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.
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).
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).
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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