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.. Demographic history and genetic structure in pre-Hispanic Central Mexico

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.