Genetic Ancestry and Structure of Four Indigenous Communities in Colombia: Embera-Kátio, Nasa-Páez, Pijao, and Wayuu

Abstract

Colombia is the second country with the highest number of Amerindian ethnic groups, with autonomy and self-governance, allowing them to preserve their culture and Amerindian genetic heritage. In some of these communities, studies using markers such as mitochondrial DNA (mtDNA), the non-recombining region of the Y chromosome (NRY), and Ancestry Informative Markers (AIMs) have helped clarify the settlement processes and genetic admixture of these populations. In this study, we analyzed genome-wide Single Nucleotide Polymorphism (SNP) data from four indigenous populations of Colombia, the Wayuu, Nasa-Páez, Pijao, and Embera-Kátio, genotyped on the Axiom SpainBA panel. We were interested in determining the genetic ancestry and structure, as well as patterns of genetic variation in these populations. We collected personal questionnaires to determine family relationships and included only unrelated individuals for further analyses. Population genetic analyses, including other Native and non-Indigenous American populations, showed genetic affinities to other Indigenous American populations and varied levels of genetic admixture with non-American sources. Furthermore, our analyses suggest that distinct demographic histories, including isolation, genetic drift associated with reduced effective population size (Ne), and admixture, have shaped patterns of genetic variation and population structure among Colombian Indigenous populations.