Dissecting the pre-Columbian genomic ancestry of Native Americans along the Andes–Amazonia divide

Guido Alberto Gnecchi-Ruscone, Stefania Sarno, Sara De Fanti, Laura Gianvincenzo, Cristina Giuliani, Alessio Boattini, Eugenio Bortolini, Tullia Di Corcia, Cesar Sanchez Mellado, Taylor Jesus Davila Francia, Davide Gentilini, Anna Maria Di Blasio, Patrizia Di Cosimo, Elisabetta Cilli, Antonio Gonzalez-Martin, Claudio Franceschi, Zelda Alice Franceschi, Olga Rickards, Marco Sazzini, Donata LuiselliDavide Pettener

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)1254-1269
Number of pages16
JournalMolecular Biology and Evolution
Issue number6
Publication statusPublished - Jun 1 2019


  • Amazonia
  • Andes
  • Genome-wide SNPs
  • Native American ancestry
  • Population genomics

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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