Whole mitogenome analysis highlights demographic history and shared connections among distal Indigenous groups of Mexico Complete mitogenome sequencing from 60 Mexican Native American groups

Abstract

47 48 The study of mitochondrial DNA is a valuable tool to delve into the demographic 49 history of human populations. Particularly in the Americas, five widespread Native 50 American specific mitochondrial lineages have been identified. Here we included the 51 complete mitogenome sequencing of 572 Indigenous individuals belonging to 60 52 populations spanning the Mexican territory. Our results show a great diversity of 53 matrilineages widespread across the country, revealing shared mtDNA haplogroups in 54 populations from distant regions. We identified all the five main Native American 55 haplogroups clades, including 83 different subhaplogroups, from which nine are novel. The 56 most frequent of the novel haplogroups was A2+64. A phylogenetic inference suggests that 57 A2+64 comes from an ancestral maternal lineage that spread into the Caribbean islands. 58 Additionally, a demographic reconstruction from whole mitogenomes showed an 59 exponential increase in female Ne around 10 Ka ago in all the tested regions. All these 60 findings suggest a genetic persistence through Mexico and possibly the Americas, in 61 agreement with the model of the Mesoamerican-related expansion into the Caribbean and 62 South America. 63 64 65 66 67 68 69 70 71 2 bioRxiv preprint doi: https://doi.org/10.1101/2023.09.03.556146; this version posted September 6, 2023. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 72