Demographic history and genetic structure in pre-Hispanic Central Mexico. We recovered and studied genome-wide and mitochondrial data from pre-Hispanic individuals from different regions in Mexico: Sierra Tarahumara, Sierra Gorda, Cañada de La Virgen and Michoacan.

Aridoamerica and Mesoamerica are two distinct cultural areas where numerous pre-Hispanic civilizations thrived between 2,500 BCE and 1,521 CE. The border between them shifted southward because of severe droughts ca. 1,100 years ago, allegedly driving demographic changes and population replacement in some sites in central Mexico. Here, we present shotgun genome-wide data from 12 individuals and 26 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity spanning the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the last 2,300 years. Lastly, we identify a contribution of an ancient unsampled 'ghost' population to pre-Hispanic populations from northern and central Mexico.

干旱美洲文化区（Aridoamerica）与中美洲文化区（Mesoamerica）是两个独立的文化区域，在公元前2500年至公元1521年间，诸多前西班牙殖民时期的文明在此繁盛发展。二者的边界在约1100年前因严重干旱向南推移，据称这一气候变化推动了墨西哥中部部分遗址的人口结构变迁与种群更替。本研究报道了来自墨西哥境内8处前西班牙殖民时期考古遗址的12名个体的全基因组鸟枪法测序数据，以及26条线粒体基因组序列，其中两处遗址正处于两个文化区的动态边界地带。我们发现，在此次气候变化事件期间，当地种群延续性得以维持，且过去2300年间，现今墨西哥境内的种群遗传结构整体保持稳定。此外，我们还确认，一支未被采样的古老“幽灵种群”对墨西哥北部与中部的前西班牙殖民时期种群存在遗传贡献。