There was a new paper published earlier this month that is really interesting for understanding the human dispersals in the Americas. Of course, with the help of some newly sequenced aDNA. From the abstract emphasis mine):
“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.”
I can’t comment in details about this very good paper that should satisfy those who are more into the history of the Americas than I am. So to those I can only recommend them to read the paper and enjoy it.
Here I’ll just comment briefly on a few details that are mentioned in the abstract excerpt above and that are somehow linked to some comments from a previous post about the population history of Northern Siberia (Sikora et al. 2018).
But first, regarding the mention of those two “Paleoamericans”, I’ll just say that they were samples that had been speculated to be from a different population due to their different cranial morphology compared to other Native Americans. However, the genetic analysis shows that they’re genetically the same as the rest, showing that cranial morphology can vary due to drift without any admixture involved.
The two other things I want to comment about are those related to the “previously unknown groups” and their relationship to that Australasian signal and to a Mesoamerican distinct one.
So about the Australasian signal, this is something that had already been found before (Skoglund et al. 2016) and that was specially showing up when comparing the affinity of Suruí (and Karitiana, though a bit less) to Mixe (and Pima, but a bit less) to Australasians (from Andaman Islands and Papua New Guinea).
My observation from the previous post about the Siberian paper was that the relationship between Anzick-1 (a ~12.5 kya sample) and Suruí/Karitiana to Ancient North Siberians (ANS) was symmetrical and it didn’t seem that there would be anything significantly different about those populations from the Amazon. Instead, I found that it was Mixe and Pima the ones who had a different relationship to ANS compared to other NA, showing some admixture from an unknown source (non-Eurasian in any case, since they didn’t show any increased affinity to any Eurasian population.
However, here they compare with D-stats directly Anzick1 and Suruí to Australasians, and from figure 4A it looks like D(Anzick1, Suruí; Australasian, Yoruba) has a Z-score of about -2. It does not reach significance, but it’s there. Interestingly, the signal is also found in a ancient samples from Lagoa Santa (SE Brazil) dated to around 10.4 kya. Using qpGraph, this Australasian admixture is estimated to be around 3% in these samples (and modern Suruí). 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.
The second thing is even more interesting: when on a similar D-stat as the above one, but with Mixe in the place of Anzick1, the result reaches significance (Z-score around 3 and a bit more in Fig. 4A). This is what had already been found before and used to argue about the signal being real and strong. However, while I don’t doubt that the signal is there, what they had failed to realize was that there is actually something specific in Mixe that makes this stat significant. And what it that? Here’s what the paper says about it (emphasis mine):
“by fitting f-statistics-based admixture graphs, and found that even though Anzick1, Spirit Cave and Lagoa Santa are separated by ~2000 years and thousands of kilometers, these three individuals can be modeled as a clade to the exclusion of the Mesoamerican Mixe (13). While we did not find evidence rejecting this clade using TreeMix and D-statistics (13), 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)”
I don’t have the tools and samples to test these things formally, but from the data provided by the paper I’d propose a slightly different interpretation. For what I see in Figure 4A, it’s clear that Mixe seems to have admixture from an outgroup too all the populations tested (see for example these 2 below):
The shift that we see to the left in the case of Mixe basically shows that while the pattern of affinities is the same as in Aymara, the number of shared alleles with all the Eurasian populations represented by the diamonds is lower than Aymara’s shared alleles. The question here is what kind of population would be an outgroup to Native Americans. And the first answer is simple: roughly anyone else. True. But then we could find the specific population in Eurasia (modern or ancient) with which Mixe would share more alleles than other NA groups (especially those without Mixe-related admixture, like Suruí). However, we don’t have such population. 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. This, to me, seems the most realistic of the options. We know that such populations (part of the main OoA) reached Siberia quite early (as Ust-Ishim shows), so why couldn’t some of them reach America and survive till the second bigger wave from around 17 kya? Archaeology has found small evidence of human habitation in America from around 50 kya (IIRC), so that could be it. For me the question in this case (but also in whichever of the previously mentioned cases) is why didn’t such population thrive in America in a similar way as the later one did as soon as they arrived?
Whatever the truth turns out to be, a very interesting question the one this paper has opened with the UPopA admixture into Mixe and other Mesoamerican populations (Huichol, it seems), though not limited to them, since there has been an expansion of these Mixe-related populations that has made that the admixture from UPopA is present in many (most?) modern NAs, just to a lower degree (in any case, keep in mind that as in the case of the Australasian-related admixture in SNA, we’re talking about a very small genetic contribution to the autosomes and none to either the paternal or maternal lineages, so the contribution itself is mostly anecdotal. What is important is to know if any of those populations were in America before actual NAs arrived).
As pointed out by Frank (personal communication), and in line with his observations about the Kennewick Man in the previous post about the population history of NE Siberia (see comment here) , on Figure 2D we can see that Kennewick Man already has Ancient Beringian admixture shown by the extra East Asian:
I confirmed this by using Global 25 datasheet and modelling Kennewick as a mixture of Clovis (Anzick1) + something else:
We can clearly see the extra NE Siberian/Beringian admixture there.
Unfortunately, trying a similar approach to detect any admixture in either Suruí or Mixe didn’t work, both coming out as 100% Clovis. A more sensitive test should be performed with these ones (well, it’s already done with Suruí, both in this paper and in Skoglund et al. 2016 showing the Australasian related admixture). For Mixe, maybe someone would like to try some of the options outlined above, like:
D(Chimp, African; Anzick1, Mixe)
Where African could be from Iberomaurusian to Ju Hoan.
D(Chimp, Archaic; Anzick1, Mixe)
Where Archaic could be Neanderthal or Denisova.
D(Chimp, Ust-Ishim; Anzick1, Mixe)
And see if any of those give a Z score of around 2 or greater.