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.现生西猯（peccary）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，从中新世至更新世时期，已灭绝的西猯物种曾遍布整个北美大陆。现生与灭绝西猯物种间的系统发育关系长期存在争议，西猯从北美迁徙至南美的具体路径与时间节点同样尚不明确。 北美平头西猯（Platygonus compressus）于更新世末期灭绝，是北美地区发现量最为丰富的亚化石类群之一。尽管拥有如此丰富的化石记录，其系统发育位置始终未能得到明确解析。本研究首次获取了平头西猯的DNA数据，并完成了所有现生西猯物种的完整线粒体基因组测序。 我们通过分子系统发育分析，探究古代与现生西猯物种间的演化关系。结果显示，平头西猯与现生西猯物种构成的演化支互为姐妹群。我们通过分子定年分析得到的分化时间估算结果表明，若现生西猯的辐射演化发生于南美洲，则其共同祖先必然早在巴拿马地峡形成之前，便已从北美扩散至南美。 我们还对来自俄亥俄州谢里登洞穴（Sheriden Cave）的平头西猯标本开展了初步种群研究，以探究其遗传多样性。结果显示，谢里登洞穴的平头西猯种群遗传多样性较高，未展现出灭绝前种群衰退的遗传信号。 未来的系统发育分析若纳入更多更新世已灭绝的西猯物种，将进一步厘清西猯的演化历程。