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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