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（peccaries）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，从中新世到更新世，现已灭绝的西猯物种曾遍布整个北美洲。长期以来，现存与灭绝西猯物种间的系统发育关系一直存在争议。同样，西猯如何以及何时从北美洲迁徙至南美洲，目前尚无定论。北美平头西猯（Platygonus compressus）于更新世末期灭绝，是北美洲发现的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，其系统发育位置仍未得到明确解析。本研究首次公布了平头西猯的DNA数据，以及所有现存西猯物种的完整线粒体基因组序列。我们通过分子系统发育分析，明确了史前与现存西猯物种间的亲缘关系。研究结果显示，平头西猯与包含所有现存西猯物种的演化支互为姊妹群。我们通过分子定年分析得到的分化时间估算结果表明：若现存西猯的物种分化发生在南美洲，则其共同祖先必然早在巴拿马地峡形成之前，就已从北美洲迁徙至南美洲。我们还对来自美国俄亥俄州谢里登洞穴的标本开展了初步种群研究，以此探讨平头西猯的遗传多样性。谢里登洞穴出土的平头西猯样本遗传多样性较为丰富，未显现出灭绝前种群数量下降的特征。未来若将更多更新世灭绝的西猯物种纳入系统发育分析，将进一步阐明西猯的演化历程。