Dissecting the Pre-Columbian Genomic Ancestry of Native Americans along the Andes–Amazonia Divide

Abstract

Extensive European and African admixture coupled with loss of Amerindian lineages makes the reconstruction of pre-Columbian history of Native Americans based on present-day genomes extremely challenging. Still open questions remain about the dispersals that occurred throughout the continent after the initial peopling from the Beringia, especially concerning the number and dynamics of diffusions into South America. Indeed, if environmental and historical factors contributed to shape distinct gene pools in the Andes and Amazonia, the origins of this East-West genetic structure and the extension of further interactions between populations residing along this divide are still not well understood. To this end, we generated new high-resolution genome-wide data for 229 individuals representative of one Central and ten South Amerindian ethnic groups from Mexico, Peru, Bolivia, and Argentina. Low levels of European and African admixture in the sampled individuals allowed the application of fine-scale haplotype-based methods and demographic modeling approaches. These analyses revealed highly specific Native American genetic ancestries and great intragroup homogeneity, along with limited traces of gene flow mainly from the Andes into Peruvian Amazonians. Substantial amount of genetic drift differentially experienced by the considered populations underlined distinct patterns of recent inbreeding or prolonged isolation. Overall, our results support the hypothesis that all non-Andean South Americans are compatible with descending from a common lineage, while we found low support for common Mesoamerican ancestors of both Andeans and other South American groups. These findings suggest extensive back-migrations into Central America from non-Andean sources or conceal distinct peopling events into the Southern Continent.

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

“…This supports the hypothesis of many migrations back to Central America different from the Andeans ancestors [39]. It has also been described that the genetic interactions between the peopling routes on both sides of the Andes were limited [39, 40].…”

“…A recent genomic study of ancient and modern populations from Central Chile and Western Patagonia further identified that they are differentiated from the Andean and Lowlands populations, supporting a differentiation process throughout South America [37]. In another recent genomic study of modern samples, in which the Southern Cone is only represented by Gran Chaco populations, it has been described a likely common lineage for non-Andean South Americans populations which do probably not share with the Andeans any common ancestor from Central America [39]. This supports the hypothesis of many migrations back to Central America different from the Andeans ancestors [39].…”

“…In another recent genomic study of modern samples, in which the Southern Cone is only represented by Gran Chaco populations, it has been described a likely common lineage for non-Andean South Americans populations which do probably not share with the Andeans any common ancestor from Central America [39]. This supports the hypothesis of many migrations back to Central America different from the Andeans ancestors [39]. It has also been described that the genetic interactions between the peopling routes on both sides of the Andes were limited [39, 40].…”

“…We argue that focusing only on indigenous communities by “implementing accurate sampling strategies and of selecting representative populations based on historical/linguistic and anthropological information”, as advocated by Gnecchi-Ruscone et al [39] for example, is not sufficient to decipher the pre-Columbian history of Native Americans. Although studies based on such sampling strategies [37–39] provide decisive information to understand the evolutionary history of Native American ancestry [22], it implies to disregard many regions of the continent. This is particularly the case of Argentinean territory where only the extreme North and South, separated by ∼ 3,700 kilometers, have been studied under this scope.…”

Fine-scale genomic analyses of admixed individuals reveal unrecognized genetic ancestry components in Argentina

“…In another genomic study of modern samples (in which the Southern Cone is only represented by the Gran Chaco region), it has been found that all non-Andean South American populations are likely to share a common lineage, while they are unlikely to share with the Andeans any common ancestor from Central America [39], supporting the hypothesis of many back migrations to Central America from non-Andean South American populations [39]. It has also been described that the genetic interactions between the peopling routes on both sides of the Andes were limited [39,40].…”