South American Genetic History

I remain skeptical that the Australasian ancestry is as ancient as claimed. It is much less than 2%, maybe a hundred times less, and the regional variation in its frequency is far too great for it to be ancient. I suspect an origin in Polynesian sea farers that may be obscured by natural selection against some signature Polynesian genes. 

I have not yet seen any really solid evidence that it has been present for 10,000+ years, or any explanation for the extremely varied frequency of these genes in the populations where they are found, indicating a very recent dispersal to these populations that hasn't had time for these frequencies to harmonize. 

South American ancient DNA samples are few and far between at that time depth, and this paper has some of them, but a lot of the references supporting this analysis are in supplementary materials and extended data, or references to other papers, and the nature of the ancient DNA sample is one I haven't been able to look at closely yet. As I've only had time to cut, paste, and highlight, rather than enough to do a proper critical analysis of this claim. 

I'll add more analysis in an update in this post, if time permits, which may or may not happen (I'm busy preparing for an upcoming jury trial).

[A] study published today in Nature reveals these migrations were anything but simple. Examining ancient and modern genomes collected from across South America and beyond, the team found that genetically diverse groups populated the continent in at least three separate pulses. And some people or communities carried with them possibly advantageous genes acquired from long-ago Australasian ancestors. . . .

His team published a complementary study today in Current Biology, finding evidence of unexpected genetic diversity and otherwise invisible migrations in 52 ancient genomes from Argentina and Uruguay.

In the Nature study, Tábita Hünemeier, a geneticist at the University of São Paulo and the Institute of Evolutionary Biology, collaborated with researchers and Indigenous communities across Latin America to sequence 128 whole genomes from living people from north Mexico to southern Argentina. The team then analyzed them alongside existing databases and previously published ancient genomes.

Previous work had identified the first two waves of settlement in South America, the earliest of which included people related to the Anzik child, who was buried in Montana 12,700 years ago. A second dispersal followed about 9000 years ago and ultimately contributed more to the genomes of most ancient and modern South Americas, including those Posth studied.

Hünemeier and her team found evidence of a third dispersal, whose genetic signature first appears in their data about 1300 years ago and then spreads widely across the continent and even into the Caribbean. The newcomers show hints of being related to Mesoamericans from Mexico and Central America, but so far, researchers don’t know exactly where they came from or who were their closest relatives. “Without the source population and more direct evidence [of a third pulse] from ancient DNA, it’s hard to really wrap our heads around” how and when a third migration might have happened, Posth says.

The study also digs deeper into a mystery that has bedeviled the genetic history of the Americas for over a decade: How did traces of Australasian ancestry end up in some ancient and modern South American genomes? Genetic variants from this lineage make up only about 2% of ancestry in the people who carry it, but that proportion has stayed remarkably consistent over the past 10,000 years. “This signal is found again and again and again,” Posth says. “It must mean something.”

Hünemeier suspects people carrying this ancestry were among several distinct populations that lived for thousands of years in Beringia, the now-drowned landmass that connected eastern Siberia to Alaska, and that it eventually spread southward into the Americas from there. (This Australasian ancestry, sometimes known as Population Y or the Ypykuéra signal after the Tupi word for “ancestor,” is different from the genetic sequences some Polynesian populations share with South American ones. Scientists continue to debate how that more recent gene flow happened—for example, whether Polynesian voyagers may have reached western South America about 800 years ago—but the findings from the Nature paper have no bearing on that mystery.)

From Science.

Both of these papers are open access.

The Nature article and its abstract:

Indigenous peoples of America represent the last principal expansion of humans across the globe, yet their genetic history remains one of the least explored. Although these populations have inhabited the continent for thousands of years, their evolutionary history remains largely unresolved, owing to the limited availability of genomic data. 

Here we present data on 128 high-coverage Indigenous American genomes and show they harbour extensive and previously uncharacterized genetic diversity, reflecting at least three dispersals into South America, followed by regional differentiation and long-term continuity. 

We identified widespread natural selection signals in genes associated with immunity, metabolism, reproduction and development, which were shaped by adaptation to diverse environmental conditions. 

Notably, several genomic regions exhibit a remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years. 

We also detected distinct contributions from archaic humans with adaptive introgression affecting key biological functions. The limited overlap between the regions of Australasian affinity and archaic ancestry indicates independent evolutionary origins of these signals. These findings challenge simplified models of continental settlements and show a more dynamic and complex evolutionary history for the Indigenous peoples in America.

Castro e Silva, M.A., Nunes, K., Ribeiro, M.R. et al. :The evolutionary history and unique genetic diversity of Indigenous Americans." Nature (April 22, 2026). https://doi.org/10.1038/s41586-026-10406-w

The section on archaic and Australasian ancestry in the body text of the Nature article states (with citations omitted):

Affinity with Australasians and archaics

Some Indigenous American populations show elevated genetic affinity to present-day Australasians relative to other groups contradicting a single non-Arctic Indigenous American clade. This affinity is best explained by admixture between the ancestors of Indigenous Americans and an unsampled ancient Asian population, termed Ypykuéra (here referred to as Ypykuéra ancestry), partially related to a sister clade of present-day Australasians.

We assessed genetic affinity between ancient and modern Indigenous Americans and present-day Australasians, the closest living proxies for Ypykuéra ancestry. We applied F-statistics to modern Indigenous American pairwise comparisons and to comparisons including ancient individuals.

Several Indigenous groups, including the Awajún, Ayoreo, Guarani, Karitiana, Sirionó, Suruí and Tsimané, show significant excess genetic affinity to Australasians relative to other present-day populations (Z > 3). These groups span eastern and western South America and the Chaco, with the strongest enrichment in the southwestern Amazon, where five of these seven populations are located.

A second analysis detected at least one individual with significant affinity in all examined clusters, except Arctic and northern North American groups, which were excluded from this analysis because of partial or complete ancestry from independent Siberian dispersals. The earliest signal occurs in the 10,400-year-old Sumidouro individual. Signals persist from the Early Holocene to the present, increasing in frequency during the Late Holocene, especially in the Andes, Pacific Coast and western South America. The partially discontinuous spatiotemporal pattern probably reflects variation in prevalence within and among populations. Taken together, these findings indicate that this ancestry was present during the initial peopling of America and that it may have contributed more strongly to Late Holocene and present-day genetic diversity.

We tested whether Ypykuéra-related ancestry in Indigenous Americans reflects shared ancestry with Australasians by means of archaic hominins (Neanderthals and/or Denisovans). We compared D(Mbuti, Onge; Mixe, X) with D(Mbuti, Neanderthal or Denisova; Mixe, X), where X denotes Indigenous American groups. Mixe served as a Mesoamerican reference to match earlier studies reporting Australasian affinity. No correlation was detected between Australasian and Neanderthal (Spearman’s r = −0.006, P = 0.971) or Denisovan affinity (r = −0.1002, P = 0.5372). By contrast, Neanderthal and Denisovan affinities were strongly correlated (r = 0.6572, P = 7.2 × 10^−6), consistent with homogeneous archaic ancestry in the founding populations.

An alternative hypothesis proposes that Australasian affinity reflects retention of the Ypykuéra component in isolated groups with high internal genetic similarity. Such populations and genomic regions, characterized by elevated ROH, would be less affected by admixture that could dilute signals of ancient Population Y ancestry. This hypothesis is not supported by our data, which show no correlation between Australasian affinity and inbreeding (FROH) (Spearman’s r = 0.2503; P = 0.1192). Moreover, ROH hotspots, defined as regions with ROH density greater than three standard deviations above the mean, show little overlap with loci of Australasian affinity, with only about 6% of such positions coinciding.

We tested whether Indigenous American affinity to present-day Australasians also includes ancient Hòabìnhian individuals, proposed ancestors of mainland Southeast Asian hunter-gatherers, including the Onge Using D(Mbuti, Y; Mixe, X), with Y as Onge or Hòabìnhian individuals (La368, La364) and X as Indigenous American populations, we evaluated correlations in affinity to Onge and Hòabìnhian individuals. La368 forms a sister branch to Onge, whereas La364 is modelled as Australasian-related plus Austronesian ancestry, sister to Ami. We observed significant correlations for La368 (Spearman’s r = 0.6444; P = 1.1856 × 10^−5) and La364 (Spearman’s r = 0.6208; P = 2.8848 × 10^−5). These results support a shared ancestry component between Indigenous Americans and Australasians that extends deep into the past.

The Current Biology article and its abstract:

• Expansion of ancestry into the Pampas, Uruguay, and Patagonia from the Middle Holocene

• Repeated mobility from southern Andean and southern Patagonian-related populations

• Genetic differentiation between the Upper and Lower Paraná River Delta ∼600 years ago

• Coastal dispersal from southern Brazil to eastern Uruguay via mound-builder societies

The Southern Cone represents the southernmost region of South America settled by humans. Although ancient genomes from southern Patagonia have been sequenced, genomes from the central Southern Cone (CSC) remain temporally and spatially sparse. Archaeology documents major cultural transformations during the Middle and Late Holocene, yet their relationship with demographic processes has been debated. 

We present genome-wide data from 52 individuals spanning 6,000 years, originating from four regions of the CSC in present-day Argentina and Uruguay: the central and southern Pampas, Northwest Patagonia, the Paraná River Delta and Lower Uruguay River, and the eastern lowlands of Uruguay. 

Genomic evidence from the Pampas reveals the presence of at least three distinct ancestries during the Middle Holocene. Although genetic contacts with southern Patagonian groups were sporadic, we identified the expansion of an ancestry of unknown geographic origin by 5,500 years ago (ya), which increased during the Late Holocene. This ancestry arrived in Northwest Patagonia by at least 600 ya and co-existed locally with a southern Andean genetic profile until colonial times. 

Genetic structure differentiates populations along the Paraná River Delta and Lower Uruguay River by 1,500 ya. 

Individuals from the eastern lowlands of Uruguay show genetic links with Sambaqui-associated populations from the southern coast of Brazil, suggesting the role of human dispersals in connecting tropical lowland cultural traditions. 

Our work documents the diffusion of genetically distinct groups across all studied regions and provides compelling evidence that large-scale human movements contributed to the remarkable cultural diversity of CSC populations during the Middle and Late Holocene.

Kim-Louise Krettek, et al., "The shared genomic history of Middle- to Late-Holocene populations from the Southern Cone of South America" Current Biology (April 22, 2026).