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