April 2026 study on the diversity of Amerindian genes & Austronesian admixing

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 Hòabìnhian 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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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2026 by Austin Whittall © 

The Genetics of Southern Patagonia

The genetics of the Southern Patagonian natives is more complex than expected. A paper published in Nature on Aug. 3, 2020 (Nakatsuka, N., Luisi, P., Motti, J.M.B. et al. Ancient genomes in South Patagonia reveal population movements associated with technological shifts and geography. Nat Commun 11, 3868 (2020). https://doi.org/10.1038/s41467-020-17656-w) explains the possible admixtures that led to the native populations in Tierra del Fuego and the Southern continental tip of Patagonia.

The authors noted that the natives that adapted to a seafaring life (marine adaptation) either "adopted the technology or invented it independently", they didn't find support that a there was a "large-scale immigration into South Patagonia of people from the north" who were already skilled in living off the sea.

Instead they found that a group of people came from the Northwest (along the Chilean Pacific Ocean coast) after the initial colonization event, around 5000 years ago (as characterized by the remains found at Ayayema ~4700 BP) these people had adopted a maritime economy and replaced the original people that had settled in this area. These latecomers:

"replac[ed] the lineages related to Punta Santa Ana (~6600 bp) and La Arcillosa2 (~5800 bp) that were previously established in South Patagonia itself. The arrival of this new stream of people could be related to the change in lithic technology between ~5500 and 3100 bp, characterized by the interruption of green obsidian use and the introduction of large biface projectile points in the Western Archipelago and Beagle Channel regions."

Archaeologists had noticed that green obsidian, a sharp volcanic glass that had been used in this region 6700 to 6300 years BP vanished, and later (5500 to 3100 BP) stone tools were made from other materials.

There was a simultaneous change in stone tools at that time.

The authors point out that "The disruption in green obsidian use has been hypothesized to reflect a loss of cultural knowledge about the location of the source of this raw material, potentially due to arrival of new people unfamiliar with the landscape."

There was another migration from the Chilean region, characterized by remains found in Central Chile. (Perhaps these people moved pushed by the migration that brought the Mapuche people into Chile?). This final group brought new genetic traits and spread between 4700 and 2000 BP. The authors wonder if the "shared linguistic family between North, Central, and South Patagonia groups in historical and modern times could be related to this signal." I assume they refer to the language of the tehuelche people, known as chon

Mapuche: Late Arrival

I have posted about the Mapuche-Guaraní link in the past. Now I have included more information on this matter in my book's second edition, a brief snippet is shown below:

Dillehay in 2007,(1) noting the similar cultural traits (ceramic, funeral practices), language similarities, and genetics, suggested an association between the Mapuche and the Amazonian natives.
A study published in 2022 analyzed ancient human DNA from the cement attaching head lice nits and found that they support a “major migration wave, occurring around 2,000 years BP from the ancient Proto Tupí/Tupí of the Amazonian lowlands (northwest Amazon) toward south Amazonia and the east Coast, spanning ∼4,000 km.”(2) The expansion continued across Argentina and reached the Andes.
This migration was probably caused by a growing population requiring new lands for farming or, as a response to a drier climate at that time. The authors concluded that “The three Calingasta [San Juan province, Argentina] ancient mummies analyzed in this study show for the first time that the original peoples of San Juan, Calingasta, came from Amazonia about 2,000 years BP… help[ing] decipher a piece of the puzzle of pre-Columbian ancient migrations within South America, of an impressive move spanning 5,000-6,500 km. [3,100-4,040 mi.]” Interestingly, Calingasta is only 160 km (100 mi.) to the east of the Mapuche homeland in Central Chile. Another study from 2023 pointed out that “the fact that together, regional varieties of Mapudungun [Mapuche language] still form a coherent single language is consistent with a relatively recent common origin, followed by geographical expansion and divergence over a timescale of the order of many centuries, but not millennia.”(3)

(1) Pedersen MW, Antunes C, De Cahsan B, et al., (2022). Ancient Human Genomes and Environmental DNA from the Cement Attaching 2,000-Year-Old Head Lice Nits. Molecular Biology and Evolution, Vol. 39, Issue 2, February 2022, msab351.
(2) Arango-Isaza E., Capodiferro MR., et al., (2023), The genetic history of the Southern Andes from present-day Mapuche ancestry. Current Biology, Vol 33:13, pp. 2602-2615.e5.
(3) Dillehay T.D. et al., (2007). Cultivated wetlands and emerging complexity in south-central Chile and long distance effects of climate change. Antiquity. 949–6.

The timing of this Out-Of-Amazon migration seems to coincide with the displacement of people into Patagonia from Central Chile

My next post will look into the Kofkeche myth, and its relation to the arrival of the Mapuche in Chile.

CAPTION HERE. Copyright © 2025 by Austin Whittall

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025by Austin Whittall © 

Americas: the language diversity problem

Ten years ago, I posted on the high diversity of languages in America, and a recent paper has added some interesting information on the subject.

The paper was published last month (June 28, 2025). It confirms the diversity and its uniqueness among the languages around the World. Furthermore, the authors can't explain why (see the bold text that I highlighted in the quote below):

"Linguistically, the Americas remain one of the most diverse parts of the world, despite the loss of many languages since European colonization (Campbell 2024). Within the Americas, the diversity of South America exceeds that of North America as measured both by the number of distinct languages as well as by the number of singular linguistic lineages (“language families”). Within South America, in turn, the Amazonian lowlands are generally more diverse than the Andes and the Southern Cone, though the uneven demographic and cultural impact of European conquest may have contributed to accentuating the observed diversity cline. About 60% of South American lineages are isolates (Seifart and Hammarström 2017), that is, consist of only one extant member whose ties with related lineages were severed at a point of time that exceeds the time horizon that can be reached by historical linguistic methods (under ideal conditions ~8000 years). This indicates high rates of linguistic diversification and cladogenesis already in an early phase of human presence. The causes of this remain poorly understood. South American languages are also characterized by extreme heterogeneity concerning their evolved sound systems and grammars—a third parameter of linguistic diversity that contributes to the overall complexity of the linguistic situation in the continent."

The paper, explored genetic and language similarities, and as you'd expect, they found "strong similarities in language and morphology between the Selk'nam and Qawaskar", the boat-people that lived in the seas of Tierra del Fuego and SW Chilean Patagonia. They were the human beings who lived furthest south in the whole World!

The Mapuche have an Amazon-Chaco origin

The paper also found affinities between Chacoan people (called Quom) and the Mapuches of Chile.

In my book, I mentioned many myths and legends of the Mapuches that are similar to myths of the natives that lived in Southern Amazonia, and the Chaco region (the Guaraní people). But the homeland of the Mapuche and the Chaco-Amazon region are nearly 1,500 miles (2,400 km) apart, with the Andes rising 6,000 m (20,000 ft.) high between them.

I also wrote a post on the subject see: Mapuche natives and their possible link to the Guarani.

The Mapuche don't like the idea of being considered as "recent" arrivals in Chile, migrants from the central South American jungles. They prefer to believe they have always lived in Chile. However, the facts are quite the opposite. This paper says:

"The Qom and Mapuche exhibit the strongest genetic similarities among the groups we studied. The Qom are a lowland group from the southern Chaco, while the Mapuche historically inhabited northern Patagonia, later expanding to the Pampas. Recent genetic studies on the Mapuche suggest that their genetic profile reflects an ancient ancestry linked to early migration waves (SNA2), followed by prolonged isolation before recent gene flow from the Central Andes (Arango-Isaza et al. 2023; Capodiferro et al. 2021). In fact, mtDNA affinities between Chaco and Andean populations have led some scholars to suggest a shared evolutionary history (Cabana et al. 2006; Russo et al. 2018). This is consistent with previous genetic studies, which have reported close biological affinities between the Qom and Mapuche (Cabana et al. 2006; Demarchi and García Ministro 2008; Sevini et al. 2013) despite the fact that they are not geographic neighbors."

Read the paper online: Menéndez, L. P., and M. Urban. 2025. “ Tracing Human Diversity in South America's Southern Cone: Linguistic, Morphometric, and Genetic Perspectives.” American Journal of Biological Anthropology 187, no. 3: e70077. https://doi.org/10.1002/ajpa.70077.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2025 by Austin Whittall ©