Abstract
The colonization of Americas is thought to have occurred 15–20 thousand years ago (Kya), with little or no subsequent migration into South America until the European expansions beginning 0.5Kya. Recently, however, haplogroup C3* Y chromosomes were discovered in two nearby Native American populations from Ecuador. Since this haplogroup is otherwise nearly absent from the Americas but is common in East Asia, and an archaeological link between Ecuador and Japan is known from 6Kya, an additional migration 6Kya was suggested. Here, we have generated high-density autosomal SNP genotypes from the Ecuadorian populations and compared them with genotypes from East Asia and elsewhere to evaluate three hypotheses: a recent migration from Japan, a single pulse of migration from Japan 6Kya, and no migration after the First Americans. First, using forward-time simulations and an appropriate demographic model, we investigated our power to detect both ancient and recent gene flow at different levels. Second, we analyzed 207,321 single nucleotide polymorphisms from 16 Ecuadorian individuals, comparing them with populations from the HGDP panel using descriptive and formal tests for admixture. Our simulations revealed good power to detect recent admixture, and that ≥5% admixture 6Kya ago could be detected. However, in the experimental data we saw no evidence of gene flow from Japan to Ecuador. In summary, we can exclude recent migration and probably admixture 6Kya as the source of the C3* Y chromosomes in Ecuador, and thus suggest that they represent a rare founding lineage lost by drift elsewhere.
Highlights
The consensus view of the peopling of the Americas, incorporating archaeological, linguistic and genetic evidence, proposes colonization by a small founder population from Northeast Asia via Beringia 15–20 Kya, followed by one or two additional migrations via Alaska, contributing only to the gene pools of North Americans, and little subsequent migration into the Americas south of the Arctic Circle before the voyages from Europe initiated by Columbus in 1492 [1]
We modelled a single pulse of migration from a Source population to produce an Admixed population; an additional population was simulated as a control
For the recent admixture model, we found that we could detect $50% or $20% of Japanese ancestry in all the individuals in the 50% or 20% artificial admixed simulations, respectively
Summary
The consensus view of the peopling of the Americas, incorporating archaeological, linguistic and genetic evidence, proposes colonization by a small founder population from Northeast Asia via Beringia 15–20 Kya (thousand years ago), followed by one or two additional migrations via Alaska, contributing only to the gene pools of North Americans, and little subsequent migration into the Americas south of the Arctic Circle before the voyages from Europe initiated by Columbus in 1492 [1]. Some inhabitants of Easter Island (Rapa Nui) carry HLA alleles characteristic of South America, most readily explained by gene flow after the colonization of the island around 1200 CE but before European contact in 1722 [5].
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