id	sid	tid	token	lemma	pos
cord-346267-l08ld2cy	1	1	key	key	JJ
cord-346267-l08ld2cy	1	2	:	:	:
cord-346267-l08ld2cy	1	3	cord-346267-l08ld2cy	cord-346267-l08ld2cy	NN
cord-346267-l08ld2cy	1	4	authors	author	NNS
cord-346267-l08ld2cy	1	5	:	:	:
cord-346267-l08ld2cy	1	6	Wertheim	Wertheim	NNP
cord-346267-l08ld2cy	1	7	,	,	,
cord-346267-l08ld2cy	1	8	Joel	Joel	NNP
cord-346267-l08ld2cy	1	9	O.	O.	NNP
cord-346267-l08ld2cy	1	10	;	;	:
cord-346267-l08ld2cy	1	11	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	1	12	Pond	Pond	NNP
cord-346267-l08ld2cy	1	13	,	,	,
cord-346267-l08ld2cy	1	14	Sergei	Sergei	NNP
cord-346267-l08ld2cy	1	15	L.	L.	NNP
cord-346267-l08ld2cy	1	16	title	title	NN
cord-346267-l08ld2cy	1	17	:	:	:
cord-346267-l08ld2cy	2	1	Purifying	purify	VBG
cord-346267-l08ld2cy	2	2	Selection	Selection	NNP
cord-346267-l08ld2cy	2	3	Can	Can	MD
cord-346267-l08ld2cy	2	4	Obscure	obscure	VB
cord-346267-l08ld2cy	2	5	the	the	DT
cord-346267-l08ld2cy	2	6	Ancient	Ancient	NNP
cord-346267-l08ld2cy	2	7	Age	Age	NNP
cord-346267-l08ld2cy	2	8	of	of	IN
cord-346267-l08ld2cy	2	9	Viral	Viral	NNP
cord-346267-l08ld2cy	2	10	Lineages	Lineages	NNPS
cord-346267-l08ld2cy	2	11	date	date	NN
cord-346267-l08ld2cy	2	12	:	:	:
cord-346267-l08ld2cy	2	13	2011	2011	CD
cord-346267-l08ld2cy	2	14	-	-	HYPH
cord-346267-l08ld2cy	2	15	06	06	CD
cord-346267-l08ld2cy	2	16	-	-	HYPH
cord-346267-l08ld2cy	2	17	24	24	CD
cord-346267-l08ld2cy	2	18	journal	journal	NN
cord-346267-l08ld2cy	2	19	:	:	:
cord-346267-l08ld2cy	3	1	Molecular	molecular	JJ
cord-346267-l08ld2cy	3	2	Biology	biology	NN
cord-346267-l08ld2cy	3	3	and	and	CC
cord-346267-l08ld2cy	3	4	Evolution	evolution	NN
cord-346267-l08ld2cy	3	5	DOI	doi	NN
cord-346267-l08ld2cy	3	6	:	:	:
cord-346267-l08ld2cy	3	7	10.1093	10.1093	CD
cord-346267-l08ld2cy	3	8	/	/	SYM
cord-346267-l08ld2cy	3	9	molbev	molbev	NNP
cord-346267-l08ld2cy	3	10	/	/	SYM
cord-346267-l08ld2cy	3	11	msr170	msr170	NNP
cord-346267-l08ld2cy	3	12	sha	sha	NNP
cord-346267-l08ld2cy	3	13	:	:	:
cord-346267-l08ld2cy	4	1	6929c0cdf46c3ce1e9c963487cc83c986a2870ef	6929c0cdf46c3ce1e9c963487cc83c986a2870ef	CD
cord-346267-l08ld2cy	5	1	doc_id	doc_id	CD
cord-346267-l08ld2cy	5	2	:	:	:
cord-346267-l08ld2cy	5	3	346267	346267	CD
cord-346267-l08ld2cy	5	4	cord_uid	cord_uid	NNS
cord-346267-l08ld2cy	5	5	:	:	:
cord-346267-l08ld2cy	5	6	l08ld2cy	l08ld2cy	NNP
cord-346267-l08ld2cy	6	1	Statistical	statistical	JJ
cord-346267-l08ld2cy	6	2	methods	method	NNS
cord-346267-l08ld2cy	6	3	for	for	IN
cord-346267-l08ld2cy	6	4	molecular	molecular	JJ
cord-346267-l08ld2cy	6	5	dating	dating	NN
cord-346267-l08ld2cy	6	6	of	of	IN
cord-346267-l08ld2cy	6	7	viral	viral	JJ
cord-346267-l08ld2cy	6	8	origins	origin	NNS
cord-346267-l08ld2cy	6	9	have	have	VBP
cord-346267-l08ld2cy	6	10	been	be	VBN
cord-346267-l08ld2cy	6	11	used	use	VBN
cord-346267-l08ld2cy	6	12	extensively	extensively	RB
cord-346267-l08ld2cy	6	13	to	to	TO
cord-346267-l08ld2cy	6	14	infer	infer	VB
cord-346267-l08ld2cy	6	15	the	the	DT
cord-346267-l08ld2cy	6	16	time	time	NN
cord-346267-l08ld2cy	6	17	of	of	IN
cord-346267-l08ld2cy	6	18	most	most	RBS
cord-346267-l08ld2cy	6	19	common	common	JJ
cord-346267-l08ld2cy	6	20	recent	recent	JJ
cord-346267-l08ld2cy	6	21	ancestor	ancestor	NN
cord-346267-l08ld2cy	6	22	for	for	IN
cord-346267-l08ld2cy	6	23	many	many	JJ
cord-346267-l08ld2cy	6	24	rapidly	rapidly	RB
cord-346267-l08ld2cy	6	25	evolving	evolve	VBG
cord-346267-l08ld2cy	6	26	pathogens	pathogen	NNS
cord-346267-l08ld2cy	6	27	.	.	.
cord-346267-l08ld2cy	7	1	However	however	RB
cord-346267-l08ld2cy	7	2	,	,	,
cord-346267-l08ld2cy	7	3	there	there	EX
cord-346267-l08ld2cy	7	4	are	be	VBP
cord-346267-l08ld2cy	7	5	a	a	DT
cord-346267-l08ld2cy	7	6	number	number	NN
cord-346267-l08ld2cy	7	7	of	of	IN
cord-346267-l08ld2cy	7	8	cases	case	NNS
cord-346267-l08ld2cy	7	9	,	,	,
cord-346267-l08ld2cy	7	10	in	in	IN
cord-346267-l08ld2cy	7	11	which	which	WDT
cord-346267-l08ld2cy	7	12	epidemiological	epidemiological	JJ
cord-346267-l08ld2cy	7	13	,	,	,
cord-346267-l08ld2cy	7	14	historical	historical	JJ
cord-346267-l08ld2cy	7	15	,	,	,
cord-346267-l08ld2cy	7	16	or	or	CC
cord-346267-l08ld2cy	7	17	genomic	genomic	JJ
cord-346267-l08ld2cy	7	18	evidence	evidence	NN
cord-346267-l08ld2cy	7	19	suggests	suggest	VBZ
cord-346267-l08ld2cy	7	20	much	much	RB
cord-346267-l08ld2cy	7	21	older	old	JJR
cord-346267-l08ld2cy	7	22	viral	viral	JJ
cord-346267-l08ld2cy	7	23	origins	origin	NNS
cord-346267-l08ld2cy	7	24	than	than	IN
cord-346267-l08ld2cy	7	25	those	those	DT
cord-346267-l08ld2cy	7	26	obtained	obtain	VBN
cord-346267-l08ld2cy	7	27	via	via	IN
cord-346267-l08ld2cy	7	28	molecular	molecular	JJ
cord-346267-l08ld2cy	7	29	dating	dating	NN
cord-346267-l08ld2cy	7	30	.	.	.
cord-346267-l08ld2cy	8	1	We	-PRON-	PRP
cord-346267-l08ld2cy	8	2	demonstrate	demonstrate	VBP
cord-346267-l08ld2cy	8	3	how	how	WRB
cord-346267-l08ld2cy	8	4	pervasive	pervasive	JJ
cord-346267-l08ld2cy	8	5	purifying	purifying	NN
cord-346267-l08ld2cy	8	6	selection	selection	NN
cord-346267-l08ld2cy	8	7	can	can	MD
cord-346267-l08ld2cy	8	8	mask	mask	VB
cord-346267-l08ld2cy	8	9	the	the	DT
cord-346267-l08ld2cy	8	10	ancient	ancient	JJ
cord-346267-l08ld2cy	8	11	origins	origin	NNS
cord-346267-l08ld2cy	8	12	of	of	IN
cord-346267-l08ld2cy	8	13	recently	recently	RB
cord-346267-l08ld2cy	8	14	sampled	sample	VBN
cord-346267-l08ld2cy	8	15	pathogens	pathogen	NNS
cord-346267-l08ld2cy	8	16	,	,	,
cord-346267-l08ld2cy	8	17	in	in	IN
cord-346267-l08ld2cy	8	18	part	part	NN
cord-346267-l08ld2cy	8	19	due	due	IN
cord-346267-l08ld2cy	8	20	to	to	IN
cord-346267-l08ld2cy	8	21	the	the	DT
cord-346267-l08ld2cy	8	22	inability	inability	NN
cord-346267-l08ld2cy	8	23	of	of	IN
cord-346267-l08ld2cy	8	24	nucleotide	nucleotide	RB
cord-346267-l08ld2cy	8	25	-	-	HYPH
cord-346267-l08ld2cy	8	26	based	base	VBN
cord-346267-l08ld2cy	8	27	substitution	substitution	NN
cord-346267-l08ld2cy	8	28	models	model	NNS
cord-346267-l08ld2cy	8	29	to	to	TO
cord-346267-l08ld2cy	8	30	properly	properly	RB
cord-346267-l08ld2cy	8	31	account	account	VB
cord-346267-l08ld2cy	8	32	for	for	IN
cord-346267-l08ld2cy	8	33	complex	complex	JJ
cord-346267-l08ld2cy	8	34	patterns	pattern	NNS
cord-346267-l08ld2cy	8	35	of	of	IN
cord-346267-l08ld2cy	8	36	spatial	spatial	JJ
cord-346267-l08ld2cy	8	37	and	and	CC
cord-346267-l08ld2cy	8	38	temporal	temporal	JJ
cord-346267-l08ld2cy	8	39	variability	variability	NN
cord-346267-l08ld2cy	8	40	in	in	IN
cord-346267-l08ld2cy	8	41	selective	selective	JJ
cord-346267-l08ld2cy	8	42	pressures	pressure	NNS
cord-346267-l08ld2cy	8	43	.	.	.
cord-346267-l08ld2cy	9	1	We	-PRON-	PRP
cord-346267-l08ld2cy	9	2	use	use	VBP
cord-346267-l08ld2cy	9	3	codon	codon	NN
cord-346267-l08ld2cy	9	4	-	-	HYPH
cord-346267-l08ld2cy	9	5	based	base	VBN
cord-346267-l08ld2cy	9	6	substitution	substitution	NN
cord-346267-l08ld2cy	9	7	models	model	NNS
cord-346267-l08ld2cy	9	8	to	to	TO
cord-346267-l08ld2cy	9	9	infer	infer	VB
cord-346267-l08ld2cy	9	10	the	the	DT
cord-346267-l08ld2cy	9	11	length	length	NN
cord-346267-l08ld2cy	9	12	of	of	IN
cord-346267-l08ld2cy	9	13	branches	branch	NNS
cord-346267-l08ld2cy	9	14	in	in	IN
cord-346267-l08ld2cy	9	15	viral	viral	JJ
cord-346267-l08ld2cy	9	16	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	9	17	;	;	:
cord-346267-l08ld2cy	9	18	these	these	DT
cord-346267-l08ld2cy	9	19	models	model	NNS
cord-346267-l08ld2cy	9	20	produce	produce	VBP
cord-346267-l08ld2cy	9	21	estimates	estimate	NNS
cord-346267-l08ld2cy	9	22	that	that	WDT
cord-346267-l08ld2cy	9	23	are	be	VBP
cord-346267-l08ld2cy	9	24	often	often	RB
cord-346267-l08ld2cy	9	25	considerably	considerably	RB
cord-346267-l08ld2cy	9	26	longer	long	RBR
cord-346267-l08ld2cy	9	27	than	than	IN
cord-346267-l08ld2cy	9	28	those	those	DT
cord-346267-l08ld2cy	9	29	obtained	obtain	VBN
cord-346267-l08ld2cy	9	30	with	with	IN
cord-346267-l08ld2cy	9	31	traditional	traditional	JJ
cord-346267-l08ld2cy	9	32	nucleotide	nucleotide	NN
cord-346267-l08ld2cy	9	33	-	-	HYPH
cord-346267-l08ld2cy	9	34	based	base	VBN
cord-346267-l08ld2cy	9	35	substitution	substitution	NN
cord-346267-l08ld2cy	9	36	models	model	NNS
cord-346267-l08ld2cy	9	37	.	.	.
cord-346267-l08ld2cy	10	1	Correcting	correct	VBG
cord-346267-l08ld2cy	10	2	the	the	DT
cord-346267-l08ld2cy	10	3	apparent	apparent	JJ
cord-346267-l08ld2cy	10	4	underestimation	underestimation	NN
cord-346267-l08ld2cy	10	5	of	of	IN
cord-346267-l08ld2cy	10	6	branch	branch	NN
cord-346267-l08ld2cy	10	7	lengths	length	NNS
cord-346267-l08ld2cy	10	8	suggests	suggest	VBZ
cord-346267-l08ld2cy	10	9	substantially	substantially	RB
cord-346267-l08ld2cy	10	10	older	old	JJR
cord-346267-l08ld2cy	10	11	origins	origin	NNS
cord-346267-l08ld2cy	10	12	for	for	IN
cord-346267-l08ld2cy	10	13	measles	measle	NNS
cord-346267-l08ld2cy	10	14	,	,	,
cord-346267-l08ld2cy	10	15	Ebola	Ebola	NNP
cord-346267-l08ld2cy	10	16	,	,	,
cord-346267-l08ld2cy	10	17	and	and	CC
cord-346267-l08ld2cy	10	18	avian	avian	JJ
cord-346267-l08ld2cy	10	19	influenza	influenza	NN
cord-346267-l08ld2cy	10	20	viruses	virus	NNS
cord-346267-l08ld2cy	10	21	.	.	.
cord-346267-l08ld2cy	11	1	This	this	DT
cord-346267-l08ld2cy	11	2	work	work	NN
cord-346267-l08ld2cy	11	3	helps	help	VBZ
cord-346267-l08ld2cy	11	4	to	to	TO
cord-346267-l08ld2cy	11	5	reconcile	reconcile	VB
cord-346267-l08ld2cy	11	6	some	some	DT
cord-346267-l08ld2cy	11	7	of	of	IN
cord-346267-l08ld2cy	11	8	the	the	DT
cord-346267-l08ld2cy	11	9	inconsistencies	inconsistency	NNS
cord-346267-l08ld2cy	11	10	between	between	IN
cord-346267-l08ld2cy	11	11	molecular	molecular	JJ
cord-346267-l08ld2cy	11	12	dating	dating	NN
cord-346267-l08ld2cy	11	13	and	and	CC
cord-346267-l08ld2cy	11	14	other	other	JJ
cord-346267-l08ld2cy	11	15	types	type	NNS
cord-346267-l08ld2cy	11	16	of	of	IN
cord-346267-l08ld2cy	11	17	evidence	evidence	NN
cord-346267-l08ld2cy	11	18	concerning	concern	VBG
cord-346267-l08ld2cy	11	19	the	the	DT
cord-346267-l08ld2cy	11	20	age	age	NN
cord-346267-l08ld2cy	11	21	of	of	IN
cord-346267-l08ld2cy	11	22	viral	viral	JJ
cord-346267-l08ld2cy	11	23	lineages	lineage	NNS
cord-346267-l08ld2cy	11	24	.	.	.
cord-346267-l08ld2cy	12	1	One	one	CD
cord-346267-l08ld2cy	12	2	of	of	IN
cord-346267-l08ld2cy	12	3	the	the	DT
cord-346267-l08ld2cy	12	4	most	most	RBS
cord-346267-l08ld2cy	12	5	powerful	powerful	JJ
cord-346267-l08ld2cy	12	6	forces	force	NNS
cord-346267-l08ld2cy	12	7	shaping	shape	VBG
cord-346267-l08ld2cy	12	8	the	the	DT
cord-346267-l08ld2cy	12	9	human	human	JJ
cord-346267-l08ld2cy	12	10	genome	genome	NN
cord-346267-l08ld2cy	12	11	is	be	VBZ
cord-346267-l08ld2cy	12	12	adaptation	adaptation	NN
cord-346267-l08ld2cy	12	13	to	to	IN
cord-346267-l08ld2cy	12	14	pathogens	pathogen	NNS
cord-346267-l08ld2cy	12	15	,	,	,
cord-346267-l08ld2cy	12	16	and	and	CC
cord-346267-l08ld2cy	12	17	the	the	DT
cord-346267-l08ld2cy	12	18	pathogens	pathogen	NNS
cord-346267-l08ld2cy	12	19	that	that	WDT
cord-346267-l08ld2cy	12	20	appear	appear	VBP
cord-346267-l08ld2cy	12	21	to	to	TO
cord-346267-l08ld2cy	12	22	have	have	VB
cord-346267-l08ld2cy	12	23	exerted	exert	VBN
cord-346267-l08ld2cy	12	24	the	the	DT
cord-346267-l08ld2cy	12	25	strongest	strong	JJS
cord-346267-l08ld2cy	12	26	influence	influence	NN
cord-346267-l08ld2cy	12	27	are	be	VBP
cord-346267-l08ld2cy	12	28	viruses	virus	NNS
cord-346267-l08ld2cy	13	1	(	(	-LRB-
cord-346267-l08ld2cy	13	2	Worobey	Worobey	NNP
cord-346267-l08ld2cy	13	3	et	et	NNP
cord-346267-l08ld2cy	13	4	al	al	NNP
cord-346267-l08ld2cy	13	5	.	.	.
cord-346267-l08ld2cy	14	1	2007	2007	CD
cord-346267-l08ld2cy	14	2	;	;	:
cord-346267-l08ld2cy	14	3	Emerman	Emerman	NNP
cord-346267-l08ld2cy	14	4	and	and	CC
cord-346267-l08ld2cy	14	5	Malik	Malik	NNP
cord-346267-l08ld2cy	14	6	2010	2010	CD
cord-346267-l08ld2cy	14	7	)	)	-RRB-
cord-346267-l08ld2cy	14	8	.	.	.
cord-346267-l08ld2cy	15	1	Genes	gene	NNS
cord-346267-l08ld2cy	15	2	which	which	WDT
cord-346267-l08ld2cy	15	3	bear	bear	VBP
cord-346267-l08ld2cy	15	4	the	the	DT
cord-346267-l08ld2cy	15	5	mark	mark	NN
cord-346267-l08ld2cy	15	6	of	of	IN
cord-346267-l08ld2cy	15	7	some	some	DT
cord-346267-l08ld2cy	15	8	of	of	IN
cord-346267-l08ld2cy	15	9	the	the	DT
cord-346267-l08ld2cy	15	10	most	most	RBS
cord-346267-l08ld2cy	15	11	potent	potent	JJ
cord-346267-l08ld2cy	15	12	selective	selective	JJ
cord-346267-l08ld2cy	15	13	forces	force	NNS
cord-346267-l08ld2cy	15	14	detected	detect	VBN
cord-346267-l08ld2cy	15	15	in	in	IN
cord-346267-l08ld2cy	15	16	the	the	DT
cord-346267-l08ld2cy	15	17	genomes	genome	NNS
cord-346267-l08ld2cy	15	18	of	of	IN
cord-346267-l08ld2cy	15	19	humans	human	NNS
cord-346267-l08ld2cy	15	20	and	and	CC
cord-346267-l08ld2cy	15	21	our	-PRON-	PRP$
cord-346267-l08ld2cy	15	22	relatives	relative	NNS
cord-346267-l08ld2cy	15	23	are	be	VBP
cord-346267-l08ld2cy	15	24	directly	directly	RB
cord-346267-l08ld2cy	15	25	related	relate	VBN
cord-346267-l08ld2cy	15	26	to	to	IN
cord-346267-l08ld2cy	15	27	combating	combat	VBG
cord-346267-l08ld2cy	15	28	RNA	RNA	NNP
cord-346267-l08ld2cy	15	29	viruses	virus	NNS
cord-346267-l08ld2cy	15	30	(	(	-LRB-
cord-346267-l08ld2cy	15	31	Meyerson	Meyerson	NNP
cord-346267-l08ld2cy	15	32	and	and	CC
cord-346267-l08ld2cy	15	33	Sawyer	Sawyer	NNP
cord-346267-l08ld2cy	15	34	2011	2011	CD
cord-346267-l08ld2cy	15	35	)	)	-RRB-
cord-346267-l08ld2cy	15	36	.	.	.
cord-346267-l08ld2cy	16	1	Moreover	moreover	RB
cord-346267-l08ld2cy	16	2	,	,	,
cord-346267-l08ld2cy	16	3	the	the	DT
cord-346267-l08ld2cy	16	4	ancient	ancient	JJ
cord-346267-l08ld2cy	16	5	history	history	NN
cord-346267-l08ld2cy	16	6	of	of	IN
cord-346267-l08ld2cy	16	7	this	this	DT
cord-346267-l08ld2cy	16	8	association	association	NN
cord-346267-l08ld2cy	16	9	with	with	IN
cord-346267-l08ld2cy	16	10	RNA	RNA	NNP
cord-346267-l08ld2cy	16	11	viruses	virus	NNS
cord-346267-l08ld2cy	16	12	is	be	VBZ
cord-346267-l08ld2cy	16	13	evidenced	evidence	VBN
cord-346267-l08ld2cy	16	14	by	by	IN
cord-346267-l08ld2cy	16	15	a	a	DT
cord-346267-l08ld2cy	16	16	diverse	diverse	JJ
cord-346267-l08ld2cy	16	17	array	array	NN
cord-346267-l08ld2cy	16	18	of	of	IN
cord-346267-l08ld2cy	16	19	defective	defective	JJ
cord-346267-l08ld2cy	16	20	viral	viral	JJ
cord-346267-l08ld2cy	16	21	remnants	remnant	NNS
cord-346267-l08ld2cy	16	22	incorporated	incorporate	VBN
cord-346267-l08ld2cy	16	23	into	into	IN
cord-346267-l08ld2cy	16	24	vertebrate	vertebrate	JJ
cord-346267-l08ld2cy	16	25	genomes	genome	NNS
cord-346267-l08ld2cy	16	26	,	,	,
cord-346267-l08ld2cy	16	27	including	include	VBG
cord-346267-l08ld2cy	16	28	mounting	mount	VBG
cord-346267-l08ld2cy	16	29	support	support	NN
cord-346267-l08ld2cy	16	30	for	for	IN
cord-346267-l08ld2cy	16	31	endogenization	endogenization	NN
cord-346267-l08ld2cy	16	32	of	of	IN
cord-346267-l08ld2cy	16	33	RNA	RNA	NNP
cord-346267-l08ld2cy	16	34	viruses	virus	NNS
cord-346267-l08ld2cy	16	35	other	other	JJ
cord-346267-l08ld2cy	16	36	than	than	IN
cord-346267-l08ld2cy	16	37	Retroviridae	Retroviridae	NNP
cord-346267-l08ld2cy	17	1	(	(	-LRB-
cord-346267-l08ld2cy	17	2	Gifford	Gifford	NNP
cord-346267-l08ld2cy	17	3	et	et	NNP
cord-346267-l08ld2cy	17	4	al	al	NNP
cord-346267-l08ld2cy	17	5	.	.	.
cord-346267-l08ld2cy	18	1	2008	2008	CD
cord-346267-l08ld2cy	18	2	;	;	:
cord-346267-l08ld2cy	18	3	Belyi	Belyi	NNP
cord-346267-l08ld2cy	18	4	et	et	FW
cord-346267-l08ld2cy	18	5	al	al	NNP
cord-346267-l08ld2cy	18	6	.	.	NNP
cord-346267-l08ld2cy	18	7	2010	2010	CD
cord-346267-l08ld2cy	18	8	;	;	:
cord-346267-l08ld2cy	18	9	Gilbert	Gilbert	NNP
cord-346267-l08ld2cy	18	10	and	and	CC
cord-346267-l08ld2cy	18	11	Feschotte	Feschotte	NNP
cord-346267-l08ld2cy	18	12	2010	2010	CD
cord-346267-l08ld2cy	18	13	;	;	:
cord-346267-l08ld2cy	18	14	Horie	Horie	NNP
cord-346267-l08ld2cy	18	15	et	et	NNP
cord-346267-l08ld2cy	18	16	al	al	NNP
cord-346267-l08ld2cy	18	17	.	.	.
cord-346267-l08ld2cy	19	1	2010	2010	CD
cord-346267-l08ld2cy	19	2	;	;	:
cord-346267-l08ld2cy	19	3	Taylor	Taylor	NNP
cord-346267-l08ld2cy	19	4	et	et	NNP
cord-346267-l08ld2cy	19	5	al	al	NNP
cord-346267-l08ld2cy	19	6	.	.	NNP
cord-346267-l08ld2cy	19	7	2010	2010	CD
cord-346267-l08ld2cy	19	8	)	)	-RRB-
cord-346267-l08ld2cy	19	9	.	.	.
cord-346267-l08ld2cy	20	1	However	however	RB
cord-346267-l08ld2cy	20	2	,	,	,
cord-346267-l08ld2cy	20	3	according	accord	VBG
cord-346267-l08ld2cy	20	4	to	to	IN
cord-346267-l08ld2cy	20	5	molecular	molecular	JJ
cord-346267-l08ld2cy	20	6	dating	dating	NN
cord-346267-l08ld2cy	20	7	analyses	analysis	NNS
cord-346267-l08ld2cy	20	8	,	,	,
cord-346267-l08ld2cy	20	9	many	many	JJ
cord-346267-l08ld2cy	20	10	RNA	RNA	NNP
cord-346267-l08ld2cy	20	11	viruses	virus	NNS
cord-346267-l08ld2cy	20	12	have	have	VBP
cord-346267-l08ld2cy	20	13	extraordinarily	extraordinarily	RB
cord-346267-l08ld2cy	20	14	recent	recent	JJ
cord-346267-l08ld2cy	20	15	origins	origin	NNS
cord-346267-l08ld2cy	20	16	(	(	-LRB-
cord-346267-l08ld2cy	20	17	Holmes	Holmes	NNP
cord-346267-l08ld2cy	20	18	2003a	2003a	CD
cord-346267-l08ld2cy	20	19	)	)	-RRB-
cord-346267-l08ld2cy	20	20	.	.	.
cord-346267-l08ld2cy	21	1	At	at	IN
cord-346267-l08ld2cy	21	2	first	first	JJ
cord-346267-l08ld2cy	21	3	glance	glance	NN
cord-346267-l08ld2cy	21	4	,	,	,
cord-346267-l08ld2cy	21	5	a	a	DT
cord-346267-l08ld2cy	21	6	recent	recent	JJ
cord-346267-l08ld2cy	21	7	introduction	introduction	NN
cord-346267-l08ld2cy	21	8	of	of	IN
cord-346267-l08ld2cy	21	9	many	many	JJ
cord-346267-l08ld2cy	21	10	RNA	RNA	NNP
cord-346267-l08ld2cy	21	11	viruses	virus	NNS
cord-346267-l08ld2cy	21	12	into	into	IN
cord-346267-l08ld2cy	21	13	the	the	DT
cord-346267-l08ld2cy	21	14	human	human	JJ
cord-346267-l08ld2cy	21	15	population	population	NN
cord-346267-l08ld2cy	21	16	is	be	VBZ
cord-346267-l08ld2cy	21	17	unsurprising	unsurprising	JJ
cord-346267-l08ld2cy	21	18	.	.	.
cord-346267-l08ld2cy	22	1	Epidemiological	epidemiological	JJ
cord-346267-l08ld2cy	22	2	,	,	,
cord-346267-l08ld2cy	22	3	historical	historical	JJ
cord-346267-l08ld2cy	22	4	,	,	,
cord-346267-l08ld2cy	22	5	and	and	CC
cord-346267-l08ld2cy	22	6	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	22	7	approaches	approach	NNS
cord-346267-l08ld2cy	22	8	agree	agree	VBP
cord-346267-l08ld2cy	22	9	that	that	IN
cord-346267-l08ld2cy	22	10	some	some	DT
cord-346267-l08ld2cy	22	11	of	of	IN
cord-346267-l08ld2cy	22	12	the	the	DT
cord-346267-l08ld2cy	22	13	most	most	RBS
cord-346267-l08ld2cy	22	14	notable	notable	JJ
cord-346267-l08ld2cy	22	15	RNA	RNA	NNP
cord-346267-l08ld2cy	22	16	viruses	virus	NNS
cord-346267-l08ld2cy	22	17	(	(	-LRB-
cord-346267-l08ld2cy	22	18	e.g.	e.g.	RB
cord-346267-l08ld2cy	22	19	,	,	,
cord-346267-l08ld2cy	22	20	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	22	21	,	,	,
cord-346267-l08ld2cy	22	22	Worobey	Worobey	NNP
cord-346267-l08ld2cy	22	23	et	et	NNP
cord-346267-l08ld2cy	22	24	al	al	NNP
cord-346267-l08ld2cy	22	25	.	.	NNP
cord-346267-l08ld2cy	22	26	2008	2008	CD
cord-346267-l08ld2cy	22	27	;	;	,
cord-346267-l08ld2cy	22	28	influenza	influenza	NN
cord-346267-l08ld2cy	22	29	A	a	DT
cord-346267-l08ld2cy	22	30	virus	virus	NN
cord-346267-l08ld2cy	22	31	,	,	,
cord-346267-l08ld2cy	22	32	Taubenberger	Taubenberger	NNP
cord-346267-l08ld2cy	22	33	et	et	NNP
cord-346267-l08ld2cy	22	34	al	al	NNP
cord-346267-l08ld2cy	22	35	.	.	NNP
cord-346267-l08ld2cy	22	36	2005	2005	CD
cord-346267-l08ld2cy	22	37	;	;	:
cord-346267-l08ld2cy	22	38	Ebola	Ebola	NNP
cord-346267-l08ld2cy	22	39	virus	virus	NN
cord-346267-l08ld2cy	22	40	[	[	-LRB-
cord-346267-l08ld2cy	22	41	EBOV	EBOV	NNP
cord-346267-l08ld2cy	22	42	]	]	-RRB-
cord-346267-l08ld2cy	22	43	Zaire	Zaire	NNP
cord-346267-l08ld2cy	22	44	,	,	,
cord-346267-l08ld2cy	22	45	Walsh	Walsh	NNP
cord-346267-l08ld2cy	22	46	et	et	NNP
cord-346267-l08ld2cy	22	47	al	al	NNP
cord-346267-l08ld2cy	22	48	.	.	NNP
cord-346267-l08ld2cy	22	49	2005	2005	CD
cord-346267-l08ld2cy	22	50	;	;	:
cord-346267-l08ld2cy	22	51	and	and	CC
cord-346267-l08ld2cy	22	52	SARS	SARS	NNP
cord-346267-l08ld2cy	22	53	coronavirus	coronavirus	NN
cord-346267-l08ld2cy	22	54	,	,	,
cord-346267-l08ld2cy	22	55	Hon	Hon	NNP
cord-346267-l08ld2cy	22	56	et	et	NNP
cord-346267-l08ld2cy	22	57	al	al	NNP
cord-346267-l08ld2cy	22	58	.	.	NNP
cord-346267-l08ld2cy	22	59	2008	2008	CD
cord-346267-l08ld2cy	22	60	)	)	-RRB-
cord-346267-l08ld2cy	22	61	emerged	emerge	VBD
cord-346267-l08ld2cy	22	62	as	as	IN
cord-346267-l08ld2cy	22	63	zoonoses	zoonosis	NNS
cord-346267-l08ld2cy	22	64	within	within	IN
cord-346267-l08ld2cy	22	65	the	the	DT
cord-346267-l08ld2cy	22	66	last	last	JJ
cord-346267-l08ld2cy	22	67	century	century	NN
cord-346267-l08ld2cy	22	68	.	.	.
cord-346267-l08ld2cy	23	1	As	as	IN
cord-346267-l08ld2cy	23	2	one	one	CD
cord-346267-l08ld2cy	23	3	looks	look	VBZ
cord-346267-l08ld2cy	23	4	further	further	RB
cord-346267-l08ld2cy	23	5	back	back	RB
cord-346267-l08ld2cy	23	6	in	in	IN
cord-346267-l08ld2cy	23	7	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	23	8	time	time	NN
cord-346267-l08ld2cy	23	9	,	,	,
cord-346267-l08ld2cy	23	10	however	however	RB
cord-346267-l08ld2cy	23	11	,	,	,
cord-346267-l08ld2cy	23	12	specific	specific	JJ
cord-346267-l08ld2cy	23	13	inconsistencies	inconsistency	NNS
cord-346267-l08ld2cy	23	14	arise	arise	VBP
cord-346267-l08ld2cy	23	15	.	.	.
cord-346267-l08ld2cy	24	1	For	for	IN
cord-346267-l08ld2cy	24	2	example	example	NN
cord-346267-l08ld2cy	24	3	,	,	,
cord-346267-l08ld2cy	24	4	defective	defective	JJ
cord-346267-l08ld2cy	24	5	remnants	remnant	NNS
cord-346267-l08ld2cy	24	6	of	of	IN
cord-346267-l08ld2cy	24	7	ancient	ancient	JJ
cord-346267-l08ld2cy	24	8	integrations	integration	NNS
cord-346267-l08ld2cy	24	9	of	of	IN
cord-346267-l08ld2cy	24	10	Filoviridae	Filoviridae	NNP
cord-346267-l08ld2cy	24	11	,	,	,
cord-346267-l08ld2cy	24	12	the	the	DT
cord-346267-l08ld2cy	24	13	viral	viral	JJ
cord-346267-l08ld2cy	24	14	family	family	NN
cord-346267-l08ld2cy	24	15	containing	contain	VBG
cord-346267-l08ld2cy	24	16	the	the	DT
cord-346267-l08ld2cy	24	17	EBOV	EBOV	NNP
cord-346267-l08ld2cy	24	18	,	,	,
cord-346267-l08ld2cy	24	19	are	be	VBP
cord-346267-l08ld2cy	24	20	found	find	VBN
cord-346267-l08ld2cy	24	21	in	in	IN
cord-346267-l08ld2cy	24	22	mammalian	mammalian	JJ
cord-346267-l08ld2cy	24	23	lineages	lineage	NNS
cord-346267-l08ld2cy	24	24	that	that	WDT
cord-346267-l08ld2cy	24	25	diverged	diverge	VBD
cord-346267-l08ld2cy	24	26	tens	ten	NNS
cord-346267-l08ld2cy	24	27	of	of	IN
cord-346267-l08ld2cy	24	28	millions	million	NNS
cord-346267-l08ld2cy	24	29	of	of	IN
cord-346267-l08ld2cy	24	30	years	year	NNS
cord-346267-l08ld2cy	24	31	ago	ago	RB
cord-346267-l08ld2cy	25	1	(	(	-LRB-
cord-346267-l08ld2cy	25	2	Belyi	Belyi	NNP
cord-346267-l08ld2cy	25	3	et	et	FW
cord-346267-l08ld2cy	25	4	al	al	NNP
cord-346267-l08ld2cy	25	5	.	.	.
cord-346267-l08ld2cy	26	1	2010	2010	CD
cord-346267-l08ld2cy	26	2	;	;	:
cord-346267-l08ld2cy	26	3	Taylor	Taylor	NNP
cord-346267-l08ld2cy	26	4	et	et	NNP
cord-346267-l08ld2cy	26	5	al	al	NNP
cord-346267-l08ld2cy	26	6	.	.	NNP
cord-346267-l08ld2cy	26	7	2010	2010	CD
cord-346267-l08ld2cy	26	8	)	)	-RRB-
cord-346267-l08ld2cy	26	9	,	,	.
cord-346267-l08ld2cy	27	1	even	even	RB
cord-346267-l08ld2cy	27	2	though	though	IN
cord-346267-l08ld2cy	27	3	molecular	molecular	JJ
cord-346267-l08ld2cy	27	4	dating	dating	NN
cord-346267-l08ld2cy	27	5	suggests	suggest	VBZ
cord-346267-l08ld2cy	27	6	a	a	DT
cord-346267-l08ld2cy	27	7	time	time	NN
cord-346267-l08ld2cy	27	8	of	of	IN
cord-346267-l08ld2cy	27	9	most	most	RBS
cord-346267-l08ld2cy	27	10	recent	recent	JJ
cord-346267-l08ld2cy	27	11	common	common	JJ
cord-346267-l08ld2cy	27	12	ancestor	ancestor	NN
cord-346267-l08ld2cy	27	13	(	(	-LRB-
cord-346267-l08ld2cy	27	14	tMRCA	tmrca	UH
cord-346267-l08ld2cy	27	15	)	)	-RRB-
cord-346267-l08ld2cy	27	16	for	for	IN
cord-346267-l08ld2cy	27	17	Filoviridae	Filoviridae	NNP
cord-346267-l08ld2cy	27	18	on	on	IN
cord-346267-l08ld2cy	27	19	the	the	DT
cord-346267-l08ld2cy	27	20	order	order	NN
cord-346267-l08ld2cy	27	21	of	of	IN
cord-346267-l08ld2cy	27	22	only	only	RB
cord-346267-l08ld2cy	27	23	thousands	thousand	NNS
cord-346267-l08ld2cy	27	24	of	of	IN
cord-346267-l08ld2cy	27	25	years	year	NNS
cord-346267-l08ld2cy	27	26	ago	ago	RB
cord-346267-l08ld2cy	27	27	(	(	-LRB-
cord-346267-l08ld2cy	27	28	Suzuki	Suzuki	NNP
cord-346267-l08ld2cy	27	29	and	and	CC
cord-346267-l08ld2cy	27	30	Gojobori	Gojobori	NNP
cord-346267-l08ld2cy	27	31	1997	1997	CD
cord-346267-l08ld2cy	27	32	)	)	-RRB-
cord-346267-l08ld2cy	27	33	.	.	.
cord-346267-l08ld2cy	28	1	Another	another	DT
cord-346267-l08ld2cy	28	2	inconsistency	inconsistency	NN
cord-346267-l08ld2cy	28	3	can	can	MD
cord-346267-l08ld2cy	28	4	be	be	VB
cord-346267-l08ld2cy	28	5	seen	see	VBN
cord-346267-l08ld2cy	28	6	in	in	IN
cord-346267-l08ld2cy	28	7	the	the	DT
cord-346267-l08ld2cy	28	8	zoonotic	zoonotic	JJ
cord-346267-l08ld2cy	28	9	origin	origin	NN
cord-346267-l08ld2cy	28	10	of	of	IN
cord-346267-l08ld2cy	28	11	measles	measles	NNP
cord-346267-l08ld2cy	28	12	virus	virus	NN
cord-346267-l08ld2cy	28	13	(	(	-LRB-
cord-346267-l08ld2cy	28	14	MeV	MeV	NNP
cord-346267-l08ld2cy	28	15	)	)	-RRB-
cord-346267-l08ld2cy	28	16	from	from	IN
cord-346267-l08ld2cy	28	17	rinderpest	rinderpest	NN
cord-346267-l08ld2cy	28	18	virus	virus	NN
cord-346267-l08ld2cy	28	19	(	(	-LRB-
cord-346267-l08ld2cy	28	20	RPV	RPV	NNP
cord-346267-l08ld2cy	28	21	)	)	-RRB-
cord-346267-l08ld2cy	28	22	and	and	CC
cord-346267-l08ld2cy	28	23	peste	peste	NNP
cord-346267-l08ld2cy	28	24	-	-	HYPH
cord-346267-l08ld2cy	28	25	des	des	NNP
cord-346267-l08ld2cy	28	26	-	-	HYPH
cord-346267-l08ld2cy	28	27	petits	petit	NNS
cord-346267-l08ld2cy	28	28	ruminants	ruminant	NNS
cord-346267-l08ld2cy	28	29	virus	virus	NN
cord-346267-l08ld2cy	28	30	(	(	-LRB-
cord-346267-l08ld2cy	28	31	PPRV	PPRV	NNP
cord-346267-l08ld2cy	28	32	)	)	-RRB-
cord-346267-l08ld2cy	28	33	,	,	.
cord-346267-l08ld2cy	29	1	two	two	CD
cord-346267-l08ld2cy	29	2	viruses	virus	NNS
cord-346267-l08ld2cy	29	3	capable	capable	JJ
cord-346267-l08ld2cy	29	4	of	of	IN
cord-346267-l08ld2cy	29	5	infecting	infect	VBG
cord-346267-l08ld2cy	29	6	large	large	JJ
cord-346267-l08ld2cy	29	7	and	and	CC
cord-346267-l08ld2cy	29	8	small	small	JJ
cord-346267-l08ld2cy	29	9	ruminants	ruminant	NNS
cord-346267-l08ld2cy	29	10	,	,	,
cord-346267-l08ld2cy	29	11	respectively	respectively	RB
cord-346267-l08ld2cy	29	12	.	.	.
cord-346267-l08ld2cy	30	1	MeV	MeV	NNP
cord-346267-l08ld2cy	30	2	required	require	VBD
cord-346267-l08ld2cy	30	3	at	at	RB
cord-346267-l08ld2cy	30	4	least	least	RBS
cord-346267-l08ld2cy	30	5	two	two	CD
cord-346267-l08ld2cy	30	6	conditions	condition	NNS
cord-346267-l08ld2cy	30	7	to	to	TO
cord-346267-l08ld2cy	30	8	emerge	emerge	VB
cord-346267-l08ld2cy	30	9	:	:	:
cord-346267-l08ld2cy	30	10	1	1	LS
cord-346267-l08ld2cy	30	11	)	)	-RRB-
cord-346267-l08ld2cy	30	12	Humans	human	NNS
cord-346267-l08ld2cy	30	13	had	have	VBD
cord-346267-l08ld2cy	30	14	to	to	TO
cord-346267-l08ld2cy	30	15	live	live	VB
cord-346267-l08ld2cy	30	16	in	in	IN
cord-346267-l08ld2cy	30	17	close	close	JJ
cord-346267-l08ld2cy	30	18	proximity	proximity	NN
cord-346267-l08ld2cy	30	19	to	to	IN
cord-346267-l08ld2cy	30	20	RPV	RPV	NNP
cord-346267-l08ld2cy	30	21	,	,	,
cord-346267-l08ld2cy	30	22	which	which	WDT
cord-346267-l08ld2cy	30	23	became	become	VBD
cord-346267-l08ld2cy	30	24	commonplace	commonplace	JJ
cord-346267-l08ld2cy	30	25	only	only	RB
cord-346267-l08ld2cy	30	26	after	after	IN
cord-346267-l08ld2cy	30	27	the	the	DT
cord-346267-l08ld2cy	30	28	domestication	domestication	NN
cord-346267-l08ld2cy	30	29	of	of	IN
cord-346267-l08ld2cy	30	30	cattle	cattle	NNS
cord-346267-l08ld2cy	30	31	over	over	IN
cord-346267-l08ld2cy	30	32	the	the	DT
cord-346267-l08ld2cy	30	33	last	last	JJ
cord-346267-l08ld2cy	30	34	10,000	10,000	CD
cord-346267-l08ld2cy	30	35	years	year	NNS
cord-346267-l08ld2cy	30	36	(	(	-LRB-
cord-346267-l08ld2cy	30	37	Perkins	Perkins	NNP
cord-346267-l08ld2cy	30	38	1969	1969	CD
cord-346267-l08ld2cy	30	39	;	;	:
cord-346267-l08ld2cy	30	40	Loftus	Loftus	NNP
cord-346267-l08ld2cy	30	41	et	et	NNP
cord-346267-l08ld2cy	30	42	al	al	NNP
cord-346267-l08ld2cy	30	43	.	.	.
cord-346267-l08ld2cy	30	44	1994	1994	CD
cord-346267-l08ld2cy	30	45	;	;	:
cord-346267-l08ld2cy	30	46	Beja	Beja	NNP
cord-346267-l08ld2cy	30	47	-	-	HYPH
cord-346267-l08ld2cy	30	48	Pereira	Pereira	NNP
cord-346267-l08ld2cy	30	49	et	et	NNP
cord-346267-l08ld2cy	30	50	al	al	NNP
cord-346267-l08ld2cy	30	51	.	.	.
cord-346267-l08ld2cy	30	52	2006	2006	CD
cord-346267-l08ld2cy	30	53	)	)	-RRB-
cord-346267-l08ld2cy	30	54	and	and	CC
cord-346267-l08ld2cy	31	1	2	2	LS
cord-346267-l08ld2cy	31	2	)	)	-RRB-
cord-346267-l08ld2cy	31	3	humans	human	NNS
cord-346267-l08ld2cy	31	4	needed	need	VBD
cord-346267-l08ld2cy	31	5	societies	society	NNS
cord-346267-l08ld2cy	31	6	with	with	IN
cord-346267-l08ld2cy	31	7	a	a	DT
cord-346267-l08ld2cy	31	8	population	population	NN
cord-346267-l08ld2cy	31	9	size	size	NN
cord-346267-l08ld2cy	31	10	above	above	IN
cord-346267-l08ld2cy	31	11	250,000	250,000	CD
cord-346267-l08ld2cy	31	12	-	-	SYM
cord-346267-l08ld2cy	31	13	500,000	500,000	CD
cord-346267-l08ld2cy	31	14	to	to	TO
cord-346267-l08ld2cy	31	15	sustain	sustain	VB
cord-346267-l08ld2cy	31	16	the	the	DT
cord-346267-l08ld2cy	31	17	epidemic	epidemic	NN
cord-346267-l08ld2cy	31	18	,	,	,
cord-346267-l08ld2cy	31	19	which	which	WDT
cord-346267-l08ld2cy	31	20	did	do	VBD
cord-346267-l08ld2cy	31	21	not	not	RB
cord-346267-l08ld2cy	31	22	exist	exist	VB
cord-346267-l08ld2cy	31	23	until	until	IN
cord-346267-l08ld2cy	31	24	about	about	RB
cord-346267-l08ld2cy	31	25	5,000	5,000	CD
cord-346267-l08ld2cy	31	26	years	year	NNS
cord-346267-l08ld2cy	31	27	ago	ago	RB
cord-346267-l08ld2cy	31	28	(	(	-LRB-
cord-346267-l08ld2cy	32	1	Black	black	JJ
cord-346267-l08ld2cy	32	2	1966	1966	CD
cord-346267-l08ld2cy	32	3	)	)	-RRB-
cord-346267-l08ld2cy	32	4	.	.	.
cord-346267-l08ld2cy	33	1	Furthermore	furthermore	RB
cord-346267-l08ld2cy	33	2	,	,	,
cord-346267-l08ld2cy	33	3	the	the	DT
cord-346267-l08ld2cy	33	4	first	first	JJ
cord-346267-l08ld2cy	33	5	unambiguous	unambiguous	JJ
cord-346267-l08ld2cy	33	6	historical	historical	JJ
cord-346267-l08ld2cy	33	7	account	account	NN
cord-346267-l08ld2cy	33	8	of	of	IN
cord-346267-l08ld2cy	33	9	measles	measle	NNS
cord-346267-l08ld2cy	33	10	dates	date	VBZ
cord-346267-l08ld2cy	33	11	back	back	RB
cord-346267-l08ld2cy	33	12	to	to	IN
cord-346267-l08ld2cy	33	13	the	the	DT
cord-346267-l08ld2cy	33	14	ninth	ninth	JJ
cord-346267-l08ld2cy	33	15	century	century	NN
cord-346267-l08ld2cy	33	16	(	(	-LRB-
cord-346267-l08ld2cy	33	17	Rāzī	Rāzī	NNP
cord-346267-l08ld2cy	33	18	1848	1848	CD
cord-346267-l08ld2cy	33	19	)	)	-RRB-
cord-346267-l08ld2cy	33	20	.	.	.
cord-346267-l08ld2cy	34	1	Therefore	therefore	RB
cord-346267-l08ld2cy	34	2	,	,	,
cord-346267-l08ld2cy	34	3	historical	historical	JJ
cord-346267-l08ld2cy	34	4	and	and	CC
cord-346267-l08ld2cy	34	5	epidemiological	epidemiological	JJ
cord-346267-l08ld2cy	34	6	considerations	consideration	NNS
cord-346267-l08ld2cy	34	7	,	,	,
cord-346267-l08ld2cy	34	8	which	which	WDT
cord-346267-l08ld2cy	34	9	place	place	VBP
cord-346267-l08ld2cy	34	10	the	the	DT
cord-346267-l08ld2cy	34	11	tMRCA	tmrca	NN
cord-346267-l08ld2cy	34	12	of	of	IN
cord-346267-l08ld2cy	34	13	MeV	MeV	NNP
cord-346267-l08ld2cy	34	14	and	and	CC
cord-346267-l08ld2cy	34	15	RPV	RPV	NNP
cord-346267-l08ld2cy	34	16	at	at	IN
cord-346267-l08ld2cy	34	17	thousands	thousand	NNS
cord-346267-l08ld2cy	34	18	of	of	IN
cord-346267-l08ld2cy	34	19	years	year	NNS
cord-346267-l08ld2cy	34	20	ago	ago	RB
cord-346267-l08ld2cy	34	21	,	,	,
cord-346267-l08ld2cy	34	22	are	be	VBP
cord-346267-l08ld2cy	34	23	at	at	IN
cord-346267-l08ld2cy	34	24	odds	odd	NNS
cord-346267-l08ld2cy	34	25	with	with	IN
cord-346267-l08ld2cy	34	26	molecular	molecular	JJ
cord-346267-l08ld2cy	34	27	dating	dating	NN
cord-346267-l08ld2cy	34	28	analysis	analysis	NN
cord-346267-l08ld2cy	34	29	,	,	,
cord-346267-l08ld2cy	34	30	which	which	WDT
cord-346267-l08ld2cy	34	31	infers	infer	VBZ
cord-346267-l08ld2cy	34	32	the	the	DT
cord-346267-l08ld2cy	34	33	tMRCA	tmrca	NN
cord-346267-l08ld2cy	34	34	to	to	TO
cord-346267-l08ld2cy	34	35	be	be	VB
cord-346267-l08ld2cy	34	36	only	only	RB
cord-346267-l08ld2cy	34	37	hundreds	hundred	NNS
cord-346267-l08ld2cy	34	38	of	of	IN
cord-346267-l08ld2cy	34	39	years	year	NNS
cord-346267-l08ld2cy	34	40	ago	ago	RB
cord-346267-l08ld2cy	35	1	(	(	-LRB-
cord-346267-l08ld2cy	35	2	Furuse	Furuse	NNP
cord-346267-l08ld2cy	35	3	et	et	NNP
cord-346267-l08ld2cy	35	4	al	al	NNP
cord-346267-l08ld2cy	35	5	.	.	NNP
cord-346267-l08ld2cy	35	6	2010	2010	CD
cord-346267-l08ld2cy	35	7	)	)	-RRB-
cord-346267-l08ld2cy	35	8	.	.	.
cord-346267-l08ld2cy	36	1	The	the	DT
cord-346267-l08ld2cy	36	2	same	same	JJ
cord-346267-l08ld2cy	36	3	phylogenetic	phylogenetic	NN
cord-346267-l08ld2cy	36	4	dating	dating	NN
cord-346267-l08ld2cy	36	5	methods	method	NNS
cord-346267-l08ld2cy	36	6	that	that	WDT
cord-346267-l08ld2cy	36	7	provide	provide	VBP
cord-346267-l08ld2cy	36	8	convincing	convincing	JJ
cord-346267-l08ld2cy	36	9	and	and	CC
cord-346267-l08ld2cy	36	10	reasonable	reasonable	JJ
cord-346267-l08ld2cy	36	11	tMRCA	tmrca	NN
cord-346267-l08ld2cy	36	12	estimates	estimate	NNS
cord-346267-l08ld2cy	36	13	for	for	IN
cord-346267-l08ld2cy	36	14	recent	recent	JJ
cord-346267-l08ld2cy	36	15	zoonotic	zoonotic	JJ
cord-346267-l08ld2cy	36	16	transfers	transfer	NNS
cord-346267-l08ld2cy	36	17	seem	seem	VBP
cord-346267-l08ld2cy	36	18	to	to	TO
cord-346267-l08ld2cy	36	19	be	be	VB
cord-346267-l08ld2cy	36	20	dramatically	dramatically	RB
cord-346267-l08ld2cy	36	21	underestimating	underestimate	VBG
cord-346267-l08ld2cy	36	22	the	the	DT
cord-346267-l08ld2cy	36	23	age	age	NN
cord-346267-l08ld2cy	36	24	of	of	IN
cord-346267-l08ld2cy	36	25	older	old	JJR
cord-346267-l08ld2cy	36	26	viral	viral	JJ
cord-346267-l08ld2cy	36	27	divergence	divergence	NN
cord-346267-l08ld2cy	36	28	events	event	NNS
cord-346267-l08ld2cy	36	29	.	.	.
cord-346267-l08ld2cy	37	1	Therefore	therefore	RB
cord-346267-l08ld2cy	37	2	,	,	,
cord-346267-l08ld2cy	37	3	over	over	IN
cord-346267-l08ld2cy	37	4	longer	long	JJR
cord-346267-l08ld2cy	37	5	periods	period	NNS
cord-346267-l08ld2cy	37	6	of	of	IN
cord-346267-l08ld2cy	37	7	time	time	NN
cord-346267-l08ld2cy	37	8	,	,	,
cord-346267-l08ld2cy	37	9	the	the	DT
cord-346267-l08ld2cy	37	10	extent	extent	NN
cord-346267-l08ld2cy	37	11	of	of	IN
cord-346267-l08ld2cy	37	12	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	37	13	change	change	NN
cord-346267-l08ld2cy	37	14	has	have	VBZ
cord-346267-l08ld2cy	37	15	been	be	VBN
cord-346267-l08ld2cy	37	16	lost	lose	VBN
cord-346267-l08ld2cy	37	17	.	.	.
cord-346267-l08ld2cy	38	1	In	in	IN
cord-346267-l08ld2cy	38	2	many	many	JJ
cord-346267-l08ld2cy	38	3	viral	viral	JJ
cord-346267-l08ld2cy	38	4	genes	gene	NNS
cord-346267-l08ld2cy	38	5	,	,	,
cord-346267-l08ld2cy	38	6	there	there	EX
cord-346267-l08ld2cy	38	7	is	be	VBZ
cord-346267-l08ld2cy	38	8	remarkable	remarkable	JJ
cord-346267-l08ld2cy	38	9	sequence	sequence	NN
cord-346267-l08ld2cy	38	10	conservation	conservation	NN
cord-346267-l08ld2cy	38	11	,	,	,
cord-346267-l08ld2cy	38	12	indicating	indicate	VBG
cord-346267-l08ld2cy	38	13	that	that	IN
cord-346267-l08ld2cy	38	14	purifying	purify	VBG
cord-346267-l08ld2cy	38	15	selection	selection	NN
cord-346267-l08ld2cy	38	16	is	be	VBZ
cord-346267-l08ld2cy	38	17	a	a	DT
cord-346267-l08ld2cy	38	18	dominant	dominant	JJ
cord-346267-l08ld2cy	38	19	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	38	20	force	force	NN
cord-346267-l08ld2cy	38	21	,	,	,
cord-346267-l08ld2cy	38	22	acting	act	VBG
cord-346267-l08ld2cy	38	23	to	to	TO
cord-346267-l08ld2cy	38	24	maintain	maintain	VB
cord-346267-l08ld2cy	38	25	evidence	evidence	NN
cord-346267-l08ld2cy	38	26	of	of	IN
cord-346267-l08ld2cy	38	27	homology	homology	NN
cord-346267-l08ld2cy	38	28	by	by	IN
cord-346267-l08ld2cy	38	29	preserving	preserve	VBG
cord-346267-l08ld2cy	38	30	amino	amino	NN
cord-346267-l08ld2cy	38	31	acid	acid	NN
cord-346267-l08ld2cy	38	32	residues	residue	NNS
cord-346267-l08ld2cy	38	33	,	,	,
cord-346267-l08ld2cy	38	34	while	while	IN
cord-346267-l08ld2cy	38	35	allowing	allow	VBG
cord-346267-l08ld2cy	38	36	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	38	37	sequences	sequence	NNS
cord-346267-l08ld2cy	38	38	to	to	TO
cord-346267-l08ld2cy	38	39	continue	continue	VB
cord-346267-l08ld2cy	38	40	evolving	evolve	VBG
cord-346267-l08ld2cy	38	41	MBE	MBE	NNP
cord-346267-l08ld2cy	38	42	(	(	-LRB-
cord-346267-l08ld2cy	38	43	Holmes	Holmes	NNP
cord-346267-l08ld2cy	38	44	2003b	2003b	NNS
cord-346267-l08ld2cy	38	45	;	;	:
cord-346267-l08ld2cy	38	46	Edwards	Edwards	NNP
cord-346267-l08ld2cy	38	47	et	et	NNP
cord-346267-l08ld2cy	38	48	al	al	NNP
cord-346267-l08ld2cy	38	49	.	.	.
cord-346267-l08ld2cy	39	1	2006	2006	CD
cord-346267-l08ld2cy	39	2	;	;	:
cord-346267-l08ld2cy	39	3	Pybus	Pybus	NNP
cord-346267-l08ld2cy	39	4	et	et	NNP
cord-346267-l08ld2cy	39	5	al	al	NNP
cord-346267-l08ld2cy	39	6	.	.	NNP
cord-346267-l08ld2cy	39	7	2007	2007	CD
cord-346267-l08ld2cy	39	8	)	)	-RRB-
cord-346267-l08ld2cy	39	9	.	.	.
cord-346267-l08ld2cy	40	1	Although	although	IN
cord-346267-l08ld2cy	40	2	the	the	DT
cord-346267-l08ld2cy	40	3	effect	effect	NN
cord-346267-l08ld2cy	40	4	of	of	IN
cord-346267-l08ld2cy	40	5	purifying	purify	VBG
cord-346267-l08ld2cy	40	6	selection	selection	NN
cord-346267-l08ld2cy	40	7	on	on	IN
cord-346267-l08ld2cy	40	8	mutations	mutation	NNS
cord-346267-l08ld2cy	40	9	in	in	IN
cord-346267-l08ld2cy	40	10	RNA	RNA	NNP
cord-346267-l08ld2cy	40	11	viruses	virus	NNS
cord-346267-l08ld2cy	40	12	is	be	VBZ
cord-346267-l08ld2cy	40	13	becoming	become	VBG
cord-346267-l08ld2cy	40	14	better	well	RBR
cord-346267-l08ld2cy	40	15	understood	understand	VBN
cord-346267-l08ld2cy	40	16	(	(	-LRB-
cord-346267-l08ld2cy	40	17	Belshaw	Belshaw	NNP
cord-346267-l08ld2cy	40	18	et	et	NNP
cord-346267-l08ld2cy	40	19	al	al	NNP
cord-346267-l08ld2cy	40	20	.	.	NNP
cord-346267-l08ld2cy	40	21	2008	2008	CD
cord-346267-l08ld2cy	40	22	)	)	-RRB-
cord-346267-l08ld2cy	40	23	,	,	,
cord-346267-l08ld2cy	40	24	the	the	DT
cord-346267-l08ld2cy	40	25	importance	importance	NN
cord-346267-l08ld2cy	40	26	of	of	IN
cord-346267-l08ld2cy	40	27	spatial	spatial	JJ
cord-346267-l08ld2cy	40	28	and	and	CC
cord-346267-l08ld2cy	40	29	temporal	temporal	JJ
cord-346267-l08ld2cy	40	30	variation	variation	NN
cord-346267-l08ld2cy	40	31	in	in	IN
cord-346267-l08ld2cy	40	32	selection	selection	NN
cord-346267-l08ld2cy	40	33	pressures	pressure	NNS
cord-346267-l08ld2cy	40	34	has	have	VBZ
cord-346267-l08ld2cy	40	35	not	not	RB
cord-346267-l08ld2cy	40	36	been	be	VBN
cord-346267-l08ld2cy	40	37	explicitly	explicitly	RB
cord-346267-l08ld2cy	40	38	explored	explore	VBN
cord-346267-l08ld2cy	40	39	in	in	IN
cord-346267-l08ld2cy	40	40	the	the	DT
cord-346267-l08ld2cy	40	41	context	context	NN
cord-346267-l08ld2cy	40	42	of	of	IN
cord-346267-l08ld2cy	40	43	tMRCA	tmrca	NN
cord-346267-l08ld2cy	40	44	estimation	estimation	NN
cord-346267-l08ld2cy	40	45	.	.	.
cord-346267-l08ld2cy	41	1	It	-PRON-	PRP
cord-346267-l08ld2cy	41	2	has	have	VBZ
cord-346267-l08ld2cy	41	3	been	be	VBN
cord-346267-l08ld2cy	41	4	well	well	RB
cord-346267-l08ld2cy	41	5	established	establish	VBN
cord-346267-l08ld2cy	41	6	that	that	IN
cord-346267-l08ld2cy	41	7	failing	fail	VBG
cord-346267-l08ld2cy	41	8	to	to	TO
cord-346267-l08ld2cy	41	9	account	account	VB
cord-346267-l08ld2cy	41	10	for	for	IN
cord-346267-l08ld2cy	41	11	site	site	NN
cord-346267-l08ld2cy	41	12	-	-	HYPH
cord-346267-l08ld2cy	41	13	to	to	IN
cord-346267-l08ld2cy	41	14	-	-	HYPH
cord-346267-l08ld2cy	41	15	site	site	NN
cord-346267-l08ld2cy	41	16	rate	rate	NN
cord-346267-l08ld2cy	41	17	variation	variation	NN
cord-346267-l08ld2cy	41	18	can	can	MD
cord-346267-l08ld2cy	41	19	lead	lead	VB
cord-346267-l08ld2cy	41	20	to	to	IN
cord-346267-l08ld2cy	41	21	an	an	DT
cord-346267-l08ld2cy	41	22	underestimation	underestimation	NN
cord-346267-l08ld2cy	41	23	of	of	IN
cord-346267-l08ld2cy	41	24	branch	branch	NN
cord-346267-l08ld2cy	41	25	lengths	length	NNS
cord-346267-l08ld2cy	41	26	due	due	JJ
cord-346267-l08ld2cy	41	27	to	to	IN
cord-346267-l08ld2cy	41	28	repeated	repeat	VBN
cord-346267-l08ld2cy	41	29	substitutions	substitution	NNS
cord-346267-l08ld2cy	41	30	at	at	IN
cord-346267-l08ld2cy	41	31	rapidly	rapidly	RB
cord-346267-l08ld2cy	41	32	evolving	evolve	VBG
cord-346267-l08ld2cy	41	33	sites	site	NNS
cord-346267-l08ld2cy	41	34	(	(	-LRB-
cord-346267-l08ld2cy	41	35	Brown	Brown	NNP
cord-346267-l08ld2cy	41	36	et	et	NNP
cord-346267-l08ld2cy	41	37	al	al	NNP
cord-346267-l08ld2cy	41	38	.	.	NNP
cord-346267-l08ld2cy	41	39	1982	1982	CD
cord-346267-l08ld2cy	41	40	;	;	:
cord-346267-l08ld2cy	41	41	Sullivan	Sullivan	NNP
cord-346267-l08ld2cy	41	42	and	and	CC
cord-346267-l08ld2cy	41	43	Joyce	Joyce	NNP
cord-346267-l08ld2cy	41	44	2005	2005	CD
cord-346267-l08ld2cy	41	45	)	)	-RRB-
cord-346267-l08ld2cy	41	46	,	,	,
cord-346267-l08ld2cy	41	47	and	and	CC
cord-346267-l08ld2cy	41	48	the	the	DT
cord-346267-l08ld2cy	41	49	use	use	NN
cord-346267-l08ld2cy	41	50	of	of	IN
cord-346267-l08ld2cy	41	51	models	model	NNS
cord-346267-l08ld2cy	41	52	,	,	,
cord-346267-l08ld2cy	41	53	which	which	WDT
cord-346267-l08ld2cy	41	54	permit	permit	VBP
cord-346267-l08ld2cy	41	55	such	such	JJ
cord-346267-l08ld2cy	41	56	variation	variation	NN
cord-346267-l08ld2cy	41	57	(	(	-LRB-
cord-346267-l08ld2cy	41	58	e.g.	e.g.	RB
cord-346267-l08ld2cy	41	59	,	,	,
cord-346267-l08ld2cy	41	60	Yang	Yang	NNP
cord-346267-l08ld2cy	41	61	1993	1993	CD
cord-346267-l08ld2cy	41	62	)	)	-RRB-
cord-346267-l08ld2cy	41	63	,	,	,
cord-346267-l08ld2cy	41	64	have	have	VBP
cord-346267-l08ld2cy	41	65	become	become	VBN
cord-346267-l08ld2cy	41	66	standard	standard	JJ
cord-346267-l08ld2cy	41	67	.	.	.
cord-346267-l08ld2cy	42	1	More	more	RBR
cord-346267-l08ld2cy	42	2	recently	recently	RB
cord-346267-l08ld2cy	42	3	,	,	,
cord-346267-l08ld2cy	42	4	Suchard	Suchard	NNP
cord-346267-l08ld2cy	42	5	and	and	CC
cord-346267-l08ld2cy	42	6	Rambaut	Rambaut	NNP
cord-346267-l08ld2cy	42	7	(	(	-LRB-
cord-346267-l08ld2cy	42	8	2009	2009	CD
cord-346267-l08ld2cy	42	9	)	)	-RRB-
cord-346267-l08ld2cy	42	10	observed	observe	VBD
cord-346267-l08ld2cy	42	11	that	that	IN
cord-346267-l08ld2cy	42	12	synonymous	synonymous	JJ
cord-346267-l08ld2cy	42	13	substitutions	substitution	NNS
cord-346267-l08ld2cy	42	14	appeared	appear	VBD
cord-346267-l08ld2cy	42	15	to	to	TO
cord-346267-l08ld2cy	42	16	saturate	saturate	VB
cord-346267-l08ld2cy	42	17	faster	fast	RBR
cord-346267-l08ld2cy	42	18	than	than	IN
cord-346267-l08ld2cy	42	19	could	could	MD
cord-346267-l08ld2cy	42	20	be	be	VB
cord-346267-l08ld2cy	42	21	handled	handle	VBN
cord-346267-l08ld2cy	42	22	by	by	IN
cord-346267-l08ld2cy	42	23	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	42	24	models	model	NNS
cord-346267-l08ld2cy	42	25	in	in	IN
cord-346267-l08ld2cy	42	26	mitochondrial	mitochondrial	JJ
cord-346267-l08ld2cy	42	27	DNA	dna	NN
cord-346267-l08ld2cy	42	28	,	,	,
cord-346267-l08ld2cy	42	29	which	which	WDT
cord-346267-l08ld2cy	42	30	is	be	VBZ
cord-346267-l08ld2cy	42	31	subject	subject	JJ
cord-346267-l08ld2cy	42	32	to	to	IN
cord-346267-l08ld2cy	42	33	strong	strong	JJ
cord-346267-l08ld2cy	42	34	overall	overall	JJ
cord-346267-l08ld2cy	42	35	purifying	purifying	NN
cord-346267-l08ld2cy	42	36	selection	selection	NN
cord-346267-l08ld2cy	42	37	.	.	.
cord-346267-l08ld2cy	43	1	Over	over	IN
cord-346267-l08ld2cy	43	2	longer	long	JJR
cord-346267-l08ld2cy	43	3	periods	period	NNS
cord-346267-l08ld2cy	43	4	of	of	IN
cord-346267-l08ld2cy	43	5	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	43	6	time	time	NN
cord-346267-l08ld2cy	43	7	(	(	-LRB-
cord-346267-l08ld2cy	43	8	i.e.	i.e.	FW
cord-346267-l08ld2cy	43	9	,	,	,
cord-346267-l08ld2cy	43	10	along	along	IN
cord-346267-l08ld2cy	43	11	long	long	JJ
cord-346267-l08ld2cy	43	12	internal	internal	JJ
cord-346267-l08ld2cy	43	13	branches	branch	NNS
cord-346267-l08ld2cy	43	14	on	on	IN
cord-346267-l08ld2cy	43	15	a	a	DT
cord-346267-l08ld2cy	43	16	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	43	17	tree	tree	NN
cord-346267-l08ld2cy	43	18	)	)	-RRB-
cord-346267-l08ld2cy	43	19	,	,	,
cord-346267-l08ld2cy	43	20	evidence	evidence	NN
cord-346267-l08ld2cy	43	21	of	of	IN
cord-346267-l08ld2cy	43	22	evolution	evolution	NN
cord-346267-l08ld2cy	43	23	at	at	IN
cord-346267-l08ld2cy	43	24	the	the	DT
cord-346267-l08ld2cy	43	25	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	43	26	level	level	NN
cord-346267-l08ld2cy	43	27	could	could	MD
cord-346267-l08ld2cy	43	28	be	be	VB
cord-346267-l08ld2cy	43	29	lost	lose	VBN
cord-346267-l08ld2cy	43	30	,	,	,
cord-346267-l08ld2cy	43	31	which	which	WDT
cord-346267-l08ld2cy	43	32	could	could	MD
cord-346267-l08ld2cy	43	33	bias	bias	VB
cord-346267-l08ld2cy	43	34	tMRCA	tmrca	NN
cord-346267-l08ld2cy	43	35	estimates	estimate	NNS
cord-346267-l08ld2cy	43	36	towards	towards	IN
cord-346267-l08ld2cy	43	37	younger	young	JJR
cord-346267-l08ld2cy	43	38	dates	date	NNS
cord-346267-l08ld2cy	43	39	(	(	-LRB-
cord-346267-l08ld2cy	43	40	i.e.	i.e.	FW
cord-346267-l08ld2cy	43	41	,	,	,
cord-346267-l08ld2cy	43	42	underestimate	underestimate	VB
cord-346267-l08ld2cy	43	43	the	the	DT
cord-346267-l08ld2cy	43	44	length	length	NN
cord-346267-l08ld2cy	43	45	of	of	IN
cord-346267-l08ld2cy	43	46	these	these	DT
cord-346267-l08ld2cy	43	47	branches	branch	NNS
cord-346267-l08ld2cy	43	48	)	)	-RRB-
cord-346267-l08ld2cy	43	49	.	.	.
cord-346267-l08ld2cy	44	1	If	if	IN
cord-346267-l08ld2cy	44	2	a	a	DT
cord-346267-l08ld2cy	44	3	substitution	substitution	NN
cord-346267-l08ld2cy	44	4	model	model	NN
cord-346267-l08ld2cy	44	5	can	can	MD
cord-346267-l08ld2cy	44	6	account	account	VB
cord-346267-l08ld2cy	44	7	for	for	IN
cord-346267-l08ld2cy	44	8	this	this	DT
cord-346267-l08ld2cy	44	9	evolution	evolution	NN
cord-346267-l08ld2cy	44	10	,	,	,
cord-346267-l08ld2cy	44	11	we	-PRON-	PRP
cord-346267-l08ld2cy	44	12	hypothesize	hypothesize	VBP
cord-346267-l08ld2cy	44	13	that	that	IN
cord-346267-l08ld2cy	44	14	a	a	DT
cord-346267-l08ld2cy	44	15	comparative	comparative	JJ
cord-346267-l08ld2cy	44	16	analysis	analysis	NN
cord-346267-l08ld2cy	44	17	of	of	IN
cord-346267-l08ld2cy	44	18	recent	recent	JJ
cord-346267-l08ld2cy	44	19	viral	viral	JJ
cord-346267-l08ld2cy	44	20	isolates	isolate	NNS
cord-346267-l08ld2cy	44	21	could	could	MD
cord-346267-l08ld2cy	44	22	be	be	VB
cord-346267-l08ld2cy	44	23	used	use	VBN
cord-346267-l08ld2cy	44	24	to	to	TO
cord-346267-l08ld2cy	44	25	make	make	VB
cord-346267-l08ld2cy	44	26	inference	inference	NN
cord-346267-l08ld2cy	44	27	about	about	IN
cord-346267-l08ld2cy	44	28	ancient	ancient	JJ
cord-346267-l08ld2cy	44	29	viral	viral	JJ
cord-346267-l08ld2cy	44	30	divergence	divergence	NN
cord-346267-l08ld2cy	44	31	events	event	NNS
cord-346267-l08ld2cy	44	32	.	.	.
cord-346267-l08ld2cy	45	1	Our	-PRON-	PRP$
cord-346267-l08ld2cy	45	2	work	work	NN
cord-346267-l08ld2cy	45	3	addresses	address	VBZ
cord-346267-l08ld2cy	45	4	two	two	CD
cord-346267-l08ld2cy	45	5	questions	question	NNS
cord-346267-l08ld2cy	45	6	.	.	.
cord-346267-l08ld2cy	46	1	First	first	RB
cord-346267-l08ld2cy	46	2	,	,	,
cord-346267-l08ld2cy	46	3	can	can	MD
cord-346267-l08ld2cy	46	4	purifying	purify	VBG
cord-346267-l08ld2cy	46	5	selection	selection	NN
cord-346267-l08ld2cy	46	6	mask	mask	NN
cord-346267-l08ld2cy	46	7	the	the	DT
cord-346267-l08ld2cy	46	8	ancient	ancient	JJ
cord-346267-l08ld2cy	46	9	history	history	NN
cord-346267-l08ld2cy	46	10	of	of	IN
cord-346267-l08ld2cy	46	11	RNA	RNA	NNP
cord-346267-l08ld2cy	46	12	viruses	virus	NNS
cord-346267-l08ld2cy	46	13	?	?	.
cord-346267-l08ld2cy	47	1	And	and	CC
cord-346267-l08ld2cy	47	2	second	second	JJ
cord-346267-l08ld2cy	47	3	,	,	,
cord-346267-l08ld2cy	47	4	by	by	IN
cord-346267-l08ld2cy	47	5	using	use	VBG
cord-346267-l08ld2cy	47	6	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	47	7	models	model	NNS
cord-346267-l08ld2cy	47	8	that	that	WDT
cord-346267-l08ld2cy	47	9	account	account	VBP
cord-346267-l08ld2cy	47	10	for	for	IN
cord-346267-l08ld2cy	47	11	selection	selection	NN
cord-346267-l08ld2cy	47	12	,	,	,
cord-346267-l08ld2cy	47	13	can	can	MD
cord-346267-l08ld2cy	47	14	we	-PRON-	PRP
cord-346267-l08ld2cy	47	15	infer	infer	VB
cord-346267-l08ld2cy	47	16	more	more	RBR
cord-346267-l08ld2cy	47	17	realistic	realistic	JJ
cord-346267-l08ld2cy	47	18	estimates	estimate	NNS
cord-346267-l08ld2cy	47	19	of	of	IN
cord-346267-l08ld2cy	47	20	the	the	DT
cord-346267-l08ld2cy	47	21	ages	age	NNS
cord-346267-l08ld2cy	47	22	of	of	IN
cord-346267-l08ld2cy	47	23	these	these	DT
cord-346267-l08ld2cy	47	24	viruses	virus	NNS
cord-346267-l08ld2cy	47	25	?	?	.
cord-346267-l08ld2cy	48	1	We	-PRON-	PRP
cord-346267-l08ld2cy	48	2	investigate	investigate	VBP
cord-346267-l08ld2cy	48	3	these	these	DT
cord-346267-l08ld2cy	48	4	questions	question	NNS
cord-346267-l08ld2cy	48	5	using	use	VBG
cord-346267-l08ld2cy	48	6	two	two	CD
cord-346267-l08ld2cy	48	7	groups	group	NNS
cord-346267-l08ld2cy	48	8	of	of	IN
cord-346267-l08ld2cy	48	9	viruses	virus	NNS
cord-346267-l08ld2cy	48	10	thought	think	VBN
cord-346267-l08ld2cy	48	11	to	to	TO
cord-346267-l08ld2cy	48	12	be	be	VB
cord-346267-l08ld2cy	48	13	older	old	JJR
cord-346267-l08ld2cy	48	14	than	than	IN
cord-346267-l08ld2cy	48	15	current	current	JJ
cord-346267-l08ld2cy	48	16	molecular	molecular	JJ
cord-346267-l08ld2cy	48	17	dating	date	VBG
cord-346267-l08ld2cy	48	18	evidence	evidence	NN
cord-346267-l08ld2cy	48	19	would	would	MD
cord-346267-l08ld2cy	48	20	suggest	suggest	VB
cord-346267-l08ld2cy	48	21	:	:	:
cord-346267-l08ld2cy	48	22	MeV	MeV	NNP
cord-346267-l08ld2cy	48	23	/	/	SYM
cord-346267-l08ld2cy	48	24	RPV	RPV	NNP
cord-346267-l08ld2cy	48	25	/	/	SYM
cord-346267-l08ld2cy	48	26	PPRV	PPRV	NNP
cord-346267-l08ld2cy	48	27	and	and	CC
cord-346267-l08ld2cy	48	28	EBOV	EBOV	NNP
cord-346267-l08ld2cy	48	29	.	.	.
cord-346267-l08ld2cy	49	1	We	-PRON-	PRP
cord-346267-l08ld2cy	49	2	also	also	RB
cord-346267-l08ld2cy	49	3	consider	consider	VBP
cord-346267-l08ld2cy	49	4	avian	avian	JJ
cord-346267-l08ld2cy	49	5	influenza	influenza	NN
cord-346267-l08ld2cy	49	6	virus	virus	NN
cord-346267-l08ld2cy	49	7	(	(	-LRB-
cord-346267-l08ld2cy	49	8	AIV)another	aiv)another	RB
cord-346267-l08ld2cy	49	9	well	well	RB
cord-346267-l08ld2cy	49	10	-	-	HYPH
cord-346267-l08ld2cy	49	11	characterized	characterize	VBN
cord-346267-l08ld2cy	49	12	viral	viral	JJ
cord-346267-l08ld2cy	49	13	lineage	lineage	NN
cord-346267-l08ld2cy	49	14	with	with	IN
cord-346267-l08ld2cy	49	15	a	a	DT
cord-346267-l08ld2cy	49	16	young	young	JJ
cord-346267-l08ld2cy	49	17	inferred	infer	VBN
cord-346267-l08ld2cy	49	18	tMRCA	tmrca	NN
cord-346267-l08ld2cy	49	19	and	and	CC
cord-346267-l08ld2cy	49	20	long	long	JJ
cord-346267-l08ld2cy	49	21	internal	internal	JJ
cord-346267-l08ld2cy	49	22	branches	branch	NNS
cord-346267-l08ld2cy	49	23	between	between	IN
cord-346267-l08ld2cy	49	24	different	different	JJ
cord-346267-l08ld2cy	49	25	serotypes	serotype	NNS
cord-346267-l08ld2cy	49	26	Holmes	Holmes	NNP
cord-346267-l08ld2cy	49	27	2006	2006	CD
cord-346267-l08ld2cy	49	28	,	,	,
cord-346267-l08ld2cy	49	29	2010	2010	CD
cord-346267-l08ld2cy	49	30	)	)	-RRB-
cord-346267-l08ld2cy	49	31	.	.	.
cord-346267-l08ld2cy	50	1	The	the	DT
cord-346267-l08ld2cy	50	2	results	result	NNS
cord-346267-l08ld2cy	50	3	presented	present	VBN
cord-346267-l08ld2cy	50	4	here	here	RB
cord-346267-l08ld2cy	50	5	demonstrate	demonstrate	VBP
cord-346267-l08ld2cy	50	6	that	that	IN
cord-346267-l08ld2cy	50	7	not	not	RB
cord-346267-l08ld2cy	50	8	accounting	account	VBG
cord-346267-l08ld2cy	50	9	for	for	IN
cord-346267-l08ld2cy	50	10	purifying	purify	VBG
cord-346267-l08ld2cy	50	11	selection	selection	NN
cord-346267-l08ld2cy	50	12	may	may	MD
cord-346267-l08ld2cy	50	13	bias	bias	VB
cord-346267-l08ld2cy	50	14	tMRCA	tmrca	NN
cord-346267-l08ld2cy	50	15	estimation	estimation	NN
cord-346267-l08ld2cy	50	16	in	in	IN
cord-346267-l08ld2cy	50	17	RNA	RNA	NNP
cord-346267-l08ld2cy	50	18	viruses	virus	NNS
cord-346267-l08ld2cy	50	19	towards	towards	IN
cord-346267-l08ld2cy	50	20	more	more	RBR
cord-346267-l08ld2cy	50	21	recent	recent	JJ
cord-346267-l08ld2cy	50	22	dates	date	NNS
cord-346267-l08ld2cy	50	23	,	,	,
cord-346267-l08ld2cy	50	24	and	and	CC
cord-346267-l08ld2cy	50	25	a	a	DT
cord-346267-l08ld2cy	50	26	degree	degree	NN
cord-346267-l08ld2cy	50	27	of	of	IN
cord-346267-l08ld2cy	50	28	correction	correction	NN
cord-346267-l08ld2cy	50	29	can	can	MD
cord-346267-l08ld2cy	50	30	be	be	VB
cord-346267-l08ld2cy	50	31	realized	realize	VBN
cord-346267-l08ld2cy	50	32	by	by	IN
cord-346267-l08ld2cy	50	33	employing	employ	VBG
cord-346267-l08ld2cy	50	34	more	more	RBR
cord-346267-l08ld2cy	50	35	realistic	realistic	JJ
cord-346267-l08ld2cy	50	36	codon	codon	NN
cord-346267-l08ld2cy	50	37	-	-	HYPH
cord-346267-l08ld2cy	50	38	based	base	VBN
cord-346267-l08ld2cy	50	39	substitution	substitution	NN
cord-346267-l08ld2cy	50	40	models	model	NNS
cord-346267-l08ld2cy	50	41	,	,	,
cord-346267-l08ld2cy	50	42	capable	capable	JJ
cord-346267-l08ld2cy	50	43	of	of	IN
cord-346267-l08ld2cy	50	44	partially	partially	RB
cord-346267-l08ld2cy	50	45	accounting	account	VBG
cord-346267-l08ld2cy	50	46	for	for	IN
cord-346267-l08ld2cy	50	47	the	the	DT
cord-346267-l08ld2cy	50	48	biasing	biasing	NN
cord-346267-l08ld2cy	50	49	effect	effect	NN
cord-346267-l08ld2cy	50	50	of	of	IN
cord-346267-l08ld2cy	50	51	purifying	purify	VBG
cord-346267-l08ld2cy	50	52	selection	selection	NN
cord-346267-l08ld2cy	50	53	.	.	.
cord-346267-l08ld2cy	51	1	For	for	IN
cord-346267-l08ld2cy	51	2	MeV	MeV	NNP
cord-346267-l08ld2cy	51	3	/	/	SYM
cord-346267-l08ld2cy	51	4	RPV	RPV	NNP
cord-346267-l08ld2cy	51	5	/	/	SYM
cord-346267-l08ld2cy	51	6	PPRV	PPRV	NNP
cord-346267-l08ld2cy	51	7	,	,	,
cord-346267-l08ld2cy	51	8	all	all	DT
cord-346267-l08ld2cy	51	9	available	available	JJ
cord-346267-l08ld2cy	51	10	full	full	JJ
cord-346267-l08ld2cy	51	11	-	-	HYPH
cord-346267-l08ld2cy	51	12	length	length	NN
cord-346267-l08ld2cy	51	13	nucleoprotein	nucleoprotein	JJ
cord-346267-l08ld2cy	51	14	sequences	sequence	NNS
cord-346267-l08ld2cy	51	15	with	with	IN
cord-346267-l08ld2cy	51	16	known	know	VBN
cord-346267-l08ld2cy	51	17	years	year	NNS
cord-346267-l08ld2cy	51	18	of	of	IN
cord-346267-l08ld2cy	51	19	isolation	isolation	NN
cord-346267-l08ld2cy	51	20	were	be	VBD
cord-346267-l08ld2cy	51	21	downloaded	download	VBN
cord-346267-l08ld2cy	51	22	from	from	IN
cord-346267-l08ld2cy	51	23	GenBank	GenBank	NNP
cord-346267-l08ld2cy	51	24	.	.	.
cord-346267-l08ld2cy	52	1	Vaccine	vaccine	NN
cord-346267-l08ld2cy	52	2	-	-	HYPH
cord-346267-l08ld2cy	52	3	associated	associate	VBN
cord-346267-l08ld2cy	52	4	sequences	sequence	NNS
cord-346267-l08ld2cy	52	5	and	and	CC
cord-346267-l08ld2cy	52	6	MeV	MeV	NNP
cord-346267-l08ld2cy	52	7	isolates	isolate	VBZ
cord-346267-l08ld2cy	52	8	implicated	implicate	VBN
cord-346267-l08ld2cy	52	9	in	in	IN
cord-346267-l08ld2cy	52	10	subacute	subacute	JJ
cord-346267-l08ld2cy	52	11	sclerosing	sclerosing	NN
cord-346267-l08ld2cy	52	12	panencephalitis	panencephalitis	NN
cord-346267-l08ld2cy	52	13	,	,	,
cord-346267-l08ld2cy	52	14	which	which	WDT
cord-346267-l08ld2cy	52	15	experience	experience	NN
cord-346267-l08ld2cy	52	16	hypermutation	hypermutation	NN
cord-346267-l08ld2cy	53	1	(	(	-LRB-
cord-346267-l08ld2cy	53	2	Woelk	Woelk	NNP
cord-346267-l08ld2cy	53	3	et	et	NNP
cord-346267-l08ld2cy	53	4	al	al	NNP
cord-346267-l08ld2cy	53	5	.	.	.
cord-346267-l08ld2cy	54	1	2001	2001	CD
cord-346267-l08ld2cy	55	1	(	(	-LRB-
cord-346267-l08ld2cy	55	2	Woelk	Woelk	NNP
cord-346267-l08ld2cy	55	3	et	et	NNP
cord-346267-l08ld2cy	55	4	al	al	NNP
cord-346267-l08ld2cy	55	5	.	.	NNP
cord-346267-l08ld2cy	55	6	,	,	,
cord-346267-l08ld2cy	55	7	2002	2002	CD
cord-346267-l08ld2cy	55	8	,	,	,
cord-346267-l08ld2cy	55	9	were	be	VBD
cord-346267-l08ld2cy	55	10	excluded	exclude	VBN
cord-346267-l08ld2cy	55	11	.	.	.
cord-346267-l08ld2cy	56	1	The	the	DT
cord-346267-l08ld2cy	56	2	curated	curate	VBN
cord-346267-l08ld2cy	56	3	MeV	MeV	NNP
cord-346267-l08ld2cy	56	4	/	/	SYM
cord-346267-l08ld2cy	56	5	RPV	RPV	NNP
cord-346267-l08ld2cy	56	6	/	/	SYM
cord-346267-l08ld2cy	56	7	PPRV	PPRV	NNP
cord-346267-l08ld2cy	56	8	virus	virus	NN
cord-346267-l08ld2cy	56	9	data	datum	NNS
cord-346267-l08ld2cy	56	10	set	set	VBN
cord-346267-l08ld2cy	56	11	contained	contain	VBD
cord-346267-l08ld2cy	56	12	145	145	CD
cord-346267-l08ld2cy	56	13	sequences	sequence	NNS
cord-346267-l08ld2cy	56	14	sampled	sample	VBN
cord-346267-l08ld2cy	56	15	between	between	IN
cord-346267-l08ld2cy	56	16	1981	1981	CD
cord-346267-l08ld2cy	56	17	and	and	CC
cord-346267-l08ld2cy	56	18	2007	2007	CD
cord-346267-l08ld2cy	56	19	.	.	.
cord-346267-l08ld2cy	57	1	Alignment	Alignment	NNP
cord-346267-l08ld2cy	57	2	was	be	VBD
cord-346267-l08ld2cy	57	3	trivial	trivial	JJ
cord-346267-l08ld2cy	57	4	due	due	IN
cord-346267-l08ld2cy	57	5	to	to	IN
cord-346267-l08ld2cy	57	6	a	a	DT
cord-346267-l08ld2cy	57	7	lack	lack	NN
cord-346267-l08ld2cy	57	8	of	of	IN
cord-346267-l08ld2cy	57	9	insertions	insertion	NNS
cord-346267-l08ld2cy	57	10	or	or	CC
cord-346267-l08ld2cy	57	11	deletions	deletion	NNS
cord-346267-l08ld2cy	57	12	and	and	CC
cord-346267-l08ld2cy	57	13	was	be	VBD
cord-346267-l08ld2cy	57	14	performed	perform	VBN
cord-346267-l08ld2cy	57	15	by	by	IN
cord-346267-l08ld2cy	57	16	eye	eye	NN
cord-346267-l08ld2cy	57	17	.	.	.
cord-346267-l08ld2cy	58	1	Next	next	RB
cord-346267-l08ld2cy	58	2	,	,	,
cord-346267-l08ld2cy	58	3	EBOV	EBOV	NNP
cord-346267-l08ld2cy	58	4	full	full	JJ
cord-346267-l08ld2cy	58	5	-	-	HYPH
cord-346267-l08ld2cy	58	6	length	length	NN
cord-346267-l08ld2cy	58	7	glycoprotein	glycoprotein	NN
cord-346267-l08ld2cy	58	8	sequences	sequence	NNS
cord-346267-l08ld2cy	58	9	with	with	IN
cord-346267-l08ld2cy	58	10	known	know	VBN
cord-346267-l08ld2cy	58	11	years	year	NNS
cord-346267-l08ld2cy	58	12	of	of	IN
cord-346267-l08ld2cy	58	13	isolation	isolation	NN
cord-346267-l08ld2cy	58	14	were	be	VBD
cord-346267-l08ld2cy	58	15	downloaded	download	VBN
cord-346267-l08ld2cy	58	16	from	from	IN
cord-346267-l08ld2cy	58	17	GenBank	GenBank	NNP
cord-346267-l08ld2cy	58	18	.	.	.
cord-346267-l08ld2cy	59	1	Regions	region	NNS
cord-346267-l08ld2cy	59	2	containing	contain	VBG
cord-346267-l08ld2cy	59	3	multiple	multiple	JJ
cord-346267-l08ld2cy	59	4	reading	reading	NN
cord-346267-l08ld2cy	59	5	frames	frame	NNS
cord-346267-l08ld2cy	59	6	(	(	-LRB-
cord-346267-l08ld2cy	59	7	Volchkov	Volchkov	NNP
cord-346267-l08ld2cy	59	8	et	et	NNP
cord-346267-l08ld2cy	59	9	al	al	NNP
cord-346267-l08ld2cy	59	10	.	.	NNP
cord-346267-l08ld2cy	59	11	1995	1995	CD
cord-346267-l08ld2cy	59	12	;	;	:
cord-346267-l08ld2cy	59	13	Sanchez	Sanchez	NNP
cord-346267-l08ld2cy	59	14	et	et	NNP
cord-346267-l08ld2cy	59	15	al	al	NNP
cord-346267-l08ld2cy	59	16	.	.	.
cord-346267-l08ld2cy	59	17	1996	1996	CD
cord-346267-l08ld2cy	59	18	)	)	-RRB-
cord-346267-l08ld2cy	59	19	and	and	CC
cord-346267-l08ld2cy	59	20	the	the	DT
cord-346267-l08ld2cy	59	21	mucin	mucin	NN
cord-346267-l08ld2cy	59	22	-	-	HYPH
cord-346267-l08ld2cy	59	23	like	like	JJ
cord-346267-l08ld2cy	59	24	region	region	NN
cord-346267-l08ld2cy	59	25	-	-	,
cord-346267-l08ld2cy	59	26	which	which	WDT
cord-346267-l08ld2cy	59	27	evolves	evolve	VBZ
cord-346267-l08ld2cy	59	28	extremely	extremely	RB
cord-346267-l08ld2cy	59	29	rapidly	rapidly	RB
cord-346267-l08ld2cy	59	30	due	due	JJ
cord-346267-l08ld2cy	59	31	to	to	IN
cord-346267-l08ld2cy	59	32	relaxed	relaxed	JJ
cord-346267-l08ld2cy	59	33	selective	selective	JJ
cord-346267-l08ld2cy	59	34	constraints	constraint	NNS
cord-346267-l08ld2cy	59	35	(	(	-LRB-
cord-346267-l08ld2cy	59	36	Wertheim	Wertheim	NNP
cord-346267-l08ld2cy	59	37	and	and	CC
cord-346267-l08ld2cy	59	38	Worobey	Worobey	NNP
cord-346267-l08ld2cy	59	39	2009b	2009b	CD
cord-346267-l08ld2cy	59	40	)	)	-RRB-
cord-346267-l08ld2cy	60	1	-were	-were	RBR
cord-346267-l08ld2cy	60	2	removed	remove	VBN
cord-346267-l08ld2cy	60	3	.	.	.
cord-346267-l08ld2cy	61	1	The	the	DT
cord-346267-l08ld2cy	61	2	curated	curate	VBN
cord-346267-l08ld2cy	61	3	EBOV	EBOV	NNP
cord-346267-l08ld2cy	61	4	data	datum	NNS
cord-346267-l08ld2cy	61	5	set	set	VBN
cord-346267-l08ld2cy	61	6	contained	contain	VBD
cord-346267-l08ld2cy	61	7	34	34	CD
cord-346267-l08ld2cy	61	8	sequences	sequence	NNS
cord-346267-l08ld2cy	61	9	sampled	sample	VBN
cord-346267-l08ld2cy	61	10	between	between	IN
cord-346267-l08ld2cy	61	11	1976	1976	CD
cord-346267-l08ld2cy	61	12	and	and	CC
cord-346267-l08ld2cy	61	13	2005	2005	CD
cord-346267-l08ld2cy	61	14	.	.	.
cord-346267-l08ld2cy	62	1	As	as	IN
cord-346267-l08ld2cy	62	2	before	before	RB
cord-346267-l08ld2cy	62	3	,	,	,
cord-346267-l08ld2cy	62	4	alignment	alignment	NN
cord-346267-l08ld2cy	62	5	was	be	VBD
cord-346267-l08ld2cy	62	6	trivial	trivial	JJ
cord-346267-l08ld2cy	62	7	and	and	CC
cord-346267-l08ld2cy	62	8	performed	perform	VBN
cord-346267-l08ld2cy	62	9	by	by	IN
cord-346267-l08ld2cy	62	10	eye	eye	NN
cord-346267-l08ld2cy	62	11	.	.	.
cord-346267-l08ld2cy	63	1	The	the	DT
cord-346267-l08ld2cy	63	2	final	final	JJ
cord-346267-l08ld2cy	63	3	alignment	alignment	NN
cord-346267-l08ld2cy	63	4	,	,	,
cord-346267-l08ld2cy	63	5	AIV	AIV	NNP
cord-346267-l08ld2cy	63	6	neuraminidase	neuraminidase	NN
cord-346267-l08ld2cy	63	7	,	,	,
cord-346267-l08ld2cy	63	8	was	be	VBD
cord-346267-l08ld2cy	63	9	provided	provide	VBN
cord-346267-l08ld2cy	63	10	by	by	IN
cord-346267-l08ld2cy	63	11	Chen	Chen	NNP
cord-346267-l08ld2cy	63	12	and	and	CC
cord-346267-l08ld2cy	63	13	Holmes	Holmes	NNP
cord-346267-l08ld2cy	63	14	(	(	-LRB-
cord-346267-l08ld2cy	63	15	2010	2010	CD
cord-346267-l08ld2cy	63	16	)	)	-RRB-
cord-346267-l08ld2cy	63	17	.	.	.
cord-346267-l08ld2cy	64	1	It	-PRON-	PRP
cord-346267-l08ld2cy	64	2	contained	contain	VBD
cord-346267-l08ld2cy	64	3	270	270	CD
cord-346267-l08ld2cy	64	4	sequences	sequence	NNS
cord-346267-l08ld2cy	64	5	sampled	sample	VBN
cord-346267-l08ld2cy	64	6	between	between	IN
cord-346267-l08ld2cy	64	7	1972	1972	CD
cord-346267-l08ld2cy	64	8	and	and	CC
cord-346267-l08ld2cy	64	9	2005	2005	CD
cord-346267-l08ld2cy	64	10	.	.	.
cord-346267-l08ld2cy	65	1	All	all	DT
cord-346267-l08ld2cy	65	2	three	three	CD
cord-346267-l08ld2cy	65	3	alignments	alignment	NNS
cord-346267-l08ld2cy	65	4	in	in	IN
cord-346267-l08ld2cy	65	5	NEXUS	NEXUS	NNP
cord-346267-l08ld2cy	65	6	format	format	NN
cord-346267-l08ld2cy	65	7	can	can	MD
cord-346267-l08ld2cy	65	8	be	be	VB
cord-346267-l08ld2cy	65	9	downloaded	download	VBN
cord-346267-l08ld2cy	65	10	from	from	IN
cord-346267-l08ld2cy	65	11	http://www.hyphy.org/wiki/codondating	http://www.hyphy.org/wiki/codondate	VBG
cord-346267-l08ld2cy	65	12	.	.	.
cord-346267-l08ld2cy	66	1	Redundant	redundant	JJ
cord-346267-l08ld2cy	66	2	sequences	sequence	NNS
cord-346267-l08ld2cy	66	3	were	be	VBD
cord-346267-l08ld2cy	66	4	excluded	exclude	VBN
cord-346267-l08ld2cy	66	5	from	from	IN
cord-346267-l08ld2cy	66	6	the	the	DT
cord-346267-l08ld2cy	66	7	alignments	alignment	NNS
cord-346267-l08ld2cy	66	8	for	for	IN
cord-346267-l08ld2cy	66	9	branch	branch	NN
cord-346267-l08ld2cy	66	10	length	length	NN
cord-346267-l08ld2cy	66	11	comparisons	comparison	NNS
cord-346267-l08ld2cy	66	12	and	and	CC
cord-346267-l08ld2cy	66	13	selection	selection	NN
cord-346267-l08ld2cy	66	14	analyses	analysis	NNS
cord-346267-l08ld2cy	66	15	.	.	.
cord-346267-l08ld2cy	67	1	We	-PRON-	PRP
cord-346267-l08ld2cy	67	2	used	use	VBD
cord-346267-l08ld2cy	67	3	a	a	DT
cord-346267-l08ld2cy	67	4	Bayesian	Bayesian	NNP
cord-346267-l08ld2cy	67	5	Markov	Markov	NNP
cord-346267-l08ld2cy	67	6	chain	chain	NN
cord-346267-l08ld2cy	67	7	Monte	Monte	NNP
cord-346267-l08ld2cy	67	8	Carlo	Carlo	NNP
cord-346267-l08ld2cy	67	9	(	(	-LRB-
cord-346267-l08ld2cy	67	10	BM	BM	NNP
cord-346267-l08ld2cy	67	11	-	-	HYPH
cord-346267-l08ld2cy	67	12	CMC	CMC	NNP
cord-346267-l08ld2cy	67	13	)	)	-RRB-
cord-346267-l08ld2cy	67	14	method	method	NN
cord-346267-l08ld2cy	67	15	implemented	implement	VBN
cord-346267-l08ld2cy	67	16	in	in	IN
cord-346267-l08ld2cy	67	17	BEAST	BEAST	NNP
cord-346267-l08ld2cy	67	18	v1.5.4	v1.5.4	NNP
cord-346267-l08ld2cy	67	19	for	for	IN
cord-346267-l08ld2cy	67	20	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	67	21	inference	inference	NN
cord-346267-l08ld2cy	67	22	and	and	CC
cord-346267-l08ld2cy	67	23	tMRCA	tmrca	NN
cord-346267-l08ld2cy	67	24	estimation	estimation	NN
cord-346267-l08ld2cy	67	25	.	.	.
cord-346267-l08ld2cy	68	1	For	for	IN
cord-346267-l08ld2cy	68	2	each	each	DT
cord-346267-l08ld2cy	68	3	data	data	NN
cord-346267-l08ld2cy	68	4	set	set	VBN
cord-346267-l08ld2cy	68	5	and	and	CC
cord-346267-l08ld2cy	68	6	substitution	substitution	NN
cord-346267-l08ld2cy	68	7	model	model	NN
cord-346267-l08ld2cy	68	8	,	,	,
cord-346267-l08ld2cy	68	9	four	four	CD
cord-346267-l08ld2cy	68	10	independent	independent	JJ
cord-346267-l08ld2cy	68	11	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	68	12	runs	run	VBZ
cord-346267-l08ld2cy	68	13	of	of	IN
cord-346267-l08ld2cy	68	14	25	25	CD
cord-346267-l08ld2cy	68	15	or	or	CC
cord-346267-l08ld2cy	68	16	50	50	CD
cord-346267-l08ld2cy	68	17	million	million	CD
cord-346267-l08ld2cy	68	18	generations	generation	NNS
cord-346267-l08ld2cy	68	19	were	be	VBD
cord-346267-l08ld2cy	68	20	performed	perform	VBN
cord-346267-l08ld2cy	68	21	.	.	.
cord-346267-l08ld2cy	69	1	A	a	DT
cord-346267-l08ld2cy	69	2	codon	codon	NN
cord-346267-l08ld2cy	69	3	-	-	HYPH
cord-346267-l08ld2cy	69	4	based	base	VBN
cord-346267-l08ld2cy	69	5	substitution	substitution	NN
cord-346267-l08ld2cy	69	6	model	model	NN
cord-346267-l08ld2cy	69	7	was	be	VBD
cord-346267-l08ld2cy	69	8	implemented	implement	VBN
cord-346267-l08ld2cy	69	9	in	in	IN
cord-346267-l08ld2cy	69	10	BEAGLE	BEAGLE	NNP
cord-346267-l08ld2cy	69	11	(	(	-LRB-
cord-346267-l08ld2cy	69	12	Suchard	Suchard	NNP
cord-346267-l08ld2cy	69	13	and	and	CC
cord-346267-l08ld2cy	69	14	Rambaut	Rambaut	NNP
cord-346267-l08ld2cy	69	15	2009	2009	CD
cord-346267-l08ld2cy	69	16	)	)	-RRB-
cord-346267-l08ld2cy	69	17	.	.	.
cord-346267-l08ld2cy	70	1	The	the	DT
cord-346267-l08ld2cy	70	2	first	first	JJ
cord-346267-l08ld2cy	70	3	10	10	CD
cord-346267-l08ld2cy	70	4	%	%	NN
cord-346267-l08ld2cy	70	5	of	of	IN
cord-346267-l08ld2cy	70	6	the	the	DT
cord-346267-l08ld2cy	70	7	generations	generation	NNS
cord-346267-l08ld2cy	70	8	were	be	VBD
cord-346267-l08ld2cy	70	9	discarded	discard	VBN
cord-346267-l08ld2cy	70	10	as	as	IN
cord-346267-l08ld2cy	70	11	burn	burn	NN
cord-346267-l08ld2cy	70	12	-	-	HYPH
cord-346267-l08ld2cy	70	13	in	in	NN
cord-346267-l08ld2cy	70	14	.	.	.
cord-346267-l08ld2cy	71	1	All	all	DT
cord-346267-l08ld2cy	71	2	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	71	3	analyses	analysis	NNS
cord-346267-l08ld2cy	71	4	were	be	VBD
cord-346267-l08ld2cy	71	5	performed	perform	VBN
cord-346267-l08ld2cy	71	6	using	use	VBG
cord-346267-l08ld2cy	71	7	an	an	DT
cord-346267-l08ld2cy	71	8	uncorrelated	uncorrelated	JJ
cord-346267-l08ld2cy	71	9	lognormal	lognormal	JJ
cord-346267-l08ld2cy	71	10	relaxed	relaxed	JJ
cord-346267-l08ld2cy	71	11	molecular	molecular	JJ
cord-346267-l08ld2cy	71	12	clock	clock	NN
cord-346267-l08ld2cy	71	13	and	and	CC
cord-346267-l08ld2cy	71	14	a	a	DT
cord-346267-l08ld2cy	71	15	Bayesian	bayesian	JJ
cord-346267-l08ld2cy	71	16	skyline	skyline	NN
cord-346267-l08ld2cy	71	17	plot	plot	NN
cord-346267-l08ld2cy	71	18	coalescent	coalescent	NN
cord-346267-l08ld2cy	71	19	prior	prior	RB
cord-346267-l08ld2cy	71	20	,	,	,
cord-346267-l08ld2cy	71	21	which	which	WDT
cord-346267-l08ld2cy	71	22	places	place	VBZ
cord-346267-l08ld2cy	71	23	the	the	DT
cord-346267-l08ld2cy	71	24	fewest	few	JJS
cord-346267-l08ld2cy	71	25	demographic	demographic	JJ
cord-346267-l08ld2cy	71	26	constraints	constraint	NNS
cord-346267-l08ld2cy	71	27	on	on	IN
cord-346267-l08ld2cy	71	28	the	the	DT
cord-346267-l08ld2cy	71	29	analysis	analysis	NN
cord-346267-l08ld2cy	71	30	.	.	.
cord-346267-l08ld2cy	72	1	Tracer	tracer	NN
cord-346267-l08ld2cy	72	2	v1.5	v1.5	NN
cord-346267-l08ld2cy	72	3	was	be	VBD
cord-346267-l08ld2cy	72	4	used	use	VBN
cord-346267-l08ld2cy	72	5	to	to	TO
cord-346267-l08ld2cy	72	6	check	check	VB
cord-346267-l08ld2cy	72	7	for	for	IN
cord-346267-l08ld2cy	72	8	convergence	convergence	NN
cord-346267-l08ld2cy	72	9	and	and	CC
cord-346267-l08ld2cy	72	10	adequate	adequate	JJ
cord-346267-l08ld2cy	72	11	mixing	mixing	NN
cord-346267-l08ld2cy	72	12	(	(	-LRB-
cord-346267-l08ld2cy	72	13	i.e.	i.e.	FW
cord-346267-l08ld2cy	72	14	,	,	,
cord-346267-l08ld2cy	72	15	estimated	estimate	VBN
cord-346267-l08ld2cy	72	16	sample	sample	NN
cord-346267-l08ld2cy	72	17	size	size	NN
cord-346267-l08ld2cy	72	18	>	>	XX
cord-346267-l08ld2cy	73	1	200	200	CD
cord-346267-l08ld2cy	73	2	for	for	IN
cord-346267-l08ld2cy	73	3	all	all	DT
cord-346267-l08ld2cy	73	4	relevant	relevant	JJ
cord-346267-l08ld2cy	73	5	parameters	parameter	NNS
cord-346267-l08ld2cy	73	6	)	)	-RRB-
cord-346267-l08ld2cy	73	7	.	.	.
cord-346267-l08ld2cy	74	1	Finally	finally	RB
cord-346267-l08ld2cy	74	2	,	,	,
cord-346267-l08ld2cy	74	3	the	the	DT
cord-346267-l08ld2cy	74	4	maximum	maximum	JJ
cord-346267-l08ld2cy	74	5	clade	clade	NN
cord-346267-l08ld2cy	74	6	credibility	credibility	NN
cord-346267-l08ld2cy	74	7	(	(	-LRB-
cord-346267-l08ld2cy	74	8	MCC	MCC	NNP
cord-346267-l08ld2cy	74	9	)	)	-RRB-
cord-346267-l08ld2cy	74	10	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	74	11	was	be	VBD
cord-346267-l08ld2cy	74	12	identified	identify	VBN
cord-346267-l08ld2cy	74	13	and	and	CC
cord-346267-l08ld2cy	74	14	annotated	annotate	VBN
cord-346267-l08ld2cy	74	15	using	use	VBG
cord-346267-l08ld2cy	74	16	the	the	DT
cord-346267-l08ld2cy	74	17	posterior	posterior	JJ
cord-346267-l08ld2cy	74	18	distribution	distribution	NN
cord-346267-l08ld2cy	74	19	of	of	IN
cord-346267-l08ld2cy	74	20	trees	tree	NNS
cord-346267-l08ld2cy	74	21	.	.	.
cord-346267-l08ld2cy	75	1	Substitution	substitution	NN
cord-346267-l08ld2cy	75	2	rates	rate	NNS
cord-346267-l08ld2cy	75	3	and	and	CC
cord-346267-l08ld2cy	75	4	tMRCAs	tmrcas	CD
cord-346267-l08ld2cy	75	5	are	be	VBP
cord-346267-l08ld2cy	75	6	reported	report	VBN
cord-346267-l08ld2cy	75	7	as	as	IN
cord-346267-l08ld2cy	75	8	mean	mean	JJ
cord-346267-l08ld2cy	75	9	and	and	CC
cord-346267-l08ld2cy	75	10	95	95	CD
cord-346267-l08ld2cy	75	11	%	%	NN
cord-346267-l08ld2cy	75	12	highest	high	JJS
cord-346267-l08ld2cy	75	13	posterior	posterior	JJ
cord-346267-l08ld2cy	75	14	density	density	NN
cord-346267-l08ld2cy	75	15	values	value	NNS
cord-346267-l08ld2cy	75	16	.	.	.
cord-346267-l08ld2cy	76	1	An	an	DT
cord-346267-l08ld2cy	76	2	earlier	early	JJR
cord-346267-l08ld2cy	76	3	study	study	NN
cord-346267-l08ld2cy	76	4	)	)	-RRB-
cord-346267-l08ld2cy	76	5	developed	develop	VBD
cord-346267-l08ld2cy	76	6	a	a	DT
cord-346267-l08ld2cy	76	7	hierarchy	hierarchy	NN
cord-346267-l08ld2cy	76	8	of	of	IN
cord-346267-l08ld2cy	76	9	five	five	CD
cord-346267-l08ld2cy	76	10	models	model	NNS
cord-346267-l08ld2cy	76	11	-	-	:
cord-346267-l08ld2cy	76	12	all	all	DT
cord-346267-l08ld2cy	76	13	extensions	extension	NNS
cord-346267-l08ld2cy	76	14	of	of	IN
cord-346267-l08ld2cy	76	15	the	the	DT
cord-346267-l08ld2cy	76	16	Muse	Muse	NNP
cord-346267-l08ld2cy	76	17	-	-	HYPH
cord-346267-l08ld2cy	76	18	Gaut	Gaut	NNP
cord-346267-l08ld2cy	76	19	probabilistic	probabilistic	JJ
cord-346267-l08ld2cy	76	20	model	model	NN
cord-346267-l08ld2cy	76	21	of	of	IN
cord-346267-l08ld2cy	76	22	sequence	sequence	NN
cord-346267-l08ld2cy	76	23	evolution	evolution	NN
cord-346267-l08ld2cy	76	24	(	(	-LRB-
cord-346267-l08ld2cy	76	25	Muse	Muse	NNP
cord-346267-l08ld2cy	76	26	and	and	CC
cord-346267-l08ld2cy	76	27	Gaut	Gaut	NNP
cord-346267-l08ld2cy	76	28	1994	1994	CD
cord-346267-l08ld2cy	76	29	)	)	-RRB-
cord-346267-l08ld2cy	77	1	-of	-of	:
cord-346267-l08ld2cy	77	2	differing	differ	VBG
cord-346267-l08ld2cy	77	3	complexities	complexity	NNS
cord-346267-l08ld2cy	77	4	that	that	WDT
cord-346267-l08ld2cy	77	5	incorporate	incorporate	VBP
cord-346267-l08ld2cy	77	6	site	site	NN
cord-346267-l08ld2cy	77	7	-	-	HYPH
cord-346267-l08ld2cy	77	8	tosite	tosite	JJ
cord-346267-l08ld2cy	77	9	and	and	CC
cord-346267-l08ld2cy	77	10	lineage	lineage	NN
cord-346267-l08ld2cy	77	11	-	-	HYPH
cord-346267-l08ld2cy	77	12	to	to	IN
cord-346267-l08ld2cy	77	13	-	-	HYPH
cord-346267-l08ld2cy	77	14	lineage	lineage	NN
cord-346267-l08ld2cy	77	15	variation	variation	NN
cord-346267-l08ld2cy	77	16	of	of	IN
cord-346267-l08ld2cy	77	17	synonymous	synonymous	JJ
cord-346267-l08ld2cy	77	18	(	(	-LRB-
cord-346267-l08ld2cy	77	19	α	α	NN
cord-346267-l08ld2cy	77	20	)	)	-RRB-
cord-346267-l08ld2cy	77	21	and	and	CC
cord-346267-l08ld2cy	77	22	nonsynonymous	nonsynonymous	NNP
cord-346267-l08ld2cy	77	23	(	(	-LRB-
cord-346267-l08ld2cy	77	24	β	β	NN
cord-346267-l08ld2cy	77	25	)	)	-RRB-
cord-346267-l08ld2cy	77	26	substitution	substitution	NN
cord-346267-l08ld2cy	77	27	rates	rate	NNS
cord-346267-l08ld2cy	77	28	.	.	.
cord-346267-l08ld2cy	78	1	We	-PRON-	PRP
cord-346267-l08ld2cy	78	2	investigated	investigate	VBD
cord-346267-l08ld2cy	78	3	the	the	DT
cord-346267-l08ld2cy	78	4	ability	ability	NN
cord-346267-l08ld2cy	78	5	of	of	IN
cord-346267-l08ld2cy	78	6	these	these	DT
cord-346267-l08ld2cy	78	7	models	model	NNS
cord-346267-l08ld2cy	78	8	to	to	TO
cord-346267-l08ld2cy	78	9	accurately	accurately	RB
cord-346267-l08ld2cy	78	10	infer	infer	VB
cord-346267-l08ld2cy	78	11	branch	branch	NN
cord-346267-l08ld2cy	78	12	lengths	length	NNS
cord-346267-l08ld2cy	78	13	on	on	IN
cord-346267-l08ld2cy	78	14	our	-PRON-	PRP$
cord-346267-l08ld2cy	78	15	viral	viral	JJ
cord-346267-l08ld2cy	78	16	data	data	NN
cord-346267-l08ld2cy	78	17	sets	set	NNS
cord-346267-l08ld2cy	78	18	.	.	.
cord-346267-l08ld2cy	79	1	The	the	DT
cord-346267-l08ld2cy	79	2	five	five	CD
cord-346267-l08ld2cy	79	3	models	model	NNS
cord-346267-l08ld2cy	79	4	are	be	VBP
cord-346267-l08ld2cy	79	5	summarized	summarize	VBN
cord-346267-l08ld2cy	79	6	below	below	IN
cord-346267-l08ld2cy	79	7	,	,	,
cord-346267-l08ld2cy	79	8	with	with	IN
cord-346267-l08ld2cy	79	9	full	full	JJ
cord-346267-l08ld2cy	79	10	details	detail	NNS
cord-346267-l08ld2cy	79	11	available	available	JJ
cord-346267-l08ld2cy	79	12	in	in	IN
cord-346267-l08ld2cy	79	13	the	the	DT
cord-346267-l08ld2cy	79	14	original	original	JJ
cord-346267-l08ld2cy	79	15	manuscript	manuscript	NN
cord-346267-l08ld2cy	79	16	.	.	.
cord-346267-l08ld2cy	80	1	Note	note	VB
cord-346267-l08ld2cy	80	2	that	that	IN
cord-346267-l08ld2cy	80	3	in	in	IN
cord-346267-l08ld2cy	80	4	all	all	DT
cord-346267-l08ld2cy	80	5	models	model	NNS
cord-346267-l08ld2cy	80	6	,	,	,
cord-346267-l08ld2cy	80	7	E	E	NNS
cord-346267-l08ld2cy	80	8	[	[	-LRB-
cord-346267-l08ld2cy	80	9	α	α	NN
cord-346267-l08ld2cy	80	10	]	]	-RRB-
cord-346267-l08ld2cy	80	11	=	=	SYM
cord-346267-l08ld2cy	80	12	1	1	CD
cord-346267-l08ld2cy	80	13	to	to	TO
cord-346267-l08ld2cy	80	14	ensure	ensure	VB
cord-346267-l08ld2cy	80	15	identifiability	identifiability	NN
cord-346267-l08ld2cy	80	16	.	.	.
cord-346267-l08ld2cy	81	1	Constant	constant	JJ
cord-346267-l08ld2cy	81	2	Rates	rate	NNS
cord-346267-l08ld2cy	81	3	:	:	:
cord-346267-l08ld2cy	81	4	The	the	DT
cord-346267-l08ld2cy	81	5	baseline	baseline	JJ
cord-346267-l08ld2cy	81	6	model	model	NN
cord-346267-l08ld2cy	81	7	,	,	,
cord-346267-l08ld2cy	81	8	which	which	WDT
cord-346267-l08ld2cy	81	9	extends	extend	VBZ
cord-346267-l08ld2cy	81	10	the	the	DT
cord-346267-l08ld2cy	81	11	original	original	JJ
cord-346267-l08ld2cy	81	12	Muse	Muse	NNP
cord-346267-l08ld2cy	81	13	-	-	HYPH
cord-346267-l08ld2cy	81	14	Gaut	Gaut	NNP
cord-346267-l08ld2cy	81	15	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	81	16	model	model	NN
cord-346267-l08ld2cy	81	17	by	by	IN
cord-346267-l08ld2cy	81	18	incorporating	incorporate	VBG
cord-346267-l08ld2cy	81	19	general	general	JJ
cord-346267-l08ld2cy	81	20	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	81	21	substitution	substitution	NN
cord-346267-l08ld2cy	81	22	biases	bias	NNS
cord-346267-l08ld2cy	81	23	(	(	-LRB-
cord-346267-l08ld2cy	81	24	MG94	MG94	NNP
cord-346267-l08ld2cy	81	25	×	×	NNP
cord-346267-l08ld2cy	81	26	REV	REV	NNP
cord-346267-l08ld2cy	81	27	)	)	-RRB-
cord-346267-l08ld2cy	81	28	.	.	.
cord-346267-l08ld2cy	82	1	α	α	NNP
cord-346267-l08ld2cy	82	2	and	and	CC
cord-346267-l08ld2cy	82	3	β	β	NN
cord-346267-l08ld2cy	82	4	rates	rate	NNS
cord-346267-l08ld2cy	82	5	are	be	VBP
cord-346267-l08ld2cy	82	6	constant	constant	JJ
cord-346267-l08ld2cy	82	7	across	across	IN
cord-346267-l08ld2cy	82	8	sites	site	NNS
cord-346267-l08ld2cy	82	9	and	and	CC
cord-346267-l08ld2cy	82	10	lineages	lineage	NNS
cord-346267-l08ld2cy	82	11	.	.	.
cord-346267-l08ld2cy	83	1	Proportional	proportional	JJ
cord-346267-l08ld2cy	83	2	:	:	:
cord-346267-l08ld2cy	84	1	A	a	DT
cord-346267-l08ld2cy	84	2	direct	direct	JJ
cord-346267-l08ld2cy	84	3	analog	analog	NN
cord-346267-l08ld2cy	84	4	to	to	TO
cord-346267-l08ld2cy	84	5	nucleotide	nucleotide	VB
cord-346267-l08ld2cy	84	6	+	+	CC
cord-346267-l08ld2cy	84	7	Γ	γ	NN
cord-346267-l08ld2cy	84	8	4	4	CD
cord-346267-l08ld2cy	84	9	models	model	NNS
cord-346267-l08ld2cy	84	10	;	;	:
cord-346267-l08ld2cy	84	11	β	β	NN
cord-346267-l08ld2cy	84	12	=	=	SYM
cord-346267-l08ld2cy	84	13	ωα	ωα	NNP
cord-346267-l08ld2cy	84	14	and	and	CC
cord-346267-l08ld2cy	84	15	α	α	NN
cord-346267-l08ld2cy	84	16	varies	vary	VBZ
cord-346267-l08ld2cy	84	17	from	from	IN
cord-346267-l08ld2cy	84	18	site	site	NN
cord-346267-l08ld2cy	84	19	to	to	IN
cord-346267-l08ld2cy	84	20	site	site	NN
cord-346267-l08ld2cy	84	21	according	accord	VBG
cord-346267-l08ld2cy	84	22	to	to	IN
cord-346267-l08ld2cy	84	23	a	a	DT
cord-346267-l08ld2cy	84	24	three	three	CD
cord-346267-l08ld2cy	84	25	-	-	HYPH
cord-346267-l08ld2cy	84	26	bin	bin	NN
cord-346267-l08ld2cy	84	27	general	general	JJ
cord-346267-l08ld2cy	84	28	discrete	discrete	JJ
cord-346267-l08ld2cy	84	29	distribution	distribution	NN
cord-346267-l08ld2cy	84	30	(	(	-LRB-
cord-346267-l08ld2cy	84	31	GDD	GDD	NNP
cord-346267-l08ld2cy	84	32	)	)	-RRB-
cord-346267-l08ld2cy	84	33	.	.	.
cord-346267-l08ld2cy	85	1	Nonsynonymous	Nonsynonymous	NNP
cord-346267-l08ld2cy	85	2	:	:	:
cord-346267-l08ld2cy	86	1	A	a	DT
cord-346267-l08ld2cy	86	2	standard	standard	JJ
cord-346267-l08ld2cy	86	3	"	"	``
cord-346267-l08ld2cy	86	4	selection	selection	NN
cord-346267-l08ld2cy	86	5	"	"	''
cord-346267-l08ld2cy	86	6	model	model	NN
cord-346267-l08ld2cy	86	7	,	,	,
cord-346267-l08ld2cy	86	8	where	where	WRB
cord-346267-l08ld2cy	86	9	α	α	NN
cord-346267-l08ld2cy	86	10	rates	rate	NNS
cord-346267-l08ld2cy	86	11	are	be	VBP
cord-346267-l08ld2cy	86	12	constant	constant	JJ
cord-346267-l08ld2cy	86	13	and	and	CC
cord-346267-l08ld2cy	86	14	β	β	NN
cord-346267-l08ld2cy	86	15	rates	rate	NNS
cord-346267-l08ld2cy	86	16	are	be	VBP
cord-346267-l08ld2cy	86	17	drawn	draw	VBN
cord-346267-l08ld2cy	86	18	from	from	IN
cord-346267-l08ld2cy	86	19	a	a	DT
cord-346267-l08ld2cy	86	20	3bin	3bin	CD
cord-346267-l08ld2cy	86	21	GDD	GDD	NNP
cord-346267-l08ld2cy	86	22	.	.	.
cord-346267-l08ld2cy	87	1	Dual	dual	JJ
cord-346267-l08ld2cy	87	2	:	:	:
cord-346267-l08ld2cy	88	1	A	a	DT
cord-346267-l08ld2cy	88	2	model	model	NN
cord-346267-l08ld2cy	88	3	,	,	,
cord-346267-l08ld2cy	88	4	where	where	WRB
cord-346267-l08ld2cy	88	5	both	both	CC
cord-346267-l08ld2cy	88	6	α	α	NN
cord-346267-l08ld2cy	88	7	and	and	CC
cord-346267-l08ld2cy	88	8	β	β	NN
cord-346267-l08ld2cy	88	9	rates	rate	NNS
cord-346267-l08ld2cy	88	10	vary	vary	VBP
cord-346267-l08ld2cy	88	11	from	from	IN
cord-346267-l08ld2cy	88	12	site	site	NN
cord-346267-l08ld2cy	88	13	to	to	IN
cord-346267-l08ld2cy	88	14	site	site	NN
cord-346267-l08ld2cy	88	15	,	,	,
cord-346267-l08ld2cy	88	16	based	base	VBN
cord-346267-l08ld2cy	88	17	on	on	IN
cord-346267-l08ld2cy	88	18	independent	independent	JJ
cord-346267-l08ld2cy	88	19	three	three	CD
cord-346267-l08ld2cy	88	20	-	-	HYPH
cord-346267-l08ld2cy	88	21	bin	bin	NN
cord-346267-l08ld2cy	88	22	GDD	GDD	NNP
cord-346267-l08ld2cy	88	23	distributions	distribution	NNS
cord-346267-l08ld2cy	88	24	.	.	.
cord-346267-l08ld2cy	89	1	Lineage+Dual	lineage+dual	CC
cord-346267-l08ld2cy	89	2	:	:	:
cord-346267-l08ld2cy	89	3	In	in	IN
cord-346267-l08ld2cy	89	4	addition	addition	NN
cord-346267-l08ld2cy	89	5	to	to	IN
cord-346267-l08ld2cy	89	6	site	site	NN
cord-346267-l08ld2cy	89	7	-	-	HYPH
cord-346267-l08ld2cy	89	8	to	to	IN
cord-346267-l08ld2cy	89	9	-	-	HYPH
cord-346267-l08ld2cy	89	10	site	site	NN
cord-346267-l08ld2cy	89	11	rate	rate	NN
cord-346267-l08ld2cy	89	12	variation	variation	NN
cord-346267-l08ld2cy	89	13	in	in	IN
cord-346267-l08ld2cy	89	14	α	α	NNP
cord-346267-l08ld2cy	89	15	and	and	CC
cord-346267-l08ld2cy	89	16	β	β	NN
cord-346267-l08ld2cy	89	17	,	,	,
cord-346267-l08ld2cy	89	18	some	some	DT
cord-346267-l08ld2cy	89	19	(	(	-LRB-
cord-346267-l08ld2cy	89	20	or	or	CC
cord-346267-l08ld2cy	89	21	all	all	DT
cord-346267-l08ld2cy	89	22	)	)	-RRB-
cord-346267-l08ld2cy	89	23	lineages	lineage	NNS
cord-346267-l08ld2cy	89	24	are	be	VBP
cord-346267-l08ld2cy	89	25	endowed	endow	VBN
cord-346267-l08ld2cy	89	26	with	with	IN
cord-346267-l08ld2cy	89	27	their	-PRON-	PRP$
cord-346267-l08ld2cy	89	28	own	own	JJ
cord-346267-l08ld2cy	89	29	mean	mean	NN
cord-346267-l08ld2cy	89	30	E	e	NN
cord-346267-l08ld2cy	89	31	[	[	-LRB-
cord-346267-l08ld2cy	89	32	β]/E	β]/e	XX
cord-346267-l08ld2cy	89	33	[	[	-LRB-
cord-346267-l08ld2cy	89	34	α	α	NN
cord-346267-l08ld2cy	89	35	]	]	-RRB-
cord-346267-l08ld2cy	89	36	ratios	ratio	NNS
cord-346267-l08ld2cy	89	37	,	,	,
cord-346267-l08ld2cy	89	38	to	to	TO
cord-346267-l08ld2cy	89	39	correct	correct	VB
cord-346267-l08ld2cy	89	40	for	for	IN
cord-346267-l08ld2cy	89	41	"	"	``
cord-346267-l08ld2cy	89	42	lineagespecific	lineagespecific	JJ
cord-346267-l08ld2cy	89	43	"	"	''
cord-346267-l08ld2cy	89	44	effects	effect	NNS
cord-346267-l08ld2cy	89	45	of	of	IN
cord-346267-l08ld2cy	89	46	selection	selection	NN
cord-346267-l08ld2cy	89	47	.	.	.
cord-346267-l08ld2cy	90	1	Unlike	unlike	IN
cord-346267-l08ld2cy	90	2	the	the	DT
cord-346267-l08ld2cy	90	3	original	original	JJ
cord-346267-l08ld2cy	90	4	implementation	implementation	NN
cord-346267-l08ld2cy	90	5	,	,	,
cord-346267-l08ld2cy	90	6	our	-PRON-	PRP$
cord-346267-l08ld2cy	90	7	version	version	NN
cord-346267-l08ld2cy	90	8	of	of	IN
cord-346267-l08ld2cy	90	9	the	the	DT
cord-346267-l08ld2cy	90	10	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	90	11	model	model	NN
cord-346267-l08ld2cy	90	12	treated	treat	VBD
cord-346267-l08ld2cy	90	13	certain	certain	JJ
cord-346267-l08ld2cy	90	14	interior	interior	JJ
cord-346267-l08ld2cy	90	15	lineages	lineage	NNS
cord-346267-l08ld2cy	90	16	differently	differently	RB
cord-346267-l08ld2cy	90	17	to	to	TO
cord-346267-l08ld2cy	90	18	better	better	RB
cord-346267-l08ld2cy	90	19	reflect	reflect	VB
cord-346267-l08ld2cy	90	20	the	the	DT
cord-346267-l08ld2cy	90	21	biological	biological	JJ
cord-346267-l08ld2cy	90	22	reality	reality	NN
cord-346267-l08ld2cy	90	23	of	of	IN
cord-346267-l08ld2cy	90	24	the	the	DT
cord-346267-l08ld2cy	90	25	sample	sample	NN
cord-346267-l08ld2cy	90	26	.	.	.
cord-346267-l08ld2cy	91	1	Branches	branch	NNS
cord-346267-l08ld2cy	91	2	which	which	WDT
cord-346267-l08ld2cy	91	3	separated	separate	VBD
cord-346267-l08ld2cy	91	4	clades	clade	NNS
cord-346267-l08ld2cy	91	5	containing	contain	VBG
cord-346267-l08ld2cy	91	6	different	different	JJ
cord-346267-l08ld2cy	91	7	viral	viral	JJ
cord-346267-l08ld2cy	91	8	species	specie	NNS
cord-346267-l08ld2cy	91	9	(	(	-LRB-
cord-346267-l08ld2cy	91	10	MeV	MeV	NNP
cord-346267-l08ld2cy	91	11	/	/	SYM
cord-346267-l08ld2cy	91	12	RPV	RPV	NNP
cord-346267-l08ld2cy	91	13	/	/	SYM
cord-346267-l08ld2cy	91	14	PPRV	PPRV	NNP
cord-346267-l08ld2cy	91	15	)	)	-RRB-
cord-346267-l08ld2cy	91	16	,	,	,
cord-346267-l08ld2cy	91	17	subtypes	subtype	NNS
cord-346267-l08ld2cy	91	18	(	(	-LRB-
cord-346267-l08ld2cy	91	19	EBOV	EBOV	NNP
cord-346267-l08ld2cy	91	20	)	)	-RRB-
cord-346267-l08ld2cy	91	21	,	,	,
cord-346267-l08ld2cy	91	22	and	and	CC
cord-346267-l08ld2cy	91	23	serotypes	serotype	NNS
cord-346267-l08ld2cy	91	24	(	(	-LRB-
cord-346267-l08ld2cy	91	25	AIV	AIV	NNP
cord-346267-l08ld2cy	91	26	)	)	-RRB-
cord-346267-l08ld2cy	91	27	were	be	VBD
cord-346267-l08ld2cy	91	28	assigned	assign	VBN
cord-346267-l08ld2cy	91	29	separate	separate	JJ
cord-346267-l08ld2cy	91	30	E	e	NN
cord-346267-l08ld2cy	91	31	[	[	-LRB-
cord-346267-l08ld2cy	91	32	β]/E	β]/e	XX
cord-346267-l08ld2cy	91	33	[	[	-LRB-
cord-346267-l08ld2cy	91	34	α	α	NN
cord-346267-l08ld2cy	91	35	]	]	-RRB-
cord-346267-l08ld2cy	91	36	ratio	ratio	NN
cord-346267-l08ld2cy	91	37	parameters	parameter	NNS
cord-346267-l08ld2cy	91	38	because	because	IN
cord-346267-l08ld2cy	91	39	they	-PRON-	PRP
cord-346267-l08ld2cy	91	40	represent	represent	VBP
cord-346267-l08ld2cy	91	41	different	different	JJ
cord-346267-l08ld2cy	91	42	timescales	timescale	NNS
cord-346267-l08ld2cy	91	43	and	and	CC
cord-346267-l08ld2cy	91	44	selective	selective	JJ
cord-346267-l08ld2cy	91	45	regimes	regime	NNS
cord-346267-l08ld2cy	91	46	compared	compare	VBN
cord-346267-l08ld2cy	91	47	with	with	IN
cord-346267-l08ld2cy	91	48	terminal	terminal	JJ
cord-346267-l08ld2cy	91	49	branches	branch	NNS
cord-346267-l08ld2cy	91	50	.	.	.
cord-346267-l08ld2cy	92	1	Longer	long	JJR
cord-346267-l08ld2cy	92	2	internal	internal	JJ
cord-346267-l08ld2cy	92	3	branches	branch	NNS
cord-346267-l08ld2cy	92	4	are	be	VBP
cord-346267-l08ld2cy	92	5	expected	expect	VBN
cord-346267-l08ld2cy	92	6	to	to	TO
cord-346267-l08ld2cy	92	7	bear	bear	VB
cord-346267-l08ld2cy	92	8	the	the	DT
cord-346267-l08ld2cy	92	9	mark	mark	NN
cord-346267-l08ld2cy	92	10	of	of	IN
cord-346267-l08ld2cy	92	11	stronger	strong	JJR
cord-346267-l08ld2cy	92	12	purifying	purifying	NN
cord-346267-l08ld2cy	92	13	selection	selection	NN
cord-346267-l08ld2cy	93	1	(	(	-LRB-
cord-346267-l08ld2cy	93	2	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	93	3	et	et	FW
cord-346267-l08ld2cy	93	4	al	al	NNP
cord-346267-l08ld2cy	93	5	.	.	.
cord-346267-l08ld2cy	94	1	2006	2006	CD
cord-346267-l08ld2cy	94	2	;	;	:
cord-346267-l08ld2cy	94	3	Pybus	Pybus	NNP
cord-346267-l08ld2cy	94	4	et	et	NNP
cord-346267-l08ld2cy	94	5	al	al	NNP
cord-346267-l08ld2cy	94	6	.	.	NNP
cord-346267-l08ld2cy	94	7	2007	2007	CD
cord-346267-l08ld2cy	94	8	)	)	-RRB-
cord-346267-l08ld2cy	94	9	.	.	.
cord-346267-l08ld2cy	95	1	We	-PRON-	PRP
cord-346267-l08ld2cy	95	2	considered	consider	VBD
cord-346267-l08ld2cy	95	3	two	two	CD
cord-346267-l08ld2cy	95	4	variations	variation	NNS
cord-346267-l08ld2cy	95	5	of	of	IN
cord-346267-l08ld2cy	95	6	this	this	DT
cord-346267-l08ld2cy	95	7	model	model	NN
cord-346267-l08ld2cy	95	8	:	:	:
cord-346267-l08ld2cy	95	9	Either	either	CC
cord-346267-l08ld2cy	95	10	1	1	LS
cord-346267-l08ld2cy	95	11	)	)	-RRB-
cord-346267-l08ld2cy	95	12	all	all	DT
cord-346267-l08ld2cy	95	13	long	long	JJ
cord-346267-l08ld2cy	95	14	internal	internal	JJ
cord-346267-l08ld2cy	95	15	lineages	lineage	NNS
cord-346267-l08ld2cy	95	16	share	share	VBP
cord-346267-l08ld2cy	95	17	the	the	DT
cord-346267-l08ld2cy	95	18	same	same	JJ
cord-346267-l08ld2cy	95	19	ratio	ratio	NN
cord-346267-l08ld2cy	95	20	parameter	parameter	NN
cord-346267-l08ld2cy	95	21	,	,	,
cord-346267-l08ld2cy	95	22	and	and	CC
cord-346267-l08ld2cy	95	23	the	the	DT
cord-346267-l08ld2cy	95	24	remaining	remain	VBG
cord-346267-l08ld2cy	95	25	branches	branch	NNS
cord-346267-l08ld2cy	95	26	share	share	VBP
cord-346267-l08ld2cy	95	27	another	another	DT
cord-346267-l08ld2cy	95	28	global	global	JJ
cord-346267-l08ld2cy	95	29	ratio	ratio	NN
cord-346267-l08ld2cy	95	30	parameter	parameter	NN
cord-346267-l08ld2cy	95	31	(	(	-LRB-
cord-346267-l08ld2cy	95	32	two	two	CD
cord-346267-l08ld2cy	95	33	-	-	HYPH
cord-346267-l08ld2cy	95	34	rate	rate	NN
cord-346267-l08ld2cy	95	35	model	model	NN
cord-346267-l08ld2cy	95	36	)	)	-RRB-
cord-346267-l08ld2cy	95	37	or	or	CC
cord-346267-l08ld2cy	95	38	2	2	CD
cord-346267-l08ld2cy	95	39	)	)	-RRB-
cord-346267-l08ld2cy	96	1	each	each	DT
cord-346267-l08ld2cy	96	2	deep	deep	JJ
cord-346267-l08ld2cy	96	3	lineage	lineage	NN
cord-346267-l08ld2cy	96	4	possesses	possess	VBZ
cord-346267-l08ld2cy	96	5	its	-PRON-	PRP$
cord-346267-l08ld2cy	96	6	own	own	JJ
cord-346267-l08ld2cy	96	7	ratio	ratio	NN
cord-346267-l08ld2cy	96	8	parameter	parameter	NN
cord-346267-l08ld2cy	96	9	,	,	,
cord-346267-l08ld2cy	96	10	and	and	CC
cord-346267-l08ld2cy	96	11	the	the	DT
cord-346267-l08ld2cy	96	12	remaining	remain	VBG
cord-346267-l08ld2cy	96	13	branches	branch	NNS
cord-346267-l08ld2cy	96	14	share	share	VBP
cord-346267-l08ld2cy	96	15	a	a	DT
cord-346267-l08ld2cy	96	16	global	global	JJ
cord-346267-l08ld2cy	96	17	ratio	ratio	NN
cord-346267-l08ld2cy	96	18	parameter	parameter	NN
cord-346267-l08ld2cy	96	19	(	(	-LRB-
cord-346267-l08ld2cy	96	20	multirate	multirate	NNP
cord-346267-l08ld2cy	96	21	model	model	NN
cord-346267-l08ld2cy	96	22	)	)	-RRB-
cord-346267-l08ld2cy	96	23	.	.	.
cord-346267-l08ld2cy	97	1	For	for	IN
cord-346267-l08ld2cy	97	2	each	each	DT
cord-346267-l08ld2cy	97	3	data	data	NN
cord-346267-l08ld2cy	97	4	set	set	VBN
cord-346267-l08ld2cy	97	5	,	,	,
cord-346267-l08ld2cy	97	6	we	-PRON-	PRP
cord-346267-l08ld2cy	97	7	selected	select	VBD
cord-346267-l08ld2cy	97	8	the	the	DT
cord-346267-l08ld2cy	97	9	model	model	NN
cord-346267-l08ld2cy	97	10	with	with	IN
cord-346267-l08ld2cy	97	11	the	the	DT
cord-346267-l08ld2cy	97	12	best	good	JJS
cord-346267-l08ld2cy	97	13	Akaike	Akaike	NNP
cord-346267-l08ld2cy	97	14	information	information	NN
cord-346267-l08ld2cy	97	15	criterion	criterion	NN
cord-346267-l08ld2cy	97	16	(	(	-LRB-
cord-346267-l08ld2cy	97	17	AIC	AIC	NNP
cord-346267-l08ld2cy	97	18	)	)	-RRB-
cord-346267-l08ld2cy	97	19	score	score	NN
cord-346267-l08ld2cy	97	20	for	for	IN
cord-346267-l08ld2cy	97	21	further	further	JJ
cord-346267-l08ld2cy	97	22	analysis	analysis	NN
cord-346267-l08ld2cy	97	23	.	.	.
cord-346267-l08ld2cy	98	1	Note	note	VB
cord-346267-l08ld2cy	98	2	that	that	IN
cord-346267-l08ld2cy	98	3	we	-PRON-	PRP
cord-346267-l08ld2cy	98	4	use	use	VBP
cord-346267-l08ld2cy	98	5	the	the	DT
cord-346267-l08ld2cy	98	6	ratio	ratio	NN
cord-346267-l08ld2cy	98	7	of	of	IN
cord-346267-l08ld2cy	98	8	the	the	DT
cord-346267-l08ld2cy	98	9	means	mean	NNS
cord-346267-l08ld2cy	98	10	E	e	NN
cord-346267-l08ld2cy	98	11	is	be	VBZ
cord-346267-l08ld2cy	98	12	possible	possible	JJ
cord-346267-l08ld2cy	98	13	under	under	IN
cord-346267-l08ld2cy	98	14	Dual	Dual	NNP
cord-346267-l08ld2cy	98	15	and	and	CC
cord-346267-l08ld2cy	98	16	Lin	Lin	NNP
cord-346267-l08ld2cy	98	17	-	-	HYPH
cord-346267-l08ld2cy	98	18	eage+Dual	eage+Dual	NNP
cord-346267-l08ld2cy	98	19	models	model	NNS
cord-346267-l08ld2cy	98	20	,	,	,
cord-346267-l08ld2cy	98	21	rendering	render	VBG
cord-346267-l08ld2cy	98	22	the	the	DT
cord-346267-l08ld2cy	98	23	mean	mean	NN
cord-346267-l08ld2cy	98	24	of	of	IN
cord-346267-l08ld2cy	98	25	the	the	DT
cord-346267-l08ld2cy	98	26	ratio	ratio	NN
cord-346267-l08ld2cy	98	27	infinite	infinite	JJ
cord-346267-l08ld2cy	98	28	.	.	.
cord-346267-l08ld2cy	99	1	For	for	IN
cord-346267-l08ld2cy	99	2	each	each	DT
cord-346267-l08ld2cy	99	3	data	data	NN
cord-346267-l08ld2cy	99	4	set	set	VBN
cord-346267-l08ld2cy	99	5	,	,	,
cord-346267-l08ld2cy	99	6	we	-PRON-	PRP
cord-346267-l08ld2cy	99	7	obtained	obtain	VBD
cord-346267-l08ld2cy	99	8	M	M	NNP
cord-346267-l08ld2cy	99	9	=	=	SYM
cord-346267-l08ld2cy	99	10	1	1	CD
cord-346267-l08ld2cy	99	11	,	,	,
cord-346267-l08ld2cy	99	12	000	000	CD
cord-346267-l08ld2cy	99	13	samples	sample	NNS
cord-346267-l08ld2cy	99	14	from	from	IN
cord-346267-l08ld2cy	99	15	the	the	DT
cord-346267-l08ld2cy	99	16	approximate	approximate	JJ
cord-346267-l08ld2cy	99	17	joint	joint	JJ
cord-346267-l08ld2cy	99	18	distribution	distribution	NN
cord-346267-l08ld2cy	99	19	of	of	IN
cord-346267-l08ld2cy	99	20	model	model	NN
cord-346267-l08ld2cy	99	21	parameter	parameter	NN
cord-346267-l08ld2cy	99	22	estimates	estimate	NNS
cord-346267-l08ld2cy	99	23	using	use	VBG
cord-346267-l08ld2cy	99	24	a	a	DT
cord-346267-l08ld2cy	99	25	modified	modify	VBN
cord-346267-l08ld2cy	99	26	Latin	Latin	NNP
cord-346267-l08ld2cy	99	27	hypercube	hypercube	NN
cord-346267-l08ld2cy	99	28	sampling	sampling	NN
cord-346267-l08ld2cy	99	29	importance	importance	NN
cord-346267-l08ld2cy	99	30	resampling	resample	VBG
cord-346267-l08ld2cy	99	31	scheme	scheme	NN
cord-346267-l08ld2cy	99	32	,	,	,
cord-346267-l08ld2cy	99	33	described	describe	VBN
cord-346267-l08ld2cy	99	34	in	in	IN
cord-346267-l08ld2cy	99	35	detail	detail	NN
cord-346267-l08ld2cy	99	36	elsewhere	elsewhere	RB
cord-346267-l08ld2cy	99	37	(	(	-LRB-
cord-346267-l08ld2cy	99	38	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	99	39	et	et	FW
cord-346267-l08ld2cy	99	40	al	al	NNP
cord-346267-l08ld2cy	99	41	.	.	NNP
cord-346267-l08ld2cy	99	42	2010	2010	CD
cord-346267-l08ld2cy	99	43	)	)	-RRB-
cord-346267-l08ld2cy	99	44	.	.	.
cord-346267-l08ld2cy	100	1	The	the	DT
cord-346267-l08ld2cy	100	2	approach	approach	NN
cord-346267-l08ld2cy	100	3	is	be	VBZ
cord-346267-l08ld2cy	100	4	meant	mean	VBN
cord-346267-l08ld2cy	100	5	to	to	TO
cord-346267-l08ld2cy	100	6	quickly	quickly	RB
cord-346267-l08ld2cy	100	7	obtain	obtain	VB
cord-346267-l08ld2cy	100	8	an	an	DT
cord-346267-l08ld2cy	100	9	approximate	approximate	JJ
cord-346267-l08ld2cy	100	10	joint	joint	JJ
cord-346267-l08ld2cy	100	11	distribution	distribution	NN
cord-346267-l08ld2cy	100	12	of	of	IN
cord-346267-l08ld2cy	100	13	maximum	maximum	JJ
cord-346267-l08ld2cy	100	14	likelihood	likelihood	NN
cord-346267-l08ld2cy	100	15	parameter	parameter	NN
cord-346267-l08ld2cy	100	16	estimators	estimator	NNS
cord-346267-l08ld2cy	100	17	.	.	.
cord-346267-l08ld2cy	101	1	First	first	RB
cord-346267-l08ld2cy	101	2	,	,	,
cord-346267-l08ld2cy	101	3	an	an	DT
cord-346267-l08ld2cy	101	4	area	area	NN
cord-346267-l08ld2cy	101	5	of	of	IN
cord-346267-l08ld2cy	101	6	parameter	parameter	NN
cord-346267-l08ld2cy	101	7	space	space	NN
cord-346267-l08ld2cy	101	8	to	to	TO
cord-346267-l08ld2cy	101	9	be	be	VB
cord-346267-l08ld2cy	101	10	sampled	sample	VBN
cord-346267-l08ld2cy	101	11	is	be	VBZ
cord-346267-l08ld2cy	101	12	defined	define	VBN
cord-346267-l08ld2cy	101	13	by	by	IN
cord-346267-l08ld2cy	101	14	constructing	construct	VBG
cord-346267-l08ld2cy	101	15	a	a	DT
cord-346267-l08ld2cy	101	16	d	d	NN
cord-346267-l08ld2cy	101	17	-dimensional	-dimensional	JJ
cord-346267-l08ld2cy	101	18	rectangle	rectangle	NN
cord-346267-l08ld2cy	101	19	,	,	,
cord-346267-l08ld2cy	101	20	in	in	IN
cord-346267-l08ld2cy	101	21	which	which	WDT
cord-346267-l08ld2cy	101	22	each	each	DT
cord-346267-l08ld2cy	101	23	dimension	dimension	NN
cord-346267-l08ld2cy	101	24	represents	represent	VBZ
cord-346267-l08ld2cy	101	25	a	a	DT
cord-346267-l08ld2cy	101	26	single	single	JJ
cord-346267-l08ld2cy	101	27	model	model	NN
cord-346267-l08ld2cy	101	28	parameter	parameter	NN
cord-346267-l08ld2cy	101	29	,	,	,
cord-346267-l08ld2cy	101	30	the	the	DT
cord-346267-l08ld2cy	101	31	corresponding	correspond	VBG
cord-346267-l08ld2cy	101	32	coordinate	coordinate	JJ
cord-346267-l08ld2cy	101	33	interval	interval	NN
cord-346267-l08ld2cy	101	34	is	be	VBZ
cord-346267-l08ld2cy	101	35	centered	center	VBN
cord-346267-l08ld2cy	101	36	on	on	IN
cord-346267-l08ld2cy	101	37	the	the	DT
cord-346267-l08ld2cy	101	38	maximum	maximum	JJ
cord-346267-l08ld2cy	101	39	likelihood	likelihood	NN
cord-346267-l08ld2cy	101	40	estimate	estimate	NN
cord-346267-l08ld2cy	101	41	of	of	IN
cord-346267-l08ld2cy	101	42	the	the	DT
cord-346267-l08ld2cy	101	43	parameter	parameter	NN
cord-346267-l08ld2cy	101	44	,	,	,
cord-346267-l08ld2cy	101	45	and	and	CC
cord-346267-l08ld2cy	101	46	the	the	DT
cord-346267-l08ld2cy	101	47	lower	low	JJR
cord-346267-l08ld2cy	101	48	and	and	CC
cord-346267-l08ld2cy	101	49	upper	upper	JJ
cord-346267-l08ld2cy	101	50	bounds	bound	NNS
cord-346267-l08ld2cy	101	51	are	be	VBP
cord-346267-l08ld2cy	101	52	determined	determine	VBN
cord-346267-l08ld2cy	101	53	by	by	IN
cord-346267-l08ld2cy	101	54	profile	profile	JJ
cord-346267-l08ld2cy	101	55	likelihood	likelihood	NN
cord-346267-l08ld2cy	101	56	.	.	.
cord-346267-l08ld2cy	102	1	Second	second	RB
cord-346267-l08ld2cy	102	2	,	,	,
cord-346267-l08ld2cy	102	3	each	each	DT
cord-346267-l08ld2cy	102	4	coordinate	coordinate	JJ
cord-346267-l08ld2cy	102	5	interval	interval	NN
cord-346267-l08ld2cy	102	6	is	be	VBZ
cord-346267-l08ld2cy	102	7	partitioned	partition	VBN
cord-346267-l08ld2cy	102	8	into	into	IN
cord-346267-l08ld2cy	102	9	N	n	NN
cord-346267-l08ld2cy	102	10	=	=	SYM
cord-346267-l08ld2cy	102	11	1	1	CD
cord-346267-l08ld2cy	102	12	,	,	,
cord-346267-l08ld2cy	102	13	000d	000d	CD
cord-346267-l08ld2cy	102	14	subintervals	subinterval	NNS
cord-346267-l08ld2cy	102	15	of	of	IN
cord-346267-l08ld2cy	102	16	approximately	approximately	RB
cord-346267-l08ld2cy	102	17	equal	equal	JJ
cord-346267-l08ld2cy	102	18	probability	probability	NN
cord-346267-l08ld2cy	102	19	,	,	,
cord-346267-l08ld2cy	102	20	based	base	VBN
cord-346267-l08ld2cy	102	21	on	on	IN
cord-346267-l08ld2cy	102	22	the	the	DT
cord-346267-l08ld2cy	102	23	asymptotic	asymptotic	JJ
cord-346267-l08ld2cy	102	24	normal	normal	JJ
cord-346267-l08ld2cy	102	25	approximation	approximation	NN
cord-346267-l08ld2cy	102	26	to	to	IN
cord-346267-l08ld2cy	102	27	the	the	DT
cord-346267-l08ld2cy	102	28	likelihood	likelihood	NN
cord-346267-l08ld2cy	102	29	surface	surface	NN
cord-346267-l08ld2cy	102	30	.	.	.
cord-346267-l08ld2cy	103	1	Third	third	JJ
cord-346267-l08ld2cy	103	2	,	,	,
cord-346267-l08ld2cy	103	3	N	n	CD
cord-346267-l08ld2cy	103	4	samples	sample	NNS
cord-346267-l08ld2cy	103	5	are	be	VBP
cord-346267-l08ld2cy	103	6	drawn	draw	VBN
cord-346267-l08ld2cy	103	7	from	from	IN
cord-346267-l08ld2cy	103	8	the	the	DT
cord-346267-l08ld2cy	103	9	d	d	NNP
cord-346267-l08ld2cy	103	10	-dimensional	-dimensional	JJ
cord-346267-l08ld2cy	103	11	rectangle	rectangle	NN
cord-346267-l08ld2cy	103	12	,	,	,
cord-346267-l08ld2cy	103	13	using	use	VBG
cord-346267-l08ld2cy	103	14	the	the	DT
cord-346267-l08ld2cy	103	15	Latin	Latin	NNP
cord-346267-l08ld2cy	103	16	Hypercube	Hypercube	NNP
cord-346267-l08ld2cy	103	17	scheme	scheme	NN
cord-346267-l08ld2cy	103	18	(	(	-LRB-
cord-346267-l08ld2cy	103	19	i.e.	i.e.	FW
cord-346267-l08ld2cy	103	20	,	,	,
cord-346267-l08ld2cy	103	21	each	each	DT
cord-346267-l08ld2cy	103	22	interval	interval	NN
cord-346267-l08ld2cy	103	23	in	in	IN
cord-346267-l08ld2cy	103	24	every	every	DT
cord-346267-l08ld2cy	103	25	coordinate	coordinate	NN
cord-346267-l08ld2cy	103	26	is	be	VBZ
cord-346267-l08ld2cy	103	27	sampled	sample	VBN
cord-346267-l08ld2cy	103	28	exactly	exactly	RB
cord-346267-l08ld2cy	103	29	once	once	RB
cord-346267-l08ld2cy	103	30	)	)	-RRB-
cord-346267-l08ld2cy	103	31	.	.	.
cord-346267-l08ld2cy	104	1	Fourth	fourth	RB
cord-346267-l08ld2cy	104	2	,	,	,
cord-346267-l08ld2cy	104	3	M	M	NNP
cord-346267-l08ld2cy	104	4	N	N	NNP
cord-346267-l08ld2cy	104	5	points	point	NNS
cord-346267-l08ld2cy	104	6	are	be	VBP
cord-346267-l08ld2cy	104	7	resampled	resample	VBN
cord-346267-l08ld2cy	104	8	based	base	VBN
cord-346267-l08ld2cy	104	9	on	on	IN
cord-346267-l08ld2cy	104	10	their	-PRON-	PRP$
cord-346267-l08ld2cy	104	11	importance	importance	NN
cord-346267-l08ld2cy	104	12	(	(	-LRB-
cord-346267-l08ld2cy	104	13	normalized	normalized	JJ
cord-346267-l08ld2cy	104	14	likelihood	likelihood	NN
cord-346267-l08ld2cy	104	15	)	)	-RRB-
cord-346267-l08ld2cy	104	16	,	,	,
cord-346267-l08ld2cy	104	17	following	follow	VBG
cord-346267-l08ld2cy	104	18	the	the	DT
cord-346267-l08ld2cy	104	19	procedure	procedure	NN
cord-346267-l08ld2cy	104	20	described	describe	VBN
cord-346267-l08ld2cy	104	21	elsewhere	elsewhere	RB
cord-346267-l08ld2cy	105	1	(	(	-LRB-
cord-346267-l08ld2cy	105	2	Skare	Skare	NNP
cord-346267-l08ld2cy	105	3	et	et	NNP
cord-346267-l08ld2cy	105	4	al	al	NNP
cord-346267-l08ld2cy	105	5	.	.	NNP
cord-346267-l08ld2cy	105	6	2003	2003	CD
cord-346267-l08ld2cy	105	7	)	)	-RRB-
cord-346267-l08ld2cy	105	8	.	.	.
cord-346267-l08ld2cy	106	1	Variance	variance	NN
cord-346267-l08ld2cy	106	2	in	in	IN
cord-346267-l08ld2cy	106	3	estimated	estimate	VBN
cord-346267-l08ld2cy	106	4	branch	branch	NN
cord-346267-l08ld2cy	106	5	lengths	length	NNS
cord-346267-l08ld2cy	106	6	was	be	VBD
cord-346267-l08ld2cy	106	7	computed	compute	VBN
cord-346267-l08ld2cy	106	8	using	use	VBG
cord-346267-l08ld2cy	106	9	this	this	DT
cord-346267-l08ld2cy	106	10	sample	sample	NN
cord-346267-l08ld2cy	106	11	.	.	.
cord-346267-l08ld2cy	107	1	All	all	DT
cord-346267-l08ld2cy	107	2	codon	codon	NN
cord-346267-l08ld2cy	107	3	-	-	HYPH
cord-346267-l08ld2cy	107	4	based	base	VBN
cord-346267-l08ld2cy	107	5	analyses	analysis	NNS
cord-346267-l08ld2cy	107	6	were	be	VBD
cord-346267-l08ld2cy	107	7	performed	perform	VBN
cord-346267-l08ld2cy	107	8	in	in	IN
cord-346267-l08ld2cy	107	9	HyPhy	HyPhy	NNP
cord-346267-l08ld2cy	107	10	v2.0020110301	v2.0020110301	CD
cord-346267-l08ld2cy	107	11	)	)	-RRB-
cord-346267-l08ld2cy	107	12	.	.	.
cord-346267-l08ld2cy	108	1	We	-PRON-	PRP
cord-346267-l08ld2cy	108	2	simulated	simulate	VBD
cord-346267-l08ld2cy	108	3	codon	codon	NN
cord-346267-l08ld2cy	108	4	sequences	sequence	NNS
cord-346267-l08ld2cy	108	5	along	along	IN
cord-346267-l08ld2cy	108	6	a	a	DT
cord-346267-l08ld2cy	108	7	single	single	JJ
cord-346267-l08ld2cy	108	8	branch	branch	NN
cord-346267-l08ld2cy	108	9	using	use	VBG
cord-346267-l08ld2cy	108	10	the	the	DT
cord-346267-l08ld2cy	108	11	MG94	MG94	NNP
cord-346267-l08ld2cy	108	12	×	×	NNP
cord-346267-l08ld2cy	108	13	REV	REV	NNP
cord-346267-l08ld2cy	108	14	codon	codon	NN
cord-346267-l08ld2cy	108	15	substitution	substitution	NN
cord-346267-l08ld2cy	108	16	model	model	NN
cord-346267-l08ld2cy	108	17	)	)	-RRB-
cord-346267-l08ld2cy	108	18	with	with	IN
cord-346267-l08ld2cy	108	19	site	site	NN
cord-346267-l08ld2cy	108	20	-	-	HYPH
cord-346267-l08ld2cy	108	21	specific	specific	JJ
cord-346267-l08ld2cy	108	22	β	β	NN
cord-346267-l08ld2cy	108	23	and	and	CC
cord-346267-l08ld2cy	108	24	α	α	NN
cord-346267-l08ld2cy	108	25	values	value	NNS
cord-346267-l08ld2cy	108	26	inferred	infer	VBN
cord-346267-l08ld2cy	108	27	using	use	VBG
cord-346267-l08ld2cy	108	28	a	a	DT
cord-346267-l08ld2cy	108	29	fixed	fix	VBN
cord-346267-l08ld2cy	108	30	effects	effect	NNS
cord-346267-l08ld2cy	108	31	likelihood	likelihood	NN
cord-346267-l08ld2cy	108	32	method	method	NN
cord-346267-l08ld2cy	108	33	on	on	IN
cord-346267-l08ld2cy	108	34	internal	internal	JJ
cord-346267-l08ld2cy	108	35	branches	branch	NNS
cord-346267-l08ld2cy	108	36	(	(	-LRB-
cord-346267-l08ld2cy	108	37	IFEL	IFEL	NNP
cord-346267-l08ld2cy	108	38	)	)	-RRB-
cord-346267-l08ld2cy	109	1	(	(	-LRB-
cord-346267-l08ld2cy	109	2	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	109	3	et	et	FW
cord-346267-l08ld2cy	109	4	al	al	NNP
cord-346267-l08ld2cy	109	5	.	.	.
cord-346267-l08ld2cy	109	6	2006	2006	CD
cord-346267-l08ld2cy	109	7	)	)	-RRB-
cord-346267-l08ld2cy	109	8	from	from	IN
cord-346267-l08ld2cy	109	9	each	each	DT
cord-346267-l08ld2cy	109	10	of	of	IN
cord-346267-l08ld2cy	109	11	the	the	DT
cord-346267-l08ld2cy	109	12	three	three	CD
cord-346267-l08ld2cy	109	13	viral	viral	JJ
cord-346267-l08ld2cy	109	14	data	data	NN
cord-346267-l08ld2cy	109	15	sets	set	NNS
cord-346267-l08ld2cy	109	16	.	.	.
cord-346267-l08ld2cy	110	1	In	in	IN
cord-346267-l08ld2cy	110	2	this	this	DT
cord-346267-l08ld2cy	110	3	method	method	NN
cord-346267-l08ld2cy	110	4	,	,	,
cord-346267-l08ld2cy	110	5	three	three	CD
cord-346267-l08ld2cy	110	6	rates	rate	NNS
cord-346267-l08ld2cy	110	7	are	be	VBP
cord-346267-l08ld2cy	110	8	inferred	infer	VBN
cord-346267-l08ld2cy	110	9	from	from	IN
cord-346267-l08ld2cy	110	10	each	each	DT
cord-346267-l08ld2cy	110	11	site	site	NN
cord-346267-l08ld2cy	110	12	:	:	:
cord-346267-l08ld2cy	111	1	α	α	NNP
cord-346267-l08ld2cy	111	2	s	s	NNP
cord-346267-l08ld2cy	111	3	,	,	,
cord-346267-l08ld2cy	111	4	β	β	NN
cord-346267-l08ld2cy	111	5	I	I	NNP
cord-346267-l08ld2cy	111	6	s	s	NNP
cord-346267-l08ld2cy	111	7	,	,	,
cord-346267-l08ld2cy	111	8	and	and	CC
cord-346267-l08ld2cy	111	9	β	β	NNP
cord-346267-l08ld2cy	111	10	T	T	NNP
cord-346267-l08ld2cy	111	11	s	s	NNP
cord-346267-l08ld2cy	111	12	.	.	.
cord-346267-l08ld2cy	112	1	Subscript	Subscript	NNP
cord-346267-l08ld2cy	112	2	s	s	NNP
cord-346267-l08ld2cy	112	3	indicates	indicate	VBZ
cord-346267-l08ld2cy	112	4	the	the	DT
cord-346267-l08ld2cy	112	5	explicit	explicit	JJ
cord-346267-l08ld2cy	112	6	dependence	dependence	NN
cord-346267-l08ld2cy	112	7	of	of	IN
cord-346267-l08ld2cy	112	8	substitution	substitution	NN
cord-346267-l08ld2cy	112	9	rates	rate	NNS
cord-346267-l08ld2cy	112	10	on	on	IN
cord-346267-l08ld2cy	112	11	the	the	DT
cord-346267-l08ld2cy	112	12	site	site	NN
cord-346267-l08ld2cy	112	13	,	,	,
cord-346267-l08ld2cy	112	14	from	from	IN
cord-346267-l08ld2cy	112	15	which	which	WDT
cord-346267-l08ld2cy	112	16	they	-PRON-	PRP
cord-346267-l08ld2cy	112	17	are	be	VBP
cord-346267-l08ld2cy	112	18	being	be	VBG
cord-346267-l08ld2cy	112	19	estimated	estimate	VBN
cord-346267-l08ld2cy	112	20	.	.	.
cord-346267-l08ld2cy	113	1	α	α	NNP
cord-346267-l08ld2cy	113	2	s	s	NNP
cord-346267-l08ld2cy	113	3	is	be	VBZ
cord-346267-l08ld2cy	113	4	the	the	DT
cord-346267-l08ld2cy	113	5	tree	tree	NN
cord-346267-l08ld2cy	113	6	-	-	HYPH
cord-346267-l08ld2cy	113	7	wide	wide	JJ
cord-346267-l08ld2cy	113	8	synonymous	synonymous	JJ
cord-346267-l08ld2cy	113	9	rate	rate	NN
cord-346267-l08ld2cy	113	10	,	,	,
cord-346267-l08ld2cy	113	11	β	β	NN
cord-346267-l08ld2cy	113	12	I	i	NN
cord-346267-l08ld2cy	113	13	s	s	NNP
cord-346267-l08ld2cy	113	14	is	be	VBZ
cord-346267-l08ld2cy	113	15	the	the	DT
cord-346267-l08ld2cy	113	16	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	113	17	rate	rate	NN
cord-346267-l08ld2cy	113	18	shared	share	VBN
cord-346267-l08ld2cy	113	19	by	by	IN
cord-346267-l08ld2cy	113	20	all	all	DT
cord-346267-l08ld2cy	113	21	internal	internal	JJ
cord-346267-l08ld2cy	113	22	branches	branch	NNS
cord-346267-l08ld2cy	113	23	,	,	,
cord-346267-l08ld2cy	113	24	and	and	CC
cord-346267-l08ld2cy	113	25	β	β	NNP
cord-346267-l08ld2cy	113	26	T	T	NNP
cord-346267-l08ld2cy	113	27	s	s	NNP
cord-346267-l08ld2cy	113	28	is	be	VBZ
cord-346267-l08ld2cy	113	29	the	the	DT
cord-346267-l08ld2cy	113	30	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	113	31	rate	rate	NN
cord-346267-l08ld2cy	113	32	shared	share	VBN
cord-346267-l08ld2cy	113	33	by	by	IN
cord-346267-l08ld2cy	113	34	all	all	DT
cord-346267-l08ld2cy	113	35	terminal	terminal	JJ
cord-346267-l08ld2cy	113	36	branches	branch	NNS
cord-346267-l08ld2cy	113	37	.	.	.
cord-346267-l08ld2cy	114	1	Only	only	RB
cord-346267-l08ld2cy	114	2	internal	internal	JJ
cord-346267-l08ld2cy	114	3	branches	branch	NNS
cord-346267-l08ld2cy	114	4	were	be	VBD
cord-346267-l08ld2cy	114	5	used	use	VBN
cord-346267-l08ld2cy	114	6	to	to	TO
cord-346267-l08ld2cy	114	7	generate	generate	VB
cord-346267-l08ld2cy	114	8	empirical	empirical	JJ
cord-346267-l08ld2cy	114	9	selection	selection	NN
cord-346267-l08ld2cy	114	10	profiles	profile	NNS
cord-346267-l08ld2cy	114	11	because	because	IN
cord-346267-l08ld2cy	114	12	substitutions	substitution	NNS
cord-346267-l08ld2cy	114	13	along	along	IN
cord-346267-l08ld2cy	114	14	tips	tip	NNS
cord-346267-l08ld2cy	114	15	in	in	IN
cord-346267-l08ld2cy	114	16	viral	viral	JJ
cord-346267-l08ld2cy	114	17	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	114	18	are	be	VBP
cord-346267-l08ld2cy	114	19	frequently	frequently	RB
cord-346267-l08ld2cy	114	20	deleterious	deleterious	JJ
cord-346267-l08ld2cy	114	21	and	and	CC
cord-346267-l08ld2cy	114	22	transient	transient	JJ
cord-346267-l08ld2cy	114	23	(	(	-LRB-
cord-346267-l08ld2cy	114	24	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	114	25	et	et	FW
cord-346267-l08ld2cy	114	26	al	al	NNP
cord-346267-l08ld2cy	114	27	.	.	.
cord-346267-l08ld2cy	115	1	2006	2006	CD
cord-346267-l08ld2cy	115	2	;	;	:
cord-346267-l08ld2cy	115	3	Pybus	Pybus	NNP
cord-346267-l08ld2cy	115	4	et	et	NNP
cord-346267-l08ld2cy	115	5	al	al	NNP
cord-346267-l08ld2cy	115	6	.	.	NNP
cord-346267-l08ld2cy	115	7	2007	2007	CD
cord-346267-l08ld2cy	115	8	)	)	-RRB-
cord-346267-l08ld2cy	115	9	.	.	.
cord-346267-l08ld2cy	116	1	Furthermore	furthermore	RB
cord-346267-l08ld2cy	116	2	,	,	,
cord-346267-l08ld2cy	116	3	we	-PRON-	PRP
cord-346267-l08ld2cy	116	4	were	be	VBD
cord-346267-l08ld2cy	116	5	primarily	primarily	RB
cord-346267-l08ld2cy	116	6	interested	interested	JJ
cord-346267-l08ld2cy	116	7	in	in	IN
cord-346267-l08ld2cy	116	8	the	the	DT
cord-346267-l08ld2cy	116	9	effects	effect	NNS
cord-346267-l08ld2cy	116	10	of	of	IN
cord-346267-l08ld2cy	116	11	selection	selection	NN
cord-346267-l08ld2cy	116	12	on	on	IN
cord-346267-l08ld2cy	116	13	long	long	JJ
cord-346267-l08ld2cy	116	14	internal	internal	JJ
cord-346267-l08ld2cy	116	15	branches	branch	NNS
cord-346267-l08ld2cy	116	16	,	,	,
cord-346267-l08ld2cy	116	17	and	and	CC
cord-346267-l08ld2cy	116	18	the	the	DT
cord-346267-l08ld2cy	116	19	IFEL	IFEL	NNP
cord-346267-l08ld2cy	116	20	profile	profile	NN
cord-346267-l08ld2cy	116	21	(	(	-LRB-
cord-346267-l08ld2cy	117	1	α	α	NNP
cord-346267-l08ld2cy	117	2	s	s	NNP
cord-346267-l08ld2cy	117	3	and	and	CC
cord-346267-l08ld2cy	117	4	β	β	NN
cord-346267-l08ld2cy	118	1	I	-PRON-	PRP
cord-346267-l08ld2cy	118	2	s	s	VBZ
cord-346267-l08ld2cy	118	3	inferred	infer	VBD
cord-346267-l08ld2cy	118	4	for	for	IN
cord-346267-l08ld2cy	118	5	each	each	DT
cord-346267-l08ld2cy	118	6	site	site	NN
cord-346267-l08ld2cy	118	7	)	)	-RRB-
cord-346267-l08ld2cy	118	8	was	be	VBD
cord-346267-l08ld2cy	118	9	meant	mean	VBN
cord-346267-l08ld2cy	118	10	to	to	TO
cord-346267-l08ld2cy	118	11	recapitulate	recapitulate	VB
cord-346267-l08ld2cy	118	12	the	the	DT
cord-346267-l08ld2cy	118	13	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	118	14	process	process	NN
cord-346267-l08ld2cy	118	15	along	along	IN
cord-346267-l08ld2cy	118	16	an	an	DT
cord-346267-l08ld2cy	118	17	"	"	``
cord-346267-l08ld2cy	118	18	average	average	JJ
cord-346267-l08ld2cy	118	19	"	"	''
cord-346267-l08ld2cy	118	20	internal	internal	JJ
cord-346267-l08ld2cy	118	21	branch	branch	NN
cord-346267-l08ld2cy	118	22	.	.	.
cord-346267-l08ld2cy	119	1	Simulations	simulation	NNS
cord-346267-l08ld2cy	119	2	were	be	VBD
cord-346267-l08ld2cy	119	3	initialized	initialize	VBN
cord-346267-l08ld2cy	119	4	using	use	VBG
cord-346267-l08ld2cy	119	5	ancestral	ancestral	JJ
cord-346267-l08ld2cy	119	6	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	119	7	sequences	sequence	NNS
cord-346267-l08ld2cy	119	8	inferred	infer	VBN
cord-346267-l08ld2cy	119	9	with	with	IN
cord-346267-l08ld2cy	119	10	marginal	marginal	JJ
cord-346267-l08ld2cy	119	11	maximum	maximum	JJ
cord-346267-l08ld2cy	119	12	likelihood	likelihood	NN
cord-346267-l08ld2cy	119	13	reconstruction	reconstruction	NN
cord-346267-l08ld2cy	119	14	(	(	-LRB-
cord-346267-l08ld2cy	119	15	Yang	Yang	NNP
cord-346267-l08ld2cy	119	16	et	et	NNP
cord-346267-l08ld2cy	119	17	al	al	NNP
cord-346267-l08ld2cy	119	18	.	.	NNP
cord-346267-l08ld2cy	119	19	1995	1995	CD
cord-346267-l08ld2cy	119	20	)	)	-RRB-
cord-346267-l08ld2cy	119	21	in	in	IN
cord-346267-l08ld2cy	119	22	HyPhy	HyPhy	NNP
cord-346267-l08ld2cy	119	23	,	,	,
cord-346267-l08ld2cy	119	24	using	use	VBG
cord-346267-l08ld2cy	119	25	the	the	DT
cord-346267-l08ld2cy	119	26	MG94	MG94	NNP
cord-346267-l08ld2cy	119	27	×	×	NNP
cord-346267-l08ld2cy	119	28	REV	REV	NNP
cord-346267-l08ld2cy	119	29	codon	codon	NN
cord-346267-l08ld2cy	119	30	substitution	substitution	NN
cord-346267-l08ld2cy	119	31	model	model	NN
cord-346267-l08ld2cy	119	32	on	on	IN
cord-346267-l08ld2cy	119	33	the	the	DT
cord-346267-l08ld2cy	119	34	MCC	MCC	NNP
cord-346267-l08ld2cy	119	35	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	119	36	obtained	obtain	VBN
cord-346267-l08ld2cy	119	37	from	from	IN
cord-346267-l08ld2cy	119	38	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	119	39	general	general	JJ
cord-346267-l08ld2cy	119	40	time	time	NN
cord-346267-l08ld2cy	119	41	reversible	reversible	JJ
cord-346267-l08ld2cy	119	42	(	(	-LRB-
cord-346267-l08ld2cy	119	43	GTR	GTR	NNP
cord-346267-l08ld2cy	119	44	)	)	-RRB-
cord-346267-l08ld2cy	119	45	+	+	CC
cord-346267-l08ld2cy	119	46	Γ	γ	NN
cord-346267-l08ld2cy	119	47	4	4	CD
cord-346267-l08ld2cy	119	48	analyses	analysis	NNS
cord-346267-l08ld2cy	119	49	.	.	.
cord-346267-l08ld2cy	120	1	The	the	DT
cord-346267-l08ld2cy	120	2	marginal	marginal	JJ
cord-346267-l08ld2cy	120	3	ancestral	ancestral	JJ
cord-346267-l08ld2cy	120	4	sequence	sequence	NN
cord-346267-l08ld2cy	120	5	was	be	VBD
cord-346267-l08ld2cy	120	6	used	use	VBN
cord-346267-l08ld2cy	120	7	to	to	TO
cord-346267-l08ld2cy	120	8	provide	provide	VB
cord-346267-l08ld2cy	120	9	a	a	DT
cord-346267-l08ld2cy	120	10	realistic	realistic	JJ
cord-346267-l08ld2cy	120	11	starting	starting	NN
cord-346267-l08ld2cy	120	12	point	point	NN
cord-346267-l08ld2cy	120	13	for	for	IN
cord-346267-l08ld2cy	120	14	our	-PRON-	PRP$
cord-346267-l08ld2cy	120	15	simulations	simulation	NNS
cord-346267-l08ld2cy	120	16	.	.	.
cord-346267-l08ld2cy	121	1	Ten	ten	CD
cord-346267-l08ld2cy	121	2	thousand	thousand	CD
cord-346267-l08ld2cy	121	3	replicates	replicate	NNS
cord-346267-l08ld2cy	121	4	were	be	VBD
cord-346267-l08ld2cy	121	5	generated	generate	VBN
cord-346267-l08ld2cy	121	6	for	for	IN
cord-346267-l08ld2cy	121	7	each	each	DT
cord-346267-l08ld2cy	121	8	branch	branch	NN
cord-346267-l08ld2cy	121	9	length	length	NN
cord-346267-l08ld2cy	121	10	ranging	range	VBG
cord-346267-l08ld2cy	121	11	from	from	IN
cord-346267-l08ld2cy	121	12	0.01	0.01	CD
cord-346267-l08ld2cy	121	13	to	to	IN
cord-346267-l08ld2cy	121	14	100	100	CD
cord-346267-l08ld2cy	121	15	expected	expect	VBN
cord-346267-l08ld2cy	121	16	substitutions	substitution	NNS
cord-346267-l08ld2cy	121	17	per	per	IN
cord-346267-l08ld2cy	121	18	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	121	19	site	site	NN
cord-346267-l08ld2cy	121	20	and	and	CC
cord-346267-l08ld2cy	121	21	analyzed	analyze	VBD
cord-346267-l08ld2cy	121	22	under	under	IN
cord-346267-l08ld2cy	121	23	the	the	DT
cord-346267-l08ld2cy	121	24	GTR	GTR	NNP
cord-346267-l08ld2cy	121	25	+	+	SYM
cord-346267-l08ld2cy	121	26	Γ	γ	NN
cord-346267-l08ld2cy	121	27	4	4	CD
cord-346267-l08ld2cy	121	28	and	and	CC
cord-346267-l08ld2cy	121	29	Dual	dual	JJ
cord-346267-l08ld2cy	121	30	substitution	substitution	NN
cord-346267-l08ld2cy	121	31	models	model	NNS
cord-346267-l08ld2cy	121	32	.	.	.
cord-346267-l08ld2cy	122	1	We	-PRON-	PRP
cord-346267-l08ld2cy	122	2	chose	choose	VBD
cord-346267-l08ld2cy	122	3	to	to	TO
cord-346267-l08ld2cy	122	4	simulate	simulate	VB
cord-346267-l08ld2cy	122	5	branches	branch	NNS
cord-346267-l08ld2cy	122	6	based	base	VBN
cord-346267-l08ld2cy	122	7	on	on	IN
cord-346267-l08ld2cy	122	8	expected	expect	VBN
cord-346267-l08ld2cy	122	9	substitutions	substitution	NNS
cord-346267-l08ld2cy	122	10	per	per	IN
cord-346267-l08ld2cy	122	11	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	122	12	site	site	NN
cord-346267-l08ld2cy	122	13	,	,	,
cord-346267-l08ld2cy	122	14	instead	instead	RB
cord-346267-l08ld2cy	122	15	of	of	IN
cord-346267-l08ld2cy	122	16	per	per	IN
cord-346267-l08ld2cy	122	17	unit	unit	NN
cord-346267-l08ld2cy	122	18	time	time	NN
cord-346267-l08ld2cy	122	19	,	,	,
cord-346267-l08ld2cy	122	20	because	because	IN
cord-346267-l08ld2cy	122	21	of	of	IN
cord-346267-l08ld2cy	122	22	the	the	DT
cord-346267-l08ld2cy	122	23	difficulty	difficulty	NN
cord-346267-l08ld2cy	122	24	in	in	IN
cord-346267-l08ld2cy	122	25	standardizing	standardize	VBG
cord-346267-l08ld2cy	122	26	time	time	NN
cord-346267-l08ld2cy	122	27	for	for	IN
cord-346267-l08ld2cy	122	28	variable	variable	JJ
cord-346267-l08ld2cy	122	29	rate	rate	NN
cord-346267-l08ld2cy	122	30	parameters	parameter	NNS
cord-346267-l08ld2cy	122	31	(	(	-LRB-
cord-346267-l08ld2cy	122	32	i.e.	i.e.	FW
cord-346267-l08ld2cy	122	33	,	,	,
cord-346267-l08ld2cy	122	34	α	α	NNP
cord-346267-l08ld2cy	122	35	s	s	NNP
cord-346267-l08ld2cy	122	36	,	,	,
cord-346267-l08ld2cy	122	37	β	β	NN
cord-346267-l08ld2cy	122	38	I	I	NNP
cord-346267-l08ld2cy	122	39	s	s	NNP
cord-346267-l08ld2cy	122	40	,	,	,
cord-346267-l08ld2cy	122	41	and	and	CC
cord-346267-l08ld2cy	122	42	substitution	substitution	NN
cord-346267-l08ld2cy	122	43	rate	rate	NN
cord-346267-l08ld2cy	122	44	)	)	-RRB-
cord-346267-l08ld2cy	122	45	in	in	IN
cord-346267-l08ld2cy	122	46	a	a	DT
cord-346267-l08ld2cy	122	47	reversible	reversible	JJ
cord-346267-l08ld2cy	122	48	model	model	NN
cord-346267-l08ld2cy	122	49	;	;	:
cord-346267-l08ld2cy	122	50	the	the	DT
cord-346267-l08ld2cy	122	51	expected	expect	VBN
cord-346267-l08ld2cy	122	52	number	number	NN
cord-346267-l08ld2cy	122	53	of	of	IN
cord-346267-l08ld2cy	122	54	substitutions	substitution	NNS
cord-346267-l08ld2cy	122	55	divided	divide	VBN
cord-346267-l08ld2cy	122	56	by	by	IN
cord-346267-l08ld2cy	122	57	the	the	DT
cord-346267-l08ld2cy	122	58	substitution	substitution	NN
cord-346267-l08ld2cy	122	59	rate	rate	NN
cord-346267-l08ld2cy	122	60	can	can	MD
cord-346267-l08ld2cy	122	61	be	be	VB
cord-346267-l08ld2cy	122	62	a	a	DT
cord-346267-l08ld2cy	122	63	proxy	proxy	NN
cord-346267-l08ld2cy	122	64	for	for	IN
cord-346267-l08ld2cy	122	65	time	time	NN
cord-346267-l08ld2cy	122	66	.	.	.
cord-346267-l08ld2cy	123	1	Using	use	VBG
cord-346267-l08ld2cy	123	2	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	123	3	analysis	analysis	NN
cord-346267-l08ld2cy	123	4	,	,	,
cord-346267-l08ld2cy	123	5	we	-PRON-	PRP
cord-346267-l08ld2cy	123	6	inferred	infer	VBD
cord-346267-l08ld2cy	123	7	the	the	DT
cord-346267-l08ld2cy	123	8	substitution	substitution	NN
cord-346267-l08ld2cy	123	9	rate	rate	NN
cord-346267-l08ld2cy	123	10	and	and	CC
cord-346267-l08ld2cy	123	11	root	root	NN
cord-346267-l08ld2cy	123	12	age	age	NN
cord-346267-l08ld2cy	123	13	under	under	IN
cord-346267-l08ld2cy	123	14	a	a	DT
cord-346267-l08ld2cy	123	15	standard	standard	JJ
cord-346267-l08ld2cy	123	16	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	123	17	substitution	substitution	NN
cord-346267-l08ld2cy	123	18	model	model	NN
cord-346267-l08ld2cy	123	19	(	(	-LRB-
cord-346267-l08ld2cy	123	20	GTR	GTR	NNP
cord-346267-l08ld2cy	123	21	+	+	CC
cord-346267-l08ld2cy	123	22	Γ	γ	NN
cord-346267-l08ld2cy	123	23	4	4	CD
cord-346267-l08ld2cy	123	24	)	)	-RRB-
cord-346267-l08ld2cy	123	25	for	for	IN
cord-346267-l08ld2cy	123	26	each	each	DT
cord-346267-l08ld2cy	123	27	of	of	IN
cord-346267-l08ld2cy	123	28	our	-PRON-	PRP$
cord-346267-l08ld2cy	123	29	three	three	CD
cord-346267-l08ld2cy	123	30	viral	viral	JJ
cord-346267-l08ld2cy	123	31	data	data	NN
cord-346267-l08ld2cy	123	32	sets	set	NNS
cord-346267-l08ld2cy	123	33	:	:	:
cord-346267-l08ld2cy	124	1	MeV	MeV	NNP
cord-346267-l08ld2cy	124	2	/	/	SYM
cord-346267-l08ld2cy	124	3	RPV	RPV	NNP
cord-346267-l08ld2cy	124	4	/	/	SYM
cord-346267-l08ld2cy	124	5	PPRV	PPRV	NNP
cord-346267-l08ld2cy	124	6	nucleoprotein	nucleoprotein	NN
cord-346267-l08ld2cy	124	7	,	,	,
cord-346267-l08ld2cy	124	8	EBOV	EBOV	NNP
cord-346267-l08ld2cy	124	9	glycoprotein	glycoprotein	NN
cord-346267-l08ld2cy	124	10	,	,	,
cord-346267-l08ld2cy	124	11	and	and	CC
cord-346267-l08ld2cy	124	12	AIV	AIV	NNP
cord-346267-l08ld2cy	124	13	neuraminidase	neuraminidase	NN
cord-346267-l08ld2cy	124	14	(	(	-LRB-
cord-346267-l08ld2cy	124	15	table	table	NN
cord-346267-l08ld2cy	124	16	1	1	CD
cord-346267-l08ld2cy	124	17	)	)	-RRB-
cord-346267-l08ld2cy	124	18	.	.	.
cord-346267-l08ld2cy	125	1	The	the	DT
cord-346267-l08ld2cy	125	2	viral	viral	JJ
cord-346267-l08ld2cy	125	3	lineages	lineage	NNS
cord-346267-l08ld2cy	125	4	examined	examine	VBN
cord-346267-l08ld2cy	125	5	here	here	RB
cord-346267-l08ld2cy	125	6	had	have	VBD
cord-346267-l08ld2cy	125	7	tMRCAs	tmrca	VBN
cord-346267-l08ld2cy	125	8	ranging	range	VBG
cord-346267-l08ld2cy	125	9	from	from	IN
cord-346267-l08ld2cy	125	10	hundreds	hundred	NNS
cord-346267-l08ld2cy	125	11	to	to	IN
cord-346267-l08ld2cy	125	12	several	several	JJ
cord-346267-l08ld2cy	125	13	thousand	thousand	CD
cord-346267-l08ld2cy	125	14	years	year	NNS
cord-346267-l08ld2cy	125	15	before	before	IN
cord-346267-l08ld2cy	125	16	present	present	JJ
cord-346267-l08ld2cy	125	17	.	.	.
cord-346267-l08ld2cy	126	1	All	all	DT
cord-346267-l08ld2cy	126	2	three	three	CD
cord-346267-l08ld2cy	126	3	viruses	virus	NNS
cord-346267-l08ld2cy	126	4	exhibited	exhibit	VBD
cord-346267-l08ld2cy	126	5	rapid	rapid	JJ
cord-346267-l08ld2cy	126	6	substitution	substitution	NN
cord-346267-l08ld2cy	126	7	rates	rate	NNS
cord-346267-l08ld2cy	126	8	,	,	,
cord-346267-l08ld2cy	126	9	on	on	IN
cord-346267-l08ld2cy	126	10	par	par	NN
cord-346267-l08ld2cy	126	11	with	with	IN
cord-346267-l08ld2cy	126	12	previous	previous	JJ
cord-346267-l08ld2cy	126	13	estimates	estimate	NNS
cord-346267-l08ld2cy	126	14	for	for	IN
cord-346267-l08ld2cy	126	15	related	relate	VBN
cord-346267-l08ld2cy	126	16	RNA	RNA	NNP
cord-346267-l08ld2cy	126	17	viruses	virus	NNS
cord-346267-l08ld2cy	126	18	(	(	-LRB-
cord-346267-l08ld2cy	126	19	Duffy	Duffy	NNP
cord-346267-l08ld2cy	126	20	et	et	NNP
cord-346267-l08ld2cy	126	21	al	al	NNP
cord-346267-l08ld2cy	126	22	.	.	NNP
cord-346267-l08ld2cy	126	23	2008	2008	CD
cord-346267-l08ld2cy	126	24	)	)	-RRB-
cord-346267-l08ld2cy	126	25	.	.	.
cord-346267-l08ld2cy	127	1	Our	-PRON-	PRP$
cord-346267-l08ld2cy	127	2	inferred	inferred	JJ
cord-346267-l08ld2cy	127	3	substitution	substitution	NN
cord-346267-l08ld2cy	127	4	rate	rate	NN
cord-346267-l08ld2cy	127	5	for	for	IN
cord-346267-l08ld2cy	127	6	the	the	DT
cord-346267-l08ld2cy	127	7	MeV	MeV	NNP
cord-346267-l08ld2cy	127	8	/	/	SYM
cord-346267-l08ld2cy	127	9	RPV	RPV	NNP
cord-346267-l08ld2cy	127	10	/	/	SYM
cord-346267-l08ld2cy	127	11	PPRV	PPRV	NNP
cord-346267-l08ld2cy	127	12	nucleoprotein	nucleoprotein	NN
cord-346267-l08ld2cy	127	13	of	of	IN
cord-346267-l08ld2cy	127	14	9.65	9.65	CD
cord-346267-l08ld2cy	127	15	×	×	NN
cord-346267-l08ld2cy	127	16	10	10	CD
cord-346267-l08ld2cy	127	17	−4	−4	CD
cord-346267-l08ld2cy	127	18	(	(	-LRB-
cord-346267-l08ld2cy	127	19	6.00	6.00	CD
cord-346267-l08ld2cy	127	20	×	×	NN
cord-346267-l08ld2cy	127	21	10	10	CD
cord-346267-l08ld2cy	127	22	−4	−4	CD
cord-346267-l08ld2cy	127	23	-1.47	-1.47	CD
cord-346267-l08ld2cy	127	24	×	×	NN
cord-346267-l08ld2cy	127	25	10	10	CD
cord-346267-l08ld2cy	127	26	−3	−3	NN
cord-346267-l08ld2cy	127	27	)	)	-RRB-
cord-346267-l08ld2cy	127	28	substitutions	substitution	NNS
cord-346267-l08ld2cy	127	29	/	/	SYM
cord-346267-l08ld2cy	127	30	site	site	NN
cord-346267-l08ld2cy	127	31	/	/	SYM
cord-346267-l08ld2cy	127	32	year	year	NN
cord-346267-l08ld2cy	127	33	under	under	IN
cord-346267-l08ld2cy	127	34	a	a	DT
cord-346267-l08ld2cy	127	35	GTR	GTR	NNP
cord-346267-l08ld2cy	127	36	+	+	SYM
cord-346267-l08ld2cy	127	37	Γ	γ	NN
cord-346267-l08ld2cy	127	38	4	4	CD
cord-346267-l08ld2cy	127	39	model	model	NN
cord-346267-l08ld2cy	127	40	was	be	VBD
cord-346267-l08ld2cy	127	41	over	over	IN
cord-346267-l08ld2cy	127	42	50	50	CD
cord-346267-l08ld2cy	127	43	%	%	NN
cord-346267-l08ld2cy	127	44	faster	fast	RBR
cord-346267-l08ld2cy	127	45	than	than	IN
cord-346267-l08ld2cy	127	46	the	the	DT
cord-346267-l08ld2cy	127	47	rate	rate	NN
cord-346267-l08ld2cy	127	48	recently	recently	RB
cord-346267-l08ld2cy	127	49	reported	report	VBN
cord-346267-l08ld2cy	127	50	by	by	IN
cord-346267-l08ld2cy	127	51	Furuse	Furuse	NNP
cord-346267-l08ld2cy	127	52	et	et	NNP
cord-346267-l08ld2cy	127	53	al	al	NNP
cord-346267-l08ld2cy	127	54	.	.	.
cord-346267-l08ld2cy	128	1	(	(	-LRB-
cord-346267-l08ld2cy	128	2	2010	2010	CD
cord-346267-l08ld2cy	128	3	)	)	-RRB-
cord-346267-l08ld2cy	128	4	:	:	:
cord-346267-l08ld2cy	128	5	6.02	6.02	CD
cord-346267-l08ld2cy	128	6	×	×	NN
cord-346267-l08ld2cy	128	7	10	10	CD
cord-346267-l08ld2cy	128	8	−4	−4	CD
cord-346267-l08ld2cy	128	9	(	(	-LRB-
cord-346267-l08ld2cy	128	10	3.62	3.62	CD
cord-346267-l08ld2cy	128	11	×	×	NN
cord-346267-l08ld2cy	128	12	10	10	CD
cord-346267-l08ld2cy	128	13	−4	−4	CD
cord-346267-l08ld2cy	128	14	-8.76	-8.76	CD
cord-346267-l08ld2cy	128	15	×	×	NN
cord-346267-l08ld2cy	128	16	10	10	CD
cord-346267-l08ld2cy	128	17	−4	−4	CD
cord-346267-l08ld2cy	128	18	)	)	-RRB-
cord-346267-l08ld2cy	128	19	substitutions	substitution	NNS
cord-346267-l08ld2cy	128	20	/	/	SYM
cord-346267-l08ld2cy	128	21	site	site	NN
cord-346267-l08ld2cy	128	22	/	/	SYM
cord-346267-l08ld2cy	128	23	year	year	NN
cord-346267-l08ld2cy	128	24	.	.	.
cord-346267-l08ld2cy	129	1	Therefore	therefore	RB
cord-346267-l08ld2cy	129	2	,	,	,
cord-346267-l08ld2cy	129	3	we	-PRON-	PRP
cord-346267-l08ld2cy	129	4	inferred	infer	VBD
cord-346267-l08ld2cy	129	5	a	a	DT
cord-346267-l08ld2cy	129	6	substantially	substantially	RB
cord-346267-l08ld2cy	129	7	younger	young	JJR
cord-346267-l08ld2cy	129	8	tMRCA	tmrca	NN
cord-346267-l08ld2cy	129	9	for	for	IN
cord-346267-l08ld2cy	129	10	MeV	MeV	NNP
cord-346267-l08ld2cy	129	11	and	and	CC
cord-346267-l08ld2cy	129	12	RPV	RPV	NNP
cord-346267-l08ld2cy	129	13	:	:	:
cord-346267-l08ld2cy	130	1	1490	1490	CD
cord-346267-l08ld2cy	130	2	CE	CE	NNP
cord-346267-l08ld2cy	130	3	(	(	-LRB-
cord-346267-l08ld2cy	130	4	1130	1130	CD
cord-346267-l08ld2cy	130	5	-	-	SYM
cord-346267-l08ld2cy	130	6	1810	1810	CD
cord-346267-l08ld2cy	130	7	CE	CE	NNP
cord-346267-l08ld2cy	130	8	)	)	-RRB-
cord-346267-l08ld2cy	130	9	,	,	,
cord-346267-l08ld2cy	130	10	instead	instead	RB
cord-346267-l08ld2cy	130	11	of	of	IN
cord-346267-l08ld2cy	130	12	1171	1171	CD
cord-346267-l08ld2cy	130	13	CE	CE	NNP
cord-346267-l08ld2cy	130	14	(	(	-LRB-
cord-346267-l08ld2cy	130	15	678	678	CD
cord-346267-l08ld2cy	130	16	-	-	SYM
cord-346267-l08ld2cy	130	17	1612	1612	CD
cord-346267-l08ld2cy	130	18	CE	ce	NN
cord-346267-l08ld2cy	130	19	)	)	-RRB-
cord-346267-l08ld2cy	130	20	.	.	.
cord-346267-l08ld2cy	131	1	We	-PRON-	PRP
cord-346267-l08ld2cy	131	2	consider	consider	VBP
cord-346267-l08ld2cy	131	3	our	-PRON-	PRP$
cord-346267-l08ld2cy	131	4	rate	rate	NN
cord-346267-l08ld2cy	131	5	estimates	estimate	NNS
cord-346267-l08ld2cy	131	6	more	more	RBR
cord-346267-l08ld2cy	131	7	reliable	reliable	JJ
cord-346267-l08ld2cy	131	8	for	for	IN
cord-346267-l08ld2cy	131	9	three	three	CD
cord-346267-l08ld2cy	131	10	reasons	reason	NNS
cord-346267-l08ld2cy	131	11	.	.	.
cord-346267-l08ld2cy	132	1	First	first	RB
cord-346267-l08ld2cy	132	2	,	,	,
cord-346267-l08ld2cy	132	3	our	-PRON-	PRP$
cord-346267-l08ld2cy	132	4	values	value	NNS
cord-346267-l08ld2cy	132	5	are	be	VBP
cord-346267-l08ld2cy	132	6	in	in	IN
cord-346267-l08ld2cy	132	7	close	close	JJ
cord-346267-l08ld2cy	132	8	agreement	agreement	NN
cord-346267-l08ld2cy	132	9	with	with	IN
cord-346267-l08ld2cy	132	10	previous	previous	JJ
cord-346267-l08ld2cy	132	11	substitution	substitution	NN
cord-346267-l08ld2cy	132	12	rate	rate	NN
cord-346267-l08ld2cy	132	13	estimates	estimate	NNS
cord-346267-l08ld2cy	132	14	in	in	IN
cord-346267-l08ld2cy	132	15	MeV	MeV	NNP
cord-346267-l08ld2cy	132	16	:	:	:
cord-346267-l08ld2cy	132	17	8.69	8.69	CD
cord-346267-l08ld2cy	132	18	×	×	NN
cord-346267-l08ld2cy	132	19	10	10	CD
cord-346267-l08ld2cy	132	20	−4	−4	CD
cord-346267-l08ld2cy	132	21	(	(	-LRB-
cord-346267-l08ld2cy	132	22	5.89	5.89	CD
cord-346267-l08ld2cy	132	23	×	×	NN
cord-346267-l08ld2cy	132	24	10	10	CD
cord-346267-l08ld2cy	132	25	−4	−4	CD
cord-346267-l08ld2cy	133	1	-1.13	-1.13	:
cord-346267-l08ld2cy	134	1	×	×	NN
cord-346267-l08ld2cy	134	2	10	10	CD
cord-346267-l08ld2cy	134	3	−3	−3	NN
cord-346267-l08ld2cy	134	4	)	)	-RRB-
cord-346267-l08ld2cy	135	1	substitutions	substitution	NNS
cord-346267-l08ld2cy	135	2	/	/	SYM
cord-346267-l08ld2cy	135	3	site	site	NN
cord-346267-l08ld2cy	135	4	/	/	SYM
cord-346267-l08ld2cy	135	5	year	year	NN
cord-346267-l08ld2cy	136	1	(	(	-LRB-
cord-346267-l08ld2cy	136	2	Pomeroy	Pomeroy	NNP
cord-346267-l08ld2cy	136	3	et	et	NNP
cord-346267-l08ld2cy	136	4	al	al	NNP
cord-346267-l08ld2cy	136	5	.	.	NNP
cord-346267-l08ld2cy	136	6	2008	2008	CD
cord-346267-l08ld2cy	136	7	)	)	-RRB-
cord-346267-l08ld2cy	136	8	.	.	.
cord-346267-l08ld2cy	137	1	Second	second	JJ
cord-346267-l08ld2cy	137	2	,	,	,
cord-346267-l08ld2cy	137	3	Furuse	Furuse	NNP
cord-346267-l08ld2cy	137	4	et	et	NNP
cord-346267-l08ld2cy	137	5	al	al	NNP
cord-346267-l08ld2cy	137	6	.	.	.
cord-346267-l08ld2cy	138	1	(	(	-LRB-
cord-346267-l08ld2cy	138	2	2010	2010	CD
cord-346267-l08ld2cy	138	3	)	)	-RRB-
cord-346267-l08ld2cy	138	4	included	include	VBD
cord-346267-l08ld2cy	138	5	both	both	DT
cord-346267-l08ld2cy	138	6	MeV	MeV	NNP
cord-346267-l08ld2cy	138	7	and	and	CC
cord-346267-l08ld2cy	138	8	RPV	RPV	NNP
cord-346267-l08ld2cy	138	9	vaccine	vaccine	NN
cord-346267-l08ld2cy	138	10	strains	strain	NNS
cord-346267-l08ld2cy	138	11	in	in	IN
cord-346267-l08ld2cy	138	12	their	-PRON-	PRP$
cord-346267-l08ld2cy	138	13	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	138	14	dating	date	VBG
cord-346267-l08ld2cy	138	15	analysis	analysis	NN
cord-346267-l08ld2cy	139	1	(	(	-LRB-
cord-346267-l08ld2cy	139	2	Rota	Rota	NNP
cord-346267-l08ld2cy	139	3	et	et	NNP
cord-346267-l08ld2cy	139	4	al	al	NNP
cord-346267-l08ld2cy	139	5	.	.	.
cord-346267-l08ld2cy	139	6	1994	1994	CD
cord-346267-l08ld2cy	139	7	;	;	:
cord-346267-l08ld2cy	139	8	Baron	Baron	NNP
cord-346267-l08ld2cy	139	9	et	et	NNP
cord-346267-l08ld2cy	139	10	al	al	NNP
cord-346267-l08ld2cy	139	11	.	.	.
cord-346267-l08ld2cy	139	12	1996	1996	CD
cord-346267-l08ld2cy	139	13	)	)	-RRB-
cord-346267-l08ld2cy	139	14	,	,	,
cord-346267-l08ld2cy	139	15	despite	despite	IN
cord-346267-l08ld2cy	139	16	evidence	evidence	NN
cord-346267-l08ld2cy	139	17	that	that	IN
cord-346267-l08ld2cy	139	18	the	the	DT
cord-346267-l08ld2cy	139	19	inclusion	inclusion	NN
cord-346267-l08ld2cy	139	20	of	of	IN
cord-346267-l08ld2cy	139	21	vaccine	vaccine	NN
cord-346267-l08ld2cy	139	22	strains	strain	NNS
cord-346267-l08ld2cy	139	23	can	can	MD
cord-346267-l08ld2cy	139	24	lead	lead	VB
cord-346267-l08ld2cy	139	25	to	to	IN
cord-346267-l08ld2cy	139	26	bias	bias	NN
cord-346267-l08ld2cy	139	27	in	in	IN
cord-346267-l08ld2cy	139	28	rate	rate	NN
cord-346267-l08ld2cy	139	29	estimation	estimation	NN
cord-346267-l08ld2cy	139	30	(	(	-LRB-
cord-346267-l08ld2cy	139	31	Bush	Bush	NNP
cord-346267-l08ld2cy	139	32	et	et	NNP
cord-346267-l08ld2cy	139	33	al	al	NNP
cord-346267-l08ld2cy	139	34	.	.	.
cord-346267-l08ld2cy	139	35	2000	2000	CD
cord-346267-l08ld2cy	139	36	;	;	:
cord-346267-l08ld2cy	139	37	Wertheim	Wertheim	NNP
cord-346267-l08ld2cy	139	38	2010	2010	CD
cord-346267-l08ld2cy	139	39	)	)	-RRB-
cord-346267-l08ld2cy	139	40	.	.	.
cord-346267-l08ld2cy	140	1	Third	third	RB
cord-346267-l08ld2cy	140	2	,	,	,
cord-346267-l08ld2cy	140	3	Furuse	Furuse	NNP
cord-346267-l08ld2cy	140	4	et	et	NNP
cord-346267-l08ld2cy	140	5	al	al	NNP
cord-346267-l08ld2cy	140	6	.	.	.
cord-346267-l08ld2cy	141	1	(	(	-LRB-
cord-346267-l08ld2cy	141	2	2010	2010	CD
cord-346267-l08ld2cy	141	3	)	)	-RRB-
cord-346267-l08ld2cy	141	4	fitted	fit	VBD
cord-346267-l08ld2cy	141	5	an	an	DT
cord-346267-l08ld2cy	141	6	exponential	exponential	JJ
cord-346267-l08ld2cy	141	7	growth	growth	NN
cord-346267-l08ld2cy	141	8	coalescent	coalescent	NN
cord-346267-l08ld2cy	141	9	prior	prior	RB
cord-346267-l08ld2cy	141	10	to	to	IN
cord-346267-l08ld2cy	141	11	viruses	virus	NNS
cord-346267-l08ld2cy	141	12	whose	whose	WP$
cord-346267-l08ld2cy	141	13	effective	effective	JJ
cord-346267-l08ld2cy	141	14	population	population	NN
cord-346267-l08ld2cy	141	15	size	size	NN
cord-346267-l08ld2cy	141	16	has	have	VBZ
cord-346267-l08ld2cy	141	17	been	be	VBN
cord-346267-l08ld2cy	141	18	declining	decline	VBG
cord-346267-l08ld2cy	141	19	-	-	HYPH
cord-346267-l08ld2cy	141	20	due	due	IN
cord-346267-l08ld2cy	141	21	to	to	IN
cord-346267-l08ld2cy	141	22	eradication	eradication	NN
cord-346267-l08ld2cy	141	23	efforts	effort	NNS
cord-346267-l08ld2cy	141	24	against	against	IN
cord-346267-l08ld2cy	141	25	both	both	DT
cord-346267-l08ld2cy	141	26	MeV	MeV	NNP
cord-346267-l08ld2cy	141	27	and	and	CC
cord-346267-l08ld2cy	141	28	RPV	RPV	NNP
cord-346267-l08ld2cy	141	29	(	(	-LRB-
cord-346267-l08ld2cy	141	30	Moss	Moss	NNP
cord-346267-l08ld2cy	141	31	2009	2009	CD
cord-346267-l08ld2cy	141	32	;	;	:
cord-346267-l08ld2cy	141	33	Normile	Normile	NNP
cord-346267-l08ld2cy	141	34	2010	2010	CD
cord-346267-l08ld2cy	141	35	)	)	-RRB-
cord-346267-l08ld2cy	141	36	.	.	.
cord-346267-l08ld2cy	142	1	Remarkably	remarkably	RB
cord-346267-l08ld2cy	142	2	,	,	,
cord-346267-l08ld2cy	142	3	our	-PRON-	PRP$
cord-346267-l08ld2cy	142	4	results	result	NNS
cord-346267-l08ld2cy	142	5	are	be	VBP
cord-346267-l08ld2cy	142	6	in	in	IN
cord-346267-l08ld2cy	142	7	even	even	RB
cord-346267-l08ld2cy	142	8	greater	great	JJR
cord-346267-l08ld2cy	142	9	conflict	conflict	NN
cord-346267-l08ld2cy	142	10	with	with	IN
cord-346267-l08ld2cy	142	11	the	the	DT
cord-346267-l08ld2cy	142	12	historical	historical	JJ
cord-346267-l08ld2cy	142	13	documentation	documentation	NN
cord-346267-l08ld2cy	142	14	of	of	IN
cord-346267-l08ld2cy	142	15	measles	measle	NNS
cord-346267-l08ld2cy	142	16	(	(	-LRB-
cord-346267-l08ld2cy	142	17	Rāzī	Rāzī	NNP
cord-346267-l08ld2cy	142	18	1848	1848	CD
cord-346267-l08ld2cy	142	19	)	)	-RRB-
cord-346267-l08ld2cy	142	20	,	,	,
cord-346267-l08ld2cy	142	21	further	further	RB
cord-346267-l08ld2cy	142	22	confirming	confirm	VBG
cord-346267-l08ld2cy	142	23	our	-PRON-	PRP$
cord-346267-l08ld2cy	142	24	conjecture	conjecture	NN
cord-346267-l08ld2cy	142	25	that	that	IN
cord-346267-l08ld2cy	142	26	traditional	traditional	JJ
cord-346267-l08ld2cy	142	27	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	142	28	substitution	substitution	NN
cord-346267-l08ld2cy	142	29	models	model	NNS
cord-346267-l08ld2cy	142	30	can	can	MD
cord-346267-l08ld2cy	142	31	underestimate	underestimate	VB
cord-346267-l08ld2cy	142	32	the	the	DT
cord-346267-l08ld2cy	142	33	age	age	NN
cord-346267-l08ld2cy	142	34	of	of	IN
cord-346267-l08ld2cy	142	35	ancient	ancient	JJ
cord-346267-l08ld2cy	142	36	viral	viral	JJ
cord-346267-l08ld2cy	142	37	divergence	divergence	NN
cord-346267-l08ld2cy	142	38	events	event	NNS
cord-346267-l08ld2cy	142	39	.	.	.
cord-346267-l08ld2cy	143	1	We	-PRON-	PRP
cord-346267-l08ld2cy	143	2	then	then	RB
cord-346267-l08ld2cy	143	3	explored	explore	VBD
cord-346267-l08ld2cy	143	4	whether	whether	IN
cord-346267-l08ld2cy	143	5	alternative	alternative	JJ
cord-346267-l08ld2cy	143	6	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	143	7	models	model	NNS
cord-346267-l08ld2cy	143	8	that	that	WDT
cord-346267-l08ld2cy	143	9	,	,	,
cord-346267-l08ld2cy	143	10	to	to	IN
cord-346267-l08ld2cy	143	11	varying	vary	VBG
cord-346267-l08ld2cy	143	12	extents	extent	NNS
cord-346267-l08ld2cy	143	13	,	,	,
cord-346267-l08ld2cy	143	14	account	account	VBP
cord-346267-l08ld2cy	143	15	for	for	IN
cord-346267-l08ld2cy	143	16	codon	codon	NN
cord-346267-l08ld2cy	143	17	structure	structure	NN
cord-346267-l08ld2cy	143	18	were	be	VBD
cord-346267-l08ld2cy	143	19	able	able	JJ
cord-346267-l08ld2cy	143	20	to	to	TO
cord-346267-l08ld2cy	143	21	recover	recover	VB
cord-346267-l08ld2cy	143	22	the	the	DT
cord-346267-l08ld2cy	143	23	expected	expect	VBN
cord-346267-l08ld2cy	143	24	older	old	JJR
cord-346267-l08ld2cy	143	25	tMRCAs	tmrca	VBD
cord-346267-l08ld2cy	143	26	for	for	IN
cord-346267-l08ld2cy	143	27	these	these	DT
cord-346267-l08ld2cy	143	28	viruses	virus	NNS
cord-346267-l08ld2cy	143	29	(	(	-LRB-
cord-346267-l08ld2cy	143	30	table	table	NN
cord-346267-l08ld2cy	143	31	1	1	CD
cord-346267-l08ld2cy	143	32	)	)	-RRB-
cord-346267-l08ld2cy	143	33	.	.	.
cord-346267-l08ld2cy	144	1	The	the	DT
cord-346267-l08ld2cy	144	2	simplest	simple	JJS
cord-346267-l08ld2cy	144	3	approach	approach	NN
cord-346267-l08ld2cy	144	4	,	,	,
cord-346267-l08ld2cy	144	5	excluding	exclude	VBG
cord-346267-l08ld2cy	144	6	the	the	DT
cord-346267-l08ld2cy	144	7	third	third	JJ
cord-346267-l08ld2cy	144	8	codon	codon	NN
cord-346267-l08ld2cy	144	9	position	position	NN
cord-346267-l08ld2cy	144	10	in	in	IN
cord-346267-l08ld2cy	144	11	a	a	DT
cord-346267-l08ld2cy	144	12	GTR	GTR	NNP
cord-346267-l08ld2cy	144	13	+	+	SYM
cord-346267-l08ld2cy	144	14	Γ	γ	NN
cord-346267-l08ld2cy	144	15	4	4	CD
cord-346267-l08ld2cy	144	16	model	model	NN
cord-346267-l08ld2cy	144	17	,	,	,
cord-346267-l08ld2cy	144	18	has	have	VBZ
cord-346267-l08ld2cy	144	19	been	be	VBN
cord-346267-l08ld2cy	144	20	used	use	VBN
cord-346267-l08ld2cy	144	21	to	to	TO
cord-346267-l08ld2cy	144	22	remove	remove	VB
cord-346267-l08ld2cy	144	23	synonymous	synonymous	JJ
cord-346267-l08ld2cy	144	24	sites	site	NNS
cord-346267-l08ld2cy	144	25	that	that	WDT
cord-346267-l08ld2cy	144	26	might	may	MD
cord-346267-l08ld2cy	144	27	have	have	VB
cord-346267-l08ld2cy	144	28	experienced	experience	VBN
cord-346267-l08ld2cy	144	29	saturation	saturation	NN
cord-346267-l08ld2cy	144	30	(	(	-LRB-
cord-346267-l08ld2cy	144	31	Worobey	Worobey	NNP
cord-346267-l08ld2cy	144	32	et	et	NNP
cord-346267-l08ld2cy	144	33	al	al	NNP
cord-346267-l08ld2cy	144	34	.	.	NNP
cord-346267-l08ld2cy	144	35	2010	2010	CD
cord-346267-l08ld2cy	144	36	)	)	-RRB-
cord-346267-l08ld2cy	144	37	.	.	.
cord-346267-l08ld2cy	145	1	A	a	DT
cord-346267-l08ld2cy	145	2	more	more	RBR
cord-346267-l08ld2cy	145	3	sophisticated	sophisticated	JJ
cord-346267-l08ld2cy	145	4	approach	approach	NN
cord-346267-l08ld2cy	145	5	,	,	,
cord-346267-l08ld2cy	145	6	the	the	DT
cord-346267-l08ld2cy	145	7	SRD06	SRD06	NNP
cord-346267-l08ld2cy	145	8	model	model	NN
cord-346267-l08ld2cy	145	9	(	(	-LRB-
cord-346267-l08ld2cy	145	10	Shapiro	Shapiro	NNP
cord-346267-l08ld2cy	145	11	et	et	NNP
cord-346267-l08ld2cy	145	12	al	al	NNP
cord-346267-l08ld2cy	145	13	.	.	.
cord-346267-l08ld2cy	145	14	2006	2006	CD
cord-346267-l08ld2cy	145	15	)	)	-RRB-
cord-346267-l08ld2cy	145	16	,	,	,
cord-346267-l08ld2cy	145	17	allows	allow	VBZ
cord-346267-l08ld2cy	145	18	first	first	JJ
cord-346267-l08ld2cy	145	19	and	and	CC
cord-346267-l08ld2cy	145	20	second	second	JJ
cord-346267-l08ld2cy	145	21	codon	codon	NN
cord-346267-l08ld2cy	145	22	positions	position	NNS
cord-346267-l08ld2cy	145	23	to	to	TO
cord-346267-l08ld2cy	145	24	have	have	VB
cord-346267-l08ld2cy	145	25	a	a	DT
cord-346267-l08ld2cy	145	26	different	different	JJ
cord-346267-l08ld2cy	145	27	transition	transition	NN
cord-346267-l08ld2cy	145	28	/	/	SYM
cord-346267-l08ld2cy	145	29	transversion	transversion	NN
cord-346267-l08ld2cy	145	30	ratio	ratio	NN
cord-346267-l08ld2cy	145	31	and	and	CC
cord-346267-l08ld2cy	145	32	Γ	γ	NN
cord-346267-l08ld2cy	145	33	4	4	CD
cord-346267-l08ld2cy	145	34	shape	shape	NN
cord-346267-l08ld2cy	145	35	parameter	parameter	NN
cord-346267-l08ld2cy	145	36	from	from	IN
cord-346267-l08ld2cy	145	37	the	the	DT
cord-346267-l08ld2cy	145	38	third	third	JJ
cord-346267-l08ld2cy	145	39	position	position	NN
cord-346267-l08ld2cy	145	40	.	.	.
cord-346267-l08ld2cy	146	1	Amino	amino	NN
cord-346267-l08ld2cy	146	2	acid	acid	NN
cord-346267-l08ld2cy	146	3	substitution	substitution	NN
cord-346267-l08ld2cy	146	4	models	model	NNS
cord-346267-l08ld2cy	146	5	have	have	VBP
cord-346267-l08ld2cy	146	6	also	also	RB
cord-346267-l08ld2cy	146	7	been	be	VBN
cord-346267-l08ld2cy	146	8	successfully	successfully	RB
cord-346267-l08ld2cy	146	9	implemented	implement	VBN
cord-346267-l08ld2cy	146	10	to	to	TO
cord-346267-l08ld2cy	146	11	estimate	estimate	VB
cord-346267-l08ld2cy	146	12	the	the	DT
cord-346267-l08ld2cy	146	13	age	age	NN
cord-346267-l08ld2cy	146	14	of	of	IN
cord-346267-l08ld2cy	146	15	RNA	RNA	NNP
cord-346267-l08ld2cy	146	16	viruses	virus	NNS
cord-346267-l08ld2cy	146	17	(	(	-LRB-
cord-346267-l08ld2cy	146	18	Zlateva	Zlateva	NNP
cord-346267-l08ld2cy	146	19	et	et	FW
cord-346267-l08ld2cy	146	20	al	al	NNP
cord-346267-l08ld2cy	146	21	.	.	NNP
cord-346267-l08ld2cy	146	22	2005	2005	CD
cord-346267-l08ld2cy	146	23	;	;	:
cord-346267-l08ld2cy	146	24	Wertheim	Wertheim	NNP
cord-346267-l08ld2cy	146	25	et	et	NNP
cord-346267-l08ld2cy	146	26	al	al	NNP
cord-346267-l08ld2cy	146	27	.	.	NNP
cord-346267-l08ld2cy	146	28	2009	2009	CD
cord-346267-l08ld2cy	146	29	)	)	-RRB-
cord-346267-l08ld2cy	146	30	.	.	.
cord-346267-l08ld2cy	147	1	Finally	finally	RB
cord-346267-l08ld2cy	147	2	,	,	,
cord-346267-l08ld2cy	147	3	we	-PRON-	PRP
cord-346267-l08ld2cy	147	4	evaluated	evaluate	VBD
cord-346267-l08ld2cy	147	5	an	an	DT
cord-346267-l08ld2cy	147	6	available	available	JJ
cord-346267-l08ld2cy	147	7	codon	codon	NN
cord-346267-l08ld2cy	147	8	-	-	HYPH
cord-346267-l08ld2cy	147	9	based	base	VBN
cord-346267-l08ld2cy	147	10	substitution	substitution	NN
cord-346267-l08ld2cy	147	11	model	model	NN
cord-346267-l08ld2cy	147	12	,	,	,
cord-346267-l08ld2cy	147	13	GY94	GY94	NNP
cord-346267-l08ld2cy	147	14	(	(	-LRB-
cord-346267-l08ld2cy	147	15	Goldman	Goldman	NNP
cord-346267-l08ld2cy	147	16	and	and	CC
cord-346267-l08ld2cy	147	17	Yang	Yang	NNP
cord-346267-l08ld2cy	147	18	1994	1994	CD
cord-346267-l08ld2cy	147	19	)	)	-RRB-
cord-346267-l08ld2cy	147	20	.	.	.
cord-346267-l08ld2cy	148	1	Generally	generally	RB
cord-346267-l08ld2cy	148	2	,	,	,
cord-346267-l08ld2cy	148	3	these	these	DT
cord-346267-l08ld2cy	148	4	alternate	alternate	JJ
cord-346267-l08ld2cy	148	5	models	model	NNS
cord-346267-l08ld2cy	148	6	either	either	CC
cord-346267-l08ld2cy	148	7	produced	produce	VBD
cord-346267-l08ld2cy	148	8	younger	young	JJR
cord-346267-l08ld2cy	148	9	tMRCAs	tmrcas	IN
cord-346267-l08ld2cy	148	10	(	(	-LRB-
cord-346267-l08ld2cy	148	11	e.g.	e.g.	RB
cord-346267-l08ld2cy	148	12	,	,	,
cord-346267-l08ld2cy	148	13	GTR	GTR	NNP
cord-346267-l08ld2cy	148	14	+	+	CC
cord-346267-l08ld2cy	148	15	Γ	γ	NN
cord-346267-l08ld2cy	148	16	4	4	CD
cord-346267-l08ld2cy	148	17	excluding	exclude	VBG
cord-346267-l08ld2cy	148	18	third	third	JJ
cord-346267-l08ld2cy	148	19	positions	position	NNS
cord-346267-l08ld2cy	148	20	and	and	CC
cord-346267-l08ld2cy	148	21	Whelan	Whelan	NNP
cord-346267-l08ld2cy	148	22	and	and	CC
cord-346267-l08ld2cy	148	23	Goldman	Goldman	NNP
cord-346267-l08ld2cy	148	24	+	+	CC
cord-346267-l08ld2cy	148	25	Γ	Γ	NNP
cord-346267-l08ld2cy	148	26	4	4	CD
cord-346267-l08ld2cy	148	27	)	)	-RRB-
cord-346267-l08ld2cy	148	28	or	or	CC
cord-346267-l08ld2cy	148	29	tMRCAs	tmrca	VBN
cord-346267-l08ld2cy	148	30	that	that	WDT
cord-346267-l08ld2cy	148	31	were	be	VBD
cord-346267-l08ld2cy	148	32	indistinguishable	indistinguishable	JJ
cord-346267-l08ld2cy	148	33	from	from	IN
cord-346267-l08ld2cy	148	34	GTR	GTR	NNP
cord-346267-l08ld2cy	148	35	+	+	CC
cord-346267-l08ld2cy	148	36	Γ	γ	NN
cord-346267-l08ld2cy	148	37	4	4	CD
cord-346267-l08ld2cy	148	38	(	(	-LRB-
cord-346267-l08ld2cy	148	39	e.g.	e.g.	RB
cord-346267-l08ld2cy	148	40	,	,	,
cord-346267-l08ld2cy	148	41	SRD06	SRD06	NNP
cord-346267-l08ld2cy	148	42	and	and	CC
cord-346267-l08ld2cy	148	43	GY94	GY94	NNP
cord-346267-l08ld2cy	148	44	+	+	CC
cord-346267-l08ld2cy	148	45	Γ	Γ	NNP
cord-346267-l08ld2cy	148	46	4	4	CD
cord-346267-l08ld2cy	148	47	)	)	-RRB-
cord-346267-l08ld2cy	148	48	.	.	.
cord-346267-l08ld2cy	149	1	A	a	DT
cord-346267-l08ld2cy	149	2	possible	possible	JJ
cord-346267-l08ld2cy	149	3	exception	exception	NN
cord-346267-l08ld2cy	149	4	was	be	VBD
cord-346267-l08ld2cy	149	5	analysis	analysis	NN
cord-346267-l08ld2cy	149	6	of	of	IN
cord-346267-l08ld2cy	149	7	the	the	DT
cord-346267-l08ld2cy	149	8	EBOV	EBOV	NNP
cord-346267-l08ld2cy	149	9	data	datum	NNS
cord-346267-l08ld2cy	149	10	set	set	VBN
cord-346267-l08ld2cy	149	11	with	with	IN
cord-346267-l08ld2cy	149	12	GY94	GY94	NNP
cord-346267-l08ld2cy	149	13	+	+	CC
cord-346267-l08ld2cy	149	14	Γ	γ	NN
cord-346267-l08ld2cy	149	15	4	4	CD
cord-346267-l08ld2cy	149	16	,	,	,
cord-346267-l08ld2cy	149	17	which	which	WDT
cord-346267-l08ld2cy	149	18	produced	produce	VBD
cord-346267-l08ld2cy	149	19	a	a	DT
cord-346267-l08ld2cy	149	20	root	root	NN
cord-346267-l08ld2cy	149	21	tMRCA	tmrca	NN
cord-346267-l08ld2cy	149	22	that	that	WDT
cord-346267-l08ld2cy	149	23	was	be	VBD
cord-346267-l08ld2cy	149	24	50	50	CD
cord-346267-l08ld2cy	149	25	%	%	NN
cord-346267-l08ld2cy	149	26	older	old	JJR
cord-346267-l08ld2cy	149	27	than	than	IN
cord-346267-l08ld2cy	149	28	the	the	DT
cord-346267-l08ld2cy	149	29	GTR	GTR	NNP
cord-346267-l08ld2cy	149	30	+	+	SYM
cord-346267-l08ld2cy	149	31	Γ	γ	NN
cord-346267-l08ld2cy	149	32	4	4	CD
cord-346267-l08ld2cy	149	33	estimate	estimate	NN
cord-346267-l08ld2cy	149	34	.	.	.
cord-346267-l08ld2cy	150	1	Finally	finally	RB
cord-346267-l08ld2cy	150	2	,	,	,
cord-346267-l08ld2cy	150	3	as	as	IN
cord-346267-l08ld2cy	150	4	a	a	DT
cord-346267-l08ld2cy	150	5	point	point	NN
cord-346267-l08ld2cy	150	6	of	of	IN
cord-346267-l08ld2cy	150	7	comparison	comparison	NN
cord-346267-l08ld2cy	150	8	,	,	,
cord-346267-l08ld2cy	150	9	we	-PRON-	PRP
cord-346267-l08ld2cy	150	10	also	also	RB
cord-346267-l08ld2cy	150	11	investigated	investigate	VBD
cord-346267-l08ld2cy	150	12	how	how	WRB
cord-346267-l08ld2cy	150	13	removing	remove	VBG
cord-346267-l08ld2cy	150	14	site	site	NN
cord-346267-l08ld2cy	150	15	-	-	HYPH
cord-346267-l08ld2cy	150	16	to	to	IN
cord-346267-l08ld2cy	150	17	-	-	HYPH
cord-346267-l08ld2cy	150	18	site	site	NN
cord-346267-l08ld2cy	150	19	rate	rate	NN
cord-346267-l08ld2cy	150	20	variation	variation	NN
cord-346267-l08ld2cy	150	21	affected	affect	VBN
cord-346267-l08ld2cy	150	22	dating	date	VBG
cord-346267-l08ld2cy	150	23	inference	inference	NN
cord-346267-l08ld2cy	150	24	by	by	IN
cord-346267-l08ld2cy	150	25	using	use	VBG
cord-346267-l08ld2cy	150	26	a	a	DT
cord-346267-l08ld2cy	150	27	GTR	GTR	NNP
cord-346267-l08ld2cy	150	28	model	model	NN
cord-346267-l08ld2cy	150	29	(	(	-LRB-
cord-346267-l08ld2cy	150	30	Tavaré	Tavaré	NNP
cord-346267-l08ld2cy	150	31	1986	1986	CD
cord-346267-l08ld2cy	150	32	)	)	-RRB-
cord-346267-l08ld2cy	150	33	;	;	:
cord-346267-l08ld2cy	150	34	ignoring	ignore	VBG
cord-346267-l08ld2cy	150	35	rate	rate	NN
cord-346267-l08ld2cy	150	36	variation	variation	NN
cord-346267-l08ld2cy	150	37	invariably	invariably	RB
cord-346267-l08ld2cy	150	38	produced	produce	VBD
cord-346267-l08ld2cy	150	39	younger	young	JJR
cord-346267-l08ld2cy	150	40	tMRCAs	tmrcas	CD
cord-346267-l08ld2cy	150	41	.	.	.
cord-346267-l08ld2cy	151	1	We	-PRON-	PRP
cord-346267-l08ld2cy	151	2	simulated	simulate	VBD
cord-346267-l08ld2cy	151	3	codon	codon	NN
cord-346267-l08ld2cy	151	4	sequences	sequence	NNS
cord-346267-l08ld2cy	151	5	along	along	IN
cord-346267-l08ld2cy	151	6	a	a	DT
cord-346267-l08ld2cy	151	7	single	single	JJ
cord-346267-l08ld2cy	151	8	branch	branch	NN
cord-346267-l08ld2cy	151	9	under	under	IN
cord-346267-l08ld2cy	151	10	a	a	DT
cord-346267-l08ld2cy	151	11	substitution	substitution	NN
cord-346267-l08ld2cy	151	12	model	model	NN
cord-346267-l08ld2cy	151	13	with	with	IN
cord-346267-l08ld2cy	151	14	site	site	NN
cord-346267-l08ld2cy	151	15	-	-	HYPH
cord-346267-l08ld2cy	151	16	to	to	IN
cord-346267-l08ld2cy	151	17	-	-	HYPH
cord-346267-l08ld2cy	151	18	site	site	NN
cord-346267-l08ld2cy	151	19	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	151	20	rate	rate	NN
cord-346267-l08ld2cy	151	21	variation	variation	NN
cord-346267-l08ld2cy	151	22	and	and	CC
cord-346267-l08ld2cy	151	23	inferred	infer	VBD
cord-346267-l08ld2cy	151	24	the	the	DT
cord-346267-l08ld2cy	151	25	length	length	NN
cord-346267-l08ld2cy	151	26	of	of	IN
cord-346267-l08ld2cy	151	27	the	the	DT
cord-346267-l08ld2cy	151	28	branch	branch	NN
cord-346267-l08ld2cy	151	29	using	use	VBG
cord-346267-l08ld2cy	151	30	GTR	GTR	NNP
cord-346267-l08ld2cy	151	31	+	+	CC
cord-346267-l08ld2cy	151	32	Γ	γ	NN
cord-346267-l08ld2cy	151	33	4	4	CD
cord-346267-l08ld2cy	151	34	.	.	.
cord-346267-l08ld2cy	152	1	An	an	DT
cord-346267-l08ld2cy	152	2	increase	increase	NN
cord-346267-l08ld2cy	152	3	in	in	IN
cord-346267-l08ld2cy	152	4	the	the	DT
cord-346267-l08ld2cy	152	5	proportion	proportion	NN
cord-346267-l08ld2cy	152	6	of	of	IN
cord-346267-l08ld2cy	152	7	sites	site	NNS
cord-346267-l08ld2cy	152	8	simulated	simulate	VBN
cord-346267-l08ld2cy	152	9	under	under	IN
cord-346267-l08ld2cy	152	10	purifying	purify	VBG
cord-346267-l08ld2cy	152	11	selection	selection	NN
cord-346267-l08ld2cy	152	12	(	(	-LRB-
cord-346267-l08ld2cy	152	13	i.e.	i.e.	FW
cord-346267-l08ld2cy	152	14	,	,	,
cord-346267-l08ld2cy	152	15	β	β	NN
cord-346267-l08ld2cy	152	16	s	s	NN
cord-346267-l08ld2cy	152	17	=	=	SYM
cord-346267-l08ld2cy	152	18	0	0	CD
cord-346267-l08ld2cy	152	19	)	)	-RRB-
cord-346267-l08ld2cy	152	20	resulted	result	VBD
cord-346267-l08ld2cy	152	21	in	in	IN
cord-346267-l08ld2cy	152	22	shorter	short	JJR
cord-346267-l08ld2cy	152	23	branches	branch	NNS
cord-346267-l08ld2cy	152	24	inferred	infer	VBN
cord-346267-l08ld2cy	152	25	by	by	IN
cord-346267-l08ld2cy	152	26	a	a	DT
cord-346267-l08ld2cy	152	27	GTR	GTR	NNP
cord-346267-l08ld2cy	152	28	+	+	SYM
cord-346267-l08ld2cy	152	29	Γ	γ	NN
cord-346267-l08ld2cy	152	30	4	4	CD
cord-346267-l08ld2cy	152	31	model	model	NN
cord-346267-l08ld2cy	152	32	(	(	-LRB-
cord-346267-l08ld2cy	152	33	fig	fig	NN
cord-346267-l08ld2cy	152	34	.	.	.
cord-346267-l08ld2cy	152	35	1A	1a	LS
cord-346267-l08ld2cy	152	36	)	)	-RRB-
cord-346267-l08ld2cy	152	37	.	.	.
cord-346267-l08ld2cy	153	1	Sufficiently	sufficiently	RB
cord-346267-l08ld2cy	153	2	strong	strong	JJ
cord-346267-l08ld2cy	153	3	purifying	purifying	NN
cord-346267-l08ld2cy	153	4	selection	selection	NN
cord-346267-l08ld2cy	153	5	could	could	MD
cord-346267-l08ld2cy	153	6	theoretically	theoretically	RB
cord-346267-l08ld2cy	153	7	lead	lead	VB
cord-346267-l08ld2cy	153	8	to	to	IN
cord-346267-l08ld2cy	153	9	underestimates	underestimate	NNS
cord-346267-l08ld2cy	153	10	of	of	IN
cord-346267-l08ld2cy	153	11	branch	branch	NN
cord-346267-l08ld2cy	153	12	lengths	length	NNS
cord-346267-l08ld2cy	153	13	by	by	IN
cord-346267-l08ld2cy	153	14	an	an	DT
cord-346267-l08ld2cy	153	15	order	order	NN
cord-346267-l08ld2cy	153	16	of	of	IN
cord-346267-l08ld2cy	153	17	magnitude	magnitude	NN
cord-346267-l08ld2cy	153	18	because	because	IN
cord-346267-l08ld2cy	153	19	purifying	purify	VBG
cord-346267-l08ld2cy	153	20	selection	selection	NN
cord-346267-l08ld2cy	153	21	slows	slow	VBZ
cord-346267-l08ld2cy	153	22	down	down	IN
cord-346267-l08ld2cy	153	23	the	the	DT
cord-346267-l08ld2cy	153	24	rate	rate	NN
cord-346267-l08ld2cy	153	25	of	of	IN
cord-346267-l08ld2cy	153	26	evolution	evolution	NN
cord-346267-l08ld2cy	153	27	relative	relative	JJ
cord-346267-l08ld2cy	153	28	to	to	IN
cord-346267-l08ld2cy	153	29	the	the	DT
cord-346267-l08ld2cy	153	30	synonymous	synonymous	JJ
cord-346267-l08ld2cy	153	31	rate	rate	NN
cord-346267-l08ld2cy	153	32	.	.	.
cord-346267-l08ld2cy	154	1	At	at	IN
cord-346267-l08ld2cy	154	2	the	the	DT
cord-346267-l08ld2cy	154	3	extreme	extreme	NN
cord-346267-l08ld2cy	154	4	(	(	-LRB-
cord-346267-l08ld2cy	154	5	β	β	NN
cord-346267-l08ld2cy	154	6	s	s	NN
cord-346267-l08ld2cy	154	7	=	=	SYM
cord-346267-l08ld2cy	154	8	0	0	CD
cord-346267-l08ld2cy	154	9	,	,	,
cord-346267-l08ld2cy	154	10	branch	branch	NN
cord-346267-l08ld2cy	154	11	length	length	NN
cord-346267-l08ld2cy	154	12	→	→	IN
cord-346267-l08ld2cy	154	13	∞	∞	NNP
cord-346267-l08ld2cy	154	14	)	)	-RRB-
cord-346267-l08ld2cy	154	15	,	,	,
cord-346267-l08ld2cy	154	16	one	one	NN
cord-346267-l08ld2cy	154	17	obtains	obtain	VBZ
cord-346267-l08ld2cy	154	18	perfectly	perfectly	RB
cord-346267-l08ld2cy	154	19	conserved	conserve	VBN
cord-346267-l08ld2cy	154	20	amino	amino	NN
cord-346267-l08ld2cy	154	21	acid	acid	NN
cord-346267-l08ld2cy	154	22	sequences	sequence	NNS
cord-346267-l08ld2cy	154	23	and	and	CC
cord-346267-l08ld2cy	154	24	completely	completely	RB
cord-346267-l08ld2cy	154	25	saturated	saturated	JJ
cord-346267-l08ld2cy	154	26	synonymous	synonymous	JJ
cord-346267-l08ld2cy	154	27	substitutions	substitution	NNS
cord-346267-l08ld2cy	154	28	.	.	.
cord-346267-l08ld2cy	155	1	For	for	IN
cord-346267-l08ld2cy	155	2	sequences	sequence	NNS
cord-346267-l08ld2cy	155	3	with	with	IN
cord-346267-l08ld2cy	155	4	10	10	CD
cord-346267-l08ld2cy	155	5	%	%	NN
cord-346267-l08ld2cy	155	6	of	of	IN
cord-346267-l08ld2cy	155	7	sites	site	NNS
cord-346267-l08ld2cy	155	8	under	under	IN
cord-346267-l08ld2cy	155	9	strict	strict	JJ
cord-346267-l08ld2cy	155	10	conservation	conservation	NN
cord-346267-l08ld2cy	155	11	,	,	,
cord-346267-l08ld2cy	155	12	the	the	DT
cord-346267-l08ld2cy	155	13	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	155	14	estimator	estimator	NN
cord-346267-l08ld2cy	155	15	approached	approach	VBD
cord-346267-l08ld2cy	155	16	the	the	DT
cord-346267-l08ld2cy	155	17	asymptote	asymptote	NN
cord-346267-l08ld2cy	155	18	of	of	IN
cord-346267-l08ld2cy	155	19	7.1	7.1	CD
cord-346267-l08ld2cy	155	20	substitutions	substitution	NNS
cord-346267-l08ld2cy	155	21	/	/	SYM
cord-346267-l08ld2cy	155	22	site	site	NN
cord-346267-l08ld2cy	155	23	,	,	,
cord-346267-l08ld2cy	155	24	even	even	RB
cord-346267-l08ld2cy	155	25	when	when	WRB
cord-346267-l08ld2cy	155	26	the	the	DT
cord-346267-l08ld2cy	155	27	simulated	simulated	JJ
cord-346267-l08ld2cy	155	28	branch	branch	NN
cord-346267-l08ld2cy	155	29	length	length	NN
cord-346267-l08ld2cy	155	30	was	be	VBD
cord-346267-l08ld2cy	155	31	increased	increase	VBN
cord-346267-l08ld2cy	155	32	to	to	IN
cord-346267-l08ld2cy	155	33	100	100	CD
cord-346267-l08ld2cy	155	34	;	;	:
cord-346267-l08ld2cy	155	35	the	the	DT
cord-346267-l08ld2cy	155	36	branch	branch	NN
cord-346267-l08ld2cy	155	37	length	length	NN
cord-346267-l08ld2cy	155	38	estimate	estimate	NN
cord-346267-l08ld2cy	155	39	was	be	VBD
cord-346267-l08ld2cy	155	40	accurate	accurate	JJ
cord-346267-l08ld2cy	155	41	for	for	IN
cord-346267-l08ld2cy	155	42	up	up	IN
cord-346267-l08ld2cy	155	43	to	to	TO
cord-346267-l08ld2cy	155	44	5	5	CD
cord-346267-l08ld2cy	155	45	substitutions	substitution	NNS
cord-346267-l08ld2cy	155	46	/	/	SYM
cord-346267-l08ld2cy	155	47	site	site	NN
cord-346267-l08ld2cy	155	48	.	.	.
cord-346267-l08ld2cy	156	1	For	for	IN
cord-346267-l08ld2cy	156	2	sequences	sequence	NNS
cord-346267-l08ld2cy	156	3	with	with	IN
cord-346267-l08ld2cy	156	4	no	no	DT
cord-346267-l08ld2cy	156	5	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	156	6	substitutions	substitution	NNS
cord-346267-l08ld2cy	156	7	(	(	-LRB-
cord-346267-l08ld2cy	156	8	i.e.	i.e.	FW
cord-346267-l08ld2cy	156	9	,	,	,
cord-346267-l08ld2cy	156	10	100	100	CD
cord-346267-l08ld2cy	156	11	%	%	NN
cord-346267-l08ld2cy	156	12	conservation	conservation	NN
cord-346267-l08ld2cy	156	13	)	)	-RRB-
cord-346267-l08ld2cy	156	14	,	,	,
cord-346267-l08ld2cy	156	15	saturation	saturation	NN
cord-346267-l08ld2cy	156	16	occurred	occur	VBD
cord-346267-l08ld2cy	156	17	much	much	RB
cord-346267-l08ld2cy	156	18	sooner	soon	RBR
cord-346267-l08ld2cy	156	19	,	,	,
cord-346267-l08ld2cy	156	20	around	around	RB
cord-346267-l08ld2cy	156	21	0.25	0.25	CD
cord-346267-l08ld2cy	156	22	substitutions	substitution	NNS
cord-346267-l08ld2cy	156	23	/	/	SYM
cord-346267-l08ld2cy	156	24	site	site	NN
cord-346267-l08ld2cy	156	25	,	,	,
cord-346267-l08ld2cy	156	26	and	and	CC
cord-346267-l08ld2cy	156	27	the	the	DT
cord-346267-l08ld2cy	156	28	corresponding	corresponding	JJ
cord-346267-l08ld2cy	156	29	asymptote	asymptote	NN
cord-346267-l08ld2cy	156	30	was	be	VBD
cord-346267-l08ld2cy	156	31	0.36	0.36	CD
cord-346267-l08ld2cy	156	32	substitutions	substitution	NNS
cord-346267-l08ld2cy	156	33	/	/	SYM
cord-346267-l08ld2cy	156	34	site	site	NN
cord-346267-l08ld2cy	156	35	.	.	.
cord-346267-l08ld2cy	157	1	The	the	DT
cord-346267-l08ld2cy	157	2	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	157	3	substitution	substitution	NN
cord-346267-l08ld2cy	157	4	model	model	NN
cord-346267-l08ld2cy	157	5	(	(	-LRB-
cord-346267-l08ld2cy	157	6	GTR	GTR	NNP
cord-346267-l08ld2cy	157	7	+	+	CC
cord-346267-l08ld2cy	157	8	Γ	γ	NN
cord-346267-l08ld2cy	157	9	4	4	CD
cord-346267-l08ld2cy	157	10	)	)	-RRB-
cord-346267-l08ld2cy	157	11	underestimated	underestimate	VBD
cord-346267-l08ld2cy	157	12	the	the	DT
cord-346267-l08ld2cy	157	13	length	length	NN
cord-346267-l08ld2cy	157	14	of	of	IN
cord-346267-l08ld2cy	157	15	branches	branch	NNS
cord-346267-l08ld2cy	157	16	simulated	simulate	VBN
cord-346267-l08ld2cy	157	17	under	under	IN
cord-346267-l08ld2cy	157	18	empirical	empirical	JJ
cord-346267-l08ld2cy	157	19	(	(	-LRB-
cord-346267-l08ld2cy	157	20	IFEL	IFEL	NNP
cord-346267-l08ld2cy	157	21	)	)	-RRB-
cord-346267-l08ld2cy	157	22	selection	selection	NN
cord-346267-l08ld2cy	157	23	regimes	regime	NNS
cord-346267-l08ld2cy	157	24	inferred	infer	VBN
cord-346267-l08ld2cy	157	25	from	from	IN
cord-346267-l08ld2cy	157	26	the	the	DT
cord-346267-l08ld2cy	157	27	three	three	CD
cord-346267-l08ld2cy	157	28	viral	viral	JJ
cord-346267-l08ld2cy	157	29	data	data	NN
cord-346267-l08ld2cy	157	30	sets	set	NNS
cord-346267-l08ld2cy	157	31	(	(	-LRB-
cord-346267-l08ld2cy	157	32	fig	fig	NNP
cord-346267-l08ld2cy	157	33	.	.	.
cord-346267-l08ld2cy	157	34	1B-1D	1b-1d	CD
cord-346267-l08ld2cy	157	35	)	)	-RRB-
cord-346267-l08ld2cy	157	36	;	;	:
cord-346267-l08ld2cy	157	37	branch	branch	NN
cord-346267-l08ld2cy	157	38	lengths	length	NNS
cord-346267-l08ld2cy	157	39	for	for	IN
cord-346267-l08ld2cy	157	40	sequences	sequence	NNS
cord-346267-l08ld2cy	157	41	simulated	simulate	VBN
cord-346267-l08ld2cy	157	42	under	under	IN
cord-346267-l08ld2cy	157	43	neutral	neutral	JJ
cord-346267-l08ld2cy	157	44	selection	selection	NN
cord-346267-l08ld2cy	157	45	(	(	-LRB-
cord-346267-l08ld2cy	157	46	i.e.	i.e.	FW
cord-346267-l08ld2cy	157	47	,	,	,
cord-346267-l08ld2cy	157	48	α	α	NN
cord-346267-l08ld2cy	157	49	s	s	NN
cord-346267-l08ld2cy	157	50	=	=	NN
cord-346267-l08ld2cy	158	1	β	β	NNP
cord-346267-l08ld2cy	158	2	s	s	NNP
cord-346267-l08ld2cy	158	3	=	=	SYM
cord-346267-l08ld2cy	158	4	1	1	CD
cord-346267-l08ld2cy	158	5	)	)	-RRB-
cord-346267-l08ld2cy	158	6	were	be	VBD
cord-346267-l08ld2cy	158	7	reliably	reliably	RB
cord-346267-l08ld2cy	158	8	inferred	infer	VBN
cord-346267-l08ld2cy	158	9	by	by	IN
cord-346267-l08ld2cy	158	10	GTR	GTR	NNP
cord-346267-l08ld2cy	158	11	+	+	CC
cord-346267-l08ld2cy	158	12	Γ	γ	NN
cord-346267-l08ld2cy	158	13	4	4	CD
cord-346267-l08ld2cy	158	14	.	.	.
cord-346267-l08ld2cy	159	1	The	the	DT
cord-346267-l08ld2cy	159	2	proportion	proportion	NN
cord-346267-l08ld2cy	159	3	of	of	IN
cord-346267-l08ld2cy	159	4	sites	site	NNS
cord-346267-l08ld2cy	159	5	under	under	IN
cord-346267-l08ld2cy	159	6	strong	strong	JJ
cord-346267-l08ld2cy	159	7	negative	negative	JJ
cord-346267-l08ld2cy	159	8	selection	selection	NN
cord-346267-l08ld2cy	159	9	(	(	-LRB-
cord-346267-l08ld2cy	159	10	i.e.	i.e.	FW
cord-346267-l08ld2cy	159	11	,	,	,
cord-346267-l08ld2cy	159	12	β	β	NNP
cord-346267-l08ld2cy	159	13	s	s	NN
cord-346267-l08ld2cy	159	14	<	<	XX
cord-346267-l08ld2cy	159	15	α	α	NNP
cord-346267-l08ld2cy	159	16	s	s	XX
cord-346267-l08ld2cy	159	17	with	with	IN
cord-346267-l08ld2cy	159	18	an	an	DT
cord-346267-l08ld2cy	159	19	IFEL	IFEL	NNP
cord-346267-l08ld2cy	159	20	P	p	NN
cord-346267-l08ld2cy	159	21	value	value	NN
cord-346267-l08ld2cy	159	22	0.05	0.05	CD
cord-346267-l08ld2cy	159	23	)	)	-RRB-
cord-346267-l08ld2cy	160	1	differed	differ	VBN
cord-346267-l08ld2cy	160	2	markedly	markedly	RB
cord-346267-l08ld2cy	160	3	among	among	IN
cord-346267-l08ld2cy	160	4	the	the	DT
cord-346267-l08ld2cy	160	5	three	three	CD
cord-346267-l08ld2cy	160	6	data	datum	NNS
cord-346267-l08ld2cy	160	7	sets	set	NNS
cord-346267-l08ld2cy	160	8	.	.	.
cord-346267-l08ld2cy	161	1	MeV	MeV	NNP
cord-346267-l08ld2cy	161	2	/	/	SYM
cord-346267-l08ld2cy	161	3	RPV	RPV	NNP
cord-346267-l08ld2cy	161	4	/	/	SYM
cord-346267-l08ld2cy	161	5	PPRV	PPRV	NNP
cord-346267-l08ld2cy	161	6	nucleoprotein	nucleoprotein	NN
cord-346267-l08ld2cy	161	7	and	and	CC
cord-346267-l08ld2cy	161	8	EBOV	EBOV	NNP
cord-346267-l08ld2cy	161	9	glycoprotein	glycoprotein	NN
cord-346267-l08ld2cy	161	10	genes	gene	NNS
cord-346267-l08ld2cy	161	11	experienced	experience	VBD
cord-346267-l08ld2cy	161	12	moderate	moderate	JJ
cord-346267-l08ld2cy	161	13	levels	level	NNS
cord-346267-l08ld2cy	161	14	of	of	IN
cord-346267-l08ld2cy	161	15	purifying	purify	VBG
cord-346267-l08ld2cy	161	16	selection	selection	NN
cord-346267-l08ld2cy	161	17	along	along	IN
cord-346267-l08ld2cy	161	18	internal	internal	JJ
cord-346267-l08ld2cy	161	19	branches	branch	NNS
cord-346267-l08ld2cy	161	20	:	:	:
cord-346267-l08ld2cy	161	21	50	50	CD
cord-346267-l08ld2cy	161	22	%	%	NN
cord-346267-l08ld2cy	161	23	and	and	CC
cord-346267-l08ld2cy	161	24	45	45	CD
cord-346267-l08ld2cy	161	25	%	%	NN
cord-346267-l08ld2cy	161	26	of	of	IN
cord-346267-l08ld2cy	161	27	sites	site	NNS
cord-346267-l08ld2cy	161	28	under	under	IN
cord-346267-l08ld2cy	161	29	strong	strong	JJ
cord-346267-l08ld2cy	161	30	purifying	purifying	NN
cord-346267-l08ld2cy	161	31	selection	selection	NN
cord-346267-l08ld2cy	161	32	,	,	,
cord-346267-l08ld2cy	161	33	respectively	respectively	RB
cord-346267-l08ld2cy	161	34	.	.	.
cord-346267-l08ld2cy	162	1	The	the	DT
cord-346267-l08ld2cy	162	2	AIV	AIV	NNP
cord-346267-l08ld2cy	162	3	neuraminidase	neuraminidase	NN
cord-346267-l08ld2cy	162	4	gene	gene	NN
cord-346267-l08ld2cy	162	5	evolved	evolve	VBN
cord-346267-l08ld2cy	162	6	under	under	IN
cord-346267-l08ld2cy	162	7	much	much	RB
cord-346267-l08ld2cy	162	8	stronger	strong	JJR
cord-346267-l08ld2cy	162	9	selective	selective	JJ
cord-346267-l08ld2cy	162	10	constraints	constraint	NNS
cord-346267-l08ld2cy	162	11	,	,	,
cord-346267-l08ld2cy	162	12	with	with	IN
cord-346267-l08ld2cy	162	13	89	89	CD
cord-346267-l08ld2cy	162	14	%	%	NN
cord-346267-l08ld2cy	162	15	of	of	IN
cord-346267-l08ld2cy	162	16	sites	site	NNS
cord-346267-l08ld2cy	162	17	under	under	IN
cord-346267-l08ld2cy	162	18	strong	strong	JJ
cord-346267-l08ld2cy	162	19	purifying	purifying	NN
cord-346267-l08ld2cy	162	20	selection	selection	NN
cord-346267-l08ld2cy	162	21	.	.	.
cord-346267-l08ld2cy	163	1	We	-PRON-	PRP
cord-346267-l08ld2cy	163	2	note	note	VBP
cord-346267-l08ld2cy	163	3	that	that	IN
cord-346267-l08ld2cy	163	4	the	the	DT
cord-346267-l08ld2cy	163	5	power	power	NN
cord-346267-l08ld2cy	163	6	to	to	TO
cord-346267-l08ld2cy	163	7	detect	detect	VB
cord-346267-l08ld2cy	163	8	selection	selection	NN
cord-346267-l08ld2cy	163	9	using	use	VBG
cord-346267-l08ld2cy	163	10	IFEL	IFEL	NNP
cord-346267-l08ld2cy	163	11	increases	increase	VBZ
cord-346267-l08ld2cy	163	12	with	with	IN
cord-346267-l08ld2cy	163	13	the	the	DT
cord-346267-l08ld2cy	163	14	size	size	NN
cord-346267-l08ld2cy	163	15	of	of	IN
cord-346267-l08ld2cy	163	16	the	the	DT
cord-346267-l08ld2cy	163	17	alignment	alignment	NN
cord-346267-l08ld2cy	164	1	(	(	-LRB-
cord-346267-l08ld2cy	164	2	Kosakovsky	Kosakovsky	NNP
cord-346267-l08ld2cy	164	3	et	et	FW
cord-346267-l08ld2cy	164	4	al	al	NNP
cord-346267-l08ld2cy	164	5	.	.	.
cord-346267-l08ld2cy	164	6	2006	2006	CD
cord-346267-l08ld2cy	164	7	)	)	-RRB-
cord-346267-l08ld2cy	165	1	;	;	:
cord-346267-l08ld2cy	165	2	hence	hence	RB
cord-346267-l08ld2cy	165	3	,	,	,
cord-346267-l08ld2cy	165	4	we	-PRON-	PRP
cord-346267-l08ld2cy	165	5	would	would	MD
cord-346267-l08ld2cy	165	6	expect	expect	VB
cord-346267-l08ld2cy	165	7	more	more	JJR
cord-346267-l08ld2cy	165	8	sites	site	NNS
cord-346267-l08ld2cy	165	9	evolving	evolve	VBG
cord-346267-l08ld2cy	165	10	under	under	IN
cord-346267-l08ld2cy	165	11	purifying	purify	VBG
cord-346267-l08ld2cy	165	12	selection	selection	NN
cord-346267-l08ld2cy	165	13	to	to	TO
cord-346267-l08ld2cy	165	14	be	be	VB
cord-346267-l08ld2cy	165	15	correctly	correctly	RB
cord-346267-l08ld2cy	165	16	detected	detect	VBN
cord-346267-l08ld2cy	165	17	as	as	IN
cord-346267-l08ld2cy	165	18	such	such	JJ
cord-346267-l08ld2cy	165	19	in	in	IN
cord-346267-l08ld2cy	165	20	the	the	DT
cord-346267-l08ld2cy	165	21	larger	large	JJR
cord-346267-l08ld2cy	165	22	AIV	AIV	NNP
cord-346267-l08ld2cy	165	23	data	datum	NNS
cord-346267-l08ld2cy	165	24	set	set	VBN
cord-346267-l08ld2cy	165	25	.	.	.
cord-346267-l08ld2cy	166	1	The	the	DT
cord-346267-l08ld2cy	166	2	simulated	simulated	JJ
cord-346267-l08ld2cy	166	3	codon	codon	NN
cord-346267-l08ld2cy	166	4	saturation	saturation	NN
cord-346267-l08ld2cy	166	5	curves	curve	NNS
cord-346267-l08ld2cy	166	6	varied	varied	JJ
cord-346267-l08ld2cy	166	7	from	from	IN
cord-346267-l08ld2cy	166	8	virus	virus	NN
cord-346267-l08ld2cy	166	9	to	to	IN
cord-346267-l08ld2cy	166	10	virus	virus	NN
cord-346267-l08ld2cy	166	11	,	,	,
cord-346267-l08ld2cy	166	12	indicating	indicate	VBG
cord-346267-l08ld2cy	166	13	that	that	IN
cord-346267-l08ld2cy	166	14	the	the	DT
cord-346267-l08ld2cy	166	15	particular	particular	JJ
cord-346267-l08ld2cy	166	16	selectiveregime	selectiveregime	NN
cord-346267-l08ld2cy	166	17	,	,	,
cord-346267-l08ld2cy	166	18	amino	amino	NN
cord-346267-l08ld2cy	166	19	acid	acid	NN
cord-346267-l08ld2cy	166	20	composition	composition	NN
cord-346267-l08ld2cy	166	21	,	,	,
cord-346267-l08ld2cy	166	22	and	and	CC
cord-346267-l08ld2cy	166	23	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	166	24	substitution	substitution	NN
cord-346267-l08ld2cy	166	25	model	model	NN
cord-346267-l08ld2cy	166	26	of	of	IN
cord-346267-l08ld2cy	166	27	each	each	DT
cord-346267-l08ld2cy	166	28	viral	viral	JJ
cord-346267-l08ld2cy	166	29	gene	gene	NN
cord-346267-l08ld2cy	166	30	have	have	VBP
cord-346267-l08ld2cy	166	31	a	a	DT
cord-346267-l08ld2cy	166	32	substantial	substantial	JJ
cord-346267-l08ld2cy	166	33	influence	influence	NN
cord-346267-l08ld2cy	166	34	on	on	IN
cord-346267-l08ld2cy	166	35	the	the	DT
cord-346267-l08ld2cy	166	36	ability	ability	NN
cord-346267-l08ld2cy	166	37	to	to	TO
cord-346267-l08ld2cy	166	38	accurately	accurately	RB
cord-346267-l08ld2cy	166	39	infer	infer	VB
cord-346267-l08ld2cy	166	40	branch	branch	NN
cord-346267-l08ld2cy	166	41	lengths	length	NNS
cord-346267-l08ld2cy	166	42	.	.	.
cord-346267-l08ld2cy	167	1	Although	although	IN
cord-346267-l08ld2cy	167	2	underestimation	underestimation	NN
cord-346267-l08ld2cy	167	3	is	be	VBZ
cord-346267-l08ld2cy	167	4	more	more	RBR
cord-346267-l08ld2cy	167	5	pronounced	pronounced	JJ
cord-346267-l08ld2cy	167	6	along	along	IN
cord-346267-l08ld2cy	167	7	longer	long	JJR
cord-346267-l08ld2cy	167	8	branches	branch	NNS
cord-346267-l08ld2cy	167	9	(	(	-LRB-
cord-346267-l08ld2cy	167	10	e.g.	e.g.	RB
cord-346267-l08ld2cy	167	11	,	,	,
cord-346267-l08ld2cy	167	12	about	about	RB
cord-346267-l08ld2cy	167	13	half	half	PDT
cord-346267-l08ld2cy	167	14	the	the	DT
cord-346267-l08ld2cy	167	15	true	true	JJ
cord-346267-l08ld2cy	167	16	length	length	NN
cord-346267-l08ld2cy	167	17	for	for	IN
cord-346267-l08ld2cy	167	18	1	1	CD
cord-346267-l08ld2cy	167	19	substitution	substitution	NN
cord-346267-l08ld2cy	167	20	/	/	SYM
cord-346267-l08ld2cy	167	21	site	site	NN
cord-346267-l08ld2cy	167	22	)	)	-RRB-
cord-346267-l08ld2cy	167	23	,	,	,
cord-346267-l08ld2cy	167	24	not	not	RB
cord-346267-l08ld2cy	167	25	accounting	account	VBG
cord-346267-l08ld2cy	167	26	for	for	IN
cord-346267-l08ld2cy	167	27	selection	selection	NN
cord-346267-l08ld2cy	167	28	can	can	MD
cord-346267-l08ld2cy	167	29	lead	lead	VB
cord-346267-l08ld2cy	167	30	to	to	IN
cord-346267-l08ld2cy	167	31	underestimation	underestimation	NN
cord-346267-l08ld2cy	167	32	of	of	IN
cord-346267-l08ld2cy	167	33	branch	branch	NN
cord-346267-l08ld2cy	167	34	lengths	length	NNS
cord-346267-l08ld2cy	167	35	even	even	RB
cord-346267-l08ld2cy	167	36	for	for	IN
cord-346267-l08ld2cy	167	37	relatively	relatively	RB
cord-346267-l08ld2cy	167	38	short	short	JJ
cord-346267-l08ld2cy	167	39	branches	branch	NNS
cord-346267-l08ld2cy	167	40	(	(	-LRB-
cord-346267-l08ld2cy	167	41	e.g.	e.g.	RB
cord-346267-l08ld2cy	167	42	,	,	,
cord-346267-l08ld2cy	167	43	0.2	0.2	CD
cord-346267-l08ld2cy	167	44	-	-	HYPH
cord-346267-l08ld2cy	167	45	0.5	0.5	CD
cord-346267-l08ld2cy	167	46	substitutions	substitution	NNS
cord-346267-l08ld2cy	167	47	/	/	SYM
cord-346267-l08ld2cy	167	48	site	site	NN
cord-346267-l08ld2cy	167	49	)	)	-RRB-
cord-346267-l08ld2cy	167	50	.	.	.
cord-346267-l08ld2cy	168	1	We	-PRON-	PRP
cord-346267-l08ld2cy	168	2	then	then	RB
cord-346267-l08ld2cy	168	3	inferred	infer	VBD
cord-346267-l08ld2cy	168	4	the	the	DT
cord-346267-l08ld2cy	168	5	length	length	NN
cord-346267-l08ld2cy	168	6	of	of	IN
cord-346267-l08ld2cy	168	7	branches	branch	NNS
cord-346267-l08ld2cy	168	8	simulated	simulate	VBN
cord-346267-l08ld2cy	168	9	under	under	IN
cord-346267-l08ld2cy	168	10	the	the	DT
cord-346267-l08ld2cy	168	11	empirical	empirical	JJ
cord-346267-l08ld2cy	168	12	selective	selective	JJ
cord-346267-l08ld2cy	168	13	regimes	regime	NNS
cord-346267-l08ld2cy	168	14	using	use	VBG
cord-346267-l08ld2cy	168	15	the	the	DT
cord-346267-l08ld2cy	168	16	Dual	dual	JJ
cord-346267-l08ld2cy	168	17	codon	codon	NN
cord-346267-l08ld2cy	168	18	model	model	NN
cord-346267-l08ld2cy	168	19	,	,	,
cord-346267-l08ld2cy	168	20	which	which	WDT
cord-346267-l08ld2cy	168	21	accounts	account	VBZ
cord-346267-l08ld2cy	168	22	for	for	IN
cord-346267-l08ld2cy	168	23	variation	variation	NN
cord-346267-l08ld2cy	168	24	in	in	IN
cord-346267-l08ld2cy	168	25	site	site	NN
cord-346267-l08ld2cy	168	26	-	-	HYPH
cord-346267-l08ld2cy	168	27	to	to	IN
cord-346267-l08ld2cy	168	28	-	-	HYPH
cord-346267-l08ld2cy	168	29	site	site	NN
cord-346267-l08ld2cy	168	30	selective	selective	JJ
cord-346267-l08ld2cy	168	31	pressures	pressure	NNS
cord-346267-l08ld2cy	168	32	(	(	-LRB-
cord-346267-l08ld2cy	168	33	fig	fig	NN
cord-346267-l08ld2cy	168	34	.	.	NNP
cord-346267-l08ld2cy	168	35	2	2	CD
cord-346267-l08ld2cy	168	36	)	)	-RRB-
cord-346267-l08ld2cy	168	37	.	.	.
cord-346267-l08ld2cy	169	1	Although	although	IN
cord-346267-l08ld2cy	169	2	the	the	DT
cord-346267-l08ld2cy	169	3	Dual	dual	JJ
cord-346267-l08ld2cy	169	4	model	model	NN
cord-346267-l08ld2cy	169	5	slightly	slightly	RB
cord-346267-l08ld2cy	169	6	underestimated	underestimate	VBN
cord-346267-l08ld2cy	169	7	lengths	length	NNS
cord-346267-l08ld2cy	169	8	for	for	IN
cord-346267-l08ld2cy	169	9	the	the	DT
cord-346267-l08ld2cy	169	10	longest	long	JJS
cord-346267-l08ld2cy	169	11	simulated	simulated	JJ
cord-346267-l08ld2cy	169	12	branches	branch	NNS
cord-346267-l08ld2cy	170	1	,	,	,
cord-346267-l08ld2cy	170	2	the	the	DT
cord-346267-l08ld2cy	170	3	bias	bias	NN
cord-346267-l08ld2cy	170	4	was	be	VBD
cord-346267-l08ld2cy	170	5	an	an	DT
cord-346267-l08ld2cy	170	6	order	order	NN
cord-346267-l08ld2cy	170	7	of	of	IN
cord-346267-l08ld2cy	170	8	magnitude	magnitude	NN
cord-346267-l08ld2cy	170	9	less	less	JJR
cord-346267-l08ld2cy	170	10	than	than	IN
cord-346267-l08ld2cy	170	11	under	under	IN
cord-346267-l08ld2cy	170	12	GTR	GTR	NNP
cord-346267-l08ld2cy	170	13	+	+	CC
cord-346267-l08ld2cy	170	14	Γ	γ	NN
cord-346267-l08ld2cy	170	15	4	4	CD
cord-346267-l08ld2cy	170	16	.	.	.
cord-346267-l08ld2cy	171	1	Furthermore	furthermore	RB
cord-346267-l08ld2cy	171	2	,	,	,
cord-346267-l08ld2cy	171	3	similar	similar	JJ
cord-346267-l08ld2cy	171	4	behavior	behavior	NN
cord-346267-l08ld2cy	171	5	was	be	VBD
cord-346267-l08ld2cy	171	6	observed	observe	VBN
cord-346267-l08ld2cy	171	7	for	for	IN
cord-346267-l08ld2cy	171	8	the	the	DT
cord-346267-l08ld2cy	171	9	longest	long	JJS
cord-346267-l08ld2cy	171	10	branches	branch	NNS
cord-346267-l08ld2cy	171	11	simulated	simulate	VBN
cord-346267-l08ld2cy	171	12	under	under	IN
cord-346267-l08ld2cy	171	13	neutrality	neutrality	NN
cord-346267-l08ld2cy	171	14	(	(	-LRB-
cord-346267-l08ld2cy	171	15	α	α	NN
cord-346267-l08ld2cy	171	16	s	s	NN
cord-346267-l08ld2cy	171	17	=	=	NN
cord-346267-l08ld2cy	172	1	β	β	NNP
cord-346267-l08ld2cy	172	2	s	s	NNP
cord-346267-l08ld2cy	172	3	)	)	-RRB-
cord-346267-l08ld2cy	172	4	and	and	CC
cord-346267-l08ld2cy	172	5	inferred	infer	VBD
cord-346267-l08ld2cy	172	6	using	use	VBG
cord-346267-l08ld2cy	172	7	GTR	GTR	NNP
cord-346267-l08ld2cy	172	8	+	+	CC
cord-346267-l08ld2cy	172	9	Γ	γ	NN
cord-346267-l08ld2cy	172	10	4	4	CD
cord-346267-l08ld2cy	173	1	(	(	-LRB-
cord-346267-l08ld2cy	173	2	fig	fig	NN
cord-346267-l08ld2cy	173	3	.	.	.
cord-346267-l08ld2cy	174	1	1B	1B	NNP
cord-346267-l08ld2cy	174	2	-1D	-1D	NNP
cord-346267-l08ld2cy	174	3	)	)	-RRB-
cord-346267-l08ld2cy	174	4	,	,	.
cord-346267-l08ld2cy	175	1	suggesting	suggest	VBG
cord-346267-l08ld2cy	175	2	that	that	IN
cord-346267-l08ld2cy	175	3	both	both	DT
cord-346267-l08ld2cy	175	4	models	model	NNS
cord-346267-l08ld2cy	175	5	perform	perform	VBP
cord-346267-l08ld2cy	175	6	equivalently	equivalently	RB
cord-346267-l08ld2cy	175	7	,	,	,
cord-346267-l08ld2cy	175	8	as	as	IN
cord-346267-l08ld2cy	175	9	expected	expect	VBN
cord-346267-l08ld2cy	175	10	.	.	.
cord-346267-l08ld2cy	176	1	Clearly	clearly	RB
cord-346267-l08ld2cy	176	2	,	,	,
cord-346267-l08ld2cy	176	3	not	not	RB
cord-346267-l08ld2cy	176	4	accounting	account	VBG
cord-346267-l08ld2cy	176	5	for	for	IN
cord-346267-l08ld2cy	176	6	purifying	purify	VBG
cord-346267-l08ld2cy	176	7	selection	selection	NN
cord-346267-l08ld2cy	176	8	can	can	MD
cord-346267-l08ld2cy	176	9	lead	lead	VB
cord-346267-l08ld2cy	176	10	to	to	IN
cord-346267-l08ld2cy	176	11	dramatic	dramatic	JJ
cord-346267-l08ld2cy	176	12	underestimation	underestimation	NN
cord-346267-l08ld2cy	176	13	of	of	IN
cord-346267-l08ld2cy	176	14	branch	branch	NN
cord-346267-l08ld2cy	176	15	lengths	length	NNS
cord-346267-l08ld2cy	176	16	;	;	:
cord-346267-l08ld2cy	176	17	this	this	DT
cord-346267-l08ld2cy	176	18	effect	effect	NN
cord-346267-l08ld2cy	176	19	is	be	VBZ
cord-346267-l08ld2cy	176	20	exacerbated	exacerbate	VBN
cord-346267-l08ld2cy	176	21	for	for	IN
cord-346267-l08ld2cy	176	22	longer	long	JJR
cord-346267-l08ld2cy	176	23	branches	branch	NNS
cord-346267-l08ld2cy	176	24	.	.	.
cord-346267-l08ld2cy	177	1	It	-PRON-	PRP
cord-346267-l08ld2cy	177	2	is	be	VBZ
cord-346267-l08ld2cy	177	3	well	well	RB
cord-346267-l08ld2cy	177	4	known	know	VBN
cord-346267-l08ld2cy	177	5	that	that	IN
cord-346267-l08ld2cy	177	6	standard	standard	JJ
cord-346267-l08ld2cy	177	7	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	177	8	models	model	NNS
cord-346267-l08ld2cy	177	9	differ	differ	VBP
cord-346267-l08ld2cy	177	10	in	in	IN
cord-346267-l08ld2cy	177	11	their	-PRON-	PRP$
cord-346267-l08ld2cy	177	12	sensitivity	sensitivity	NN
cord-346267-l08ld2cy	177	13	to	to	IN
cord-346267-l08ld2cy	177	14	multiple	multiple	JJ
cord-346267-l08ld2cy	177	15	substitutions	substitution	NNS
cord-346267-l08ld2cy	177	16	at	at	IN
cord-346267-l08ld2cy	177	17	the	the	DT
cord-346267-l08ld2cy	177	18	same	same	JJ
cord-346267-l08ld2cy	177	19	site	site	NN
cord-346267-l08ld2cy	177	20	(	(	-LRB-
cord-346267-l08ld2cy	177	21	Sullivan	Sullivan	NNP
cord-346267-l08ld2cy	177	22	and	and	CC
cord-346267-l08ld2cy	177	23	Joyce	Joyce	NNP
cord-346267-l08ld2cy	177	24	2005	2005	CD
cord-346267-l08ld2cy	177	25	)	)	-RRB-
cord-346267-l08ld2cy	177	26	.	.	.
cord-346267-l08ld2cy	178	1	We	-PRON-	PRP
cord-346267-l08ld2cy	178	2	explored	explore	VBD
cord-346267-l08ld2cy	178	3	how	how	WRB
cord-346267-l08ld2cy	178	4	various	various	JJ
cord-346267-l08ld2cy	178	5	methods	method	NNS
cord-346267-l08ld2cy	178	6	of	of	IN
cord-346267-l08ld2cy	178	7	modeling	model	VBG
cord-346267-l08ld2cy	178	8	rate	rate	NN
cord-346267-l08ld2cy	178	9	variation	variation	NN
cord-346267-l08ld2cy	178	10	affected	affect	VBN
cord-346267-l08ld2cy	178	11	branch	branch	NN
cord-346267-l08ld2cy	178	12	length	length	NN
cord-346267-l08ld2cy	178	13	inference	inference	NN
cord-346267-l08ld2cy	178	14	in	in	IN
cord-346267-l08ld2cy	178	15	our	-PRON-	PRP$
cord-346267-l08ld2cy	178	16	three	three	CD
cord-346267-l08ld2cy	178	17	viral	viral	JJ
cord-346267-l08ld2cy	178	18	data	data	NN
cord-346267-l08ld2cy	178	19	sets	set	NNS
cord-346267-l08ld2cy	178	20	,	,	,
cord-346267-l08ld2cy	178	21	using	use	VBG
cord-346267-l08ld2cy	178	22	a	a	DT
cord-346267-l08ld2cy	178	23	fixed	fix	VBN
cord-346267-l08ld2cy	178	24	MCC	MCC	NNP
cord-346267-l08ld2cy	178	25	tree	tree	NN
cord-346267-l08ld2cy	178	26	from	from	IN
cord-346267-l08ld2cy	178	27	the	the	DT
cord-346267-l08ld2cy	178	28	GTR	GTR	NNP
cord-346267-l08ld2cy	178	29	+	+	SYM
cord-346267-l08ld2cy	178	30	Γ	γ	NN
cord-346267-l08ld2cy	178	31	4	4	CD
cord-346267-l08ld2cy	178	32	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	178	33	analyses	analysis	NNS
cord-346267-l08ld2cy	178	34	.	.	.
cord-346267-l08ld2cy	179	1	First	first	RB
cord-346267-l08ld2cy	179	2	,	,	,
cord-346267-l08ld2cy	179	3	we	-PRON-	PRP
cord-346267-l08ld2cy	179	4	examined	examine	VBD
cord-346267-l08ld2cy	179	5	two	two	CD
cord-346267-l08ld2cy	179	6	extremes	extreme	NNS
cord-346267-l08ld2cy	179	7	among	among	IN
cord-346267-l08ld2cy	179	8	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	179	9	substitution	substitution	NN
cord-346267-l08ld2cy	179	10	models	model	NNS
cord-346267-l08ld2cy	179	11	that	that	WDT
cord-346267-l08ld2cy	179	12	do	do	VBP
cord-346267-l08ld2cy	179	13	not	not	RB
cord-346267-l08ld2cy	179	14	adjust	adjust	VB
cord-346267-l08ld2cy	179	15	for	for	IN
cord-346267-l08ld2cy	179	16	rate	rate	NN
cord-346267-l08ld2cy	179	17	variation	variation	NN
cord-346267-l08ld2cy	179	18	across	across	IN
cord-346267-l08ld2cy	179	19	sites	site	NNS
cord-346267-l08ld2cy	179	20	:	:	:
cord-346267-l08ld2cy	179	21	JC69	JC69	NNP
cord-346267-l08ld2cy	179	22	(	(	-LRB-
cord-346267-l08ld2cy	179	23	Jukes	Jukes	NNP
cord-346267-l08ld2cy	179	24	and	and	CC
cord-346267-l08ld2cy	179	25	Cantor	Cantor	NNP
cord-346267-l08ld2cy	179	26	1969	1969	CD
cord-346267-l08ld2cy	179	27	)	)	-RRB-
cord-346267-l08ld2cy	179	28	and	and	CC
cord-346267-l08ld2cy	179	29	GTR	GTR	NNP
cord-346267-l08ld2cy	179	30	.	.	.
cord-346267-l08ld2cy	180	1	JC69	JC69	NNP
cord-346267-l08ld2cy	180	2	assumes	assume	VBZ
cord-346267-l08ld2cy	180	3	a	a	DT
cord-346267-l08ld2cy	180	4	single	single	JJ
cord-346267-l08ld2cy	180	5	substitution	substitution	NN
cord-346267-l08ld2cy	180	6	rate	rate	NN
cord-346267-l08ld2cy	180	7	and	and	CC
cord-346267-l08ld2cy	180	8	equal	equal	JJ
cord-346267-l08ld2cy	180	9	base	base	NN
cord-346267-l08ld2cy	180	10	frequencies	frequency	NNS
cord-346267-l08ld2cy	180	11	,	,	,
cord-346267-l08ld2cy	180	12	whereas	whereas	IN
cord-346267-l08ld2cy	180	13	GTR	GTR	NNP
cord-346267-l08ld2cy	180	14	allows	allow	VBZ
cord-346267-l08ld2cy	180	15	each	each	DT
cord-346267-l08ld2cy	180	16	class	class	NN
cord-346267-l08ld2cy	180	17	of	of	IN
cord-346267-l08ld2cy	180	18	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	180	19	substitution	substitution	NN
cord-346267-l08ld2cy	180	20	to	to	TO
cord-346267-l08ld2cy	180	21	occur	occur	VB
cord-346267-l08ld2cy	180	22	at	at	IN
cord-346267-l08ld2cy	180	23	a	a	DT
cord-346267-l08ld2cy	180	24	unique	unique	JJ
cord-346267-l08ld2cy	180	25	rate	rate	NN
cord-346267-l08ld2cy	180	26	and	and	CC
cord-346267-l08ld2cy	180	27	estimates	estimate	VBZ
cord-346267-l08ld2cy	180	28	base	base	VBP
cord-346267-l08ld2cy	180	29	frequencies	frequency	NNS
cord-346267-l08ld2cy	180	30	from	from	IN
cord-346267-l08ld2cy	180	31	the	the	DT
cord-346267-l08ld2cy	180	32	data	datum	NNS
cord-346267-l08ld2cy	180	33	.	.	.
cord-346267-l08ld2cy	181	1	As	as	IN
cord-346267-l08ld2cy	181	2	expected	expect	VBN
cord-346267-l08ld2cy	181	3	,	,	,
cord-346267-l08ld2cy	181	4	failure	failure	NN
cord-346267-l08ld2cy	181	5	to	to	TO
cord-346267-l08ld2cy	181	6	account	account	VB
cord-346267-l08ld2cy	181	7	for	for	IN
cord-346267-l08ld2cy	181	8	site	site	NN
cord-346267-l08ld2cy	181	9	-	-	HYPH
cord-346267-l08ld2cy	181	10	to	to	IN
cord-346267-l08ld2cy	181	11	-	-	HYPH
cord-346267-l08ld2cy	181	12	site	site	NN
cord-346267-l08ld2cy	181	13	rate	rate	NN
cord-346267-l08ld2cy	181	14	variation	variation	NN
cord-346267-l08ld2cy	181	15	led	lead	VBD
cord-346267-l08ld2cy	181	16	to	to	IN
cord-346267-l08ld2cy	181	17	severe	severe	JJ
cord-346267-l08ld2cy	181	18	underestimation	underestimation	NN
cord-346267-l08ld2cy	181	19	of	of	IN
cord-346267-l08ld2cy	181	20	longer	long	JJR
cord-346267-l08ld2cy	181	21	branches	branch	NNS
cord-346267-l08ld2cy	181	22	in	in	IN
cord-346267-l08ld2cy	181	23	all	all	DT
cord-346267-l08ld2cy	181	24	three	three	CD
cord-346267-l08ld2cy	181	25	viral	viral	JJ
cord-346267-l08ld2cy	181	26	data	data	NN
cord-346267-l08ld2cy	181	27	sets	set	NNS
cord-346267-l08ld2cy	181	28	(	(	-LRB-
cord-346267-l08ld2cy	181	29	JC69	JC69	NNP
cord-346267-l08ld2cy	181	30	or	or	CC
cord-346267-l08ld2cy	181	31	GTR	GTR	NNP
cord-346267-l08ld2cy	181	32	vs.	vs.	IN
cord-346267-l08ld2cy	181	33	GTR	GTR	NNP
cord-346267-l08ld2cy	181	34	+	+	CC
cord-346267-l08ld2cy	181	35	Γ	γ	NN
cord-346267-l08ld2cy	181	36	4	4	CD
cord-346267-l08ld2cy	181	37	,	,	,
cord-346267-l08ld2cy	181	38	fig	fig	NN
cord-346267-l08ld2cy	181	39	.	.	.
cord-346267-l08ld2cy	182	1	3	3	LS
cord-346267-l08ld2cy	183	1	the	the	DT
cord-346267-l08ld2cy	183	2	importance	importance	NN
cord-346267-l08ld2cy	183	3	of	of	IN
cord-346267-l08ld2cy	183	4	modeling	model	VBG
cord-346267-l08ld2cy	183	5	site	site	NN
cord-346267-l08ld2cy	183	6	-	-	HYPH
cord-346267-l08ld2cy	183	7	to	to	IN
cord-346267-l08ld2cy	183	8	-	-	HYPH
cord-346267-l08ld2cy	183	9	site	site	NN
cord-346267-l08ld2cy	183	10	rate	rate	NN
cord-346267-l08ld2cy	183	11	variation	variation	NN
cord-346267-l08ld2cy	183	12	to	to	IN
cord-346267-l08ld2cy	183	13	accurate	accurate	JJ
cord-346267-l08ld2cy	183	14	inference	inference	NN
cord-346267-l08ld2cy	183	15	.	.	.
cord-346267-l08ld2cy	184	1	Allowing	allow	VBG
cord-346267-l08ld2cy	184	2	for	for	IN
cord-346267-l08ld2cy	184	3	multiple	multiple	JJ
cord-346267-l08ld2cy	184	4	substitution	substitution	NN
cord-346267-l08ld2cy	184	5	rates	rate	NNS
cord-346267-l08ld2cy	184	6	and	and	CC
cord-346267-l08ld2cy	184	7	empirical	empirical	JJ
cord-346267-l08ld2cy	184	8	base	base	NN
cord-346267-l08ld2cy	184	9	frequencies	frequency	NNS
cord-346267-l08ld2cy	184	10	had	have	VBD
cord-346267-l08ld2cy	184	11	a	a	DT
cord-346267-l08ld2cy	184	12	negligible	negligible	JJ
cord-346267-l08ld2cy	184	13	impact	impact	NN
cord-346267-l08ld2cy	184	14	on	on	IN
cord-346267-l08ld2cy	184	15	branch	branch	NN
cord-346267-l08ld2cy	184	16	length	length	NN
cord-346267-l08ld2cy	184	17	estimation	estimation	NN
cord-346267-l08ld2cy	184	18	(	(	-LRB-
cord-346267-l08ld2cy	184	19	fig	fig	NN
cord-346267-l08ld2cy	184	20	.	.	.
cord-346267-l08ld2cy	184	21	3	3	CD
cord-346267-l08ld2cy	184	22	)	)	-RRB-
cord-346267-l08ld2cy	184	23	.	.	.
cord-346267-l08ld2cy	185	1	Underestimation	underestimation	NN
cord-346267-l08ld2cy	185	2	of	of	IN
cord-346267-l08ld2cy	185	3	long	long	JJ
cord-346267-l08ld2cy	185	4	branches	branch	NNS
cord-346267-l08ld2cy	185	5	likely	likely	RB
cord-346267-l08ld2cy	185	6	explains	explain	VBZ
cord-346267-l08ld2cy	185	7	why	why	WRB
cord-346267-l08ld2cy	185	8	the	the	DT
cord-346267-l08ld2cy	185	9	GTR	GTR	NNP
cord-346267-l08ld2cy	185	10	model	model	NN
cord-346267-l08ld2cy	185	11	inferred	infer	VBD
cord-346267-l08ld2cy	185	12	younger	young	JJR
cord-346267-l08ld2cy	185	13	root	root	VB
cord-346267-l08ld2cy	185	14	tMRCAs	tmrcas	CD
cord-346267-l08ld2cy	185	15	for	for	IN
cord-346267-l08ld2cy	185	16	all	all	PDT
cord-346267-l08ld2cy	185	17	all	all	DT
cord-346267-l08ld2cy	185	18	three	three	CD
cord-346267-l08ld2cy	185	19	viral	viral	JJ
cord-346267-l08ld2cy	185	20	data	data	NN
cord-346267-l08ld2cy	185	21	sets	set	NNS
cord-346267-l08ld2cy	185	22	(	(	-LRB-
cord-346267-l08ld2cy	185	23	table	table	NN
cord-346267-l08ld2cy	185	24	1	1	CD
cord-346267-l08ld2cy	185	25	)	)	-RRB-
cord-346267-l08ld2cy	185	26	.	.	.
cord-346267-l08ld2cy	186	1	We	-PRON-	PRP
cord-346267-l08ld2cy	186	2	hypothesized	hypothesize	VBD
cord-346267-l08ld2cy	186	3	that	that	IN
cord-346267-l08ld2cy	186	4	codon	codon	NN
cord-346267-l08ld2cy	186	5	substitution	substitution	NN
cord-346267-l08ld2cy	186	6	models	model	NNS
cord-346267-l08ld2cy	186	7	,	,	,
cord-346267-l08ld2cy	186	8	which	which	WDT
cord-346267-l08ld2cy	186	9	explicitly	explicitly	RB
cord-346267-l08ld2cy	186	10	account	account	VBP
cord-346267-l08ld2cy	186	11	for	for	IN
cord-346267-l08ld2cy	186	12	the	the	DT
cord-346267-l08ld2cy	186	13	differences	difference	NNS
cord-346267-l08ld2cy	186	14	between	between	IN
cord-346267-l08ld2cy	186	15	synonymous	synonymous	JJ
cord-346267-l08ld2cy	186	16	and	and	CC
cord-346267-l08ld2cy	186	17	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	186	18	substitutions	substitution	NNS
cord-346267-l08ld2cy	186	19	,	,	,
cord-346267-l08ld2cy	186	20	would	would	MD
cord-346267-l08ld2cy	186	21	permit	permit	VB
cord-346267-l08ld2cy	186	22	a	a	DT
cord-346267-l08ld2cy	186	23	more	more	RBR
cord-346267-l08ld2cy	186	24	accurate	accurate	JJ
cord-346267-l08ld2cy	186	25	estimation	estimation	NN
cord-346267-l08ld2cy	186	26	of	of	IN
cord-346267-l08ld2cy	186	27	sequence	sequence	NN
cord-346267-l08ld2cy	186	28	divergence	divergence	NN
cord-346267-l08ld2cy	186	29	well	well	RB
cord-346267-l08ld2cy	186	30	past	past	IN
cord-346267-l08ld2cy	186	31	the	the	DT
cord-346267-l08ld2cy	186	32	point	point	NN
cord-346267-l08ld2cy	186	33	a	a	DT
cord-346267-l08ld2cy	186	34	standard	standard	JJ
cord-346267-l08ld2cy	186	35	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	186	36	model	model	NN
cord-346267-l08ld2cy	186	37	would	would	MD
cord-346267-l08ld2cy	186	38	reach	reach	VB
cord-346267-l08ld2cy	186	39	saturation	saturation	NN
cord-346267-l08ld2cy	186	40	.	.	.
cord-346267-l08ld2cy	187	1	Therefore	therefore	RB
cord-346267-l08ld2cy	187	2	,	,	,
cord-346267-l08ld2cy	187	3	it	-PRON-	PRP
cord-346267-l08ld2cy	187	4	may	may	MD
cord-346267-l08ld2cy	187	5	be	be	VB
cord-346267-l08ld2cy	187	6	possible	possible	JJ
cord-346267-l08ld2cy	187	7	to	to	TO
cord-346267-l08ld2cy	187	8	use	use	VB
cord-346267-l08ld2cy	187	9	RNA	RNA	NNP
cord-346267-l08ld2cy	187	10	virus	virus	NN
cord-346267-l08ld2cy	187	11	genes	gene	NNS
cord-346267-l08ld2cy	187	12	,	,	,
cord-346267-l08ld2cy	187	13	which	which	WDT
cord-346267-l08ld2cy	187	14	evolve	evolve	VBP
cord-346267-l08ld2cy	187	15	extremely	extremely	RB
cord-346267-l08ld2cy	187	16	rapidly	rapidly	RB
cord-346267-l08ld2cy	187	17	(	(	-LRB-
cord-346267-l08ld2cy	187	18	e.g.	e.g.	RB
cord-346267-l08ld2cy	187	19	,	,	,
cord-346267-l08ld2cy	187	20	0.0001	0.0001	CD
cord-346267-l08ld2cy	187	21	-	-	HYPH
cord-346267-l08ld2cy	187	22	0.001	0.001	CD
cord-346267-l08ld2cy	187	23	substitutions	substitution	NNS
cord-346267-l08ld2cy	187	24	/	/	SYM
cord-346267-l08ld2cy	187	25	site	site	NN
cord-346267-l08ld2cy	187	26	/	/	SYM
cord-346267-l08ld2cy	187	27	year	year	NN
cord-346267-l08ld2cy	187	28	)	)	-RRB-
cord-346267-l08ld2cy	187	29	,	,	,
cord-346267-l08ld2cy	187	30	to	to	TO
cord-346267-l08ld2cy	187	31	estimate	estimate	VB
cord-346267-l08ld2cy	187	32	ancient	ancient	JJ
cord-346267-l08ld2cy	187	33	viral	viral	JJ
cord-346267-l08ld2cy	187	34	divergence	divergence	NN
cord-346267-l08ld2cy	187	35	events	event	NNS
cord-346267-l08ld2cy	187	36	using	use	VBG
cord-346267-l08ld2cy	187	37	codon	codon	NN
cord-346267-l08ld2cy	187	38	substitution	substitution	NN
cord-346267-l08ld2cy	187	39	models	model	NNS
cord-346267-l08ld2cy	187	40	.	.	.
cord-346267-l08ld2cy	188	1	A	a	DT
cord-346267-l08ld2cy	188	2	crude	crude	JJ
cord-346267-l08ld2cy	188	3	approximation	approximation	NN
cord-346267-l08ld2cy	188	4	of	of	IN
cord-346267-l08ld2cy	188	5	a	a	DT
cord-346267-l08ld2cy	188	6	codon	codon	NN
cord-346267-l08ld2cy	188	7	model	model	NN
cord-346267-l08ld2cy	188	8	,	,	,
cord-346267-l08ld2cy	188	9	SRD06	SRD06	NNP
cord-346267-l08ld2cy	188	10	,	,	,
cord-346267-l08ld2cy	188	11	produced	produce	VBN
cord-346267-l08ld2cy	188	12	branch	branch	NN
cord-346267-l08ld2cy	188	13	lengths	length	NNS
cord-346267-l08ld2cy	188	14	that	that	WDT
cord-346267-l08ld2cy	188	15	were	be	VBD
cord-346267-l08ld2cy	188	16	essentially	essentially	RB
cord-346267-l08ld2cy	188	17	the	the	DT
cord-346267-l08ld2cy	188	18	same	same	JJ
cord-346267-l08ld2cy	188	19	as	as	IN
cord-346267-l08ld2cy	188	20	those	those	DT
cord-346267-l08ld2cy	188	21	from	from	IN
cord-346267-l08ld2cy	188	22	the	the	DT
cord-346267-l08ld2cy	188	23	GTR	GTR	NNP
cord-346267-l08ld2cy	188	24	+	+	SYM
cord-346267-l08ld2cy	188	25	Γ	γ	NN
cord-346267-l08ld2cy	188	26	4	4	CD
cord-346267-l08ld2cy	188	27	model	model	NN
cord-346267-l08ld2cy	188	28	(	(	-LRB-
cord-346267-l08ld2cy	188	29	fig	fig	NN
cord-346267-l08ld2cy	188	30	.	.	.
cord-346267-l08ld2cy	188	31	3	3	LS
cord-346267-l08ld2cy	188	32	)	)	-RRB-
cord-346267-l08ld2cy	188	33	,	,	,
cord-346267-l08ld2cy	188	34	which	which	WDT
cord-346267-l08ld2cy	188	35	may	may	MD
cord-346267-l08ld2cy	188	36	explain	explain	VB
cord-346267-l08ld2cy	188	37	why	why	WRB
cord-346267-l08ld2cy	188	38	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	188	39	tMRCA	tmrca	XX
cord-346267-l08ld2cy	188	40	inference	inference	NN
cord-346267-l08ld2cy	188	41	using	use	VBG
cord-346267-l08ld2cy	188	42	these	these	DT
cord-346267-l08ld2cy	188	43	two	two	CD
cord-346267-l08ld2cy	188	44	models	model	NNS
cord-346267-l08ld2cy	188	45	was	be	VBD
cord-346267-l08ld2cy	188	46	so	so	RB
cord-346267-l08ld2cy	188	47	similar	similar	JJ
cord-346267-l08ld2cy	188	48	.	.	.
cord-346267-l08ld2cy	189	1	The	the	DT
cord-346267-l08ld2cy	189	2	inference	inference	NN
cord-346267-l08ld2cy	189	3	under	under	IN
cord-346267-l08ld2cy	189	4	the	the	DT
cord-346267-l08ld2cy	189	5	GY94	GY94	NNP
cord-346267-l08ld2cy	189	6	+	+	CC
cord-346267-l08ld2cy	189	7	Γ	γ	NN
cord-346267-l08ld2cy	189	8	4	4	CD
cord-346267-l08ld2cy	189	9	codon	codon	NN
cord-346267-l08ld2cy	189	10	model	model	NN
cord-346267-l08ld2cy	189	11	resulted	result	VBD
cord-346267-l08ld2cy	189	12	in	in	IN
cord-346267-l08ld2cy	189	13	longer	long	JJR
cord-346267-l08ld2cy	189	14	internal	internal	JJ
cord-346267-l08ld2cy	189	15	branch	branch	NN
cord-346267-l08ld2cy	189	16	lengths	length	NNS
cord-346267-l08ld2cy	189	17	only	only	RB
cord-346267-l08ld2cy	189	18	for	for	IN
cord-346267-l08ld2cy	189	19	EBOV	EBOV	NNP
cord-346267-l08ld2cy	189	20	(	(	-LRB-
cord-346267-l08ld2cy	190	1	fig	fig	NNP
cord-346267-l08ld2cy	190	2	.	.	.
cord-346267-l08ld2cy	190	3	3	3	LS
cord-346267-l08ld2cy	190	4	)	)	-RRB-
cord-346267-l08ld2cy	190	5	,	,	,
cord-346267-l08ld2cy	190	6	which	which	WDT
cord-346267-l08ld2cy	190	7	was	be	VBD
cord-346267-l08ld2cy	190	8	in	in	IN
cord-346267-l08ld2cy	190	9	agreement	agreement	NN
cord-346267-l08ld2cy	190	10	with	with	IN
cord-346267-l08ld2cy	190	11	our	-PRON-	PRP$
cord-346267-l08ld2cy	190	12	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	190	13	tMRCA	tmrca	NN
cord-346267-l08ld2cy	190	14	inference	inference	NN
cord-346267-l08ld2cy	190	15	using	use	VBG
cord-346267-l08ld2cy	190	16	this	this	DT
cord-346267-l08ld2cy	190	17	model	model	NN
cord-346267-l08ld2cy	190	18	.	.	.
cord-346267-l08ld2cy	191	1	Based	base	VBN
cord-346267-l08ld2cy	191	2	on	on	IN
cord-346267-l08ld2cy	191	3	the	the	DT
cord-346267-l08ld2cy	191	4	simulations	simulation	NNS
cord-346267-l08ld2cy	191	5	along	along	IN
cord-346267-l08ld2cy	191	6	a	a	DT
cord-346267-l08ld2cy	191	7	single	single	JJ
cord-346267-l08ld2cy	191	8	branch	branch	NN
cord-346267-l08ld2cy	191	9	,	,	,
cord-346267-l08ld2cy	191	10	we	-PRON-	PRP
cord-346267-l08ld2cy	191	11	anticipated	anticipate	VBD
cord-346267-l08ld2cy	191	12	that	that	IN
cord-346267-l08ld2cy	191	13	longer	long	JJR
cord-346267-l08ld2cy	191	14	branches	branch	NNS
cord-346267-l08ld2cy	191	15	would	would	MD
cord-346267-l08ld2cy	191	16	be	be	VB
cord-346267-l08ld2cy	191	17	disproportionately	disproportionately	RB
cord-346267-l08ld2cy	191	18	affected	affect	VBN
cord-346267-l08ld2cy	191	19	by	by	IN
cord-346267-l08ld2cy	191	20	site	site	NN
cord-346267-l08ld2cy	191	21	-	-	HYPH
cord-346267-l08ld2cy	191	22	to	to	IN
cord-346267-l08ld2cy	191	23	-	-	HYPH
cord-346267-l08ld2cy	191	24	site	site	NN
cord-346267-l08ld2cy	191	25	variation	variation	NN
cord-346267-l08ld2cy	191	26	in	in	IN
cord-346267-l08ld2cy	191	27	selection	selection	NN
cord-346267-l08ld2cy	191	28	pressures	pressure	NNS
cord-346267-l08ld2cy	191	29	.	.	.
cord-346267-l08ld2cy	192	1	Therefore	therefore	RB
cord-346267-l08ld2cy	192	2	,	,	,
cord-346267-l08ld2cy	192	3	we	-PRON-	PRP
cord-346267-l08ld2cy	192	4	investigated	investigate	VBD
cord-346267-l08ld2cy	192	5	how	how	WRB
cord-346267-l08ld2cy	192	6	extensions	extension	NNS
cord-346267-l08ld2cy	192	7	of	of	IN
cord-346267-l08ld2cy	192	8	the	the	DT
cord-346267-l08ld2cy	192	9	MG94	MG94	NNP
cord-346267-l08ld2cy	192	10	model	model	NN
cord-346267-l08ld2cy	192	11	that	that	WDT
cord-346267-l08ld2cy	192	12	incorporate	incorporate	VBP
cord-346267-l08ld2cy	192	13	β	β	XX
cord-346267-l08ld2cy	192	14	,	,	,
cord-346267-l08ld2cy	192	15	α	α	NN
cord-346267-l08ld2cy	192	16	,	,	,
cord-346267-l08ld2cy	192	17	and	and	CC
cord-346267-l08ld2cy	192	18	lineage	lineage	NN
cord-346267-l08ld2cy	192	19	-	-	HYPH
cord-346267-l08ld2cy	192	20	specific	specific	JJ
cord-346267-l08ld2cy	192	21	rate	rate	NN
cord-346267-l08ld2cy	192	22	variation	variation	NN
cord-346267-l08ld2cy	192	23	affected	affect	VBN
cord-346267-l08ld2cy	192	24	branch	branch	NN
cord-346267-l08ld2cy	192	25	length	length	NN
cord-346267-l08ld2cy	192	26	inference	inference	NN
cord-346267-l08ld2cy	192	27	(	(	-LRB-
cord-346267-l08ld2cy	192	28	table	table	NN
cord-346267-l08ld2cy	192	29	2	2	CD
cord-346267-l08ld2cy	192	30	)	)	-RRB-
cord-346267-l08ld2cy	192	31	.	.	.
cord-346267-l08ld2cy	193	1	For	for	IN
cord-346267-l08ld2cy	193	2	MeV	MeV	NNP
cord-346267-l08ld2cy	193	3	and	and	CC
cord-346267-l08ld2cy	193	4	AIV	AIV	NNP
cord-346267-l08ld2cy	193	5	,	,	,
cord-346267-l08ld2cy	193	6	the	the	DT
cord-346267-l08ld2cy	193	7	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	193	8	(	(	-LRB-
cord-346267-l08ld2cy	193	9	two	two	CD
cord-346267-l08ld2cy	193	10	-	-	HYPH
cord-346267-l08ld2cy	193	11	rate	rate	NN
cord-346267-l08ld2cy	193	12	)	)	-RRB-
cord-346267-l08ld2cy	193	13	model	model	NN
cord-346267-l08ld2cy	193	14	that	that	WDT
cord-346267-l08ld2cy	193	15	allowed	allow	VBD
cord-346267-l08ld2cy	193	16	longer	long	JJR
cord-346267-l08ld2cy	193	17	internal	internal	JJ
cord-346267-l08ld2cy	193	18	branches	branch	NNS
cord-346267-l08ld2cy	193	19	to	to	TO
cord-346267-l08ld2cy	193	20	share	share	VB
cord-346267-l08ld2cy	193	21	their	-PRON-	PRP$
cord-346267-l08ld2cy	193	22	own	own	JJ
cord-346267-l08ld2cy	193	23	ratio	ratio	NN
cord-346267-l08ld2cy	194	1	E	e	LS
cord-346267-l08ld2cy	194	2	[	[	-LRB-
cord-346267-l08ld2cy	194	3	β]/E	β]/e	XX
cord-346267-l08ld2cy	194	4	[	[	-LRB-
cord-346267-l08ld2cy	194	5	α	α	NN
cord-346267-l08ld2cy	194	6	]	]	-RRB-
cord-346267-l08ld2cy	194	7	provided	provide	VBD
cord-346267-l08ld2cy	194	8	the	the	DT
cord-346267-l08ld2cy	194	9	best	good	JJS
cord-346267-l08ld2cy	194	10	fit	fit	NN
cord-346267-l08ld2cy	194	11	to	to	IN
cord-346267-l08ld2cy	194	12	the	the	DT
cord-346267-l08ld2cy	194	13	data	datum	NNS
cord-346267-l08ld2cy	194	14	.	.	.
cord-346267-l08ld2cy	195	1	For	for	IN
cord-346267-l08ld2cy	195	2	EBOV	EBOV	NNP
cord-346267-l08ld2cy	195	3	,	,	,
cord-346267-l08ld2cy	195	4	a	a	DT
cord-346267-l08ld2cy	195	5	more	more	RBR
cord-346267-l08ld2cy	195	6	complicated	complicated	JJ
cord-346267-l08ld2cy	195	7	(	(	-LRB-
cord-346267-l08ld2cy	195	8	eight	eight	CD
cord-346267-l08ld2cy	195	9	-	-	HYPH
cord-346267-l08ld2cy	195	10	rate	rate	NN
cord-346267-l08ld2cy	195	11	)	)	-RRB-
cord-346267-l08ld2cy	195	12	model	model	NN
cord-346267-l08ld2cy	195	13	,	,	,
cord-346267-l08ld2cy	195	14	in	in	IN
cord-346267-l08ld2cy	195	15	which	which	WDT
cord-346267-l08ld2cy	195	16	each	each	DT
cord-346267-l08ld2cy	195	17	intersubtype	intersubtype	NNP
cord-346267-l08ld2cy	195	18	branch	branch	NN
cord-346267-l08ld2cy	195	19	and	and	CC
cord-346267-l08ld2cy	195	20	the	the	DT
cord-346267-l08ld2cy	195	21	long	long	JJ
cord-346267-l08ld2cy	195	22	terminal	terminal	NN
cord-346267-l08ld2cy	195	23	branches	branch	NNS
cord-346267-l08ld2cy	195	24	leading	lead	VBG
cord-346267-l08ld2cy	195	25	to	to	IN
cord-346267-l08ld2cy	195	26	Côte	Côte	NNP
cord-346267-l08ld2cy	195	27	d'Ivoire	d'Ivoire	NNP
cord-346267-l08ld2cy	195	28	and	and	CC
cord-346267-l08ld2cy	195	29	Bundibugyo	Bundibugyo	NNP
cord-346267-l08ld2cy	195	30	had	have	VBD
cord-346267-l08ld2cy	195	31	their	-PRON-	PRP$
cord-346267-l08ld2cy	195	32	own	own	JJ
cord-346267-l08ld2cy	195	33	rates	rate	NNS
cord-346267-l08ld2cy	195	34	,	,	,
cord-346267-l08ld2cy	195	35	was	be	VBD
cord-346267-l08ld2cy	195	36	fit	fit	JJ
cord-346267-l08ld2cy	195	37	because	because	IN
cord-346267-l08ld2cy	195	38	E	e	NN
cord-346267-l08ld2cy	195	39	[	[	-LRB-
cord-346267-l08ld2cy	195	40	β]/E	β]/e	XX
cord-346267-l08ld2cy	195	41	[	[	-LRB-
cord-346267-l08ld2cy	195	42	α	α	NN
cord-346267-l08ld2cy	195	43	]	]	-RRB-
cord-346267-l08ld2cy	195	44	varied	vary	VBN
cord-346267-l08ld2cy	195	45	dramatically	dramatically	RB
cord-346267-l08ld2cy	195	46	among	among	IN
cord-346267-l08ld2cy	195	47	the	the	DT
cord-346267-l08ld2cy	195	48	intersubtype	intersubtype	NNP
cord-346267-l08ld2cy	195	49	branches	branch	NNS
cord-346267-l08ld2cy	195	50	.	.	.
cord-346267-l08ld2cy	196	1	The	the	DT
cord-346267-l08ld2cy	196	2	inclusion	inclusion	NN
cord-346267-l08ld2cy	196	3	of	of	IN
cord-346267-l08ld2cy	196	4	variation	variation	NN
cord-346267-l08ld2cy	196	5	in	in	IN
cord-346267-l08ld2cy	196	6	β	β	NN
cord-346267-l08ld2cy	196	7	and	and	CC
cord-346267-l08ld2cy	196	8	α	α	NN
cord-346267-l08ld2cy	196	9	in	in	IN
cord-346267-l08ld2cy	196	10	the	the	DT
cord-346267-l08ld2cy	196	11	Nonsynonymous	Nonsynonymous	NNP
cord-346267-l08ld2cy	196	12	and	and	CC
cord-346267-l08ld2cy	196	13	Dual	dual	JJ
cord-346267-l08ld2cy	196	14	models	model	NNS
cord-346267-l08ld2cy	196	15	resulted	result	VBD
cord-346267-l08ld2cy	196	16	in	in	IN
cord-346267-l08ld2cy	196	17	notable	notable	JJ
cord-346267-l08ld2cy	196	18	increases	increase	NNS
cord-346267-l08ld2cy	196	19	in	in	IN
cord-346267-l08ld2cy	196	20	the	the	DT
cord-346267-l08ld2cy	196	21	cumulative	cumulative	JJ
cord-346267-l08ld2cy	196	22	length	length	NN
cord-346267-l08ld2cy	196	23	of	of	IN
cord-346267-l08ld2cy	196	24	deep	deep	JJ
cord-346267-l08ld2cy	196	25	internal	internal	JJ
cord-346267-l08ld2cy	196	26	branches	branch	NNS
cord-346267-l08ld2cy	196	27	(	(	-LRB-
cord-346267-l08ld2cy	196	28	table	table	NN
cord-346267-l08ld2cy	196	29	2	2	CD
cord-346267-l08ld2cy	196	30	;	;	,
cord-346267-l08ld2cy	196	31	supplementary	supplementary	JJ
cord-346267-l08ld2cy	196	32	fig	fig	NN
cord-346267-l08ld2cy	196	33	.	.	.
cord-346267-l08ld2cy	197	1	S1	S1	NNP
cord-346267-l08ld2cy	197	2	,	,	,
cord-346267-l08ld2cy	197	3	Supplementary	Supplementary	NNP
cord-346267-l08ld2cy	197	4	Material	Material	NNP
cord-346267-l08ld2cy	197	5	online	online	RB
cord-346267-l08ld2cy	197	6	)	)	-RRB-
cord-346267-l08ld2cy	197	7	.	.	.
cord-346267-l08ld2cy	198	1	In	in	IN
cord-346267-l08ld2cy	198	2	all	all	DT
cord-346267-l08ld2cy	198	3	three	three	CD
cord-346267-l08ld2cy	198	4	viral	viral	JJ
cord-346267-l08ld2cy	198	5	data	data	NN
cord-346267-l08ld2cy	198	6	sets	set	NNS
cord-346267-l08ld2cy	198	7	,	,	,
cord-346267-l08ld2cy	198	8	however	however	RB
cord-346267-l08ld2cy	198	9	,	,	,
cord-346267-l08ld2cy	198	10	the	the	DT
cord-346267-l08ld2cy	198	11	most	most	RBS
cord-346267-l08ld2cy	198	12	substantial	substantial	JJ
cord-346267-l08ld2cy	198	13	differences	difference	NNS
cord-346267-l08ld2cy	198	14	were	be	VBD
cord-346267-l08ld2cy	198	15	seen	see	VBN
cord-346267-l08ld2cy	198	16	with	with	IN
cord-346267-l08ld2cy	198	17	the	the	DT
cord-346267-l08ld2cy	198	18	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	198	19	model	model	NN
cord-346267-l08ld2cy	198	20	,	,	,
cord-346267-l08ld2cy	198	21	which	which	WDT
cord-346267-l08ld2cy	198	22	produced	produce	VBD
cord-346267-l08ld2cy	198	23	lengths	length	NNS
cord-346267-l08ld2cy	198	24	for	for	IN
cord-346267-l08ld2cy	198	25	long	long	JJ
cord-346267-l08ld2cy	198	26	internal	internal	JJ
cord-346267-l08ld2cy	198	27	branches	branch	NNS
cord-346267-l08ld2cy	198	28	that	that	WDT
cord-346267-l08ld2cy	198	29	were	be	VBD
cord-346267-l08ld2cy	198	30	substantially	substantially	RB
cord-346267-l08ld2cy	198	31	greater	great	JJR
cord-346267-l08ld2cy	198	32	than	than	IN
cord-346267-l08ld2cy	198	33	those	those	DT
cord-346267-l08ld2cy	198	34	inferred	infer	VBN
cord-346267-l08ld2cy	198	35	under	under	IN
cord-346267-l08ld2cy	198	36	GTR	GTR	NNP
cord-346267-l08ld2cy	198	37	+	+	CC
cord-346267-l08ld2cy	198	38	Γ	γ	NN
cord-346267-l08ld2cy	198	39	4	4	CD
cord-346267-l08ld2cy	198	40	(	(	-LRB-
cord-346267-l08ld2cy	198	41	fig	fig	NN
cord-346267-l08ld2cy	198	42	.	.	.
cord-346267-l08ld2cy	198	43	3	3	CD
cord-346267-l08ld2cy	198	44	)	)	-RRB-
cord-346267-l08ld2cy	198	45	.	.	.
cord-346267-l08ld2cy	199	1	Importantly	importantly	RB
cord-346267-l08ld2cy	199	2	,	,	,
cord-346267-l08ld2cy	199	3	the	the	DT
cord-346267-l08ld2cy	199	4	lengths	length	NNS
cord-346267-l08ld2cy	199	5	of	of	IN
cord-346267-l08ld2cy	199	6	the	the	DT
cord-346267-l08ld2cy	199	7	more	more	RBR
cord-346267-l08ld2cy	199	8	recent	recent	JJ
cord-346267-l08ld2cy	199	9	intraspecies	intraspecie	NNS
cord-346267-l08ld2cy	199	10	/	/	SYM
cord-346267-l08ld2cy	199	11	subtype	subtype	NN
cord-346267-l08ld2cy	199	12	/	/	SYM
cord-346267-l08ld2cy	199	13	serotype	serotype	NN
cord-346267-l08ld2cy	199	14	branches	branch	NNS
cord-346267-l08ld2cy	199	15	were	be	VBD
cord-346267-l08ld2cy	199	16	relatively	relatively	RB
cord-346267-l08ld2cy	199	17	unchanged	unchanged	JJ
cord-346267-l08ld2cy	199	18	between	between	IN
cord-346267-l08ld2cy	199	19	these	these	DT
cord-346267-l08ld2cy	199	20	two	two	CD
cord-346267-l08ld2cy	199	21	models	model	NNS
cord-346267-l08ld2cy	199	22	for	for	IN
cord-346267-l08ld2cy	199	23	all	all	DT
cord-346267-l08ld2cy	199	24	three	three	CD
cord-346267-l08ld2cy	199	25	data	datum	NNS
cord-346267-l08ld2cy	199	26	sets	set	NNS
cord-346267-l08ld2cy	199	27	;	;	:
cord-346267-l08ld2cy	199	28	this	this	DT
cord-346267-l08ld2cy	199	29	observation	observation	NN
cord-346267-l08ld2cy	199	30	confirms	confirm	VBZ
cord-346267-l08ld2cy	199	31	that	that	IN
cord-346267-l08ld2cy	199	32	when	when	WRB
cord-346267-l08ld2cy	199	33	the	the	DT
cord-346267-l08ld2cy	199	34	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	199	35	is	be	VBZ
cord-346267-l08ld2cy	199	36	comprised	comprise	VBN
cord-346267-l08ld2cy	199	37	of	of	IN
cord-346267-l08ld2cy	199	38	relatively	relatively	RB
cord-346267-l08ld2cy	199	39	short	short	JJ
cord-346267-l08ld2cy	199	40	branches	branch	NNS
cord-346267-l08ld2cy	199	41	,	,	,
cord-346267-l08ld2cy	199	42	it	-PRON-	PRP
cord-346267-l08ld2cy	199	43	is	be	VBZ
cord-346267-l08ld2cy	199	44	appropriate	appropriate	JJ
cord-346267-l08ld2cy	199	45	to	to	TO
cord-346267-l08ld2cy	199	46	rely	rely	VB
cord-346267-l08ld2cy	199	47	on	on	IN
cord-346267-l08ld2cy	199	48	common	common	JJ
cord-346267-l08ld2cy	199	49	approximations	approximation	NNS
cord-346267-l08ld2cy	199	50	,	,	,
cord-346267-l08ld2cy	199	51	such	such	JJ
cord-346267-l08ld2cy	199	52	as	as	IN
cord-346267-l08ld2cy	199	53	the	the	DT
cord-346267-l08ld2cy	199	54	GTR	GTR	NNP
cord-346267-l08ld2cy	199	55	+	+	SYM
cord-346267-l08ld2cy	199	56	Γ	γ	NN
cord-346267-l08ld2cy	199	57	4	4	CD
cord-346267-l08ld2cy	199	58	model	model	NN
cord-346267-l08ld2cy	199	59	.	.	.
cord-346267-l08ld2cy	200	1	This	this	DT
cord-346267-l08ld2cy	200	2	increase	increase	NN
cord-346267-l08ld2cy	200	3	in	in	IN
cord-346267-l08ld2cy	200	4	the	the	DT
cord-346267-l08ld2cy	200	5	length	length	NN
cord-346267-l08ld2cy	200	6	of	of	IN
cord-346267-l08ld2cy	200	7	only	only	JJ
cord-346267-l08ld2cy	200	8	deep	deep	JJ
cord-346267-l08ld2cy	200	9	internal	internal	JJ
cord-346267-l08ld2cy	200	10	branches	branch	NNS
cord-346267-l08ld2cy	200	11	was	be	VBD
cord-346267-l08ld2cy	200	12	likely	likely	JJ
cord-346267-l08ld2cy	200	13	due	due	IN
cord-346267-l08ld2cy	200	14	to	to	IN
cord-346267-l08ld2cy	200	15	the	the	DT
cord-346267-l08ld2cy	200	16	dramatically	dramatically	RB
cord-346267-l08ld2cy	200	17	stronger	strong	JJR
cord-346267-l08ld2cy	200	18	purifying	purifying	NN
cord-346267-l08ld2cy	200	19	selection	selection	NN
cord-346267-l08ld2cy	200	20	which	which	WDT
cord-346267-l08ld2cy	200	21	we	-PRON-	PRP
cord-346267-l08ld2cy	200	22	inferred	infer	VBD
cord-346267-l08ld2cy	200	23	along	along	IN
cord-346267-l08ld2cy	200	24	these	these	DT
cord-346267-l08ld2cy	200	25	lineages	lineage	NNS
cord-346267-l08ld2cy	200	26	(	(	-LRB-
cord-346267-l08ld2cy	200	27	table	table	NN
cord-346267-l08ld2cy	200	28	2	2	CD
cord-346267-l08ld2cy	200	29	)	)	-RRB-
cord-346267-l08ld2cy	200	30	.	.	.
cord-346267-l08ld2cy	201	1	In	in	IN
cord-346267-l08ld2cy	201	2	AIV	AIV	NNP
cord-346267-l08ld2cy	201	3	,	,	,
cord-346267-l08ld2cy	201	4	for	for	IN
cord-346267-l08ld2cy	201	5	instance	instance	NN
cord-346267-l08ld2cy	201	6	,	,	,
cord-346267-l08ld2cy	201	7	E	e	LS
cord-346267-l08ld2cy	201	8	[	[	-LRB-
cord-346267-l08ld2cy	201	9	β]/E	β]/e	XX
cord-346267-l08ld2cy	201	10	[	[	-LRB-
cord-346267-l08ld2cy	201	11	α	α	NN
cord-346267-l08ld2cy	201	12	]	]	-RRB-
cord-346267-l08ld2cy	201	13	was	be	VBD
cord-346267-l08ld2cy	201	14	two	two	CD
cord-346267-l08ld2cy	201	15	orders	order	NNS
cord-346267-l08ld2cy	201	16	of	of	IN
cord-346267-l08ld2cy	201	17	magnitude	magnitude	NN
cord-346267-l08ld2cy	201	18	lower	low	JJR
cord-346267-l08ld2cy	201	19	on	on	IN
cord-346267-l08ld2cy	201	20	deep	deep	JJ
cord-346267-l08ld2cy	201	21	interior	interior	JJ
cord-346267-l08ld2cy	201	22	branches	branch	NNS
cord-346267-l08ld2cy	201	23	,	,	,
cord-346267-l08ld2cy	201	24	compared	compare	VBN
cord-346267-l08ld2cy	201	25	with	with	IN
cord-346267-l08ld2cy	201	26	the	the	DT
cord-346267-l08ld2cy	201	27	rest	rest	NN
cord-346267-l08ld2cy	201	28	of	of	IN
cord-346267-l08ld2cy	201	29	the	the	DT
cord-346267-l08ld2cy	201	30	tree	tree	NN
cord-346267-l08ld2cy	201	31	.	.	.
cord-346267-l08ld2cy	202	1	One	one	CD
cord-346267-l08ld2cy	202	2	outcome	outcome	NN
cord-346267-l08ld2cy	202	3	of	of	IN
cord-346267-l08ld2cy	202	4	including	include	VBG
cord-346267-l08ld2cy	202	5	variation	variation	NN
cord-346267-l08ld2cy	202	6	in	in	IN
cord-346267-l08ld2cy	202	7	selection	selection	NN
cord-346267-l08ld2cy	202	8	pressures	pressure	NNS
cord-346267-l08ld2cy	202	9	across	across	IN
cord-346267-l08ld2cy	202	10	branches	branch	NNS
cord-346267-l08ld2cy	202	11	into	into	IN
cord-346267-l08ld2cy	202	12	the	the	DT
cord-346267-l08ld2cy	202	13	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	202	14	model	model	NN
cord-346267-l08ld2cy	202	15	was	be	VBD
cord-346267-l08ld2cy	202	16	that	that	IN
cord-346267-l08ld2cy	202	17	several	several	JJ
cord-346267-l08ld2cy	202	18	branches	branch	NNS
cord-346267-l08ld2cy	202	19	were	be	VBD
cord-346267-l08ld2cy	202	20	inferred	infer	VBN
cord-346267-l08ld2cy	202	21	to	to	TO
cord-346267-l08ld2cy	202	22	have	have	VB
cord-346267-l08ld2cy	202	23	essentially	essentially	RB
cord-346267-l08ld2cy	202	24	infinite	infinite	JJ
cord-346267-l08ld2cy	202	25	lengths	length	NNS
cord-346267-l08ld2cy	202	26	in	in	IN
cord-346267-l08ld2cy	202	27	the	the	DT
cord-346267-l08ld2cy	202	28	EBOV	EBOV	NNP
cord-346267-l08ld2cy	202	29	and	and	CC
cord-346267-l08ld2cy	202	30	AIV	AIV	NNP
cord-346267-l08ld2cy	202	31	trees	tree	NNS
cord-346267-l08ld2cy	202	32	.	.	.
cord-346267-l08ld2cy	203	1	The	the	DT
cord-346267-l08ld2cy	203	2	inference	inference	NN
cord-346267-l08ld2cy	203	3	of	of	IN
cord-346267-l08ld2cy	203	4	an	an	DT
cord-346267-l08ld2cy	203	5	infinite	infinite	JJ
cord-346267-l08ld2cy	203	6	branch	branch	NN
cord-346267-l08ld2cy	203	7	length	length	NN
cord-346267-l08ld2cy	203	8	is	be	VBZ
cord-346267-l08ld2cy	203	9	likely	likely	RB
cord-346267-l08ld2cy	203	10	caused	cause	VBN
cord-346267-l08ld2cy	203	11	by	by	IN
cord-346267-l08ld2cy	203	12	the	the	DT
cord-346267-l08ld2cy	203	13	complete	complete	JJ
cord-346267-l08ld2cy	203	14	saturation	saturation	NN
cord-346267-l08ld2cy	203	15	of	of	IN
cord-346267-l08ld2cy	203	16	synonymous	synonymous	JJ
cord-346267-l08ld2cy	203	17	substitutions	substitution	NNS
cord-346267-l08ld2cy	203	18	along	along	IN
cord-346267-l08ld2cy	203	19	the	the	DT
cord-346267-l08ld2cy	203	20	branch	branch	NN
cord-346267-l08ld2cy	203	21	in	in	IN
cord-346267-l08ld2cy	203	22	question	question	NN
cord-346267-l08ld2cy	203	23	;	;	:
cord-346267-l08ld2cy	203	24	even	even	RB
cord-346267-l08ld2cy	203	25	after	after	IN
cord-346267-l08ld2cy	203	26	accounting	account	VBG
cord-346267-l08ld2cy	203	27	for	for	IN
cord-346267-l08ld2cy	203	28	variation	variation	NN
cord-346267-l08ld2cy	203	29	in	in	IN
cord-346267-l08ld2cy	203	30	α	α	NNP
cord-346267-l08ld2cy	203	31	s	s	NNP
cord-346267-l08ld2cy	203	32	and	and	CC
cord-346267-l08ld2cy	203	33	β	β	NNP
cord-346267-l08ld2cy	203	34	s	s	NNP
cord-346267-l08ld2cy	203	35	,	,	,
cord-346267-l08ld2cy	203	36	the	the	DT
cord-346267-l08ld2cy	203	37	true	true	JJ
cord-346267-l08ld2cy	203	38	branch	branch	NN
cord-346267-l08ld2cy	203	39	length	length	NN
cord-346267-l08ld2cy	203	40	was	be	VBD
cord-346267-l08ld2cy	203	41	inestimable	inestimable	JJ
cord-346267-l08ld2cy	203	42	.	.	.
cord-346267-l08ld2cy	204	1	In	in	IN
cord-346267-l08ld2cy	204	2	the	the	DT
cord-346267-l08ld2cy	204	3	EBOV	EBOV	NNP
cord-346267-l08ld2cy	204	4	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	204	5	,	,	,
cord-346267-l08ld2cy	204	6	complete	complete	JJ
cord-346267-l08ld2cy	204	7	saturation	saturation	NN
cord-346267-l08ld2cy	204	8	was	be	VBD
cord-346267-l08ld2cy	204	9	observed	observe	VBN
cord-346267-l08ld2cy	204	10	on	on	IN
cord-346267-l08ld2cy	204	11	the	the	DT
cord-346267-l08ld2cy	204	12	branch	branch	NN
cord-346267-l08ld2cy	204	13	leading	lead	VBG
cord-346267-l08ld2cy	204	14	to	to	IN
cord-346267-l08ld2cy	204	15	EBOV	EBOV	NNP
cord-346267-l08ld2cy	204	16	Sudan	Sudan	NNP
cord-346267-l08ld2cy	204	17	and	and	CC
cord-346267-l08ld2cy	204	18	on	on	IN
cord-346267-l08ld2cy	204	19	the	the	DT
cord-346267-l08ld2cy	204	20	branch	branch	NN
cord-346267-l08ld2cy	204	21	connecting	connect	VBG
cord-346267-l08ld2cy	204	22	EBOV	EBOV	NNP
cord-346267-l08ld2cy	204	23	Reston	Reston	NNP
cord-346267-l08ld2cy	204	24	/	/	SYM
cord-346267-l08ld2cy	204	25	Sudan	Sudan	NNP
cord-346267-l08ld2cy	204	26	to	to	IN
cord-346267-l08ld2cy	204	27	EBOV	EBOV	NNP
cord-346267-l08ld2cy	204	28	Zaire	Zaire	NNP
cord-346267-l08ld2cy	204	29	/	/	SYM
cord-346267-l08ld2cy	204	30	Côte	Côte	NNP
cord-346267-l08ld2cy	204	31	d'Ivoire	d'Ivoire	NNP
cord-346267-l08ld2cy	204	32	/	/	SYM
cord-346267-l08ld2cy	204	33	Bundibugyo	Bundibugyo	NNP
cord-346267-l08ld2cy	204	34	(	(	-LRB-
cord-346267-l08ld2cy	204	35	supplementary	supplementary	JJ
cord-346267-l08ld2cy	204	36	fig	fig	NN
cord-346267-l08ld2cy	204	37	.	.	.
cord-346267-l08ld2cy	205	1	S2	S2	NNP
cord-346267-l08ld2cy	205	2	,	,	,
cord-346267-l08ld2cy	205	3	Supplementary	Supplementary	NNP
cord-346267-l08ld2cy	205	4	Material	Material	NNP
cord-346267-l08ld2cy	205	5	online	online	RB
cord-346267-l08ld2cy	205	6	)	)	-RRB-
cord-346267-l08ld2cy	205	7	.	.	.
cord-346267-l08ld2cy	206	1	In	in	IN
cord-346267-l08ld2cy	206	2	the	the	DT
cord-346267-l08ld2cy	206	3	AIV	AIV	NNP
cord-346267-l08ld2cy	206	4	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	206	5	,	,	,
cord-346267-l08ld2cy	206	6	each	each	DT
cord-346267-l08ld2cy	206	7	of	of	IN
cord-346267-l08ld2cy	206	8	the	the	DT
cord-346267-l08ld2cy	206	9	nine	nine	CD
cord-346267-l08ld2cy	206	10	neuraminidase	neuraminidase	NN
cord-346267-l08ld2cy	206	11	serotypes	serotype	NNS
cord-346267-l08ld2cy	206	12	naturally	naturally	RB
cord-346267-l08ld2cy	206	13	found	find	VBN
cord-346267-l08ld2cy	206	14	in	in	IN
cord-346267-l08ld2cy	206	15	avian	avian	JJ
cord-346267-l08ld2cy	206	16	hosts	host	NNS
cord-346267-l08ld2cy	206	17	was	be	VBD
cord-346267-l08ld2cy	206	18	separated	separate	VBN
cord-346267-l08ld2cy	206	19	by	by	IN
cord-346267-l08ld2cy	206	20	branches	branch	NNS
cord-346267-l08ld2cy	206	21	that	that	WDT
cord-346267-l08ld2cy	206	22	experienced	experience	VBD
cord-346267-l08ld2cy	206	23	saturation	saturation	NN
cord-346267-l08ld2cy	206	24	at	at	IN
cord-346267-l08ld2cy	206	25	synonymous	synonymous	JJ
cord-346267-l08ld2cy	206	26	sites	site	NNS
cord-346267-l08ld2cy	206	27	under	under	IN
cord-346267-l08ld2cy	206	28	the	the	DT
cord-346267-l08ld2cy	206	29	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	206	30	model	model	NN
cord-346267-l08ld2cy	206	31	(	(	-LRB-
cord-346267-l08ld2cy	206	32	supplementary	supplementary	JJ
cord-346267-l08ld2cy	206	33	fig	fig	NN
cord-346267-l08ld2cy	206	34	.	.	.
cord-346267-l08ld2cy	207	1	S3	S3	NNP
cord-346267-l08ld2cy	207	2	,	,	,
cord-346267-l08ld2cy	207	3	Supplementary	Supplementary	NNP
cord-346267-l08ld2cy	207	4	Material	Material	NNP
cord-346267-l08ld2cy	207	5	online	online	RB
cord-346267-l08ld2cy	207	6	)	)	-RRB-
cord-346267-l08ld2cy	207	7	.	.	.
cord-346267-l08ld2cy	208	1	The	the	DT
cord-346267-l08ld2cy	208	2	Latin	latin	JJ
cord-346267-l08ld2cy	208	3	hypercube	hypercube	NN
cord-346267-l08ld2cy	208	4	resampling	resampling	NN
cord-346267-l08ld2cy	208	5	scheme	scheme	NN
cord-346267-l08ld2cy	208	6	suggested	suggest	VBD
cord-346267-l08ld2cy	208	7	relatively	relatively	RB
cord-346267-l08ld2cy	208	8	narrow	narrow	JJ
cord-346267-l08ld2cy	208	9	variance	variance	NN
cord-346267-l08ld2cy	208	10	in	in	IN
cord-346267-l08ld2cy	208	11	the	the	DT
cord-346267-l08ld2cy	208	12	expansion	expansion	NN
cord-346267-l08ld2cy	208	13	under	under	IN
cord-346267-l08ld2cy	208	14	the	the	DT
cord-346267-l08ld2cy	208	15	Lin	Lin	NNP
cord-346267-l08ld2cy	208	16	-	-	HYPH
cord-346267-l08ld2cy	208	17	eage+Dual	eage+Dual	NNP
cord-346267-l08ld2cy	208	18	model	model	NN
cord-346267-l08ld2cy	208	19	.	.	.
cord-346267-l08ld2cy	209	1	The	the	DT
cord-346267-l08ld2cy	209	2	total	total	JJ
cord-346267-l08ld2cy	209	3	increase	increase	NN
cord-346267-l08ld2cy	209	4	in	in	IN
cord-346267-l08ld2cy	209	5	MeV	MeV	NNP
cord-346267-l08ld2cy	209	6	/	/	SYM
cord-346267-l08ld2cy	209	7	RPV	RPV	NNP
cord-346267-l08ld2cy	209	8	/	/	SYM
cord-346267-l08ld2cy	209	9	PPRV	PPRV	NNP
cord-346267-l08ld2cy	209	10	tree	tree	NN
cord-346267-l08ld2cy	209	11	relative	relative	JJ
cord-346267-l08ld2cy	209	12	to	to	IN
cord-346267-l08ld2cy	209	13	GTR	GTR	NNP
cord-346267-l08ld2cy	209	14	+	+	CC
cord-346267-l08ld2cy	209	15	Γ	γ	NN
cord-346267-l08ld2cy	209	16	4	4	CD
cord-346267-l08ld2cy	209	17	was	be	VBD
cord-346267-l08ld2cy	209	18	1.93	1.93	CD
cord-346267-l08ld2cy	209	19	(	(	-LRB-
cord-346267-l08ld2cy	209	20	approximate	approximate	JJ
cord-346267-l08ld2cy	209	21	95	95	CD
cord-346267-l08ld2cy	209	22	%	%	NN
cord-346267-l08ld2cy	209	23	confidence	confidence	NN
cord-346267-l08ld2cy	209	24	interval	interval	NN
cord-346267-l08ld2cy	209	25	:	:	:
cord-346267-l08ld2cy	209	26	1.76	1.76	CD
cord-346267-l08ld2cy	209	27	-	-	HYPH
cord-346267-l08ld2cy	209	28	2.16	2.16	CD
cord-346267-l08ld2cy	209	29	)	)	-RRB-
cord-346267-l08ld2cy	209	30	.	.	.
cord-346267-l08ld2cy	210	1	Due	due	IN
cord-346267-l08ld2cy	210	2	to	to	IN
cord-346267-l08ld2cy	210	3	the	the	DT
cord-346267-l08ld2cy	210	4	inference	inference	NN
cord-346267-l08ld2cy	210	5	of	of	IN
cord-346267-l08ld2cy	210	6	branch	branch	NN
cord-346267-l08ld2cy	210	7	lengths	length	NNS
cord-346267-l08ld2cy	210	8	that	that	WDT
cord-346267-l08ld2cy	210	9	experienced	experience	VBD
cord-346267-l08ld2cy	210	10	saturation	saturation	NN
cord-346267-l08ld2cy	210	11	in	in	IN
cord-346267-l08ld2cy	210	12	EBOV	EBOV	NNP
cord-346267-l08ld2cy	210	13	and	and	CC
cord-346267-l08ld2cy	210	14	AIV	AIV	NNP
cord-346267-l08ld2cy	210	15	,	,	,
cord-346267-l08ld2cy	210	16	the	the	DT
cord-346267-l08ld2cy	210	17	overall	overall	JJ
cord-346267-l08ld2cy	210	18	increase	increase	NN
cord-346267-l08ld2cy	210	19	in	in	IN
cord-346267-l08ld2cy	210	20	tree	tree	NN
cord-346267-l08ld2cy	210	21	length	length	NN
cord-346267-l08ld2cy	210	22	was	be	VBD
cord-346267-l08ld2cy	210	23	more	more	RBR
cord-346267-l08ld2cy	210	24	dramatic	dramatic	JJ
cord-346267-l08ld2cy	210	25	under	under	IN
cord-346267-l08ld2cy	210	26	the	the	DT
cord-346267-l08ld2cy	210	27	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	210	28	model	model	NN
cord-346267-l08ld2cy	210	29	,	,	,
cord-346267-l08ld2cy	210	30	relative	relative	JJ
cord-346267-l08ld2cy	210	31	to	to	IN
cord-346267-l08ld2cy	210	32	GTR	GTR	NNP
cord-346267-l08ld2cy	210	33	+	+	CC
cord-346267-l08ld2cy	210	34	Γ	γ	NN
cord-346267-l08ld2cy	210	35	4	4	CD
cord-346267-l08ld2cy	210	36	:	:	:
cord-346267-l08ld2cy	210	37	32.14	32.14	CD
cord-346267-l08ld2cy	210	38	(	(	-LRB-
cord-346267-l08ld2cy	210	39	approximate	approximate	JJ
cord-346267-l08ld2cy	210	40	95	95	CD
cord-346267-l08ld2cy	210	41	%	%	NN
cord-346267-l08ld2cy	210	42	confidence	confidence	NN
cord-346267-l08ld2cy	210	43	interval	interval	NN
cord-346267-l08ld2cy	210	44	:	:	:
cord-346267-l08ld2cy	210	45	12.14	12.14	CD
cord-346267-l08ld2cy	210	46	-	-	SYM
cord-346267-l08ld2cy	210	47	32.22	32.22	CD
cord-346267-l08ld2cy	210	48	)	)	-RRB-
cord-346267-l08ld2cy	210	49	for	for	IN
cord-346267-l08ld2cy	210	50	EBOV	EBOV	NNP
cord-346267-l08ld2cy	210	51	and	and	CC
cord-346267-l08ld2cy	210	52	107.34	107.34	CD
cord-346267-l08ld2cy	210	53	(	(	-LRB-
cord-346267-l08ld2cy	210	54	approximate	approximate	JJ
cord-346267-l08ld2cy	210	55	95	95	CD
cord-346267-l08ld2cy	210	56	%	%	NN
cord-346267-l08ld2cy	210	57	confidence	confidence	NN
cord-346267-l08ld2cy	210	58	interval	interval	NN
cord-346267-l08ld2cy	210	59	:	:	:
cord-346267-l08ld2cy	210	60	101.06	101.06	CD
cord-346267-l08ld2cy	210	61	-	-	SYM
cord-346267-l08ld2cy	210	62	117.36	117.36	CD
cord-346267-l08ld2cy	210	63	)	)	-RRB-
cord-346267-l08ld2cy	210	64	for	for	IN
cord-346267-l08ld2cy	210	65	AIV	AIV	NNP
cord-346267-l08ld2cy	210	66	.	.	.
cord-346267-l08ld2cy	211	1	It	-PRON-	PRP
cord-346267-l08ld2cy	211	2	is	be	VBZ
cord-346267-l08ld2cy	211	3	clear	clear	JJ
cord-346267-l08ld2cy	211	4	that	that	IN
cord-346267-l08ld2cy	211	5	purifying	purifying	NN
cord-346267-l08ld2cy	211	6	selection	selection	NN
cord-346267-l08ld2cy	211	7	can	can	MD
cord-346267-l08ld2cy	211	8	obscure	obscure	VB
cord-346267-l08ld2cy	211	9	the	the	DT
cord-346267-l08ld2cy	211	10	ancient	ancient	JJ
cord-346267-l08ld2cy	211	11	evolution	evolution	NN
cord-346267-l08ld2cy	211	12	of	of	IN
cord-346267-l08ld2cy	211	13	the	the	DT
cord-346267-l08ld2cy	211	14	RNA	RNA	NNP
cord-346267-l08ld2cy	211	15	viruses	virus	NNS
cord-346267-l08ld2cy	211	16	examined	examine	VBN
cord-346267-l08ld2cy	211	17	here	here	RB
cord-346267-l08ld2cy	211	18	.	.	.
cord-346267-l08ld2cy	212	1	A	a	DT
cord-346267-l08ld2cy	212	2	comparison	comparison	NN
cord-346267-l08ld2cy	212	3	of	of	IN
cord-346267-l08ld2cy	212	4	the	the	DT
cord-346267-l08ld2cy	212	5	MeV	MeV	NNP
cord-346267-l08ld2cy	212	6	/	/	SYM
cord-346267-l08ld2cy	212	7	RPV	RPV	NNP
cord-346267-l08ld2cy	212	8	/	/	SYM
cord-346267-l08ld2cy	212	9	PPRV	PPRV	NNP
cord-346267-l08ld2cy	212	10	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	212	11	optimized	optimize	VBN
cord-346267-l08ld2cy	212	12	under	under	IN
cord-346267-l08ld2cy	212	13	GTR	GTR	NNP
cord-346267-l08ld2cy	212	14	+	+	CC
cord-346267-l08ld2cy	212	15	Γ	γ	NN
cord-346267-l08ld2cy	212	16	4	4	CD
cord-346267-l08ld2cy	212	17	and	and	CC
cord-346267-l08ld2cy	212	18	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	212	19	(	(	-LRB-
cord-346267-l08ld2cy	212	20	two	two	CD
cord-346267-l08ld2cy	212	21	-	-	HYPH
cord-346267-l08ld2cy	212	22	rate	rate	NN
cord-346267-l08ld2cy	212	23	)	)	-RRB-
cord-346267-l08ld2cy	212	24	models	model	NNS
cord-346267-l08ld2cy	212	25	showed	show	VBD
cord-346267-l08ld2cy	212	26	that	that	IN
cord-346267-l08ld2cy	212	27	the	the	DT
cord-346267-l08ld2cy	212	28	elongation	elongation	NN
cord-346267-l08ld2cy	212	29	of	of	IN
cord-346267-l08ld2cy	212	30	branches	branch	NNS
cord-346267-l08ld2cy	212	31	occurred	occur	VBD
cord-346267-l08ld2cy	212	32	along	along	IN
cord-346267-l08ld2cy	212	33	the	the	DT
cord-346267-l08ld2cy	212	34	deep	deep	JJ
cord-346267-l08ld2cy	212	35	internal	internal	JJ
cord-346267-l08ld2cy	212	36	branches	branch	NNS
cord-346267-l08ld2cy	212	37	,	,	,
cord-346267-l08ld2cy	212	38	leaving	leave	VBG
cord-346267-l08ld2cy	212	39	the	the	DT
cord-346267-l08ld2cy	212	40	relationships	relationship	NNS
cord-346267-l08ld2cy	212	41	among	among	IN
cord-346267-l08ld2cy	212	42	recently	recently	RB
cord-346267-l08ld2cy	212	43	divergent	divergent	JJ
cord-346267-l08ld2cy	212	44	lineages	lineage	NNS
cord-346267-l08ld2cy	212	45	within	within	IN
cord-346267-l08ld2cy	212	46	viral	viral	JJ
cord-346267-l08ld2cy	212	47	species	specie	NNS
cord-346267-l08ld2cy	212	48	relatively	relatively	RB
cord-346267-l08ld2cy	212	49	unchanged	unchanged	JJ
cord-346267-l08ld2cy	212	50	(	(	-LRB-
cord-346267-l08ld2cy	212	51	fig	fig	NN
cord-346267-l08ld2cy	212	52	.	.	.
cord-346267-l08ld2cy	212	53	4	4	LS
cord-346267-l08ld2cy	212	54	)	)	-RRB-
cord-346267-l08ld2cy	212	55	.	.	.
cord-346267-l08ld2cy	213	1	The	the	DT
cord-346267-l08ld2cy	213	2	depth	depth	NN
cord-346267-l08ld2cy	213	3	of	of	IN
cord-346267-l08ld2cy	213	4	the	the	DT
cord-346267-l08ld2cy	213	5	split	split	NN
cord-346267-l08ld2cy	213	6	between	between	IN
cord-346267-l08ld2cy	213	7	MeV	MeV	NNP
cord-346267-l08ld2cy	213	8	and	and	CC
cord-346267-l08ld2cy	213	9	RPV	RPV	NNP
cord-346267-l08ld2cy	213	10	under	under	IN
cord-346267-l08ld2cy	213	11	a	a	DT
cord-346267-l08ld2cy	213	12	GTR	GTR	NNP
cord-346267-l08ld2cy	213	13	+	+	SYM
cord-346267-l08ld2cy	213	14	Γ	γ	NN
cord-346267-l08ld2cy	213	15	4	4	CD
cord-346267-l08ld2cy	213	16	model	model	NN
cord-346267-l08ld2cy	213	17	was	be	VBD
cord-346267-l08ld2cy	213	18	0.4921	0.4921	CD
cord-346267-l08ld2cy	213	19	substitutions	substitution	NNS
cord-346267-l08ld2cy	213	20	/	/	SYM
cord-346267-l08ld2cy	213	21	site	site	NN
cord-346267-l08ld2cy	213	22	,	,	,
cord-346267-l08ld2cy	213	23	which	which	WDT
cord-346267-l08ld2cy	213	24	,	,	,
cord-346267-l08ld2cy	213	25	according	accord	VBG
cord-346267-l08ld2cy	213	26	to	to	IN
cord-346267-l08ld2cy	213	27	the	the	DT
cord-346267-l08ld2cy	213	28	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	213	29	analysis	analysis	NN
cord-346267-l08ld2cy	213	30	,	,	,
cord-346267-l08ld2cy	213	31	occurred	occur	VBD
cord-346267-l08ld2cy	213	32	in	in	IN
cord-346267-l08ld2cy	213	33	the	the	DT
cord-346267-l08ld2cy	213	34	year	year	NN
cord-346267-l08ld2cy	213	35	1483	1483	CD
cord-346267-l08ld2cy	213	36	Table	Table	NNP
cord-346267-l08ld2cy	213	37	2	2	CD
cord-346267-l08ld2cy	213	38	.	.	.
cord-346267-l08ld2cy	214	1	Goodness	goodness	NN
cord-346267-l08ld2cy	214	2	of	of	IN
cord-346267-l08ld2cy	214	3	fit	fit	NN
cord-346267-l08ld2cy	214	4	for	for	IN
cord-346267-l08ld2cy	214	5	various	various	JJ
cord-346267-l08ld2cy	214	6	codon	codon	NN
cord-346267-l08ld2cy	214	7	models	model	NNS
cord-346267-l08ld2cy	214	8	and	and	CC
cord-346267-l08ld2cy	214	9	the	the	DT
cord-346267-l08ld2cy	214	10	effect	effect	NN
cord-346267-l08ld2cy	214	11	of	of	IN
cord-346267-l08ld2cy	214	12	model	model	NN
cord-346267-l08ld2cy	214	13	choice	choice	NN
cord-346267-l08ld2cy	214	14	on	on	IN
cord-346267-l08ld2cy	214	15	the	the	DT
cord-346267-l08ld2cy	214	16	estimates	estimate	NNS
cord-346267-l08ld2cy	214	17	of	of	IN
cord-346267-l08ld2cy	214	18	the	the	DT
cord-346267-l08ld2cy	214	19	branch	branch	NN
cord-346267-l08ld2cy	214	20	lengths	length	NNS
cord-346267-l08ld2cy	214	21	of	of	IN
cord-346267-l08ld2cy	214	22	deep	deep	JJ
cord-346267-l08ld2cy	214	23	and	and	CC
cord-346267-l08ld2cy	214	24	recent	recent	JJ
cord-346267-l08ld2cy	214	25	lineages	lineage	NNS
cord-346267-l08ld2cy	214	26	.	.	.
cord-346267-l08ld2cy	215	1	Model	model	NN
cord-346267-l08ld2cy	215	2	(	(	-LRB-
cord-346267-l08ld2cy	215	3	597	597	CD
cord-346267-l08ld2cy	215	4	-	-	SYM
cord-346267-l08ld2cy	215	5	1144	1144	CD
cord-346267-l08ld2cy	215	6	CE	CE	NNP
cord-346267-l08ld2cy	215	7	)	)	-RRB-
cord-346267-l08ld2cy	215	8	.	.	.
cord-346267-l08ld2cy	216	1	This	this	DT
cord-346267-l08ld2cy	216	2	extrapolation	extrapolation	NN
cord-346267-l08ld2cy	216	3	is	be	VBZ
cord-346267-l08ld2cy	216	4	meant	mean	VBN
cord-346267-l08ld2cy	216	5	as	as	IN
cord-346267-l08ld2cy	216	6	a	a	DT
cord-346267-l08ld2cy	216	7	rather	rather	RB
cord-346267-l08ld2cy	216	8	crude	crude	JJ
cord-346267-l08ld2cy	216	9	approximation	approximation	NN
cord-346267-l08ld2cy	216	10	of	of	IN
cord-346267-l08ld2cy	216	11	the	the	DT
cord-346267-l08ld2cy	216	12	age	age	NN
cord-346267-l08ld2cy	216	13	of	of	IN
cord-346267-l08ld2cy	216	14	this	this	DT
cord-346267-l08ld2cy	216	15	divergence	divergence	NN
cord-346267-l08ld2cy	216	16	event	event	NN
cord-346267-l08ld2cy	216	17	;	;	:
cord-346267-l08ld2cy	216	18	nevertheless	nevertheless	RB
cord-346267-l08ld2cy	216	19	,	,	,
cord-346267-l08ld2cy	216	20	these	these	DT
cord-346267-l08ld2cy	216	21	dates	date	NNS
cord-346267-l08ld2cy	216	22	are	be	VBP
cord-346267-l08ld2cy	216	23	more	more	RBR
cord-346267-l08ld2cy	216	24	likely	likely	JJ
cord-346267-l08ld2cy	216	25	to	to	TO
cord-346267-l08ld2cy	216	26	be	be	VB
cord-346267-l08ld2cy	216	27	closer	close	JJR
cord-346267-l08ld2cy	216	28	to	to	IN
cord-346267-l08ld2cy	216	29	the	the	DT
cord-346267-l08ld2cy	216	30	true	true	JJ
cord-346267-l08ld2cy	216	31	split	split	NN
cord-346267-l08ld2cy	216	32	between	between	IN
cord-346267-l08ld2cy	216	33	MeV	MeV	NNP
cord-346267-l08ld2cy	216	34	and	and	CC
cord-346267-l08ld2cy	216	35	RPV	RPV	NNP
cord-346267-l08ld2cy	216	36	than	than	IN
cord-346267-l08ld2cy	216	37	previous	previous	JJ
cord-346267-l08ld2cy	216	38	estimates	estimate	NNS
cord-346267-l08ld2cy	216	39	and	and	CC
cord-346267-l08ld2cy	216	40	are	be	VBP
cord-346267-l08ld2cy	216	41	not	not	RB
cord-346267-l08ld2cy	216	42	inconsistent	inconsistent	JJ
cord-346267-l08ld2cy	216	43	with	with	IN
cord-346267-l08ld2cy	216	44	recorded	record	VBN
cord-346267-l08ld2cy	216	45	history	history	NN
cord-346267-l08ld2cy	216	46	of	of	IN
cord-346267-l08ld2cy	216	47	measles	measle	NNS
cord-346267-l08ld2cy	216	48	.	.	.
cord-346267-l08ld2cy	217	1	The	the	DT
cord-346267-l08ld2cy	217	2	degree	degree	NN
cord-346267-l08ld2cy	217	3	of	of	IN
cord-346267-l08ld2cy	217	4	synonymous	synonymous	JJ
cord-346267-l08ld2cy	217	5	saturation	saturation	NN
cord-346267-l08ld2cy	217	6	observed	observe	VBN
cord-346267-l08ld2cy	217	7	along	along	IN
cord-346267-l08ld2cy	217	8	the	the	DT
cord-346267-l08ld2cy	217	9	EBOV	EBOV	NNP
cord-346267-l08ld2cy	217	10	and	and	CC
cord-346267-l08ld2cy	217	11	AIV	AIV	NNP
cord-346267-l08ld2cy	217	12	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	217	13	indicate	indicate	VBP
cord-346267-l08ld2cy	217	14	an	an	DT
cord-346267-l08ld2cy	217	15	inability	inability	NN
cord-346267-l08ld2cy	217	16	to	to	TO
cord-346267-l08ld2cy	217	17	reliably	reliably	RB
cord-346267-l08ld2cy	217	18	infer	infer	VB
cord-346267-l08ld2cy	217	19	tMRCAs	tmrcas	CD
cord-346267-l08ld2cy	217	20	for	for	IN
cord-346267-l08ld2cy	217	21	these	these	DT
cord-346267-l08ld2cy	217	22	viruses	virus	NNS
cord-346267-l08ld2cy	217	23	.	.	.
cord-346267-l08ld2cy	218	1	Too	too	RB
cord-346267-l08ld2cy	218	2	many	many	JJ
cord-346267-l08ld2cy	218	3	sites	site	NNS
cord-346267-l08ld2cy	218	4	have	have	VBP
cord-346267-l08ld2cy	218	5	sunk	sink	VBN
cord-346267-l08ld2cy	218	6	beyond	beyond	IN
cord-346267-l08ld2cy	218	7	the	the	DT
cord-346267-l08ld2cy	218	8	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	218	9	horizon	horizon	NN
cord-346267-l08ld2cy	218	10	.	.	.
cord-346267-l08ld2cy	219	1	Nevertheless	nevertheless	RB
cord-346267-l08ld2cy	219	2	,	,	,
cord-346267-l08ld2cy	219	3	these	these	DT
cord-346267-l08ld2cy	219	4	estimates	estimate	NNS
cord-346267-l08ld2cy	219	5	could	could	MD
cord-346267-l08ld2cy	219	6	provide	provide	VB
cord-346267-l08ld2cy	219	7	meaningful	meaningful	JJ
cord-346267-l08ld2cy	219	8	minimum	minimum	JJ
cord-346267-l08ld2cy	219	9	bounds	bound	NNS
cord-346267-l08ld2cy	219	10	for	for	IN
cord-346267-l08ld2cy	219	11	the	the	DT
cord-346267-l08ld2cy	219	12	tMRCAs	tmrcas	NN
cord-346267-l08ld2cy	219	13	.	.	.
cord-346267-l08ld2cy	220	1	Thus	thus	RB
cord-346267-l08ld2cy	220	2	,	,	,
cord-346267-l08ld2cy	220	3	for	for	IN
cord-346267-l08ld2cy	220	4	both	both	CC
cord-346267-l08ld2cy	220	5	EBOV	EBOV	NNP
cord-346267-l08ld2cy	220	6	and	and	CC
cord-346267-l08ld2cy	220	7	AIV	AIV	NNP
cord-346267-l08ld2cy	220	8	,	,	,
cord-346267-l08ld2cy	220	9	we	-PRON-	PRP
cord-346267-l08ld2cy	220	10	applied	apply	VBD
cord-346267-l08ld2cy	220	11	the	the	DT
cord-346267-l08ld2cy	220	12	mean	mean	JJ
cord-346267-l08ld2cy	220	13	substitution	substitution	NN
cord-346267-l08ld2cy	220	14	rate	rate	NN
cord-346267-l08ld2cy	220	15	inferred	infer	VBN
cord-346267-l08ld2cy	220	16	in	in	IN
cord-346267-l08ld2cy	220	17	the	the	DT
cord-346267-l08ld2cy	220	18	BMCMC	BMCMC	NNP
cord-346267-l08ld2cy	220	19	GTR	GTR	NNP
cord-346267-l08ld2cy	220	20	+	+	CC
cord-346267-l08ld2cy	220	21	Γ	γ	NN
cord-346267-l08ld2cy	220	22	4	4	CD
cord-346267-l08ld2cy	220	23	analyses	analysis	NNS
cord-346267-l08ld2cy	220	24	to	to	IN
cord-346267-l08ld2cy	220	25	the	the	DT
cord-346267-l08ld2cy	220	26	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	220	27	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	220	28	.	.	.
cord-346267-l08ld2cy	221	1	This	this	DT
cord-346267-l08ld2cy	221	2	approach	approach	NN
cord-346267-l08ld2cy	221	3	suggested	suggest	VBD
cord-346267-l08ld2cy	221	4	that	that	IN
cord-346267-l08ld2cy	221	5	the	the	DT
cord-346267-l08ld2cy	221	6	minimum	minimum	JJ
cord-346267-l08ld2cy	221	7	tMRCA	tmrca	NN
cord-346267-l08ld2cy	221	8	estimates	estimate	NNS
cord-346267-l08ld2cy	221	9	for	for	IN
cord-346267-l08ld2cy	221	10	EBOV	EBOV	NNP
cord-346267-l08ld2cy	221	11	and	and	CC
cord-346267-l08ld2cy	221	12	AIV	AIV	NNP
cord-346267-l08ld2cy	221	13	are	be	VBP
cord-346267-l08ld2cy	221	14	approximately	approximately	RB
cord-346267-l08ld2cy	221	15	70,000	70,000	CD
cord-346267-l08ld2cy	221	16	and	and	CC
cord-346267-l08ld2cy	221	17	200,000	200,000	CD
cord-346267-l08ld2cy	221	18	years	year	NNS
cord-346267-l08ld2cy	221	19	ago	ago	RB
cord-346267-l08ld2cy	221	20	,	,	,
cord-346267-l08ld2cy	221	21	respectively	respectively	RB
cord-346267-l08ld2cy	221	22	.	.	.
cord-346267-l08ld2cy	222	1	The	the	DT
cord-346267-l08ld2cy	222	2	actual	actual	JJ
cord-346267-l08ld2cy	222	3	tMRCAs	tmrcas	NN
cord-346267-l08ld2cy	222	4	may	may	MD
cord-346267-l08ld2cy	222	5	be	be	VB
cord-346267-l08ld2cy	222	6	much	much	RB
cord-346267-l08ld2cy	222	7	older	old	JJR
cord-346267-l08ld2cy	222	8	.	.	.
cord-346267-l08ld2cy	223	1	Our	-PRON-	PRP$
cord-346267-l08ld2cy	223	2	results	result	NNS
cord-346267-l08ld2cy	223	3	suggest	suggest	VBP
cord-346267-l08ld2cy	223	4	that	that	IN
cord-346267-l08ld2cy	223	5	the	the	DT
cord-346267-l08ld2cy	223	6	ancient	ancient	JJ
cord-346267-l08ld2cy	223	7	age	age	NN
cord-346267-l08ld2cy	223	8	of	of	IN
cord-346267-l08ld2cy	223	9	RNA	RNA	NNP
cord-346267-l08ld2cy	223	10	viruses	virus	NNS
cord-346267-l08ld2cy	223	11	may	may	MD
cord-346267-l08ld2cy	223	12	be	be	VB
cord-346267-l08ld2cy	223	13	partially	partially	RB
cord-346267-l08ld2cy	223	14	masked	mask	VBN
cord-346267-l08ld2cy	223	15	behind	behind	IN
cord-346267-l08ld2cy	223	16	a	a	DT
cord-346267-l08ld2cy	223	17	veil	veil	NN
cord-346267-l08ld2cy	223	18	of	of	IN
cord-346267-l08ld2cy	223	19	purifying	purify	VBG
cord-346267-l08ld2cy	223	20	selection	selection	NN
cord-346267-l08ld2cy	223	21	.	.	.
cord-346267-l08ld2cy	224	1	The	the	DT
cord-346267-l08ld2cy	224	2	same	same	JJ
cord-346267-l08ld2cy	224	3	forces	force	NNS
cord-346267-l08ld2cy	224	4	of	of	IN
cord-346267-l08ld2cy	224	5	purifying	purify	VBG
cord-346267-l08ld2cy	224	6	selection	selection	NN
cord-346267-l08ld2cy	224	7	that	that	WDT
cord-346267-l08ld2cy	224	8	maintain	maintain	VBP
cord-346267-l08ld2cy	224	9	evidence	evidence	NN
cord-346267-l08ld2cy	224	10	of	of	IN
cord-346267-l08ld2cy	224	11	protein	protein	NN
cord-346267-l08ld2cy	224	12	sequence	sequence	NN
cord-346267-l08ld2cy	224	13	homology	homology	NN
cord-346267-l08ld2cy	224	14	over	over	IN
cord-346267-l08ld2cy	224	15	great	great	JJ
cord-346267-l08ld2cy	224	16	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	224	17	distances	distance	NNS
cord-346267-l08ld2cy	224	18	also	also	RB
cord-346267-l08ld2cy	224	19	truncate	truncate	VBP
cord-346267-l08ld2cy	224	20	long	long	JJ
cord-346267-l08ld2cy	224	21	ancestral	ancestral	JJ
cord-346267-l08ld2cy	224	22	branches	branch	NNS
cord-346267-l08ld2cy	224	23	deep	deep	RB
cord-346267-l08ld2cy	224	24	within	within	IN
cord-346267-l08ld2cy	224	25	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	224	26	trees	tree	NNS
cord-346267-l08ld2cy	224	27	.	.	.
cord-346267-l08ld2cy	225	1	We	-PRON-	PRP
cord-346267-l08ld2cy	225	2	observed	observe	VBD
cord-346267-l08ld2cy	225	3	this	this	DT
cord-346267-l08ld2cy	225	4	pattern	pattern	NN
cord-346267-l08ld2cy	225	5	MBE	MBE	NNP
cord-346267-l08ld2cy	225	6	in	in	IN
cord-346267-l08ld2cy	225	7	three	three	CD
cord-346267-l08ld2cy	225	8	different	different	JJ
cord-346267-l08ld2cy	225	9	groups	group	NNS
cord-346267-l08ld2cy	225	10	of	of	IN
cord-346267-l08ld2cy	225	11	rapidly	rapidly	RB
cord-346267-l08ld2cy	225	12	evolving	evolve	VBG
cord-346267-l08ld2cy	225	13	negative	negative	JJ
cord-346267-l08ld2cy	225	14	-	-	HYPH
cord-346267-l08ld2cy	225	15	sense	sense	NN
cord-346267-l08ld2cy	225	16	RNA	RNA	NNP
cord-346267-l08ld2cy	225	17	viruses	virus	NNS
cord-346267-l08ld2cy	225	18	:	:	:
cord-346267-l08ld2cy	226	1	MeV	MeV	NNP
cord-346267-l08ld2cy	226	2	/	/	SYM
cord-346267-l08ld2cy	226	3	RPV	RPV	NNP
cord-346267-l08ld2cy	226	4	/	/	SYM
cord-346267-l08ld2cy	226	5	PPRV	PPRV	NNP
cord-346267-l08ld2cy	226	6	,	,	,
cord-346267-l08ld2cy	226	7	EBOV	EBOV	NNP
cord-346267-l08ld2cy	226	8	,	,	,
cord-346267-l08ld2cy	226	9	and	and	CC
cord-346267-l08ld2cy	226	10	AIV	AIV	NNP
cord-346267-l08ld2cy	226	11	.	.	.
cord-346267-l08ld2cy	227	1	Estimating	estimate	VBG
cord-346267-l08ld2cy	227	2	branch	branch	NN
cord-346267-l08ld2cy	227	3	lengths	length	NNS
cord-346267-l08ld2cy	227	4	under	under	IN
cord-346267-l08ld2cy	227	5	a	a	DT
cord-346267-l08ld2cy	227	6	codon	codon	NN
cord-346267-l08ld2cy	227	7	-	-	HYPH
cord-346267-l08ld2cy	227	8	based	base	VBN
cord-346267-l08ld2cy	227	9	substitution	substitution	NN
cord-346267-l08ld2cy	227	10	model	model	NN
cord-346267-l08ld2cy	227	11	that	that	WDT
cord-346267-l08ld2cy	227	12	accounts	account	VBZ
cord-346267-l08ld2cy	227	13	for	for	IN
cord-346267-l08ld2cy	227	14	spatial	spatial	JJ
cord-346267-l08ld2cy	227	15	and	and	CC
cord-346267-l08ld2cy	227	16	temporal	temporal	JJ
cord-346267-l08ld2cy	227	17	variation	variation	NN
cord-346267-l08ld2cy	227	18	in	in	IN
cord-346267-l08ld2cy	227	19	selection	selection	NN
cord-346267-l08ld2cy	227	20	pressures	pressure	NNS
cord-346267-l08ld2cy	227	21	yielded	yield	VBD
cord-346267-l08ld2cy	227	22	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	227	23	trees	tree	NNS
cord-346267-l08ld2cy	227	24	that	that	WDT
cord-346267-l08ld2cy	227	25	were	be	VBD
cord-346267-l08ld2cy	227	26	more	more	JJR
cord-346267-l08ld2cy	227	27	than	than	IN
cord-346267-l08ld2cy	227	28	twice	twice	RB
cord-346267-l08ld2cy	227	29	as	as	RB
cord-346267-l08ld2cy	227	30	long	long	RB
cord-346267-l08ld2cy	227	31	as	as	IN
cord-346267-l08ld2cy	227	32	those	those	DT
cord-346267-l08ld2cy	227	33	obtained	obtain	VBN
cord-346267-l08ld2cy	227	34	under	under	IN
cord-346267-l08ld2cy	227	35	standard	standard	JJ
cord-346267-l08ld2cy	227	36	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	227	37	models	model	NNS
cord-346267-l08ld2cy	227	38	.	.	.
cord-346267-l08ld2cy	228	1	Modeling	model	VBG
cord-346267-l08ld2cy	228	2	synonymous	synonymous	JJ
cord-346267-l08ld2cy	228	3	,	,	,
cord-346267-l08ld2cy	228	4	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	228	5	,	,	,
cord-346267-l08ld2cy	228	6	and	and	CC
cord-346267-l08ld2cy	228	7	lineage	lineage	NN
cord-346267-l08ld2cy	228	8	-	-	HYPH
cord-346267-l08ld2cy	228	9	specific	specific	JJ
cord-346267-l08ld2cy	228	10	rate	rate	NN
cord-346267-l08ld2cy	228	11	variation	variation	NN
cord-346267-l08ld2cy	228	12	indicates	indicate	VBZ
cord-346267-l08ld2cy	228	13	that	that	IN
cord-346267-l08ld2cy	228	14	current	current	JJ
cord-346267-l08ld2cy	228	15	estimates	estimate	NNS
cord-346267-l08ld2cy	228	16	of	of	IN
cord-346267-l08ld2cy	228	17	the	the	DT
cord-346267-l08ld2cy	228	18	age	age	NN
cord-346267-l08ld2cy	228	19	of	of	IN
cord-346267-l08ld2cy	228	20	these	these	DT
cord-346267-l08ld2cy	228	21	,	,	,
cord-346267-l08ld2cy	228	22	and	and	CC
cord-346267-l08ld2cy	228	23	possibly	possibly	RB
cord-346267-l08ld2cy	228	24	other	other	JJ
cord-346267-l08ld2cy	228	25	,	,	,
cord-346267-l08ld2cy	228	26	viral	viral	JJ
cord-346267-l08ld2cy	228	27	lineages	lineage	NNS
cord-346267-l08ld2cy	228	28	may	may	MD
cord-346267-l08ld2cy	228	29	be	be	VB
cord-346267-l08ld2cy	228	30	dramatically	dramatically	RB
cord-346267-l08ld2cy	228	31	underestimated	underestimate	VBN
cord-346267-l08ld2cy	228	32	.	.	.
cord-346267-l08ld2cy	229	1	Codon	Codon	NNP
cord-346267-l08ld2cy	229	2	models	model	NNS
cord-346267-l08ld2cy	229	3	used	use	VBN
cord-346267-l08ld2cy	229	4	in	in	IN
cord-346267-l08ld2cy	229	5	this	this	DT
cord-346267-l08ld2cy	229	6	study	study	NN
cord-346267-l08ld2cy	229	7	do	do	VBP
cord-346267-l08ld2cy	229	8	not	not	RB
cord-346267-l08ld2cy	229	9	circumvent	circumvent	VB
cord-346267-l08ld2cy	229	10	the	the	DT
cord-346267-l08ld2cy	229	11	issue	issue	NN
cord-346267-l08ld2cy	229	12	of	of	IN
cord-346267-l08ld2cy	229	13	substitutional	substitutional	JJ
cord-346267-l08ld2cy	229	14	saturation	saturation	NN
cord-346267-l08ld2cy	229	15	but	but	CC
cord-346267-l08ld2cy	229	16	merely	merely	RB
cord-346267-l08ld2cy	229	17	extend	extend	VB
cord-346267-l08ld2cy	229	18	the	the	DT
cord-346267-l08ld2cy	229	19	horizon	horizon	NN
cord-346267-l08ld2cy	229	20	further	further	RB
cord-346267-l08ld2cy	229	21	back	back	RB
cord-346267-l08ld2cy	229	22	in	in	IN
cord-346267-l08ld2cy	229	23	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	229	24	time	time	NN
cord-346267-l08ld2cy	229	25	;	;	:
cord-346267-l08ld2cy	229	26	the	the	DT
cord-346267-l08ld2cy	229	27	application	application	NN
cord-346267-l08ld2cy	229	28	of	of	IN
cord-346267-l08ld2cy	229	29	more	more	RBR
cord-346267-l08ld2cy	229	30	complex	complex	JJ
cord-346267-l08ld2cy	229	31	and	and	CC
cord-346267-l08ld2cy	229	32	biologically	biologically	RB
cord-346267-l08ld2cy	229	33	realistic	realistic	JJ
cord-346267-l08ld2cy	229	34	models	model	NNS
cord-346267-l08ld2cy	229	35	is	be	VBZ
cord-346267-l08ld2cy	229	36	likely	likely	JJ
cord-346267-l08ld2cy	229	37	to	to	TO
cord-346267-l08ld2cy	229	38	extend	extend	VB
cord-346267-l08ld2cy	229	39	these	these	DT
cord-346267-l08ld2cy	229	40	branches	branch	NNS
cord-346267-l08ld2cy	229	41	even	even	RB
cord-346267-l08ld2cy	229	42	further	far	RBR
cord-346267-l08ld2cy	229	43	into	into	IN
cord-346267-l08ld2cy	229	44	the	the	DT
cord-346267-l08ld2cy	229	45	past	past	NN
cord-346267-l08ld2cy	229	46	.	.	.
cord-346267-l08ld2cy	230	1	Eventually	eventually	RB
cord-346267-l08ld2cy	230	2	,	,	,
cord-346267-l08ld2cy	230	3	however	however	RB
cord-346267-l08ld2cy	230	4	,	,	,
cord-346267-l08ld2cy	230	5	even	even	RB
cord-346267-l08ld2cy	230	6	the	the	DT
cord-346267-l08ld2cy	230	7	most	most	RBS
cord-346267-l08ld2cy	230	8	realistic	realistic	JJ
cord-346267-l08ld2cy	230	9	models	model	NNS
cord-346267-l08ld2cy	230	10	are	be	VBP
cord-346267-l08ld2cy	230	11	likely	likely	JJ
cord-346267-l08ld2cy	230	12	to	to	TO
cord-346267-l08ld2cy	230	13	fail	fail	VB
cord-346267-l08ld2cy	230	14	and	and	CC
cord-346267-l08ld2cy	230	15	external	external	JJ
cord-346267-l08ld2cy	230	16	information	information	NN
cord-346267-l08ld2cy	230	17	,	,	,
cord-346267-l08ld2cy	230	18	such	such	JJ
cord-346267-l08ld2cy	230	19	as	as	IN
cord-346267-l08ld2cy	230	20	biogeography	biogeography	NN
cord-346267-l08ld2cy	230	21	and	and	CC
cord-346267-l08ld2cy	230	22	homology	homology	NN
cord-346267-l08ld2cy	230	23	to	to	IN
cord-346267-l08ld2cy	230	24	endogenous	endogenous	JJ
cord-346267-l08ld2cy	230	25	viral	viral	JJ
cord-346267-l08ld2cy	230	26	elements	element	NNS
cord-346267-l08ld2cy	230	27	,	,	,
cord-346267-l08ld2cy	230	28	must	must	MD
cord-346267-l08ld2cy	230	29	be	be	VB
cord-346267-l08ld2cy	230	30	brought	bring	VBN
cord-346267-l08ld2cy	230	31	into	into	IN
cord-346267-l08ld2cy	230	32	consideration	consideration	NN
cord-346267-l08ld2cy	230	33	to	to	TO
cord-346267-l08ld2cy	230	34	estimate	estimate	VB
cord-346267-l08ld2cy	230	35	truly	truly	RB
cord-346267-l08ld2cy	230	36	ancient	ancient	JJ
cord-346267-l08ld2cy	230	37	events	event	NNS
cord-346267-l08ld2cy	230	38	(	(	-LRB-
cord-346267-l08ld2cy	230	39	Katzourakis	Katzourakis	NNP
cord-346267-l08ld2cy	230	40	et	et	NNP
cord-346267-l08ld2cy	230	41	al	al	NNP
cord-346267-l08ld2cy	230	42	.	.	.
cord-346267-l08ld2cy	230	43	2009	2009	CD
cord-346267-l08ld2cy	230	44	;	;	.
cord-346267-l08ld2cy	231	1	Katzourakis	Katzourakis	NNP
cord-346267-l08ld2cy	231	2	and	and	CC
cord-346267-l08ld2cy	231	3	Gifford	Gifford	NNP
cord-346267-l08ld2cy	231	4	2010	2010	CD
cord-346267-l08ld2cy	231	5	)	)	-RRB-
cord-346267-l08ld2cy	231	6	.	.	.
cord-346267-l08ld2cy	232	1	The	the	DT
cord-346267-l08ld2cy	232	2	precise	precise	JJ
cord-346267-l08ld2cy	232	3	age	age	NN
cord-346267-l08ld2cy	232	4	of	of	IN
cord-346267-l08ld2cy	232	5	measles	measle	NNS
cord-346267-l08ld2cy	232	6	in	in	IN
cord-346267-l08ld2cy	232	7	the	the	DT
cord-346267-l08ld2cy	232	8	human	human	JJ
cord-346267-l08ld2cy	232	9	population	population	NN
cord-346267-l08ld2cy	232	10	remains	remain	VBZ
cord-346267-l08ld2cy	232	11	elusive	elusive	JJ
cord-346267-l08ld2cy	232	12	.	.	.
cord-346267-l08ld2cy	233	1	The	the	DT
cord-346267-l08ld2cy	233	2	domestication	domestication	NN
cord-346267-l08ld2cy	233	3	of	of	IN
cord-346267-l08ld2cy	233	4	cattle	cattle	NNS
cord-346267-l08ld2cy	233	5	beginning	begin	VBG
cord-346267-l08ld2cy	233	6	10	10	CD
cord-346267-l08ld2cy	233	7	,	,	,
cord-346267-l08ld2cy	233	8	000	000	CD
cord-346267-l08ld2cy	233	9	years	year	NNS
cord-346267-l08ld2cy	233	10	ago	ago	RB
cord-346267-l08ld2cy	233	11	provided	provide	VBD
cord-346267-l08ld2cy	233	12	the	the	DT
cord-346267-l08ld2cy	233	13	necessary	necessary	JJ
cord-346267-l08ld2cy	233	14	exposure	exposure	NN
cord-346267-l08ld2cy	233	15	to	to	IN
cord-346267-l08ld2cy	233	16	RPV	RPV	NNP
cord-346267-l08ld2cy	233	17	,	,	,
cord-346267-l08ld2cy	233	18	and	and	CC
cord-346267-l08ld2cy	233	19	the	the	DT
cord-346267-l08ld2cy	233	20	development	development	NN
cord-346267-l08ld2cy	233	21	of	of	IN
cord-346267-l08ld2cy	233	22	agriculture	agriculture	NN
cord-346267-l08ld2cy	233	23	allowed	allow	VBD
cord-346267-l08ld2cy	233	24	human	human	JJ
cord-346267-l08ld2cy	233	25	populations	population	NNS
cord-346267-l08ld2cy	233	26	to	to	TO
cord-346267-l08ld2cy	233	27	reach	reach	VB
cord-346267-l08ld2cy	233	28	sizes	size	NNS
cord-346267-l08ld2cy	233	29	necessary	necessary	JJ
cord-346267-l08ld2cy	233	30	to	to	TO
cord-346267-l08ld2cy	233	31	sustain	sustain	VB
cord-346267-l08ld2cy	233	32	an	an	DT
cord-346267-l08ld2cy	233	33	epidemic	epidemic	NN
cord-346267-l08ld2cy	233	34	.	.	.
cord-346267-l08ld2cy	234	1	However	however	RB
cord-346267-l08ld2cy	234	2	,	,	,
cord-346267-l08ld2cy	234	3	the	the	DT
cord-346267-l08ld2cy	234	4	historical	historical	JJ
cord-346267-l08ld2cy	234	5	record	record	NN
cord-346267-l08ld2cy	234	6	of	of	IN
cord-346267-l08ld2cy	234	7	measles	measle	NNS
cord-346267-l08ld2cy	234	8	is	be	VBZ
cord-346267-l08ld2cy	234	9	ambiguous	ambiguous	JJ
cord-346267-l08ld2cy	234	10	until	until	IN
cord-346267-l08ld2cy	234	11	the	the	DT
cord-346267-l08ld2cy	234	12	ninth	ninth	JJ
cord-346267-l08ld2cy	234	13	century	century	NN
cord-346267-l08ld2cy	234	14	,	,	,
cord-346267-l08ld2cy	234	15	when	when	WRB
cord-346267-l08ld2cy	234	16	Rhazes	Rhazes	NNP
cord-346267-l08ld2cy	234	17	(	(	-LRB-
cord-346267-l08ld2cy	234	18	a	a	DT
cord-346267-l08ld2cy	234	19	Persian	persian	JJ
cord-346267-l08ld2cy	234	20	physician	physician	NN
cord-346267-l08ld2cy	234	21	)	)	-RRB-
cord-346267-l08ld2cy	234	22	outlined	outline	VBD
cord-346267-l08ld2cy	234	23	the	the	DT
cord-346267-l08ld2cy	234	24	criteria	criterion	NNS
cord-346267-l08ld2cy	234	25	for	for	IN
cord-346267-l08ld2cy	234	26	differentiating	differentiate	VBG
cord-346267-l08ld2cy	234	27	between	between	IN
cord-346267-l08ld2cy	234	28	measles	measle	NNS
cord-346267-l08ld2cy	234	29	and	and	CC
cord-346267-l08ld2cy	234	30	smallpox	smallpox	NN
cord-346267-l08ld2cy	234	31	(	(	-LRB-
cord-346267-l08ld2cy	234	32	Rāzī	Rāzī	NNP
cord-346267-l08ld2cy	234	33	1848	1848	CD
cord-346267-l08ld2cy	234	34	)	)	-RRB-
cord-346267-l08ld2cy	234	35	.	.	.
cord-346267-l08ld2cy	235	1	Rhazes	Rhazes	NNP
cord-346267-l08ld2cy	235	2	discusses	discuss	VBZ
cord-346267-l08ld2cy	235	3	both	both	DT
cord-346267-l08ld2cy	235	4	ailments	ailment	NNS
cord-346267-l08ld2cy	235	5	as	as	IN
cord-346267-l08ld2cy	235	6	immemorial	immemorial	JJ
cord-346267-l08ld2cy	235	7	,	,	,
cord-346267-l08ld2cy	235	8	indicating	indicate	VBG
cord-346267-l08ld2cy	235	9	that	that	IN
cord-346267-l08ld2cy	235	10	both	both	DT
cord-346267-l08ld2cy	235	11	diseases	disease	NNS
cord-346267-l08ld2cy	235	12	predated	predate	VBD
cord-346267-l08ld2cy	235	13	him	-PRON-	PRP
cord-346267-l08ld2cy	235	14	by	by	IN
cord-346267-l08ld2cy	235	15	many	many	JJ
cord-346267-l08ld2cy	235	16	generations	generation	NNS
cord-346267-l08ld2cy	235	17	.	.	.
cord-346267-l08ld2cy	236	1	Although	although	IN
cord-346267-l08ld2cy	236	2	there	there	EX
cord-346267-l08ld2cy	236	3	are	be	VBP
cord-346267-l08ld2cy	236	4	historical	historical	JJ
cord-346267-l08ld2cy	236	5	records	record	NNS
cord-346267-l08ld2cy	236	6	of	of	IN
cord-346267-l08ld2cy	236	7	earlier	early	JJR
cord-346267-l08ld2cy	236	8	plagues	plague	NNS
cord-346267-l08ld2cy	236	9	that	that	WDT
cord-346267-l08ld2cy	236	10	could	could	MD
cord-346267-l08ld2cy	236	11	be	be	VB
cord-346267-l08ld2cy	236	12	interpreted	interpret	VBN
cord-346267-l08ld2cy	236	13	as	as	IN
cord-346267-l08ld2cy	236	14	measles	measle	NNS
cord-346267-l08ld2cy	236	15	,	,	,
cord-346267-l08ld2cy	236	16	notably	notably	RB
cord-346267-l08ld2cy	236	17	in	in	IN
cord-346267-l08ld2cy	236	18	eighth	eighth	JJ
cord-346267-l08ld2cy	236	19	century	century	NN
cord-346267-l08ld2cy	236	20	France	France	NNP
cord-346267-l08ld2cy	236	21	during	during	IN
cord-346267-l08ld2cy	236	22	the	the	DT
cord-346267-l08ld2cy	236	23	battle	battle	NN
cord-346267-l08ld2cy	236	24	of	of	IN
cord-346267-l08ld2cy	236	25	Tours	Tours	NNP
cord-346267-l08ld2cy	236	26	(	(	-LRB-
cord-346267-l08ld2cy	236	27	Rolleston	Rolleston	NNP
cord-346267-l08ld2cy	236	28	1937	1937	CD
cord-346267-l08ld2cy	236	29	)	)	-RRB-
cord-346267-l08ld2cy	236	30	,	,	,
cord-346267-l08ld2cy	236	31	it	-PRON-	PRP
cord-346267-l08ld2cy	236	32	is	be	VBZ
cord-346267-l08ld2cy	236	33	also	also	RB
cord-346267-l08ld2cy	236	34	possible	possible	JJ
cord-346267-l08ld2cy	236	35	that	that	IN
cord-346267-l08ld2cy	236	36	this	this	DT
cord-346267-l08ld2cy	236	37	plague	plague	NN
cord-346267-l08ld2cy	236	38	could	could	MD
cord-346267-l08ld2cy	236	39	have	have	VB
cord-346267-l08ld2cy	236	40	been	be	VBN
cord-346267-l08ld2cy	236	41	smallpox	smallpox	NN
cord-346267-l08ld2cy	236	42	or	or	CC
cord-346267-l08ld2cy	236	43	another	another	DT
cord-346267-l08ld2cy	236	44	disease	disease	NN
cord-346267-l08ld2cy	236	45	with	with	IN
cord-346267-l08ld2cy	236	46	similar	similar	JJ
cord-346267-l08ld2cy	236	47	presentation	presentation	NN
cord-346267-l08ld2cy	236	48	.	.	.
cord-346267-l08ld2cy	237	1	Even	even	RB
cord-346267-l08ld2cy	237	2	after	after	IN
cord-346267-l08ld2cy	237	3	Rhazes	Rhazes	NNPS
cord-346267-l08ld2cy	237	4	description	description	NN
cord-346267-l08ld2cy	237	5	,	,	,
cord-346267-l08ld2cy	237	6	Western	western	JJ
cord-346267-l08ld2cy	237	7	medicine	medicine	NN
cord-346267-l08ld2cy	237	8	still	still	RB
cord-346267-l08ld2cy	237	9	confounded	confound	VBD
cord-346267-l08ld2cy	237	10	measles	measle	NNS
cord-346267-l08ld2cy	237	11	,	,	,
cord-346267-l08ld2cy	237	12	smallpox	smallpox	NN
cord-346267-l08ld2cy	237	13	,	,	,
cord-346267-l08ld2cy	237	14	and	and	CC
cord-346267-l08ld2cy	237	15	scarlet	scarlet	JJ
cord-346267-l08ld2cy	237	16	fever	fever	NN
cord-346267-l08ld2cy	237	17	until	until	IN
cord-346267-l08ld2cy	237	18	the	the	DT
cord-346267-l08ld2cy	237	19	17th	17th	JJ
cord-346267-l08ld2cy	237	20	century	century	NN
cord-346267-l08ld2cy	237	21	(	(	-LRB-
cord-346267-l08ld2cy	237	22	Rolleston	Rolleston	NNP
cord-346267-l08ld2cy	237	23	1937	1937	CD
cord-346267-l08ld2cy	237	24	)	)	-RRB-
cord-346267-l08ld2cy	237	25	.	.	.
cord-346267-l08ld2cy	238	1	In	in	IN
cord-346267-l08ld2cy	238	2	light	light	NN
cord-346267-l08ld2cy	238	3	of	of	IN
cord-346267-l08ld2cy	238	4	this	this	DT
cord-346267-l08ld2cy	238	5	confusion	confusion	NN
cord-346267-l08ld2cy	238	6	,	,	,
cord-346267-l08ld2cy	238	7	the	the	DT
cord-346267-l08ld2cy	238	8	lack	lack	NN
cord-346267-l08ld2cy	238	9	of	of	IN
cord-346267-l08ld2cy	238	10	a	a	DT
cord-346267-l08ld2cy	238	11	definitive	definitive	JJ
cord-346267-l08ld2cy	238	12	description	description	NN
cord-346267-l08ld2cy	238	13	of	of	IN
cord-346267-l08ld2cy	238	14	measles	measle	NNS
cord-346267-l08ld2cy	238	15	before	before	IN
cord-346267-l08ld2cy	238	16	Rhazes	Rhazes	NNPS
cord-346267-l08ld2cy	238	17	(	(	-LRB-
cord-346267-l08ld2cy	238	18	e.g.	e.g.	RB
cord-346267-l08ld2cy	238	19	,	,	,
cord-346267-l08ld2cy	238	20	Galen	Galen	NNP
cord-346267-l08ld2cy	238	21	,	,	,
cord-346267-l08ld2cy	238	22	an	an	DT
cord-346267-l08ld2cy	238	23	ancient	ancient	JJ
cord-346267-l08ld2cy	238	24	Roman	roman	JJ
cord-346267-l08ld2cy	238	25	physician	physician	NN
cord-346267-l08ld2cy	238	26	,	,	,
cord-346267-l08ld2cy	238	27	described	describe	VBD
cord-346267-l08ld2cy	238	28	smallpox	smallpox	NN
cord-346267-l08ld2cy	238	29	but	but	CC
cord-346267-l08ld2cy	238	30	not	not	RB
cord-346267-l08ld2cy	238	31	measles	measles	NN
cord-346267-l08ld2cy	238	32	)	)	-RRB-
cord-346267-l08ld2cy	238	33	does	do	VBZ
cord-346267-l08ld2cy	238	34	not	not	RB
cord-346267-l08ld2cy	238	35	establish	establish	VB
cord-346267-l08ld2cy	238	36	that	that	IN
cord-346267-l08ld2cy	238	37	the	the	DT
cord-346267-l08ld2cy	238	38	virus	virus	NN
cord-346267-l08ld2cy	238	39	was	be	VBD
cord-346267-l08ld2cy	238	40	absent	absent	JJ
cord-346267-l08ld2cy	238	41	(	(	-LRB-
cord-346267-l08ld2cy	238	42	McNeill	McNeill	NNP
cord-346267-l08ld2cy	238	43	1976	1976	CD
cord-346267-l08ld2cy	238	44	)	)	-RRB-
cord-346267-l08ld2cy	238	45	.	.	.
cord-346267-l08ld2cy	239	1	It	-PRON-	PRP
cord-346267-l08ld2cy	239	2	is	be	VBZ
cord-346267-l08ld2cy	239	3	plausible	plausible	JJ
cord-346267-l08ld2cy	239	4	that	that	IN
cord-346267-l08ld2cy	239	5	MeV	MeV	NNP
cord-346267-l08ld2cy	239	6	might	may	MD
cord-346267-l08ld2cy	239	7	have	have	VB
cord-346267-l08ld2cy	239	8	not	not	RB
cord-346267-l08ld2cy	239	9	entered	enter	VBN
cord-346267-l08ld2cy	239	10	the	the	DT
cord-346267-l08ld2cy	239	11	human	human	JJ
cord-346267-l08ld2cy	239	12	population	population	NN
cord-346267-l08ld2cy	239	13	until	until	IN
cord-346267-l08ld2cy	239	14	the	the	DT
cord-346267-l08ld2cy	239	15	first	first	JJ
cord-346267-l08ld2cy	239	16	millennium	millennium	NN
cord-346267-l08ld2cy	239	17	of	of	IN
cord-346267-l08ld2cy	239	18	the	the	DT
cord-346267-l08ld2cy	239	19	Common	Common	NNP
cord-346267-l08ld2cy	239	20	Era	Era	NNP
cord-346267-l08ld2cy	239	21	,	,	,
cord-346267-l08ld2cy	239	22	as	as	IN
cord-346267-l08ld2cy	239	23	our	-PRON-	PRP$
cord-346267-l08ld2cy	239	24	analysis	analysis	NN
cord-346267-l08ld2cy	239	25	suggests	suggest	VBZ
cord-346267-l08ld2cy	239	26	.	.	.
cord-346267-l08ld2cy	240	1	Alternatively	alternatively	RB
cord-346267-l08ld2cy	240	2	,	,	,
cord-346267-l08ld2cy	240	3	MeV	MeV	NNP
cord-346267-l08ld2cy	240	4	could	could	MD
cord-346267-l08ld2cy	240	5	have	have	VB
cord-346267-l08ld2cy	240	6	emerged	emerge	VBN
cord-346267-l08ld2cy	240	7	thousands	thousand	NNS
cord-346267-l08ld2cy	240	8	of	of	IN
cord-346267-l08ld2cy	240	9	years	year	NNS
cord-346267-l08ld2cy	240	10	ago	ago	RB
cord-346267-l08ld2cy	240	11	,	,	,
cord-346267-l08ld2cy	240	12	and	and	CC
cord-346267-l08ld2cy	240	13	the	the	DT
cord-346267-l08ld2cy	240	14	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	240	15	models	model	NNS
cord-346267-l08ld2cy	240	16	employed	employ	VBN
cord-346267-l08ld2cy	240	17	here	here	RB
cord-346267-l08ld2cy	240	18	are	be	VBP
cord-346267-l08ld2cy	240	19	too	too	RB
cord-346267-l08ld2cy	240	20	crude	crude	JJ
cord-346267-l08ld2cy	240	21	to	to	TO
cord-346267-l08ld2cy	240	22	recover	recover	VB
cord-346267-l08ld2cy	240	23	the	the	DT
cord-346267-l08ld2cy	240	24	true	true	JJ
cord-346267-l08ld2cy	240	25	age	age	NN
cord-346267-l08ld2cy	240	26	of	of	IN
cord-346267-l08ld2cy	240	27	the	the	DT
cord-346267-l08ld2cy	240	28	virus	virus	NN
cord-346267-l08ld2cy	240	29	.	.	.
cord-346267-l08ld2cy	241	1	Regardless	regardless	RB
cord-346267-l08ld2cy	241	2	of	of	IN
cord-346267-l08ld2cy	241	3	which	which	WDT
cord-346267-l08ld2cy	241	4	scenario	scenario	NN
cord-346267-l08ld2cy	241	5	is	be	VBZ
cord-346267-l08ld2cy	241	6	correct	correct	JJ
cord-346267-l08ld2cy	241	7	,	,	,
cord-346267-l08ld2cy	241	8	accounting	account	VBG
cord-346267-l08ld2cy	241	9	for	for	IN
cord-346267-l08ld2cy	241	10	variable	variable	JJ
cord-346267-l08ld2cy	241	11	selective	selective	JJ
cord-346267-l08ld2cy	241	12	pressures	pressure	NNS
cord-346267-l08ld2cy	241	13	is	be	VBZ
cord-346267-l08ld2cy	241	14	an	an	DT
cord-346267-l08ld2cy	241	15	important	important	JJ
cord-346267-l08ld2cy	241	16	step	step	NN
cord-346267-l08ld2cy	241	17	in	in	IN
cord-346267-l08ld2cy	241	18	revealing	reveal	VBG
cord-346267-l08ld2cy	241	19	the	the	DT
cord-346267-l08ld2cy	241	20	ancient	ancient	JJ
cord-346267-l08ld2cy	241	21	history	history	NN
cord-346267-l08ld2cy	241	22	of	of	IN
cord-346267-l08ld2cy	241	23	RNA	RNA	NNP
cord-346267-l08ld2cy	241	24	viruses	virus	NNS
cord-346267-l08ld2cy	241	25	.	.	.
cord-346267-l08ld2cy	242	1	The	the	DT
cord-346267-l08ld2cy	242	2	different	different	JJ
cord-346267-l08ld2cy	242	3	timescales	timescale	NNS
cord-346267-l08ld2cy	242	4	affecting	affect	VBG
cord-346267-l08ld2cy	242	5	mutation	mutation	NN
cord-346267-l08ld2cy	242	6	rates	rate	NNS
cord-346267-l08ld2cy	242	7	and	and	CC
cord-346267-l08ld2cy	242	8	substitution	substitution	NN
cord-346267-l08ld2cy	242	9	rates	rate	NNS
cord-346267-l08ld2cy	242	10	make	make	VBP
cord-346267-l08ld2cy	242	11	it	-PRON-	PRP
cord-346267-l08ld2cy	242	12	difficult	difficult	JJ
cord-346267-l08ld2cy	242	13	to	to	TO
cord-346267-l08ld2cy	242	14	extrapolate	extrapolate	VB
cord-346267-l08ld2cy	242	15	population	population	NN
cord-346267-l08ld2cy	242	16	-	-	HYPH
cord-346267-l08ld2cy	242	17	based	base	VBN
cord-346267-l08ld2cy	242	18	estimates	estimate	NNS
cord-346267-l08ld2cy	242	19	of	of	IN
cord-346267-l08ld2cy	242	20	rates	rate	NNS
cord-346267-l08ld2cy	242	21	over	over	IN
cord-346267-l08ld2cy	242	22	a	a	DT
cord-346267-l08ld2cy	242	23	long	long	JJ
cord-346267-l08ld2cy	242	24	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	242	25	time	time	NN
cord-346267-l08ld2cy	242	26	(	(	-LRB-
cord-346267-l08ld2cy	242	27	Ho	Ho	NNP
cord-346267-l08ld2cy	242	28	et	et	FW
cord-346267-l08ld2cy	242	29	al	al	NNP
cord-346267-l08ld2cy	242	30	.	.	NNP
cord-346267-l08ld2cy	242	31	2005	2005	CD
cord-346267-l08ld2cy	242	32	)	)	-RRB-
cord-346267-l08ld2cy	242	33	;	;	:
cord-346267-l08ld2cy	242	34	however	however	RB
cord-346267-l08ld2cy	242	35	,	,	,
cord-346267-l08ld2cy	242	36	it	-PRON-	PRP
cord-346267-l08ld2cy	242	37	is	be	VBZ
cord-346267-l08ld2cy	242	38	unlikely	unlikely	JJ
cord-346267-l08ld2cy	242	39	that	that	IN
cord-346267-l08ld2cy	242	40	purifying	purify	VBG
cord-346267-l08ld2cy	242	41	selection	selection	NN
cord-346267-l08ld2cy	242	42	alone	alone	RB
cord-346267-l08ld2cy	242	43	can	can	MD
cord-346267-l08ld2cy	242	44	account	account	VB
cord-346267-l08ld2cy	242	45	for	for	IN
cord-346267-l08ld2cy	242	46	this	this	DT
cord-346267-l08ld2cy	242	47	difference	difference	NN
cord-346267-l08ld2cy	242	48	between	between	IN
cord-346267-l08ld2cy	242	49	short	short	JJ
cord-346267-l08ld2cy	242	50	-	-	HYPH
cord-346267-l08ld2cy	242	51	and	and	CC
cord-346267-l08ld2cy	242	52	long	long	JJ
cord-346267-l08ld2cy	242	53	-	-	HYPH
cord-346267-l08ld2cy	242	54	term	term	NN
cord-346267-l08ld2cy	242	55	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	242	56	rates	rate	NNS
cord-346267-l08ld2cy	242	57	(	(	-LRB-
cord-346267-l08ld2cy	242	58	Woodhams	Woodhams	NNP
cord-346267-l08ld2cy	242	59	2006	2006	CD
cord-346267-l08ld2cy	242	60	)	)	-RRB-
cord-346267-l08ld2cy	242	61	.	.	.
cord-346267-l08ld2cy	243	1	Furthermore	furthermore	RB
cord-346267-l08ld2cy	243	2	,	,	,
cord-346267-l08ld2cy	243	3	short	short	JJ
cord-346267-l08ld2cy	243	4	-	-	HYPH
cord-346267-l08ld2cy	243	5	term	term	NN
cord-346267-l08ld2cy	243	6	estimates	estimate	NNS
cord-346267-l08ld2cy	243	7	of	of	IN
cord-346267-l08ld2cy	243	8	viral	viral	JJ
cord-346267-l08ld2cy	243	9	substitution	substitution	NN
cord-346267-l08ld2cy	243	10	rates	rate	NNS
cord-346267-l08ld2cy	243	11	(	(	-LRB-
cord-346267-l08ld2cy	243	12	inferred	infer	VBN
cord-346267-l08ld2cy	243	13	from	from	IN
cord-346267-l08ld2cy	243	14	population	population	NN
cord-346267-l08ld2cy	243	15	-	-	HYPH
cord-346267-l08ld2cy	243	16	based	base	VBN
cord-346267-l08ld2cy	243	17	rate	rate	NN
cord-346267-l08ld2cy	243	18	estimates	estimate	NNS
cord-346267-l08ld2cy	243	19	at	at	IN
cord-346267-l08ld2cy	243	20	the	the	DT
cord-346267-l08ld2cy	243	21	tips	tip	NNS
cord-346267-l08ld2cy	243	22	of	of	IN
cord-346267-l08ld2cy	243	23	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	243	24	)	)	-RRB-
cord-346267-l08ld2cy	243	25	are	be	VBP
cord-346267-l08ld2cy	243	26	often	often	RB
cord-346267-l08ld2cy	243	27	found	find	VBN
cord-346267-l08ld2cy	243	28	to	to	TO
cord-346267-l08ld2cy	243	29	be	be	VB
cord-346267-l08ld2cy	243	30	several	several	JJ
cord-346267-l08ld2cy	243	31	orders	order	NNS
cord-346267-l08ld2cy	243	32	of	of	IN
cord-346267-l08ld2cy	243	33	magnitude	magnitude	NN
cord-346267-l08ld2cy	243	34	faster	fast	RBR
cord-346267-l08ld2cy	243	35	than	than	IN
cord-346267-l08ld2cy	243	36	long	long	JJ
cord-346267-l08ld2cy	243	37	-	-	HYPH
cord-346267-l08ld2cy	243	38	term	term	NN
cord-346267-l08ld2cy	243	39	estimates	estimate	NNS
cord-346267-l08ld2cy	243	40	of	of	IN
cord-346267-l08ld2cy	243	41	substitution	substitution	NN
cord-346267-l08ld2cy	243	42	rates	rate	NNS
cord-346267-l08ld2cy	243	43	(	(	-LRB-
cord-346267-l08ld2cy	243	44	inferred	infer	VBN
cord-346267-l08ld2cy	243	45	from	from	IN
cord-346267-l08ld2cy	243	46	external	external	JJ
cord-346267-l08ld2cy	243	47	calibrations	calibration	NNS
cord-346267-l08ld2cy	243	48	located	locate	VBN
cord-346267-l08ld2cy	243	49	deeper	deeply	RBR
cord-346267-l08ld2cy	243	50	in	in	IN
cord-346267-l08ld2cy	243	51	the	the	DT
cord-346267-l08ld2cy	243	52	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	243	53	)	)	-RRB-
cord-346267-l08ld2cy	243	54	.	.	.
cord-346267-l08ld2cy	244	1	This	this	DT
cord-346267-l08ld2cy	244	2	inconsistency	inconsistency	NN
cord-346267-l08ld2cy	244	3	has	have	VBZ
cord-346267-l08ld2cy	244	4	been	be	VBN
cord-346267-l08ld2cy	244	5	reported	report	VBN
cord-346267-l08ld2cy	244	6	for	for	IN
cord-346267-l08ld2cy	244	7	hepatitis	hepatitis	NN
cord-346267-l08ld2cy	244	8	B	B	NNP
cord-346267-l08ld2cy	244	9	virus	virus	NN
cord-346267-l08ld2cy	244	10	(	(	-LRB-
cord-346267-l08ld2cy	244	11	Zhou	Zhou	NNP
cord-346267-l08ld2cy	244	12	and	and	CC
cord-346267-l08ld2cy	244	13	Holmes	Holmes	NNP
cord-346267-l08ld2cy	244	14	2007	2007	CD
cord-346267-l08ld2cy	244	15	;	;	:
cord-346267-l08ld2cy	244	16	Gilbert	Gilbert	NNP
cord-346267-l08ld2cy	244	17	and	and	CC
cord-346267-l08ld2cy	244	18	Feschotte	Feschotte	NNP
cord-346267-l08ld2cy	244	19	2010	2010	CD
cord-346267-l08ld2cy	244	20	)	)	-RRB-
cord-346267-l08ld2cy	244	21	and	and	CC
cord-346267-l08ld2cy	244	22	simian	simian	JJ
cord-346267-l08ld2cy	244	23	immunodeficiency	immunodeficiency	NN
cord-346267-l08ld2cy	244	24	virus	virus	NN
cord-346267-l08ld2cy	244	25	(	(	-LRB-
cord-346267-l08ld2cy	244	26	Wertheim	Wertheim	NNP
cord-346267-l08ld2cy	244	27	and	and	CC
cord-346267-l08ld2cy	244	28	Worobey	Worobey	NNP
cord-346267-l08ld2cy	244	29	2009a	2009a	CD
cord-346267-l08ld2cy	244	30	;	;	:
cord-346267-l08ld2cy	244	31	Worobey	Worobey	NNP
cord-346267-l08ld2cy	244	32	et	et	NNP
cord-346267-l08ld2cy	244	33	al	al	NNP
cord-346267-l08ld2cy	244	34	.	.	NNP
cord-346267-l08ld2cy	244	35	2010	2010	CD
cord-346267-l08ld2cy	244	36	)	)	-RRB-
cord-346267-l08ld2cy	244	37	,	,	.
cord-346267-l08ld2cy	245	1	suggesting	suggest	VBG
cord-346267-l08ld2cy	245	2	that	that	IN
cord-346267-l08ld2cy	245	3	long	long	JJ
cord-346267-l08ld2cy	245	4	-	-	HYPH
cord-346267-l08ld2cy	245	5	term	term	NN
cord-346267-l08ld2cy	245	6	substitution	substitution	NN
cord-346267-l08ld2cy	245	7	rates	rate	NNS
cord-346267-l08ld2cy	245	8	can	can	MD
cord-346267-l08ld2cy	245	9	be	be	VB
cord-346267-l08ld2cy	245	10	orders	order	NNS
cord-346267-l08ld2cy	245	11	of	of	IN
cord-346267-l08ld2cy	245	12	magnitude	magnitude	NN
cord-346267-l08ld2cy	245	13	lower	low	JJR
cord-346267-l08ld2cy	245	14	than	than	IN
cord-346267-l08ld2cy	245	15	short	short	JJ
cord-346267-l08ld2cy	245	16	-	-	HYPH
cord-346267-l08ld2cy	245	17	term	term	NN
cord-346267-l08ld2cy	245	18	substitution	substitution	NN
cord-346267-l08ld2cy	245	19	rates	rate	NNS
cord-346267-l08ld2cy	245	20	.	.	.
cord-346267-l08ld2cy	246	1	An	an	DT
cord-346267-l08ld2cy	246	2	alternative	alternative	NN
cord-346267-l08ld2cy	246	3	,	,	,
cord-346267-l08ld2cy	246	4	and	and	CC
cord-346267-l08ld2cy	246	5	more	more	RBR
cord-346267-l08ld2cy	246	6	parsimonious	parsimonious	JJ
cord-346267-l08ld2cy	246	7	,	,	,
cord-346267-l08ld2cy	246	8	explanation	explanation	NN
cord-346267-l08ld2cy	246	9	is	be	VBZ
cord-346267-l08ld2cy	246	10	that	that	IN
cord-346267-l08ld2cy	246	11	a	a	DT
cord-346267-l08ld2cy	246	12	single	single	JJ
cord-346267-l08ld2cy	246	13	substitution	substitution	NN
cord-346267-l08ld2cy	246	14	rate	rate	NN
cord-346267-l08ld2cy	246	15	(	(	-LRB-
cord-346267-l08ld2cy	246	16	albeit	albeit	IN
cord-346267-l08ld2cy	246	17	one	one	CD
cord-346267-l08ld2cy	246	18	possibly	possibly	RB
cord-346267-l08ld2cy	246	19	slower	slow	JJR
cord-346267-l08ld2cy	246	20	than	than	IN
cord-346267-l08ld2cy	246	21	that	that	DT
cord-346267-l08ld2cy	246	22	inferred	infer	VBN
cord-346267-l08ld2cy	246	23	using	use	VBG
cord-346267-l08ld2cy	246	24	short	short	JJ
cord-346267-l08ld2cy	246	25	-	-	HYPH
cord-346267-l08ld2cy	246	26	term	term	NN
cord-346267-l08ld2cy	246	27	population	population	NN
cord-346267-l08ld2cy	246	28	-	-	HYPH
cord-346267-l08ld2cy	246	29	based	base	VBN
cord-346267-l08ld2cy	246	30	data	datum	NNS
cord-346267-l08ld2cy	246	31	)	)	-RRB-
cord-346267-l08ld2cy	246	32	predominates	predominate	VBZ
cord-346267-l08ld2cy	246	33	throughout	throughout	IN
cord-346267-l08ld2cy	246	34	the	the	DT
cord-346267-l08ld2cy	246	35	history	history	NN
cord-346267-l08ld2cy	246	36	of	of	IN
cord-346267-l08ld2cy	246	37	these	these	DT
cord-346267-l08ld2cy	246	38	viruses	virus	NNS
cord-346267-l08ld2cy	246	39	.	.	.
cord-346267-l08ld2cy	247	1	And	and	CC
cord-346267-l08ld2cy	247	2	our	-PRON-	PRP$
cord-346267-l08ld2cy	247	3	inability	inability	NN
cord-346267-l08ld2cy	247	4	to	to	TO
cord-346267-l08ld2cy	247	5	accurately	accurately	RB
cord-346267-l08ld2cy	247	6	estimate	estimate	VB
cord-346267-l08ld2cy	247	7	branch	branch	NN
cord-346267-l08ld2cy	247	8	lengths	length	NNS
cord-346267-l08ld2cy	247	9	creates	create	VBZ
cord-346267-l08ld2cy	247	10	the	the	DT
cord-346267-l08ld2cy	247	11	appearance	appearance	NN
cord-346267-l08ld2cy	247	12	of	of	IN
cord-346267-l08ld2cy	247	13	dramatically	dramatically	RB
cord-346267-l08ld2cy	247	14	lower	low	JJR
cord-346267-l08ld2cy	247	15	substitution	substitution	NN
cord-346267-l08ld2cy	247	16	rates	rate	NNS
cord-346267-l08ld2cy	247	17	deep	deep	JJ
cord-346267-l08ld2cy	247	18	in	in	IN
cord-346267-l08ld2cy	247	19	the	the	DT
cord-346267-l08ld2cy	247	20	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	247	21	tree	tree	NN
cord-346267-l08ld2cy	247	22	.	.	.
cord-346267-l08ld2cy	248	1	Although	although	IN
cord-346267-l08ld2cy	248	2	the	the	DT
cord-346267-l08ld2cy	248	3	methods	method	NNS
cord-346267-l08ld2cy	248	4	presented	present	VBN
cord-346267-l08ld2cy	248	5	here	here	RB
cord-346267-l08ld2cy	248	6	do	do	VBP
cord-346267-l08ld2cy	248	7	not	not	RB
cord-346267-l08ld2cy	248	8	correct	correct	VB
cord-346267-l08ld2cy	248	9	for	for	IN
cord-346267-l08ld2cy	248	10	branch	branch	NN
cord-346267-l08ld2cy	248	11	lengths	length	NNS
cord-346267-l08ld2cy	248	12	on	on	IN
cord-346267-l08ld2cy	248	13	the	the	DT
cord-346267-l08ld2cy	248	14	order	order	NN
cord-346267-l08ld2cy	248	15	needed	need	VBD
cord-346267-l08ld2cy	248	16	to	to	TO
cord-346267-l08ld2cy	248	17	reconcile	reconcile	VB
cord-346267-l08ld2cy	248	18	short	short	JJ
cord-346267-l08ld2cy	248	19	-	-	HYPH
cord-346267-l08ld2cy	248	20	term	term	NN
cord-346267-l08ld2cy	248	21	substitution	substitution	NN
cord-346267-l08ld2cy	248	22	rates	rate	NNS
cord-346267-l08ld2cy	248	23	with	with	IN
cord-346267-l08ld2cy	248	24	deep	deep	JJ
cord-346267-l08ld2cy	248	25	calibrations	calibration	NNS
cord-346267-l08ld2cy	248	26	,	,	,
cord-346267-l08ld2cy	248	27	they	-PRON-	PRP
cord-346267-l08ld2cy	248	28	provide	provide	VBP
cord-346267-l08ld2cy	248	29	a	a	DT
cord-346267-l08ld2cy	248	30	glimpse	glimpse	NN
cord-346267-l08ld2cy	248	31	at	at	IN
cord-346267-l08ld2cy	248	32	the	the	DT
cord-346267-l08ld2cy	248	33	missing	missing	JJ
cord-346267-l08ld2cy	248	34	evolution	evolution	NN
cord-346267-l08ld2cy	248	35	that	that	IN
cord-346267-l08ld2cy	248	36	most	most	JJS
cord-346267-l08ld2cy	248	37	current	current	JJ
cord-346267-l08ld2cy	248	38	methods	method	NNS
cord-346267-l08ld2cy	248	39	of	of	IN
cord-346267-l08ld2cy	248	40	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	248	41	inference	inference	NN
cord-346267-l08ld2cy	248	42	fail	fail	VBP
cord-346267-l08ld2cy	248	43	to	to	TO
cord-346267-l08ld2cy	248	44	capture	capture	VB
cord-346267-l08ld2cy	248	45	.	.	.
cord-346267-l08ld2cy	249	1	Although	although	IN
cord-346267-l08ld2cy	249	2	we	-PRON-	PRP
cord-346267-l08ld2cy	249	3	are	be	VBP
cord-346267-l08ld2cy	249	4	unable	unable	JJ
cord-346267-l08ld2cy	249	5	to	to	TO
cord-346267-l08ld2cy	249	6	provide	provide	VB
cord-346267-l08ld2cy	249	7	a	a	DT
cord-346267-l08ld2cy	249	8	full	full	JJ
cord-346267-l08ld2cy	249	9	remedy	remedy	NN
cord-346267-l08ld2cy	249	10	to	to	IN
cord-346267-l08ld2cy	249	11	the	the	DT
cord-346267-l08ld2cy	249	12	problem	problem	NN
cord-346267-l08ld2cy	249	13	of	of	IN
cord-346267-l08ld2cy	249	14	underestimated	underestimated	JJ
cord-346267-l08ld2cy	249	15	branch	branch	NN
cord-346267-l08ld2cy	249	16	lengths	length	NNS
cord-346267-l08ld2cy	249	17	due	due	JJ
cord-346267-l08ld2cy	249	18	to	to	IN
cord-346267-l08ld2cy	249	19	purifying	purify	VBG
cord-346267-l08ld2cy	249	20	selection	selection	NN
cord-346267-l08ld2cy	249	21	,	,	,
cord-346267-l08ld2cy	249	22	our	-PRON-	PRP$
cord-346267-l08ld2cy	249	23	results	result	NNS
cord-346267-l08ld2cy	249	24	do	do	VBP
cord-346267-l08ld2cy	249	25	point	point	NN
cord-346267-l08ld2cy	249	26	to	to	IN
cord-346267-l08ld2cy	249	27	a	a	DT
cord-346267-l08ld2cy	249	28	couple	couple	NN
cord-346267-l08ld2cy	249	29	of	of	IN
cord-346267-l08ld2cy	249	30	guidelines	guideline	NNS
cord-346267-l08ld2cy	249	31	when	when	WRB
cord-346267-l08ld2cy	249	32	inferring	infer	VBG
cord-346267-l08ld2cy	249	33	tMRCAs	tmrcas	CD
cord-346267-l08ld2cy	249	34	in	in	IN
cord-346267-l08ld2cy	249	35	RNA	RNA	NNP
cord-346267-l08ld2cy	249	36	viruses	virus	NNS
cord-346267-l08ld2cy	249	37	.	.	.
cord-346267-l08ld2cy	250	1	First	first	RB
cord-346267-l08ld2cy	250	2	,	,	,
cord-346267-l08ld2cy	250	3	the	the	DT
cord-346267-l08ld2cy	250	4	inference	inference	NN
cord-346267-l08ld2cy	250	5	of	of	IN
cord-346267-l08ld2cy	250	6	substantially	substantially	RB
cord-346267-l08ld2cy	250	7	different	different	JJ
cord-346267-l08ld2cy	250	8	selective	selective	JJ
cord-346267-l08ld2cy	250	9	regimes	regime	NNS
cord-346267-l08ld2cy	250	10	on	on	IN
cord-346267-l08ld2cy	250	11	longer	long	JJR
cord-346267-l08ld2cy	250	12	internal	internal	JJ
cord-346267-l08ld2cy	250	13	branches	branch	NNS
cord-346267-l08ld2cy	250	14	compared	compare	VBN
cord-346267-l08ld2cy	250	15	with	with	IN
cord-346267-l08ld2cy	250	16	shorter	short	JJR
cord-346267-l08ld2cy	250	17	shallower	shallow	JJR
cord-346267-l08ld2cy	250	18	branches	branch	NNS
cord-346267-l08ld2cy	250	19	(	(	-LRB-
cord-346267-l08ld2cy	250	20	e.g.	e.g.	RB
cord-346267-l08ld2cy	250	21	,	,	,
cord-346267-l08ld2cy	250	22	using	use	VBG
cord-346267-l08ld2cy	250	23	Lineage+Dual	lineage+dual	JJ
cord-346267-l08ld2cy	250	24	,	,	,
cord-346267-l08ld2cy	250	25	,	,	,
cord-346267-l08ld2cy	250	26	or	or	CC
cord-346267-l08ld2cy	250	27	Free	Free	NNP
cord-346267-l08ld2cy	250	28	Ratio	Ratio	NNP
cord-346267-l08ld2cy	250	29	,	,	,
cord-346267-l08ld2cy	250	30	Yang	Yang	NNP
cord-346267-l08ld2cy	250	31	1998	1998	CD
cord-346267-l08ld2cy	250	32	,	,	,
cord-346267-l08ld2cy	250	33	codon	codon	NN
cord-346267-l08ld2cy	250	34	models	model	NNS
cord-346267-l08ld2cy	250	35	)	)	-RRB-
cord-346267-l08ld2cy	250	36	appears	appear	VBZ
cord-346267-l08ld2cy	250	37	to	to	TO
cord-346267-l08ld2cy	250	38	be	be	VB
cord-346267-l08ld2cy	250	39	a	a	DT
cord-346267-l08ld2cy	250	40	sign	sign	NN
cord-346267-l08ld2cy	250	41	that	that	IN
cord-346267-l08ld2cy	250	42	older	old	JJR
cord-346267-l08ld2cy	250	43	tMRCAs	tmrcas	PRP
cord-346267-l08ld2cy	250	44	may	may	MD
cord-346267-l08ld2cy	250	45	be	be	VB
cord-346267-l08ld2cy	250	46	underestimated	underestimate	VBN
cord-346267-l08ld2cy	250	47	.	.	.
cord-346267-l08ld2cy	251	1	Second	second	RB
cord-346267-l08ld2cy	251	2	,	,	,
cord-346267-l08ld2cy	251	3	if	if	IN
cord-346267-l08ld2cy	251	4	the	the	DT
cord-346267-l08ld2cy	251	5	synonymous	synonymous	JJ
cord-346267-l08ld2cy	251	6	substitution	substitution	NN
cord-346267-l08ld2cy	251	7	rate	rate	NN
cord-346267-l08ld2cy	251	8	approaches	approach	VBZ
cord-346267-l08ld2cy	251	9	saturation	saturation	VBP
cord-346267-l08ld2cy	251	10	along	along	IN
cord-346267-l08ld2cy	251	11	a	a	DT
cord-346267-l08ld2cy	251	12	branch	branch	NN
cord-346267-l08ld2cy	251	13	or	or	CC
cord-346267-l08ld2cy	251	14	group	group	NN
cord-346267-l08ld2cy	251	15	of	of	IN
cord-346267-l08ld2cy	251	16	branches	branch	NNS
cord-346267-l08ld2cy	251	17	,	,	,
cord-346267-l08ld2cy	251	18	it	-PRON-	PRP
cord-346267-l08ld2cy	251	19	is	be	VBZ
cord-346267-l08ld2cy	251	20	likely	likely	JJ
cord-346267-l08ld2cy	251	21	that	that	IN
cord-346267-l08ld2cy	251	22	the	the	DT
cord-346267-l08ld2cy	251	23	tMRCA	tmrca	NN
cord-346267-l08ld2cy	251	24	can	can	MD
cord-346267-l08ld2cy	251	25	not	not	RB
cord-346267-l08ld2cy	251	26	be	be	VB
cord-346267-l08ld2cy	251	27	reliably	reliably	RB
cord-346267-l08ld2cy	251	28	inferred	infer	VBN
cord-346267-l08ld2cy	251	29	.	.	.
cord-346267-l08ld2cy	252	1	If	if	IN
cord-346267-l08ld2cy	252	2	either	either	DT
cord-346267-l08ld2cy	252	3	of	of	IN
cord-346267-l08ld2cy	252	4	these	these	DT
cord-346267-l08ld2cy	252	5	patterns	pattern	NNS
cord-346267-l08ld2cy	252	6	is	be	VBZ
cord-346267-l08ld2cy	252	7	encountered	encounter	VBN
cord-346267-l08ld2cy	252	8	,	,	,
cord-346267-l08ld2cy	252	9	the	the	DT
cord-346267-l08ld2cy	252	10	inferred	infer	VBN
cord-346267-l08ld2cy	252	11	tMRCA	tmrca	NN
cord-346267-l08ld2cy	252	12	estimates	estimate	NNS
cord-346267-l08ld2cy	252	13	should	should	MD
cord-346267-l08ld2cy	252	14	be	be	VB
cord-346267-l08ld2cy	252	15	interpreted	interpret	VBN
cord-346267-l08ld2cy	252	16	with	with	IN
cord-346267-l08ld2cy	252	17	caution	caution	NN
cord-346267-l08ld2cy	252	18	.	.	.
cord-346267-l08ld2cy	253	1	Rapid	rapid	JJ
cord-346267-l08ld2cy	253	2	advances	advance	NNS
cord-346267-l08ld2cy	253	3	in	in	IN
cord-346267-l08ld2cy	253	4	cheap	cheap	JJ
cord-346267-l08ld2cy	253	5	and	and	CC
cord-346267-l08ld2cy	253	6	accessible	accessible	JJ
cord-346267-l08ld2cy	253	7	computational	computational	JJ
cord-346267-l08ld2cy	253	8	power	power	NN
cord-346267-l08ld2cy	253	9	will	will	MD
cord-346267-l08ld2cy	253	10	undoubtedly	undoubtedly	RB
cord-346267-l08ld2cy	253	11	move	move	VB
cord-346267-l08ld2cy	253	12	the	the	DT
cord-346267-l08ld2cy	253	13	fields	field	NNS
cord-346267-l08ld2cy	253	14	of	of	IN
cord-346267-l08ld2cy	253	15	paleovirology	paleovirology	NN
cord-346267-l08ld2cy	253	16	and	and	CC
cord-346267-l08ld2cy	253	17	molecular	molecular	JJ
cord-346267-l08ld2cy	253	18	dating	date	VBG
cord-346267-l08ld2cy	253	19	towards	towards	IN
cord-346267-l08ld2cy	253	20	increasingly	increasingly	RB
cord-346267-l08ld2cy	253	21	more	more	RBR
cord-346267-l08ld2cy	253	22	realistic	realistic	JJ
cord-346267-l08ld2cy	253	23	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	253	24	models	model	NNS
cord-346267-l08ld2cy	253	25	that	that	WDT
cord-346267-l08ld2cy	253	26	account	account	VBP
cord-346267-l08ld2cy	253	27	for	for	IN
cord-346267-l08ld2cy	253	28	variation	variation	NN
cord-346267-l08ld2cy	253	29	in	in	IN
cord-346267-l08ld2cy	253	30	selective	selective	JJ
cord-346267-l08ld2cy	253	31	regimes	regime	NNS
cord-346267-l08ld2cy	253	32	(	(	-LRB-
cord-346267-l08ld2cy	253	33	Suchard	Suchard	NNP
cord-346267-l08ld2cy	253	34	and	and	CC
cord-346267-l08ld2cy	253	35	Rambaut	Rambaut	NNP
cord-346267-l08ld2cy	253	36	2009	2009	CD
cord-346267-l08ld2cy	253	37	)	)	-RRB-
cord-346267-l08ld2cy	253	38	.	.	.
cord-346267-l08ld2cy	254	1	Our	-PRON-	PRP$
cord-346267-l08ld2cy	254	2	results	result	NNS
cord-346267-l08ld2cy	254	3	provide	provide	VBP
cord-346267-l08ld2cy	254	4	compelling	compelling	JJ
cord-346267-l08ld2cy	254	5	evidence	evidence	NN
cord-346267-l08ld2cy	254	6	that	that	IN
cord-346267-l08ld2cy	254	7	such	such	PDT
cord-346267-l08ld2cy	254	8	a	a	DT
cord-346267-l08ld2cy	254	9	movement	movement	NN
cord-346267-l08ld2cy	254	10	should	should	MD
cord-346267-l08ld2cy	254	11	be	be	VB
cord-346267-l08ld2cy	254	12	accelerated	accelerate	VBN
cord-346267-l08ld2cy	254	13	.	.	.
cord-346267-l08ld2cy	255	1	In	in	IN
cord-346267-l08ld2cy	255	2	this	this	DT
cord-346267-l08ld2cy	255	3	study	study	NN
cord-346267-l08ld2cy	255	4	,	,	,
cord-346267-l08ld2cy	255	5	we	-PRON-	PRP
cord-346267-l08ld2cy	255	6	demonstrate	demonstrate	VBP
cord-346267-l08ld2cy	255	7	the	the	DT
cord-346267-l08ld2cy	255	8	need	need	NN
cord-346267-l08ld2cy	255	9	to	to	TO
cord-346267-l08ld2cy	255	10	include	include	VB
cord-346267-l08ld2cy	255	11	relevant	relevant	JJ
cord-346267-l08ld2cy	255	12	biological	biological	JJ
cord-346267-l08ld2cy	255	13	and	and	CC
cord-346267-l08ld2cy	255	14	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	255	15	forces	force	NNS
cord-346267-l08ld2cy	255	16	in	in	IN
cord-346267-l08ld2cy	255	17	substitution	substitution	NN
cord-346267-l08ld2cy	255	18	models	model	NNS
cord-346267-l08ld2cy	255	19	.	.	.
cord-346267-l08ld2cy	256	1	It	-PRON-	PRP
cord-346267-l08ld2cy	256	2	was	be	VBD
cord-346267-l08ld2cy	256	3	not	not	RB
cord-346267-l08ld2cy	256	4	until	until	IN
cord-346267-l08ld2cy	256	5	we	-PRON-	PRP
cord-346267-l08ld2cy	256	6	permitted	permit	VBD
cord-346267-l08ld2cy	256	7	different	different	JJ
cord-346267-l08ld2cy	256	8	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	256	9	regimes	regime	NNS
cord-346267-l08ld2cy	256	10	for	for	IN
cord-346267-l08ld2cy	256	11	different	different	JJ
cord-346267-l08ld2cy	256	12	branches	branch	NNS
cord-346267-l08ld2cy	256	13	in	in	IN
cord-346267-l08ld2cy	256	14	the	the	DT
cord-346267-l08ld2cy	256	15	tree	tree	NN
cord-346267-l08ld2cy	256	16	that	that	WDT
cord-346267-l08ld2cy	256	17	we	-PRON-	PRP
cord-346267-l08ld2cy	256	18	saw	see	VBD
cord-346267-l08ld2cy	256	19	the	the	DT
cord-346267-l08ld2cy	256	20	most	most	RBS
cord-346267-l08ld2cy	256	21	dramatic	dramatic	JJ
cord-346267-l08ld2cy	256	22	changes	change	NNS
cord-346267-l08ld2cy	256	23	in	in	IN
cord-346267-l08ld2cy	256	24	branch	branch	NN
cord-346267-l08ld2cy	256	25	length	length	NN
cord-346267-l08ld2cy	256	26	estimates	estimate	NNS
cord-346267-l08ld2cy	256	27	.	.	.
cord-346267-l08ld2cy	257	1	Current	current	JJ
cord-346267-l08ld2cy	257	2	codon	codon	NN
cord-346267-l08ld2cy	257	3	models	model	NNS
cord-346267-l08ld2cy	257	4	take	take	VBP
cord-346267-l08ld2cy	257	5	a	a	DT
cord-346267-l08ld2cy	257	6	very	very	RB
cord-346267-l08ld2cy	257	7	simplistic	simplistic	JJ
cord-346267-l08ld2cy	257	8	mechanistic	mechanistic	JJ
cord-346267-l08ld2cy	257	9	view	view	NN
cord-346267-l08ld2cy	257	10	of	of	IN
cord-346267-l08ld2cy	257	11	the	the	DT
cord-346267-l08ld2cy	257	12	action	action	NN
cord-346267-l08ld2cy	257	13	of	of	IN
cord-346267-l08ld2cy	257	14	purifying	purify	VBG
cord-346267-l08ld2cy	257	15	selection	selection	NN
cord-346267-l08ld2cy	257	16	,	,	,
cord-346267-l08ld2cy	257	17	and	and	CC
cord-346267-l08ld2cy	257	18	we	-PRON-	PRP
cord-346267-l08ld2cy	257	19	expect	expect	VBP
cord-346267-l08ld2cy	257	20	that	that	IN
cord-346267-l08ld2cy	257	21	incorporating	incorporate	VBG
cord-346267-l08ld2cy	257	22	processes	process	NNS
cord-346267-l08ld2cy	257	23	such	such	JJ
cord-346267-l08ld2cy	257	24	as	as	IN
cord-346267-l08ld2cy	257	25	directional	directional	JJ
cord-346267-l08ld2cy	257	26	selection	selection	NN
cord-346267-l08ld2cy	257	27	(	(	-LRB-
cord-346267-l08ld2cy	257	28	Seoighe	Seoighe	NNP
cord-346267-l08ld2cy	257	29	et	et	NNP
cord-346267-l08ld2cy	257	30	al	al	NNP
cord-346267-l08ld2cy	257	31	.	.	NNP
cord-346267-l08ld2cy	257	32	2007	2007	CD
cord-346267-l08ld2cy	257	33	)	)	-RRB-
cord-346267-l08ld2cy	257	34	,	,	,
cord-346267-l08ld2cy	257	35	toggling	toggle	VBG
cord-346267-l08ld2cy	257	36	selection	selection	NN
cord-346267-l08ld2cy	257	37	(	(	-LRB-
cord-346267-l08ld2cy	257	38	Delport	Delport	NNP
cord-346267-l08ld2cy	257	39	et	et	NNP
cord-346267-l08ld2cy	257	40	al	al	NNP
cord-346267-l08ld2cy	257	41	.	.	NNP
cord-346267-l08ld2cy	257	42	2008	2008	CD
cord-346267-l08ld2cy	257	43	)	)	-RRB-
cord-346267-l08ld2cy	257	44	,	,	,
cord-346267-l08ld2cy	257	45	and	and	CC
cord-346267-l08ld2cy	257	46	residue	residue	NN
cord-346267-l08ld2cy	257	47	-	-	HYPH
cord-346267-l08ld2cy	257	48	specific	specific	JJ
cord-346267-l08ld2cy	257	49	(	(	-LRB-
cord-346267-l08ld2cy	257	50	Doron	Doron	NNP
cord-346267-l08ld2cy	257	51	-	-	HYPH
cord-346267-l08ld2cy	257	52	Faigenboim	Faigenboim	NNP
cord-346267-l08ld2cy	257	53	and	and	CC
cord-346267-l08ld2cy	257	54	Pupko	Pupko	NNP
cord-346267-l08ld2cy	257	55	2007	2007	CD
cord-346267-l08ld2cy	257	56	)	)	-RRB-
cord-346267-l08ld2cy	257	57	or	or	CC
cord-346267-l08ld2cy	257	58	site	site	NN
cord-346267-l08ld2cy	257	59	-	-	HYPH
cord-346267-l08ld2cy	257	60	specific	specific	JJ
cord-346267-l08ld2cy	257	61	substitution	substitution	NN
cord-346267-l08ld2cy	257	62	(	(	-LRB-
cord-346267-l08ld2cy	257	63	Lartillot	Lartillot	NNP
cord-346267-l08ld2cy	257	64	and	and	CC
cord-346267-l08ld2cy	257	65	Philippe	Philippe	NNP
cord-346267-l08ld2cy	257	66	2004	2004	CD
cord-346267-l08ld2cy	257	67	)	)	-RRB-
cord-346267-l08ld2cy	257	68	biases	bias	NNS
cord-346267-l08ld2cy	257	69	can	can	MD
cord-346267-l08ld2cy	257	70	further	further	RB
cord-346267-l08ld2cy	257	71	refine	refine	VB
cord-346267-l08ld2cy	257	72	tMRCA	tmrca	NN
cord-346267-l08ld2cy	257	73	estimates	estimate	NNS
cord-346267-l08ld2cy	257	74	.	.	.
cord-346267-l08ld2cy	258	1	It	-PRON-	PRP
cord-346267-l08ld2cy	258	2	is	be	VBZ
cord-346267-l08ld2cy	258	3	still	still	RB
cord-346267-l08ld2cy	258	4	unclear	unclear	JJ
cord-346267-l08ld2cy	258	5	how	how	WRB
cord-346267-l08ld2cy	258	6	correcting	correct	VBG
cord-346267-l08ld2cy	258	7	for	for	IN
cord-346267-l08ld2cy	258	8	the	the	DT
cord-346267-l08ld2cy	258	9	effects	effect	NNS
cord-346267-l08ld2cy	258	10	of	of	IN
cord-346267-l08ld2cy	258	11	purifying	purify	VBG
cord-346267-l08ld2cy	258	12	selection	selection	NN
cord-346267-l08ld2cy	258	13	may	may	MD
cord-346267-l08ld2cy	258	14	affect	affect	VB
cord-346267-l08ld2cy	258	15	dating	dating	NN
cord-346267-l08ld2cy	258	16	and	and	CC
cord-346267-l08ld2cy	258	17	branch	branch	NN
cord-346267-l08ld2cy	258	18	length	length	NN
cord-346267-l08ld2cy	258	19	estimation	estimation	NN
cord-346267-l08ld2cy	258	20	in	in	IN
cord-346267-l08ld2cy	258	21	other	other	JJ
cord-346267-l08ld2cy	258	22	types	type	NNS
cord-346267-l08ld2cy	258	23	of	of	IN
cord-346267-l08ld2cy	258	24	viruses	virus	NNS
cord-346267-l08ld2cy	258	25	(	(	-LRB-
cord-346267-l08ld2cy	258	26	e.g.	e.g.	RB
cord-346267-l08ld2cy	258	27	,	,	,
cord-346267-l08ld2cy	258	28	DNA	dna	NN
cord-346267-l08ld2cy	258	29	viruses	virus	NNS
cord-346267-l08ld2cy	258	30	)	)	-RRB-
cord-346267-l08ld2cy	258	31	and	and	CC
cord-346267-l08ld2cy	258	32	cellular	cellular	JJ
cord-346267-l08ld2cy	258	33	organisms	organism	NNS
cord-346267-l08ld2cy	258	34	.	.	.
cord-346267-l08ld2cy	259	1	The	the	DT
cord-346267-l08ld2cy	259	2	bias	bias	NN
cord-346267-l08ld2cy	259	3	we	-PRON-	PRP
cord-346267-l08ld2cy	259	4	observed	observe	VBD
cord-346267-l08ld2cy	259	5	in	in	IN
cord-346267-l08ld2cy	259	6	the	the	DT
cord-346267-l08ld2cy	259	7	estimation	estimation	NN
cord-346267-l08ld2cy	259	8	of	of	IN
cord-346267-l08ld2cy	259	9	branch	branch	NN
cord-346267-l08ld2cy	259	10	lengths	length	NNS
cord-346267-l08ld2cy	259	11	appears	appear	VBZ
cord-346267-l08ld2cy	259	12	to	to	TO
cord-346267-l08ld2cy	259	13	be	be	VB
cord-346267-l08ld2cy	259	14	related	relate	VBN
cord-346267-l08ld2cy	259	15	to	to	IN
cord-346267-l08ld2cy	259	16	the	the	DT
cord-346267-l08ld2cy	259	17	intensity	intensity	NN
cord-346267-l08ld2cy	259	18	of	of	IN
cord-346267-l08ld2cy	259	19	selection	selection	NN
cord-346267-l08ld2cy	259	20	and	and	CC
cord-346267-l08ld2cy	259	21	the	the	DT
cord-346267-l08ld2cy	259	22	length	length	NN
cord-346267-l08ld2cy	259	23	of	of	IN
cord-346267-l08ld2cy	259	24	the	the	DT
cord-346267-l08ld2cy	259	25	branches	branch	NNS
cord-346267-l08ld2cy	259	26	in	in	IN
cord-346267-l08ld2cy	259	27	question	question	NN
cord-346267-l08ld2cy	259	28	.	.	.
cord-346267-l08ld2cy	260	1	The	the	DT
cord-346267-l08ld2cy	260	2	genome	genome	NN
cord-346267-l08ld2cy	260	3	sequence	sequence	NN
cord-346267-l08ld2cy	260	4	of	of	IN
cord-346267-l08ld2cy	260	5	the	the	DT
cord-346267-l08ld2cy	260	6	virulent	virulent	JJ
cord-346267-l08ld2cy	260	7	Kabete	Kabete	NNP
cord-346267-l08ld2cy	260	8	'	'	``
cord-346267-l08ld2cy	260	9	O	o	UH
cord-346267-l08ld2cy	260	10	'	'	''
cord-346267-l08ld2cy	260	11	strain	strain	NN
cord-346267-l08ld2cy	260	12	of	of	IN
cord-346267-l08ld2cy	260	13	rinderpest	rinderpest	NN
cord-346267-l08ld2cy	260	14	virus	virus	NN
cord-346267-l08ld2cy	260	15	:	:	:
cord-346267-l08ld2cy	260	16	comparison	comparison	NN
cord-346267-l08ld2cy	260	17	with	with	IN
cord-346267-l08ld2cy	260	18	the	the	DT
cord-346267-l08ld2cy	260	19	derived	derived	JJ
cord-346267-l08ld2cy	260	20	vaccine	vaccine	NN
cord-346267-l08ld2cy	260	21	The	the	DT
cord-346267-l08ld2cy	260	22	origin	origin	NN
cord-346267-l08ld2cy	260	23	of	of	IN
cord-346267-l08ld2cy	260	24	European	european	JJ
cord-346267-l08ld2cy	260	25	cattle	cattle	NNS
cord-346267-l08ld2cy	260	26	:	:	:
cord-346267-l08ld2cy	260	27	evidence	evidence	NN
cord-346267-l08ld2cy	260	28	from	from	IN
cord-346267-l08ld2cy	260	29	modern	modern	JJ
cord-346267-l08ld2cy	260	30	and	and	CC
cord-346267-l08ld2cy	260	31	ancient	ancient	JJ
cord-346267-l08ld2cy	260	32	DNA	dna	NN
cord-346267-l08ld2cy	260	33	Pacing	pace	VBG
cord-346267-l08ld2cy	260	34	a	a	DT
cord-346267-l08ld2cy	260	35	small	small	JJ
cord-346267-l08ld2cy	260	36	cage	cage	NN
cord-346267-l08ld2cy	260	37	:	:	:
cord-346267-l08ld2cy	260	38	mutation	mutation	NN
cord-346267-l08ld2cy	260	39	and	and	CC
cord-346267-l08ld2cy	260	40	RNA	RNA	NNP
cord-346267-l08ld2cy	260	41	viruses	virus	NNS
cord-346267-l08ld2cy	260	42	Unexpected	unexpected	JJ
cord-346267-l08ld2cy	260	43	inheritance	inheritance	NN
cord-346267-l08ld2cy	260	44	:	:	:
cord-346267-l08ld2cy	260	45	multiple	multiple	JJ
cord-346267-l08ld2cy	260	46	integrations	integration	NNS
cord-346267-l08ld2cy	260	47	of	of	IN
cord-346267-l08ld2cy	260	48	ancient	ancient	JJ
cord-346267-l08ld2cy	260	49	bornavirus	bornavirus	NN
cord-346267-l08ld2cy	260	50	and	and	CC
cord-346267-l08ld2cy	260	51	ebolavirus/	ebolavirus/	NN
cord-346267-l08ld2cy	260	52	marburgvirus	marburgvirus	JJ
cord-346267-l08ld2cy	260	53	sequences	sequence	NNS
cord-346267-l08ld2cy	260	54	in	in	IN
cord-346267-l08ld2cy	260	55	vertebrate	vertebrate	JJ
cord-346267-l08ld2cy	260	56	genomes	genome	NNS
cord-346267-l08ld2cy	260	57	Measles	measles	VBP
cord-346267-l08ld2cy	260	58	endemicity	endemicity	NN
cord-346267-l08ld2cy	260	59	in	in	IN
cord-346267-l08ld2cy	260	60	insular	insular	JJ
cord-346267-l08ld2cy	260	61	populations	population	NNS
cord-346267-l08ld2cy	260	62	:	:	:
cord-346267-l08ld2cy	260	63	critical	critical	JJ
cord-346267-l08ld2cy	260	64	community	community	NN
cord-346267-l08ld2cy	260	65	size	size	NN
cord-346267-l08ld2cy	260	66	and	and	CC
cord-346267-l08ld2cy	260	67	its	-PRON-	PRP$
cord-346267-l08ld2cy	260	68	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	260	69	implication	implication	NN
cord-346267-l08ld2cy	260	70	Mitochondrial	mitochondrial	IN
cord-346267-l08ld2cy	260	71	DNA	dna	NN
cord-346267-l08ld2cy	260	72	sequences	sequence	NNS
cord-346267-l08ld2cy	260	73	of	of	IN
cord-346267-l08ld2cy	260	74	primates	primate	NNS
cord-346267-l08ld2cy	260	75	:	:	:
cord-346267-l08ld2cy	260	76	tempo	tempo	NN
cord-346267-l08ld2cy	260	77	and	and	CC
cord-346267-l08ld2cy	260	78	mode	mode	NN
cord-346267-l08ld2cy	260	79	of	of	IN
cord-346267-l08ld2cy	260	80	evolution	evolution	NN
cord-346267-l08ld2cy	260	81	Effects	effect	NNS
cord-346267-l08ld2cy	260	82	of	of	IN
cord-346267-l08ld2cy	260	83	passage	passage	NN
cord-346267-l08ld2cy	260	84	history	history	NN
cord-346267-l08ld2cy	260	85	and	and	CC
cord-346267-l08ld2cy	260	86	sampling	sampling	NN
cord-346267-l08ld2cy	260	87	bias	bias	NN
cord-346267-l08ld2cy	260	88	on	on	IN
cord-346267-l08ld2cy	260	89	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	260	90	reconstruction	reconstruction	NN
cord-346267-l08ld2cy	260	91	of	of	IN
cord-346267-l08ld2cy	260	92	human	human	JJ
cord-346267-l08ld2cy	260	93	influenza	influenza	NN
cord-346267-l08ld2cy	260	94	A	a	DT
cord-346267-l08ld2cy	260	95	evolution	evolution	NN
cord-346267-l08ld2cy	260	96	Avian	avian	JJ
cord-346267-l08ld2cy	260	97	influenza	influenza	NN
cord-346267-l08ld2cy	260	98	virus	virus	NN
cord-346267-l08ld2cy	260	99	exhibits	exhibit	VBZ
cord-346267-l08ld2cy	260	100	rapid	rapid	JJ
cord-346267-l08ld2cy	260	101	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	260	102	dynamics	dynamic	NNS
cord-346267-l08ld2cy	260	103	Hitchhiking	Hitchhiking	NNP
cord-346267-l08ld2cy	260	104	and	and	CC
cord-346267-l08ld2cy	260	105	the	the	DT
cord-346267-l08ld2cy	260	106	population	population	NN
cord-346267-l08ld2cy	260	107	genetic	genetic	JJ
cord-346267-l08ld2cy	260	108	structure	structure	NN
cord-346267-l08ld2cy	260	109	of	of	IN
cord-346267-l08ld2cy	261	1	avian	avian	JJ
cord-346267-l08ld2cy	261	2	influenza	influenza	NN
cord-346267-l08ld2cy	261	3	virus	virus	NN
cord-346267-l08ld2cy	261	4	Frequent	frequent	JJ
cord-346267-l08ld2cy	261	5	toggling	toggle	VBG
cord-346267-l08ld2cy	261	6	between	between	IN
cord-346267-l08ld2cy	261	7	alternative	alternative	JJ
cord-346267-l08ld2cy	261	8	amino	amino	NN
cord-346267-l08ld2cy	261	9	acids	acid	NNS
cord-346267-l08ld2cy	261	10	is	be	VBZ
cord-346267-l08ld2cy	261	11	driven	drive	VBN
cord-346267-l08ld2cy	261	12	by	by	IN
cord-346267-l08ld2cy	261	13	selection	selection	NN
cord-346267-l08ld2cy	261	14	in	in	IN
cord-346267-l08ld2cy	261	15	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	261	16	A	A	NNP
cord-346267-l08ld2cy	261	17	combined	combine	VBN
cord-346267-l08ld2cy	261	18	empirical	empirical	JJ
cord-346267-l08ld2cy	261	19	and	and	CC
cord-346267-l08ld2cy	261	20	mechanistic	mechanistic	JJ
cord-346267-l08ld2cy	261	21	codon	codon	NN
cord-346267-l08ld2cy	261	22	model	model	NN
cord-346267-l08ld2cy	261	23	Relaxed	relaxed	JJ
cord-346267-l08ld2cy	261	24	phylogenetics	phylogenetic	NNS
cord-346267-l08ld2cy	261	25	and	and	CC
cord-346267-l08ld2cy	261	26	dating	date	VBG
cord-346267-l08ld2cy	261	27	with	with	IN
cord-346267-l08ld2cy	261	28	confidence	confidence	NN
cord-346267-l08ld2cy	261	29	BEAST	BEAST	NNP
cord-346267-l08ld2cy	261	30	:	:	:
cord-346267-l08ld2cy	262	1	Bayesian	bayesian	JJ
cord-346267-l08ld2cy	262	2	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	262	3	analysis	analysis	NN
cord-346267-l08ld2cy	262	4	by	by	IN
cord-346267-l08ld2cy	262	5	sampling	sampling	NN
cord-346267-l08ld2cy	262	6	trees	tree	NNS
cord-346267-l08ld2cy	262	7	Bayesian	bayesian	JJ
cord-346267-l08ld2cy	262	8	coalescent	coalescent	JJ
cord-346267-l08ld2cy	262	9	inference	inference	NN
cord-346267-l08ld2cy	262	10	of	of	IN
cord-346267-l08ld2cy	262	11	past	past	JJ
cord-346267-l08ld2cy	262	12	population	population	NN
cord-346267-l08ld2cy	262	13	dynamics	dynamic	NNS
cord-346267-l08ld2cy	262	14	from	from	IN
cord-346267-l08ld2cy	262	15	molecular	molecular	JJ
cord-346267-l08ld2cy	262	16	sequences	sequence	NNS
cord-346267-l08ld2cy	262	17	Rates	rate	NNS
cord-346267-l08ld2cy	262	18	of	of	IN
cord-346267-l08ld2cy	262	19	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	262	20	change	change	NN
cord-346267-l08ld2cy	262	21	in	in	IN
cord-346267-l08ld2cy	262	22	viruses	virus	NNS
cord-346267-l08ld2cy	262	23	:	:	:
cord-346267-l08ld2cy	263	1	patterns	pattern	NNS
cord-346267-l08ld2cy	263	2	and	and	CC
cord-346267-l08ld2cy	263	3	determinants	determinant	NNS
cord-346267-l08ld2cy	263	4	Evolution	evolution	NN
cord-346267-l08ld2cy	263	5	of	of	IN
cord-346267-l08ld2cy	263	6	the	the	DT
cord-346267-l08ld2cy	263	7	human	human	JJ
cord-346267-l08ld2cy	263	8	immunodeficiency	immunodeficiency	NN
cord-346267-l08ld2cy	263	9	virus	virus	NN
cord-346267-l08ld2cy	263	10	envelope	envelope	NN
cord-346267-l08ld2cy	263	11	gene	gene	NN
cord-346267-l08ld2cy	263	12	is	be	VBZ
cord-346267-l08ld2cy	263	13	dominated	dominate	VBN
cord-346267-l08ld2cy	263	14	by	by	IN
cord-346267-l08ld2cy	263	15	purifying	purify	VBG
cord-346267-l08ld2cy	263	16	selection	selection	NN
cord-346267-l08ld2cy	263	17	Paleovirology	paleovirology	NN
cord-346267-l08ld2cy	263	18	-	-	HYPH
cord-346267-l08ld2cy	263	19	modern	modern	JJ
cord-346267-l08ld2cy	263	20	consequences	consequence	NNS
cord-346267-l08ld2cy	263	21	of	of	IN
cord-346267-l08ld2cy	263	22	ancient	ancient	JJ
cord-346267-l08ld2cy	263	23	viruses	virus	NNS
cord-346267-l08ld2cy	263	24	Origin	Origin	NNP
cord-346267-l08ld2cy	263	25	of	of	IN
cord-346267-l08ld2cy	263	26	measles	measles	NNP
cord-346267-l08ld2cy	263	27	virus	virus	NN
cord-346267-l08ld2cy	263	28	:	:	:
cord-346267-l08ld2cy	263	29	divergence	divergence	NN
cord-346267-l08ld2cy	263	30	from	from	IN
cord-346267-l08ld2cy	263	31	rinderpest	rinderpest	NN
cord-346267-l08ld2cy	263	32	virus	virus	NN
cord-346267-l08ld2cy	263	33	between	between	IN
cord-346267-l08ld2cy	263	34	the	the	DT
cord-346267-l08ld2cy	263	35	11th	11th	JJ
cord-346267-l08ld2cy	263	36	and	and	CC
cord-346267-l08ld2cy	263	37	12th	12th	NN
cord-346267-l08ld2cy	263	38	centuries	century	NNS
cord-346267-l08ld2cy	264	1	A	a	DT
cord-346267-l08ld2cy	264	2	transitional	transitional	JJ
cord-346267-l08ld2cy	264	3	endogenous	endogenous	JJ
cord-346267-l08ld2cy	264	4	lentivirus	lentivirus	NN
cord-346267-l08ld2cy	264	5	from	from	IN
cord-346267-l08ld2cy	264	6	the	the	DT
cord-346267-l08ld2cy	264	7	genome	genome	NN
cord-346267-l08ld2cy	264	8	of	of	IN
cord-346267-l08ld2cy	264	9	a	a	DT
cord-346267-l08ld2cy	264	10	basal	basal	NN
cord-346267-l08ld2cy	264	11	primate	primate	NN
cord-346267-l08ld2cy	264	12	and	and	CC
cord-346267-l08ld2cy	264	13	implications	implication	NNS
cord-346267-l08ld2cy	264	14	for	for	IN
cord-346267-l08ld2cy	264	15	lentivirus	lentivirus	NN
cord-346267-l08ld2cy	264	16	evolution	evolution	NN
cord-346267-l08ld2cy	264	17	Genomic	genomic	JJ
cord-346267-l08ld2cy	264	18	fossils	fossil	NNS
cord-346267-l08ld2cy	264	19	calibrate	calibrate	VBP
cord-346267-l08ld2cy	264	20	the	the	DT
cord-346267-l08ld2cy	264	21	long	long	JJ
cord-346267-l08ld2cy	264	22	-	-	HYPH
cord-346267-l08ld2cy	264	23	term	term	NN
cord-346267-l08ld2cy	264	24	evolution	evolution	NN
cord-346267-l08ld2cy	264	25	of	of	IN
cord-346267-l08ld2cy	264	26	hepadnaviruses	hepadnavirus	NNS
cord-346267-l08ld2cy	265	1	A	a	DT
cord-346267-l08ld2cy	265	2	codon	codon	NN
cord-346267-l08ld2cy	265	3	-	-	HYPH
cord-346267-l08ld2cy	265	4	based	base	VBN
cord-346267-l08ld2cy	265	5	model	model	NN
cord-346267-l08ld2cy	265	6	of	of	IN
cord-346267-l08ld2cy	265	7	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	265	8	substitution	substitution	NN
cord-346267-l08ld2cy	265	9	for	for	IN
cord-346267-l08ld2cy	265	10	protein	protein	NN
cord-346267-l08ld2cy	265	11	-	-	HYPH
cord-346267-l08ld2cy	265	12	coding	code	VBG
cord-346267-l08ld2cy	265	13	DNA	dna	NN
cord-346267-l08ld2cy	265	14	sequences	sequence	NNS
cord-346267-l08ld2cy	265	15	Time	Time	NNP
cord-346267-l08ld2cy	265	16	dependency	dependency	NN
cord-346267-l08ld2cy	265	17	of	of	IN
cord-346267-l08ld2cy	265	18	molecular	molecular	JJ
cord-346267-l08ld2cy	265	19	rate	rate	NN
cord-346267-l08ld2cy	265	20	estimates	estimate	NNS
cord-346267-l08ld2cy	265	21	and	and	CC
cord-346267-l08ld2cy	265	22	systematic	systematic	JJ
cord-346267-l08ld2cy	265	23	overestimation	overestimation	NN
cord-346267-l08ld2cy	265	24	of	of	IN
cord-346267-l08ld2cy	265	25	recent	recent	JJ
cord-346267-l08ld2cy	265	26	divergence	divergence	NN
cord-346267-l08ld2cy	265	27	times	time	NNS
cord-346267-l08ld2cy	265	28	Molecular	Molecular	NNP
cord-346267-l08ld2cy	265	29	clocks	clock	NNS
cord-346267-l08ld2cy	265	30	and	and	CC
cord-346267-l08ld2cy	265	31	the	the	DT
cord-346267-l08ld2cy	265	32	puzzle	puzzle	NN
cord-346267-l08ld2cy	265	33	of	of	IN
cord-346267-l08ld2cy	265	34	RNA	RNA	NNP
cord-346267-l08ld2cy	265	35	virus	virus	NN
cord-346267-l08ld2cy	265	36	origins	origin	VBZ
cord-346267-l08ld2cy	265	37	Patterns	pattern	NNS
cord-346267-l08ld2cy	265	38	of	of	IN
cord-346267-l08ld2cy	265	39	intra	intra	JJ
cord-346267-l08ld2cy	265	40	-	-	:
cord-346267-l08ld2cy	265	41	and	and	CC
cord-346267-l08ld2cy	265	42	interhost	interhost	NNP
cord-346267-l08ld2cy	265	43	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	265	44	variation	variation	NN
cord-346267-l08ld2cy	265	45	reveal	reveal	VBP
cord-346267-l08ld2cy	265	46	strong	strong	JJ
cord-346267-l08ld2cy	265	47	purifying	purifying	NN
cord-346267-l08ld2cy	265	48	selection	selection	NN
cord-346267-l08ld2cy	265	49	in	in	IN
cord-346267-l08ld2cy	265	50	dengue	dengue	NN
cord-346267-l08ld2cy	265	51	virus	virus	NN
cord-346267-l08ld2cy	265	52	Evidence	evidence	NN
cord-346267-l08ld2cy	265	53	of	of	IN
cord-346267-l08ld2cy	265	54	the	the	DT
cord-346267-l08ld2cy	265	55	recombinant	recombinant	JJ
cord-346267-l08ld2cy	265	56	origin	origin	NN
cord-346267-l08ld2cy	265	57	of	of	IN
cord-346267-l08ld2cy	265	58	a	a	DT
cord-346267-l08ld2cy	265	59	bat	bat	NN
cord-346267-l08ld2cy	265	60	severe	severe	JJ
cord-346267-l08ld2cy	265	61	acute	acute	JJ
cord-346267-l08ld2cy	265	62	respiratory	respiratory	JJ
cord-346267-l08ld2cy	265	63	syndrome	syndrome	NN
cord-346267-l08ld2cy	265	64	(	(	-LRB-
cord-346267-l08ld2cy	265	65	SARS)-like	sars)-like	CD
cord-346267-l08ld2cy	265	66	coronavirus	coronavirus	NN
cord-346267-l08ld2cy	265	67	and	and	CC
cord-346267-l08ld2cy	265	68	its	-PRON-	PRP$
cord-346267-l08ld2cy	265	69	implications	implication	NNS
cord-346267-l08ld2cy	265	70	on	on	IN
cord-346267-l08ld2cy	265	71	the	the	DT
cord-346267-l08ld2cy	265	72	direct	direct	JJ
cord-346267-l08ld2cy	265	73	ancestor	ancestor	NN
cord-346267-l08ld2cy	265	74	of	of	IN
cord-346267-l08ld2cy	265	75	SARS	SARS	NNP
cord-346267-l08ld2cy	265	76	coronavirus	coronavirus	NN
cord-346267-l08ld2cy	265	77	Endogenous	endogenous	JJ
cord-346267-l08ld2cy	265	78	non	non	JJ
cord-346267-l08ld2cy	265	79	-	-	JJ
cord-346267-l08ld2cy	265	80	retroviral	retroviral	JJ
cord-346267-l08ld2cy	265	81	RNA	RNA	NNP
cord-346267-l08ld2cy	265	82	virus	virus	NN
cord-346267-l08ld2cy	265	83	elements	element	NNS
cord-346267-l08ld2cy	265	84	in	in	IN
cord-346267-l08ld2cy	265	85	mammalian	mammalian	JJ
cord-346267-l08ld2cy	265	86	genomes	genome	NNS
cord-346267-l08ld2cy	265	87	Evolution	evolution	NN
cord-346267-l08ld2cy	265	88	of	of	IN
cord-346267-l08ld2cy	265	89	protein	protein	NN
cord-346267-l08ld2cy	265	90	molecules	molecule	NNS
cord-346267-l08ld2cy	265	91	Endogenous	endogenous	JJ
cord-346267-l08ld2cy	265	92	viral	viral	JJ
cord-346267-l08ld2cy	265	93	elements	element	NNS
cord-346267-l08ld2cy	265	94	in	in	IN
cord-346267-l08ld2cy	265	95	animal	animal	NN
cord-346267-l08ld2cy	265	96	genomes	genome	NNS
cord-346267-l08ld2cy	265	97	Macroevolution	macroevolution	NN
cord-346267-l08ld2cy	265	98	of	of	IN
cord-346267-l08ld2cy	265	99	complex	complex	JJ
cord-346267-l08ld2cy	265	100	retroviruses	retrovirus	NNS
cord-346267-l08ld2cy	265	101	Adaptation	adaptation	NN
cord-346267-l08ld2cy	265	102	to	to	IN
cord-346267-l08ld2cy	265	103	different	different	JJ
cord-346267-l08ld2cy	265	104	human	human	JJ
cord-346267-l08ld2cy	265	105	populations	population	NNS
cord-346267-l08ld2cy	265	106	by	by	IN
cord-346267-l08ld2cy	265	107	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	265	108	revealed	reveal	VBN
cord-346267-l08ld2cy	265	109	by	by	IN
cord-346267-l08ld2cy	265	110	codon	codon	NN
cord-346267-l08ld2cy	265	111	-	-	HYPH
cord-346267-l08ld2cy	265	112	based	base	VBN
cord-346267-l08ld2cy	265	113	analyses	analysis	NNS
cord-346267-l08ld2cy	266	1	HyPhy	HyPhy	NNP
cord-346267-l08ld2cy	266	2	:	:	:
cord-346267-l08ld2cy	266	3	hypothesis	hypothesis	NN
cord-346267-l08ld2cy	266	4	testing	testing	NN
cord-346267-l08ld2cy	266	5	using	use	VBG
cord-346267-l08ld2cy	266	6	phylogenies	phylogeny	NNS
cord-346267-l08ld2cy	266	7	Site	site	NN
cord-346267-l08ld2cy	266	8	-	-	HYPH
cord-346267-l08ld2cy	266	9	to	to	IN
cord-346267-l08ld2cy	266	10	-	-	HYPH
cord-346267-l08ld2cy	266	11	site	site	NN
cord-346267-l08ld2cy	266	12	variation	variation	NN
cord-346267-l08ld2cy	266	13	of	of	IN
cord-346267-l08ld2cy	266	14	synonymous	synonymous	JJ
cord-346267-l08ld2cy	266	15	substitution	substitution	NN
cord-346267-l08ld2cy	266	16	rates	rate	NNS
cord-346267-l08ld2cy	266	17	Evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	266	18	fingerprinting	fingerprinting	NN
cord-346267-l08ld2cy	266	19	of	of	IN
cord-346267-l08ld2cy	266	20	genes	gene	NNS
cord-346267-l08ld2cy	267	1	A	a	DT
cord-346267-l08ld2cy	267	2	Bayesian	bayesian	JJ
cord-346267-l08ld2cy	267	3	mixture	mixture	NN
cord-346267-l08ld2cy	267	4	model	model	NN
cord-346267-l08ld2cy	267	5	for	for	IN
cord-346267-l08ld2cy	267	6	across	across	IN
cord-346267-l08ld2cy	267	7	-	-	HYPH
cord-346267-l08ld2cy	267	8	site	site	NN
cord-346267-l08ld2cy	267	9	heterogeneities	heterogeneity	NNS
cord-346267-l08ld2cy	267	10	in	in	IN
cord-346267-l08ld2cy	267	11	the	the	DT
cord-346267-l08ld2cy	267	12	amino	amino	NN
cord-346267-l08ld2cy	267	13	-	-	HYPH
cord-346267-l08ld2cy	267	14	acid	acid	NN
cord-346267-l08ld2cy	267	15	replacement	replacement	NN
cord-346267-l08ld2cy	267	16	process	process	NN
cord-346267-l08ld2cy	267	17	Evidence	evidence	NN
cord-346267-l08ld2cy	267	18	for	for	IN
cord-346267-l08ld2cy	267	19	two	two	CD
cord-346267-l08ld2cy	267	20	independent	independent	JJ
cord-346267-l08ld2cy	267	21	domestications	domestication	NNS
cord-346267-l08ld2cy	267	22	of	of	IN
cord-346267-l08ld2cy	267	23	cattle	cattle	NNS
cord-346267-l08ld2cy	267	24	Plagues	plague	NNS
cord-346267-l08ld2cy	267	25	and	and	CC
cord-346267-l08ld2cy	267	26	peoples	people	NNS
cord-346267-l08ld2cy	268	1	Bias	Bias	NNP
cord-346267-l08ld2cy	269	1	Due	due	IN
cord-346267-l08ld2cy	269	2	to	to	IN
cord-346267-l08ld2cy	269	3	Purifying	Purifying	NNP
cord-346267-l08ld2cy	269	4	Selection	Selection	NNP
cord-346267-l08ld2cy	269	5	·	·	NFP
cord-346267-l08ld2cy	269	6	Two	two	CD
cord-346267-l08ld2cy	269	7	-	-	HYPH
cord-346267-l08ld2cy	269	8	stepping	step	VBG
cord-346267-l08ld2cy	269	9	through	through	IN
cord-346267-l08ld2cy	269	10	time	time	NN
cord-346267-l08ld2cy	269	11	:	:	:
cord-346267-l08ld2cy	269	12	mammals	mammal	NNS
cord-346267-l08ld2cy	269	13	and	and	CC
cord-346267-l08ld2cy	269	14	viruses	virus	NNS
cord-346267-l08ld2cy	269	15	Measles	measle	NNS
cord-346267-l08ld2cy	269	16	control	control	NN
cord-346267-l08ld2cy	269	17	and	and	CC
cord-346267-l08ld2cy	269	18	the	the	DT
cord-346267-l08ld2cy	269	19	prospect	prospect	NN
cord-346267-l08ld2cy	269	20	of	of	IN
cord-346267-l08ld2cy	269	21	eradication	eradication	NN
cord-346267-l08ld2cy	270	1	A	a	DT
cord-346267-l08ld2cy	270	2	likelihood	likelihood	NN
cord-346267-l08ld2cy	270	3	approach	approach	NN
cord-346267-l08ld2cy	270	4	for	for	IN
cord-346267-l08ld2cy	270	5	comparing	compare	VBG
cord-346267-l08ld2cy	270	6	synonymous	synonymous	JJ
cord-346267-l08ld2cy	270	7	and	and	CC
cord-346267-l08ld2cy	270	8	nonsynonymous	nonsynonymous	JJ
cord-346267-l08ld2cy	270	9	nucleotide	nucleotide	JJ
cord-346267-l08ld2cy	270	10	substitution	substitution	NN
cord-346267-l08ld2cy	270	11	rates	rate	NNS
cord-346267-l08ld2cy	270	12	,	,	,
cord-346267-l08ld2cy	270	13	with	with	IN
cord-346267-l08ld2cy	270	14	application	application	NN
cord-346267-l08ld2cy	270	15	to	to	IN
cord-346267-l08ld2cy	270	16	the	the	DT
cord-346267-l08ld2cy	270	17	chloroplast	chloroplast	NN
cord-346267-l08ld2cy	270	18	genome	genome	NN
cord-346267-l08ld2cy	270	19	Animal	Animal	NNP
cord-346267-l08ld2cy	270	20	science	science	NN
cord-346267-l08ld2cy	270	21	.	.	.
cord-346267-l08ld2cy	271	1	rinderpest	rinderpest	NN
cord-346267-l08ld2cy	271	2	,	,	,
cord-346267-l08ld2cy	271	3	deadly	deadly	JJ
cord-346267-l08ld2cy	271	4	for	for	IN
cord-346267-l08ld2cy	271	5	cattle	cattle	NNS
cord-346267-l08ld2cy	271	6	,	,	,
cord-346267-l08ld2cy	271	7	joins	join	VBZ
cord-346267-l08ld2cy	271	8	smallpox	smallpox	NN
cord-346267-l08ld2cy	271	9	as	as	IN
cord-346267-l08ld2cy	271	10	a	a	DT
cord-346267-l08ld2cy	271	11	vanquished	vanquish	VBN
cord-346267-l08ld2cy	271	12	disease	disease	NN
cord-346267-l08ld2cy	271	13	Fauna	Fauna	NNP
cord-346267-l08ld2cy	271	14	of	of	IN
cord-346267-l08ld2cy	271	15	Catal	Catal	NNP
cord-346267-l08ld2cy	271	16	Hüyük	Hüyük	NNP
cord-346267-l08ld2cy	271	17	:	:	:
cord-346267-l08ld2cy	271	18	evidence	evidence	NN
cord-346267-l08ld2cy	271	19	for	for	IN
cord-346267-l08ld2cy	271	20	early	early	JJ
cord-346267-l08ld2cy	271	21	cattle	cattle	NNS
cord-346267-l08ld2cy	271	22	domestication	domestication	NN
cord-346267-l08ld2cy	271	23	in	in	IN
cord-346267-l08ld2cy	271	24	Anatolia	Anatolia	NNP
cord-346267-l08ld2cy	272	1	The	the	DT
cord-346267-l08ld2cy	272	2	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	272	3	and	and	CC
cord-346267-l08ld2cy	272	4	epidemiological	epidemiological	JJ
cord-346267-l08ld2cy	272	5	dynamics	dynamic	NNS
cord-346267-l08ld2cy	272	6	of	of	IN
cord-346267-l08ld2cy	272	7	the	the	DT
cord-346267-l08ld2cy	272	8	paramyxoviridae	paramyxoviridae	JJ
cord-346267-l08ld2cy	272	9	Phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	272	10	evidence	evidence	NN
cord-346267-l08ld2cy	272	11	for	for	IN
cord-346267-l08ld2cy	272	12	deleterious	deleterious	JJ
cord-346267-l08ld2cy	272	13	mutation	mutation	NN
cord-346267-l08ld2cy	272	14	load	load	NN
cord-346267-l08ld2cy	272	15	in	in	IN
cord-346267-l08ld2cy	272	16	RNA	RNA	NNP
cord-346267-l08ld2cy	272	17	viruses	virus	NNS
cord-346267-l08ld2cy	272	18	and	and	CC
cord-346267-l08ld2cy	272	19	its	-PRON-	PRP$
cord-346267-l08ld2cy	272	20	contribution	contribution	NN
cord-346267-l08ld2cy	272	21	to	to	IN
cord-346267-l08ld2cy	272	22	viral	viral	JJ
cord-346267-l08ld2cy	272	23	evolution	evolution	NN
cord-346267-l08ld2cy	273	1	Rāzī	Rāzī	NNP
cord-346267-l08ld2cy	273	2	ABMiZ.	ABMiZ.	NNP
cord-346267-l08ld2cy	273	3	1848	1848	CD
cord-346267-l08ld2cy	273	4	.	.	.
cord-346267-l08ld2cy	274	1	A	a	DT
cord-346267-l08ld2cy	274	2	treatise	treatise	NN
cord-346267-l08ld2cy	274	3	on	on	IN
cord-346267-l08ld2cy	274	4	the	the	DT
cord-346267-l08ld2cy	274	5	small	small	JJ
cord-346267-l08ld2cy	274	6	-	-	HYPH
cord-346267-l08ld2cy	274	7	pox	pox	NN
cord-346267-l08ld2cy	274	8	and	and	CC
cord-346267-l08ld2cy	274	9	measles	measle	NNS
cord-346267-l08ld2cy	275	1	The	the	DT
cord-346267-l08ld2cy	275	2	history	history	NN
cord-346267-l08ld2cy	275	3	of	of	IN
cord-346267-l08ld2cy	275	4	the	the	DT
cord-346267-l08ld2cy	275	5	acute	acute	JJ
cord-346267-l08ld2cy	275	6	exanthemata	exanthemata	JJ
cord-346267-l08ld2cy	275	7	Comparison	comparison	NN
cord-346267-l08ld2cy	275	8	of	of	IN
cord-346267-l08ld2cy	275	9	sequences	sequence	NNS
cord-346267-l08ld2cy	275	10	of	of	IN
cord-346267-l08ld2cy	275	11	the	the	DT
cord-346267-l08ld2cy	275	12	H	H	NNP
cord-346267-l08ld2cy	275	13	,	,	,
cord-346267-l08ld2cy	275	14	F	F	NNP
cord-346267-l08ld2cy	275	15	,	,	,
cord-346267-l08ld2cy	275	16	and	and	CC
cord-346267-l08ld2cy	275	17	N	n	CD
cord-346267-l08ld2cy	275	18	coding	coding	NN
cord-346267-l08ld2cy	275	19	genes	gene	NNS
cord-346267-l08ld2cy	275	20	of	of	IN
cord-346267-l08ld2cy	275	21	measles	measles	NN
cord-346267-l08ld2cy	275	22	-	-	HYPH
cord-346267-l08ld2cy	275	23	virus	virus	NN
cord-346267-l08ld2cy	275	24	vaccine	vaccine	NN
cord-346267-l08ld2cy	275	25	strains	strain	VBZ
cord-346267-l08ld2cy	275	26	The	the	DT
cord-346267-l08ld2cy	275	27	virion	virion	NN
cord-346267-l08ld2cy	275	28	glycoproteins	glycoprotein	NNS
cord-346267-l08ld2cy	275	29	of	of	IN
cord-346267-l08ld2cy	275	30	Ebola	Ebola	NNP
cord-346267-l08ld2cy	275	31	viruses	virus	NNS
cord-346267-l08ld2cy	275	32	are	be	VBP
cord-346267-l08ld2cy	275	33	encoded	encode	VBN
cord-346267-l08ld2cy	275	34	in	in	IN
cord-346267-l08ld2cy	275	35	two	two	CD
cord-346267-l08ld2cy	275	36	reading	read	VBG
cord-346267-l08ld2cy	275	37	frames	frame	NNS
cord-346267-l08ld2cy	275	38	and	and	CC
cord-346267-l08ld2cy	275	39	are	be	VBP
cord-346267-l08ld2cy	275	40	expressed	express	VBN
cord-346267-l08ld2cy	275	41	through	through	IN
cord-346267-l08ld2cy	275	42	transcriptional	transcriptional	JJ
cord-346267-l08ld2cy	275	43	editing	edit	VBG
cord-346267-l08ld2cy	275	44	A	a	DT
cord-346267-l08ld2cy	275	45	model	model	NN
cord-346267-l08ld2cy	275	46	of	of	IN
cord-346267-l08ld2cy	275	47	directional	directional	JJ
cord-346267-l08ld2cy	275	48	selection	selection	NN
cord-346267-l08ld2cy	275	49	applied	apply	VBN
cord-346267-l08ld2cy	275	50	to	to	IN
cord-346267-l08ld2cy	275	51	the	the	DT
cord-346267-l08ld2cy	275	52	evolution	evolution	NN
cord-346267-l08ld2cy	275	53	of	of	IN
cord-346267-l08ld2cy	275	54	drug	drug	NN
cord-346267-l08ld2cy	275	55	resistance	resistance	NN
cord-346267-l08ld2cy	275	56	in	in	IN
cord-346267-l08ld2cy	275	57	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	275	58	Choosing	choose	VBG
cord-346267-l08ld2cy	275	59	appropriate	appropriate	JJ
cord-346267-l08ld2cy	275	60	substitution	substitution	NN
cord-346267-l08ld2cy	275	61	models	model	NNS
cord-346267-l08ld2cy	275	62	for	for	IN
cord-346267-l08ld2cy	275	63	the	the	DT
cord-346267-l08ld2cy	275	64	phylogenetic	phylogenetic	JJ
cord-346267-l08ld2cy	275	65	analysis	analysis	NN
cord-346267-l08ld2cy	275	66	of	of	IN
cord-346267-l08ld2cy	275	67	proteincoding	proteincode	VBG
cord-346267-l08ld2cy	275	68	sequences	sequence	NNS
cord-346267-l08ld2cy	275	69	Improved	Improved	NNP
cord-346267-l08ld2cy	275	70	sampling	sampling	NN
cord-346267-l08ld2cy	275	71	-	-	HYPH
cord-346267-l08ld2cy	275	72	importance	importance	NN
cord-346267-l08ld2cy	275	73	resampling	resampling	NN
cord-346267-l08ld2cy	275	74	and	and	CC
cord-346267-l08ld2cy	275	75	reduced	reduced	JJ
cord-346267-l08ld2cy	275	76	bias	bias	NN
cord-346267-l08ld2cy	275	77	importance	importance	NN
cord-346267-l08ld2cy	275	78	sampling	sample	VBG
cord-346267-l08ld2cy	275	79	Many	many	JJ
cord-346267-l08ld2cy	275	80	-	-	HYPH
cord-346267-l08ld2cy	275	81	core	core	NN
cord-346267-l08ld2cy	275	82	algorithms	algorithm	NNS
cord-346267-l08ld2cy	275	83	for	for	IN
cord-346267-l08ld2cy	275	84	statistical	statistical	JJ
cord-346267-l08ld2cy	275	85	phylogenetics	phylogenetic	NNS
cord-346267-l08ld2cy	275	86	Model	Model	NNP
cord-346267-l08ld2cy	275	87	selection	selection	NN
cord-346267-l08ld2cy	275	88	in	in	IN
cord-346267-l08ld2cy	275	89	phylogenetics	phylogenetic	NNS
cord-346267-l08ld2cy	275	90	The	the	DT
cord-346267-l08ld2cy	275	91	origin	origin	NN
cord-346267-l08ld2cy	275	92	and	and	CC
cord-346267-l08ld2cy	275	93	evolution	evolution	NN
cord-346267-l08ld2cy	275	94	of	of	IN
cord-346267-l08ld2cy	275	95	Ebola	Ebola	NNP
cord-346267-l08ld2cy	275	96	and	and	CC
cord-346267-l08ld2cy	275	97	Marburg	Marburg	NNP
cord-346267-l08ld2cy	276	1	viruses	virus	NNS
cord-346267-l08ld2cy	277	1	Characterization	characterization	NN
cord-346267-l08ld2cy	277	2	of	of	IN
cord-346267-l08ld2cy	277	3	the	the	DT
cord-346267-l08ld2cy	277	4	1918	1918	CD
cord-346267-l08ld2cy	277	5	influenza	influenza	NN
cord-346267-l08ld2cy	277	6	virus	virus	NN
cord-346267-l08ld2cy	277	7	polymerase	polymerase	NN
cord-346267-l08ld2cy	277	8	genes	gene	NNS
cord-346267-l08ld2cy	278	1	Some	some	DT
cord-346267-l08ld2cy	278	2	probabilistic	probabilistic	JJ
cord-346267-l08ld2cy	278	3	and	and	CC
cord-346267-l08ld2cy	278	4	statistical	statistical	JJ
cord-346267-l08ld2cy	278	5	problems	problem	NNS
cord-346267-l08ld2cy	278	6	in	in	IN
cord-346267-l08ld2cy	278	7	the	the	DT
cord-346267-l08ld2cy	278	8	analysis	analysis	NN
cord-346267-l08ld2cy	278	9	of	of	IN
cord-346267-l08ld2cy	278	10	DNA	dna	NN
cord-346267-l08ld2cy	278	11	sequences	sequence	NNS
cord-346267-l08ld2cy	278	12	Filoviruses	Filoviruses	NNPS
cord-346267-l08ld2cy	278	13	are	be	VBP
cord-346267-l08ld2cy	278	14	ancient	ancient	JJ
cord-346267-l08ld2cy	278	15	and	and	CC
cord-346267-l08ld2cy	278	16	integrated	integrate	VBN
cord-346267-l08ld2cy	278	17	into	into	IN
cord-346267-l08ld2cy	278	18	mammalian	mammalian	JJ
cord-346267-l08ld2cy	278	19	genomes	genome	NNS
cord-346267-l08ld2cy	278	20	GP	GP	NNP
cord-346267-l08ld2cy	278	21	mRNA	mrna	NN
cord-346267-l08ld2cy	278	22	of	of	IN
cord-346267-l08ld2cy	278	23	Ebola	Ebola	NNP
cord-346267-l08ld2cy	278	24	virus	virus	NN
cord-346267-l08ld2cy	278	25	is	be	VBZ
cord-346267-l08ld2cy	278	26	edited	edit	VBN
cord-346267-l08ld2cy	278	27	by	by	IN
cord-346267-l08ld2cy	278	28	the	the	DT
cord-346267-l08ld2cy	278	29	Ebola	Ebola	NNP
cord-346267-l08ld2cy	278	30	virus	virus	NN
cord-346267-l08ld2cy	278	31	polymerase	polymerase	NN
cord-346267-l08ld2cy	278	32	and	and	CC
cord-346267-l08ld2cy	278	33	by	by	IN
cord-346267-l08ld2cy	278	34	T7	T7	NNP
cord-346267-l08ld2cy	278	35	and	and	CC
cord-346267-l08ld2cy	278	36	vaccinia	vaccinia	NN
cord-346267-l08ld2cy	278	37	virus	virus	NN
cord-346267-l08ld2cy	278	38	polymerases	polymerases	VBP
cord-346267-l08ld2cy	278	39	Wave	wave	NN
cord-346267-l08ld2cy	278	40	-	-	HYPH
cord-346267-l08ld2cy	278	41	like	like	JJ
cord-346267-l08ld2cy	278	42	spread	spread	NN
cord-346267-l08ld2cy	278	43	of	of	IN
cord-346267-l08ld2cy	278	44	Ebola	Ebola	NNP
cord-346267-l08ld2cy	278	45	Zaire	Zaire	NNP
cord-346267-l08ld2cy	279	1	The	the	DT
cord-346267-l08ld2cy	279	2	re	re	NN
cord-346267-l08ld2cy	279	3	-	-	NN
cord-346267-l08ld2cy	279	4	emergence	emergence	NN
cord-346267-l08ld2cy	279	5	of	of	IN
cord-346267-l08ld2cy	279	6	H1N1	H1N1	NNP
cord-346267-l08ld2cy	279	7	influenza	influenza	NN
cord-346267-l08ld2cy	279	8	virus	virus	NN
cord-346267-l08ld2cy	279	9	in	in	IN
cord-346267-l08ld2cy	279	10	1977	1977	CD
cord-346267-l08ld2cy	279	11	:	:	:
cord-346267-l08ld2cy	279	12	a	a	DT
cord-346267-l08ld2cy	279	13	cautionary	cautionary	JJ
cord-346267-l08ld2cy	279	14	tale	tale	NN
cord-346267-l08ld2cy	279	15	for	for	IN
cord-346267-l08ld2cy	279	16	estimating	estimate	VBG
cord-346267-l08ld2cy	279	17	divergence	divergence	NN
cord-346267-l08ld2cy	279	18	times	time	NNS
cord-346267-l08ld2cy	279	19	using	use	VBG
cord-346267-l08ld2cy	279	20	biologically	biologically	RB
cord-346267-l08ld2cy	279	21	unrealistic	unrealistic	JJ
cord-346267-l08ld2cy	279	22	sampling	sampling	NN
cord-346267-l08ld2cy	279	23	dates	date	VBZ
cord-346267-l08ld2cy	279	24	A	a	DT
cord-346267-l08ld2cy	279	25	quick	quick	JJ
cord-346267-l08ld2cy	279	26	fuse	fuse	NN
cord-346267-l08ld2cy	279	27	and	and	CC
cord-346267-l08ld2cy	279	28	the	the	DT
cord-346267-l08ld2cy	279	29	emergence	emergence	NN
cord-346267-l08ld2cy	279	30	of	of	IN
cord-346267-l08ld2cy	279	31	taura	taura	NNP
cord-346267-l08ld2cy	279	32	syndrome	syndrome	NNP
cord-346267-l08ld2cy	279	33	virus	virus	NN
cord-346267-l08ld2cy	279	34	Dating	date	VBG
cord-346267-l08ld2cy	279	35	the	the	DT
cord-346267-l08ld2cy	279	36	age	age	NN
cord-346267-l08ld2cy	279	37	of	of	IN
cord-346267-l08ld2cy	279	38	the	the	DT
cord-346267-l08ld2cy	279	39	SIV	SIV	NNP
cord-346267-l08ld2cy	279	40	lineages	lineage	NNS
cord-346267-l08ld2cy	279	41	that	that	WDT
cord-346267-l08ld2cy	279	42	gave	give	VBD
cord-346267-l08ld2cy	279	43	rise	rise	NN
cord-346267-l08ld2cy	279	44	to	to	IN
cord-346267-l08ld2cy	279	45	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	279	46	and	and	CC
cord-346267-l08ld2cy	280	1	HIV-2	HIV-2	NNP
cord-346267-l08ld2cy	280	2	Relaxed	relaxed	JJ
cord-346267-l08ld2cy	280	3	selection	selection	NN
cord-346267-l08ld2cy	280	4	and	and	CC
cord-346267-l08ld2cy	280	5	the	the	DT
cord-346267-l08ld2cy	280	6	evolution	evolution	NN
cord-346267-l08ld2cy	280	7	of	of	IN
cord-346267-l08ld2cy	280	8	RNA	RNA	NNP
cord-346267-l08ld2cy	280	9	virus	virus	NN
cord-346267-l08ld2cy	280	10	mucin	mucin	NN
cord-346267-l08ld2cy	280	11	-	-	HYPH
cord-346267-l08ld2cy	280	12	like	like	JJ
cord-346267-l08ld2cy	280	13	pathogenicity	pathogenicity	NN
cord-346267-l08ld2cy	280	14	factors	factor	NNS
cord-346267-l08ld2cy	280	15	Immune	immune	JJ
cord-346267-l08ld2cy	280	16	and	and	CC
cord-346267-l08ld2cy	280	17	artificial	artificial	JJ
cord-346267-l08ld2cy	280	18	selection	selection	NN
cord-346267-l08ld2cy	280	19	in	in	IN
cord-346267-l08ld2cy	280	20	the	the	DT
cord-346267-l08ld2cy	280	21	haemagglutinin	haemagglutinin	NNP
cord-346267-l08ld2cy	280	22	(	(	-LRB-
cord-346267-l08ld2cy	280	23	H	H	NNP
cord-346267-l08ld2cy	280	24	)	)	-RRB-
cord-346267-l08ld2cy	280	25	glycoprotein	glycoprotein	NN
cord-346267-l08ld2cy	280	26	of	of	IN
cord-346267-l08ld2cy	280	27	measles	measle	NNS
cord-346267-l08ld2cy	280	28	virus	virus	NN
cord-346267-l08ld2cy	280	29	Increased	increase	VBD
cord-346267-l08ld2cy	280	30	positive	positive	JJ
cord-346267-l08ld2cy	280	31	selection	selection	NN
cord-346267-l08ld2cy	280	32	pressure	pressure	NN
cord-346267-l08ld2cy	280	33	in	in	IN
cord-346267-l08ld2cy	280	34	persistent	persistent	JJ
cord-346267-l08ld2cy	280	35	(	(	-LRB-
cord-346267-l08ld2cy	280	36	SSPE	SSPE	NNP
cord-346267-l08ld2cy	280	37	)	)	-RRB-
cord-346267-l08ld2cy	280	38	versus	versus	IN
cord-346267-l08ld2cy	280	39	acute	acute	JJ
cord-346267-l08ld2cy	280	40	measles	measle	NNS
cord-346267-l08ld2cy	280	41	virus	virus	NN
cord-346267-l08ld2cy	280	42	infections	infection	NNS
cord-346267-l08ld2cy	280	43	Can	Can	MD
cord-346267-l08ld2cy	280	44	deleterious	deleterious	JJ
cord-346267-l08ld2cy	280	45	mutations	mutation	NNS
cord-346267-l08ld2cy	280	46	explain	explain	VBP
cord-346267-l08ld2cy	280	47	the	the	DT
cord-346267-l08ld2cy	280	48	time	time	NN
cord-346267-l08ld2cy	280	49	dependency	dependency	NN
cord-346267-l08ld2cy	280	50	of	of	IN
cord-346267-l08ld2cy	280	51	molecular	molecular	JJ
cord-346267-l08ld2cy	280	52	rate	rate	NN
cord-346267-l08ld2cy	280	53	estimates	estimate	NNS
cord-346267-l08ld2cy	280	54	?	?	.
cord-346267-l08ld2cy	281	1	Point	point	NN
cord-346267-l08ld2cy	281	2	,	,	,
cord-346267-l08ld2cy	281	3	counterpoint	counterpoint	NN
cord-346267-l08ld2cy	281	4	:	:	:
cord-346267-l08ld2cy	282	1	the	the	DT
cord-346267-l08ld2cy	282	2	evolution	evolution	NN
cord-346267-l08ld2cy	282	3	of	of	IN
cord-346267-l08ld2cy	282	4	pathogenic	pathogenic	JJ
cord-346267-l08ld2cy	282	5	viruses	virus	NNS
cord-346267-l08ld2cy	282	6	and	and	CC
cord-346267-l08ld2cy	282	7	their	-PRON-	PRP$
cord-346267-l08ld2cy	282	8	human	human	JJ
cord-346267-l08ld2cy	282	9	hosts	host	NNS
cord-346267-l08ld2cy	282	10	Direct	direct	JJ
cord-346267-l08ld2cy	282	11	evidence	evidence	NN
cord-346267-l08ld2cy	282	12	of	of	IN
cord-346267-l08ld2cy	282	13	extensive	extensive	JJ
cord-346267-l08ld2cy	282	14	diversity	diversity	NN
cord-346267-l08ld2cy	282	15	of	of	IN
cord-346267-l08ld2cy	282	16	HIV-1	HIV-1	NNP
cord-346267-l08ld2cy	282	17	in	in	IN
cord-346267-l08ld2cy	282	18	Kinshasa	Kinshasa	NNP
cord-346267-l08ld2cy	282	19	by	by	IN
cord-346267-l08ld2cy	282	20	1960	1960	CD
cord-346267-l08ld2cy	282	21	Island	Island	NNP
cord-346267-l08ld2cy	282	22	biogeography	biogeography	NN
cord-346267-l08ld2cy	282	23	reveals	reveal	VBZ
cord-346267-l08ld2cy	282	24	the	the	DT
cord-346267-l08ld2cy	282	25	deep	deep	JJ
cord-346267-l08ld2cy	282	26	history	history	NN
cord-346267-l08ld2cy	282	27	of	of	IN
cord-346267-l08ld2cy	282	28	SIV	SIV	NNP
cord-346267-l08ld2cy	282	29	Maximum	Maximum	NNP
cord-346267-l08ld2cy	282	30	-	-	HYPH
cord-346267-l08ld2cy	282	31	likelihood	likelihood	NN
cord-346267-l08ld2cy	282	32	estimation	estimation	NN
cord-346267-l08ld2cy	282	33	of	of	IN
cord-346267-l08ld2cy	282	34	phylogeny	phylogeny	NN
cord-346267-l08ld2cy	282	35	from	from	IN
cord-346267-l08ld2cy	282	36	DNA	dna	NN
cord-346267-l08ld2cy	282	37	sequences	sequence	NNS
cord-346267-l08ld2cy	282	38	when	when	WRB
cord-346267-l08ld2cy	282	39	substitution	substitution	NN
cord-346267-l08ld2cy	282	40	rates	rate	NNS
cord-346267-l08ld2cy	282	41	differ	differ	VBP
cord-346267-l08ld2cy	282	42	over	over	IN
cord-346267-l08ld2cy	282	43	sites	site	NNS
cord-346267-l08ld2cy	282	44	Likelihood	likelihood	NN
cord-346267-l08ld2cy	282	45	ratio	ratio	NN
cord-346267-l08ld2cy	282	46	tests	test	NNS
cord-346267-l08ld2cy	282	47	for	for	IN
cord-346267-l08ld2cy	282	48	detecting	detect	VBG
cord-346267-l08ld2cy	282	49	positive	positive	JJ
cord-346267-l08ld2cy	282	50	selection	selection	NN
cord-346267-l08ld2cy	282	51	and	and	CC
cord-346267-l08ld2cy	282	52	application	application	NN
cord-346267-l08ld2cy	282	53	to	to	IN
cord-346267-l08ld2cy	282	54	primate	primate	JJ
cord-346267-l08ld2cy	282	55	lysozyme	lysozyme	NNS
cord-346267-l08ld2cy	282	56	evolution	evolution	NN
cord-346267-l08ld2cy	282	57	A	a	DT
cord-346267-l08ld2cy	282	58	new	new	JJ
cord-346267-l08ld2cy	282	59	method	method	NN
cord-346267-l08ld2cy	282	60	of	of	IN
cord-346267-l08ld2cy	282	61	inference	inference	NN
cord-346267-l08ld2cy	282	62	of	of	IN
cord-346267-l08ld2cy	282	63	ancestral	ancestral	JJ
cord-346267-l08ld2cy	282	64	nucleotide	nucleotide	NN
cord-346267-l08ld2cy	282	65	and	and	CC
cord-346267-l08ld2cy	282	66	amino	amino	NN
cord-346267-l08ld2cy	282	67	acid	acid	NN
cord-346267-l08ld2cy	282	68	sequences	sequence	NNS
cord-346267-l08ld2cy	282	69	Bayesian	bayesian	JJ
cord-346267-l08ld2cy	282	70	estimates	estimate	NNS
cord-346267-l08ld2cy	282	71	of	of	IN
cord-346267-l08ld2cy	282	72	the	the	DT
cord-346267-l08ld2cy	282	73	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	282	74	rate	rate	NN
cord-346267-l08ld2cy	282	75	and	and	CC
cord-346267-l08ld2cy	282	76	age	age	NN
cord-346267-l08ld2cy	282	77	of	of	IN
cord-346267-l08ld2cy	282	78	hepatitis	hepatitis	NN
cord-346267-l08ld2cy	282	79	B	B	NNP
cord-346267-l08ld2cy	282	80	virus	virus	NN
cord-346267-l08ld2cy	282	81	Genetic	genetic	JJ
cord-346267-l08ld2cy	282	82	variability	variability	NN
cord-346267-l08ld2cy	282	83	and	and	CC
cord-346267-l08ld2cy	282	84	molecular	molecular	JJ
cord-346267-l08ld2cy	282	85	evolution	evolution	NN
cord-346267-l08ld2cy	282	86	of	of	IN
cord-346267-l08ld2cy	282	87	the	the	DT
cord-346267-l08ld2cy	282	88	human	human	JJ
cord-346267-l08ld2cy	282	89	respiratory	respiratory	JJ
cord-346267-l08ld2cy	282	90	syncytial	syncytial	JJ
cord-346267-l08ld2cy	282	91	virus	virus	NN
cord-346267-l08ld2cy	282	92	subgroup	subgroup	NN
cord-346267-l08ld2cy	282	93	B	b	NN
cord-346267-l08ld2cy	282	94	attachment	attachment	NN
cord-346267-l08ld2cy	282	95	G	g	NN
cord-346267-l08ld2cy	282	96	protein	protein	NN
cord-346267-l08ld2cy	283	1	We	-PRON-	PRP
cord-346267-l08ld2cy	283	2	thank	thank	VBP
cord-346267-l08ld2cy	283	3	the	the	DT
cord-346267-l08ld2cy	283	4	Associate	Associate	NNP
cord-346267-l08ld2cy	283	5	Editor	Editor	NNP
cord-346267-l08ld2cy	283	6	Alexei	Alexei	NNP
cord-346267-l08ld2cy	283	7	Drummond	Drummond	NNP
cord-346267-l08ld2cy	283	8	,	,	,
cord-346267-l08ld2cy	283	9	Jeff	Jeff	NNP
cord-346267-l08ld2cy	283	10	Thorne	Thorne	NNP
cord-346267-l08ld2cy	283	11	,	,	,
cord-346267-l08ld2cy	283	12	and	and	CC
cord-346267-l08ld2cy	283	13	two	two	CD
cord-346267-l08ld2cy	283	14	anonymous	anonymous	JJ
cord-346267-l08ld2cy	283	15	reviewers	reviewer	NNS
cord-346267-l08ld2cy	283	16	for	for	IN
cord-346267-l08ld2cy	283	17	their	-PRON-	PRP$
cord-346267-l08ld2cy	283	18	valuable	valuable	JJ
cord-346267-l08ld2cy	283	19	comments	comment	NNS
cord-346267-l08ld2cy	283	20	.	.	.
cord-346267-l08ld2cy	284	1	This	this	DT
cord-346267-l08ld2cy	284	2	research	research	NN
cord-346267-l08ld2cy	284	3	was	be	VBD
cord-346267-l08ld2cy	284	4	supported	support	VBN
cord-346267-l08ld2cy	284	5	in	in	IN
cord-346267-l08ld2cy	284	6	part	part	NN
cord-346267-l08ld2cy	284	7	by	by	IN
cord-346267-l08ld2cy	284	8	the	the	DT
cord-346267-l08ld2cy	284	9	National	National	NNP
cord-346267-l08ld2cy	284	10	Institutes	Institutes	NNPS
cord-346267-l08ld2cy	284	11	of	of	IN
cord-346267-l08ld2cy	284	12	Health	Health	NNP
cord-346267-l08ld2cy	284	13	(	(	-LRB-
cord-346267-l08ld2cy	284	14	 	 	_SP
cord-346267-l08ld2cy	284	15	The	the	DT
cord-346267-l08ld2cy	284	16	relative	relative	JJ
cord-346267-l08ld2cy	284	17	importance	importance	NN
cord-346267-l08ld2cy	284	18	of	of	IN
cord-346267-l08ld2cy	284	19	these	these	DT
cord-346267-l08ld2cy	284	20	factors	factor	NNS
cord-346267-l08ld2cy	284	21	in	in	IN
cord-346267-l08ld2cy	284	22	understanding	understand	VBG
cord-346267-l08ld2cy	284	23	the	the	DT
cord-346267-l08ld2cy	284	24	evolutionary	evolutionary	JJ
cord-346267-l08ld2cy	284	25	history	history	NN
cord-346267-l08ld2cy	284	26	of	of	IN
cord-346267-l08ld2cy	284	27	other	other	JJ
cord-346267-l08ld2cy	284	28	taxa	taxon	NNS
cord-346267-l08ld2cy	284	29	remains	remain	VBZ
cord-346267-l08ld2cy	284	30	to	to	TO
cord-346267-l08ld2cy	284	31	be	be	VB
cord-346267-l08ld2cy	284	32	seen	see	VBN
cord-346267-l08ld2cy	284	33	.	.	.
cord-346267-l08ld2cy	285	1	Supplementary	supplementary	JJ
cord-346267-l08ld2cy	285	2	figs	fig	NNS
cord-346267-l08ld2cy	285	3	.	.	.
cord-346267-l08ld2cy	286	1	S1-S3	S1-S3	NNP
cord-346267-l08ld2cy	286	2	are	be	VBP
cord-346267-l08ld2cy	286	3	available	available	JJ
cord-346267-l08ld2cy	286	4	at	at	IN
cord-346267-l08ld2cy	286	5	Molecular	Molecular	NNP
cord-346267-l08ld2cy	286	6	Biology	Biology	NNP
cord-346267-l08ld2cy	286	7	and	and	CC
cord-346267-l08ld2cy	286	8	Evolution	Evolution	NNP
cord-346267-l08ld2cy	286	9	online	online	RB
cord-346267-l08ld2cy	286	10	(	(	-LRB-
cord-346267-l08ld2cy	286	11	http://www.mbe	http://www.mbe	ADD
cord-346267-l08ld2cy	286	12	.	.	.
cord-346267-l08ld2cy	287	1	oxfordjournals.org/	oxfordjournals.org/	NNP
cord-346267-l08ld2cy	287	2	)	)	-RRB-
cord-346267-l08ld2cy	287	3	.	.	.