Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the intial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.

The large and diverse population of Latin America is potentially a powerful resource for elucidating the genetic basis of complex traits through admixture mapping. However, no genome-wide characterization of admixture across Latin America has yet been attempted. Here, we report an analysis of admixture in thirteen Mestizo populations (i.e. in regions of mainly European and Native settlement) from seven countries in Latin America based on data for 678 autosomal and 29 X-chromosome microsatellites. We found extensive variation in Native American and European ancestry (and generally low levels of African ancestry) among populations and individuals, and evidence that admixture across Latin America has often involved predominantly European men and both Native and African women. An admixture analysis allowing for Native American population subdivision revealed a differentiation of the Native American ancestry amongst Mestizos. This observation is consistent with the genetic structure of pre-Columbian populations and with admixture having involved Natives from the area where the Mestizo examined are located. Our findings agree with available information on the demographic history of Latin America and have a number of implications for the design of association studies in population from the region. The history of Latin America has entailed a complex process of population mixture between Native and recent immigrants across a vast geographic region. Few details are known about this process or about how it has shaped the genetic makeup of contemporary Latin American populations. To perform a broad exploration of the genetic diversity of Latin America we carried out genome-wide analyses in 13 mestizo populations sampled from 7 countries across the region. We observe a marked variation in ancestry both within and between mestizo populations. This variation in ancestry correlates with pre-Columbian Native population density in the areas examined and with recent patterns of demographic growth of the sites sampled. We also find evidence that the mixture at the origin of these populations involved mainly immigrant European men and Native and African women. Finally, mestizo populations show a differentiated Amerindian genetic background, consistent with a predominantly local Native ancestry. Mestizos thus still reveal the genetic imprint of the pre-Columbian Native American population diversification. Our study helps delineate the genetic landscape of Latin America and has a number of implications for gene identification analyses in populations from the region.

Similarly to other populations across the Americas, Argentinean populations trace back their genetic ancestry into African, European and Native American ancestors, reflecting a complex demographic history with multiple migration and admixture events in pre- and post-colonial times. However, little is known about the sub-continental origins of these three main ancestries. We present new high-throughput genotyping data for 87 admixed individuals across Argentina. This data was combined to previously published data for admixed individuals in the region and then compared to different reference panels specifically built to perform population structure analyses at a sub-continental level. Concerning the Native American ancestry, we could identify four Native American components segregating in modern Argentinean populations. Three of them are also found in modern South American populations and are specifically represented in Central Andes, Central Chile/Patagonia, and Subtropical and Tropical Forests geographic areas. The fourth component might be specific to the Central Western region of Argentina, and it is not well represented in any genomic data from the literature. As for the European and African ancestries, we confirmed previous results about origins from Southern Europe, Western and Central Western Africa, and we provide evidences for the presence of Northern European and Eastern African ancestries.

To confirm the geographic and ethnic segregation of HTLV-I and HTLV-II carriers in native populations in South America, we have conducted a seroepidemiological study of native populations in South America, including HTLV-I carriers distributed among seven ethnic groups in the Andes highlands of Colombia, Peru, Bolivia, Argentina, and Chile, and two ethnic groups on Chiloe Island and Easter Island; and HTLV-II carriers distributed among seven ethnic groups of the lowlands along the Atlantic coast of Colombia, Orinoco, Amazon, and Patagonia, and one ethnic group on Chiloe Island. The incidence rate of HTLV-I and HTLVII carriers varied among the ethnic groups, ranging from 0.8 to 6.8% for HTLV-I seropositivity and from 1.4 to 57.9% for HTLV-II seropositivity. A new HTLV-I focus was found among the Peruvian Aymara (1.6%), the Bolivian Aymara (5.3%) and Quechua (4.5%), the Argentine Puna (2.3%), and the Chilean Atacama (4.1%), while on HTLV-II focus was found among the Brazilian Kayapo (57.9%), the Paraguayan Chaco (16.4%), and the Chilean Alacalf (34.8%) and Yahgan (9.1%). The distribution of HTLV-I/II foci showed a geographic clustering of HTLV-I foci in the Andes highlands and of HTLV-II foci in the lowlands of South America. It was thus suggested that South American natives might be divided into two major ethnic groups by HTLV-I and HTLV-II carrier state.

We analyzed 391 samples from 12 Argentinian populations from the Center-West, East and North-West regions with the Illumina Human Exome Beadchip v1.0 (HumanExome-12v1-A). We did Principal Components analysis to infer patterns of populational divergence and migrations. We identified proportions and patterns of European, African and Native American ancestry and found a correlation between distance to Buenos Aires and proportion of Native American ancestry, where the highest proportion corresponds to the Northernmost populations, which is also the furthest from the Argentinian capital. Most of the European sources are from a South European origin, matching historical records, and we see two different Native American components, one that spreads all over Argentina and another specifically Andean. The highest percentages of African ancestry were in the Center West of Argentina, where the old trade routes took the slaves from Buenos Aires to Chile and Peru. Subcontinentaly, sources of this African component are represented by both West Africa and groups influenced by the Bantu expansion, the second slightly higher than the first, unlike North America and the Caribbean, where the main source is West Africa. This is reasonable, considering that a large proportion of the ships arriving at the Southern Hemisphere came from Mozambique, Loango and Angola.