N1b1 and N1b2 subclades

[ronin92]

I want to continue the discussion about the N1b clades that started in in the Shandong thread but I have moved it to a separate thread to avoid hijacking that discussion which has samples of other haplogroups.  sg_jun raised some interesting points there that are worth discussing.

While N1b may have been a major component of some north China populations earlier in prehistory, that was no longer the case later.  This makes it more difficult to determine how it spread.  The attached figure shows the modern distribution of N1b1 and N1b2 and their relative proportions in China.  Sites from which N1b ancient DNA was collected are marked in panel C.

   

It may be easier understanding what happened with N1b1.  As already pointed out by sg_jun earlier, N1b1 was prominent around the Bohai Sea.  And it does seem plausible that West Liao was N1b1 too.  Even if N1b1 may have been eventually diluted by later incomers, in those regions, they were remained in areas that would participate in the dispersals from Yangshao areas southward and eventually moved to the southeastern coast, displacing the proto-Austronesians there.  That would be consistent with their current representation in and around Fujian.  They also appear to have migrated as far as Thailand by the Iron Age.

N1b2 is more complicated.  N1b2 differentiated itself from N1b later and is not found in the older sites like N1b1.  The earliest site where it was found was Zongri in Qinghai, 5.1 kybp.  Data from the Zongri sites showed that that first Zongri N1b sample was devoid of YR ancestry, unlike samples from 4.7 kybp and after, indicating that N1b2 did not reach Zongri via the demic diffusion that brought millet and presumably Tibeto-Burman to this site.  N1b2 was also found at sites south of the Tibetan plateau 2-2.5 kybp.  One question is whether these Tibetan related sites had any role in subsequent spread of N1b2 elsewhere.  N1b2 is relatively common in Sichuan today but it is impossible to attribute with any confidence, its presence by a spread of N1b2 from Tibet/Qinghai.  Sichuan has had such a disturbed population history that it is difficult to infer anything about the distant past from its genetics today.  Hunan is also relatively enriched in N1b2 relative to N1b1 today but has also had large amounts of immigration historically.  Given higher minority populations in Hunan, could N1b2 have been mostly associated with one or more of those rather than with YR populations?  It is more commonly seen in Tujia etc.  Then the spread of N1b2 is significantly driven by displacement of these groups by Han expansion and its presence in Han populations is through assimilation of these non-Han minorities.  It may explain why it is so rarely sampled at Han-associated ancient sites.  Would that be plausible?

[Ebizur]

Percentage of males of each ethnic group in China that belong to N-M1819 according to 23mofang (unless otherwise noted)
Guizhou Yi 9/43 = 20.93%
Yi from Zhaojue County, Sichuan 20/205 = 9.76% (cf. Table S4 of He Guanglin et al. 2023)
Tujia 34/593 = 5.73%
Yunnan Yi 10/180 = 5.56%
Yi from Meigu County, Sichuan 10/222 = 4.50% (cf. Table S4 of He Guanglin et al. 2023)
Sichuan Yi 2/54 = 3.70%
Miao 10/329 = 3.04%
Chinese average 2.38%
Manchu 52/2938 = 1.77%
Zhuang 14/801 = 1.75%
Tibetan 8/485 = 1.65%
Hui 42/2553 = 1.65%
Mongol 21/1521 = 1.38%

In regard to ancient specimens that have been found to belong to haplogroup N-M1819, it should be noted that the two specimens from the Pingliangtai site of the Longshan culture in Henan have been assigned to a rare primary subclade, N-M1819 > N-MF21116, that is very rarely found among present-day males (even among Han Chinese in Henan). Nearly all extant members of N-M1819 belong to another primary subclade, N-M1819 > N-F1020, and that subclade has been found among specimens from Zongri culture sites in Qinghai as well as other ancient specimens from Tibet and Thailand and in a Western Zhou burial at the Xinancheng cemetery in Zhangzi County, Shanxi.

[ronin92]

Percentage of males of each ethnic group in China that belong to N-M1819 according to 23mofang (unless otherwise noted)
Guizhou Yi 9/43 = 20.93%
Yi from Zhaojue County, Sichuan 20/205 = 9.76% (cf. Table S4 of He Guanglin et al. 2023)
Tujia 34/593 = 5.73%
Yunnan Yi 10/180 = 5.56%
Yi from Meigu County, Sichuan 10/222 = 4.50% (cf. Table S4 of He Guanglin et al. 2023)
Sichuan Yi 2/54 = 3.70%
Miao 10/329 = 3.04%
Chinese average 2.38%
Manchu 52/2938 = 1.77%
Zhuang 14/801 = 1.75%
Tibetan 8/485 = 1.65%
Hui 42/2553 = 1.65%
Mongol 21/1521 = 1.38%

In regard to ancient specimens that have been found to belong to haplogroup N-M1819, it should be noted that the two specimens from the Pingliangtai site of the Longshan culture in Henan have been assigned to a rare primary subclade, N-M1819 > N-MF21116, that is very rarely found among present-day males (even among Han Chinese in Henan). Nearly all extant members of N-M1819 belong to another primary subclade, N-M1819 > N-F1020, and that subclade has been found among specimens from Zongri culture sites in Qinghai as well as other ancient specimens from Tibet and Thailand and in a Western Zhou burial at the Xinancheng cemetery in Zhangzi County, Shanxi.

Thanks for the stats.
Yes, the Pingliangtai distribution is different:-

  pingliangtai.png (Size: 68.66 KB / Downloads: 77)
All 23mofang samples are north of Yangtze and none from the prefecture that Pingliangtai lies in.  I think I've chosen the right group within 23mofang corresponding to that in theYtree.

[Ebizur]

Percentage of males of each ethnic group in China that belong to N-M1819 according to 23mofang (unless otherwise noted)
Guizhou Yi 9/43 = 20.93%
Yi from Zhaojue County, Sichuan 20/205 = 9.76% (cf. Table S4 of He Guanglin et al. 2023)
Tujia 34/593 = 5.73%
Yunnan Yi 10/180 = 5.56%
Yi from Meigu County, Sichuan 10/222 = 4.50% (cf. Table S4 of He Guanglin et al. 2023)
Sichuan Yi 2/54 = 3.70%
Miao 10/329 = 3.04%
Chinese average 2.38%
Manchu 52/2938 = 1.77%
Zhuang 14/801 = 1.75%
Tibetan 8/485 = 1.65%
Hui 42/2553 = 1.65%
Mongol 21/1521 = 1.38%

In regard to ancient specimens that have been found to belong to haplogroup N-M1819, it should be noted that the two specimens from the Pingliangtai site of the Longshan culture in Henan have been assigned to a rare primary subclade, N-M1819 > N-MF21116, that is very rarely found among present-day males (even among Han Chinese in Henan). Nearly all extant members of N-M1819 belong to another primary subclade, N-M1819 > N-F1020, and that subclade has been found among specimens from Zongri culture sites in Qinghai as well as other ancient specimens from Tibet and Thailand and in a Western Zhou burial at the Xinancheng cemetery in Zhangzi County, Shanxi.

The corresponding figures for haplogroup N-CTS582, the other subclade of N1b-F2930, are as follows:

Mongol 19/1521 = 1.25%
Chinese average 1.24%
Manchu 34/2938 = 1.16%
Tibetan 5/485 = 1.03%
Hui 22/2553 = 0.86%
Tujia 5/593 = 0.84%
Zhuang 2/801 = 0.25%
Guizhou Yi 0/43
Sichuan Yi 0/54
Yunnan Yi 0/180
Miao 0/329

Table S4 of He et al. (2023) does not indicate results for testing of N1b1 (= N-CTS582). However, it does indicate results for N1b1a1b~, which should be a subclade of N-CTS582.

Yi from Meigu County, Sichuan 1/222 = 0.45% N1b1a1b~ + 2/222 = 0.90% N1(xN1b1a1b~, N1b2a1b~) = 1.35% maximum potential N-CTS582
Yi from Zhaojue County, Sichuan 0/205 potential N-CTS582

So, N1b2-M1819 tends to be found in relatively great percentages of Tibeto-Burman people, whereas N1b1-CTS582 tends to be found in relatively great percentages of Mongol and Han people.

Another trend that is apparent in data derived from present-day males (including Mongol, Manchu, and the Chinese average, this last being primarily determined by "Han") is for N1b1a-Y6374/Z8029 to be more common than N1b1b-CTS962. (However, cf. Ren Z, Yang M, Jin X, Wang Q, Liu Y, Zhang H, Ji J, Wang C-C and Huang J (2022) "Genetic substructure of Guizhou Tai-Kadai-speaking people inferred from genome-wide single nucleotide polymorphisms data": 19/33 = 57.6% N1b1b-Y23802 in a sample of Gelao from Wuchuan Gelao and Miao Autonomous County, Zunyi, Guizhou.) According to TheYtree, EDM176 from the Lower Xiajiadian layer at the Erdaojingzi site in Chifeng, Inner Mongolia belongs to N-CTS582 > N-Y6374 > N-L727 > N-Y13910 > N-CTS6498 > N-TYT63444. However, the N-CTS6498 subclade to which this specimen from the Erdaojingzi site has been assigned is extremely rare among present-day males in China (accounting for less than 0.06% of the total male population of China according to 23mofang), and the TMRCA of N-Y13910 is estimated by 23mofang to be 12650 ybp, so this specimen from the Erdaojingzi site is not necessarily relevant to determining the origin of the common ancestor of the majority of present-day members of N-CTS582. (In other words, most present-day members of haplogroup N-CTS582 belong to N-CTS582 > N-Y6374(xCTS6498).) The ancient DNA samples from Shandong that have recently been uploaded by Wen Shaoqing of Fudan University and that are suspected to represent samples from some site(s) of the Dawenkou culture belong to N-CTS962, so they cannot represent the direct ancestors of the majority of present-day members of N-CTS582, either.

[CLTVTE]

Recently, a new commentary from the Institute of Vertebrate Paleontology and Paleoanthropology has become available.
Ancient genomes and the evolutionary path of modern humans
E. Andrew Bennett, Qiaomei Fu
https://doi.org/10.1016/j.cell.2024.01.047
“Ancient genomes from modern human populations with no present-day descendants have been found in Europe, Siberia, and East Asia [7], each representing a distinct facet of humanity that has vanished, reminding us that one truly universally shared genetic feature of modern humans has been their diversity.”

In [7], the Tianyuan Man, that is, the ancient human from the population of the Huanghe River basin of East Asia (Northern China), was marked as an ancient individual that did not contribute to modern populations. His mtDNA was B4’5*, his yDNA was assigned to K2b*, but additionally produced the result of yDNA O, rather than yDNA NO. AR33K of the Amur River basin shared the genetic drift with the Tianyuan Man in “The deep population history of northern East Asia from the Late Pleistocene to the Holocene”.

Unlike the eastern part of the Yangtze River basin, which was occupied by ancestors of modern yDNA O-M122, O-M119, O1b*/O1b1-related populations in “Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans”, “Human genetic history on the Tibetan Plateau in the past 5100 years” observed the maximization of some components, which were present in the Early Neolithic Shandong individuals, in the ancient DNA from China’s part of the area, adjacent to the Lancang River basin, which is in turn adjacent to the western part of the Yangtze River basin. "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago" produced an indirect relative estimate that the ancestors of the “Early Neolithic Shandong-related” population should have entered the Lancang River basin by 38000 years ago, having separated from their yDNA O relatives.



However, some distant y chromosome relatives of Early Neolithic Shandong individuals formed a cline with the Hmong-Mien-related ancient Dushan (yDNA O-M7) and an ancient Tai-Kadai individual (close to Dushan on the PCA), who was a relative of the ancient basal yDNA O1b*-related specimen, also found in ancient Tai-Kadais in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", while when the ancestor of the “Austronesian” yDNA O-M119 was born, he had to reside in the common homeland, shared by the basal yDNA O1b* (in the eastern part of the Yangtze River basin in “Ancient genomes reveal the complex genetic history of Prehistoric Eurasian modern humans”). Such a grouping on the PCA should remind of the so-called “Austro-Tai” linguistic grouping from the book “Japanese/Austro-Tai” by Paul King Benedict (1990). Apparently, some “Proto-Austro-Tai” yDNA O1b* individuals used to reach the Upper Yangtze River basin in the Paleolithic, but their lineages were substituted by lineages of ancestors, whose descendants gave birth to Early Neolithic Shandong individuals . Similarly, the deeply diverged “Para-Austroasiatic”-related O1b1* lineage is also observed in the same part of the Upper Yangtze River basin in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago".

Melinda Yang placed the population dispersal via the most coastal “Para-Austronesian” yDNA O-M119-related Lower Yangtze area to ancient Shandong and to Fujian, a neighbour of Taiwan, in “A genetic history of migration, diversification, and admixture in Asia”.

The most interesting ancient individual is yDNA N-M1819 individual from Pingliangtai. In "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", he formed a cline with the basal yDNA O-M175* ancient individual of Suogang from the Penghu Islands between mainland China and Taiwan, in whose settlement ancient jade implements were found. Similarly, jade, similar to the jade of the rice-farming Shijiahe “civilization” was found in Pingliangtai. However, we know that the Shijiahe jade culture formed under the influence of the jade working of the rice-farming Liangzhu “civilization” of the Lower Yangtze River basin, and members of the Liangzhu “civilization” migrated to the north. However, the Liangzhu “civilization” should have also influenced the appearance of the rice farming in the southern Tanshishan culture of Fujian, which brought rice farming to Austronesian ancestors in Taiwan. To put it in a more simple way, both yDNA N-M1819 Pingliangtai individuals (PLTM311 and PLTM312) formed a genetic cline with the ancient rice farming Tanshishan culture’s individual in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago".

The distribution of rice farming individuals of the Liangzhu descent to the north should also have been even much more complicated. For example, in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", some ancient Pingliangtai individuals should have been related to mtDNA M7c1a5-affiliated individuals, distantly akin to the Hmong-Miens and Tai-Kadais, whereas mtDNA M7c1a5 was classified as belonging to the Koreans in “Ancient Mitogenomes Reveal the Origins and Genetic Structure of the Neolithic Shimao Population in Northern China”. Some ancient rice farmers joined the Koreans. However, some jade artifacts were also observed in the rice farming Songgukri culture. The main path joining the Liangzhu culture of the Lower Yangtze to both Pingliangtai’s Henan area and more northern Jiangsu territories should have passed through the area of the modern Jiangsu Province.

The Hongshan-related part of the Miaozigou population could have only contributed to the Liangzhu areas via the culture of Lingjiatan, which resulted in the alignment on the PCA, which would only suit the formation of the Aichi Prefecture population, in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago", while the population, ancestral to the population of the Chongming Island of Shanghai, could have only formed from local individuals, as well as newcoming individuals having ancestors in Late Yangshao, when the Liangzhu culture had already collapsed, according to genetic connections, uncovered in "Human population history at the crossroads of East and Southeast Asia since 11,000 years ago".