Abstract
There is great scientific and popular interest in understanding the genetic
history of populations in the Americas. We wish to understand when different
regions of the continent were inhabited, where settlers came from, and how
current inhabitants relate genetically to earlier populations. Recent studies
unraveled parts of the genetic history of the continent using genotyping arrays
and uniparental markers. The 1000 Genomes Project provides a unique opportunity
for improving our understanding of population genetic history by providing over
a hundred sequenced low coverage genomes and exomes from Colombian (CLM),
Mexican-American (MXL), and Puerto Rican (PUR) populations. Here, we explore
the genomic contributions of African, European, and especially Native American
ancestry to these populations. Estimated Native American ancestry is 48% in
MXL, 25% in CLM, and 13% in PUR. Native American ancestry in PUR appears most
closely related to Equatorial-Tucanoan-speaking populations, supporting a
Southern America ancestry of the Taino people of the Caribbean. We present new
methods to estimate the allele frequencies in the Native American fraction of
the populations, and model their distribution using a three-population
demographic model. The ancestral populations to the three groups likely split
in close succession: the most likely scenario, based on a peopling of the
Americas 16 thousand years ago (kya), supports that the MXL Ancestors split
12.2kya, with a subsequent split of the ancestors to CLM and PUR 11.7kya. The
model also features a Mexican population of 62,000, a Colombian population of
8,700, and a Puerto Rican population of 1,900. Modeling Identity-by-descent
(IBD) and ancestry tract length, we show that post-contact populations also
differ markedly in their effective sizes and migration patterns, with Puerto
Rico showing the smallest size and the earlier migration from Europe.
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