Admixture and genetic diversity distribution patterns of non-recombining lineages of Native American ancestry in Colombian populations.

Catarina Xavier,Ana Goios,Juliana Aquino,Jose Miguel Ospino,Juan José Builes,Verónica Gomes,António Amorim,Leonor Gusmão,Walther Parson,Francesc Calafell

doi:10.1371/journal.pone.0120155

Abstract

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.

Highlights

Colombia was the major entrance point into South America during the peopling of the continent by the Paleoindians [1]
The colonization by the Spaniards reshaped Native slavery in 1503, and later introduced the African slave trade, leading to severe alterations in the demography of Native groups [5,6,7], so that the genetic background of Colombia results from a mixture of Native American, African and European contributions
MtDNA control region haplotypes observed in the studied Colombian Native American population groups, together with their classification in haplogroups, are described in detail in S1 Table

Summary

Introduction

Colombia was the major entrance point into South America during the peopling of the continent by the Paleoindians [1]. Two major migratory routes took place resulting in the colonization of South America: (a) along the Pacific coastline and the Andean regions and (b) towards the Amazonian plains (Fig. 1) [2,3,4]. The demography of Native ethnic groups in Colombia endured several changes since precolonial times, through the Spanish domain and into present day. Several linguistic groups coexist in Colombia since before the Spanish colonization, some of the most relevant being: the Chibchan, Carib and Arawakan, in the Atlantic coast, Chocoan in the Pacific coast and Paezan, Barbacoan and Quechua in the Southern Andean region (Fig. 1) [5,6,7]. The Native groups inhabit mainly rural zones and small villages of the country or indigenous reserves; there is a small minority that lives in the cities normally due to the lack of lands in the reserves or to difficulties in re-adapting to the social/cultural indigenous lifestyle [7]

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