DataSheet1_Indigenous Ancestry and Admixture in the Uruguayan Population.pdf

The Amerindian group known as the Charrúas inhabited Uruguay at the timing of European colonial contact. Even though they were extinguished as an ethnic group as a result of a genocide, Charrúan heritage is part of the Uruguayan identity both culturally and genetically. While mitochondrial DNA studies have shown evidence of Amerindian ancestry in living Uruguayans, here we undertake whole-genome sequencing of 10 Uruguayan individuals with self-declared Charruan heritage. We detect chromosomal segments of Amerindian ancestry supporting the presence of indigenous genetic ancestry in living descendants. Specific haplotypes were found to be enriched in “Charrúas” and rare in the rest of the Amerindian groups studied. Some of these we interpret as the result of positive selection, as we identified selection signatures and they were located mostly within genes related to the infectivity of specific viruses. Historical records describe contacts of the Charrúas with other Amerindians, such as Guaraní, and patterns of genomic similarity observed here concur with genomic similarity between these groups. Less expected, we found a high genomic similarity of the Charrúas to Diaguita from Argentinian and Chile, which could be explained by geographically proximity. Finally, by fitting admixture models of Amerindian and European ancestry for the Uruguayan population, we were able to estimate the timing of the first pulse of admixture between European and Uruguayan indigenous peoples in approximately 1658 and the second migration pulse in 1683. Both dates roughly concurring with the Franciscan missions in 1662 and the foundation of the city of Colonia in 1680 by the Spanish.

在欧洲殖民接触时期，查鲁阿（Charrúas）印第安族群曾定居于乌拉圭境内。尽管该族群因种族灭绝而作为民族实体消亡，但其文化与遗传层面的遗产仍是乌拉圭身份认同的重要组成部分。此前的线粒体DNA（mitochondrial DNA）研究已在当代乌拉圭人群中发现印第安血统的证据，本研究针对10名自称具有查鲁阿血统的乌拉圭个体开展全基因组测序，成功检测到携带印第安血统的染色体片段，证实当代查鲁阿后裔体内仍留存原住民遗传血统。研究发现，特定单倍型（haplotype）在"查鲁阿人群"中富集，而在其余被纳入研究的印第安族群中较为罕见；其中部分单倍型被推断为正向选择的产物：我们识别出了选择信号，且这些单倍型大多位于与特定病毒感染性相关的基因区域内。历史文献记载了查鲁阿人与瓜拉尼（Guaraní）等其他印第安族群的接触史，本研究观察到的基因组相似性模式与这些族群间的基因组相似性结果一致。出乎意料的是，我们发现查鲁阿人群与来自阿根廷、智利的迪亚吉塔（Diaguita）人群具有高度的基因组相似性，这一结果可通过地理邻近性得到合理解释。最后，通过为乌拉圭人群构建印第安与欧洲血统的混合模型，我们估算出欧洲人与乌拉圭原住民的首次混血事件发生于约1658年，第二次混血事件发生于1683年，这两个时间节点大致与1662年的方济各会传教活动（Franciscan missions）以及1680年西班牙建立科洛尼亚（Colonia）城的史实相吻合。