Data from: Archaeogenomic evidence from the southwestern US points to a pre-Hispanic scarlet macaw breeding colony

Hundreds of scarlet macaw (Ara macao cyanoptera) skeletons have been recovered from archaeological contexts in the southwestern United States and northwestern Mexico (SW/NW). The location of these skeletons, >1,000 km outside their Neotropical endemic range, has suggested a far-reaching pre-Hispanic acquisition network. Clear evidence for scarlet macaw breeding within this network is only known from the settlement of Paquimé in NW dating between 1250 and 1450 CE. Although some scholars have speculated on the probable existence of earlier breeding centers in the SW/NW region, there has been no supporting evidence. In this study, we performed an ancient DNA analysis of scarlet macaws recovered from archaeological sites in Chaco Canyon and the contemporaneous Mimbres area of New Mexico. All samples were directly radiocarbon dated between 900 and 1200 CE. We reconstructed complete or near-complete mitochondrial genome sequences of 14 scarlet macaws from five different sites. We observed remarkably low genetic diversity in this sample, consistent with breeding of a small founder population translocated outside their natural range. Phylogeographic comparisons of our ancient DNA mitogenomes with mitochondrial sequences from macaws collected during the last 200 years from their endemic Neotropical range identified genetic affinity between the ancient macaws and a single rare haplogroup (Haplo6) observed only among wild macaws in Mexico and northern Guatemala. Our results suggest that people at an undiscovered pre-Hispanic settlement dating between 900 and 1200 CE managed a macaw breeding colony outside their endemic range and distributed these symbolically important birds through the SW.数百件猩红金刚鹦鹉（Ara macao cyanoptera）骨骼发掘自美国西南部与墨西哥西北部（SW/NW）的考古遗存中。这些骨骼的出土地点距离其新热带界自然分布范围超过1000公里，这表明当时存在一套覆盖范围极广的前西班牙时期物种获取网络。目前该网络中存在猩红金刚鹦鹉人工繁育的明确证据，仅来自墨西哥西北部的帕基梅（Paquimé）遗址，其年代可追溯至公元1250至1450年。尽管有学者推测美国西南部与墨西哥西北部地区可能存在更早的繁育中心，但一直缺乏相关佐证证据。本研究对出土于美国新墨西哥州查科峡谷（Chaco Canyon）及同期明布雷斯（Mimbres）地区考古遗址的猩红金刚鹦鹉样本开展了古DNA分析。所有样本均经直接放射性碳定年法测定，年代介于公元900至1200年之间。我们从5处不同遗址的14件猩红金刚鹦鹉样本中，重建了完整或近完整的线粒体基因组（mitochondrial genome）序列。本样本的遗传多样性极低，这与一小群被迁移至其自然分布区外的奠基种群的繁育模式相符。我们将本次研究获得的古DNA线粒体基因组，与过去200年间采集自新热带界自然分布区的金刚鹦鹉线粒体序列进行系统地理学（phylogeographic）比较后发现，古代金刚鹦鹉与仅见于墨西哥及危地马拉北部野生种群的单一稀有单倍群（haplogroup，Haplo6）存在遗传亲缘关系。研究结果表明，在公元900至1200年间的一处尚未被发现的前西班牙时期聚落中，先民们曾在自然分布区外运营一处金刚鹦鹉繁育种群，并将这些具有重要象征意义的鸟类传播至美国西南部地区。