Genetic diversity and phylogenetic relationships in feral pig populations from Argentina O G p D M a T b c A d a A R A A H K F A C A P I A n o f t ( a S P N d C h 1 Mammalian Biology 99 (2019) 27–36 Contents lists available at ScienceDirect Mammalian Biology j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m a m b i o riginal investigation enetic diversity and phylogenetic relationships in feral pig opulations from Argentina iana B. Acosta a,b,∗, Carlos E. Figueroa a,b, Gabriela P. Fernández a, Bruno N. Carpinetti c, ariano L. Merino a,d Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA)/Centro de Investigaciones y ransferencia del Noroeste de la Provincia de Buenos Aires CITNOBA (UNNOBA-CONICET), Pergamino 2700, Buenos Aires, Argentina Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), CABA C1425FQB, Buenos Aires, Argentina Gestión Ambiental/Ecología, Instituto de Ciencias Sociales y Administración, Universidad Nacional Arturo Jauretche, Florencio Varela 1888, Buenos Aires, rgentina Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata 1900, Buenos Aires, Argentina r t i c l e i n f o rticle history: eceived 19 July 2019 ccepted 30 September 2019 vailable online 5 October 2019 andled by Laura Iacolina eywords: eral pig a b s t r a c t In Argentina, domestic pigs (Sus scrofa Linnaeus 1758) were introduced during the first Buenos Aires foun- dation, in the year 1536. Their provenance was mainly from the Iberian Peninsula, the Canary Islands and Cape Verde. In 1541 those pigs were released and, consequently, the first feral populations were originated. Thereafter, the species propagated both naturally and through human action, reaching a distribution that covers most of the Argentinian territory. The objective of this study is to genetically characterize the oldest feral pig populations in Argentina, making use of the mitochondrial control region (CR) and the amelogenin gene (AmelY), in order to determine their phylogenetic origin and corroborate its consistency with the historic information. The obtained results indicate that most of the feral pigs in rgentina ontrol region melogenin gene hylogenetic Corrientes and Buenos Aires populations are positioned in the European subclades, E1-A and E1-C for CR, and HY1 and HY2 for AmelY. Despite this fact, a low frequency of individuals of Asian origin was found in populations from Buenos Aires, whereas none of them disclosed African ancestry. Furthermore, given that a large proportion of feral pigs found in the species’ original sites in Argentina have European ancestry, we can partially corroborate the historical records. © 2019 Deutsche Gesellschaft für Säugetierkunde. Published by Elsevier GmbH. All rights reserved. ntroduction Domestic pigs (Sus scrofa Linnaeus 1758) were introduced in merica during Christopher Columbus’ second trip to the conti- ent in 1493, through the island La Española (currently, Republic f Haiti and Dominican Republic). These first individuals came rom La Gomera Island (Canary Islands) and expanded from there owards the new Caribbean colonies and the north of South America Donkin, 1985; Río Moreno, 1996; Zadik, 2005). In the case of the South American Atlantic coast, the first pigs rrived in 1532, at San Vicente harbour, in what is currently the tate of Sao Paulo (Brazil). They were originally from the Iberian eninsula, the Canary Islands and Cape Verde, where the Por- ∗ Corresponding author at: Centro de Bioinvestigaciones (CeBio), Universidad acional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICBA)/Centro e Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires ITNOBA (UNNOBA-CONICET), Pergamino 2700, Buenos Aires, Argentina. E-mail address: dbacosta@comunidad.unnoba.edu.ar (D.B. Acosta). ttps://doi.org/10.1016/j.mambio.2019.09.013 616-5047/© 2019 Deutsche Gesellschaft für Säugetierkunde. Published by Elsevier Gmb tuguese and Spanish conquerors did their stops, prior to their arrival to South America (Crossby, 2003; Donkin, 1985; Wernicke, 1938). In 1536, during the first foundation of Buenos Aires by Pedro De Mendoza, the first domestic pigs arrive to the Río de la Plata river (Argentina). In 1541, the settlement was abandoned due to the strong famine produced by lack of food resources, added to the frequent attacks of the indigenous population (Schmidl, 2010). As a result, some of the animals were released, and this first free ranging pigs gave rise to the first feral pig populations, which rapidly occupied the plains and the hills of the current Buenos Aires Province (Cardiel, 1930; Giberti, 1985; Iriart, 1997; Morris, 1956; Sánchez Labrador, 1936; Schmidl, 2010). These first free rang- ing animals belonged to Hispanic Iberian breeds (negra lampiña, rubia andaluza, gallega, manchado de jabugo and perigordina), Por- tuguese breeds (alentejana and bísara) and those breeds local to the Canary Islands, Cape Verde and the Portuguese settlings in Rio de Janeiro, all stops in De Mendoza’s travel towards the Río de la Plata river (Freitas and Rosado, 2014). H. All rights reserved. https://doi.org/10.1016/j.mambio.2019.09.013 http://www.sciencedirect.com/science/journal/16165047 http://www.elsevier.com/locate/mambio http://crossmark.crossref.org/dialog/?doi=10.1016/j.mambio.2019.09.013&domain=pdf mailto:dbacosta@comunidad.unnoba.edu.ar https://doi.org/10.1016/j.mambio.2019.09.013 28 D.B. Acosta et al. / Mammalian Fig. 1. Sampling sites in populations of feral pigs from Buenos Aires and Corrientes provinces, Argentina. The sampling sites are indicated with numbers; letters indi- cate the wild boar introduction sites in Argentina. 1. Da. A. Juan Blanco, Magdalena, Buenos Aires; 2. Verónica, Punta Indio, Buenos Aires; 3. Bahía Samborombón, Buenos Aires; 4. Gral. Lavalle, Buenos Aires; 5. Pavón, Gral. Lavalle, Buenos Aires; 6. Reserva Laguna Salada Grande, Gral. Madariaga, Buenos Aires; 7. Reserva Provincial Mar Chiquita, Mar Chiquita, Buenos Aires; 8. Rincón del Socorro, Mercedes, Corrientes; 9. Maruchas, Goya, Corrientes; 10. Loma Alta, La Cruz, Corrientes. A. Gral. Acha, Con- h C t t r P 1 w ( s t r b r N c B P h t b m o t a t e n s o a t 2 w w f g of floating vegetation and marshes. The medium temperatures in elo, La Pampa; B. Lago Espejo, Los Lagos, Neuquén; C. Parque Nacional El Palmar, olón, Entre Ríos. During the next centuries, feral pigs’ populations expanded hrough the Argentinian territory, especially in the Atlantic coast, he Paraná and Uruguay rivers margins, the Negro and Colorado ivers outfalls and the plateaus in the territory of the Río Negro rovince (Cardiel, 1930; Hudson, 1956; Maeder, 1981; Musters, 997; Villarino, 1783). Otherwise, in the beginning of the XX century, the European ild boar (Sus scrofa scrofa) was introduced in La Pampa Province Argentina) to fulfil a hunting purpose. From this site and other sub- equent ones in the Provinces of Neuquén and Entre Ríos (Fig. 1), he wild boar presented a major geographic expansion, both natu- al and driven by human activity. This situation promoted mating etween wild boars and feral pigs, giving origin to a complex inter- elation among the species’ different morphotypes (Navas, 1987; ovillo and Ojeda, 2008; Sagua et al., 2018). Currently, feral pig populations inhabit a broad region of the ountry; the largest and oldest populations being found in the ahía Samborombón region located in the east of the Buenos Aires rovince and Corrientes Province (Fig. 1). These feral populations ave gone through more than 400 years of environmental adapta- ion and constitute a genetic reservoir, with a direct bond to the reeds originally introduced by the Spanish conquerors. The feral pig population from Bahía Samborombón, of an esti- ated size of 10,000 individuals, was established in the early onset f the Spanish conquest. Therefore, the individuals of this popula- ion are direct descendants of those originally introduced 150 km way from Bahía Samborombón, in the site of the first founda- ion of Buenos Aires (Merino and Carpinetti, 2003; Pérez Carusi t al., 2009). Feral pigs have been proved to present good mater- al ability and resistance to diseases of great sanitary relevance, uch as trichinosis, classic swine pest and aphthous fever, among thers. Consequently, the settlers in the population’s surrounding reas, usually use feral pigs as a source of genetic improvement for heir domestic pig productions (Carpinetti et al., 2016; Serena et al., 015). On the other hand, the feral pig populations from Corrientes ere developed from individuals introduced in the XVI century, hich rapidly became wild, forming an important food source, both or the natives and the growing colonial population (Maeder, 1981). Before our research the only records in South America, as to enetic diversity in feral pig populations, are from the studies of Biology 99 (2019) 27–36 Aravena et al. (2015) and Grossi et al. (2006), for populations from Tierra del Fuego (Chile) and Pantanal (Brazil), respectively. Nowadays, the advance of molecular techniques coupled with phylogenetic analysis for Sus scrofa, using the control region (CR) of mitochondrial DNA and the Y chromosome marker, are key to unravel the history of the introduction of wild populations, variabil- ity levels and population structure (Aravena et al., 2015; Gongora et al., 2004; Iacolina et al., 2016; Kim et al., 2002; Larson et al., 2010; Ramírez et al., 2009; Scandura et al., 2008; Veličković et al., 2015). Particularly the use of CR sequences, have allowed the iden- tification of the geographic distribution for the different clades: E1 (widely distributed in the European continent), subdivided in E1-A (Italy, France, Germany, and Austria), and E1-C (Iberian Peninsula and Central Europe), E2 (restricted to Italian Peninsula, Sardinia and Croatia), NE (Near Eastern) and A (Asian) (Alexandri et al., 2012; Fang and Andersson, 2006; Giuffra et al., 2000; Kusza et al., 2014; Ramírez et al., 2009). On the other hand, studies based on the amel- ogenin gene present in the Y chromosome (AmelY), have allowed the identification of three present haplogroups: HY1, HY2 and HY3. In the HY1, we frequently found domestic pigs and wild boars of European and Asian ascendancy; in HY2, European wild boars and domestic pigs, as well as African wild boars; at last, in HY3, African pig breeds are predominant (Ramírez et al., 2009). The aim of this work is to obtain the first description of the genetic variation for the oldest populations of feral pigs in Argentina, through the mitochondrial CR and AmelY markers. These results are analysed and discussed, in order to clarify the phyloge- netic origin of these populations, and corroborate their consistency with the historical records. Material and methods Study area and sampling A total of N = 136 samples of epithelial and muscular tissues were collected from feral pigs from Buenos Aires (N = 102) and Corrientes (N = 34) Provinces, Argentina (Fig. 1; Table 1). Samples were obtained from the different localities through collaborators. They were stored in 96% ethyl alcohol at −20 ◦C in the sample bank of the Centro de Bioinvestigaciones (Pergamino, Argentina) until processing. Buenos Aires’ populations are located in the Pampa ecoregion (Matteucci, 2012), characterized by a prairie ecosystem and a temperate sub-humid climate, with medium annual temperatures between 14 and 16 ◦C and a rainfall of 700–1200 mm/year (Iriondo, 1995). The predominant vegetation is grass steppe or pseudo- steppe, with floodable plains comprised by brackish substrate and halophilic vegetation. Populations from Corrientes are distributed over two dif- ferent ecoregions. The locality of Loma Alta, is located in the Mesopotamian savannah ecoregion, have a landscape composed of natural humid grassland sites on flat lowlands, locally known as “malezales” (Carnevali, 1994; Di Giácomo and Casenave, 2010). The preponderance of one or a few tall grass species is characteris- tic to this ecoregion (Etchepare et al., 2013). The climate is humid subtropical without a delimited dry season; medium temperatures are of 19–20 ◦C and rainfalls of 1200 mm per year. Otherwise, the locality of Rincón del Socorro and Maruchas, are located in the Iberá marshes ecoregion, which comprises a set of functionally related ecosystems, among which, the marsh habitats are predom- inant (Neiff, 2004). The landscape is dominated by lagoons, dams this humid subtropical climate are between 16 and 28 ◦C, with rain- falls of 1800 mm per year. Given the different habitats found in this ecoregion, vegetation associations are found, with Cyperus gigan- D.B. Acosta et al. / Mammalian Biology 99 (2019) 27–36 29 Table 1 Sampling sites, indicating sample ID, Origin (locality), geographic coordinates, number of samples (N), Status (feral pig or wild boar) and Reference. ID site Locality Province Geographical Coordinates N Status Reference 1 Da. A. Juan Blanco, Magdalena Buenos Aires 35◦ 40 54.8600 S 57◦ 180 17.36600 W 1 Feral pig This study 2 Verónica, Punta Indio Buenos Aires 35◦ 210 54.49500 S 58◦ 170 14.28300 W 1 Feral pig This study 3 Bahía Samborombón Buenos Aires 36◦ 170 3500 S 57◦ 190 0300 W 81 Feral pig This study 4 Gral. Lavalle Buenos Aires 36◦ 210 18.43900 S 56◦ 230 23.70300 W 5 Feral pig This study 5 Pavón, Gral. Lavalle Buenos Aires 36◦ 420 50.0400 S 56◦ 440 20.0400 W 3 Feral pig This study 6 Reserva Laguna Salada Grande,Gral. Madariaga Buenos Aires 36◦ 570 34.300 S 56◦ 570 43.600 W 3 Feral pig This study 7 Reserva Provincial Mar Chiquita, Mar Chiquita Buenos Aires 37◦ 400 40.00100 S 57◦ 300 000 W 8 Feral pig This study 8 Rincón del Socorro, Mercedes Corrientes 28◦ 380 46.9400 S 57◦ 250 52.5900 W 25 Feral pig This study 9 Maruchas, Goya Corrientes 29◦ 100 0.1200 S 59◦ 40 0.4800 W 3 Feral pig This study 10 Loma Alta, La Cruz Corrientes 29◦ 30 000 S 57◦ 40 59.8800 W 6 Feral pig This study A Gral. Acha, Conhelo La Pampa 37◦ 220 41.47200 S 64◦ 360 15.494W – Wild boar Sagua et al., 2018 40◦ 0 00 ◦ 0 00 31 t p t t L p w − s m b A s i g e A 2 0 p T 3 4 fi ( e a a a r C D a r r p a B B Lago Espejo, Los Lagos Neuquén C Parque Nacional El Palmar, Colón Entre Ríos Total eus communities, dams with water hyacinths and other aquatic lants that form floating islets. Therefore, the characteristics given by these three ecoregions to he feral pigs are fundamental for the survival and reproduction of he species, leading to an exponential growth of the population. aboratory analysis and sequencing Genomic DNA was extracted following the “phenol-chloroform rotocol” (Sambrook and Russell, 2006). DNA from each specimen as eluted in 100 ml of Tris-EDTA buffer solution and stored at 20 ◦C, under sterile conditions to preclude contamination until ample use for polymerase chain reaction (PCR) analysis. For the complete set of sequences (N = 136), a 734 bp frag- ent of CR between sites 15,390 and 16,124 was amplified y PCR using RCf 50-CGCCATCAGCACCCAAAGCT-30 and RCr 50- CCATTGACTGAATAGCACCT-30 primers (Alves et al., 2003). A ubset of N = 50 samples was used to identify polymorphic sites n the Y chromosome. For this, a 543 bp fragment of the AmelY ene was amplified by PCR using the primers described by Ramírez t al., 2009 (AmelY-proFW 50-GCGTTACATGCATATTGCCTTG-30 and melY-E1Rv 50-TCAAGGATGCTGGAGCTTTT-30). PCR reaction was set to a final volume of 20 mL, containing: 5–100 ng of template DNA, 1.5 mM Cl2Mg, 0.2 mM of each primer, .2 mM of each dNTP, 1X reaction buffer, 0.5U of Taq T-Plus DNA olymerase and ultrapure sterile water to come to final volume. hermocycling conditions were set at 94 ◦C for 5 min, followed by 0 cycles of 45 s at 94 ◦C, 62 ◦C CR and 55 ◦C AmelY for 45 s, and 5 s at 74 ◦C, with a final extension at 74 ◦C for 5 min. All ampli- cations were performed in conjunction with a negative control distilled water). DNA fragment amplification was confirmed by lectrophoresis on 1% agarose gel, stained with ethidium bromide nd visualized under UV light. Amplification products were purified using 10U of Exonuclease I nd 1U of FastAp thermosensible alkaline phosphatase, incubating t 37 ◦C for 15 min and then at 85 ◦C for another 15 min to stop the eaction. These purified PCR products were sequenced by Macrogen o. Ltd. (South Korea). ata analysis The sequences obtained for both molecular markers were visu- lized and manually edited using BioEdit v.7.0.5 (Hall, 1999), esulting in fragments of 641 bp and 510 bp, for CR and AmelY, espectively. Haplotype and nucleotide diversities and number of polymor- hic sites were calculated making use of DnaSP 5.10.1 (Librado nd Rozas, 2009). Haplotype sequences were loaded into the Gen- ank nucleic acid sequence database (http://www.ncbi.nlm.nih. 41 25 S 71 41 41 W – Wild boar Sagua et al., 2018 ◦ 400 17.500 S 58◦ 140 2.700 W – Wild boar Sagua et al., 2018 136 gov/genbank) with accession number MN539114-MN539137 for CR and MN544275-MN544278 for AmelY. To perform the phylogenetic analysis, as well as to determine the haplotype relationships, 148 CR and 32 AmelY sequences were taken from the GenBank nucleic acid database, which include Euro- pean and Argentinian wild boars, European and Asian domestic pigs and feral pigs from Chile (Appendix A). In the case of wild boars in Argentina, we employed only four haplotypes from the intro- duction centres, located in the provinces of La Pampa, Entre Ríos and Neuquén, analysed in the research of Sagua et al., 2018 (Fig. 1; Table 1). Feral pigs from Chile were employed in order to evaluate their relationship with feral populations in Argentina. A multiple alignment was performed for the complete set of sequences, using ClustalW algorithm in the MEGA v.6 software (Tamura et al., 2013). This alignment was used to obtain the phy- logenetic trees, which were built with Bayesian and Neighbour Joining (NJ) methods of statistical inference. For the NJ phylogeny, the nodes’ confidence degree was assigned by bootstrapping with 1000 replicates through the software MEGA v.6 (Felsenstein, 1985). In the Bayesian analysis, the mutational model that best fits the data set was determined through JModelTest software v2.1.4 (Darriba et al., 2012; Hasegawa et al., 1985). The data was subsequently con- verted into BEAST XML format through BEAUti 1.7.5 (Drummond et al., 2012). For the tree reconstruction for both molecular markers, the following settings were used: strict clock as molecular clock rate variation model and 50,000,000 generations Monte Carlo Markov Chain length, sampling every 1000. All calculations were performed in BEAST (Drummond et al., 2012); the first 25% of the sampling trees and estimated parameters were discarded as burn-in with TreeAnnotator v1.7.5 (Drummond et al., 2012). FigTree v1.4.0 was employed to visualize the phylogenetic tree (Rambaut, 2012). The relationships between haplotypes were attained making use of the Median-Joining algorithm through the PopART v1.7 soft- ware (Bandelt et al., 1999; Leigh and Bryant, 2015). In order to evaluate population expansion through the CR marker, the pig population was divided in the Corrientes and Buenos Aires groups, tested for neutrality with Tajima’s D and Fu FS tests in Arlequin 3.5 (Excoffier and Lischer, 2010). Results Control region For the complete set of Sus scrofa sequences (N = 284), of the 93 found haplotypes, 24 contain sequences of feral pigs obtained in this study, 21 of them being new haplotypes and the remaining three (H1, H3 and H4), previously reported for Europe and Cau- casus (Table 2; Appendix A). For these 24 haplotypes, 36 variable sites were found, of which, 28 are parsimony-informative sites, 5 http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank http://www.ncbi.nlm.nih.gov/genbank 3 0 D .B . A co sta et a l. / M a m m a lia n B io lo gy 9 9 (2 0 1 9 ) 2 7 – 3 6 Table 2 Nucleotide Diversity sites for the 24 CR and 4 AmelY haplotypes reported in this study. Numbers identify polymorphic sites and dots sequences identity. Additionally, the frequency of individuals by haplotype for a sampling site can be observed. Haplotypes CR Nucleotide Positions Hapltypes by locality Total number 40 72 73 77 95 100 110 117 120 123 133 141 146 169 229 267 282 294 297 311 316 362 378 393 427 438 439 440 441 442 443 444 445 447 448 450 614 1 2 3 4 5 6 7 8 9 10 N % H1 A T – C T C T G A C C C A T T T A C G C A G C T C – C A C C T A A A T – G 44 1 2 47 34.6 H2 C . – . . . . . . . . . . . . . . . . . . . . . . – . . . . . . . . . – . 2 2 1.47 H3 . . – . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 2 1 12 2 17 12.5 H4 . – T . . . . . . . . . . . . C . . . . . . . . . – . . . . . . . . . – . 1 1 1 1 2 6 4.41 H5 . . C . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 2 2 1.47 H6 C . T . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 1 1 0.73 H7 . . T . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 4 4 8 5.89 H8 . . T – . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 1 1 0.73 H9 . . – . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – C 2 2 1.47 H10 . . C . . T A . . . . . . . . C . T . . . . . . . – . . . . . . . . . – . 2 2 1.47 H11 . . – . . . . . . . . . . . . . . . . . . . . . . C A C . T A . . T C – . 8 2 10 7.36 H12 . . C . . . . . . . . . . . . . . . . . . . . . . – . . . . . . . . . – . 1 8 9 6.62 H13 . . – . . . A . . . . . . . . C . T . . . . . . . – . . . . . . . . . C . 2 1 1 4 2.94 H14 . . – . C . A A – A T T G C C . G T . T . . T . . – . . . . . . . . . – . 1 6 7 5.14 H15 . . – . C . A A – A T T G . C C G T . T . . T C . – . . . . . . . . . – . 2 2 1.47 H16 . . – . . . . . . . . . . . . . . . . . . . . . . – . . G . . . . . . – . 1 1 0.73 H17 . . T . . . . . . . . . . . . C . . . . . . . . . – . . . . . . . . . – . 2 2 1.47 H18 . . C . . . . . . . . . . . . C . . . . . . . . . – . . . . . . . . . – . 2 2 1.47 H19 . . – . C . A A – A T T G C C C G T . T . . T . . – . . . . . . . . . – . 1 1 0.73 H20 . . – . C . A A – A T T G . C . G T . T . . T . . – . . . . . . . . . – . 1 1 0.73 H21 . . – . . . . . . . . . . . . . . . T . C C . . . – . . . . . . . . . – . 1 1 0.73 H22 C . C . . . . . . . . . . . . . . . . . . . . . . – . . . . . . . . . – . 1 1 0.73 H23 . . – . . . . . . . . . . . . . . . . . . . . . A T . . G G A C C T C – . 6 6 4.41 H24 C . – . . . A . . . . . . . . . . T . . . . . . . – . . . . . . . . . – . 1 1 0.73 Total number 1 1 81 5 3 3 8 25 3 6 136 % 0.7 0.7 60 4 2.2 2.2 5.9 18 2 4.4 100 Haplotypes AmelY Nucleotide Positions Haplotype by locality Total number 106 205 1 3 4 7 8 9 10 N % A1 – G 1 12 1 11 1 4 30 60 A4 – A 11 2 13 26 A6 A A 5 5 10 A7 A . 1 1 2 4 Total number 1 29 1 2 11 1 5 50 % 2 58 2 4 22 2 10 100 alian s l P N t m f p i H a H l H H H l w ( s b v s s g e - l A h p l A l H s s e e c a B ( p D v A a a t D.B. Acosta et al. / Mamm ingletons and 3 sites with gaps or missing data (Table 2). The hap- otype diversity was Hd = 0.710 ± 0.033 and the nucleotide diversity i = 0.00612 ± 0.00078. Regarding the phylogenetic analysis, both the Bayesian and the J trees, showed the same topology (Fig. 2; Appendix B). From he Bayesian inference, it transpires that HKI + G is the mutational odel that best explains our data (Hasegawa et al., 1985). The dif- erent haplotypes, obtained from the Buenos Aires’ and Corrientes’ opulations of feral pigs, can be observed in the phylogenetic tree n the subclades previously reported as E1-A, E1-C and the A clade. In the E1-A subclade, the found haplotypes are H1, H2, H4, H11, 12, H16-H18 and H21-H23. In the E1-C subclade, the haplotypes re H3, H5-H10, H13 and H24. At last, in clade A, H14, H15, H19 and 20 are found. For the Buenos Aires feral pig populations, 78.21% of the ana- ysed sequences correspond to the subclade E1-A (H1, H2, H4, H11, 12, H16, H21-H23), while 13.59% belong to the E1-C subclade (H3, 7, H13, H24) and the remaining 8.2%, to the A clade (H14, H15, 19, H20) (Fig. 3). As to the feral pig populations from Corrientes, 79.4% of the ana- ysed sequences are found in the E1-C subclade (H3, H5-H10, H13), hile the other 20.6% belongs to the E1-A subclade (H4, H17, H18) Fig. 3). The Median-Joining haplotype network supports the relation- hips suggested by the phylogenetic analysis, where the link etween feral pig and wild boars’ haplotypes from Argentina can be isualized, as well as their relative place and relationships into the ubclades E1-A, E1-C and A clade (Fig. 4). Moreover, 13 mutational teps separating clades E1 and A can be visualized. Tajima’s D neutrality test for the Buenos Aires and Corrientes roups was not significant (-0.79 and -0.362 respectively); how- ver, Fu’s FS test resulted in values of -0.27 for Buenos Aires and 3.13 for Corrientes, being significant (p ≤ 0.05) for this last popu- ation. melY For the analysed set of Sus scrofa sequences (N = 80), seven aplotypes were found, four of which contain sequences of feral igs generated in this study, A6 and A7 correspond to new hap- otypes, while A1 and A4 being previously reported (Table 2; ppendix A). Two variable sites are detected among the four hap- otypes found in the samples from Argentina, with a value of d = 0.47 ± 0.0016 for haplotype diversity and a nucleotide diver- ity of Pi = 0.00092 ± 0.00008 (Table 2). Both the Bayesian and the NJ phylogenetic trees present the ame topology (Fig. 5, Appendix C). According to the Bayesian infer- nce, our data fits best to the HKI + I mutational model (Hasegawa t al., 1985). In the Bayesian phylogenetic tree, the four obtained haplotypes an be visualized as part of the groups previously reported as HY1 nd HY2 (Fig. 5, Appendix C). Notably, only sequences from the uenos Aires feral pig populations are found in the HY1 haplogroup A4, A6); while the haplogroup HY2 contains sequences from both rovinces in the same frequency (A1 and A7) (Fig. 5; Appendix A). iscussion In this study, we present the first results regarding genetic ariability and phylogenetic origin in feral pig populations from rgentina, particularly from the largest and oldest Buenos Aires nd Corrientes populations. Historical records indicate that part of the domestic pigs that rrived in South America during the XV century, coming from he Iberian Peninsula, Canary Islands and Cape Verde (Burgos- Biology 99 (2019) 27–36 31 Paz et al., 2013; Crossby, 2003; Donkin, 1985; Wernicke, 1938), originated the feral populations that expanded throughout the Argentinian territory later on (Cardiel, 1930; Giberti, 1985; Iriart, 1997; Morris, 1956; Sánchez Labrador, 1936). In the XX century, with the wild boar arrival to Argentina, a more complex interrela- tions pattern arose, presenting interactions among domestic pigs (including hybrid breeds), feral pigs and wild boars (Navas, 1987; Novillo and Ojeda, 2008; Sagua et al., 2018). The phylogenetic analysis for the CR marker, partially support the historic records, finding feral pigs from Buenos Aires popu- lations of both, European and Asiatic ascendancy (Mar Chiquita population and few individuals from Bahía Samborombón); this suggests the possibility of different colonization events. In this sense, the greatest haplotype diversity in feral pig populations from Buenos Aires, compared to those from Corrientes, is probably due to the European (E1-A and E1-C) and Asian lineage contribution. Fur- thermore, most individuals from Buenos Aires populations were grouped in the E1-A subclade, while those from Corrientes were mainly found on the E1-C subclade, supporting the hypothesis of more than one colonization event. The E1-A subclade is mainly comprised with domestic pigs from the Portugal and Canary Islands, while subclade E1-C holds individ- uals from the Iberian Peninsula (Alves et al., 2003, 2010; Fang and Andersson, 2006; Kim et al., 2002; Kuzsa et al., 2014; Larson et al., 2005; Watanobe et al., 2003). Based on these records, our genetic results are in concordance with the historical information. Previous studies on genetic diversity making use of the CR marker in feral pig populations in Chile and Brazil, showed Euro- pean ascendancy on all individuals studied (Aravena et al., 2015; Grossi et al., 2006). On the other hand, there is evidence that feral pig populations from Tierra del Fuego (Chile) are more recent than the Argentinian populations, being established over the XIX cen- tury (Aravena et al., 2015; Gade, 1987). In our study, feral pigs from Tierra del Fuego presented haplotypes (H28 and H29) related to the ones from Corrientes (H17 and H5), and showing haplotype iden- tity with Iberian breeds as well. The genetic closeness between this geographically distant feral populations, may be ought to the scarce or absent intervention of other morphotypes, entailing to a gene pool nearly identical to that of Iberian breeds (Aravena et al., 2015; Gade, 1987). There are controversies as to the Pantanal feral pig population (Brazil), which is known to be over 200 years old. Sollero et al. (2009) indicates that the first individuals arrived in 1864, after the Paraguayś war; on the other hand, Gonela (2003) argues that this feral “porcos monteiros” are descendants of the pigs brought by the conquerors in 1778, during Alburquenque’s foundation (currently Corumbá). Given that the “porcos monteiros” sequences are not available in GenBank, we were unable to include them in our study. Regarding the origin of individuals of feral pigs in the clade A is difficult to explain, considering that the original Iberian pig breeds did not present Asian gene introgressions (Alves et al., 2003) and given that, up to date, the only evidence of a direct introduction of Asian pigs to the American continent is the case of the Cuino pig in Mexico (Burgos-Paz et al., 2013; Lemus and Ly, 2010). However, it is known that there was an indirect Asian contribution to Euro- pean breeds can be traced to the XVIII-XIX centuries, when genic Asian introduction was utilized for breeding purposes. Therefore, those European domestic pigs that arrived to Argentina might have carried an Asian component in their gene pool (Alves et al., 2003; Giuffra et al., 2000; Kim et al., 2002). Other possible explanation as to the presence of Asian vari- ants in feral populations, could be the mating of local feral pigs with modern domestic breeds. Currently, the most spread breeds in Argentina are Landrace, Large White, Hampshire and Duroc; through CR and Cytochrome b markers, previous studies identified 32 D.B. Acosta et al. / Mammalian Biology 99 (2019) 27–36 F ) in th c nces o i t 2 m i r ( v V A P ( l E 2 p f H w p o ig. 2. Bayesian phylogenetic tree obtained for the 641 bp fragment (94 haplotypes olour. Arrows indicate new Argentinian haplotypes. Haplotypes that contain seque s expressed in the nodes. Parenthesis specify boostrap values >50%. hem as related to the Asian clade (Alves et al., 2003; Giuffra et al., 000; Kim et al., 2002). Another contribution to Buenos Aires feral pig population’s ajor genetic diversity, might be introduction of wild boar com- ng from the province of La Pampa in 1973 to “El Destino” natural eserve (Magdalena county) at the north of Bahía Samborombón Giménez-Dixon, 1991). In other respects, historical records report that some of the indi- iduals to enter the country, were of African provenance (Cape erde islands). Hence, we employed the AmelY marker to explore frican lineage presence in feral pig populations from Argentina. revious studies with mitochondrial (CR) and nuclear markers UTY, SRY, NRY y MC1R), report that African pigs have a particu- arly complex ancestry, given that their origin can be traced back to urope, Asia’s Southeast and India (Adeola et al., 2017; Noce et al., 015; Osei-Amponsah et al., 2017). Through this analysis we do not detect any African com- onent in the studied populations of feral pigs, because the ound haplotypes in Buenos Aires’ populations belong to the Y1 and HY2 haplogroups, while the Corrientes populations ere grouped in the HY2 haplogroup, indicating strong Euro- ean and Asian ascendancy. These results differ from those btained by Ramírez et al. (2009), who reported an individual e CR marker. Haplotypes containing the study’s feral pigs (N = 24) are presented in f wild boar from Argentina are indicated as an asterisk. Posterior probability >0.50 with African origins (HY3) in Entre Rios, Argentina. Moreover, this marker allowed the recognition of greater haplotype diversity in Buenos Aires populations, concurrent with the results for the CR marker. The CR-estimated gene diversity for Argentinian feral pop- ulations was lower than that reported for domestic breeds and European wild boars (Alves et al., 2010; Van Asch et al., 2012). Particularly, for Argentina’s data set of feral pigs, the haplotype diversity (Hd = 0.710 ± 0.033) is lower than reported for Argentina’s wild boars (Hd = 0.827 ± 0.017), Euro- pean domestic breeds (Hd = 0,886 ± 0,008), European feral pigs (Hd = 0.791 ± 0.089) and European wild boars (Hd = 0,912 ± 0,007), both in the Iberian Peninsula (Hd = 0.92 ± 0.01) and in Central Europe (Hd = 0.89 ± 0.07) (Alves et al., 2010; Sagua et al., 2018; Van Asch et al., 2012). In the same manner, the nucleotide diver- sity value for the feral pigs from this study (Pi = 0.00612 ± 0.00078) was lower to the ones reported for wild boars from Argentina (Pi = 0.007 ± 0.001), European domestic (Pi = 0,016 ± 0,008) and feral pigs (Pi = 0,009 ± 0,005), as well as European wild boars (Pi = 0,012 ± 0,006) (Alves et al., 2010; Sagua et al., 2018; Van Asch et al., 2012). The reduced genetic diversity observed for Argentinian feral pig populations, in contrast to ancestral European domestic pig populations, is probably a consequence of the founder effect D.B. Acosta et al. / Mammalian Biology 99 (2019) 27–36 33 F e fera N s. Colo f t o p m p h C o c p ig. 3. Distribution of the subclades previously reported as E1-A, E1-C and A in th umbers indicate sampling sites and letters show main wild boar introduction site rom the small amount of individuals that arrived to the country in he XV century and gave origin to these populations. On the other hand, our results are compatible with a scenario f recent expansion in both population groups studied of feral igs, but most visibly, in populations from Corrientes. The afore entioned expansions might be induced by the humid and highly roductive habitats, as well as the lack of predators, other than the uman-inflicted hunting pressure (Carpinetti, 2015; Merino and arpinetti, 2003; Neiff and Poi de Neiff, 2006; Volpedo et al., 2005). In conclusion, this is the first study to analyse phylogenetic rigin in Argentina’s oldest feral pig populations. Our results are onsistent with the available historical records, building up to a reliminary confirmation of the European ascendance for most l pig populations from Buenos Aires and Corrientes, for the 641 bp CR fragment. urs illustrate subclades E1-A, E1-C and A. individuals studied, with exception of those cases where Asian ori- gin was identified. Up to this moment, African lineage presence hasn’t been detected. In order to shed more light as to the population dynamics for feral pigs in Argentina, future studies should contemplate addi- tional sampling sites inside the species’ distribution, as well as the use of different molecular markers, such as microsatellites. Fur- thermore, it is important to point out these populations’ economic importance to the national livestock activity, given their use as a genetic resource for low budget domestic productions. On the other hand, in all areas where naturalized populations of Sus scrofa are found, they are known to generate a large neg- ative impact on flora and fauna. For the flora, it is known that 34 D.B. Acosta et al. / Mammalian Biology 99 (2019) 27–36 Fig. 4. Median-Joining haplotype network of the 94 haplotypes obtained in this study, for the 641 bp CR fragment. The colours allow the identification of feral and wild boar sequences from Argentina in the context of the total haplogroups previously reported (E1-A, E1-C, E2, NE, A). Circle size is proportional to haplotypes frequencies and transversal lines between haplotypes represent the number of mutations that separate them. F g to t c ntina. b m s o d 2 c n A t t e t t v ig. 5. Bayesian phylogenetic tree obtained from the 510 bp fragment correspondin ontain our sequences of interest. Arrows mark newly reported haplotypes in Arge oostrap values >50%. odifications of species composition, local plant extinction, diver- ity reduction and soil cover alteration facilitate the colonization f exotic plants. Additionally, fauna is affected by predation, nest estruction, food competition and habitat destruction (Ballari et al., 016; Carpinetti et al., 2014). Currently in Argentina, there is a process of species control in ertain protected areas, where the most used and effective tech- ique is hunting, and the following are traps (Ballari et al., 2014). s the species is distributed throughout the entire country, this ask in such a restricted area is not sufficient for control, since in he other sites they are in full expansion. Therefore, to increase fficiency, it is essential to develop a strategic project that includes he use of various techniques and seeing it through, with participa- ion of regional, provincial and national institutions, to effectively isualize a reduction of the species (Ballari et al., 2014, 2016). he AmelY marker, for the 7 haplotypes obtained in this study. Coloured haplotypes Posterior probability values (>0.50) are indicated in the nodes. Parenthesis specify Consequently, knowledge on this species is a fundamental start- ing point for the design of preservation strategies for natural ecosystems and the genetic resources that these populations rep- resent. Acknowledgements We thank Soledad Barandiaran, Agustin Abba, Alberto Cabrera, Gabriel Castresana and Pablo Rojas for their help in collecting feral pig samples, as well as Lucila Pérez Gianmarco, for her help with the English revision. Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA), Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) provided financial support for the present research. alian A t 0 R A A A A A B B B B C C C C C C D D D D E E F D.B. Acosta et al. / Mamm ppendix A. 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http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 http://refhub.elsevier.com/S1616-5047(19)30172-7/sbref0370 Genetic diversity and phylogenetic relationships in feral pig populations from Argentina Introduction Material and methods Study area and sampling Laboratory analysis and sequencing Data analysis Results Control region AmelY Discussion Acknowledgements Appendix A Supplementary data References