The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America.

We examined genetic diversity and population structure in the American landmass using 678 autosomal microsatellite markers genotyped in 422 individuals representing 24 Native American populations sampled from North, Central, and South America. These data were analyzed jointly with similar data available in 54 other indigenous populations worldwide, including an additional five Native American groups. The Native American populations have lower genetic diversity and greater differentiation than populations from other continental regions. We observe gradients both of decreasing genetic diversity as a function of geographic distance from the Bering Strait and of decreasing genetic similarity to Siberians—signals of the southward dispersal of human populations from the northwestern tip of the Americas. We also observe evidence of: (1) a higher level of diversity and lower level of population structure in western South America compared to eastern South America, (2) a relative lack of differentiation between Mesoamerican and Andean populations, (3) a scenario in which coastal routes were easier for migrating peoples to traverse in comparison with inland routes, and (4) a partial agreement on a local scale between genetic similarity and the linguistic classification of populations. These findings offer new insights into the process of population dispersal and differentiation during the peopling of the Americas.

No abstract

An appropriate model of recent human evolution is not only important to understand our own history, but it is necessary to disentangle the effects of demography and selection on genome diversity. Although most genetic data support the view that our species originated recently in Africa, it is still unclear if it completely replaced former members of the Homo genus, or if some interbreeding occurred during its range expansion. Several scenarios of modern human evolution have been proposed on the basis of molecular and paleontological data, but their likelihood has never been statistically assessed. Using DNA data from 50 nuclear loci sequenced in African, Asian and Native American samples, we show here by extensive simulations that a simple African replacement model with exponential growth has a higher probability (78%) as compared with alternative multiregional evolution or assimilation scenarios. A Bayesian analysis of the data under this best supported model points to an origin of our species Ϸ141 thousand years ago (Kya), an exit out-of-Africa Ϸ51 Kya, and a recent colonization of the Americas Ϸ10.5 Kya. We also find that the African replacement model explains not only the shallow ancestry of mtDNA or Y-chromosomes but also the occurrence of deep lineages at some autosomal loci, which has been formerly interpreted as a sign of interbreeding with Homo erectus.Bayesian analysis ͉ DNA nuclear data ͉ multiregional hypothesis ͉ out of Africa hypothesis

We report here a simulation study examining the effect of a recent spatial expansion on the pattern of molecular diversity within a deme. We first simulate a range expansion in a virtual world consisting in a two-dimensional array of demes exchanging a given proportion of migrants (m) with their neighbors. The recorded demographic and migration histories are then used under a coalescent approach to generate the genetic diversity in a sample of genes. We find that the shape of the gene genealogies and the overall pattern of diversity within demes depend not only on the age of the expansion but also on the level of gene flow between neighboring demes, as measured by the product Nm, where N is the size of a deme. For small Nm values (< approximately 20 migrants sent outwards per generation), a substantial proportion of coalescent events occur early in the genealogy, whereas with larger levels of gene flow, most coalescent events occur around the time of the onset of the spatial expansion. Gene genealogies are star shaped, and mismatch distributions are unimodal after a range expansion for large Nm values. In contrast, gene genealogies present a mixture of both very short and very long branch lengths, and mismatch distributions are multimodal for small Nm values. It follows that statistics used in tests of selective neutrality like Tajima's D statistic or Fu's F(S) statistic will show very significant negative values after a spatial expansion only in demes with high Nm values. In the context of human evolution, this difference could explain very simply the fact that analyses of samples of mitochondrial DNA sequences reveal multimodal mismatch distributions in hunter-gatherers and unimodal distributions in post-Neolithic populations. Indeed, the current simulations show that a recent increase in deme size (resulting in a larger Nm value) is sufficient to prevent recent coalescent events and thus lead to unimodal mismatch distributions, even if deme sizes (and therefore Nm values) were previously much smaller. The fact that molecular diversity within deme is so dependent on recent levels of gene flow suggests that it should be possible to estimate Nm values from samples drawn from a single deme.