Population admixture structure and demographic history of North East Asians

[MNOPSC1b]

Ok, back to topic.

After long periods of thinking back and forth, I think I have a quite good grasp of how the population movements might have been in East Asia for the past 40,000 years.

So 40,000 years ago, there were at least 3 distinct East Eurasian populations inhabiting East Asia. How they arrived at East Asia though is anyone's guess, they could have taken either a northern route or a southern route, we don't have enough evidence for what happened before 40,000 years ago, so I will leave that part out.

The first group, which I tentatively name "Proto-Americans", inhabited what is now Northern China, Manchuria, and Eastern Siberia. The earliest representative of this group is probably the Tianyuan Man found in the outskirts of Beijing, and his age is around 40,000 years BP. He belonged to Y-chromosome haplogroup K2b* and Mt-haplogroup B*, both of which are ancestral to some of the haplogroups found among Native Americans and East Asians today (K2b is ancestral to PQR, while B is ancestral/upstream of B4 and B5). Genetic studies indicate that the Tianyuan Man is already on the East Eurasian line, meaning that he has already separated from West Eurasians, and is closer to Native Americans and East Asians than to West Eurasians. However, within the East Eurasian family he is closer to some Native American groups (particularly native Amazonians like Surui and Karitiana) than to modern East Asians.

If I were to pick a photo to represent this group, I would pick the cacique of the Sapanawa tribe Shina. His tribe had been an uncontacted tribe living on the Peruvian side of the border between Brazil and Peru, but illegal loggers forced them to emerge from their forest dwellings and made contact with the Brazilian department in charge of indigenous affairs. Now his tribe lives on the Brazilian side of the border.



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The second group, Jomon, was largely confined to Korea and Japan. There're no Jomon remains from 40,000 years BP available to us for DNA studies, but based on later Jomon remains, their dominant Y-chromosome haplogroup is likely D1a2a, while their Mt-haplogroups are likely M7a and D4.

This old Ainu man is probably the best representative I can find to represent Jomon.



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The third group refers to whoever that was living in Southern China / SE Asia at that time, and this refers to the ancestors of Longlin, Dushan, Hoabinhian, Leang Panninge, Onge/Jarawa, Aeta, Jehai, etc. We might tentatively call this group Proto-Hoabinhian or Proto-Southern East Eurasian. Granted they might not even be a single group, but due to the scarcity of evidence and for simplicity's sake, I'd group together for this thread. They might have carried Y-chromosome haplogroups C*, D*, C1b, D1a2b, D1b, F2 etc., and their Mt-haplogroups are likely the numerous small clades of M that we still find in the same region nowadays, like M5, M71, M74, M33, M21 etc., and as well as certain subclades of N and R.

For a modern representative of this group, I picked the famous Muay Thai boxer Buakaw Banchamek. Granted he might not be a pure descendant of the third group, but judging by his appearance I believe he still carries a significant portion of their bloodline.



Purer descendants of the aforementioned group would be the Batek people (considered to be Orang Asli or "native men" of Malaysia)



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Now a question arises, where do the ancestors of modern East Asians come from? Do they fit in any of the above groups? Well, the direct ancestors of modern East Asians were certainly affiliated to them by the token that they were all East Eurasians, however I would tentatively say they didn't directly come from any of the three but a related side group (or the fourth group if you prefer). And 40,000 years BP this fourth group probably hasn't even arrived in East Asia yet, but was roaming somewhere between Eastern Europe and Siberia. They left their marks in those places, such Ust-Ishim, Oase, and Bacho Kiro. From what I heard we've detected Y-chromosome haplogroup K2a in all three sites, and K2a is ancestral to modern East Asian N and O.

Starting from 30,000 years BP however, in one part due to the cooling of temperature towards the LGM, and in another part due to the spread of UP West Eurasians, this fourth IUP East Eurasian group had no choice but to migrate eastwards to East Asia. According to Chinese archaeologists, starting from around 30,000 to 28,000 years BP a new culture began to appear in Northern China, the 下川 Xiachuan culture. They carried a type of stone tool named by Chinese archaeologists as 船型细石器 or boat-shaped microlith, and this type of tool was different from the traditional flake tools in Northern China or the Hoabinhian cobble choppers in Southern China/SE Asia, but was more similar to the tools found in Northern Eurasia at that time. I believe the Xiachuan people might be the direct ancestors of modern East Asians. All modern East Asian groups, regardless of Sino-Tibetan, Mongolic, Turkic, Tungusic, Japonic, Koreanic, Hmong-Mien, Austronesian, Austroasiatic, and Tai-Kradai, ultimately trace their origin to the Xiachuan that entered Northern China around 30,000 years BP.

The arrival of Xiachuan to East Asia had great consequences in the region. After they entered Northern China, they pushed away the Tianyuan-like Proto-Americans (the aforementioned first group) that used to inhabit the region, and the Proto-Americans had no choice but to migrate further to the north, eventually crossed the Bering land bridge to the Americas. The second group (Jomon) had been pushed out of the mainland and lingered on the Japanese isles. The third group (Proto-Southern) had also been pushed away from the Yangtse region that they presumably had inhabited and they had to migrate further and further to the south, took refuge in the jungles and forests of SE Asia.

However the Xiachuan didn't just simply push away those groups, they also intermingled with them, and this likely led to their eventual break up into Northern East Asians and Southern East Asians sometime around 23,000 to 20,000 years BP. The ones who stayed in Northern China and who likely intermingled with the Proto-Americans (and the Jomons to a lesser extent) became the ancestors of Sino-Tibetan, Mongolic, Tungusic, Turkic, Koreanic, and Japonic peoples. On the other hand, the ones who moved south to the Yangtse region and beyond and who intermingled with the Proto-Southern group became the ancestors of Austroasiatic, Austronesian, Tai-Kradai, and Hmong-Mien peoples.

A modern representative of Northern East Asians, the Sinitic people (a branch of Sino-Tibetan)



A modern representative of Northern East Asians, the Japanese people (a branch of Japonic)



A modern representative of Southern East Asians, the Dayak people (a branch of Austronesians)



A modern representative of Southern East Asians, the Hlai people (a branch of Tai-Kradai)



Sorry if any of the costumes in the above photos might be inaccurate, I already tried my best to search for photos with traditional costumes.

And this basically sums up of my theory on the movement of peoples in East Asia for the last 40,000 years.

[VladimirTaraskin]

Ok, back to topic.

After long periods of thinking back and forth, I think I have a quite good grasp of how the population movements might have been in East Asia for the past 40,000 years.

So 40,000 years ago, there were at least 3 distinct East Eurasian populations inhabiting East Asia. How they arrived at East Asia though is anyone's guess, they could have taken either a northern route or a southern route, we don't have enough evidence for what happened before 40,000 years ago, so I will leave that part out.

The first group, which I tentatively name "Proto-Americans", inhabited what is now Northern China, Manchuria, and Eastern Siberia. The earliest representative of this group is probably the Tianyuan Man found in the outskirts of Beijing, and his age is around 40,000 years BP. He belonged to Y-chromosome haplogroup K2b* and Mt-haplogroup B*, both of which are ancestral to some of the haplogroups found among Native Americans and East Asians today (K2b is ancestral to PQR, while B is ancestral/upstream of B4 and B5). Genetic studies indicate that the Tianyuan Man is already on the East Eurasian line, meaning that he has already separated from West Eurasians, and is closer to Native Americans and East Asians than to West Eurasians. However, within the East Eurasian family he is closer to some Native American groups (particularly native Amazonians like Surui and Karitiana) than to modern East Asians.

If I were to pick a photo to represent this group, I would pick the cacique of the Sapanawa tribe Shina. His tribe had been an uncontacted tribe living on the Peruvian side of the border between Brazil and Peru, but illegal loggers forced them to emerge from their forest dwellings and made contact with the Brazilian department in charge of indigenous affairs. Now his tribe lives on the Brazilian side of the border.



-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

The second group, Jomon, was largely confined to Korea and Japan. There're no Jomon remains from 40,000 years BP available to us for DNA studies, but based on later Jomon remains, their dominant Y-chromosome haplogroup is likely D1a2a, while their Mt-haplogroups are likely M7a and D4.

This old Ainu man is probably the best representative I can find to represent Jomon.



------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

The third group refers to whoever that was living in Southern China / SE Asia at that time, and this refers to the ancestors of Longlin, Dushan, Hoabinhian, Leang Panninge, Onge/Jarawa, Aeta, Jehai, etc. We might tentatively call this group Proto-Hoabinhian or Proto-Southern East Eurasian. Granted they might not even be a single group, but due to the scarcity of evidence and for simplicity's sake, I'd group together for this thread. They might have carried Y-chromosome haplogroups C*, D*, C1b, D1a2b, D1b, F2 etc., and their Mt-haplogroups are likely the numerous small clades of M that we still find in the same region nowadays, like M5, M71, M74, M33, M21 etc., and as well as certain subclades of N and R.

For a modern representative of this group, I picked the famous Muay Thai boxer Buakaw Banchamek. Granted he might not be a pure descendant of the third group, but judging by his appearance I believe he still carries a significant portion of their bloodline.



Purer descendants of the aforementioned group would be the Batek people (considered to be Orang Asli or "native men" of Malaysia)



-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Now a question arises, where do the ancestors of modern East Asians come from? Do they fit in any of the above groups? Well, the direct ancestors of modern East Asians were certainly affiliated to them by the token that they were all East Eurasians, however I would tentatively say they didn't directly come from any of the three but a related side group (or the fourth group if you prefer). And 40,000 years BP this fourth group probably hasn't even arrived in East Asia yet, but was roaming somewhere between Eastern Europe and Siberia. They left their marks in those places, such Ust-Ishim, Oase, and Bacho Kiro. From what I heard we've detected Y-chromosome haplogroup K2a in all three sites, and K2a is ancestral to modern East Asian N and O.

Starting from 30,000 years BP however, in one part due to the cooling of temperature towards the LGM, and in another part due to the spread of UP West Eurasians, this fourth IUP East Eurasian group had no choice but to migrate eastwards to East Asia. According to Chinese archaeologists, starting from around 30,000 to 28,000 years BP a new culture began to appear in Northern China, the 下川 Xiachuan culture. They carried a type of stone tool named by Chinese archaeologists as 船型细石器 or boat-shaped microlith, and this type of tool was different from the traditional flake tools in Northern China or the Hoabinhian cobble choppers in Southern China/SE Asia, but was more similar to the tools found in Northern Eurasia at that time. I believe the Xiachuan people might be the direct ancestors of modern East Asians. All modern East Asian groups, regardless of Sino-Tibetan, Mongolic, Turkic, Tungusic, Japonic, Koreanic, Hmong-Mien, Austronesian, Austroasiatic, and Tai-Kradai, ultimately trace their origin to the Xiachuan that entered Northern China around 30,000 years BP.

The arrival of Xiachuan to East Asia had great consequences in the region. After they entered Northern China, they pushed away the Tianyuan-like Proto-Americans (the aforementioned first group) that used to inhabit the region, and the Proto-Americans had no choice but to migrate further to the north, eventually crossed the Bering land bridge to the Americas. The second group (Jomon) had been pushed out of the mainland and lingered on the Japanese isles. The third group (Proto-Southern) had also been pushed away from the Yangtse region that they presumably had inhabited and they had to migrate further and further to the south, took refuge in the jungles and forests of SE Asia.

However the Xiachuan didn't just simply push away those groups, they also intermingled with them, and this likely led to their eventual break up into Northern East Asians and Southern East Asians sometime around 23,000 to 20,000 years BP. The ones who stayed in Northern China and who likely intermingled with the Proto-Americans (and the Jomons to a lesser extent) became the ancestors of Sino-Tibetan, Mongolic, Tungusic, Turkic, Koreanic, and Japonic peoples. On the other hand, the ones who moved south to the Yangtse region and beyond and who intermingled with the Proto-Southern group became the ancestors of Austroasiatic, Austronesian, Tai-Kradai, and Hmong-Mien peoples.

A modern representative of Northern East Asians, the Sinitic people (a branch of Sino-Tibetan)



A modern representative of Northern East Asians, the Japanese people (a branch of Japonic)



A modern representative of Southern East Asians, the Dayak people (a branch of Austronesians)



A modern representative of Southern East Asians, the Hlai people (a branch of Tai-Kradai)



Sorry if any of the costumes in the above photos might be inaccurate, I already tried my best to search for photos with traditional costumes.

And this basically sums up of my theory on the movement of peoples in East Asia for the last 40,000 years.

In general, I agree. But I would add some nuances. There are no people of haplogroups N and O among Native Americans, so I think that N and O did not meet with group Q. Perhaps N and O entered East Asia through Central Asia, for example, through Dzungaria. And this is due to another group you missed C2a, which was really located between Q in the north and NO in the south of it.

Another nuance concerning the northern P/QR group. Just in the period of 30-20 thousand years before our time, they all or already their separate subclades (probably R and separate subclades Q) met with groups similar to the Kostenki that came from the West (possibly C1a-M8 or C1b-K281), resulting in the formation of the ANE group with 75% Kostenki and 25% Tianyuans.

[MNOPSC1b]

In general, I agree. But I would add some nuances. There are no people of haplogroups N and O among Native Americans, so I think that N and O did not meet with group Q. Perhaps N and O entered East Asia through Central Asia, for example, through Dzungaria. And this is due to another group you missed C2a, which was really located between Q in the north and NO in the south of it.

Another nuance concerning the northern P/QR group. Just in the period of 30-20 thousand years before our time, they all or already their separate subclades (probably R and separate subclades Q) met with groups similar to the Kostenki that came from the West (possibly C1a-M8 or C1b-K281), resulting in the formation of the ANE group with 75% Kostenki and 25% Tianyuans.

My theory is very general, there're of course many nuances that can be further discussed, but the general scheme is there.

Where to place P/QR is one of the mysteries yet to be solved. I'm not even sure if they were originally East or West Eurasians. On the one hand the earliest K2b individual known so far is Tianyuan who was East Eurasian, and K2b is ancestral to P/QR; on the other hand, apart from Native Americans (who are actually a mixed group composed of ANE + East Eurasian), P/QR has very little presence among the majority of East Eurasians, who are predominantly NO. Perhaps the Tianyuan group had already spread by 40,000 years BP, with one group moving to the west in a counter-clockwise pattern and this group eventually gave rise to P/QR, whereas the ones that stayed behind in Northern China/Manchuria were mostly C2 with some K2b? C2 is found among Native Americans though, so my theory still makes sense.

The migration pattern of C1b is another mystery. On the one hand the earliest C1b individual known so far is Kostenki, who was West Eurasian; on the other hand, modern-day C1b is mostly found in India, Southern China, SE Asia, and Oceania.

[MNOPSC1b]

The info on ancient DNA is updating rapidly and even what I said above is somewhat outdated. I've just read a Chinese article about the new discoveries on Y-chromosome haplogroup C in 2020-21, and I have to make a few corrections to what I said above.

1. The earliest identified C1b individual isn't Kostenki anymore but the sample CC7-335 from Bacho Kiro Cave, with an estimated age of around 44k to 46k. And according to DNA analysis the Bacho Kiro individuals are closer to East Eurasians than to West Eurasians. It's very likely that C1b was part of both the IUP (East Eurasian) and UP (West Eurasian) migrations, or that there was no clear boundary between early East and West Eurasians people traveled freely between the two groups.

2. The earliest identified C2 individual is the sample NE56 from the AR19K site in Northeastern China, with an estimated age of only 19k. This is too late for C2 to be part of the Proto-American group. It's more likely that C2 belonged to the same group as K2a/NO, but after entering Northern China C2 and NO diverged, with C2 moving north to Northeastern China/Manchuria and displaced the Proto-American group, whereas NO likely stayed on the Yellow River Plains (which extended to the Yellow Sea at that time due to lower sea levels) and had very little contact with the PA group. The PA group should be predominantly K2b/PQ.

Here's the link to that new Chinese article I used as reference, in case if anyone is interested: https://mp.weixin.qq.com/s?__biz=Mzk...&lang=zh_CN#rd

[MNOPSC1b]

Another surprising data that I discovered from the Chinese website https://mp.weixin.qq.com/s?__biz=Mzk...&lang=zh_CN#rd

Back in 2018, the Laos Hoabinhian La368 sample was assigned to C* (neither C1 nor C2), but now after a few years of analysis it seems they decided to place him near the root position of C1b, quite close to the position of Kostenki14. This would push the existence of C1b in Southern China / SE Asia to 8,000 years BP or perhaps even further, effectively making C1b native to that part of the world and perhaps one of the earliest Homo Sapien to inhabit that region. And since C1b still occurs among the modern inhabitants of that region, this shows that Hoabinhian hunter-gatherers didn't simply get pushed away or exterminated by the expanding farmers, but were assimilated.

This is the new C1b tree that I found on the Chinese website, it's in Chinese but I don't think I need to translate anything cause it's quite obvious.

[Howard23]

Chinese anthropology blogs are full of guesswork, and it is difficult to communicate with those bloggers, who are immersed in their own fantasies. The following is more reliable statements about Kostenki14 and IUP-BKs.

From Mateja Hajdinjak1,et al. 2021. Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

We enriched the libraries from the male individuals using probes that targeted about 6.9 Mb of the Y chromosome25 (Supplementary Information 4) and arrived at 15.2-fold coverage for F6-620, 2.5-fold for BB7-240 and 1.5-fold for CC7-335. F6-620 carries a basal lineage of the Y chromosome haplogroup F (F-M89), whereas BB7-240 and CC7-335 carry haplogroup C1 (C-F3393).

About IUP-BKs:

From Pribislav:

Thread: Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria

Similarly to BB7-240, CC7-335 also could've been pre-C1-F3393. Derived calls at C1b-F1370 level are aDNA damage IMO.

C1-F3393 level: F3393/Z1426+ C>A (1A); K29+ G>T (1T); F1171? G>A (3G-3A); K36- G>A (8G-2A)

C1a-CTS11043 level: CTS11043- G>T (1G); CTS8718/V7127- T>C (1T); Z7106- C>T (2C); Z7105- G>A (2G); F14743/Z7109/K667? G>A (1G-1A)

C1b-F1307 level: K164+ C>T (1T); K116+ C>T (2T)

After checking all five BAMs for sample BB7-240 (A11199, A12359, A12555, A12946, A15718), it seems he might've been pre-C1. Ancestral calls at C level are present in every BAM, but occasional ancestral calls are present at almost every major upstream level (A0-T, A1, A1b, BT, CT), so those are likely the consequence of aDNA damage. More importantly, in four of five BAMs derived calls at C1-F3393 level are present, so I think it's safe to assign this sample to (pre-)C1-F3393.


C1-F3393 level: F3393/Z1426+ C>A (2A); F1171+ G>A (2A); K31+ G>A (1A); K36- G>A (4G-1A)

C1a-CTS11043 level: CTS11043- G>T (1G); Z7976- G>T (1G); CTS8718/V7127- T>C (1T)

C1b-F1370 level: K384- G>T (5G); K116- C>T (1C)

Nothing to add here. BK-1653 is consistent with P, but since derived SNPs at all three P-levels are G>A transitions we can't know for sure to which one exactly he belonged to.

Thread: C-B65 subclade: Closest Relatives of Kostenki-14?

Kostenki14 was obviously incorrectly assigned to pre-B65 by their software. 3700K BAM of Kostenki14 from Fu et al. 2016 has 145 ancestral and no derived SNPs at B65 level, while shotgun BAM from the original paper (Seguin-Orlando et al. 2014) has only 1 derived SNP at B65 level (Z33130/F12012+ A>T (1T)) and 198 ancestral SNPs. This alone should've caused suspicion if the BAMs were manually checked, but their software just follows the sequence of derived SNPs, while not considering ancestral SNPs at all. The rest of SNPs currently at Z33130 level in YFull's live tree are not covered in Kostenki14, but they were counted as derived, which is another fault in their software that I've pointed out several times in the past. Finally, Kostenki14 has ancestral SNPs at upstream level K281, which means he should in fact split K281 level:


Kostenki14 (3700K BAM; Fu et al. 2016):

K281 level: K380- C>T (11C-1T); B66/Z16458- A>G (5A)


Kostenki14 (Shotgun BAM; Seguin-Orlando et al. 2014):

K281 level: K281+ G>A (1A); K458- T>A (1T); K380- C>T (1C)

I don't know where Kostenki14 will be in the next version of YFull tree, but since he has (at least) 3 ancestral SNPs at K281 level it is pretty clear that Z31330+ is a false positive, despite being a transversion. Even K281 assignment wouldn't be particularly strong, since the only derived SNP is a G>A transition covered with only one read. He also has one ancestral SNP at level F1370 (above K281), so I think the safest assignment considering all of the above would be pre-F1370.

F1370 level (merged calls from both BAMs): F1370+ G>C (13C); K384+ G>T (4T); K116+ C>T (4T); Z16480+ T>C (1C); K164+ C>T (1T); Y27076/F19598- C>T (1C)

[SG_Jun]

There is actually little evidence from published uniparentals for an origin of Koreans or Japanese in either the Neolithic to Bronze Age Liao River basin or Neolithic Shandong, or even a great amount of gene flow from either of those regions to Korea or Japan during the stipulated time frame.

Niuheliang site (the border of Lingyuan County and Jianping County, Liaoning Province, PRC)/Hongshan culture/approx. 6500 YBP ~ 5000 YBP/Neolithic (Cui et al. 2013)
2/6 N-M231(xN1c2a-M128, N1c1-Tat)
2/6 N-M231(xN1c1-Tat)
1/6 C-M216 (subclade undetermined)
1/6 O3-M122 (subclade undetermined)
(Too much N to be a major direct contributor to the Korean or Japanese population)

Halahaigou site (Yuanbaoshan County, Chifeng City, Inner Mongolian Autonomous Region, PRC)/Xiaoheyan culture/approx. 5000 YBP ~ 4200 YBP/Neolithic (Cui et al. 2013)
8/12 N-M231(xN1c2a-M128, N1c1-Tat)
4/12 N-M231(xN1c1-Tat)
(Again, far too much N-M231)

Dadianzi site (Aohan Banner, Chifeng City, Inner Mongolian Autonomous Region, PRC)/Lower Xiajiadian culture/approx. 4200 YBP ~ 3600 YBP/Early Bronze Age (Cui et al. 2013)
3/5 N-M231(xN1c1-Tat)
2/5 O3-M122 (subclade undetermined)
(Too much N)

Dashanqian site (Harqin Banner, Chifeng City, Inner Mongolian Autonomous Region, PRC)/Upper Xiajiadian culture/approx. 3000 YBP ~ 2700 YBP/Late Bronze Age (Cui et al. 2013)
1/9 C2c-P53.1
2/9 O3a-M324(xO3a2-P201)
2/9 O3a2c1a-M117
1/9 N-M231(xN1c2a-M128, N1c1-Tat)
3/9 N1c1-Tat
(This is somewhat closer than the other samples to the composition of present-day Koreans and Japanese, but it is still not a good match; the ratio of N-M231 to O2-M122 is ten times too great (1, whereas the ratio among present-day Koreans and Japanese is 0.1). Furthermore, N1c1-Tat does not seem to be so predominant among the small fractions of present-day Koreans and Japanese who belong to haplogroup N-M231.)

Jinggouzi site (Linxi County, Chifeng City, Inner Mongolian Autonomous Region, PRC)/Northern nomad culture/approx. 3000 YBP ~ 2500 YBP/Late Bronze Age (Cui et al. 2013)
12/12 C2c-P53.1
(Far too much C2)

Banlashan site (south of Chaoyang city, Liaoning, PRC/Hongshan culture/approx. 5500 YBP ~ 4500 YBP/Middle Neolithic (Ning et al. 2020)
Two females D5a3a1
One male O2a
(The male O2a is inconclusive. The mtDNA of the two female specimens should be related to a lineage that has contributed to present-day Sami people, neither to Koreans nor Japanese.)

Erdaojingzi site (north of the village of Erdaojingzi in the Hongshan District in Chifeng, Inner Mongolia/Lower Xiajiadian culture/approx. 4000 YBP ~ 3300 YBP/Late Neolithic (Ning et al. 2020)
One male with mtDNA haplogroup B5b1a and Y-DNA haplogroup O2a1c (EDM124)
One female with mtDNA haplogroup A22 (EDM139)
One male with mtDNA haplogroup N9a1 and Y-DNA haplogroup unreported (EDM176)
(The male O2a1c is inconclusive. MtDNA haplogroup A22 has been found among present-day Chinese. MtDNA haplogroups B5b1a1 and B5b1a2 have been found in approximately 0.2% and 0.8% of present-day Japanese, respectively. MtDNA haplogroup B5b1a(xB5b1a1, B5b1a2) has been found in a present-day Shan from northwestern Thailand and in a Chinese esophageal cancer patient from the Taihang area in Henan province. YFull currently estimates the TMRCA of B5b1a1 to be 3800 ybp, the TMRCA of B5b1a2 to be 2400 ybp, and the TMRCA of B5b1a to be 9400 ybp. Therefore, a sister or other close matrilineal relative of EDM124 could be ancestral to either B5b1a1 or B5b1a2, both of which have been found among present-day Japanese, but there is no way that such a close matrilineal relative of EDM124 could be ancestral to both B5b1a1 and B5b1a2, and there is no strong reason to assume that either of these Japanese haplogroups is descended from this B5b1a lineage found at the Erdaojingzi site. MtDNA haplogroup N9a1 has been found in 0.2% of present-day Japanese and it also has been found among present-day Koreans, Khamnigans, Mongolians, Tu, Tuvans, Kyrgyz, Uyghurs, Han Chinese, She, and Tai people in Vietnam and Thailand. Its TMRCA is currently estimated by YFull to be 9100 ybp. Again, there is no reason to suspect that this N9a1 lineage found at the Erdaojingzi site of the Lower Xiajiadian culture might be directly ancestral to any of the few present-day Japanese members of haplogroup N9a1.)

Longtoushan site (about 6 km south of Tuchengzi town, Hexigten, Chifeng, Inner Mongolia/Upper Xiajiadian culture/approx. 3000 ~ 2300 YBP/Bronze Age (Ning et al. 2020)
One female with mtDNA haplogroup D4m1 (91KLH11)
One male with mtDNA haplogroup D4j14 and Y-DNA haplogroup NO (91KLH18; this individual has been AMS dated to 2717±30 BP)
One male "outlier" with mtDNA haplogroup B4c1a2 and Y-DNA haplogroup C2b1a1 (91KLM2)
(In Eurasia, Y-DNA haplogroup C2b1a1 is currently found with greatest frequency (approx. 15%) among Khalkha Mongols. Y-DNA haplogroup NO is utterly inconclusive. As for the mtDNA haplogroups assigned to these specimens, haplogroups D4m1 and D4j14 have in fact been found in approximately 0.5% and 0.1% of present-day Japanese, respectively. However, D4j14 has formed 15900 ybp according to the current version of the YFull tree, and the two tabulated Japanese members of this clade have an estimated TMRCA of 9600 ybp. D4m1 has formed 16700 ybp, and the three tabulated Japanese members of this clade have an estimated TMRCA of 4700 ybp. The estimated TMRCA for the Japanese members of each of these clades currently tabulated by YFull exceeds the archaeological date for the Longtoushan site, so it is unlikely that 91KLH11 or a close female matrilineal relative of 91KLH18 should be ancestral to all present-day Japanese members of D4m1 or even the extremely rare D4j14. (This is all the more relevant when one considers that Japanese people are very poorly represented on YFull; the fact that these haplogroups that are very rare among the Japanese each already has two or more Japanese members tabulated by YFull with estimated TMRCA exceeding the date for the onset of even the Lower Xiajiadian culture is quite significant.) As for the "outlier," haplogroup B4c1a2a has been found in Kyrgyz from Artux x2, Khamnigan from South Siberia x1, Barghut from Hulun Buir x1 with TMRCA estimated by YFull to be 3300 ybp, and haplogroup B4c1a2(xB4c1a2a) has been found in Buryat from South Siberia x3, Buryat from Inner Mongolia x1, and Yakut from Central Siberia x1; the TMRCA of the entire B4c1a2 clade is estimated to be 12000 ybp. B4c1a2 also has been found in a male specimen from the Early Neolithic layer at Houtaomuga at the southern edge of the Amur River basin whose Y-DNA belongs to N-Tat. Although there is no Japanese member of B4c1a2 currently tabulated by YFull, there is evidence that a small percentage (~0.3%) of present-day Japanese should belong to this clade; however, there is no way to check where these Japanese members might fit in the phylogeny of B4c1a2, which has an estimated TMRCA of 12000 ybp. Furthermore, haplogroup B4c1a2's nearest outgroup, B4c1a1, happens to be a mainly Japanese (and marginally also Korean and Chinese) haplogroup; YFull currently has tabulated eighteen Japanese members of this clade (with an estimated TMRCA of 11400 ybp) plus one of unreported origin (cf. Behar et al. 2012) and one from a large study of HIV patients from eastern China. The individual of unreported origin from the study by Behar et al. has an estimated TMRCA with a Japanese individual of 1300 ybp; YFull has assigned these two to a newly created "B4c1a1a3" subclade. The individual from the study of HIV patients from eastern China has been assigned to B4c1a1a*; this individual's TMRCA with Japanese members of B4c1a1a is estimated to be 8800 ybp. The mtDNA of the BS11 specimen from Early Neolithic Boshan in Shandong has been assigned to B4c1a*; the TMRCA of the entire B4c1a clade is estimated to be 18400 ybp.)

Large proportions of both the Y-DNA and mtDNA pools of present-day Japanese are comprised of clades that are not regularly found among Chinese. (That is not to say that none of them has ever been found in any Chinese individual; some of these clades have been found sporadically in China, like the B4c1a1a* mtDNA found in the aforementioned individual from a study of HIV patients in eastern China. The point is that they are not found regularly among Chinese, whereas they are regularly found among Japanese and also among Koreans, though their frequencies among Koreans tend to be lower than among Japanese.) It appears rather unlikely that these clades might have been introduced to Japan recently from anywhere in China, including Shandong and the Liao River basin. For many of these clades, one cannot yet exclude a possibility of an introduction to Japan from the Korean Peninsula within the past several millennia (largely because of a dearth of high-resolution Y-DNA and especially mtDNA data from present-day Koreans as well as a dearth of ancient specimens from the Korean Peninsula).

It appears much more likely from present-day Y-DNA and mtDNA distributions that present-day so-called Koreans should be in the main a hybrid of indigenous inhabitants of the Korean Peninsula (whom I am loath to call "Koreans"; the ethnic group called "Koreans" as an exonym in the English language probably have very little genetic, cultural, or linguistic connection with the historical "Koreans," so calling them "Koreans" is rather like calling all present-day Italians "Lombards") and historical Han Chinese (I mean Han Chinese proper -- i.e. people of the state ruled by the Han Dynasty of China). The indigenous inhabitants of the Korean Peninsula appear to have been related to the Japanese rather than to the people of the Neolithic-to-Bronze Age Liao River basin. (The historical "Koreans," on the other hand, may have been descendants of the people of the Upper Xiajiadian culture of the Liao River basin. However, those people probably have next to nothing to do with present-day so-called "Koreans." I wish someone would start a movement to popularize among English speakers a more appropriate ethnonym for the present-day ethnic majority of the Korean Peninsula -- how about Joseonese? "Joseon people" is what present-day North Koreans and Koreans in China call themselves, after all. Calling them "Han people," as South Koreans call themselves, would cause too much confusion with the Han of China. However, it is also questionable how much connection the present-day "Koreans" have with the "Joseon" of ancient Chinese history as opposed to the "Joseon" of the medieval Korean Peninsula; the latter Joseon is very clearly a country of the ancestors of present-day "Koreans," whereas the former Joseon's connection with the latter Joseon and with present-day "Koreans" is about as tenuous as the connection of the historical Koreans with the present-day "Koreans." Maybe we should borrow the Mongolian exonym and start calling them "Solongos"; it coincidentally sounds like the Mongolian word for "rainbow," though it historically has no connection with that word and is most likely derived from the name of the first millennium CE kingdom of "Silla," which according to historical records ought to be the direct ancestor of the so-called "Koreans.")

Hi, I wish to add that Y-DNA of EDM176 of the Lower Xiajiadian Culture at Erdaojingzi has been announced as N1b1-CTS582, which is the same haplotype as the three ancient samples in Bianbian, Xiaojingshan and Boshan in Fu Qiaomei's study in Shandong Early Neolithic. It should be added that in terms of autosomal DNA these samples from Bianbian, Xiaojingshan and Boshan seem to be even more northern-shifted than the autosomal DNA of Lower Xiajiadian (which presents some degree of admixture with Yellow River populations), instead clustering more closely together with the autosomal DNA of Upper Xiajiadian.

As for the sample of NO at Longtoushan (Upper Xiajiadian), it has been re-classified as N1a1a3-F4063.

In my opinion this possibly points to a link between Shandong_EN and WLR populations

Source: https://mt-y.cn/

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[alchemist223]

It may be so, but the Y-DNA of the present study's specimen from Taejungni appears to be atypical for present-day Koreans. Kwon et al. 2015 have found C2b-L1373 in only 0.7% (5/706) of a pooled sample of Koreans from Seoul (n=573) and Daejeon (n=133). Furthermore, two of two examples of C-L1373 from Korea on the current YFull tree belong to rare basal subclades (C-ACT1932 and C-Y176542, respectively) that have not been found anywhere besides the area along the coast of the Asian continent extending from Liaoning through Korea to the mouth of the Amur and in the Japanese Archipelago. The TMRCA between the more basal of these two clades (C-ACT1932) and "Altaic" subclades of C-L1373 is currently estimated to be 16100 (95% CI 17400 <-> 14800) ybp, and the TMRCA between the less basal of these two clades (C-Y176542) and the frequently observed "Altaic" subclades of C-L1373 is currently estimated to be TMRCA 14300 (95% CI 15700 <-> 12900) ybp. These genealogical splits should have occurred roughly around the time of the initial spread of humans into the American continent, perhaps even before that event.

A greater number of specimens is needed before any sense can be made of these initial results. I would especially like to see a historical transect of specimens from the Korean Peninsula (especially the areas of northern Korea that have been governed by the Han Dynasty and the areas of southern Korea from which the Silla kingdom has expanded) in order to elucidate how and when the closely Chinese-related lineages that currently predominate among Koreans have come to do so.

Is there not a single specimen from Jōmon-era Western Japan that has yielded useful amounts of endogenous DNA? Why do researchers always set up admixture models using these specimens from Eastern Japan, sometimes even only the specimen from the Funadomari site, which is located on the northern tip of Rebun Island (which is on average the northernmost island of Japan, although Cape Sōya at the northern tip of Hokkaidō extends slightly further to the north), less than 100 km from Sakhalin Island, Russia? I always find it to be a bit curious.

Just as an update, a Japanese sample was recently uploaded to YFull as C-BY72441*, being basal to the samples from South Korea and Liaoning, China. Unfortunately, the uploader seemingly did not pay for the sample, which has since disappeared from YFull's tree. I do not recall any specific region of Japan being listed.

[Q-M242-is-Papuan-related]

In Table S2 of the article ‘Human population history at the crossroads of East and Southeast Asia (11000bP)’, the 8000-year-old Yumin individual is closer to the ancient Baojianshan individual (f4(Mbuti,Baojianshan;Yumin,Kolyma), Z=-6,8) from the Guangxi Province than to the ancient Dushan individual from the Guangxi Province (f4(Mbuti,Dushan;Yumin,Kolyma), Z=-5,9) in comparison with the northern samples. According to the same article, the Baojianshan individual additionally acquired the Hoabinhian-related DNA found in Southeast Asia, while it was discovered in the Admixture model in the article ‘Multiple migrations to the Philippines during the last 50,000 years’ (Figure S9) that the Yumin individual had a small amount of ancestry looking like that of the Negrito Ayta people, distantly related to the Hoabinhians.

[Skhznamk]

It may be so, but the Y-DNA of the present study's specimen from Taejungni appears to be atypical for present-day Koreans. Kwon et al. 2015 have found C2b-L1373 in only 0.7% (5/706) of a pooled sample of Koreans from Seoul (n=573) and Daejeon (n=133). Furthermore, two of two examples of C-L1373 from Korea on the current YFull tree belong to rare basal subclades (C-ACT1932 and C-Y176542, respectively) that have not been found anywhere besides the area along the coast of the Asian continent extending from Liaoning through Korea to the mouth of the Amur and in the Japanese Archipelago. The TMRCA between the more basal of these two clades (C-ACT1932) and "Altaic" subclades of C-L1373 is currently estimated to be 16100 (95% CI 17400 <-> 14800) ybp, and the TMRCA between the less basal of these two clades (C-Y176542) and the frequently observed "Altaic" subclades of C-L1373 is currently estimated to be TMRCA 14300 (95% CI 15700 <-> 12900) ybp. These genealogical splits should have occurred roughly around the time of the initial spread of humans into the American continent, perhaps even before that event.

A greater number of specimens is needed before any sense can be made of these initial results. I would especially like to see a historical transect of specimens from the Korean Peninsula (especially the areas of northern Korea that have been governed by the Han Dynasty and the areas of southern Korea from which the Silla kingdom has expanded) in order to elucidate how and when the closely Chinese-related lineages that currently predominate among Koreans have come to do so.

Is there not a single specimen from Jōmon-era Western Japan that has yielded useful amounts of endogenous DNA? Why do researchers always set up admixture models using these specimens from Eastern Japan, sometimes even only the specimen from the Funadomari site, which is located on the northern tip of Rebun Island (which is on average the northernmost island of Japan, although Cape Sōya at the northern tip of Hokkaidō extends slightly further to the north), less than 100 km from Sakhalin Island, Russia? I always find it to be a bit curious.

There is a saying that Osaka and Nara, Kyoto are more connected to the continent referring to Korea and China. Eastern Japan and the North are where Jomon-related groups such as Emishi or Ainu lived. I haven’t looked much into it but this might explain their peculiar sampling. Small groups of people won’t change the average national gene pool though.