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Saturday, January 17, 2015

Ancient Jomon people not like present-day East Asians


Here's an abstract about a couple of ancient Jomon genomes from the recent OIST Ancient DNA Symposium in Japan.

Hideaki Kanzawa-Kiriyama, Nuclear Genome Analysis of Ancient Japanese Archipelago Humans

The Jomon period, characterized by chord-marked potteries, lasted from ~16,000 to <3,000 years before present (YBP), and abundant human skeletal remains have been excavated from shell mounds and other sites throughout the Japanese Archipelago. However, their genetic origin and the relationships with modern populations are largely unknown. Here we determined 10% and 80% of the genomic DNA sequences from two Jomon individuals, excavated at Yugura cave site, Nagano, and Shitsukariabe cave site, Aomori, respectively, and compared their genome sequences with worldwide populations. We found a unique genetic position of the Jomon people who had diverged before the diversification of most of present-day East Eurasian populations including East Eurasian Islanders. This indicates that Jomon people were a basal population in East Eurasia and genetically isolated from other East Eurasians for long time. However, their genetic affinities to modern East Eurasians are uneven. The heterogeneity might be a hint to clarify human migration and gene flow in East Eurasia after the divergence of Jomon ancestors.

Hopefully the full paper and genomes are published soon. It'll be interesting to see how these Jomon individuals compare to Western European Hunter-Gatherers (WHG) like Loschbour and Ancient North Eurasians (ANE) like MA-1.

Update 17/01/2015: In fact, the author of this abstract analyzed a variety of Jomon samples, including the two mentioned above, as well as an Upper Paleolithic individual from Ryukyu, for his doctoral thesis back in 2013. The thesis is freely available here.

Update 09/02/2016: The paper is now available and open access at Human Genetics. See here: A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan

65 comments:

Chad Rohlfsen said...

Yeah, that one looked interesting! There's quite a few that I'm looking forward to on those links.

Chad Rohlfsen said...

From sources at Wiki:

Initial Jōmon, exhibits some of the highest densities known for foraging populations.[16] Genetic mapping studies by Cavalli-Sforza have shown a pattern of genetic expansion from the area of the Sea of Japan towards the rest of eastern Asia. This appears as the third principal component of genetic variation in Eurasia (after the "Great expansion" from the African continent, and a second expansion from the area of Northern Siberia), which suggests geographical expansion during the early Jōmon period.[17] These studies also suggest that the Jōmon demographic expansion may have reached America along a path following the Pacific coast.[18]

It would be interesting to see how the Jomon compare to the East Eurasian in Native Americans!

Tone said...

It would be very interesting indeed to see how Jomon compares to the East Eurasian in Native Americans.

Furthermore, I wish we could extract DNA from early first Americans like Kenewick Man. Just more religious/cultural hokum standing in the way of science.

Krefter said...

The Jomen samples are to east Asians what Loschbour and Stuttgart are to us. They're around 8,000 years old.

http://ci.nii.ac.jp/naid/130003363110/en/

" We found a unique genetic position of the Jomon people who had diverged before the diversification of most of present-day East Eurasian populations including East Eurasian Islanders. This indicates that Jomon people were a basal population in East Eurasia and genetically isolated from other East Eurasians for long time."

Does this mean all east Asians today are more related to each other than to Jomon people?

As people dive into ancient east Asian DNA like they did for European, I doubt they'll find as complicated of a story. East Asians don't have signs of something basal Eurasian-like and are distinct from MA-1. If they're mixed they're mixed with other east Asians.

ryukendo kendow said...

WOW!

This is absolutely incredible.

I've always wondered about the position of Ainus in the ENA clade, and wanted an ainu genome to be made open for the rest of us to analyse. A year ago--I think--we had data, but that was not released. But data from the jomon itself beats Ainu any day.

ADMIXTURE often detects something 'ainu' in Koreans and Northern Chinese. Wonder how that will play out.

@ Krefter
"who had diverged before the diversification of most of present-day East Eurasian populations including East Eurasian Islanders"

That seems to suggest that present-day East Eurasian, Southeast Asian and Pacific islanders form a clade to the exclusion of Ainu. AKA Ainu is outside of Dai in the (Papuan(ASI-Dai)) branching.

The really interesting thing to me is what relationship they will have with ASI and papuan. Probably no relationship. The other thing is uncovering whether the ENA in native Americans, Uralics and Altaics branched before Southeast Asian split from East Asian, or did the northern movements branch off after the Southeast Asians did, and whether or not any of the northern branches had anything to do with Ainu/Jomons.

Krefter said...

Ryuk,

Since when were Ainu, the same thing as people Jomon. Has this been confirmed?

Do you know how Andmanese, Papuan, Austrlians, and other isolated Asian pops relate to east Asians? Do southern Indians have ANE and near eastern-like ancestry?

ryukendo kendow said...

@ Krefter
No, they are by no means identical, but multiple lines of evidence, incl. ancient mtDNA and modern YDNA distribution, point to a connection, at least among most researchers currently. Archaeologically Ainus are seen to be a descendant of the fusion of the Okhotsk and Satsumon cultures, the latter of which descended from Jomon. The okhotsk culture might have ferried influences from paleosiberians, which mean that ainus are not unadmixed descendants of the Jomon.

The current model in both Rasmussen and Reich is Papuan(ASI(Dai)), where Papuan and Australian form a clade which also accounts for part of the ancestry of Philippine negritos, where Onge and most ancestry in Sundaland negritos and some ancestry of south Indians and a little ancestry in Southeast Asians form the ASI clade, and all the rest is part of the East Asian clade.

Krefter said...

Has anyone noticed a decent percent of Karitiana have a G allele in rs12913832?

It looks like some must have blue eyes because they have GG. This gives me more confidence in the ANE-western ancestry in native Americans, because no Han have a G allele. I think most Caucasoid facial features are mostly Neolithic near eastern derived, which is why native Americans look more east Asian than west Eurasian.

rs12913832 GG might have first arisen in the WHG-ANE branch.

Krefter said...

Here's the link. I'm not very confident in it.

https://genetiker.wordpress.com/2013/06/01/frequencies-for-blue-eyes-snp-rs12913832-in-hgdp-populations/

Krefter said...

"The current model in both Rasmussen and Reich is Papuan(ASI(Dai)), where Papuan and Australian form a clade which also accounts for part of the ancestry of Philippine negritos, where Onge and most ancestry in Sundaland negritos and some ancestry of south Indians and a little ancestry in Southeast Asians form the ASI clade, and all the rest is part of the East Asian clade."

So, southern Asians and native Australians are not in the east Asian branch with Han? And south Indians and other southern Asians are something Papuan-like+East Asian?

ryukendo kendow said...

South Asians have approx half ancestry from the Onge branch, which is closest to Han.

Papuans and Australian also have approx half ancestry from that clade, and half from a clade restricted to themselves and phillipine negrito.

Otherwise there is no connection except at the ENA level.

Krefter said...

Kenniwick man was Amerindian.

http://dienekes.blogspot.com/2015/01/kennewick-man-was-native-american.html

Chad Rohlfsen said...

Might not be so much..
http://www.washingtonpost.com/national/health-science/scientists-mysterious-kennewick-man-looked-polynesian-and-came-from-far-away/2014/08/25/45411b2a-27b3-11e4-86ca-6f03cbd15c1a_story.html

Davidski said...

Ancient DNA trumps anthropological reconstructions.

Chad Rohlfsen said...

They laid out more than just a facial reconstruction. He could be a little different than modern natives in the area.

Davidski said...

He probably had a higher level of ANE and lower level of East Asian ancestry compared to modern North Amerindians, like Anzick-1 did.

That's why Anzick-1 clusters with Central Amerindians, rather than North Amerindians. It seems that fresh waves of Siberian migrants entered the Americas after 10K YBP, bringing with them more East Asian admixture and less ANE.

Chad Rohlfsen said...

Maybe, maybe not. He likely originated much closer to the coast. Nw coastal natives are more East Eurasian. The ranges up the coast were a good barrier. Their morphology and culture are different than their neighbors. Preliminary results have him more like North American Natives. Jomon genomes could slightly change the picture.

Krefter said...

Davidski why did you change the title to "not like present-day East Asians". That's like saying K-14 is unlike modern Europeans. He had an extinct U2, an extinct C, but his relatives are the main ancestors of modern Europeans.

The Jomon clustered with East Asians, which is a start. They may be apart of an extinct east Asian lineage(except for those people in Japan Ryuk mentioned), but they do show present-day east Asian's ancestors were living somewhere in east Asia at that time.

Matt said...

Comparisons with the Sherpa population and their estimated high altitude ancestors would be interesting as well, since that population seems to form a "pole" in East Asia when it is included.

from http://www.nature.com/ncomms/2014/140210/ncomms4281/pdf/ncomms4281.pdf

Admixture facilitates genetic adaptations to high altitude in Tibet - C Jeong

http://i.imgur.com/wZFpuLr.png - PCA Eurasia+Africa

http://i.imgur.com/ALonsYi.jpg - PCA intra-East Asia

There is public data for the Sherpas from the above paper, unforunately only in the form of 2 100GB genome sequence samples http://www.ncbi.nlm.nih.gov/bioproject/PRJNA232645, not the 49 Sherpa and sundry Tibetans included in the study.

Chad Rohlfsen said...

The Japanese look significantly Jomon. Maybe that is why you get South Eurasian on them. Andaman/onge might be closer to the Jomon. I wonder if the authors would release the data.

http://www.nature.com/srep/2012/120405/srep00355/full/srep00355.html

Krefter said...

It looks like Jomon to Japanese is what WHG is to Europeans.

Chad Rohlfsen said...

I've sent a message to Eske, regarding the Kennewick man, as well as Yungang He, about the Jomon genomes from the study. Hopefully, we can have something to run through the calculators very soon.

Chad Rohlfsen said...

Let's hope that the Jomon aren't a jumbled mess, like Kostenki.

David,
Would you separate the Jomon part from any other East Eurasian components in a future run if it is clearly distinct? It would be interesting to see the spread of this component across Eurasia and the Americas.

Davidski said...

Sure, but there has to be a strong signal of the Jomon component in modern populations, like there is of ANE and WHG, otherwise I won't be able to pick it up.

ryukendo kendow said...

@ Chad
Thank you for that.

@ Matt
In one of the 'big' papers, I frustratingly cannot remember which one, an ADMIXTURE run shows a Tibet-centered component emerging in the Kusunda isolate in India and was present in successively lower levels in Tibetans, naxis and northern Han.

The paper you cited by Jeong models Tibetans as a mixture of Sherpas and a Han-like population.

If we can analyse the genomes, hopefully we might find signs of interesting pop struct. Maybe a relict population in Tibet assoc with Hap D, just like the Jomon? Hmm.

Grey said...

Cormac O'Mitsubishi

Chad Rohlfsen said...

Those k runs make it appear to be present across the board, but higher in the Japanese, then followed by other NE Asians. It would be interesting to see how East Eurasian behaves when it is split up. This could be useful in deciphering what the hell the South Asian component is.

Chad Rohlfsen said...

It could be useful in at least splitting up NE and SE Eurasian, then working to South Eurasian. A bit of a long process, like pulling ANE out of 100 pops, but it could lead to a breakthrough.

Krefter said...

"Sure, but there has to be a strong signal of the Jomon component in modern populations, like there is of ANE and WHG, otherwise I won't be able to pick it up."

Are east Asian pops less diverse than West Eurasian pops? Maybe if someone created an ADMIXTURE test only with east Asians a Jomon type component will pop up.

The title is still incorrect because Jomons were east Asians, and they contributed significant ancestry to modern Japanese.

These Jomon samples are 8,000 years old, and the fact they can differentiate Jomon from mainland east Asians, means the east Asian branch had already been diversifying by that time.

You can see the same distinct east Asian physical features in Siberians, Ameridians, Ryukyuans, Chinese, Finno-Urgics, Vietnamese, suggesting it was around in the Palaeolithic, and that light skin is older in east Asia than in west Eurasia.

The north European-type physical appearance must be the most recent example in human history of a radical change in physical appearance. The facial features are a mix of 3 different Mesolithic-Neolithic populations and the pigmentation became mainstream in the bronze age, and then spread to the Baltic, west Europe, and central Asia.

Chad Rohlfsen said...

It looks like the Jomon are about 3x the distance of the Japanese from the North Chinese. If we have a PCA of those two, we could figure out where the Jomon should plot.

Davidski said...

I'm leaving the title, because it seems from the abstract that the Jomon genomes represent a basal but also parallel (note the use of the word "unique" in the abstract) lineage to the main modern East Asian lineage, which has diversified into various sub-lineages during the last ~9,000 years.

And we don't know yet whether the Jomon lineage contributed significant ancestry to the modern Japanese. The abstract doesn't say.

What it says is that modern East Asians are unevenly related to this lineage, which suggests that they harbor varied amounts of admixture from it or closely related lineages. The Japanese, especially those of partly Ainu origin, probably do have more of it than other East Asians, but we don't know how much.

Chad Rohlfsen said...

The other paper I posted has given the possibility of 23% in mainlanders and up to 62% in Ryukyuans. This next paper should be quite interesting.

Matt said...

@ Ryukendo: If we can analyse the genomes, hopefully we might find signs of interesting pop struct. Maybe a relict population in Tibet assoc with Hap D, just like the Jomon? Hmm.

Apparently an archaeology paper linked up on Razib Khan's blog makes a pretty forceful case for non-permanent habitation of Tibet prior to agriculture (really prior to crops coming from both East and West). Yet there should have been some humans up there or where could the climatic adaptations come from? Sherpas don't seem any closer to West Eurasians on world PCA, unlike Northeast Asians who have shared ancestry with ANE.

@ Krefter: Unlike West Eurasia, it seems we don't really understand skin lightening in East Asians at the moment. The genes in Amerinds could be different from East Asians, Siberians / the main East Asian cluster that encompasses everyone else.

Siberians themselves seem more East Asian than whoever the proto-Amerind blend, so there might be some recent gene flow from China to them, bringing some new skin lightening genes, which are probably more likely after agriculture booms lead to more mutations, etc.

Ainu are supposed to fit lighter skin than others in Japan while Ryukyuans aren't, according to what studies there are, yet both seem likely to have a Jomon inheritance.

Re: genetic distance between East Asians, based on FST (which is a pretty good measure of differentiation with its own caveats), HGDP Japanese and Dai from Southern China are about as separated as HGDP Russians and Georgians. HGDP Cambodians and Japanese are about as separate as HGDP Russians and Bedouin (HGDP Kargopol Russian and Bedouin probably have a slice of 5% East Asian and 10% African ancestry respectively that plays a role in inflating their dissimilarity). Differentiation per distance may be lesser in Asia(?).

See the "by population" overall FST matrix from http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234374/ (in the supplement at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234374/bin/mmc1.pdf). This table shows FST of the Filipino population with others in addition - http://i.imgur.com/xQm2fkk.jpg.

(I have adjusted the labeling as the original was incorrectly labeled to show populations having non-zero FSTs with themselves. The original can be found via Google. Some of the small populations that aren't samples from large countries are probably composed of close relatives so FST doesn't work as well as a measure of differentiation.)

I think East Asia will prove to be different than West Eurasia in that it will be more of a genetically intermediate central population from China largely expanding towards the edges, which are all quite different from one another, less edge populations expanding towards the centre.

@Chad: The paper by Timothy Jinam et al, based on direct gene sampling of Ainu (as opposed to estimating contributions and then creating zombies from that) shows mainland Japanese as perhaps a quarter or third of the distance between China to Ainu.

If the Ainu themselves aren't 100% Jomon (either due to Northeast Asians or Japanese), more like 50% say, then it could be that the contribution to mainland Japanese falls more to 10-15% or so (which would make some sense with patterns in certain genes like alcohol dehydrogenases I think).

Matt said...

CR: Let's hope that the Jomon aren't a jumbled mess, like Kostenki.

As we find more samples, I think we may find MA-1 and Loschbour are closer to a jumble than K14.

IIRC K14 seems to violate the initial model from Lazaridis - IRC no further from Ust Ishim compared to WHG and ANE (from David's stats), at the same time as being further from ENA compared to WHG and ANE and the same distance from ENA as Stuttgart (from the paper). (and K14 is further from Stuttgart than Loschbour and MA1 are is, on top.)

That's a challenge for the idea that Basal Eurasian is an element moving into Stuttgart and pushing it away from UI and ENA and that WHG-ANE's greater similarity to ENA only comes from a lack of BE, as it seems to be possible to be as close to UI as WHG while being as far from ENA as Stuttgart.

So maybe integrating both UI and K14 into their models is part of what is adding some time into the new paper.

ryukendo kendow said...

@ Matt

"I think East Asia will prove to be different than West Eurasia in that it will be more of a genetically intermediate central population from China largely expanding towards the edges, which are all quite different from one another, less edge populations expanding towards the centre."

Agree largely.

It seems that SEA, incl. Vietnam, was non mongoloid until after the neolithic. In the Shang Dynasty sacrificial burials, crania with 'oceanic negroid' morphology were described by Chinese anthropologists. The Onge/ASI cluster in HUGO pan-Asian at low K is present all the way up to central China. And we know that Siberia was not ENA at first.

My own very speculative hypothesis is that an ASI-like pop moved north and diverged into East Asians, gaining cold-adaptions in the process, before 1) a wave that contributed to amerindians, then 2) a wave that contributed to Uralics and topped up ENA in Kets, then 3) a wave that contributed to altaics, branched off in that order. The remaining clusters in SEA and Pacific, incl. the Sinitic, Austroasiatic, Hmong-Mien, and Austronesian-Tai clusters seem to be a product of linguistic/agricultural expansions in neolithic and post-neolithic periods, so much more recent.

ryukendo kendow said...

@ Matt

I think some new aDNA discoveries will cause us to revise the tree, with new ghost populations or new introgressions. I think K14 cannot answer very many things though, we need more genomes so we have more resolution.

"no further from Ust Ishim compared to WHG and ANE (from David's stats), at the same time as being further from ENA compared to WHG and ANE..."

This is intriguing... it means that a model where K14 has some ancestry in Crown Eurasian that is not in ((WHG-ANE)(ENA)), and that this ancestry is only shared with Middle Easterns today, is going to fail. It also suggests that something in K14 exposes a difference between WHG+ANE+U-I on one hand, and ENA on the other... Where did you find it again?

David, did you do a D-stat for K14 between an ENA population and Ust-Ishim? e.g. Dai and U-I?

Matt said...

RK, I think David gave the D stats as follows, I have them from a document called "D-stats9" I downloaded when he was doing lots of D stats for K14 and UI in the wake of those papers. Not sure where the link is, David might be able to say where they are on his Google Drive:

Outgroup, Target, Pop1, Pop2, D-stat, Z-score
"MbutiPygmy Ust'-Ishim : Kostenki14 Loschbour 0.0004 0.055
MbutiPygmy Ust'-Ishim : Kostenki14 Dai 0.0006 0.096
Primate_Chimp Ust'-Ishim : Kostenki14 Loschbour 0.0032 0.389
Primate_Chimp Ust'-Ishim : Kostenki14 Dai 0.0043 0.635"

IUC these aren't statistically significant differences.

From the paper on UI itself (Fu 2014 - "Genome sequence of a 45,000-year-old modern human from western Siberia" - paper and SM available at http://genetics.med.harvard.edu/reich/Reich_Lab/Publications.html), we know that present day Europeans and Stuttgart have a lower relatedness to UI than East Asians or Loschbour, but no statistical difference between EA and Loschbour / MA1 in relatedness to UI.

At the same time from the paper on K14 (actually Seguin-Orlando 2014 [not Sikora as I wrongy said] (http://www.sciencemag.org/content/early/2014/11/05/science.aaa0114.abstract) we know that East Asian is no closer to K14 or Stuttgart and that K14 is further from East Asian compared to "HG" (Motala, Losch, MA-1, etc). See the statistics on the tree model - http://1.bp.blogspot.com/-jlF6eSOWmnk/VFwpvCk9MjI/AAAAAAAAJ1o/lkmfDp204OU/s1600/F2.large.jpg (graphic posted up on Dienekes blog).

So the statistics taken together, if they hold up, ultimately seem to show that K14 is as close to UI as HGs and East Asians while being only as close to East Asians as Stuttgart (while Stuttgart is further away from UI than the rest).

Davidski said...

I can't remember, but I think that both Ust'-Ishim and K14 are too old, and perhaps the latter too low coverage, to be informative about the population movements and mixing in West Eurasia during the early Neolithic and Chalcolithic.

And the main angle in the K14 paper about Basal Eurasian already being in Europe 36K years ago just seems a bit weird to me, especially since they didn't fit their model formally and didn't compare K14 to Ust'-Ishim.

ryukendo kendow said...

This is weird and difficult to interpret. I suspect David that you are right, and we are looking at weird stuff at the edge of significance.

Agree that the Middle Eastern sharing in K14 is not the same basal as that in Stuttgart. Or at least, that's not proven formally.

Matt said...

Yeah, I older genomes probably aren't going to add anything to Neolithic / post-Neolithic explanations of difference necessarily, but will tell us about how the ANE, WHG and EEF / ENF components formed in the Paleolithc / pre-Mesolithic, maybe in ways that violate the idea that ENA-(WHG/ANE) experienced a tree like split with no later admixture.

Mainly my comment was just in skeptical reaction to the idea that K14 is a jumble or mixed population that doesn't tell us anything about the formation of WHG-ANE, etc. It seems as likely to me at the moment that K14 is less admixed than WHG, ANE.

Krefter said...

Matt,

My point was that there are many genetically distant pops in east Asia who pretty much have the exact same physical appearance, meaning it's very old.

West Eurasians have a mix of WHG, BB, and ANE features, and there's more variation in their facial features as a result, while east Asians are much more uniform.

The lighting process in Europe, which changed the appearance, probably occurred much later than in east Asia to. Add to that the current genetic makeups(ANE into WHG/Near eastern( in west Asia and Europe formed in the bronze age.

Chad Rohlfsen said...

Matt,
I'm not saying that K-14 is admixed, but that I hope the Jomon genome doesn't pull ridiculous stuff like Kostenki did. I don't think that there is a pure WHG or ANE, or that EEF is simply a basal and WHG mix. I believe that it is a lot more complicated and only several genomes from the Near East, South Asia, Caucasus, and such, can clear it up.

Chad Rohlfsen said...

Personally, I hope that Eske does check out the Red Lady of Paviland and rechecks Kostenki. I think that it would be interesting just to create a calculator with Kostenki and Ust-Ishim as separate components, along with the other ones. Just to see what happens. Without a few dozen genomes ranging from 20-40kya, it will be hard to infer a whole lot.

Chad Rohlfsen said...

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&ved=0CDYQFjAE&url=http%3A%2F%2Fir.soken.ac.jp%2F%3Faction%3Drepository_uri%26item_id%3D4960%26file_id%3D19%26file_no%3D2&ei=CIO9VLeFO4OYyASv7oCgAw&usg=AFQjCNE9l1_7Z3jO3v28v_UJztOt2YVYTw&sig2=B6gIGkRtkOeHfNNSOazbPA

This should link to a PDF with a Jomon study in 2013. It includes PC plots and fst distances. Very, very interesting so far.

Chad Rohlfsen said...

"Compared to modern East Asian populations, the Tohoku and Hokkaido Jomon people
were genetically close to the Udegey of southern Siberia (Udegey and Tohoku Jomon, Fst =
0.088, P =0.01; Udegey and Hokkaido Jomon, Fst = 0.138, P =0.00) (Table 2.9). The Udegey is
also geographically closer to the Jomon populations than are the other southern Siberian
populations (Figure 2.1). In the phylogenetic network shown in Figure 2.3, based on shared
mtDNA haplogroups M7a and N9b (Table 2.5), it seems possible that the Udegey represents
admixture of southern Siberian populations and the northern (Hokkaido and Tohoku) Jomon
people. This implies some degree of gene flow between the Udegey people ancestors and the
northern Jomon. Moreover, as I mentioned earlier, haplogroup N9b and M7a2 are hardly
observed in the other East Asian populations except in the Japanese Archipelago (Table 2.7 and
2.8)"

Matt said...

Ah, yeah, OK. I agree I would definitely hope for a new genome that solved questions more than it raised as well (preferably)! That's a version of hoping the Jomon genomes are not jumbles I can get behind.

CR: I think that it would be interesting just to create a calculator with Kostenki and Ust-Ishim as separate components, along with the other ones.

It would be ideal, but so hard to do as estimating any contribution to any present day populations, which the calculator would then use to trigger components would be difficult, since any contributions UI or K14 did make to present day people seem tenuous at the moment.

With rechecking K14 and getting other UP samples, yes.

And maybe that pattern where K14 seems to be related to Ust-Ishim exactly like Loschbour and MA1 while being related to East Asians exactly like Stuttgart (in violation of our prior expectations for Basal Eurasian admixture) will resolve itself or is just a statistical issue (relating to SNP overlap or somesuch as David suggests). Food for thought at the moment.

Chad Rohlfsen said...

This has me wondering how close the Jomon are to Ust-Ishim.. that would be interesting!

Chad Rohlfsen said...

You guys have to check out that paper. It's full of great info!!

Chad Rohlfsen said...

The frequency of allele sharing with Sanganji Jomon is
relatively high in Northern and Southern East Eurasian ethnic minorities (such as Xibo, Tujia,
and Naxi), and is low in Han Chinese, She, and Dai (although the degree of differences are not
significant). Within Japanese populations, Ainu people retain Jomon component the most, and
Ryukyuan was second most.

Chad Rohlfsen said...

Last one here... you guys can read it. Tons of d-stats included!

"PCA shows that Sanganji Jomon was located in
between Cambodian and Yakut (Figure 3.8), and it looks like that Sanganji Jomons were the
admixed populations between Cambodian and Yakut. I think that it is artifact of PCA, because
Sanganji Jomons was outgroup of all modern East Eurasians in the phylogenetic tree.
Importantly, the phylogenetic relationship implies that modern genetic population structure in
East Eurasians was constructed after the divergence between the ancestors of Sanganji Jomon
and modern East Eurasians"

Chad Rohlfsen said...

If I am reading one of the tables correctly, the Ainu could be 71% Jomon.

Matt said...

Great find Chad. Thanks, I didn't know there had been any work on adna work on Jomon other than mtdna. I don't know about the quality of this sample but seems very interesting. Probably a preview of what we will find with the full paper in this post's title.

The PCA here seems to show the Jomon sample relatively central, I guess because it doesn't fit into poles of differentiation as defined by East Asians, Africans and Europeans as well as any of those 3? There seems like some differentiation between the Ainu samples and Sanganji Jomon that isn't the Ainu samples being on a cline from SJ to mainland Japanese, which is suggested here to be from gene flow from South Siberians.

Interesting comments are that D-stats seem to indicate SJ has higher levels of Denisovan ancestry ("Network analysis demonstrates that there was weak gene flow between Denisovan and Sanganji Jomon, and D-statistic analysis show the genetic contribution of Denisovan to Sanganji
Jomon at significant level. I observed same pattern in Japanese and Dai, but the Zrevision-score was
not significant in D-statistic analysis. However, Jinam et al. (unpublished) shows Ainu and
Japanese were significantly and genetically closer to Denisovan than Europeans."
).

Also "Interestingly, I observed splits of ((European, Native American) (Sanganji Jomon, East Eurasian)) (Figures 3.19, 3.20, 3.22, 3.23). D-statistic analysis also shows not significant but negative D-value in D(Africans, French; Native American, East Asians) (Table 3.10). This suggests two possibilities: one is the gene flow between Sanganji Jomon and East Eurasians after the first divergence from the ancestry of East Eurasian and Native Americans; another is the gene flow between Native American and European after the split between East Eurasian and Native Americans .... A draft genome of Siberian boy from 24,000 YBP suggests that western Eurasian genetic signatures in modern-day Native Americans derived not only from post-Columbian admixture, but also from a mixed ancestry of the First Americans (Raghavan et al., 2013). The position of Sanganji Jomon in Figure 3.19 and 3.20 seems to indicate no gene flow with Europeans. So, Sanganji Jomons were mostly genetically derived from Southeast Asia.". D-stats also don't seem to indicate any affinity to Europeans, unlike for NA.

One caveat is that the author seems concerned about contamination and post-mortem change, hopefully they're cracked that. "The genomic information of Sanganji Jomons was only 2% of total genome", so looks good for the larger samples mentioned in the forthcoming paper, especially if they can be cross checked.

Matt said...

Wow, actually there's a lot more to this than I thought on page 124 onwards. Really looks worth checking out Chad's link.

Chad Rohlfsen said...

It's probably just about as good as the paper that'll be coming. I'm enjoying it.

Chad Rohlfsen said...

Someone should write this guy and get the genomes. Holy shit... Is it the same guy that is putting out the new study???

Matt said...

Yep, Kanzawa-Kiriyama and it even includes the two samples in the upcoming paper in the analysis from p124 onwards.

Looking at the D-stats for the higher Jomon sample, Shikkariabe Jomon, it seems like:

- Shikkariabe Jomon is no closer to Papuan, French or Bedouin than Han is

- Shikkariabe Jomon is closer to French or Bedouin than Papuan is.

- Shikkariabe Jomon does not seem to have a closer relationship to Denisovan than other populations do.

The Denisovan link, at least more than other East Asians, seems found by a network analysis, not found by statistical comparisons very strongly. I get the impression Kanzawa-Kiriyama is trying to push that as far as it can go to not eliminate it. It seems far from clear.

Jomon doesn't seem much more than a very differentiated ENA group, but it's interesting that their affinities, to the extent they exist with present day East Eurasians, lie in both North and Southeast Asia. So perhaps something is moving in to China from the centre - makes me wonder more about whether anything interesting happened in China from Tibet early on.

There's a lot here though, lots of information - I imagine the new paper will be a lot more succinct in its organisation and key findings.

ryukendo kendow said...

@ Chad
Wow, thanks for this! Why hasn't this gotten more press??

Chad Rohlfsen said...

Is there anything in the numbers to go against them being an early break-away group, then contributing back into East Eurasians. Sort of a Basal East Eurasian, or similar to the hypothesis for Basal Eurasian?

ryukendo kendow said...

Hi guys, reviewing the paper quickly:

1) neighbour-joining suggests that Jomon splits off after papuan but before Karitiana.

2) Network analysis determines that jomon split off after papuan but cannot determine if jomon split off before or after karitiana.

3) PCA shows quite clearly that jomon are an outgroup to all east asian, and the dimension differentiating Dai from Yakut is not the same differentiating jomon from all east asian groups. However, PCA cannot determine if jomon split off before or after karitiana.

For some reason, they did not do a pca with East Asian, jomon and Karitiana but no papuans. This would inform the previous question.

4) Jomon appear to have more denisova than the average east asian, but this is difficult to detect, appearing only in sequencing data but not snp data. It appears that han have less denisova than japanese, dai, cambodian, papuan, or jomon.

The author proposes a first movement into both NE and SE Asia with Denisova, and a second expansion from NEAsia with little/no denisova. But Tianyuan has no denisova, implying some complex dynamics here.

5) Network analysis uncovers a weak signal of sharing between Tianyuan, french and Sardinian to the exclusion of ENA.

6) Japanese and ryukyuans are a mix of jomon and northern han. Ainu are a mix of Jomon and paleosiberians.

7) When PCA compresses variation, jomon is always close to east eurasians, but pca pushes jomon preferentially towards 1) the West Eurasian side of East Eurasian vs. the African side in a world plot, 2) Papuan vs. karitiana side in an ENA plot, and 3) Yakut vs. papuan in Oceanian + East Asian plot. 4) It does not choose sides between Yakut and Cambodian in a east-asian-only plot.

This suggests that jomon are 1) in the eurasian clade, and 3) in the ENA clade including Yakuts and excluding papuan, and 4) outside of the clade containing Yakut and Cambodian and influencing neither. It is impossible to tell however if 2) is because of the ANE in karitiana or not.

This would be so good for f-stats and D-stats!

Cantonese Taishanese said...

Chad Rohlfsen. I have never in my entire life saw a Japanese that look Jomon or even significantly Jomon.
I don't know about Okinawans but judging from their pictures their Jomon phenotypes is small to non-existant. The only Japanese/Okinawans that look they have some Jomon admixture are some celebrity and individual pictures but that's is extremely few, like 1 out of 1000. Not something you won't find in the public of Tokyo

The only ethnic group in Japan that still look partly Jomon are the Ainu although many don't look Jomon at all. So I seriously doubt there is any significant jomon DNA ancestry in Okinawans and Japanese.


I've seen many mix race who 3/4 Chinese and 1/4 white and still look much less East Asian than Japanese and Okinawans.

The Uyghurs of Xinjiang/East Turkistan are mixture of 30%-60% Caucasian. But their faces can look from typical Caucasian to Asian. Where as 99.99% of Japanese/Okinawans look almost no different to their neighbors

Cantonese Taishanese said...

Ryukendo kendow,

What you said don't make much sense to me. You say Ainu, Ryukuan, Japanese are all part Jomon?

What I don't understand is how can Ainu who are mixture of Jomon and Paleo-Siberian and still have 60% of their physical appearance look from Jomon to mix, and around 40% that look Paleo-Siberians.


While for Japanese and Ryukyuan who you claim to be mixture of Northern Han and Jomon have 99.99% of their population's physical appearance look like Northern Han or Korean and only like 0.001% like mix with Jomon???

Japanese that look part Jomom like Ken Hirai and Abe hiroshi is like 1 out of 1000 ( maybe even 100,000 ).
Of course I haven't seen every Japanese in the world but I also use google.

Now I'm not saying Japanese and Okinawans don't have Jomon ancestry, But if you guys do have it than it has to be small portion, not significant.

I'm just comparing. It doesn't make sense for Japanese/Okinawan to be hybrid and still be shorter and Skinner than Northern Han and Koreans. Although I will say you have bigger eyes but than I've seen much more Vietnamese with bigger eyes.

Having seen Uyghurs Turkic of Xinjiang ( aka East Turkistan ). I can confessed these people are definitely mix race looking from predominately Caucasian to the South to predominately Mongoloid to the North. You can find many that look straight up Caucasian like Afghan, European, Gypsy, Persian to more mix race looking, and some who look very Mongoloid.

35% look Caucasian, 50% mix race, 15% completely Mongoloid

However even the Kazakh ethnic minority of Xinjiang who Mongoloid with some Caucasian still look far more less East Asian than Japanese and Okinawans. 50 of them look Mongoloid and 50% of them look mixed

pokeanimal said...

@Ryuk

"The other thing is uncovering whether the ENA in native Americans, Uralics and Altaics branched before Southeast Asian split from East Asian, or did the northern movements branch off after the Southeast Asians did, and whether or not any of the northern branches had anything to do with Ainu/Jomons."

Based on Cavalli-Sforza's genetic distance maps, I'd put the SE Asian split before any divergence from NE Asians.

Large genetic distance between AmerIndians/Siberians and other NE Asians probably comes from ANE Caucasoid admixture, and even then SE Asians are far more divergent.

Cantonese Taishanese said...

Amerindians/Siberian have only little Caucasian admixture. Even African Americans have more Caucasian admixture than they do.

Anyway can anyone estimate the percentage of Ainu/jomon blood in Japanese and Okinawans? I'm guessing it's only 1-10%. Judging by the fact even 85% of Ainu today look totally East Asian.

Davidski said...

Jomon genomes haven't been published yet. But once they are it'll be possible to check how much Jomon ancestry present-day Japanese have.

Normandie Kent said...

No....that is what happens when the immigrant colonialist population thinks it owns the indigenous native populations ancestors remains, because anything before the 1700s has nothing to do the colonialist immigrants. So get over it.