David Reich's take on the Y population and Australasians

The mysterious and ancient ghost population known as "Y" Population mentioned in yesterday's post (and in several other posts over the past years) was explored in depth by Harvard geneticist, David Reich in his 2018 book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past 🔓.

In Chapter 7 (starts on p. 155), dedicated to the original ancestors of the Native Americans, Reich explains the theories and timing of the peopling of America based on current archaeological and genetic data.

Reich tells how the one wave peopled South America mutated over the years, and now we believe that at least four separate migrations led to the current makeup of Native Americans. Of relevance is the section starting on p. 176 that looks into the Y population.

The basics are the following: Walter Neves was the first to propose (see post) base on skull morphology, that ancient Brazilian paleoindians, like those found in Lagoa Santa were very similar to those of Australian aboriginals and Melanesians from Papua New Guinea.

Fig 21 in Reich's book, original caption reads: Despite extraordinary geographic distance, populations in the Amazon share ancestry with Australians, New Guineans, and Andamanese to a greater extent than with other Eurasians. This may reflect an early movement of humans into the Americas from a source population that is no longer substantially represented in northeast Asia.

This was very controversial, and opposed by the mainstream anthropologists. However, Pontus Skoglund investigated this possibility and after looking into the genetics of different native people, "found two Native American populations, both from the Amazon region of Brazil, that are more closely related to Australasians than to other world populations... Skoglund found weaker signals of genetic affinity to Australasians, but still probably real, in other Native American populations ringing the Amazon basin. He estimated that the proportion of ancient ancestry in these populations was small—1 to 6 percent—with the rest being consistent with First American ancestry."

This pattern appeared not only in Skoglund's data (by the way, Skoglund was working with Reich as a postdoctoral student), but in other data sets collected by other scientists. Furthermore, they also showed that it wasn't a recent admixture with people from Australia or Papua New Guinea, nor the result of Polynesians carrying these alleles across the Pacific to America.

The remarkable findings are that:

• Similar yet not closely related: "while Amazonians had their strongest affinity to indigenous people from Australia, New Guinea, and the Andaman Islands (compared to East Asians as a baseline), they were not particularly close to any of them"
• It was highest among the Suruí, Karitiana, and Xavante groups, and almost absent elsewhere: "We found little or no Population Y ancestry in Mesoamerica or in South Americans to the west of the high Andes. We also did not detect Population Y ancestry in the almost thirteen-thousand-year old genome of the Clovis culture infant from the northern United States, or in present-day Algonquin speakers from Canada. The Population Y geographic distribution is largely limited to Amazonia, providing yet more evidence for an ancient origin" Reich attributes this limited distribution to an "original pioneering population that was once more broadly distributed and was then marginalized by the expansion of other groups."
• Two groups of Native Americans with skulls similar to those of Neves' Paleoindians were tested by other researchers, they were Pericués of Baja California, and Fuegians in Argentina, however, neither group carried the signal of Population Y alleles.

This evidence suggests different population possibilities to Reich: (1) Population Y reached America first, spread across the continent and later, when the "First Americans" (actually, the current ones, but not first, they were second) arrived they displaced and replaced the Population Y people "either completely or only partially, as in Amazonia. Population Y ancestry may have survived better in Amazonia than it did elsewhere because of the relative impenetrability of the Amazonian environment." So, in the Amazons the original Population Y was not razed, but admixed gradually with the newcomers.

The current levels of Population Y ancestry in the Amazonians may be small (~2%), Reich states that the impact of the ghost populations should not be dismissed. Reich proposes a second theory (2) in which he supposes that the Population Y people as they walked across Asia and Siberia into "northern North America where the ancestors of First Americans were also living. It is likely that Population Y was already mixed with large amounts of First American–related ancestry when it started expanding into South America. If so, then the ancestry derived from a lineage related to southern Asians is only a kind of “tracer dye” for Population Y ancestry—like the heavy metals injected into patients’ veins in hospitals to track the paths of their blood vessels in a CT scan. Our estimate of around 2 percent Population Y ancestry in the Suruí is based on the assumption that Population Y traversed the entirety of Northeast Asia and America without mixing with other people it encountered. If we allow for the likelihood that there was mixture with populations related to First Americans on the way, the proportion of Population Y in the Suruí could be as high as 85 percent and still produce the observed statistical evidence of relatedness to Australasians. If the true proportion is even a fraction of this, then the story of First Americans expanding into virgin territory is profoundly misleading. Instead, we need to think in terms of an expansion of a highly substructured founding population of the Americas. The history and timing of the arrival of Population Y in the Americas is likely to be resolved only with recovery of ancient DNA from skeletons with Population Y ancestry."

So, in this second scenario, the Y Population isn't the original one, instead it was part of the First People reaching America, in a very highly structured population which somehow (Reich does not explain the mechanism though!) had already admixed with other Native groups, yet did not leave any signal in North America or Central America, or anwyhere other than the Amazon region.

I agree that further studies are needed, and finding Population Y remains will be of capital intererst, but also, we need a theory proposing a clear mechanism, other than Bottlenecks and genetic drift, to explain how the Population Y signal was erased, and is absent among present day Amerindians all across America —except for these three Amazonian groups.

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

Tianyuan Man's DNA (40 ky old) linked to present South American Natives

I have read online that an analysis of the remains of the "Tianyuan Man", from China, dating back to 40,000 years ago, have revealed some unexpected findings.

I will quote Phys.org below: (I highlighted part of the text in bold)

"... With a close relationship to present-day Asians, they expected him to be similar to present-day Asian populations with respect to Europeans. It was a surprise when they found that a 35,000-year-old individual from Belgium, GoyetQ116-1, who in other ways seemed to be an ancient European, shared some genetic similarity to the Tianyuan individual that no other ancient Europeans shared.
...
A second unexpected result sheds some light on human genetic diversity in prehistoric East Asia. In 2015, a study comparing present-day populations in Asia, the Pacific and the Americas showed that some Native American populations from South America had an unusual connection to some populations south of mainland Asia, most notably the Melanesian Papuan and the Andamanese Onge. That study proposed that the population that crossed into the Americas around 20,000 years ago could not be thought of as a single unit. Instead, one or more related but distinct populations crossed at around the same time period, and at least one of these groups had additional ties to an Asian population that also contributed to the present-day Papuan and Onge.
No trace of this connection is observed in present-day East Asians and Siberians, but unlike them, the Tianyuan man also possesses genetic similarities to the same South Americans, in a pattern similar to that found for the Papuan and Onge. The new study directly confirms that the multiple ancestries represented in Native Americans were all from populations in mainland Asia. What is intriguing, however, is that the migration to the Americas occurred approximately 20,000 years ago, but the Tianyuan individual is twice that age. Thus, the population diversity represented in the Americas must have persisted in mainland Asia in two or more distinct populations since 40,000 years ago."

A simple answer for the "intriguing" finding is that either:

(a) The ancestors of Tianyuan man came from South American stock, crossed North America before it was peopled by later Siberian-origin humans, and entered Asia via Bering heading south and peopling China, Melanesia and the Andamans first, and then heading west into Europe where the ancestors of the GoyetQ116-1 remains picked up these genes.

(b) The Asian ancestors of South Americans entered America at least 40,000 years ago, before Siberian-Asians peopled North America. This eliminates the need for a persistance in Asia of "two or more distinct populations since 40,000 years ago".

According to Science:

"... Tianyuan Man inherited about as much Neandertal DNA—4% to 5%—as ancient Europeans and Asians of similar age. That’s a bit higher than the 1.8% to 2.6% of Neandertal DNA in living Europeans and Asians. The Tianyuan Man did not have any detectable DNA from Denisovans...
Native Americans living today in the Amazon of South America, such as the Karitiana and Surui peoples of Brazil and the Chane people of northern Argentina and southern Bolivia. They inherited about 9% to 15% of their DNA from an ancestral population in Asia that also gave rise to the Tianyuan Man. "

Or rather the Tianyuan man "inherited" this DNA from the American ancestors of the present Amerindian populations in South America.

The lack of Denisovan DNA is interesting and we should find out how come Melanesians which have a very high content of Denisovan DNA also have a very close link to Tianyuan man which has no Denisovan genes!

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Patagonian Monsters - Cryptozoology, Myths & legends in Patagonia Copyright 2009-2017 by Austin Whittall ©