The genomic formation of First American ancestors in East and Northeast Asia:
Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000-18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia.
Read the preprint. I’ll note three things
– The authors suggested that differentiation between American native lineages occurred in eastern Siberia, not Beringia. In other words, there’s a lot of ancient structure in the New World that dates to the Last Glacial Maximum
– Speaking of ancient structure, using the new methods in this paper they detect more pervasive “Australo-Melanesian” ancestry in lower quality ancient remains. It seems clear ta this point that this isn’t about Australo-Melanesian, as much as genetic variation in East Eurasia during the Pleistocene that we have a poor grasp of at this point
– In Europe ancient DNA quickly converged on the trihybrid model of Mesolithic hunter-gatherers, and early farmers, and steppe pastoralists. The tsunami of ancient DNA has fleshed out a lot of details, but the basic framework has been in place for five years. The situation in other parts of the world seems to be more unsettled and dynamic. More sophisticated models and more ancient DNA keeps returning surprise on the margin
Does this mean that the Austronesian ancestry David Reich talks about in the Amazonians isn’t likely from admixture with that some truly Austronesian group that was in the Americas or mixed before hand? Or is it something else?
it’s not austronesian. it’s australomelanesian
this doesn’t resolve the details of that. but it opens up more space of diverse admixture in siberia
At least it becomes possible to see where that ancestry might have come from, without invoking some implausible explanation.
Imagine all the ancient lineages which have disappeared, simply because they hadn’t been able to reach far-away places. The Native Americans, Ainu, Andamanese, Australomelanesians and Austronesians are all relicts of this ancient diversity which were preserved by virtue of geography. The missing links aren’t the ones in-between but the ones in the periphery. Fascinating stuff!
Impressively, the authors find a suggestive linguistic connection as well.
“Lexical remnants of a substrate language presumably spoken on the Denali territory before the Athabaskan radiation ca. 2000 – 3000 cal yr BP show similarity with the ChukotkoKamchatkan language family. This suggests that this substrate pre-Athabaskan language could be a member of the hypothetical Chukotko-Kamchatkan–Nivkh linguistic clade. There is also evidence for a distant relationship between the latter clade on the Asian side and Salishan and Algic language families in North America. Since the Nivkh speakers are prominent present-day representatives of the ARB gene pool, it is possible that these linguistic traces reflect the Pleistocene gene flow revealed in this study between the ARB cluster and Ancient Beringians.”
The Nivkh people are the closest modern descendants of the Amur River Basin (ARB) population believed to be one of the sources of ancestry for this 11,500 year old Beringian individual with 81% of their ancestry derived from the same source.
The macro-linguistic connections being made in this analysis seem far less fanciful and speculative than those of the Russian linguistic lumpers that don’t have genetics and archaeological narratives to back them up.
It seems like an interesting paper, I couldn’t follow the methods at a glance as got used to with for many of these papers, so must re-read fully, and the supplements, to understand.
There’s some interesting commentary by Flegentov on Davidski’s blog; he is talking about some questions about how the use the qpAdm and qpWave methods have developed in use, and thinks there are some issues with the array / SNPs sets used, potentially thrown off by lack of rare variants, biased gene conversions, etc. He’s referenced the Bergstrom 2020 whole genome HGDP paper which surprised me as I thought it mainly showed linear correlation of D-stats on whole genome or ascertained on archaics, with Human Origins array. Deviations mainly relating to African splits, mainly the former producing lower significance stats due to relatively fewer polymorphic sites and more fixed variation overall in modern humans. But could be that there is some more devil in the details when they look at specific non-African populations and test with adna.
Slightly disappointed no exhaustive D-stats actually published with paper showing the 12kya sample against all the very plentiful East Asian adna that’s come out this year, and present day Ulchi. Really no geneflow into this region? (Absolutely no Jomon / Nivkh / Yellow River / Boshan related?).
I still do wonder how much of the specific scenario they lay in Fig 4, where an early dispersal proto-NA East Asia population migrates into NE Siberia early in 36-25 kya and then experiences one way gene flow with Ancient North Siberians like Yana, and isolation for about 20 kya (see here for excerpt: https://imgur.com/a/9dhHKhq) really actually is or is going to be backed up by anything in adna…
Even their tree in Fig S21 that provides some basis for dates doesn’t really work with this, with split between the roughly 13-12kya sample being very shallow, and only happening 19kya (e.g. about 7kya before this sample is actually attested). E.g. https://imgur.com/a/BvUp4qt .
The East Asian ancestry in NA looks fairly shallowly divergent from Houtaomuga13-12kya (less divergent that present day SEA ancestry in their graph), not deeply divergent at 30kya?
Need samples between the time of early East Eurasians Tianyuan and Salkhit (40-36 kya) and earliest East Asian sample (the roughly 13-12kya sample above) to try and examine this. Working with perilously little directt adna for these questions atm.