untitled


Volume 132, 2015, pp. 481–485
DOI: 10.1642/AUK-15-1.1

COMMENTARY

Subspecies and the philosophy of science

Michael A. Patten

Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
mpatten@ou.edu

Submitted January 3, 2015; Accepted January 13, 2015; Published March 25, 2015

ABSTRACT
Phylogenetic methods increasingly are brought to bear on questions of subspecies taxonomy, but several recent
examples highlight the need for a clear and consistent philosophical approach to how genetic data are used to assess
subspecies limits. Such standards are crucial conceptually, whether or not taxonomic decisions affect conservation
decisions, as they might in a recent study focused on the California Gnatcatcher (Polioptila californica), a taxon
currently protected under the U.S. Endangered Species Act. It is also crucial that any adopted framework allows each of
a full range of alternatives to be either supported or rejected. In this spirit, in addition to recommending best practices,
I propose an amendment to the phylogenetic species concept to include a subspecies category.

Keywords: diagnosability, effect size, Polioptila californica, reciprocal monophyly, subspecies

Subespecies y la Filosofı́a de la Ciencia

RESUMEN
Los métodos filogenéticos influencian cada vez más los cuestionamientos sobre la taxonomı́a de las subespecies, pero
varios ejemplos recientes destacan la necesidad de un abordaje filosófico claro y consistente de cómo los datos
genéticos son usados para determinar los ĺımites de las subespecies. Estos estándares son conceptualmente cruciales
si las decisiones taxonómicas afectan o no a las decisiones de conservación, como podrı́an haberlo hecho en un
estudio reciente enfocado en Polioptila californica, un taxón actualmente protegido por la Ley de Especies en Peligro
de Estados Unidos. También es crucial que el marco adoptado permita que cada una de las alternativas de un rango
completo sea apoyada o rechazada. Con este espı́ritu, además de recomendar buenas prácticas, propongo una adenda
al concepto filogenético de especie para incluir una categorı́a de subespecie.

Palabras clave: diagnosticabilidad, monofilia recı́proca, Polioptila californica, subespecie, tamaño del efecto

The Subspecies Debate

No taxonomic rank has been more maligned or misun-

derstood than the subspecies. Attacks on this rank’s value

date back to the early 1950s (e.g., Wilson and Brown 1953),

the principal argument against it being that subspecies are

‘‘arbitrary,’’ a charge that could be levied with equal force

at the genus, family, or any other higher rank (which tend

not to correspond across phyla or kingdoms; Avise and

Mitchell 2007). Although there may be merit in setting

aside the whole of the Linnaean hierarchy (Ereshefsky

2001), it remains the dominant way in which we classify

organisms and, hence, communicate about ecological

communities, phylogenetic relationships, biogeographic

processes, and a host of other basic topics in ecology and

evolutionary biology. Linnaeus’s scheme is likely to be with

us for years to come, so we ought to determine how best to

standardize its use across all organisms and ensure that

classification into established ranks follows a logical and

repeatable procedure. This last point, repeatability, is an

often neglected cornerstone of the scientific process. Many

criticized Sibley and Ahlquist (1990) when they opted to

allow particular levels of Dt50, a measure of the difference
in temperature at which DNA heteroduplexes and

homoduplexes denature, to assign ranks of family, tribe,

order, and the like—yet, if nothing else, the procedure and

the assignment were repeatable.

Strides have been made to reduce subjectivity in other

ranks, most notably that of species, a rank even Darwin

refused to define despite its appearing prominently in the

title of his famous book. Darwin considered species limits

arbitrary, and modern debates about the relative virtues of

particular species concepts have done little to address the

inherent subjectivity of, say, what exactly it means to be

reproductively isolated (how much hybridization is too

much?) or how exactly to identify a clade that corresponds

to something above an isolated population yet below a

wholesale radiation (i.e. the ‘‘diagnosable clusters’’ of the

phylogenetic species concept; Cracraft 1983). A crucial

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step in the direction of objectivity has been a recent

emphasis on effect size (of trait variability) to determine

species and subspecies limits (Patten 2010, Tobias et al.

2010, Winker 2010). Akin to Sibley and Ahlquist’s (1990)

Dt50 thresholds, the idea is that differences of a particular
magnitude—a large effect size—for a trait being examined

will indicate whether 2 populations are 2 species (Tobias et

al. 2010). A similar argument can be made to assess

whether 2 populations correspond to 2 subspecies (Patten

2010), provided it is clear that there are distinct thresholds

that determine species limits and subspecies limits.

This last point, that different taxonomic ranks have

different thresholds of distinctiveness, should go without

saying, given that the whole of Linnaean hierarchy is

predicated on this view; but a failure to set distinct

thresholds is common, even if a particular study did not

assess effect size per se. A prevalent example is when

researchers bring molecular methods to bear on questions

of subspecies with the (often unstated) expectation that

subspecies ought to differ in the same way that (phyloge-

netic or other lineage-based) species would. Nowhere is

this situation clearer than in assessments, implicit or

explicit, of subspecies’ ‘‘validity’’ in which one or several
neutral genetic markers are found not to be reciprocally

monophyletic (or yield unique haplotypes or form distinct

clusters) among populations under study, as in recent

papers on intraspecific variation in the green comma

(Polygonia faunus; Kodandaramaiah et al. 2012), California

Gnatcatcher (Polioptila californica; Zink et al. 2013; cf.

McCormack and Maley 2015), and western shovel-nosed

snake (Chionactis occipitalis; Wood et al. 2014). In each

case, the authors drew broad conclusions about subspecies

validity after they had failed to meet genetic expectations

for species limits, and in no case did the authors explain

how they would assess subspecies limits in relation to a
particular definition of the term ‘‘subspecies.’’

What Is a Subspecies?
It is incumbent on any scientist, no matter the field of

inquiry, to adhere to (or at least specify) definitions. It is

senseless for particle physicists to argue about whether a

Higgs boson exists if they do not agree on what a Higgs

boson is. The taxonomic rank of subspecies has been

defined for many decades (e.g., Mayr 1942, Amadon 1949,

Rand and Traylor 1950), and that definition can be

summarized simply as ‘‘a collection of populations
occupying a distinct breeding range and diagnosably

distinct from other such populations’’ (Patten 2009), with
the crucial caveat that these populations comprise

‘‘completely fertile individuals’’ (Mayr 1942:106); that is,
populations are not reproductively isolated from one

another. Compared with a biological species, Patten and

Unitt (2002:27) noted that ‘‘Concealed by the nesting of
the two categories in the Linnaean hierarchy is that they

address qualitatively different aspects of biology: the

species addresses reproductive and behavioral criteria,

the subspecies morphological diagnosability.’’
The diagnosability issue has received attention for well

over a half-century (Rand and Traylor 1950, Amadon and

Short 1992), and a host of practitioners have argued for a

standard statistical threshold, the ‘‘75% rule’’ being the
predominant (and most widely accepted) example (Ama-

don 1949, Pimentel 1959, Baker et al. 2002, Patten and

Unitt 2002, Haig et al. 2006). The 75% rule means that

subspecies A is recognized taxonomically if, and only if,

�75% of the individuals in group A lie outside 99% of the
range of variation of group B for the character or set of

characters under consideration (Patten and Unitt 2002).

Taxonomic recognition of subspecies B requires meeting

the opposite criterion: 75% of its individuals outside 99% of

the variation in group A. In terms of a joint probability, a

more liberal 75% rule (i.e. 75% of group A from 75% of

group B) is equivalent to a difference of 5% of group A

from 99.9% of group B (Pimentel 1959), a level of

separation akin to the accepted standard type I error rate

of a ¼ 0.05. Accordingly, the stricter 75% rule defined
above conforms more than adequately to statistical (i.e.

probabilistic) convention in ecology and evolutionary
biology.

It is unclear how ‘‘subspecies’’ was defined in the studies
of the butterfly, bird, and snake mentioned above. It may

be that a subspecies was viewed as ‘‘lower than a species,’’
however that would be defined, or perhaps it was viewed as

an ‘‘incipient species,’’ even though Mayr (1942:155)
admonished that although under a model of geographic

(as opposed to ecological, polyploid, or other) speciation,

every biological species must go through a subspecies

stage, this condition does not mean that every subspecies

will become a species. Regardless, it does not follow that

the same criteria for assessing species limits can be used to

assess subspecies limits, chiefly because a simple conse-

quence of the definition of subspecies is that gene flow (or

its inferred possibility in contact) has not been severed.

The possibility of ongoing gene flow changes the equation,

and so it makes no sense to expect clusters of genes or

reciprocal monophyly among groups, at least with respect

to neutral markers. Some nuclear genes under natural

selection are expected to differ, given that subspecies

characters are assumed to have a genetic basis (Remsen

2010); that is, the ‘‘typical characters of [a] group of
individuals are genetically fixed’’ (Mayr 1942:106).

Detecting Subspecies Genetically
We might rephrase our definition of ‘‘subspecies’’ to
emphasize that the term refers to ‘‘heritable geographic
variation in phenotype.’’ Each of these 3 components—the
heritable, the geographic, and the phenotypic—is crucial to

a proper understanding of what this taxonomic rank

The Auk: Ornithological Advances 132:481–485, Q 2015 American Ornithologists’ Union

482 A philosophy of subspecies M. A. Patten



encapsulates. A clear implication of this rephrasing is that

for any given subspecies, there will be a gene or set of

genes that determines phenotype of individuals in a

particular geographic area. As such, any genetic assess-

ment of subspecies ought to focus on identification and

elucidation of these genes. Today, avian systematists have

access to 0.5% of avian genomes (see Jarvis et al. 2014,

Zhang et al. 2014), but one day soon, avian systematists

will have access to whole genomes of any species they wish

to study, coupled with a key of how specific phenotypic

traits map to that genome. With these tools, researchers

will be able to identify which genes correspond to key

phenotypic traits that vary geographically; with such data

in hand, basic assignment tests (Piry et al. 2004, Manel et

al. 2007) could be used to classify genetically screened

individuals into geographically circumscribed populations.

The foregoing assessment postulates the existence of

‘‘subspecies genes,’’ genes responsible for phenotypic
variation associated with different geographic populations.

A key implication of this view is that phenotypic variation

is not merely a product of environment. If it can be shown

that environmental variance rather than genetic variation

(i.e. in the sense of quantitative genetics) principally shapes

phenotype, then subspecies ought not be named. Little
work has been devoted to this question, although there are

some preliminary ventures, such as a reported common

garden experiment (which failed the test of a true common

garden, but it was a step in the right direction) of Swamp

Sparrow (Melospiza georgiana) subspecies (Ballentine and

Greenberg 2010). Another implication is that the ‘‘sub-
species genes’’ will be nonneutral—they are postulated to
be under natural selection for local adaptation to

environmental conditions, particularly of plumage color

and pattern (Remsen 2010), most often, I suggest, via a

process of phylogenetic niche conservatism (sensu Pyron et

al. 2015). Postulated genetic variation does not imply that a

researcher may choose any gene(s), neutral or not, with an

expectation that any gene(s) will resolve phylogenetic

history or systematic relationships.

Indeed, modern genetic tools can zero in on especially

fine-scaled variation among human populations (e.g., Xing

et al. 2009), and there is no reason to think we could not

do the same with other organisms. As a result, we are

increasingly likely to identify genetic variation at a spatial

extent so small that it is meaningless for subspecific

identification, yet genetic differentiation is insufficient, by

itself, to diagnosis a subspecies: Morphological variation is

needed as well (Mousseau and Sikes 2011). The problem,

then, is to state clearly and explicitly what the expectations

are for how a subspecies will be detected. On one hand,

some modern methods (e.g., single-nucleotide polymor-

phism) may yield a surfeit of distinction unsuitable to

subspecies diagnosis. On the other hand, one cannot, for

reasons of ongoing gene flow and of heritable variation in

phenotype, expect implicitly that use of neutral genetic

markers will demonstrate reciprocal monophyly among

subspecies or that subspecies otherwise will form distinct

clusters. Use of such neutral genes might reasonably yield

no difference among populations, even if those popula-

tions differ markedly in phenotype, so a finding of no

difference in neutral markers cannot be construed to mean

anything. (Conversely, finding a difference in neutral

markers means only that sufficient time has elapsed since

the sampled populations were isolated but does not

necessarily mean that the subspecies are valid, and they

would not be valid unless phenotype differed.) It goes

against basic philosophy of science to fail to reject a null

hypothesis and then conclude that the null is true. At the

least, any ‘‘acceptance’’ of the null must be accompanied
by an a priori analysis of statistical power, although such an

analysis necessitates that a suitable statistical analysis was

performed—and in the case of the California Gnatcatcher,

Zink et al. (2013) did not conduct basic analyses of

molecular variance (see McCormack and Maley 2015).

Likewise, a researcher who finds that taxa do not differ in,

say, cytochrome-b sequence has a responsibility to report

that this is not equivalent to finding that the taxa ‘‘do not
differ genetically.’’ The latter (decidedly common) short-
hand implies that no aspect of the genotype differs, which

was not the null hypothesis tested; rather, it is attribute

substitution, the answering of an easier question than what

was asked (sensu Kahneman 2011). Readers rightly would

scoff if a researcher found no variation in the lesser wing

coverts among populations only to proclaim that pheno-
type did not vary geographically.

Another aspect of philosophy of science bears scrutiny,

an aspect McCormack and Maley (2015) touched upon but

did not explore fully: Subspecies have no place in the

schema of the phylogenetic species concept, so adherents
to that concept are predisposed to a finding of ‘‘no
subspecies’’ because below the generic level a taxon is
either a species or it is nothing. A basic tenet of the

hypothetico-deductive framework, the bedrock of scientif-

ic inquiry, is that valid alternatives are tested, yet Zink et al.

(2013) tested implicitly only 2 alternatives, both of which

would have yielded the same conclusion. Had they

concluded that distinct genetic clusters were present, they

would have declared the gnatcatcher taxa to be species and

trumpeted this example of cryptic species others had

overlooked. Had they concluded (as they did with their

visual inspection of haplotype networks but with no

statistical tests) that no geographic pattern was present,

they would have declared no taxa to be discernible (which

they did). Their ideology left them no other options. In

other words, if a conclusion of species¼A, subspecies¼B,
and no taxa¼C, then under the framework adopted, only
A or C could be reached; there is no suitable alternative, in

the hypothetico-deductive sense, under which conclusion

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M. A. Patten A philosophy of subspecies 483



B could have been reached. This situation is acceptable if

researchers do not intend to draw an inference about

subspecies limits, but it is patently unacceptable if they do.

A Way Forward
In light of increased reliance on phylogenetic methods, it is

imperative that systematists identify and adopt standards

to determine species limits and subspecies limits, ‘‘to
establish a standard method to determine the species–

subspecies boundary in order to effectively use the

subspecies classification for research and conservation

purposes’’ (Torstrom et al. 2014). This task will mean that
we must consider both phenotype and genotype (see

Winker 2009), even in the face of an overwhelming push to

consider only the latter. As it stands, we can assess

concordance between aspects of subspecific phenotype

and genotype (e.g., Pruett et al. 2008, Miller et al. 2011),

especially if we use a range of genes, and it possible to

meld the two in increasingly sophisticated ways (e.g.,

Hawlitschek et al. 2012). Better still, we can establish an a

priori set of explicit genetic predictions to assess
subspecies limits (for a superb example, see Sackett et al.

2014).

In the interim, I suggest a simple solution to resolve the

problem: Add alterative B to the framework of the
phylogenetic species concept. In principle, this addition

is simple. Because a subspecies is defined by its

morphological diagnosability (Patten and Unitt 2002), a

researcher needs to account for phenotype as well as

genotype, and genetic differences alone are not enough to

define a subspecies (Mousseau and Sikes 2011). Under the

biological species concept, a diagnosably distinct, geo-

graphically circumscribed segment not reproductively

isolated from other such segments would be deemed a

subspecies and not a species. I propose that under the

phylogenetic species concept, a (morphologically) diag-

nosably distinct, geographically circumscribed clade that

does not form a distinct (neutral) genetic cluster or is not

reciprocally monophyletic (I mention this because its

assessment is common practice, not because it is a

criterion inherent to the concept) in relation to other

such clades be deemed a subspecies and not a species.

Only a failure to achieve both phenotypic and genotypic

distinctiveness—by which I mean a large effect size (Patten

2010, Tobias et al. 2010)—ought to lead a researcher to

conclude that a subspecies is taxonomically invalid.

As a final thought, I wish to emphasize that it is

incumbent upon a researcher who wishes to make a good-

faith effort to examine phenotypic variation to begin with

diagnoses in the type descriptions of the subspecies. It is

incorrect, for example, to assess a subspecies’ taxonomic

status that is based on plumage color by instead using wing

length, when body size was never claimed to differ. Only

with rigorous analysis of phenotype, using modern

methods such as colorimetry and computer-based analysis

of shape, wed to rigorous analysis of genotype and a clear

sense of what we expect to see in such data (e.g., Sackett et

al. 2014), can we move forward in the field of subspecies

systematics. Short of that, we run the risk of further

imperiling Earth’s already unconscionably imperiled biodi-

versity when we accept null hypotheses of no difference, fail

to state expectations explicitly, and adopt frameworks that

do not allow us to reach reasonable scientific conclusions.

ACKNOWLEDGMENTS

My thanks to K. Winker and R. M. Zink for comments on the
manuscript.

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