Reconstructing Native American Migrations from Whole-genome and Whole-exome Data

Reconstructing Native American Migrations from Whole-genome and Whole-exome Data
Simon Gravel, Fouad Zakharia, Jake K Byrnes, Marina Muzzio, Andres Moreno-Estrada, Juan L. Rodriguez-Flores, Eimear E. Kenny, Christopher R. Gignoux, Brian K. Maples, Wilfried Guiblet, Julie Dutil, Karla Sandoval, Gabriel Bedoya, The 1000 Genomes Project, Taras K Oleksyk, Andres Ruiz-Linares, Esteban G Burchard, Juan Carlos Martinez-Cruzado, Carlos D. Bustamante
(Submitted on 17 Jun 2013)

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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