There’s a new amazing preprint at bioRxiv about the population history of Siberia, which also deals with the origin of Native Americans. The new study brings a good amount of new samples spanning from the UP (~32 kya) to ca. 1250 AD that clarify the genetic history of the region. While it does not show anything too surprising or new, it basically confirms with samples and provides more accurate dates and places for what could already be envisaged from the previous limited amount of aDNA available. Here’s the abstract (emphasis mine):
Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of “Ancient North Siberians” (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the “Neosiberians” from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.
So let’s start with the oldest samples from Yana RHS, dating to around 31.6 kya and referred to as Ancient North Siberians (ANS). This represent a new population in the ancient DNA (aDNA) record, at least partially so. A note a bout the name: whenever a new population is found it needs a name, which usually corresponds to the geographical location where the specific samples are found, and sometimes to the economical subsistence strategy or the time when they lived. I this case, the choice of Ancient North Siberian does not imply that this population was restricted at that time to North Siberia (since it’s very likely that people living in South Siberia at that time were part of the same population), nor does it imply the place where it originated (since it’s very unlikely that it was actually in North Siberia). So let’s just take the name for what it is: a way to refer to this population due to the location and time of the samples.
So who were these ANS? Probably many already have guessed that they must be related to another population known as the Ancient North Eurasians (ANE). Indeed, ANS represent an early stage in the development of the ANE population, and therefor ancestral to ANE, as seen both in the autosomes and the Y chromosome (P1 in these 2 samples). This population is somewhat intermediate between West Eurasians (WE) and East Eurasians (EE), but closer to West Eurasians (it can be modelled as 75% WE and 25% EE). Whether this is because the split from West Eurasians soon after the split between WE and EE alone or because of subsequent admixture with EE is unclear, though in theory I guess that admixture is the only way to explain a higher affinity to EE (or otherwise WE admixed into some other more divergent ghost population that separated them further from EE, but this is quite more speculative).
As for the origin of this ANS population, it seems quite clear that it was to the south west. A population that is in between WE and EE must be from somewhere around Central Eurasia. And after all, ANE was already in high proportions in 10 kya samples from West Iran, in pre-BA sample presumably from the Indus Valley Civilization and it’s present all the way to South Indian tribals.
The paper draws what I think it’s a very good picture of the dynamics of the populations that occupied difficult climatic zones such as Siberia during the last glacial period. While it’s amazing that populations could actually live in North Siberia at that time, it’s not surprising that whatever subsistence strategies and ecological niches they managed to find and exploit, they were quite fragile and could easily break with any change in the climatic conditions. The paper documents the discontinuities during, for example, the LGM and investigates through climate modelling the possible areas where these populations might have found refuge during each period.
Following the LGM, this ANS population is replaced by a different one, the Ancient Paleosiberians (AP), who are the ones who went further to colonize the American continent. This population was partly descended from ANS, via ANE, but had a large amount of East Asian admixture (from around North China/SE Siberia, represented by other ancient samples from the Devil’s Gate cave). In this part is where I find the only issue with an otherwise exemplary paper. When arguing the possible place where this AP population formed, they write the following:
Conditions in the region became less suitable during the LGM, supporting the lack of genetic continuity between Yana RHS and later groups. Interestingly, we find evidence for a potential refuge in southeastern Beringia, as well as a possible coastal corridor along the Sea of Okhotsk and the Kamchatka Peninsula during the LGM (e.g. panel 22ka, Alaska, Extended Data Fig. 8a), in line with previous reports48. A possible scenario for the ANS gene flow during the formation of Native Americans and AP might therefore have involved early ANS surviving in southeastern Beringia during the LGM, with subsequent admixture with EEA [Early East Asians] arriving by a coastal migration ~20 kya. This scenario would also be consistent with a divergence of Ancient Beringians from ancestral Native Americans in eastern Beringia rather than in Siberia, which is also supported by genetic data (Scenario 2 in41).
I think that this scenario is incompatible with their current genetic data. The “ANS gene flow during the formation of Native Americans” is not a precise statement, since it’s not really ANS, but more precisely ANE. Their scenario implies that the evolution from ANS to ANE happened simultaneously and independently in Beringia/Kamchatka and in South Siberia (Laka Baikal) and SW Siberia (Altai), something that is not really possible. They show in different stats and figures in the paper that the Malta1 (near Lake Baikal, ca. 24 kya) shares more drift with Native Americans than the Yana samples. And AfontovaGora3 (Altai region, 17 kya) shares even more drift with Native Americans than Malta1 does. This makes is basically impossible that ANS survived in NE Siberia and contributed to the formation of Native Americans (it would require a very convoluted scenario of back migrations from NE Siberia to Altai that I won’t extend in outlining here due to its various complications).
So what it seems to have really happened is that those ANS populations from N/NE Siberia went extinct sooner or later, and subsequently the area was repopulated from people coming from around the Amur basin who mixed with people coming from much further west, maybe the Altai region. This seems rather clear, as the evolution from ANS to ANE seems to imply an increased affinity to West Eurasians (shown in some graphs as admixture from a branch related to CHG, but without Basal Eurasian admixture). They go on saying:
Alternatively, the closer affinity of both Kolyma1 and Native Americans to Mal’ta rather than Yana could suggest a more southern location (Lake Baikal region) for the admixture, with a subsequent northward expansion following the LGM. While the archaeological evidence of a movement south during the LGM supports this scenario, the genetic isolation between Asians and ancestral Native Americans after ~24 kya would have been difficult to maintain if several populations sought refuge in the region. Our results nevertheless support the broader implication that glacial and post-glacial climate change was a major driver of human population history across Northern Eurasia.
I’m not really sure what they mean by the “genetic isolation between Asians and ancestral Native Americans after ~24 kya” (I might have missed the specific part in the paper – will check), but in any case this could mean that it was these EEA who were in the Beringia and/or Kamchatka area prior to the LGM, since we don’t have direct genetic evidence from that region at that time. Or any other scenario. But clearly (IMHO) not the first one proposed.
Regarding the higher affinity of ANE to some WE branch related to CHG (I wouldn’t take this very literally, since it probably means something more similar to Kostenki), it further goes on to show that in the formation of EHG there is admixture fro CHG (this time CHG-proper, or closely related), and shows the presence of Basal Eurasian admixture in EHG too. This has been known by many of us for a long time now, but it’s the first time it appears documented in a scientific paper, so that’s another good point in the paper.
Continuing with Native Americans, there’s this other mysterious Australasian (Onge/Papuan related) admixture found in previous studies in populations from the Amazon, like Surui and Karitiana, specifically when compared to the Mixe and Pima populations from the SW part of North America. For what I see here, however, the relatedness of the Yana samples to Anzick-1 (a 12.4 kya sample from the Clovis complex) and to Karitiana and Surui is symmetrical, while it becomes asymmetrical with Mixe and Pima. This suggests that whatever Australasian “admixture” (if it can be called admixture at all) present in modern samples from the Amazon might have been already present in the Anzick-1 sample, and it’s rather Mixe and Pima who would have later experienced some genetic shift that makes them further away from Australasians (but apparently IIRC, there’s no evidence of admixture from any known source in Pima and Mixe, which makes the case complicated. Maybe if these 2 population went through a bottleneck that triggered a strong selection that affected specific regions of the genome associated with Australasians it could lead to these results, but this is something that’s purely speculative on my part and would need to be tested as an alternative).
Holocene transformations across Siberia and Beringia
The paper further investigates the Holocene genetic shifts across Siberia, but I’m afraid that in order to keep this post at a reasonable length I’ll have to just outline a few headlines and leave further analysis for either a second part or the comments section.
- A second migration from Beringia to North America and Greenland represented by the ancient Saqqaq sample (Paleoeskimo, from Greenland) harbouring an excess of DGC-related ancestry.
- A back migration of Native Americans to Siberia represented by Uelen and Ekven Neo-Eskimo sites (2.7-1.6 kya) that strongly resemble contemporary Inuit and could harbour some 30% Native American admixture
- The replacement of Ancient Paleosiberians by Neosiberians in most of Siberia. While they show that AP ancestry was still common by the Early Bronze Age, by the late Bronze Age it was largely restricted to NE Siberia, with populations that closely resemble contemporary Koryak and Itelmen.
Finally, there’s a linguistic discussion on the supplements that I think it’s quite an interesting read. I find that they have managed to get a good understanding of the genetic and archaeological data to try to correlate it with the linguistic hypothesis that exist so far. It’s an informed and balanced summary that doesn’t take any strong stance (which would be quite difficult to do knowing the region we’re dealing with). I think that maybe some of the references to Uralic or to macrofamilies might be already a bit outdated, but that’s not a big issue since they’re just mentioning what’s been hypothesized so far, and anyway it’s not the place or time to go into such issue. Overall, I think that it’s a necessary addition to any aDNA paper, much in line with what I wrote about in a recent post about it.[UPDATE 27th June 2019: the final version has been published already with an important correction about the issue discussed above:
For both Ancient Palaeo-Siberians and Native Americans, ANS-related ancestry is more closely related to Mal’ta than to the Yana individuals (Extended Data Fig. 3f), which rejects the hypothesis that the Yana lineage contributed directly to later Ancient Palaeo-Siberians or Native American groups.
Good news to see that part being addressed in the final version.]