A survey of genetic variation in Native American and Siberian populations reveals that Native Americans are descended from at least three streams of gene flow from Asia: after the initial peopling of the continent there was a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. The settlement of the Americas occurred at least 15,000 years ago by means of the Beringia land bridge that existed between Asia and America during the ice ages. Key questions about how many migrations were involved and subsequent dispersal patterns within the Americas remain unresolved. This new survey of genetic variation in Native American and Siberian populations shows that Native Americans descend from at least three waves of migration from Asia. After the initial peopling of the continent there was a southward expansion along the coast, with sequential population splits and little gene flow after divergence, particularly in South America. The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1,2,3,4,5. One contentious issue is whether the settlement occurred by means of a single6,7,8 migration or multiple streams of migration from Siberia9,10,11,12,13,14,15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here 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.

Despite being located at the crossroads of Asia, genetics of the Afghanistan populations have been largely overlooked. It is currently inhabited by five major ethnic populations: Pashtun, Tajik, Hazara, Uzbek and Turkmen. Here we present autosomal from a subset of our samples, mitochondrial and Y- chromosome data from over 500 Afghan samples among these 5 ethnic groups. This Afghan data was supplemented with the same Y-chromosome analyses of samples from Iran, Kyrgyzstan, Mongolia and updated Pakistani samples (HGDP-CEPH). The data presented here was integrated into existing knowledge of pan-Eurasian genetic diversity. The pattern of genetic variation, revealed by structure-like and Principal Component analyses and Analysis of Molecular Variance indicates that the people of Afghanistan are made up of a mosaic of components representing various geographic regions of Eurasian ancestry. The absence of a major Central Asian-specific component indicates that the Hindu Kush, like the gene pool of Central Asian populations in general, is a confluence of gene flows rather than a source of distinctly autochthonous populations that have arisen in situ: a conclusion that is reinforced by the phylogeography of both haploid loci.

A population in a natural crossroad within Europe reveals multiple ancient contributions and substantial population structure.

Summary: We report an integrated analysis of nuclear (autosomal, X‐ and Y‐chromosome) short tandem repeat (STR) data and mtDNA D‐loop sequences obtained in the same set of 22 Native populations from across the Americas. A north to south gradient of decreasing population diversity was observed, in agreement with a settlement of the Americas from the extreme northwest of the continent. This correlation is stronger with “least cost distances,” which consider the coasts as facilitators of migration. Continent‐wide estimates of population structure are highest for the Y‐chromosome and lowest for the autosomes, consistent with the effective size of the different marker systems examined. Population differentiation is highest in East South America and lowest in Meso America and the Andean region. Regional analyses suggest a deviation from mutation–drift equilibrium consistent with population expansion in Meso America and the Andes and population contraction in Northwest and East South America. These data hint at an early divergence of Andean and non‐Andean South Americans and at a contrasting demographic history for populations from these regions.