Different models have been proposed to elucidate the origins of the founding populations of America, along with the number of migratory waves and routes used by these first explorers. Settlements, both along the Pacific coast and on land, have been evidenced in genetic and archeological studies. However, the number of migratory waves and the origin of immigrants are still controversial topics.
Here, we show the Australasian genetic signal is present in the Pacific coast region, indicating a more widespread signal distribution within South America and implicating an ancient contact between Pacific and Amazonian dwellers.
We demonstrate that the Australasian population contribution was introduced in South America through the Pacific coastal route before the formation of the Amazonian branch, likely in the ancient coastal Pacific/Amazonian population.
In addition, we detected a significant amount of interpopulation and intrapopulation variation in this genetic signal in South America. This study elucidates the genetic relationships of different ancestral components in the initial settlement of South America and proposes that the migratory route used by migrants who carried the Australasian ancestry led to the absence of this signal in the populations of Central and North America.
Marcos Araújo Castro e Silva, et al., "Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry" 118 (14) PNAS e2025739118 (April 6, 2021) https://doi.org/10.1073/pnas.2025739118 (Hat Tip to DDeden in the comments). Supplemental materials here. Data here.
As the body text explains:
A signal of genetic affinity between present-day and ancient natives from South America and present-day indigenous groups of South Asia, Australia, and Melanesia has been previously reported. This Australasian−Native American connection persists as one of the most intriguing and poorly understood events in human history.
The controversial Australasian population genetic component (i.e., “Ypikuéra population” or “Y population” component) was identified exclusively in the present-day Amazonian populations suggesting at least two different founding waves leading to the formation of the people of this region.
The first wave was inferred to be composed of direct descendants of the Beringian standstill population, and a second wave was formed by an admixed population of Beringian and southeast Asian ancestors that reached Beringia more recently. Both these populations would have settled and admixed in the Amazon region.The contribution of an unsampled population to the autochthonous gene pool is thought to have led to the origin of the Australasian shared ancestry. In this sense, the Y population would be part of the first colonizing groups of the American continent. However, data from ancient South American samples indicated a weak Y signal around 10,000 yBP. This evidence indicates that, rather than a second wave entering South America from southeast Asia, the Y ancestry might be traced back to common ancestors of Native Americans, who lived in northeast Asia.
Furthermore, a new line of evidence indicates that the first American clades split in East Asia, not in Beringia, which makes the gene flow of the Y ancestry from the ancestral East Asian groups even more likely.
However, the paucity of the signal among present-day and ancient groups, along with the endemic and apparently random pattern of detection, has raised the possibility that it could be a false-positive detection, likely due to the strong genetic drift effects experienced by the Amazonian populations (and other indigenous South Americans). However, it might be the other way around, a scenario in which the signal went below the significance level in some populations, due to the high drift effects they experienced (i.e., false negatives).We explored our dataset, which is currently the most comprehensive set of genomic data from South American populations (383 individuals; 438,443 markers), to shed light on this question.
. . .Our results showed that the Australasian genetic signal, previously described as exclusive to Amazonian groups, was also identified in the Pacific coastal population, pointing to a more widespread signal distribution within South America, and possibly implicating an ancient contact between Pacific and Amazonian dwellers. In addition, a significant amount of interpopulation and intrapopulation variation of this genetic signal was detected.To test the existence of this excess allele sharing, we calculated the D(Mbuti, Australasian; Y, Z) statistic for every pair of Y and Z indigenous groups or individuals in our dataset, where “Australasian” is also iterated over the Australasian groups, namely Australian (and Australian.DG), Melanesian, Onge (i.e., ONG.SG), and Papuan. In the tests between groups, signal detection was reproduced in Karitiana and Suruí (Amazonia), but it was also observed in Chotuna (Mochica descendants from the Pacific coast), Guaraní Kaiowá (central west Brazil), and Xavánte (Central Brazilian Plateau).
When we used the maximum unrelated set of individuals, the signal lost significance level in Karitiana, Suruí, and Guaraní Kaiowá . However, the signal was still evident in the Pacific coast population and in the central Brazilian natives.
. . .
the loss of signal significance upon the shift from the complete set to the maximum unrelated set of samples was caused by the exclusion of specific individuals with higher levels of allele sharing with Australasians rather than by the removal of a bias caused by the relatedness among the tested samples in the first place. . . . .
This provides strong evidence that a significant variability of this signal exists not only at an interpopulation level but also between individuals from the same populations. These results suggest that the intrapopulation variability of this signal is not rare and is observed in several groups (Apalai, Guaraní Nãndeva, Karitiana, Munduruku, Parakanã, and Xavánte). Most significant tests detected this excess signal in Tupí-speaking individuals, but the signal was also detected in individuals from every major linguistic group and, at the same time, presented a widespread geographic distribution within South America. Conversely, a considerable number of samples were inferred to have a deficit of allele sharing with Australasians.
Strikingly, the individual PAR137 (Parakanã) presented an extremely high proportion of significant tests (31.64%), indicating a relative deficit. This individual is not an outlier neither in the principal component analysis of the Native American samples, nor regarding its missingness rate, nor in a multidimensional scaling (MDS) of pairwise genetic distances between samples in the unrelated and unadmixed subset. Besides, the distribution of Y-population ancestry among present-day indigenous groups of South America showed no relationship with ethnolinguistic diversity or geographic location.
. . .Different migration routes to the South American region have been previously proposed and evidenced. Archeological and genetic data demonstrated that both routes, Pacific coastal and inland, were likely used by the first migrants.
Our models point to an ancient genetic affinity between the Pacific coast and Amazonian populations that could be explained by the presence of Y ancestry in both geographic regions.
In addition, this shared ancestry seems to precede the separation of the Pacific and Amazon branches, showing an entry through the west coast, followed by successive events of genetic drift in the Brazilian populations. This genetic evidence for the presence of Y ancestry on the South American Pacific coast indicates that this ancestry likely reached this region through the Pacific coastal route, and therefore could explain absence of this genetic component in the populations of North and Central America studied so far.