Several studies have reported an Austronesian component in Native Americans, and I have mentioned this in various posts. A recent paper published on April 22, 2026 in Nature (Castro e Silva, M.A., Nunes, K., Ribeiro, M.R. et al. The evolutionary history and unique genetic diversity of Indigenous Americans. Nature 653, 134–145 (2026). https://doi.org/10.1038/s41586-026-10406-w) explores these matters as well as the diversity, ages, distribution, and population waves ov the people that peopled America.
In the abstract, the authors point out that Native Americans "harbour extensive and previously uncharacterized genetic diversity" and attribute it to "at least three dispersals into South America". They also suggest that natural selection has acted on Neanderthal, Denisovan, and ancient Australasian alleles because they conferred adaptative advantages.
An imporant finding is the Australasian signal: "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."
Diversity
The paper says that scholars in general believe that America is "less genetically diverse than other continental human groups" (due to the Beringian bottleneck, founding effects and the European and African slave trade admixtures, however in this study they found new single-nucleotide variants (SNVs), roughly 11,000 new variants per individual, which, although lower than the African level of 27.800 per person is very similar to that of the Oceanians.
The paper states that "despite lower overall diversity, Indigenous Americans carry many previously unreported variants. This reflects both substantial genetic variation and long-standing underrepresentation in genomic resources." One measure of lack of diversity caused by isolation and small founder populations which lead to inbreeding. This is seen in the genome by a higher number of runs of homozygosity (ROHs). However, the expected higher ROH due to "serial bottlenecks following entry into the Americas" was not observed, because ROH does not show any "significant correlation with geographic distance from Alaska, longitude or latitude." Instead there were hotspots with high ROH in specific regions of the Americas, such as areas around the Amazonia in Brazil, Bolivia, and Peru.
Ancient Splits
The split from other Old World people is ancient, definitively pre-Clovis, and in my opinion, the older boundary is really ancient, suggesting an early peopling of America: "Cross-coalescence rate estimates (Methods) show that Indigenous American populations, grouped by genetic cluster, diverged from other continental groups between about 70,000 and 15,000 years ago." I mean the 70 ky limit. Very old indeed!
A Replacement 9,000 years ago
The paper mentions that some 9 kya a new genetic lineage sperad across Central America and the Caribbean, reaching South America and affected groups that still exist, like the Quechua of the Peruvian and Bolivian highlands, and the Tehuelche of Pataonia. These people partially replaced ancient lineages older than 9 kya. Then came a third wave around 1,300 years ago.
North American natives are very different "Indigenous North American populations are the most genetically distinct from South American groups."
Mapuches and the Amazon
Interestingly the paper finds that although the Tehuelche people of Patagonia have managed to retain their original genomic makeup, they "derive most ancestry from a Chaco sister branch (third dispersal)", and a similar effect is noticed among the Quechua. I have posted about a possible Southern Amazonian or Chacoan origin for the Mapuche people (see here and here), who live between Quechua and Tehuelches, and who have admixed with modern Tehuelches. The recent arrival of a Guarani component into the Mapuche could account for their similar myths and legendary beasts. This paper with its 3rd-wave seems to support this notion.
Affinity with Australasians
The similarity between genes of some Native Americans and contemporary Australasians has been explained as follows: the ancestors of Amerindians admixed in the distant past with some ancient archaic Asian people, known as Ypykuéra (a Tupi word meaning "Ancestors") or "Y" population, which is "partially related to a sister clade of present-day Australasians." (see my post and this one too).
The study found that the highest affinity with Australasians was centered in the Chaco Region, eastern and western South American as well as the Southwestern Amazon region (Paraguay, Bolivia, Northern Argentina, and South-southeastern Brazil. It is found among the Giarani, Surui, Awaj&uactue;, Ayoreo, Karitiana, Sirionó amd Tsimané people. It dates back to an ancient sample found in Sumidouro, Brazil, 10,400 years old. It increased from there on, "especially in the Andes, Pacific Coast and western South America." But the Pacific area, despite suggesting a transoceanic contact is disregarded by the authors, who instead prefer to support the idea 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".
They tested if the Australasian link was due to introgression of archaics, like Neanderthals and Denisovans. This makes sense, Oceanian people have a high contribution of Denisovan ancestry. But, "No correlation was detected between Australasian and Neanderthal or Denisovan affinity. By contrast, Neanderthal and Denisovan affinities were strongly correlated, consistent with homogeneous archaic ancestry in the founding populations" In other words, the Neanderthal and Denisovan component of Amerindians is not linked to Australasians. So my suggestions in this post and this one, are not valid.
They also rejected the idea that the similarity with Australasians is due to isolation, where different groups retained the "Y" component. Isolation, marked by higher ROHs is not linked to Australasian affinity or inbreeding. Furthermore, those natives with higher ROH, and higher inbreeding have low Australasian affinity.
They also tested the link between the ancient Southeast Asian people, the H&oagrave;abìnhian people, and compared them with two samples of this population, La368 and La364. They found "significant correlations for La368 and La364. These results support a shared ancestry component between Indigenous Americans and Australasians that extends deep into the past." A short, laconic, explains-nothing phrase. How does the signal reach America? See my post on the H&oagrave;abìnhian and Austronesians here.
Finally the low prevalence 1-3% of Y genes in Amerindians suggests that at least some of these alleles were positively selected for and maintained over the past 10,000 years: "these findings indicate that several genomic regions sharing alleles with present-day Australasians were probably targets of positive selection. The candidate genes in these loci participate in critical biological processes that may have shaped the health and adaptive history of Indigenous American populations. However, positive selection seems to have acted on only a subset of Ypykuéra ancestry loci, whereas the remaining regions show no evidence of selection and are probably shaped by neutral evolutionary processes."
Conclusion
There is an Austronesian imprint in Amerindians, but we don't know why. The Native American people are diverse, and ROHs are not a sign of lack of diversity due to bottlenecks. Mapuche people have a recent 1,300 year-old ancestry from Guarani people. Deeper research and more samples will show a clearer picture.
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