A new paper came out today on ancient East Asian DNA. More precisely, this work focused on early and late Neolithic samples from China, especially the lower Yellow river basin (north-central China) and the Fujian in southeast China. A major result can be boiled down to the Admixturegraph to the right.
The first ancient DNA out of East Eurasia was that from Tianyuan cave near modern Beijing. As you can see that individual is basal to other ancient (and modern) East Asians. That is, it isn’t representative of the ancestors of modern East Asians. But, the Tianyuan individual was already closer to modern East Asians than West Eurasians. Since the Tianyuan individual is ~40,000 years old, that means the bifurcation between eastern and western Eurasian groups predates 40,000 years ago.
This is not a surprising result, as the bifurcations between various “eastern” Eurasian groups (e.g., the ancestors of the Andamanese and East Asians) date to close to 50,000 years ago. The separation from Western Eurasians had to have happened after ~55,000 years ago since that’s about when the common shared Neanderthal admixture occurred.
The graph also shows that some ancient West Eurasian ancestry did come into the ancestors of East Asians through Siberians. More precisely, the Paleo-Siberian populations (replaced more recently by Neo-Siberian groups) had some ancestry from Ancient North Eurasians, who themselves were ~70% West Eurasian in ancestry (the other ~30% being a deeply basal East Eurasian). These Paleo-Siberians contributed ancestry to many northern East Asian groups, and likely explain the affinity between these groups and the Mal’ta-related individuals.
Finally, most of the edges show the separations between northern and southern East Asians and differences between inland and coastal populations. Though there is a deep distinction between northern and southern groups, the paper makes it clear that there is gene flow between coastal groups. This may explain affinities between the Japanese and Koreans, and peoples in southern China.
In terms of broad dynamics, one pattern that is evident, and repeats what we see all across Eurasia, is that the more recent periods seem to have undergone some level of panmixia. Ancient samples from northern and southern China are well differentiated, with pairwise Fst of around 0.04. Modern individuals sampled from these regions are closer to 0.02. Part of this is due to a significant expansion of “northern” ancestry at the expense of “southern”. But there is also some flow northward of “southern” ancestry. Though not highlighted in this paper because they lacked the samples, the movement throughout the Chinese Empire over the last 2,000 years is surely mediating this. In instances of famine or war resulting in depopulation in a province, the Chinese central authorities routinely encouraged migration from overpopulated provinces (modern Sichuan was repopulated from Hunan after a series of wars during the Ming-Qing transition). After 800 AD the demographic center China was in the Yangzi river valley, and south.
Unsurprisingly, the authors find that the southern samples from Fujian seem most similar to Austronesians. Today no one from these regions is “pure” southern. Rather, they are a mix. The Austronesians migrated out early enough that they carry southern East Asian ancestry exclusively. This recapitulates a common phenomenon where the ancestral “homeland” of a given group changes over time, reducing the ability to infer origins (e.g., the percentage of “Middle Eastern” ancestry in Southern Europe was underestimated because Anatolian farmers were partially replaced in Anatolia by migrants from the east).
There are also details in the supplements which confirm earlier inferences. For example, the Tianyuan individual has affinities with the Goyet Aurginacian sample from Belgium which dates to 35,000 years ago. But other East Asians do not. This seems to imply that Tianyuan was much more closely connected to a population that had trans-Eurasian affinities (another possibility is ancient structure, but the bifurcation between eastern and western Eurasian populations was more than 15,000 years before the time of Goyet so I am skeptical). Additionally, they also detect possible gene flow into Mesolithic Europeans from a population with East Asian ancestry (one possibility here that doesn’t seem to be explored is shared Ancient North Eurasian ancestry into both groups).
What is the overall takeaway? I think this confirms the other early papers that East Asia exhibits more continuity with its past that Europe and South Asian, rather like West Asia. While Europeans and South Asians have substantial ancestry from profoundly intrusive groups during the Holocene, the Han Chinese are in many ways “sons of the soil.” They did to some extent marginalize and absorb many other peoples in the modern area of “China proper”, and are themselves as a compound of two ancestral streams, but at the end of the last Ice Age, more than 90% of their ancestors were living within the boundaries of China proper.
More generally, modern imperial polities are exactly what some of their critics accuse of them of being: panmixia machines. Pre-state people were more genetically differentiated across local spatial scales. This seems the case everywhere there are good transects.
Related: The Deep Origins Of East Eurasians.
“Additionally, they also detect possible gene flow into Mesolithic Europeans from a population with East Asian ancestry (one possibility here that doesn’t seem to be explored is shared Ancient North Eurasian ancestry into both groups).”
Interesting, which part of the paper are you referring to?
Razib: But there is also some flow northward of “southern” ancestry. Though not highlighted in this paper because they lacked the samples, the movement throughout the Chinese Empire over the last 2,000 years is surely mediating this.
Yes… That’s a solid point (and I think something the authors’ may be alluding to).
Though I’d add to consider the Damgaard et al “Xiongnu”. Of those “Xiongnu” which are East Asian. There are these two Xiongnu samples, DA43 and DA45, who basically cluster with present-day Northern Han Chinese, at least in the Eurogenes Global 25. There’s also one, DA39 who clusters with Daur and Hezhen.
Interestingly, DA43 and DA45 come from this Omnogobi site that’s basically a mass grave, while DA39 actually comes from a formal burial.
Anyway, DA43 and DA45 are from 100 BCE. Their genetic structure suggests to me that either they were Han who joined the Xiongnu, or perhaps were Han soldiers who just ended up in a mass grave. But either way, Northern Han Chinese like people seem to have been present at around 100 BCE, before the last 2000 years.
So it seems to me it can’t be too much that early neolithic Northern Boshan like people were still about at this time, and then the Chinese Empire changed that. Rather genetic exchange must have already happened quite a bit.
The neolithic sequence in the north ends at 6000BCE, while in the south in continues to 2000BCE! So we can’t really know if anything happened through the subsequent period.
…
On this topic, under their modelling in supplement page 47, the following proportions for pooled Han: Boshan 0.38, Kolyma 0.15, Liangdao 0.47.
Boshan = Early Neolithic Northern East Asian 6000BCE, Kolyma = Mesolithic/Neolithic NE Siberian 8000BCE, Liangdao = Early Neolithic Southern East Asian 6000BCE.
So Han seem about equally derived overall from the Southern and Northern Neolithic East Asian populations.
(Maybe slightly less specifically from Yellow River people than the coastal south, due to the influence of the steppes?).
This varies per province from 23% Boshan related in Chongqing to 60% in Shangdong.
Their modelling might need a sense check with some other methods, as they are trying to distinguish between groups that don’t have many outgroups. But the strategy of using in qpAdm a mix of previous adna that has some differential affinities within East Asia, and some of their early Neolithic samples here, makes sense to me. (Notwithstanding questions generally about modelling modern people with ancients in qpAdm!)
If accurate, suggests that the coastal Southern East Asian Neolithic may be one of the more successful (most successful?) demographic expansions in human pre-history. About half the ancestry of Han Chinese + most of ancestry of Mainland South East Asia + most of ancestry of Austronesian expansions.
Note that the Liangdao and Qihe crania were classified on the basis of craniometry here (https://www.nature.com/articles/s41598-018-35426-z) as being “first layer” Hoabhinian like East Eurasians, but here they are really more part of this “second layer” genetically. Liangdao is the population that contributes about 27-66% of Han ancestry, depending on province. So that suggests that even where crania are good for telling if a distinctive people moves in, there’s still a lot of potential for mis-classification of higher level affinities. It may be that previous analyses were a bit too “eager” to find a fit that placed these with the Hoabinhians from SE Asia, and it may be that re-analysis finds that actually they should have been clustered with their closer genetic kin instead.
(As the authors note – “In a principal component analysis (PCA) including ancient and present-day Asians (14), all Neolithic East Asians cluster with populations of East Asian an-cestry (Fig. 1C and fig. S1), who include present-day East Asians and Neolithic Asians from Siberia, Tibet, Southeast Asia, and the Southwest Pacific who possess primarily East Asian-related ancestry (8–10, 21). Notably, this includes Early Neolithic southern East Asians (Qihe, Liangdao), who possess cranial morphology that clustered with ‘early Asians’ “).
Massive accomplishment of a paper.
Paper: “A test of genetic differentiation (Fst) shows that coastal Neolithic northern East Asians and coastalNeolithic southern East Asians are more highly differentiated from each other (Fst=0.042, sd=0.004) “
Comparing differentiation with a couple of European populations at about 4000 BCE; Piedmont_Steppe_Eneolithic (which is Yamnaya without a bit of 15% extra EEF ancestry that Yamnaya at 3000 BCE has) has Fst of 0.06 with Iberian and Polish Middle Neolithic farmers. So a bit higher in Europe (between the populations that were living in Europe and then went on to form the main ancestry of Europeans).
Differentiation of Piedmont_Eneolithic with the Anatolian Barcin_farmers from 6600BCE, who had none of the Euro HG ancestry that the MN have, is also approximately 0.06.
The Piedmont Steppe samples are about 4000 BCE, but Davidski suggests that some unpublished samples like them from Northern Black Sea coast are about at 5000 BCE, which makes a pretty apples to apples comparison with the early Neolithic samples in this paper.
The ChinaMAP analytics of deep whole genome sequences in 10,588 individuals
https://www.nature.com/articles/s41422-020-0322-9
This study shows northern Han and Japanese in one group, Manchurian as close relatives.
I have a question about the eastern affinity in mesolithic Europeans. Was it present in all of them or in specific subgroups? There were 3 main subgroups : WHGs that weren’t on a known cline (grotta continenza, sicily); WHGs that formed a cline toward ANE (Villabruna had very little ANE while EHGs would an example of the other extreme end and in between there would be east and southeast European HGs); and WHGs that formed a cline with Aurignacians (El Miron, Goyet Q2 would be examples with a lot of this Aurignacian ancestry, while later examples like La Brana would have a much smaller Aurignacian component).
Did all of these WHGs have the eastern affinity or was it only certain subgroups?
Another quick comment continuing on theme from above post.
There is actually more adna from North China after the EN that’s in this paper, of course – Wang’s preprint with the Wuzhuanguoliang samples from 3000 BCE (https://www.biorxiv.org/content/10.1101/2020.03.25.004606v1).
That’s about 5000 ybp, 3000 years later than the EN coastal Northern Neolithic samples here.
They found “Specifically, we can model almost all present-day Han Chinese as mixtures of two ancestral populations, in a variety of proportions, with 77-93% related to Neolithic Wuzhuangguoliang from the Yellow River basin”.
How to integrate that with proportions of 27-66% Liangdao2 ancestry in present day Han Chinese in Melinda Yang’s paper? We could just say that the data in Wang’s paper is weird exome capture stuff and may be an artefact of sequencing method, and Yang’s paper uses more “normal, standard” capture (I think?) so is more informative, and we should just pass over the Wuzhuangguoliang for now. But that’s a less approach interesting.
Assuming both are true, we might reconcile it by Wuzhuangguoliang Yellow River population already having 20% Liangdao2 related ancestry?
A full transect will help to understand how much what happened in China was a model of pulses, vs just slow but stable exchanges of fairly low numbers of migrants over the centuries, well before recorded history.
@DaThing
As per David Reich and Mark Lipson, all contemporary West Eurasian populations have substantial ENA admixture (with the possible exception of Bedouins and similar Near Easterners).
A few years ago, I had a discussion with them (over email) concerning their paper on the deep phylogeny of Eurasian “lineages”.
This one:
https://academic.oup.com/mbe/article/34/4/889/2838774
“… these signals in fact appear to reflect shared drift between a subset of western Eurasian hunter-gatherers (including MA1 and Mesolithic Europeans such as Loschbour) and East Asians.”
“We also repeated the computation with other western Eurasian populations in place of MA1 and found the same signal of eastern Eurasian relatedness, including the same preferred directionality, in WHG (defined as in table 2; Z = 2.04 for the difference), Caucasus hunter-gatherers (CHG; Jones et al. 2015; Z = 1.77), and Afontova Gora 3 (AG3, a ∼17 kya individual from Siberia closely related to MA1; Fu et al. 2016; Z = 2.17).”
“Lastly, we also briefly studied two other ancient European lineages. First, we built a version of our model with WHG in place of MA1 and found that it fit in a similar fashion (majority component of WHG’s ancestry as a sister group to K14, plus eastern Eurasian gene flow).”
Basically, if “ANE” populations had ENA admixture, then so did Mesolithic Europeans.
For whatever reason though, the influx of ENA admixture into WHG seems to be glossed over in the online discussions, while we see a focus on the ANE. Maybe because with ANE, we’re dealing with Siberia, so just easier to imagine them as ENA-admixed?
Anyway, an interesting nugget with regard to contemporary West Eurasians:
“… we did build an extended graph with French added (25 individuals). A good fit was obtained with four ancestry components, related to western (K14), northern (near the base of the MA1 lineage), and eastern (specified as the same source as for MA1) Eurasians, plus Basal Eurasian (specified without Neanderthal introgression; Lazaridis et al. 2016). The inferred proportions were 27.7%, 34.9%, 23.2%, and 14.2%, respectively, with essentially no change in the list of residuals.”
In terms of deep ancestry, even contemporary Western Europeans can be modelled as 25% ENA! More than MA1.
This post seems as good a place as any to note the recent discoveries being made at the Shimao site from ca. 2000 BCE in Northern Shaanxi, China. They reveal more advanced architecture and more trade and exchange with West Eurasia than was expected to exist at that time, and suggest that Chinese civilization may have had origins removed from the Central Plains where Chinese civilization is widely assumed to have arisen.
“As Ralph E. Turner puts it, “almost nothing is known about Chinese architecture before the age of Qin (3rd c BC),” because dominant building materials had been rammed earth &timber. But at Shimao, we see a stone city with monumental structures which look like stepped pyramids. Shimao reveals a lost culture that seemed to have the most advanced building & manufacturing techniques of the time, highly sophisticated ritual & artistic activities. However, it is located far away from the Central Plains where Chinese civilization has been assumed to emerge. Such stone construction & carvings… had no parallel in any parts of China, but recall those produced by Indo-European Kurgan culture…. In fact, the city is on the eastern edge of Eurasian steppe, which served as a highway between East Asia & Europe in the ancient times. While the terracotta soldiers suggest contacts between China & the rest of Eurasian world at the beginning of the imperial age, the Shimao city might show such contacts already started at the very beginning of Chinese civilization.”
https://languagelog.ldc.upenn.edu/nll/?p=47047
Related, author of this paper Melinda Yang and some colleagues published this month a paper on Japan –
https://www.researchgate.net/publication/341159838_Japan_considered_from_the_hypothesis_of_farmerlanguage_spread
Looks to have some reference to samples in the paper under the post.
Interesting, which part of the paper are you referring to?
look in the supplements
re: when ENA ancestry. the villabruna culture has it. 15K BP and after. the pre-villabruna don’t. except for goyet
@Razib Khan
Yes, found it. thank you. But that was known for some time now.
@Matt
“On this topic, under their modelling in supplement page 47, the following proportions for pooled Han: Boshan 0.38, Kolyma 0.15, Liangdao 0.47.”
I think their use of Kolyma in that model is eating away some of the Boshan component.
@James, yeah it probably does that… but if that’s the 3-way model that fits best, that’s what fits I guess.
Their qpGraph with a 2-way model between Coastal nEastAsia:Coastal sEastAsia fits at 60:40 though, less than 50:50, but pretty close. If you applied that to the province spread of ancestries, you’d get max nEastAsia (Boshan) at 77:23 Shandong and minimum in Chongqing at 44:66.
I guess Kolyma provides a better fit in part because you can get what would be 4% ANE into Han (29% in Kolyma, 15% Kolyma in Han), which Boshan doesn’t provide.
Possibly that could’ve come more directly than via Kolyma though. Maybe one of the “West Siberian” / ANE rich “Central Steppe” populations who are still about in the BA interacted with an ancestral North Chinese population directly or something, which might allow for a bit more Boshan? E.g. Han could be doable as 50:10:40 Boshan:Okunevo:Liangdao2, or something like this. It might make more sense to have an “early” post EN edge of ANE here.
Or else its due to divergence in East Asian related ancestries (needs something N East Asian related, but not Boshan).
@Matt
Southern Han having West Eurasian is a first though. I understand that some North Siberian-type was needed,but a very unexpected conclusion.
I don’t know how the presence of West Eurasian ancestry in Han also affects the estimation of their southern ancestry. Might have no impact but might also increase it in qpAdm I think.
“you’d get max nEastAsia (Boshan) at 77:23 Shandong and minimum in Chongqing at 44:66”
That sounds quite realistic to me, but then again I am no expert.
@James, sometimes these things show up a bit more once there are more exact references to cross-check against; I guess I am speculating here about why their model required Kolyma, there may be some more explanation in the paper somewhere. (I should have put 44:56 for Chongqing btw!)
@Matt
Only future papers will tell. For example, their conclusions differed a bit from Wang et al (2020) as you mentioned.
@James, yeah, though I think more should be possible even with just these data if bloggers and researchers in the scientific community are able to access them and really work at squeezing out what are possible models and why particular models fail and succeed.
Really, I’m happy that this paper indicates that there is at least some possibility of ongoing collaboration between Chinese researchers and Reich’s group, involving samples from within the present-day boundaries of PRC.
Wang’s 2020 paper seemed to be a sign of this kind of forbidding possibility that we would only be seeing data which was closed access / in different sampling methods from what the main players in adna use. Methods which could present confounds / incompatibility in modelling. This presents some possibilities that samples will build up over time in a more useful way and that the researchers in Wang’s may have been following a comparative advantage by sampling as they did. (We will not end up in this farcical situation with very deep time transects in everywhere the rings the PRC – Taiwan, Mongolia, Japan, Vietnam – and then a complete lacuna in PRC, which covers the territories which are kind of at the core of all of this.)
Though, I do have to admit to having some bias towards those qpAdm models (where Han have only a substantial minority or slim majority of early Northern Chinese coastal neolithic ancestry).
Firstly and most basically, because if true they remove a lot of the kind of idea where China was presented as a possibility that the early ideas of Cavalli-Sforza and Renfrew, severely moderated elsewhere by ancient dna, actually still applied *somewhere*.
Those were models where you notionally just had this sort of “demographic steamroller” of the earliest regions to develop agriculture sending out this wave of advance that stomped flat everything that came before it. Then lesser waves that spread out from that same region. Without any real turnover or reflux *within* the region of origin.
So I prefer the models here that indicate North China was more normal and consistent with what we know from other regions, where the regions which first farmed have themselves seen lots of turnover, and there is lots of reflux of other ancestry (even turnover *within* the Near East). No “For China, it was different…”
Secondly, having an impression of China as more multi-regional within itself (with lots of ancestry from the south moving into the north well before the Chinese Empire, and well before the earliest Chinese Dynasties, and with some potential ancestry from Siberia moving into North China as well) also fits more with some of my conjectures that de-centre the North China Plain / Yellow River as an inherently special region that advanced particularly quickly on its own and sent out waves of migrants.
Seems to instead add more plausibility to sort of ideas I have more sympathy with, where the Yellow River region was actually not so special in early epochs, but contact with wider Eurasian civilization, perhaps via sites like Shimao (which Andrew mentions), was crucial in the 3rd and 2nd millennium BCE, and this later prefigures larger cultural differences emerging in emergence of civilization in North China in the 1st millennium BCE. That is, where the origin and expanse of Chinese civilization is more plausibly due to connections with the rest of Eurasia, which emerged after the initial neolithic, less due to a pre-existing, invariable specialness of the Yellow River region. No, “Ex Borealis Lux in East Asia, even since the early Neolithic”.
So I have a slight bias towards those models for those reasons. But whatever the most accurate models will be, they’ll be.
I’m a little bit confused when it comes to the Jomon. McColl et al. (2018) suggest that the Jomon shares a special relationship with the Hòabìnhians, but this new study rejects that hypothesis and instead purposes that the Jomon do share a special relationship with coastal neolithic southern East Asians…can anyone enlight me when regarding this contradiction???
@Roberto, I don’t really know why McColl came up with that tree topology. In this paper, they find that the f4 and f3 statistics connecting G1 (Hoabinhian) to the Iwakazu Jomon are generally non-significant for other ancient and modern East Asian groups, with the exception of the Northern Mongolic/Tungusic groups who have some Ancient North / West Eurasian ancestry, and the Tibetan+Sherpa who have their own thing that’s basal to the East Eurasian clade (both of which make them less close in f4 to G1).
I’ve collected these here: https://imgur.com/a/i5z9Imd
It seems reasonable to me that there’s no special connection with Jomon to Hoabinhian.
Yang’s new paper on Japan I’ve put in comments upthread has another Fig 2 displaying the f4(Mbuti, Hoabinhian; Ikawazu Jōmon, East Asians) and some more discussion of issue.
Anyone have any guesses about how the Coastal East Asian-Jomon relationship will resolve?
I’d guess two poles of options:
A) Geneflow into Jomon from coastal EA’s ancestral pops (one of them, as they likely are composites themselves, probably not evolving as a single population since early UP). No geneflow into coastal EA groups from groups that form a clade with main trunk of Jomon ancestors.
B) Epi-Jomon groups that form an ancient clade with Jomon once diverse in coastal East Asia, then fused with Inner East Asian related groups to form the composite Coastal Neolithic groups. No geneflow into Jomon from Coastal N ancestors following split of epi-Jomon ancestry.
Probably both scenarios happened to some degree; hopefully Upper Palaeolithic adna will sort it out. The Neolithic adna boundary has been broken, if we are lucky UP will soon as well.
http://www.asahi.com/sp/ajw/articles/AJ201908160051.html – news article from mid 2019 on a adna study by Shinoda (referenced in Yang’s recent paper on Japan above), which finds admixed Jomon related individual from Yahoo period in Japan.
@Sein
Do you really think WHG had ENA and modern Western Europeans can be modeled as 25%+ ENA?
@ Matt
Out of curiosity, do you have any opinion of what the ENA side of Yana might be most closely related to? I believe in the original Yana paper the ENA ancestry was said to be even more basal than Tianyuan, and I don’t think Yana had more affinity with any particular Asian population over another.
@Mick, no, sorry, I don’t really have a strong opinion on it.
Will say, I do think it’ll be difficult to pin it on any extent East Eurasian group, because there was probably a lot of initial branching of ENA that were subsequently replaced that we can only really see fairly dimly (if at all).
That would make it likely that we probably don’t have a good proxy for any branch that contributed to Yana. Like you say, quite probably not any more affinity particularly with any extent group, strongly, that is easy to detect.
Quick illustration of one reason why I think that (lots of branching and turnover), cross-plot of difference in outgroup Mbuti f3 stat against Ust-Ishim for X: Kostenki14, Y: Tianyuan – https://imgur.com/a/XK8FyOw
(That’s effectively more or less equivalent to plotting X: f4(Mbuti,X;Ust-Ishim,Kostenki14), Y: f4(Mbuti,X;Ust-Ishim,Tianyuan), but I don’t have those to hand).
Effectively that should give a rough measure of continuity between Kostenki14 and Tianyuan (earliest Upper Paleolithic specimins with some continuity with present day people, K14 about 3k later) and subsequent populations that mostly cancels for Basal Eurasian effect (not entirely, as BEu will still make a pop tend to 0, but mostly). Taking advantage that Ust Ishim almost trifurcates with the early East and West Eurasian split.
You can see that plotted this way, the sharing with Tianyuan in present day North East Asia is not really higher than in present day Northern Europe with Kostenki14, if mostly removing (as much as possible) the Basal Eurasian effect.
The sharing with Tianyuan is also fairly low in Han and North East Asia, compared to the continuity between late Upper Paleolithic HGs in Europe, and Kostenki14, which are in turn lower than earlier UP specimins like Vestonice16 and Sunghir.
That suggests to me that to there was probably a *lot* of turnover, and a lot of initial branching. (Additionally, I think is this backed by high uniparental diversity)
Hopefully that Salkhit genome from slightly later than Tianyuan will throw more light on this. (Shouldn’t be too long, tweets about this: https://twitter.com/jjhublin/status/1174979389026553857, https://twitter.com/AmandaGHenry/status/1174985030361374720, https://twitter.com/ZCofran/status/1174977833904427011)
@Matt
“Really, I’m happy that this paper indicates that there is at least some possibility of ongoing collaboration between Chinese researchers and Reich’s group, involving samples from within the present-day boundaries of PRC.”
Yes, certainly agree here. Though I am not too convinced about the current qpAdm models,I still feel they underestimated the northern ancestry (which might not really be from a Boshan-like population anyways). In any case, I would not be surprised if their models turn out to be quite accurate either.
Re: Jomon, both scenarios seem plausible to me, but I think b is more likely. There almost certainly is a deep connection Jomon-coastal Neolithic. You have Y haplogroup D present in the northern coastal neolithic area as well.
@James, yeah, I’m still not really sure about the models with Kolyma Meso, as there really seems to be no very obvious cline evident in f-stats within Han->SE Asia in affinity to ANE groups (Afontova-Gora3, Yana_UP, MA-1).
I think that is very likely as well re; Jomon relationships, and these distributions of haplogroup D are connected with what is described here as early East Asian ancestry that does not seem to be equated wih Hoabinhians (and Tibet also is what we think about when we think about this).
Actually on the topic of early East Asian ancestry, I wonder if this paper changes our broader view of where the main trunk of East Asian ancestry is likely to have evolved.
We had the paper of Yana Upper Paleolithic by Sikora which suggested that at 32kya, Northeast Siberia was inhabited by these ANE groups, and then the paper estimates that “20 and 11 kya, the ANS population was largely replaced by peoples with ancestry related to present-day East Asians, giving rise to ancestral Native Americans and “Ancient Paleosiberians” (AP), represented by a 9.8 kya skeleton from Kolyma River”, and also the expansions into the Americas at probably 16kya(?).
That was somewhat surprising to some folks who’d thought that the main trunk of East Asian ancestry was probably evolving in NE Siberia since 45kya or something like this (1/2 to 1/3 the time depth), and instead it seemed to have come from somewhere else.
But when it came to where East Asian ancestry was still evolving, there was still an idea that this must be fairly far north, if not as far as NE Siberia. This because South China was presumed to have been inhabited by these Hoabinhian related hunter-gatherer groups, really until quite late in the Neolithic even, until East Asian like ancestry was thought to come in along with Neolithic food producing technology.
This paper seems to be indicate that, at least by around 8kya, there were hunting and gathering groups in South China who were pretty genetically East Asian, and who lacked any signal of relatedness to Hoabinhians.
I’d add to this that when I look at the f3 statistics, the population structure in South China (among samples that seem to have no affinity to Hoabinhians) seems to be relatively diverse – Qihe has lower outgroup f3 with the Liangdao samples than the North East Asia Coastal Neolithic have with each other, or which NEACN have with the North East Asia Inland Neolithic sample, Yumin. So the centre of diversity among phylogenetically East Asian ancient populations *may* have been in the south.
Both of these would add weight to ideas that East Asian ancestors may have been evolving across a lot of different environments in East Asia, including South China.
There could be some other explanations for those patterns though. Taking adna into the LGM era will help to sort this stuff out, I reckon.
(One probably final comment is that with this paper, finding of more alleles relating to adaptation to fatty acids in seafood, in South China compared to North, makes more sense, if some ancestry actually coming from southern coastal groups with relatively large of such component in diet.)
@Matt
” there really seems to be no very obvious cline evident in f-stats within Han->SE Asia in affinity to ANE groups (Afontova-Gora3, Yana_UP, MA-1).”
Yes, looking through past papers, I don’t see this ANE affinity in Han relative to other East Asians. Tibetans on the other hand, should have some low West Eurasian ancestry that this paper did not consider.
“Actually on the topic of early East Asian ancestry, I wonder if this paper changes our broader view of where the main trunk of East Asian ancestry is likely to have evolved.”
In my opinion, given the presence of Hoabinhian/Onge groups in the south and ANE-heavy groups in the north, the main trunk of East Asian was probably located in the (south)west. I think more samples from Tibet and Western China would be really useful to resolve this.
“in South China compared to North, makes more sense, if some ancestry actually coming from southern coastal groups with relatively large of such component in diet”
Yes, I agree.
Apparently there are some other papers published recently relating to North China from Jilin University & Max Planck:
http://kns.cnki.net/kcms/detail/detail.aspx?doi=10.16143/j.cnki.1001-9928.2019.04.004 – title translates – “DNA Analysis of Ancient Residents of Longshan Period in Wadian Ruins of Yuzhou, Henan”
https://kns.cnki.net/kcms/detail/detail.aspx?filename=1019162097.nh&dbcode=CMFD&dbname=CMFDTEMP&v= – title translates – “Study on the Genomics of the Ancient Population from Yangshao to Longshan in Central Plains”
Apparently this suggest that Longshan population (3000 – 1900 BCE) had more southern ancestry than Yangshao population (5000 BC – 3000 BCE), which would be consistent with results here, suggesting ongoing between northern and southern pools admixture.
Another paper today finds the earliest individual in Eastern Eurasia to show a similar blend of ANE+East Asian related ancestry to Native Americans, at Lake Baikal (site on the border of Mongolia and Russia today) – https://www.cell.com/cell/pdf/S0092-8674(20)30502-X.pdf. This is 14kya (12000 BCE).
Their graphical abstract here suggests that they view that as the result of migration from Eastern Asian ancestry from Amur region and ANE Mal’ta boy (Baikal) / AfontovaGora (Altai) ancestry, meeting in North Siberia, then back-migrating down to Baikal.
I wonder if it wouldn’t be simpler to have the migration just be from directly to the south to Baikal, possibly from a more inland location, and then on from there.
Their graphical abstract seems to show increasing amounts of Native American like ancestry (e.g. ANE) over time in the Baikal region, since the initial neolithic, following it being reduced at the initial neolithic period (after their UP sample).
How much ANE did that Baikal population have?
Also how far spread were the ANS people?
I guess that the Kolyma ancestry in present-day Han in qpAdm is likely due to the Okunevo_EMBA, which possibly has some Kolyma-related ancestry.