Archaeogenomic distinctiveness of the Isthmo-Colombian area

Abstract

Summary The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.

Weaving Mitochondrial DNA and Y-Chromosome Variation in the Panamanian Genetic Canvas

“…This genome-wide analysis also provided some clues about the impact of European colonization. As expected, present-day Morenos show prevalent African ancestry (≈62%), but with a significant European contribution (≈13%), in ADMIXTURE analyses [36]. Surprisingly, Mestizos present a larger fraction of Indigenous (≈44%) than African (≈32%) and European (≈13%) genomic components and traces of East Asian variants (≈11%).…”

“…Another outcome of the present work is the similarity between the two systems with respect to the significant difference in the haplogroup distribution among the Panamanian Indigenous groups (p-value < 0.001 for both systems). Indeed, mtDNA haplogroup A2w, previously found in North and Central American modern individuals [36,[68][69][70][71][72][73] and more recently in an ancient pre-Hispanic individual excavated in Panama City [36], is only present in the Ngäbe group of our present sample. Likewise, in our sample, the male paragroup Q-M925* is exclusively found (except for one Guna individual) in the Ngäbe.…”

“…A total of 301 unrelated Panamanian males were sampled. Of these, 248 were successfully classified into Y-chromosome haplogroups (Table S1), including 43 male subjects genotyped with the Affymetrix Human origin 600K chip and previously analyzed in [36]. The Y-chromosome haplogroup classification was obtained by hierarchical order analysis of 54 biallelic markers of the male-specific region of Y chromosome (MSY), following the latest Y-chromosome phylogeny (https://www.yfull.com/tree/; https://isogg.org/, both accessed on 7 October 2021) and according to [41].…”

The Mitochondrial DNA Landscape of Modern Mexico

“…Both clines were also observed in Indigenous and admixed populations when analyzed at a country-wide scale [ 2 , 3 , 12 , 14 , 17 , 18 , 62 ]. These findings illustrate the heterogeneity of lineage dispersal within America, since they contrast with the overall gradients in the double continent [ 8 , 18 ].…”

“…Mesoamerica had a pivotal role in this process, providing a bridge and geographic bottleneck into South America and continuous interethnic space. Archaeological evidence has shown human presence in today’s Mexico since 12–15 thousand years (ky) [ 5 , 6 , 10 , 11 , 12 ]. The extensive and arid North and the rainy and narrow central and Southern valleys and mountains required different subsistence strategies: while Northern human populations were hunter-gatherers, Indigenous American (also called Native American) groups in South-Central Mexico began to settle in communities following the development of (maize) agriculture from 7–5 ky ago [ 2 , 3 , 5 , 13 , 14 ].…”