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 in MXL, in CLM, and in PUR. Native American ancestry in PUR is most closely related to populations surrounding the Orinoco River basin, confirming the Southern America ancestry of the Taíno 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 demographic model for three ancestral Native American populations. These ancestral populations likely split in close succession: the most likely scenario, based on a peopling of the Americas thousand years ago (kya), supports that the MXL Ancestors split kya, with a subsequent split of the ancestors to CLM and PUR kya. The model also features effective populations of in Mexico, in Colombia, and in Puerto Rico. 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 effective size and the earlier migration from Europe. Finally, we compare IBD and ancestry assignments to find evidence for relatedness among European founders to the three populations.
Populations of the Americas have a rich and heterogeneous genetic and cultural heritage that draws from a diversity of pre-Columbian Native American, European, and African populations. Characterizing this diversity facilitates the development of medical genetics research in diverse populations and the transfer of medical knowledge across populations. It also represents an opportunity to better understand the peopling of the Americas, from the crossing of Beringia to the post-Columbian era. Here, we take advantage sequencing of individuals of Colombian (CLM), Mexican (MXL), and Puerto Rican (PUR) origin by the 1000 Genomes project to improve our demographic models for the peopling of the Americas. The divergence among African, European, and Native American ancestors to these populations enables us to infer the continent of origin at each locus in the sampled genomes. The resulting patterns of ancestry suggest complex post-Columbian migration histories, starting later in CLM than in MXL and PUR. Whereas European ancestral segments show evidence of relatedness, a demographic model of synonymous variation suggests that the Native American Ancestors to MXL, PUR, and CLM panels split within a few hundred years over 12 thousand years ago. Together with early archeological sites in South America, these results support rapid divergence during the initial peopling of the Americas.