Denisovan admixture within America?

Last may I published a brief post about a paper by Castro e Silva et al., (2026). The evolutionary history and unique genetic diversity of Indigenous Americans. Nature. https://doi.org/10.1038/s41586-026-10406-w. The paper is an in-depth study of South American natives' genetics, the three waves that peopled the subcontinent, and the "remarkable allele sharing with Australasian populations, probably originating from an ancient admixture event and partly maintained by selection for more than 10,000 years." It attributes this permanence across ten millennia because this admixture was positively selected for due to benefits these alleles provided to those carrying them.

Archaic Introgression

I re-read the article and took note of the part that says that the Australasian signal is not the result of an archaic introgression, which means that Denisovans didn't share these same genes with Oceanian and American natives, there were different groups admixing with each population. The paper states: "Furthermore, we identified candidate regions of adaptive archaic introgression from Neanderthals and Denisovans that contribute to functions related to immunity, metabolism and epidermal integrity, thereby reinforcing the role of archaic alleles in shaping the evolutionary trajectory of non-African populations. Importantly, our data indicate minimal overlap between genomic regions with Australasian affinity and those introgressed from archaic hominins, supporting the interpretation that these signals represent distinct evolutionary phenomena."

Australasian signal

The Australasian signal in Amerindians is very very peculiar, it has a high prevalence in some groups that live in the Southwestern Amazon region and Chaco (these groups are the Awajún, Ayoreo, Guarani, Karitiana, Sirionó, Suruí, and Tsimané). This is known as the introgression from a "Y" population, or Ypykuéra (a Tupi word meaning "ancestor") which is a "ghost lineage" of ancient Amerindians with a high Australasian genetic content.

The paper confirms that the distribution of Australasian "alleles" is not uniform, it shows a "partially discontinuous spatiotemporal pattern" which suggests, according to the authors that "this ancestry was present during the initial peopling of America." It is also very ancient because the paper finds that Amerindians "diverged from other continental groups between about 70,000 and 15,000 years ago."

The paper states that isolation of these Amazonian groups that carry the highest frequencies of these introgressed alleles and their inbreeding and small population sizes are all factors that led them to have such a high prevalence of them. However, I wonder if another factor was at play: Denisovans lived in that region and encountered humans there, admixing in that area with them. After all it is a kind of cul-de-sac in the Amazonian rainforest nowadays, why wouldn't it have been one for the Denisovans? They also seem to have thrived in the jungles of Indonesia, and the Philippines in Southeast Asia.

The comparison between different groups within America, outside of America, and archaics, didn't detect any "correlation... 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."

This is interesting because the Australasian signal is independent from the two archaic introgressions. This suggests that the Denisovans and Neanderthals that admixed with the first Amerindians were different from those who admixed with Australasians (including the Onge people and the Hòabìnhian people from Laos).

The authors wondered if the Australasian-Amerindian similarity was due to "shared archaic ancestry" but when the checked the introgression from Denisovans and Neanderthals in both groups, they found a "minimal overlap of 0.4%, corresponding to 11 genes/genomic regions... This minimal overlap indicates that the Ypykuéra ancestry is unlikely to have been derived from a known archaic hominin." (This is not clear, what do they mean by "a known archaic hominin"?)

The paper did find a "shared ancestry component between Indigenous Americans and Australasians that extends deep into the past." So this shared ancestry probably came from a similar modern human group, yet, as mentioned further up, the ancestors of the Amerindians split from other H. sapiens 15 to 70,000 years ago. I favor the older date. But, intriguingly, these people did not admix with the same Denisovans or Neanderthals that the Australasians bred with!

This could be explained by a split in this basal Homo sapiens: one group went into Australasia and admixed there with a group of Denisovans, the other headed north into East Asia mixing with other Denisovans, and eventually reached America. However, why is there no presence of other East Asian signals in Amerindians? This leads to a second alternative: the admixture event between Denisovans and the modern human ancestors of Amerindians took place inside America?

The map below outlines this possibility, with the Denisovans splitting from the Neanderthals somewhere in the South Caucasus, and moving into East Asia along different routes, a northern one to Altai, and then Tibet and East Asia, another along South Asia, and South East Asia into the Philippines and Papua New Guinea. Another hypothetical route could have led them across Siberia into America. Their last stand was in the Tropical Amazon region. They seemed to thrive in all types of climate, from icy siberia and Altai, to the highlands of Tibet, and the jungles of Sundaland and Sahul. America offers all of them: Cold Alaska, Canada and Northern USA, Patagonia, high mountains and plateaus in Bolivia and Peru, as well as along the Andes in Chile and Argentina, and of course the Jungles east of the Andes from Colombia, Venezuela and Bolivia to Brazil, Paraguay and Argentina.

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

On the Australasian imprint in Paleoindians (Part 1)

See part 2 here

In this post I am sharing text from a paper published in 2022 (Silva, M. A. C. e ., Ferraz, T., & Hünemeier, T.. (2022). A genomic perspective on South American human history. Genetics and Molecular Biology, 45(3), e20220078. https://doi.org/10.1590/1678-4685-GMB-2022-0078. Online) that summarizes the current (in 2022) knowledge about the peopling of South America, and provides early dates and information on the Australasian genetic imprint found there:

Taken together, the current archeological evidence supports that humans were present in the Americas at least 20 ka BP during the peak of the LGM (Ardelean et al., 2020; Bennett et al., 2021). Although the identity of these first Americans remains an open question, genetics has given us some insight into who they may have been, as revealed by the faint signal of shared ancestry with modern-day Australasian peoples (Skoglund et al., 2015; Castro e Silva et al., 2021). This data supports the hypothesis that the initial settlers were more closely related to the ancestors of modern Australasians than to those of East Asians and also implies that their contribution to post-LGM Native American populations was mostly absent and seldom minimal. In this scenario, these first human groups to reach the continent would have been later replaced by the ANA descendants, starting by the end of the LGM, and only rarely would have admixed with them. Furthermore, our recent findings show a lot of variation within populations (Castro e Silva et al., 2021), which suggests that some of these first Americans could have lived in relative isolation until very recently when admixed with SNA populations. Furthermore, most of the genetic contribution from these early ancestors might have been erased by the intense population dynamics during the Holocene and by the successive inflows of distinct SNA groups in the case of South America (Posth et al., 2018).
Considering that continental glaciers completely blocked northern North America throughout the LGM period, an early settlement of the Americas requires an alternate pathway. This alternative is provided by the so-called coastal migration theory (CMT) (Davis and Madsen, 2020), which proposes that the Pacific Rim shorelines were used as a route into the Americas from Asia by groups of humans adapted to a seaside lifestyle, likely based on the exploitation of the resourcefully rich environments of kelp forests present along both continents’ Pacific coasts (Erlandson et al., 2007). In that case, it could also help explain the absence of the Australasian signal in North America if the dispersal was rapid and mostly restricted along the Pacific coast, resulting in more significant population growth in South America at the expense of North America. Most interestingly new evidence points to the existence of a very large number of islands in the Bering Sea to the south of Beringia between 30 and 8 ka BP, named the Bering Transitory Archipelago (BTA), which would have greatly enhanced the availability of marine resources and also facilitated sea travel through more easily navigable and protected waters (Dobson et al., 2021).
Finally, some genetic and morphometric analyses of Northeastern and Southeastern Asians (NEA and SEA, respectively) provide some intriguing pieces of evidence on the origins of the Native American-Australasian connection. First, a link between the Onge and the ancient SEA hunter-gatherers, known as Hòabìnhians, is demonstrated by the genetic affinity between the Onge and two Hòabìnhians from Laos and Malaysia with approximately 8 and 4 ka BP (McColl et al., 2018), implying that the latter are closely related to the Onge’s ancestors. Second, morphological affinities between the Onge (a SEA population) and the NEA (Matsumura et al., 2019) support the hypothesis that a group closely linked to the Onge - thus also likely related to the Hòabìnhians - was involved in an admixture event with the ANA and thus responsible for the Australasian genetic affinity observed in indigenous Americans (Skoglund et al., 2015). There is also solid evidence that the distribution of modern-day Australasian and East Asian ancestors was significantly different across East Asia during the Pleistocene and that populations like the Jomon from Japan show very clear indications of a mixture of northern and southern Asian ancestries (McColl et al., 2018; Wang et al., 2020); this is particularly meaningful given that Japan is a likely candidate and the proposed birthplace of the First Americans in the CMT framework. These findings illustrate how important it is to comprehensively elucidate East Asian population history in order to grasp the full picture of the Americas’ peopling. "

Below is the map in Skoglund et al.'s 2015 paper regarding Australasian and Amerindian affinities.

Original image caption: heatmap of CHROMOPAINTER statistics. For non-Americans we display the symmetry statistic S(non-American; Mixe, Suruí & Karitiana) for donating as many haplotypes to Mixe as to Suruí & Karitiana. For the Americas we plot S(Onge; Mixe, American) for receiving as many haplotypes from the Onge as do the Mixe.. Fig 1 in Skoglund et al.

The Population-Y

Skoglund et al. 2015 paper discovered this Australasian signal. They write the following:

" we do find that a model where Amazonians receive ancestry from the lineage leading to the Andamanese fits the data in the sense that its predicted f4-statistics are all within 2 standard errors of statistics computed on the empirical data (Extended Data Figure 6; Extended Data Figure 7; Extended Data Table 3). These results do not imply that an unmixed population related anciently to Australasians migrated to the Americas. While this is a formal possibility, an alternative model that we view as plausible is that the ‘Population Y’ (we use ‘Population Y’ after Ypykuéra, which means ‘ancestor’ in the Tupi language family spoken by the Suruí and Kartiana) that contributed Australian related ancestry to Amazonians was already mixed with a lineage related to First Americans at the time it reached Amazonia. When we model such a scenario, we obtain a fit for models that specify 2%-85% of the ancestry of the Suruí, Karitiana, and Xavante as coming from Population Y (Figure 2). These results show that quite a high fraction of Amazonian ancestry today plausibly comes from Population Y. At the same time, the results constrain the fraction of Amazonian ancestry that comes from an Australasian related population (via Population Y) to a much tighter range of 1%-2% (Figure 2).
We have provided compelling evidence that a Population Y that has ancestry from a lineage more closely related to present-day Australasians than to present-day East Asians and Siberians, contributed a small fraction of the DNA of Native Americans from Amazonia and the Central Brazilian Plateau."

Onge people

You can see some Onge people in the following picutre (source):

These people in the Anadaman islands of the Gulf of Bengal, in the Indian Ocean close to both India and Myanmar, are among the oldest (if you accept the Out of Africa hypothesis) humans after H. sapiens left Africa, and lived in isolation on their insular territory.

Their dark African-like skin is convergent evolution to adapt to their tropical habitat.

How did it reach America and the Amazon?

A paper from 2021 analyzed the matter in depth (to validate its reality -the signal could have been an artifact in the tools used, that mistook a strong genetic drift in the Amazonian people it was found in, for an ancient Australasian imprint.

It confirmed it was a real signal: "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.."

The study found the signal not only in Amazonian Suruí and Karitiana, and also among people living on the NW Pacific Coast of Peru like the Sechura, Chotuna, and Narihuala. The authors conclude that "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."

But no explanation on how did these genes end up in South America. Yes, the current belief is that the predecessors of modern East Asians were related to the Onge, and that these people moved by boat along the sea, bypassing Beringia and reaching America first, where they were later diluted by successive waves from Beringia.

To be Continued in Part 2.

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

Australasian signal in the DNA of Amerindians

BBack in 2015 (Skoglund P, Mallick S, Bortolini MC, et al. Genetic evidence for two founding populations of the Americas. Nature. 2015;525(7567):104–108. doi:10.1038/nature14895) an article showed that " show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent or at all in present-day Northern and Central Americans or a ~12,600 year old Clovis genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".

This is quite a remarkable discovery, and the authors quickly clarified that "These results do not imply that an unmixed population related anciently to Australasians migrated to the Americas. While this is a formal possibility, an alternative model that we view as plausible is that the 'Population Y' (we use 'Population Y' after Ypykuéra, which means 'ancestor' in the Tupi language family spoken by the Suruí and Kartiana) that contributed Australian related ancestry to Amazonians was already mixed with a lineage related to First Americans at the time it reached Amazonia."

They concluded that "he genetic data allow us to say with confidence that Population Y ancestry arrived south of the ice sheets anciently: the fact that the geographically diverse Andamanese, Australian and New Guinean populations are all similarly related to this source suggests that the population is no longer extant, and the absence of long-range admixture linkage disequilibrium suggests that the population mixture did not occur in the last few thousand years."

Last year another study (Reconstructing the Deep Population History of Central and South America Posth C. et al., (2018) Cell, Vol 175:5 P1185-1197.E22, Nov. 15, 2018) looked into the peopling of America but didn't manage to find this Australasian signal in "ancient remains" that they analyzed:

"failure to find significant evidence of Australasian or Paleolithic East Asian affinities in any of the ancient Central and South American individuals raises the question of what ancient populations could have contributed the Population Y signal in Surui and other Amazonian groups and increases the previously small chance that this signal—despite the strong statistical evidence for it—was a false-positive."

But shortly after another paper was published in Science (Early human dispersals within the Americas, Moreno-Mayar et al., Science 07 Dec 2018: Vol. 362, Issue 6419, eaav2621 DOI: 10.1126/science.aav2621) that sequenced the DNA of ancient remains from all across America, Alaska to Patagonia and found that prior to the main migration into America, there was an earlier one, with Australasian traits:

"... there are genomic and archaeological hints of an earlier human presence. How these early groups are related or structured, particularly those with Australasian ancestry, remains unknown.... [there were] multiple independent, geographically uneven migrations into South America. One such migration provides clues of Late Pleistocene Australasian ancestry in South America, [which] contributed to present-day South American ancestry."

"... we find that the Amazonian Surui share a larger proportion of alleles with Australasian groups (represented by Papuans, Australians and Andaman Islanders), with respect to Mixe. Lagoa Santa yielded similar results to those obtained for the Surui. When compared to Mesoamerican groups (Mixe and Huichol), Lagoa Santa also shares a larger proportion of alleles with Australasian groups but not with other Eurasians."

Remarkably, these first wave individuals with Austronesian genes somehow reached South America without leaving any traces in North America: "[a populaton] that harbored an Australasian signal in the Late Pleistocene and reached South America, yet left no apparent traces in North America".

-- New, Sept. 4, 2019 --

I had originally written:

So the facial reconstruction of "Luzia", one of the 12,500 year-old Lagoa Santa crania (and almost lost in the fire that razed the Rio de Janeiro National Museum -fortunately the skull survived) which originally depicted her with an African look now has her looking more Asian:

One of Luzia's relatives - African look has gone. Source

Luzia before, more "African".

Reader feedback:

D. Parker wrote an e-mail to me with the following text:

your source: http://agencia.fapesp.br/the-new-face-of-luzia-and-the-lagoa-santa-people/29168/. Notice caption ^^^ does not say that that picture is Luzia.
The Brazilian researchers’ contribution to the study was fundamental. Among the 49 individuals from which fossil DNA was taken, seven skeletons dated to between 10,100 and 9,100 years ago came from Lapa do Santo, a rock shelter in Lagoa Santa. A new bust has replaced Luzia in the Brazilian scientific pantheon. Caroline Wilkinson, a forensic anthropologist at Liverpool John Moores University in the UK and a disciple of Neave, has produced a facial reconstruction of one of the individuals exhumed at Lapa do Santo. The reconstruction was based on a retrodeformed digital model of the skull.
Estudos genéticos dão nova cara ao Povo de Luzia Representação do fóssil humano mais fa...
Facial reconstruction of the People of Luzia by Caroline Wilkinson of Liverpool John Moores University in England, based on a retroformed digital skull model of the Lapa do Santo archaeological site. The skull used as a reference is from a young man, cataloged as Burial 26.
Also in regard to the Caroline Wilkinson reconstruction. None of the articles, not the one you sourced said the Caroline Wilkinson reconstruction. looks more Asian. The eye fold is not depicted Asian. None of the features are particularly Asian. The nose is not as flat as many Asians. It's true that the ancestors of Native are believed to be Asian but the reconstruction is intended to depict someone looking Native American and though they have Asian ancestry they dont always look exactly like,Asians. People have said it looks racially ambiguous or could even pass for a dark skinned European or Middle Eastern person, Nevertheless these reconstructions include speculation from the forensic artist
regards,
D. Parker

I thank Mr. Parker for his comments. And I promise to write a specific post on these Brazilian remains (the whole group).

See this post here:Lagoa Santa sites and remains: old and odd

.

My remark on the features of the reconstructed face still stands however. The overall impression of the original bust is that of an African, now it is more Eurasian, it does not look like the typical Amerindian people one sees -today- in South America which have distinct features.

-- end of comment--

So the question remains open: where did this signal come from? And why is it not present in North America or Asia? Below is a map from Skoglund's 2015 paper, and the white circles show this lack of Australasian DNA in those regions, and the red and yellow cicles indicate their presence in South America:

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2019 by Austin Whittall © 

The "unsampled population" in America: archaic hominins?

I want to share an excellent article from "Ancient DNA Era", published on Nov. 27, 2018 by Alberto (Early human dispersals within the Americas – Moreno-Mayar et al. 2018).

In this article Alberto discusses a recent paper (Early human dispersals within the Americas, J. Victor Moreno-Mayar, Lasse Vinner, Peter de Barros Damgaard, Constanza de la Fuente et al, Science 08 Nov 2018 DOI: 10.1126/science.aav2621) which deals with "multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America."

Moreno-Mayar mentions:

"We sequenced 15 ancient human genomes spanning Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans (NA), including an Ancient Beringian individual, and two morphologically distinct "Paleoamericans." We find evidence of rapid dispersal and early diversification, including previously unknown groups, as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, and a later Mesoamerican-related expansion."

Alberto focuses on the "previously unknown groups" and the "Australasian genetic signal" and he quotes the original paper:

"...further SFS-based modeling indicates that Mixe most likely carry gene flow from an unsampled outgroup […] Hereafter we refer to that outgroup as 'Unsampled population A' (UPopA), which is neither AB, NNA or SNA [Ancient Beringians, Northern Native Americans or Southern Native Americans], and which we infer split off from Native Americans ~24.7 ka, ranging from 30-22 ka (95% CI; this large range is a result of the analytical challenge of estimating divergence and admixture times in the absence of UPopA genome data).[…] Under a model with a pulse-like gene flow, we inferred a probability of ~11% gene flow from UPopA into Mixe ~8.7 ka (95% CI: 0.4-13.9 ka; the wide interval potentially reflects unmodeled continuous migration)"

Alberto then reasons as follows: (I quote him extensively below)

" When they say "unsampled", they mean unsampled. So no, we’re not talking about potentially "anyone", but quite specifically about a population that does not only seem to be an outgroup to NA, but also an outgroup to Eurasians.
If this is true, then who can be an outgroup to Eurasians? Basically there are 4 options:
– An African population (meaning a population that went Out of Africa after the main OoA event that gave birth to most Eurasians, and that somehow reached Central America some 9 kya). This one is the least likely, really.
– An early OoA population (meaning a population that went OoA before the main OoA event). We know from archaeology (and with some support from genetics) that such early events did occur but they hardly contributed to later Eurasian populations (maybe a tiny bit to some SE Asian/Australasian populations?). So this one would mean that such population made it to the Americas and survived somewhere around Central America until the second major wave arrived.
– Archaic hominins. Like Neandertals or Denisovans. A small admixture from such groups (on top of what other NA already have) would make the shared drift of Mixe with all other AMH be lower. So is it possible that some form of archaic hominin lived in America and survived until some 9 kya?
– A fourth option would be an early "generic" Eurasian population, something similar to Ust-Ishim samples from 45 kya, but not directly related to Ust-Ishim."

I favor option three "Archaic hominins" but Alberto believes option four is the most likely one.

Finally Alberto remarks: "Using qpGraph, this Australasian admixture is estimated to be around 3% in these samples (and modern Surui). How it got there (if it’s real, that it well could be) is unknown at this point, but it’s important to keep in mind that it was already present at least 10.4 kya, so it cannot be from any kind of Holocene migration of Australasians to South America. The possibility is that there was a small (?) population of Australasian origin at the arrival of the migrants of NE Siberian origin."

Skoglund already noticed the Australasian link in Native American DNA (See paper here and the other paper here) back in 2015.

In my book Monsters of Patagonia y point out the similarity between Australian and Patagonian native myths (read more), and conclude " Human remains discovered in Brazil show a very strong resemblance to modern South Pacific people, suggesting that America was first colonized by the generalized human (Homo sapiens) population that inhabited East Asia in the Late Pleistocene. These people arrived in America in very ancient times long before the Mongolid morphology of the forbearers of the Clovis had evolved."

We will have to wait for more evidence to learn about the unsampled population and the Australasian migrants.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2018 by Austin Whittall © 

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 Australasian and Denisovan admixture in Amerindians

A paper published in 2022 (Campelo dos Santos Andre Luiz, Owings Amanda, Sullasi Henry Socrates Lavalle, Gokcumen Omer, DeGiorgio Michael and Lindo John (2022). Genomic evidence for ancient human migration routes along South America's Atlantic coast. Proc. R. Soc. B.28920221078 http://doi.org/10.1098/rspb.2022.1078) reported the genomes of two ancient paleoindians from Northeastern Brazil, on the Atlantic coastal region and placed them in the context of other South American specimens.

The authors report that "...we also detect greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Moreover, we find a strong Australasian signal in an ancient genome from Panama".

Australasian signal

The paper indicates that "A strong signal of Australasian ancestry, previously reported only for the Lagoa Santa individual and present-day Surui, was also observed for the previously published PAPV173, from Panama. The Piapoco, Surui and Karitiana, however, harbour high affinities with Brazil-2 and thus may have received contributions coming from Central America (in the form of the Australasian signal, in a north-to-south directionality) and South America's Atlantic coast (in a south-to-north directionality)."

The PAPV173 individual from Panama also harbored a very high proportion of Denisovan genes (see map below) while in the rest of South America the opposite is true: they have a higher proportion of Neanderthal to Denisovan ancestry. Why?

In the map below, the "Pie chart radius reflects the proportion of shared archaic loci in the individual."

Genetic components (Fig. 2). Source

An article pulbished on the Florida Atlantic University news site (some of the authors are researchers at the FAU) includes some comments by the authors

"“There is an entire Pacific Ocean between Australasia and the Americas, and we still don’t know how these ancestral genomic signals appeared in Central and South America without leaving traces in North America,” said Andre Luiz Campelo dos Santos, Ph.D., first author, an archaeologist and a postdoctoral fellow in FAU’s Department of Electrical Engineering and Computer Science.
To further add to the existing complexity, researchers also detected greater Denisovan than Neanderthal ancestry in ancient Uruguay and Panama individuals. Denisovans are a group of extinct humans first identified from DNA sequences from the tip of finger bone discovered around 2008.
“It’s phenomenal that Denisovan ancestry made it all the way to South America,” says John Lindo, Ph.D., a co-corresponding author of the article who specializes in ancient DNA analysis and is an assistant professor in the Department of Anthropology at Emory University. “The admixture must have occurred a long time before, perhaps 40,000 years ago. The fact that the Denisovan lineage persisted and its genetic signal made it into an ancient individual from Uruguay that is only 1,500 years old suggests that it was a large admixture event between a population of humans and Denisovans.”"

Unanswered questions

Is the Australasian signal an artifact of the models and computer analysis programs? Does the Denisovan genetic content indicate a link to Austronesians? (There is a high Denisovan content among people in that region). Why do the ancient South American natives have a higher proportion of Neanderthal than Denisovan content?

A recent paper published on Oct. 20, 2025 (An early East Asian lineage with unexpectedly low Denisovan ancestry, Yang, Jiaqi et al., Current Biology, Volume 35, Issue 20, 4898 - 4908.e4) found that the 40,000 year-old Tianyuan had the highest Denisovan genetic admixture among ancient Asians: "Among individuals from continental Eurasia, we find the highest proportion of detectable Denisovan ancestry in Tianyuan (∼0.25%), while other pre-LGM individuals from Eastern Eurasia had lower levels of Denisovan ancestry, comparable to those of later East Asians and Siberians."

It also noted that the Laos Hoabinhian hunter-gatherers also have high levels of Denisovan admixture "we found more Denisovan ancestry in the Hoabinhian individual La36846 than in the Jomon individuals, with the Hoabinhian individual carrying more segments covering a larger part of the genome." However, they report that "our results support the existence of a deep modern human lineage in East Asia with limited, if any, Denisovan ancestry, suggesting that at least one early East Asian lineage was not in contact, or in limited contact, with Denisovans. This implies different dispersals for modern humans into East Asia and suggests that Denisovans were sparsely distributed in the region."

The Panama sample PAPV173 is only 520-650 years BP yet it still carries a very high Denisovan signal, could this link it to the ancient Tianyuan man? The other South Americans have a lower signal, perhaps diluted by admixture with other groups of Asians who arrived later and had the limited contact suggested by Yang's paper?

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

On the Australasian imprint in Paleoindians (Part 2)

See part 1 here

This post continues my analysis on how did the Australasian genetic imprint (from Southeast Asia and the Andaman Islands) reach the ancient Amerindians and current tribes in the Amazon and NW Peruvian coast without leaving any traces in the North American Natives, ancient North Amerindian remains, or their Beringian ancestors.

I thought it would be pretty straightforward, but it isn't. The genetics of the Late Pleistocene in Asia are not simple. There were several groups there around 50,000 years ago, and the current populations don't reflect the situation at that time.

Assuming Out of Africa as correct, it seems that humans moved across Asia and diversified into different "Basal" populations.

Tianyuan Man

Genetic analysis of a male found in Northern China, close to Beijing, in the Tianyuan cave, confirmed he had 4-5% of Neanderthal introgression. He was dated at 41,000 years ago. "three South American populations—the Surui and Karitiana in Brazil (“Amazonians”) and the Chane in northern Argentina and southern Bolivia—share more alleles with the Tianyuan individual than other Native American populations do." (source), these Amazonians are the ones with the Australasian imprint. The paper adds that "we find that the Amazonians can be described as a mixture of other Native American populations and 9%–15% of an ancestral population related to the Tianyuan individual, the Papuan, or the Onge (SE 4%–10%)." So here we add another "ancient" Asian component to the Australasian imprint, the Tianyuan man's genes.

The paper reasons that "The fact that the Tianyuan individual, who lived in mainland Asia about 40,000 years ago, has affinities to some South American populations that is as strong as or stronger than that observed for the Papuan and Onge suggests that a population related to the Tianyuan individual, as well as to the present-day Papuan and Onge, was once widespread in eastern Asia. This group or another Asian population related to this group persisted at least until the colonization of the Americas and contributed to the genomes of some Native American populations."

A 2025 paper found that "Among individuals from continental Eurasia, we find the highest proportion of detectable Denisovan ancestry in Tianyuan (∼0.25%), while other pre-LGM individuals from Eastern Eurasia had lower levels of Denisovan ancestry, comparable to those of later East Asians and Siberians."

Onge and Hòabìnhian

The Onge from the Andaman Islands are Australasians, and their signal is found in the Amazonian tribes. They were part of a basal population in Southeast Asia, a 2022 paper includes the following map showing a possible entry route into the area, and the current levels of this ancient basal component. Note how high it is in some areas.

Basal Asians. Fig. 2 in Deng et al. (2022)

The paper continues: " We speculate this basal Asian (bASN) ancestry to be an ancient lineage... the bASN ancestry is negatively correlated with the Altai Neanderthal introgression in Asian populations... suggesting that the peopling of Asia might have occurred prior to the Altai Neanderthal introgression (directly or indirectly) to the modern human populations in this region." Which makes sense, the Neanderthals lived in the colder central and NW regions of Asia, and possibly in NE Asia. So the people that moved along the coast of Southern and SE Asia didn't encounter Neanderthals on their journey.

An extremely interesting paper by Silcocks & Dunstan (2023) on dispersal of humans and two strains of tuberculosis across Asia finds a similar distribution of ancient people in Asia, the basal one in SE Asia, a later wave in northern and central Asia. (map below from the paper).

!--image captions-->

Original caption: "Fig. 7: Our proposed model of human-Mtb co-expansion, including population dispersal trajectories, and the predominant Mtb and Y-chromosome lineages they carried.". Source

A paper published in Science by McColl et al., (2018) indicates that there are "at least four ancient populations [in Asia] The oldest layer consists of mainland Hòabìnhians (group 1), who share ancestry with present-day Andamanese Önge, Malaysian Jehai, and the ancient Japanese Ikawazu Jōmon." The paper includes the following map, which shows an even older migration (black arrows) heading norteast to Tianyuan and southeast into Sahul, Papua New Guinea and Australia. The Onge and Hòabìnhians split later (red arrows).

Original Caption: Fig. 4 Model for plausible migration routes into SEA. This schematic is based on ancestry patterns observed in the ancient genomes. Because we do not have ancient samples to accurately resolve how the ancestors of Jōmon and Japanese populations entered the Japanese archipelago, these migrations are represented by dashed arrows. A mainland component in Indonesia is depicted by the dashed red-green line. Gr, group; Kra, Kradai. Fig. 4 McColl et al.

A similar route is suggested by Larena et al. (2021) which analyzes the genetics of the Philippine population. It mentions a first wave of human beings that reachied Sundaland (at that time it was not submerged) and peopled Australia, Papua New Guinea, the Indonesian Islands, the Philippines, and Andaman Islands around 50,000 years ago. This basal group put the Negrito people in the Philippines. Below is Fig. 2A from the paper, where I have added these place names and the comment on the exposed continental shelf

This wave comprised "Paleolithic hunter-gatherer groups, linked genetically to the Basal Australasian branch of modern humans"" it led to the Negritos, PNG people and Australian Aboriginal people, and also, in Southern China to another basal group, shown in the image above, the "Basal East Asian".

These Basal East Asians could have moved along the Pacific coast, northwards into Japan, and the Siberian coast, reaching America with their Onge genetic imprint. Moving along the coast of North America they didn't leave an imprint in its interior. Then, when they reached South America they moved inland. Plausible, but strange.

I have not yet found a paper with a convincing explanation of the "Gap" in Beringia, ancient North American and Mesoamerican paleoindians and most of the later Amerindians in the continent.

False Signal?

A study published in 2018 by Posth et al. failed to find the Population Y signal:

"We tested for this signal in the ancient South American individuals with statistics of the form f4(Mbuti, Australasian; X, Mixe or ancient South American), and while we replicated the originally reported signal when X was present-day Karitiana or Surui, we could not detect a signal when X was any of the ancient South Americans (Table S6). We also studied the statistic f4(Mbuti, Tianyuan; Ancient1, Ancient2) to test if any ancient individual is differentially related to Tianyuan (Yang et al., 2017), but no statistic was significant (Table S6). We finally applied qpWave to all pairs of South American groups, testing whether they were homogeneously related to a set of diverse non-Native American outgroups (Mbuti, Han, Onge, French, and Papuan) and found no pair of ancient South Americans that consistently gave significant signals (p < 0.01), as expected if all the ancient South Americans we analyzed derived from the same stem Native American population (Table S6). Our failure to find significant evidence of Australasian or Paleolithic East Asian affinities in any of the ancient Central and South American individuals raises the question of what ancient populations could have contributed the Population Y signal in Surui and other Amazonian groups and increases the previously small chance that this signal—despite the strong statistical evidence for it—was a false-positive. A priority is to search for the Population Y signal in additional ancient genomes."

Another paper searched for the Population Y signal using f4 statistics: f4(Mbuti, Papuan/Onge/Australian; present-day Mexicans, ancient Brazilians). The authors noted that:

"The only ancient Brazilian group showing significant affinity to Onge, compared with present-day Mexicans, is the JabuticabeiraII_~2400BP group. The signal is mainly driven by one individual (JBT009—burial 38), but it remains for the entire group even after the exclusion of JBT009. Similarly, there is significant genetic attraction between Onge and one individual from the Cabeçuda_3200BP group (CBE004—burial 15), while all other tests do not reach values close to significance (Supplementary Data 7). However, no evidence of the Population Y signal is found in the recent Amazonian individual Palmeiras Xingu_500BP, despite the fact that this ancestry was first described in present-day Amazonian populations; or in Capelinha_10400BP, despite its association with the paleoamerican cranial morphology. We further tested the presence of differential affinity of ancient Brazilian individuals to present-day Papuans, Onge and Australians, as well as the 40,000-year-old Tianyuan genome-wide data from China using f4 statistics of the form f4(Mbuti, Papuan/Onge/Australian/Tianyuan; Ancient Brazilian A, Ancient Brazilian B). Only the JabuticabeiraII_~2400BP group reaches significant attraction to both Onge and Papuans, and only in comparison to LapaDoSanto_9600BP (ref. 63). This suggests either that the Population Y signal is equally widespread in most tested ancient individuals from Brazil or that previously reported attractions to non-American ancestries are exacerbated by the use of present-day Mexican populations in comparison to ancient groups (Supplementary Data 7)."

Modern Mexicans are a mixture of European and North American native people. It is reasonable that they are different from secluded Amazonian natives. The Mixe natives are North American, which lack this Population-Y signal. It does not appear to me that they "exacerbate" the population Y signal.

Posth et al. didn't detect it among the ancient samples they used, this does not mean it is a false positive, perhaps their sample did not include the members of this first peopling wave which was erased by later "ancient" people via Beringia, with Siberian genetic imprints.

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

Ancient Australasian signal found in South American natives

A paper published earlier this year (Deep genetic affinity between coastal Pacific and Amazonian natives evidenced by Australasian ancestry. Marcos Araújo Castro e Silva, et al. PNAS April 6, 2021 118 (14) e2025739118; https://doi.org/10.1073/pnas.2025739118), suggest that the very early or even the earliest people to reach South America carried a genetic component that is not found in North or Central America, and that is linked to a "Y Population" the genetic signal inherited from this group (called "Y" after "Ypikuéra" or "ancestral" in Tupi language") is only found among Australasian people.

The paper reports that the Y-population signal originally found among Amazonian Amerindians is also found in natives from other parts of Brazil, and also in the Pacific coastal population of South America.

The authors write: "The best-fitted model showed that the Pacific coast is a mixed group of South American ancestry and a small non-American contribution associated with a sister branch of Onge, as also observed for Karitiana and Suruí. They suggest that the presence of this signal on the Pacific coast suggests that the original population reached the area following a coastal route.

The Onge are people that live in the Andaman islands, in the Bay of Bengal, dark skinned isolated people... and they are linked to South American natives.

Did they land in North America and Mesoamerica and die out? Did they bypass the northern part of the Americas and settle in the South?. The lack of this signal in the northern part of the continent is not explained in the paper.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2021 by Austin Whittall © 

More on the Amerindian - Australasian link: Denisovans?

I I have already posted about this The link between Negritos, Papuans and Amerindians!, but the paper by P. Skoglund et al., published online on July 21, 2015 [1], found a close relationship between the genetic makeup of some Amazonian Native Americans and a group of Oceanian or Austalasian people. Namely, the team found "genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.".

Being beind a paywall, since that first posts I have read other online sources who have accessed the paper found some interesting points to share in this post:

Skoglund et al., found that the Amazonian Amerindians like the Suruí, the Xavante and Karitiana share around 1 or 2% of their genes with aboriginal Andamanese, Papuans and Australians. Furthermore, the 12,600 year-old remains from Anzic, Montana, US, don't have any links to these Australasians suggesting that the Anzic child and modern Amazonians have different origins.

Their explanation is the following:

A simple migration from Melanesia north to Bering and then south into America does not seem likely because there are no traces of Australasian genes along the route. It is improbable that they would have covered such a long route without dallying with the locals and spreading their genes.

Instead they suggest that an ancestral population which is now extinct (that is why their genes cannot be found in Asia), lived in eastern Asia and split into two groups, one that moved south into South East Asia, PNG and Australia and another that marched north across eastern Asia and entered America.

They named these mysterious people as "Population Y" (Y from the Tupi word "Ypykuéra", which means "ancestor").

As I am not constrained by the rigidity of orthodox science, I can suggest that there is a Denisovan link involved in this process:

As Austronesians have a very high share of Denisovan genetic input, the hypothetical "Population Y" may well be the group that admixed with Denisovans, and therefore Denisovan genes in America could have this origin.

An alternative explanation however for the lack of "Population Y" traces in Asia could be that the Denisovans lived both in Asia and America, and admixed with the first wave of humans that went into America and also with the first wave through their Asian homeland: the ancestors of the modern Australasians. Later, they became extinct, but their genes lived on. Later still, Asians with a different genetic make up entered America and swept the first people away. Nowadays only 2% of the old genome survives in the Amazonian forests.

Since the very old hg M mtDNA was found in some ancient native remains in America, but is also found in parts of South East Asia, PNG, India and Tibet. Could this be a signal of the first people to reach America from South East Asia?

We have evidence of humans in Southern Asia aroung 120 kya, a very archaic population of humans; and they probably moved into America and mixed with Denisovans there or in Asia. What is the mtDNA of these people? If the hypothetical Out of Africa move took place earlier, then they could be Haplogroup M. We will have to wait for more evidence.

Source

[1] Pontus Skoglund, et al. (2015) Genetic evidence for two founding populations of the Americas, Nature 525, 104–108 (03 September 2015) doi:10.1038/nature14895.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2015 by Austin Whittall © 

Malaria and the Peopling of America

Today's post will explore the pathogens that cause Malaria, and how they reached America.

A paper published in April 2021 (Population genomic evidence of a Southeast Asian origin of Plasmodium vivax J. Daron, A. Boissière, L. Boundenga, B. Ngoubangoye, S. Houze, C. Arnathau, C. Sidobre, J.-F. Trape, P. Durant, F. Renaud, M.C. Fontaine, F. Prugnolle, V. Rougeron. bioRxiv 2020.04.29.067439; doi: https://doi.org/10.1101/2020.04.29.067439 Now published in Science Advances doi: 10.1126/sciadv.abc3713) proposed a Southeast Asian origin (below we will see two other papers, one, suggesting an African origin, the other an Asian one.)

The paper includes the following phylogenetic tree. Notice how America forms one of the three branches, with two separate clades, and the other two branches are: Most Asian countries, and India, Madagascar and Africa (perhaps linked by trade across the Indian Ocean).

P. vivax phylogenetic tree. Fig. 3 in Daron et al.

For America the authors suggest two possible explanations: "Across the Americas, P. vivax strains were structured in two distinct ancestral populations (Fig. 3, B to D). This is consistent with two putative evolutionary scenarios of the parasite in America. The first scenario hypothesizes that both ancestral populations originated from the isolation between Amazonian and non-Amazonian populations, after a single introduction during the European colonization in the 15th century. In the second scenario, two distinct waves of introduction occurred from the same or from different sources. Disentangling these two hypotheses will require more samples and statistical population genetic modeling."

The original online publication in Bioarxiv included text that was ommitted in the Science publication:

"Across the Americas, P. vivax strains were structured into two distinct ancestral populations. This is consistent with recent findings suggesting two successive migratory waves responsible for the introduction of P. vivax in America (37). The first wave has been suggested to occur following a reverse Kon-Tiki route, with a long-range oceanic crossing from the Western Pacific to the Americas. The second wave, has been recently attributed to an introduction by the European colonization of the Americas during the 15th century, and represents the major genetic contributors to the New World P. vivax lineages."

The paper cited as (37) is the following: Rodrigues, P. T., Valdivia, H. O., De Oliveira, T. C., Alves, J. M. P., Duarte, A. M. R., Cerutti-Junior, C., ... & Ferreira, M. U. (2018). Human migration and the spread of malaria parasites to the New World. Scientific reports, 8(1), 1993.🔓

The paper analyzes the genetics and relationship between the different lineages of malaria-causing parasites. It says it originated in Africa ("Plasmodium falciparum is currently hypothesized to have originated from a lateral transfer from gorillas to humans in Western Africa between 10,000 and 100,000 years ago" and spread globally.

In the case of American variants it notes that: "The TMRCA estimates for SAM populations of P. falciparum (37,002 years; 95% HPD interval, 21,385–56,606 years before present) and P. vivax (52,149 years; 95% HPD interval, 29,896–60,659 years before present) indicate that the hypothetical most recent common ancestor of New World malaria parasites largely predates the first human migrations to the continent."

Ah! the question of the arrival in America makes them say that being 37 or 52 ky old means that they "predate the first human migration" into America. Why not accept the facts, and suppose that there were humans in America 37-52 ky ago and that these parasites evolved there, in America?

They continue the analysis looking at the African variant (AFR) and point out that "Moreover, these estimates are rather similar to those obtained for populations of AFR P. falciparum (35,384 years; 95% HPD interval, 21,101–54,974 years before present) and P. vivax (41,685 years; 95% HPD interval, 28,630-57,563 years before present). Therefore, skyline analysis and TMRCA estimates argue against a severe population bottleneck associated with the recent malaria parasite migration to the Americas; to the contrary, SAM lineages appear to have retained much of the diversity that preexisted in their ancestral populations." Which is interesting: the parasite didn't have a bottleneck like the one that is always argued, happened to the humans that peopled America -and carried it there. And also, that the American variant is as old as the Old World African clade.

The paper concludes that slave trade and European navigation brought malaria parasites from Africa to America, and from India and Asia via Madagascar, and South Africa. There may have been a transpacific route from Asia to Central America. They also note that Melanesian variants could have also reached America in pre-Hispanic times: "We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans... While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax."

However, the great diversity observed in America surprises them and they try to explain it as sampling errors or, the successive waves from different places: "The lack of an apparent bottleneck in South American populations of P. falciparum is somewhat surprising. Not only parasite migration events, but also selective sweeps induced by large-scale antimalarial use in more recent years could have drastically reduced parasite diversity in this continent. We argue, however, that the current diversity levels have originated from the very many introductions of this parasite into the continent over centuries, from several different source populations in Africa. The substantial differentiation between present-day SAM and AFR lineages of P. falciparum likely results from the fact that we have not sampled all potential AFR source populations (Supplementary Fig. 15) or all P. falciparum subpopulations currently found in the Americas."

But looking at the phylogenetic tree from this paper, below, we see that the American (and the Atlantic rainforest simian variety) clades clearly are nested within the SE Asian and Melanesian clades, while the African and some other Asian clades form a different branch (with some -few- American samples, these surely came with the Slave Trade.

Global Malaria phlogenetic tree. Adapted from Fig. 2 in Rodrigues et al.

Polynesian - Melanesian migration?

As mentioned above, this paper also mentions the transpacific route and also adds: "Carter has speculated that a relapsing parasite such as P. vivax might have survived long-range, pre-Columbian oceanic crossings from the Western Pacific to the Americas through a reverse Kon-Tiki route." citing: Carter, R. Speculations on the origins of Plasmodium vivax malaria. Trends Parasitol. 19, 214–219 (2003).🔒

Carter suggests a South Asian origin for P. vivax" from where it moved aroun 1 million years ago into Europe and Africa, surviving in warm, humid places until humans were infected some 10 to 20 ky ago.

Closing Comments

There are three separate clusters, or branches on the malaria pathogen tree: Africa, Asia, and America. If the parasites originated in Asia and moved to Africa 20-50,000 years ago (or vice versa) and originated a seprate branch there, it took 20 to 50 ky to acquire its present diversity. So, why are we expected to imagine that these same pathogens came to America barely 400 years ago and suddenly evolved into another separate branch with equally enormous diversity?

Perhaps the pathogens reached America 50 ky (or even 100, or 200 ky earlier, via a migration from Asia by infected Neanderthals, Denisovans, or even older hominins like H. erectus then they diversified there, in the New World, where they infected monkeys in the Brazilian rainforests.

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

A Philippine group of people have the highest level of Denisovan ancestry

Another recent publication that caught my eye refers to Denisovans (Philippine Ayta possess the highest level of Denisovan ancestry in the world, by Maximilian Larena et al, August 12, 2021. Cuurent Biology. DOI:https://doi.org/10.1016/j.cub.2021.07.022).

The paper tells us:

"Highlights:... Ayta Magbukon display ∼30%–40% greater Denisovan ancestry than Australopapuans. The model is explained by a distinct admixture event into Negritos from Denisovans. Prior to modern humans, Islander Denisovans may have been present in the Philippines
Summary
... We show that Ayta Magbukon possess the highest level of Denisovan ancestry in the world—∼30%–40% greater than that of Australians and Papuans—consistent with an independent admixture event into Negritos from Denisovans. Together with the recently described Homo luzonensis, we suggest that there were multiple archaic species that inhabited the Philippines prior to the arrival of modern humans and that these archaic groups may have been genetically related. Altogether, our findings unveil a complex intertwined history of modern and archaic humans in the Asia-Pacific region, where distinct Islander Denisovan populations differentially admixed with incoming Australasians across multiple locations and at various points in time."

The paper argues that "The significantly higher level of Denisovan ancestry in Ayta Magbukon relative to Papuans highlights the possibility of an independent Denisovan introgression event in the Philippines among Negritos that is different from the Denisovan introgression event into the ancestors of Australopapuans. This observation is consistent with recent studies suggesting multiple pulses of Denisovan introgression into humans, that Denisovans were probably widespread throughout ISEA, and that Ayta Negritos were likely to have experienced a second Denisovan introgression event."

Furthermore, the Denisovans had split into different groups in the region and admixed separately with Papuans and Aytas: "our simulations provide support for the presence of two separate Denisovan lineages that independently introgressed into the ancestors of Ayta Negritos and Papuans, likely occurring around the same time after the Negrito-Papuan divergence 53 kya (95% CI: 41–64 kya). Upon entry of the first modern human migrants into Sunda and Sahul (ancestors of Negritos and Australopapuans), these ancestral Australasian groups likely experienced admixture with deeply divergent Denisovan-related populations scattered all throughout the ISEA and the Oceania region."

It also has an interesting suggestion regarding the different archaic hominins in the region (but it does not mention H. erectus): "Additionally, the physical evidence for a previously undescribed hominin in Luzon 67 kya, where present-day Negritos reside, combined with the genetic evidence presented here, raises the possibility that the suggested Homo luzonensis and Denisovans were likely genetically related, either as distinct forms or possibly belonging to the same group residing on the islands. Furthermore, it is not entirely impossible that the recently identified new species of archaic hominins in the Indonesian island of Flores, the Homo floresiensis,38 may also be related to Denisovans. Hence, the presence of multiple archaic human remains in the region, together with the genomic evidence presented here and elsewhere, raises the possibility that the Denisovans comprised deeply structured populations with considerable genetic and phenotypic diversity,"

Let's hope that we can soon identify the links between Denisovans and these other hominins.

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2021 by Austin Whittall © 

Black dwarves or pygmies in America

This is another post in our series on Armando Vivante's article* (Online here - Spanish) about pygmies in America. In it we will look into the section on "Little Black Men" (section 13, p.250 of his article).

* Vivante, A. (1963). Estado actual de la discución sobre los pigmeos americanos. 1. El primer contexto de este problema. Revista del Museo de La Plata. Nueva Serie. Sección Antropología, Artículos, Vol 5, No 28.

Little Black Men

Vivante cites Lehmann, who in turn cites Nordenskjöld who mentioned a book (Geografí de Colombia - See p. 878) that included a reference about these black pygmies in the Darien, in the border region between Panama and Colombia, which features a thick jungle.

This article was written at the time that Panama was still a province of Colombia (1901) shortly before the U.S. president Theodore "Teddy" Roosevelt promoted the independence of Panama (1902) in order to build the transoceanic canal there and exert direct control over it. Below is the text on the Darien people:

"According to reports from one of their main chiefs, in those mountains there existed ten years ago remains of an aboriginal population, small in stature, with black skin, very scarce in my region (100 to 200) and entirely savage: he reported that the Cunacunas took from that people the land they occupy today, after a great massacre, and they fear finding any of those who remained, believing them to be sorcerers and even demons."

The Debunked Negrito-Tasmanian Theory

Vivante then mentions that Italian anthropologist Giuseppe Sergi who studied cranial forms and concluded that America had been populated in different waves, one came from Western Africa, and was comprised by Negrito people, "we can certainly affirm that, besides those of the Tasmanian type, another human branch entered America, this one of short stature, which is usually called pygmy with a short cunciform skull Sphenoidis brevis." (from Gl'indigeni Americane: ricerche antropologiche, Rome, 1928 p.164).

Despite living under Mussolini's fascist regime, Sergi was a pacifist, anti-German, and not at all racist. Unfortunately his theory on "Mediterraneanism" was co-opted by the fascists to back their racist ideology.

These racialist Tasmanian-Negrito-Pygmy migration theories were in vogue in the late 1800s and early 1900s (see, for instance, an article on Pygmies in the U.S. from 1896). Since the mid 1900s, they have been debunked. Closer to Patagonia, Argentine anthropologist José Imbelloni supported a similar notion where South America was populated by several waves of people, and the first were pygmies, ancestors of both the Tasmanians and the Fuegian Yamana people (see Imbelloni, J. The peopling of America. Acta Americana. vol. I, No 3, Jul.-Sept. 1943).

Vivante states that he mentions these theories as potential evidence of an "ancient pygmy layer or layers then fragmented and liquidated, leaving behind reduced nuclei and tiny islands" when the later Amerindians arrived and wiped them out.

Tasmanian. Source

Nowadays the ancient Lagoa Santa remains from Brazil, and the Australasian genetic imprint suggest that the original inhabitants of Southeastern Asia somehow played a role in the peopling of America.

Mythical Dwarfs

Vivante's paper also mentions the mythical dwarves across America, and he also mentions some Patagonian examples, such as a reference from 1863 by Cox about the "peuquenes" close to Puerto Blest in Neuquén, the "'pichuchu', tiny men" (citing Daniel Hammerly Dupuy, 1953. Nahuel Huapi. Panoramas, Leyendas, Historias, Soc. Geogr. Americana, B. Aires, pp. 72-74) and several authors about the "Anchimallén".

Below is an excerpt from my book, on Cox and the Peuquén (also posted here):

"“Peuquen” – the Patagonian gnome
Guillermo Cox is the only reference that I have found regarding the Peuquen. He wrote about them in 1862, calling them “mountain genies […] small men that are clothed in avellano [Gevuina avellana, a native Chilean tree] leaves […] they also have a hat made from its bark, and an axe made of its wood.” Like Trauco, it lives in the forests of Chiloé, chopping trees. Yet like Yosi, it does not use its wood to light fires. Those who come across him face a nasty fate: their heads are turned backward for the rest of their lives. Like Yosi and Trauco, he is a lewd creature and seeks sexual intercourse with women. The children conceived during these trysts are born with their skin like the bark of an avellano, that is, rough and light brown.

I cite his work: Cox, G., (2006). Expedición de la Patagonia Norte: un viajero en el Nahuel Huapi: 1862-1863. B. Aires: Continente-Pax. pp.67-69

I also mentioned Kossler-Ilg, Francisco Moreno, Gregorio Álvarez, Father Mascardi, and Parodi regarding the Anchimallén (also posted here). However, this is the first time I hear about "pichuchu" the name applied to a dwarf. The word is used as a friendly, affectionate diminutive for tiny, sounding tender or childlike. But I have never encountered it in the Patagonian dwarves context until now.

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