The Mystery of Population Y

This fabulous portrait by celebrated photographer Carlos Monforte shows an Aborigine elder in Darwin, Australia in 2017.  Monforte specializes in images of indigenous cultures and people as well as scenery, especially in Asia and Oceania.  He lives in Singapore and says his photography is about “capturing souls, not smiles.”  (See his National Geographic link here.)  I thought the image would make a cool introduction to our discussion …

Is it possible that a group of humans related to Australian Aborigines somehow made its way into South America before Native Americans crossed the Bering Strait and entered the New World over 13,000 years ago?  In other words, were the First Americans actually the Second Americans?

Believe it or not, that is the scenario that has emerged from several studies over the past three years … or at least, it’s one of a couple scenarios that have been suggested.  Researchers have dubbed this mystery group “Population Y” after the word ypykuera, which means ancestor in a Brazilian language called Tupi.

Until the mystery of Population Y emerged, genetic studies in concert with archaeological finds have tended to point toward the conclusion that all native people in the New World descend from a common origin – that is, from Siberians who crossed the Bering Straits over 15,000 years ago (ya).  North and South America are, of course, the last two continents to be populated by homo sapiens.

However, in 2015, two studies quite independently discovered that certain tribes deep in the Amazon jungle shared a genetic affinity to Australasians.  (The ancestry of these tribe members remains primarily Native American; it is only a small portion of their DNA that links them to Australasians.)

Australasians is the term used to describe Aborigines, Papua New Guineans, Andaman Islanders, Mamanwa Negritos, and other groups in the Philippines.  The Andaman Islands were recently in the news because an American missionary, John Chau, was killed when he attempted to make illegal contact with natives on North Sentinel Island in November 2018.

The tribes that show the genetic linkage included the Surui, Kiritania, and Xavante, all three of which inhabit remote regions in Brazil.  No such genetic link was found in North American Indians, or for that matter, in any other Central or Southern Americans who were not related to these three tribes.  The amounts involved were not great but were nevertheless pronounced.  It was a completely unexpected result and led to much head scratching.  David Reich, the head of a Harvard research group which contributed to one of the 2015 studies, was quoted as saying:

“We spent a lot of time being skeptical and incredulous about the finding and trying to make it go away, but it just got stronger.”1)Ewen Callaway, “Ghost population hints at long-lost migration to the Americas,” Nature: International Weekly Journal of Science, 21 July 2015.

The 2015 studies were published in the journals Nature2)Skoglund, P. et alNature (2015). and Science3)Raghavan, M. et alScience (2015).

Surui man (Source: Paulo Whitaker/Reuters/Corbis)

At the time of the discovery in 2015, the DNA of very few ancient Native American remains had been tested.  The genetic link was discovered only in current humans who agreed to be tested.  The connection is not linear – that is, the Brazilian tribes in question are not directly descended from Australian Aborigines, nor are Aborigines descended from them.  Instead, today’s Australasians and some members of these three Brazilian tribes today are very distant cousins who are likely descended from a common population, and it is that hypothesized common population which has been dubbed Population Y.  As Pontus Skoglund who worked with Professor Reich points out, Population Y is “an unknown group that doesn’t exist anymore.”4)Callaway, “Ghost population,” Nature, 21 July 2015.  The theory is that Population Y would have existed somewhere in East Asia, time frame unclear, and then split – one group went south and one north, with the northern group eventually making its way across the Bering Strait and into the Americas.

Then, late last year, two more studies were published by the same research labs which further expanded on the possibility of an Australasian connection to these Brazilian tribes.  Although the research groups are independent of one another, they published collaboratively on the same day: November 8.  The results of David Reich’s Harvard team were published in the journal Cell,5)Posth et al. “Reconstructing the Deep Population History of Central and South America.” Cell, 2018 DOI: 10.1016/j.cell.2018.10.027, while the results of Eske Willerslev’s Copenhagen/Cambridge team were published in Science.6)“Early human dispersals within the Americas.” Science, 2018; eaav2621 DOI: 10.1126/science.aav2621

The two new studies represent the first major effort to systematically test and analyze multiple ancient human DNA samples from the Americas.  The Harvard team decoded 49 ancient genomes going as far back as 12,800 ya while the Copenhagen/ Cambridge team decoded 15 ancient genomes going as far back as 10,600 ya.  Previously less than 10 ancient genomes in the New World had been analyzed by anyone.  A lot of interesting insights came out of the two studies, with the Australasian connection being only one small aspect of their overall findings.

Disappointingly, none of the 49 ancient samples in the Cell study revealed an Australasian genetic signature.  One sample from the Science study, however did: the 10,400-year-old Lagoa Santa remains in Brazil.  That would appear to be evidence that descendants of the “ghost” population known as Population Y were in South America at least 10,000 ya.

Migration of Native Americans into the New World (Source: Posth et al./Cell)

But that still doesn’t answer the question of who came first.  We already know that the ancestors of today’s Native Americans left Siberia as a structured population about 23,000 ya, resided in Beringia during the Last Glacial Maximum for about 8,000 years, and then began to enter North America after 15,000 ya when the melting of ice sheets permitted.  There is also evidence of an ancient split within the original Native American population that occurred about 13,000 ya, with one group heading east across Canada (called ANC-B), and another that headed south, populating the rest of the New World (ANC-A).  So a group carrying the Population Y signature either was already in South America when Native Americans arrived or they entered afterward.  If it was afterward, they somehow traveled through North America without leaving any genetic trace.  Quoting Dr. Peter de Barros Damgaard, University of Copehagen:

If we assume that the migratory route that brought this Australasian ancestry to South America went through North America, either the carriers … came in as a structured population and went straight to South America where they later mixed with new incoming groups, or they entered later.  At the moment, we cannot resolve which …7)St John’s College, University of Cambridge, “DNA of world’s oldest natural mummy unlocks secrets of Ice Age tribes in the Americas,” ScienceDaily, 8 November 2018 (

The emphasis now is on continuing to find and test more ancient remains.  That will help verify the existence of Population Y and pin down the timing of its entrance into the New World.

To me, imagining that Population Y came after Native Americans seems like quite a stretch.  I don’t know how a separate population travels all the way from Asia through North America to the Amazon jungle without leaving some trace of their existence along the way.  (Arriving in South America across the oceans 10 or 20 thousand years ago seems even more fantastic.)  It makes much more sense that the Population Y group is more ancient than the Paleoamericans who arrived 15,000 ya.  They could have easily been more widespread and were displaced.

Interestingly, I have not seen any comment about Neanderthals, or especially Denisovans, in connection with the Population Y signal in Brazil.  Since we know that Australasians have a higher proportion of Denisovan introgression than any other population, one would think that checking for Denisovan alleles in the Brazilian tribes would contribute to the discussion.  Just a thought.

References   [ + ]

1. Ewen Callaway, “Ghost population hints at long-lost migration to the Americas,” Nature: International Weekly Journal of Science, 21 July 2015.
2. Skoglund, P. et alNature (2015).
3. Raghavan, M. et alScience (2015
4. Callaway, “Ghost population,” Nature, 21 July 2015.
5. Posth et al. “Reconstructing the Deep Population History of Central and South America.” Cell, 2018 DOI: 10.1016/j.cell.2018.10.027
6. “Early human dispersals within the Americas.” Science, 2018; eaav2621 DOI: 10.1126/science.aav2621
7. St John’s College, University of Cambridge, “DNA of world’s oldest natural mummy unlocks secrets of Ice Age tribes in the Americas,” ScienceDaily, 8 November 2018 (