Demographic history and genetic structure in pre-Hispanic Central Mexico

Abstract

Aridoamerica and Mesoamerica are two distinct cultural areas in northern and central Mexico, respectively, that hosted numerous pre-Hispanic civilizations between 2500 BCE and 1521 CE. The division between these regions shifted southward because of severe droughts ~1100 years ago, which allegedly drove a population replacement in central Mexico by Aridoamerican peoples. In this study, we present shotgun genome-wide data from 12 individuals and 27 mitochondrial genomes from eight pre-Hispanic archaeological sites across Mexico, including two at the shifting border of Aridoamerica and Mesoamerica. We find population continuity that spans the climate change episode and a broad preservation of the genetic structure across present-day Mexico for the past 2300 years. Lastly, we identify a contribution to pre-Hispanic populations of northern and central Mexico from two ancient unsampled “ghost” populations.

TheMUC19gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection

“…Genomic data for MUC19 in ancient individuals was generated by combining high coverage (>1X) pre-European contact genomes from the literature, including nine individuals from California, one from Ontario [Scheib et al, 2018], four from Peru [Lindo et al, 2018] four from Patagonia [de la Fuente et al, 2018], one from Alaska [Moreno-Mayar et al, 2018], one from Montana [Rasmussen et al, 2014], and three from Central Mexico [Villa-Islas et al, 2023].…”

Genomic analyses correspond with deep persistence of peoples of Blackfoot Confederacy from glacial times

“…The finding of a previously unidentified lineage in the Americas that emerged in the Late Pleistocene builds on a pattern of multiple lineages being identified prior to the split of the Northern and Southern Native American lineages including the Ancient Beringian lineage ( 2 ), the population represented by the lineage associated with the Big Bar ancestor ( 3 ), and “ghost” populations contributing to the genomic diversity in the Americas most recently identified through statistical analyses ( 5, 6 ). These findings are potentially consistent with models of multiple populations radiating from a single source into vast geographic lands, evolving in relative isolation into different lineages early on, before interacting with nearby communities later in time as we infer here with the Blood/Blackfoot.…”

“…However, the ancient lineages identified in these studies have not been observed in Indigenous peoples of the Americas living today. Research in Mesoamerica and South America suggests that certain sampled populations (e.g., Mixe) have at least partial ancestry in present-day Indigenous groups from unknown genomic lineages in the Americas, possibly dating as far back as 25,000 years ago ( 3, 5, 6 )…”

“…However, the ancient lineages identified in these studies have not been observed in Indigenous peoples of the Americas living today. Research in Mesoamerica and South America suggests that certain sampled populations (e.g., Mixe) have at least partial ancestry in present-day Indigenous groups from unknown genomic lineages in the Americas, possibly dating as far back as 25,000 years ago (3,5,6) In addition to providing information about the population histories of Indigenous peoples in the Americas, genomic studies have the potential to further Indigenous communities' social, educational, legal, and political goals. Equitable partnerships between scientists and these communities are essential for advancing the fragmentary genomic knowledge of ancient and present-day Indigenous populations (7)(8)(9).…”

Improving data archiving practices in ancient genomics

“…The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 8 , PRJEB51180 (ENA) 9 , PRJCA005576 (GSA) 10 , PRJEB52849 (ENA) 11 , PRJEB42656 (ENA) 12 , PRJEB52230 (ENA) 13 , PRJNA786530 (SRA) 14 , PRJNA1005336 (SRA) 15 , PRJEB51440 (ENA) 16 , PRJEB56773 (ENA) 17 , PRJEB49291 (ENA) 18 , PRJEB42781 (ENA) 19 , PRJEB46734 (ENA) 20 , PRJNA798381 (SRA) 21 , PRJEB42269 (ENA) 22 , PRJEB47891 (ENA) 23 , PRJEB54899 (ENA) 24 , PRJEB43715 (ENA) 25 , PRJEB39134 (ENA) 26 , PRJEB46162 (ENA) 27 , PRJEB46875 (ENA) 28 , PRJEB44430 (ENA) 29 , PRJEB42199 (ENA) 30 , PRJEB38555 (ENA) 31 , PRJEB55327 (ENA) 32 , PRJEB56213 (ENA) 33 , PRJEB51862 (ENA) 34 , PRJEB58698 (ENA) 35 , PRJEB62503 (ENA) 36 , PRJEB66319 (ENA) 37 , PRJEB59008 (ENA) 38 , PRJEB61818 (ENA) 39 , PRJEB50368 (ENA) 40 , PRJEB50857 (ENA) 41 , PRJCA003870 (GSA) 42 , PRJCA003699 (GSA) 43 , PRJEB53475 (ENA) 44 , PRJEB37782 (ENA) 45 , PRJNA687817 (SRA) 46 , PRJEB42372 (ENA) 47 , PRJEB66422 (ENA) 48 , PRJEB57364 (ENA) 49 .…”