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Mol Biol Evol. 2019 Jun 1;36(6):1254-1269. doi: 10.1093/molbev/msz066.

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

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Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy.
Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
Department of Cultural Heritage, University of Bologna, Ravenna, Italy.
Department of Biology, University of Rome Tor Vergata, Rome, Italy.
Faculty of Intercultural Education and Humanity, National Intercultural University of Amazon, Ucayali, Peru.
Center for Biomedical Research and Technologies, Italian Auxologic Institute IRCCS, Milan, Italy.
Takesi Project, University of Bologna, Bologna, Italy.
Department of Zoology and Physical Anthropology, Complutense University of Madrid, Madrid, Spain.
Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.
Department of History and Cultures, University of Bologna, Bologna, Italy.


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.


Amazonia; Andes; Native American ancestry; genome-wide SNPs; population genomics


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