Data from: Ancient DNA analysis of the extinct North American flat-headed peccary (Platygonus compressus)

The geographical range of extant peccaries extends from the southwestern United States through Central America and into northern Argentina. However, from the Miocene until the Pleistocene now-extinct peccary species inhabited the entirety of North America. Relationships among the living and extinct species have long been contentious. Similarly, how and when peccaries moved from North to South America is unclear. The North American flat-headed peccary (Platygonus compressus) became extinct at the end of the Pleistocene and is one of the most abundant subfossil taxa found in North America, yet despite this extensive fossil record its phylogenetic position has not been resolved. This study is the first to present DNA data from the flat-headed peccary and full mitochondrial genome sequences of all the extant peccary species. We performed a molecular phylogenetic analysis to determine the relationships among ancient and extant peccary species. Our results suggested that the flat-headed peccary is sister-taxon to a clade comprising the extant peccary species. Divergence date estimates from our molecular dating analyses suggest that if extant peccary diversification occurred in South America then their common ancestor must have dispersed from North America to South America well before the establishment of the Isthmus of Panama. We also investigated the genetic diversity of the flat-headed peccary by performing a preliminary population study on specimens from Sheriden Cave, Ohio. Flat-headed peccaries from Sheriden Cave appear to be genetically diverse and show no signature of population decline prior to extinction. Including additional extinct Pleistocene peccary species in future phylogenetic analyses will further clarify peccary evolution.现存西猯的地理分布范围从美国西南部延伸至中美洲，直至阿根廷北部。然而在中新世至更新世时期，现已灭绝的西猯物种曾遍布整个北美洲。现存与灭绝西猯物种间的演化关系长期存在争议，而西猯如何、何时从北美洲迁徙至南美洲这一问题也尚未明晰。北美平头西猯（Platygonus compressus）于更新世末期灭绝，是北美洲出土量最丰富的亚化石类群之一。尽管拥有如此详尽的化石记录，其系统发育位置仍未得到明确解析。本研究首次获取了平头西猯的DNA数据，以及所有现存西猯物种的完整线粒体基因组（mitochondrial genome）序列。我们通过分子系统发育分析（molecular phylogenetic analysis），旨在明确远古与现存西猯物种间的演化关系。研究结果显示，平头西猯与现存西猯物种构成的演化支（clade）互为姊妹群（sister-taxon）。分子定年分析得到的分化时间估算表明，若现存西猯的物种多样化过程发生在南美洲，则其共同祖先必定早在巴拿马地峡形成之前，就已从北美洲扩散至南美洲。我们还对来自俄亥俄州谢里登洞（Sheriden Cave）的标本开展了初步种群研究，以探究平头西猯的遗传多样性。来自谢里登洞的平头西猯样本展现出较高的遗传多样性，未显示出灭绝前种群衰退的迹象。未来的系统发育分析若纳入更多更新世灭绝的西猯物种，将进一步厘清西猯的演化历程。