Human Migration To South America

A new, rather mediocre, study that emphasizes genetic diversity in South America tends to track the New World settlement paradigm rather closely. Honestly, for a major new paper in a major scientific journal, it adds surprisingly little to existing knowledge. 

Uncontacted or recently contacted populations in Amazonia and Papuans are the least genetically diverse.  This study, by not mentioning it at all, seems to disfavor the hypothesis of ancient Papuan/Australasian ancestry in Amazonian populations in South America, although this is a key issue in South American population history that really should have been at least discussed in this paper, even if it couldn't reach a definitive conclusion regarding this point with its own data.

The paper also, implicitly suggests (consistent with prior research), that progenitor modern human populations that left foot prints in New Mexico about 23,000 years ago made only an indiscernible impact, if any, on the primary founding population of the Americas starting around 14,000 years ago. A better discussion of how the genetic profiles of Native American in North America differs from those in South America would also have been welcome. It seems to suggest a somewhat older than conventional population history for the founding population of North America, but does so with little meaningful discussion of North American population genetics.

The lack of data from the Atlantic coast of South America and the very thin data from the Amazon, even compared to prior studies of South American genetics, also suggests to me that it is possible that there could be five rather than four main branches of South American settlement. Even if one can't find "pure" indigenous South American ancestry in this region, it should be possible from large databases of modern populations in this region from prior studies, which is home to a large share of all South Americans, to make strong inferences about it from individuals modern populations in the region with indigenous admixture.

There is also too little discussion of the population genetic impact of the Columbian Exchange on either the main different population groups it infers in South America or on the strength of the inferences it is making. We would expect this event in the last 500 years to cause strong fitness based selection, and possibly hard selective sweeps on HLA genetic diversity, an rate unprecedented in the previous 13,500 years, and HLA genetic diversity is one of the important pieces of data that the study examines. But this question isn't elevated or focused upon by the authors.

Editor’s summary

From our origins in Africa, humans have migrated and settled across the world. Perhaps none of these migrations has been the subject of as much debate as the expansion into and throughout the Americas. Gusareva et al. used 1537 whole-genome sequenced samples from 139 populations in South America and Northeast Eurasia to shed light on the population history of Native Americans. Collected as a part of the GenomeAsia 100K consortium, analysis of these data showed that there are four main ancestral lineages that contributed to modern South Americans. These lineages diverged from each other between 10,000 and 14,000 years ago, and this analysis reveals more details of the population history dynamics in these groups. —Corinne Simonti

Abstract

Genome sequencing of 1537 individuals from 139 ethnic groups reveals the genetic characteristics of understudied populations in North Asia and South America. Our analysis demonstrates that West Siberian ancestry, represented by the Kets and Nenets, contributed to the genetic ancestry of most Siberian populations. West Beringians, including the Koryaks, Inuit, and Luoravetlans, exhibit genetic adaptation to Arctic climate, including medically relevant variants. 

In South America, early migrants split into four groups—Amazonians, Andeans, Chaco Amerindians, and Patagonians—~13,900 years ago. Their longest migration led to population decline, whereas settlement in South America’s diverse environments caused instant spatial isolation, reducing genetic and immunogenic diversity. These findings highlight how population history and environmental pressures shaped the genetic architecture of human populations across North Asia and South America.

Abstract

INTRODUCTION

During the late Pleistocene, humans expanded across Eurasia and eventually migrated to the Americas. Those who reached Patagonia, at the southern tip of South America, completed the longest migration out of Africa.

RATIONALE

The extent of basal divergences, admixture, and degrees of isolation among Indigenous North Eurasian and Native South American populations remain debated, with most insights derived from genome-wide genotyping data. This study aims to deepen our understanding of the ancient dynamics that shaped contemporary populations in North Eurasia and the Americas. By using large-scale whole-genome sequencing of 1537 individuals from 139 ethnic groups in these regions, we examined population structures, elucidated prehistoric migrations, and explored the influence of past environmental factors on the diversification of human populations.

RESULTS

Advances in large-scale genomic sequencing have considerably enhanced our understanding of the genetic ancestry of human populations across North Eurasia and South America. Our analysis reveals that all contemporary Siberians, as well as some Northeast Europeans and Central Asians, share ancestry with the West Siberian groups, represented by the Kets and Nenets. Their ancestors were widespread across Siberia 10,000 years ago (ya), but now these groups face population decline by 73.6% and are becoming a minority.

The populations of west Beringia, including the Koryaks, Inuit, and Luoravetlans, are the most genetically distinct from other Siberians. These groups have adapted to Arctic conditions with genetic variations related to lipid metabolism, thermogenesis, sensory perception, and the regulation of reproductive and immune functions. 

We were not able to identify a specific Siberian group as the direct ancestors of Native Americans owing to deep divergence and limited genetic continuity. However, west Beringian populations remain closely related to Native Americans. Koryaks and Inuit show 5 and 28% Native American ancestry, respectively, owing to gene flow between 700 and 5100 ya.

We estimated the split time of Native South Americas into Amazonians, Andeans, Chaco Amerindians, and Patagonians to have occurred 13,900 to 10,000 ya. Migration and settlement across the continent led to population isolations due to geographic boundaries and a reduction in their genetic diversity, particularly affecting immune genes, such as the human leukocyte antigen (HLA) genes. Over the past 10,000 years, all four Native South American lineages have experienced population declines ranging from 38 to 80%. This dramatic decline, combined with the loss of traditional lifestyles, cultural practices, and languages, has pushed some Indigenous communities, such as the Kawésqar, to the brink of extinction.

CONCLUSION

The migration to an uninhabited continent of South America through the narrow Isthmus of Panama resulted in a founder effect among Native South Americans, leading to reduced genetic diversity compared with that of Indigenous populations of North Eurasia. Over 13,900 years, geographic barriers within the continent further isolated Indigenous groups, subsequently reducing genetic diversity. These groups faced a profound challenge with the arrival of European colonists in the 1600s, who introduced new adversities that threatened their long-standing endurance. 

Genetic ancestry and nucleotide diversity. 

Colors represent genetic ancestries estimated by whole-genome sequencing data of contemporary human populations. Countries having no data remained empty. Circle size indicates the average nucleotide diversity of each population.

Elena S. Gusareva, et al., "From North Asia to South America: Tracing the longest human migration through genomic sequencing" 388 (6748) Science (May 15, 2025) DOI: 10.1126/science.adk5081

The introduction in the body text puts the findings in context:

The late Pleistocene saw the expansion of humans into the frigid lands of Eurasia. The earliest known presence of modern humans in northern Eurasia at latitudes greater than 50°N was around 45,000 years ago (ya) in West Siberia, and by 31,600 ya, humans had migrated far east toward Beringia, north of the Arctic Circle at 71° N. The earliest human remains identified in this region are two Yana Rhinoceros Horn Site individuals that, despite their extreme Northeast Siberian geographical location, show substantial genetic relatedness to early West Eurasian hunter-gatherers. 

The Upper Palaeolithic people who initially populated Northeast Siberia were then replaced by arrivals from East Asia. The Kolyma1 remains, excavated near the Chukotka region and dated as being from 9800 ya, demonstrate greater affinity to East Asians and present-day west Beringian populations, such as Koryaks and Luoravetlans (also known as Chukchi), as well as to Native Americans. The linguistic and cultural diversity of present-day Indigenous Siberian populations is mirrored by the complex patterns of admixture, as shown by genome-wide genotype data analysis. This genetic structure in Siberians, comprising several ancestral components, is estimated to have emerged within the past 10,000 to ~3400 years. The Western Eurasian ancestry component presented in a majority of Indigenous Siberian populations is not the result of postcolonial Russian admixture but one of the ancient components dating back to 12,500 to 25,000 ya in different Siberian populations. Among the present-day populations of Northeast Eurasia, the Koryaks from the Kamchatka Peninsula and the Inuit from Chukotka show the closest genetic relatedness to Native North Americans. 

The migration of humans to the Americas occurred when the Bering Land Bridge was still open, with the earliest human remains in North America found in the Clovis burial site in western Montana dating back to around 12,700 ya. However, recent evidence suggests human presence in North America from at least 23,000 ya. By the time the Ice-Free Corridor opened up and became suitable for travel around 13,300 ya, humans were already widely dispersed in North America, likely owing to Pacific coastal migration routes. The divergence between northern and southern Native American populations is estimated to have occurred between 17,500 and 14,600 ya south of the North American ice sheets, according to modern and ancient genomic analyses. The rapid dispersal of humans in South America is suggested by archaeological records, which date the earliest human presence in North Patagonia, the southernmost tip of the Americas, to 14,500 ya. However, the number of basal divergences, founding populations, admixture, and the degrees of isolation among Native South American populations remain a subject of debate, with most of the current understanding coming from analyses of genome-wide genotyping or ancient DNA data. Additionally, fine-scale population genetic studies based on high-coverage whole-genome sequencing datasets for contemporary populations of North Eurasia and South America have not been performed to date.

The body text's discussion of population decline in South America (which has been continuous and not just entirely due to the Columbian exchange) is notable since rare haplotypes and ancestrally informative genes are strongly prone to being purged in periods of declining population (while happens only rarely in expanding populations). Consistent with this these populations have low genetic diversity.

The population split time estimates also suggest that the divergence of the four Native South American lineages occurred over a short period, from 13,900 to 10,000 ya. All four lineages show a continuous population decline. However, the Andean highlanders managed to maintain their population size during the rise of maize horticulture around 5200 to 3700 ya. It has declined by 45.1% since then (Ne from 1771 to 972), whereas Chaco Amerindians have declined by 46.89% (Ne from 1448 to 769) since 10,000 ya. Amazonians and especially Patagonians have seen a dramatic decrease in population size over the past 10,000 years, with declines of 66.59% (Ne from 1368 to 457) and 79.68% (Ne from 1171 to 238), respectively.

To assess the impact of population decline on genetic diversity, we estimated genome-wide runs of homozygosity (ROHs) segments. In Native South Americans, the average number and length of ROHs segments estimated across all populations were 10.5 and 1.3 times higher than those in Africans (Yoruba) and 3.75 and 1.2 times higher than those in Northeast Europeans, respectively. The highest abundance of extended ROHs was observed in Amazonians, Patagonian Kawésqar, and Chaco Amerindians and was similar to that seen in isolated island populations, such as the Andamanese and Baining. This high homozygosity is likely the result of the founder effect due to long-distance migration and/or population isolation. The strong correlation between the average total number of ROHs and the average nucleotide diversity (Pearson correlation coefficient r = –0.78) supports the idea that the extended homozygosity is a result of population history.

The body text of the discussion section notes that:

Our analysis of whole-genome datasets also allowed us to infer the split time between North Eurasians and Native Americans, which occurred between 26,800 and 19,300 ya. This finding is consistent with estimates based on the recently published paleontological discovery of human footprints in North America (south-central New Mexico) dating back to 23,000 and 21,000 ya, as well as with other genetic studies, despite differences in the cohorts that were investigated. 

A previous study of ancient genomes suggests limited genetic continuity in Beringia, as the most recent Arctic colonization occurred 6000 ya. Therefore, it is likely that the first ancestors of the Native Americans in this region were replaced by the most recent wave of migration. We could not identify a specific Siberian group as direct Native American ancestors among the contemporary Indigenous populations in our dataset. However, we show that west Beringian populations, such as Inuit, Luoravetlans, and Koryaks, are genetically the closest to Native Americans. Moreover, we revealed the gene flow from Native Americans back to Inuit and Koryaks in Chukotka and the Kamchatka Peninsula between 700 to 5100 ya. Our analyses also demonstrated the shared ancestry between the west Beringian populations and contemporary Native North Americans, particularly the Chipewyan from Canada. This genetic relatedness is consistent with the PCA results. These findings are in line with previous reports that describe multiple waves of Northeast Asian gene flow into North Americans, including Neo-Inuit lineages. 

By using our genome sequencing data from diverse Native South Americans, we have discovered that the simultaneous split of the four Native South American ancestral lineages occurred between 13,900 and 10,000 ya from a common ancestral population in Mesoamerica. This rapid radial dispersal and the establishment of sedentary settlements across South America are supported by previous genetic studies and the archaeological findings of early technologies (such as stone tools) that indicate regional cultural diversification in South America from at least 13,000 ya. This divergence occurred shortly after the split of the ancestral Native American lineages into northern and southern branches, which happened between 17,500 and 14,600 ya south of the North American ice sheets. By the time the Ice-Free Corridor was fully opened 14,300 to 13,300 ya during the abrupt warming, humans were already widely dispersed in North America. 

Our study shows that the human migration across South America resulted in population splits with a loss of genetic diversity due to founder effects. Geographical and environmental boundaries caused population isolation and further enhanced the genetic homogenization, similar to islander populations. The demographic history has greatly influenced the Patagonian Kawésqar, whose ancestors migrated the farthest distance out of Africa. They have the smallest effective population size and one of the smallest genetic distances between community members. It has been reported that contemporary Native Patagonians (including the Kawésqar) show the highest genetic affinity to ancient Patagonian maritime individuals that lived 1000 ya, indicating genetic continuity in the region. Our study cannot provide evidence for the reported back migration from the Southern Cone along South America's Atlantic coast owing to a lack of data on east coastal Native South American populations. 

Our study also suggests that close genetic relatedness in Indigenous populations, along with reduced heterozygosity in HLA genes, may impact antigen recognition ability to new unexposed pathogens. In combination with socioeconomic factors and limited access to medical care, this could pose a potential health risk. High–pathogen load regions, such as Southeast Asia, tend to have a higher diversity of promiscuous HLA-DRB1 alleles, which allows them to respond to a wider range of extracellular pathogens. However, emerging evidence that divergent allele advantage (a mechanism where the HLA genotypes present a broader set of epitopes) and increase in HLA alleles promiscuity level may counterplay the effect of loss of heterozygosity in HLA genes. Our work highlights a noteworthy implication for future research in population-based disease cohorts: Epitope-binding repertoire studies are essential for identifying the dynamic effects of limited HLA diversity on disease susceptibility. 

Access to the vastness of the South American continent was constrained by the relatively small landmass of the Isthmus of Panama. Consequently, migrating groups could only inhabit the continent from a singular direction, limiting the genetic diversity of human individuals. This ultimately led to the emergence of the four ancestries described in our analysis. Although Indigenous groups managed to maintain their populations for over 13 millennia with minimal interaction with other groups, their endurance faced a critical challenge with the arrival of the initial colonists in the 1600s.