May 31, 2013

Ancient mtDNA of Tohoku district Jomon

Anthropological Science

Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan

Hideaki KANZAWA-KIRIYAMA et al.

Abstract We investigated mitochondrial DNA haplogroups of four Jomon individuals from the Sanganji shell mound in Fukushima, Tohoku district, Japan. Partial nucleotide sequences of the coding and control region of mitochondrial DNA were determined. The success rate of sequencing increased when we analyzed short DNA sequences. We identified haplogroups from all four samples that were analyzed; haplogroup frequencies were 50% (n = 2) for N9b and 50% (n = 2) for M7a2. Haplogroup N9b has been previously observed in high frequencies in the other Tohoku Jomon, Hokkaido Jomon, Okhotsk, and Ainu peoples, whereas its frequency was reported to be low in the Kanto Jomon and the modern mainland Japanese. Sub-haplogroup M7a2 has previously been reported in the Hokkaido Jomon, Okhotsk, and modern Udegey (southern Siberia) peoples, but not in the Kanto Jomon, Ainu, or Ryukyuan peoples. Principal component analysis and phylogenetic network analysis revealed that, based on haplogroup frequencies, the Tohoku Jomon was genetically closer to the Hokkaido Jomon and Udegey people, than to the Kanto Jomon or mainland modern Japanese. The available evidence suggests genetic differences between the Tohoku and Kanto regions in the Jomon period, and greater genetic similarity between the Tohoku Jomon and the other investigated ancient (Hokkaido Jomon, Okhotsk) and modern (Siberian, Udegey in particular) populations. At the same time, the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history.

Link

25 comments:

terryt said...

"the Tohoku and Hokkaido Jomon seem to differ in sub-haplotype representations, suggesting complexity in Jomon population structure and history".

I would be far more surprised to learn that the Jomon were a homogeneous population. They must have developed over a considerable period and be the product of numerous migrations into Japan.

Justin said...

I find it strange that the Southern Chinese and Taiwanese Aboriginies are closer to Udegey (northern Asians) than Koreans are.

Another study that shows that mtDNA haplogroups are not a good indicator of genetic distance.

Kristiina said...

Udegey seem to have very particular mtdna and ydna composition:
mtdna
N9 30%
M* 29%
C2 17%
CSZ*(S) 15%
F 8.7%
Ydna:
C3c 60 %
M9 25%
Q 10%
R1a 5%
On the East Coast of China men carry quite much ydna C3 and mtdna M9E and F are very common in Taiwanese Aboriginals.

andrew said...

The persistence of non-farmer Jomon genetics in the modern Japanese population through the Neolithic revolution there continues to be remarkable and almost unprecedented to that degree seen in Japan.

terryt said...

What is the Y-DNA M9? Or is it a misprint for mt-DNA M9? Y-DNA M is New Guinea, with no M9.

terryt said...

Sorry. Y-DNA M9 is obviously K(xIJ), probably O of some sort.

Ebizur said...

I do not know the original sources of this study's Taiwanese Aboriginals and Udegey data sets, but the data I have on Taiwanese aborigines is nothing like the Udegey data that Kristiina has posted above.

Taiwan aborigines (Peng et al. 2011)
100/640 = 15.63% B4a
47/640 = 7.34% B4b1 (This is a sister clade to the American type of Haplogroup B.)
25/640 = 3.91% B4c1b
172/640 = 26.88% B4 total

33/640 = 5.16% B5a

8/640 = 1.25% D4
26/640 = 4.06% D5'6
34/640 = 5.31% D total

77/640 = 12.03% E

14/640 = 2.19% F1a(xF1a1)
21/640 = 3.28% F1a1(xF1a1a)
1/640 = 0.16% F2
54/640 = 8.44% F3
72/640 = 11.25% F4
162/640 = 25.31% F total

1/640 = 0.16% G
2/640 = 0.31% M12

4/640 = 0.63% M10

74/640 = 11.56% M7b(xM7b1)
5/640 = 0.78% M7b1
42/640 = 6.56% M7c1'2
121/640 = 18.91% M7 total

10/640 = 1.56% N9a
9/640 = 1.41% Y
19/640 = 2.97% N9 total

15/640 = 2.34% R9c

The frequency of F is three times greater in Taiwan aborigines than in Udegeys, the frequency of N9 is ten times greater in Udegeys than in Taiwan aborigines, and Taiwan aborigines completely lack the M8 clade, which includes C and Z and seems to be the modal haplogroup among the Udegey.

On the Y-DNA side of things, Taiwan aborigines are heavily O1a-M119, with a few particular subclades of O3-M122 or O2a1-M95 also represented in some tribes. Taiwan aborigines completely lack the typically Siberian C3c and Q lineages that predominate among the Udegey, and they also do not exhibit R1a, which may reflect limited geneflow from the Russian majority population into the indigenous Udegey minority.

Frankly, the mtDNA pool of the Udegey looks quite typically Siberian, with a definite majority of M (and especially M8) subclades accompanied by a small amount of F. N9 is rare in most of Siberia, being generally a more southerly East Asian group, but it is quite common (especially in the form of its Y subclade) in populations around the Sea of Okhotsk in the extreme east of Siberia, who are close to the Udegey geographically and culturally. (This is similar to the distribution of mtDNA haplogroup G, which is also generally rare in Siberia and more typically East/Central Asian, but with a branch extending up the eastern fringe of Siberia into Kamchatka.)

In contrast, the mtDNA pool of Taiwan aborigines is very typical of Southeast Asian populations, with an overwhelming majority of R subclades (especially B and F), and representatives of mtDNA macrohaplogroup M being mostly limited to M7b/c (branches of M7, another branch of which is common in Japan) and E (a branch of M9, another branch of which is common in Tibet).

I cannot explain why the Taiwan aborigines and the Udegey have been placed so close together on this study's PC plot without access to their raw data.

terryt said...

"I cannot explain why the Taiwan aborigines and the Udegey have been placed so close together on this study's PC plot"

Thanks for that information. I was more than just a little surprised at the connection too.

Kristiina said...

Terry, M9 must be just K. Do not know more precisely as I only copied the values.

To me Udegey mtDNA pool is not so typically Siberian or Korean. They lack mtDNA haplogroups D, G and A and yDNA N and O. The lack of D is very unusual, as D is extremely widespread in Northern East-Asia, including Korea. Their CSZ*(S) is specific to Udegey. I do not really say that Udegey and Taiwanese aboriginals have the same mtDNA pool. I just find some interesting lacks (G, A, M10, and Taiwanese Aboriginals have a low frequency of D haplogroups) and similarities (presence of N9, F) which may explain why the Udegey are placed closer to Taiwanese than Koreans. Mtdna haplogroups frequencies of Udegey were taken from Starikovskaya et al study. According to this paper, one of Udegey M* lines has been detected in the Vietnamese and Taiwanese Han, and the other M* line has similarities with a M line detected in China. Taiwanese aboriginals also have a considerable amount of M7 which was found in this ancient Jomon sample.

Ebizur said...

Kristiina wrote,

"Terry, M9 must be just K. Do not know more precisely as I only copied the values."

The "M9" (i.e. K-M9(xQ, R1a, ...?)) category is almost certainly not "just K," but rather a hodgepodge of derivatives of N-M231 and O-M175. Many researchers, unfortunately, continue to provide readers with very shallow phylogenetic resolution of their samples. However, in the case of the Udegeys, at least one other study has demonstrated that some of them possess Y-DNA derived from O-M175, such as O2b-SRY465.

Kristiina wrote,

"To me Udegey mtDNA pool is not so typically Siberian or Korean. They lack mtDNA haplogroups D, G and A and yDNA N and O. The lack of D is very unusual, as D is extremely widespread in Northern East-Asia, including Korea. Their CSZ*(S) is specific to Udegey. I do not really say that Udegey and Taiwanese aboriginals have the same mtDNA pool. I just find some interesting lacks (G, A, M10, and Taiwanese Aboriginals have a low frequency of D haplogroups) and similarities (presence of N9, F) which may explain why the Udegey are placed closer to Taiwanese than Koreans. Mtdna haplogroups frequencies of Udegey were taken from Starikovskaya et al study. According to this paper, one of Udegey M* lines has been detected in the Vietnamese and Taiwanese Han, and the other M* line has similarities with a M line detected in China. Taiwanese aboriginals also have a considerable amount of M7 which was found in this ancient Jomon sample."

Would you mind sharing the title of that study by Starikovskaya et al. with us? Are you sure that the "M* 29%" figure for this study's sample of Udeghe explicitly excludes haplogroup D and/or haplogroup G, and not only some subclades (including that allegedly Udeghe-specific type) of M8CZ? It is difficult for me to imagine that the Udeghe population could entirely lack mtDNA haplogroups D and G; G is very common in other populations of the greater circum-Okhotsk region that also share haplogroup N9Y with the Udeghe, and haplogroup D is generally the second most common mtDNA haplogroup in North Asia after haplogroup C. Please keep in mind that the Udeghe are not isolated in any way; they are just one of many populations of Tungusic speakers in the general region, whose language is quite cosmopolitan for a Tungusic language, sharing some features with the dialects of the more northerly Evenks and other features with the dialects of the other Amurians. They do not even live on an island or in mountains, but rather along rivers in the lower watershed of the Amur.

As for the high frequency of M7 among the aborigines of Taiwan, it is completely attributable to the typically South Chinese/Southeast Asian subclades M7b and M7c. The M7 that is often brought up in discussions about the ethnogenesis of populations of the Japanese Archipelago actually refers to the M7a subclade, which has been found almost exclusively in ancient remains from the Japanese Archipelago (e.g. Jōmon) and in modern Japanese, Ryūkyūans, Ainus, and Koreans.

Kristiina said...

Ebizur, please, go and see the study yourself (Table 2). I am not making up things. http://onlinelibrary.wiley.com/doi/10.1046/j.1529-8817.2003.00127.x/pdf

If you are aware of another study where the Udegey have been sampled, please let me know.

The same applies to this ydna study. Please go and check what kind of M9 it is. I would also like to know!
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC384887/

I agree that their M9 is not at all very clear, but this M9 is anyway absent in Buryat and Yenisey Evenks, so it should not be O line, as Buryats have O2b and O3. They also say that ”The Tat-C haplogroup was absent in the Lower Amur and Sea of Okhotsk region populations that have maintained greater geographic and/or linguistic isolation (e.g., the Udegeys, Nivkhs, and Upriver Negidals) and was only detected in the populations likely to have had recent contact or shared origins with the populations of southern Middle Siberia (e.g., the Okhotsk Evenks, Ulchi/Nanai, and Downriver Negidals)”. M9 could be upstream N3 but I am not aware of N1a or N1b or N1 LLY22g being found in Amur area.

Ebizur, would you kindly like to share the link (or the name) of the study where O2b is found in Udegey.

terryt said...

"the mtDNA pool of Taiwan aborigines is very typical of Southeast Asian populations, with an overwhelming majority of R subclades (especially B and F)"

Indeed. So much so that I am certain that research will eventually reveal that mt-DNA R developed from N in Southern Wallacea, specifically in the triangle formed by Sumba, Timor, Alor and Flores. R22's root is claimed to lie in the Lombok/Alor region, although it has been found elsewhere in Malaysia and Indonesia. R14's root is also most likely in the triangle, although it has been found as far away as the Nicobar Islands in the west and New Guinea in the east. R23 straddles the Wallace Line to the west of the triangle. To me it seems obvious that P developed to the east of the island triangle: in Australia. Both R9/F and the haplogroup collection making up the R11'B6, B4'5 and R24 group obviously developed northwest of the Wallace Line, as did all the other R haplogroups.

"Terry, M9 must be just K. Do not know more precisely as I only copied the values".

I don't think so. K is unlikely so far north whereas N and/or O are extremely likely, and not listed as being present. Y-DNA M9 includes both these haplogroups.

"Ebizur, would you kindly like to share the link (or the name) of the study where O2b is found in Udegey".

At this stage I don't require a reference to accept that this is an extremely likely find.

Kristiina said...

In my first post, I mixed up lines F and Y and wrote that Udegey have 8.7% of F, but it is in fact Y, descendant of N9. So, what Taiwanese aboriginals and Udegey have in common, is not what they share but what they lack.

Anyway, in the Starikovskaya et al paper they say that “branching patterns of the Lower Amur and adjacent Okhotsk Sea coast/Kamchatkan populations, relative to those located in Western and Middle Siberia, may reflect relatively recent demic expansions which have brought haplogroups G, S, Y and Z into the Sea of Okhotsk/ Kamchatka region. The observed geographical distribution of these haplogroups (tables 1 and 2) would be expected from anthropological, archaeological and linguistic evidence indicating the expansion of the Altaic-speakers from the Lower Amur/Manchuria region during the Neolithic.”

Then there was another incongruity in my previous mail. I should have used according to the new nomenclature N1c and not N3.

Ebizur said...

Thank you for the link, Kristiina.

First, I would like to correct a slight error in your previous tabulation of the Udegey mtDNA data from Starikovskaya et al. 2005. According to this study's Table 2, the authors' sample of Udegey mtDNA contained 14/46 = 30.4% N9(xY) and 4/46 = 8.7% Y for a total of 18/46 = 39.1% N9. Y was found in the following samples besides the Udegeys: 37/56 = 66.1% Nivkhi, 33/87 = 37.9% Ulchi, 7/33 = 21.2% Negidal, 15/155 = 9.7% Koriak, 2/47 = 4.3% Itelmen. This is consistent with other studies' findings of high frequencies of mtDNA haplogroup Y in populations surrounding the Sea of Okhotsk, especially in the vicinity of its southwestern shores (i.e. Tungusic peoples of the lower Amur region, Nivkhs, and Ainus). Haplogroup N9(xY), which tends to be a more typical East/Southeast Asian mtDNA haplogroup, was found with high frequency only in the Udegey sample, but it was also detected in the samples of Tubalars (5/72 = 6.9%), Ulchi (6/87 = 6.9%), and Tuvans (3/95 = 3.2%). They have reported finding mtDNA haplogroup F, a typically Chinese/Vietnamese haplogroup, mainly in the Yeniseyan Kets (9/38 = 23.7% F) and the Turkic Tofalars (4/46 = 8.7% F) and Tuvans (4/95 = 4.2% F), with singletons found in their samples of Evenki (1/71), Tubalars (1/72), Ulchi (1/87), and Mansi (1/98). MtDNA haplogroup F was absent from the study's samples of Nganasans (0/24), Buryats (0/25), Negidals (0/33), Udegey (0/46), Itelmens (0/47), Nivkhi (0/56), Chukchi (0/66), Eskimos (0/79), and Koriaks (0/155).

Anyway, you are correct that the Udegeys do stand out in the Siberian genetic landscape for their high frequencies of N9(xY) and M(xM8CZ, D, G), which are generally much more common in East/Southeast Asia than in North Asia. However, despite this vague "East Asian" tendency, the mtDNA pool of the Udegeys according to this study is still nowhere close to that of the Taiwan aborigines, as the Taiwan aborigines exhibit a typically Southeast Asian mtDNA pool dominated by R (B & F & R9) and complemented by subclades of M7 and M9, whereas this sample of Udegeys is completely devoid of any representative of haplogroup R.

Ebizur said...

The following are the only data I have regarding Udegey Y-DNA:

Lell et al. 2002
Udegey
12/20 = 60% C3c-M48
5/20 = 25% K-M9(xO1a-M119, N1c-Tat, P-M45) [It now appears that these should turn out to be O2b* or O3.]
2/20 = 10% P-M45(xR1a1a-M17, Q1a3a-M3)
1/20 = 5% R1a1a-M17

Jin, Han-Jun; Kim, Ki-Cheol; Kim, Wook (2009). "Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia," American Journal of Physical Anthropology. doi:10.1002/ajpa.21232
14/21 = 66.7% C-RPS4Y711
2/21 = 9.5% K-M9(xNO-M214)
2/21 = 9.5% O2b-SRY465(xO2b1-DXYS5Y)
1/21 = 4.8% O3-M122(xLINE1)
1/21 = 4.8% O3-M122(+LINE1)
1/21 = 4.8% Y*(xC, DE, K)

I would like to know more precisely the classification of the 2/20 = 10% P-M45(xR1a1a-M17, Q1a3a-M3) in the Udegey sample of Lell et al. 2002 and the 2/21 = 9.5% K-M9(xNO-M214) in the Udegey sample of Jin et al. 2009. Is it really some sort of haplogroup Q, as Kristiina seems to have assumed, or is it rather some type of R (R1b, R2, etc.)? Both R1b and R2 have been found in some Buryats.

In any case, the Y-DNA pool of the Udegeys seems to share an extremely high frequency of C3c-M48 with Northern Tungusic (Evenk, Even, Negidal) populations of North Asia, but the Udegeys also exhibit O3-M122 and O2b-SRY465, which is similar to Koreans and Southern Tungusic peoples of Manchuria (Manchus, Solon Evenks, Hezhes).

terryt said...

"what Taiwanese aboriginals and Udegey have in common, is not what they share but what they lack".

But that cannot be used to explain any genetic connection. Taiwanese and Europeans have very few haplogroups in common for example. I see no surprises in the data for either Taiwanese aboriginals or Udegey. Unless Udegey do actually have a complete absence of either N or O Y-DNA.

Kristiina said...

If an analysis shows an unexpected result, I think that it is only normal to try to find an explanation. So, it is a fundamental thing to look into the haplogroup distribution of that particular group, and that is what we have done. I think that picture is now much clearer to everybody.

That M9 in the Lell study should not be O3 as they specifically say that ”Interestingly, none of the Y chromosomes analyzed in the present study contained the M122 marker, which has been shown to represent a large proportion of northern Chinese and East Asian Y chromosomes”. So O2b-SRY465(xO2b1-DXYS5Y) seems to be the most plausible option. In that case, O2b (and O2b1) would be a clear link between Koreans and Japanese, on one hand, and Udegey, Nivkh, Ulchi, on the other, if this M9 is now O2b in all these Okhotsk groups.

It seems that O2b-SRY465(xO2b1-DXYS5Y) is not very widespread in Siberia. Daur have it, and they also have O2a-M95(xO2a1-M88), but Mongols have instead O2*-P31(xO2a-M95, O2b-SRY+465). This O2*-P31(xO2a-M95, O2b-SRY465) is detected in outer and inner Mongolians and Daur.

In a study on Nivkh ydna (Tajima et al.) they have used the formula 28.6% of O-AS1(xO3-M122, O1a-M119).

Moreover, I think that there is surprisingly much O1-M119 in the easternmost populations of the Northeast: Daur 5.1% O1a-M119 (Xue et al. 2006), Yenisey Evenks 3.2% O1a-M119 (Jeffrey et al, 2001), Ulchi/Nanai 3.8% O1a-M119 (Jeffrey et al, 2001) and Nivkh 5.9% O1a-M119 (Jeffrey et al, 2001).

That P-M45(xR1a1a-M17, Q1a3a-M3) could, in fact, be R1b or R1a, if Udegey have some western mtdna haplogroups as it seems on the basis of this summary (http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21232/abstract).

Udegey seem to differ from other Siberians in that they lack ydna N and mtdna D, G and A, and if their P-M45 is only R, they lack also Q. As O3 is detected only in Han-Jun et al. study, it is possible that it is quite recent in Udegey. The Japanese seem to consider that O3a lines are quite recent:
Early Yayoi Intra-Mainland Migration - Circa 800-400 BCE (Northern Kyushu)
O3a4-LINE1 3.10% Sanmiao (Dongye-Huiji) Jar Borial Lower Dolmen Lelang Sea Folk Wo
O2b1-47z 22.00% Wo (Songunni-Ongagawa)

Middle Yayoi Immigration - Circa 400-1 BCE (North Kyushu)
O3-M122* 6.60% Jizi Emigrant Hebei Farmers Higher Dolmen Bronze Dagger

Tumuli Period Circa 369 AD
(Yuezhi-Silla Immigration Ojin aka "Hormusta" Dynasty Yamato-Baekje Pact/Seven Branch Sword)
(Purported Equestrian Conquerers' Dynasty)
O3a3c-M134 10.40% Qi-Qins Emigre

I found also this comment on Internet ”previous O3-LINE1 among Miao and Yao people are proven mostly O3a3b-M7, but in other populations, ex: previous O3-LINE1 among Taiwan Han people are now mostly O3a3-P201 and O3a4-002611. I tend to suppose O3-LINE1 in Koreans and Japanese are O3a3-P201 and O3a4-002611”.

I still think that Udegey are not typical Siberians or extreme North-Easterners.

Kristiina said...

I got acces to the data in “Genetic Diversity of Two Haploid Markers in the Udegey Population From Southeastern Siberia” (Jin et al. 2009). It seems that they share a strange Y*(xC, DE, K) line at a frequency of 1/21 = 4.8% with at least the following groups: Beijing Han (the highest frequency), Koreans, Buryats, Khalk, Yunnan, Philippines, Thais. They also share with the same groups K-M9 (xO) that should not be R or Q as they say-that “in addition, unlike on the maternal side, very little contribution from European Y chromosome haplogroups was observed in the Udegeys studied here, although non-differentiated Y chromosomes (e.g., haplogroups Y* and K-M9) need further analysis of their classification. It is unusual to find European mtDNA input, and not European Y input in the Udegey population, since male-biased Europeangene flow is much more common.” According to Jin paper, Udegey have some D4c, but this clade seems to be, in fact, typical of East-Asians and not of Northeast-Asians and Siberians who carry other D4 clades, for example D4e and D4j.

On the origin of O2-SRY465 they say that “In the median-joining network, the haplogroup O2-SRY465 chromosomes of the Udegeys are also connected to the East Asian populations (e.g., Koreans and Manchurians). This finding of the occurrence of haplogroup O2-SRY465 chromosomes in the Udegeys may be considered concordant with the historical views about the early connection between ancient Udegeys and northeast Asians (e.g., Qing Dynasty of China and the Ancient Koguryo/Parhae States of Korea).”

To me the original Udegey group consisted of ydna C3c-M48 and mtdna N9. According to Zhong study (Zhong et al. 2010), the age of STR variation of C3c is 10.8kya and the divergence time 9.3kya, and the highest frequencies are in Oroquens, Ewenki and Mongolians of Inner Mongolia, Manchu and Hezhe of Heilongjiang and Kyrgyz of Xinjiang. They also say that “We believe that M48 originated in NEAS populations, which agrees well with the suggested recent migration (for example, the Mongol expansion) of M48-derived individuals into Central Asia and Siberia”. On C3 they say that “The Han Chinese display a high STR diversity, especially those in the eastern coastal region (0.467) as well as other eastern populations (Korean,0.463; Japanese, 0.453), whereas populations in the north and west show low diversities (Altaic, 0.281; Tibetan, 0.366). Therefore, the distribution and gene diversities of the M217-derived lineages support a single eastward migration through the southern route and the subsequent northward migration of Hg C along the coastline of mainland East Asia in prehistory. The evidence from dental morphological
traits pointed to the same direction.”

terryt said...

"This O2*-P31(xO2a-M95, O2b-SRY465) is detected in outer and inner Mongolians and Daur".

That is extrememly interesting. I don't think O2*-P31(xO2a-M95, O2b-SRY465) has been found anywhere in the south so this finding indicates a northern origin for O2 as a whole, as I have long suspected.

"O3a3c-M134 10.40% Qi-Qins Emigre"

O3-M134 is now O3a2c1. This haplogroup is strongly associated with Sino-Tibetan speakers although it is spread from Tibet to Japan.

"previous O3-LINE1 among Miao and Yao people are proven mostly O3a3b-M7, but in other populations, ex: previous O3-LINE1 among Taiwan Han people are now mostly O3a3-P201 and O3a4-002611".

O3-M7 is now O3a2b, predominantly a Hmong-Mien/Mon-Kmer haplogroup (ie. south of the Yangtze). O3a3-P201 is now basal O3a2, widespread through East Asia but especially in the Han. O3a4-002611 is O3a1c, also high in China, especially south of the Yangtze.

Tha above would suggest that, apart from O2 and C3, the Udegey are partly the product of a northward movement from within China. So they may have some K-M9(xNOPS).

Ebizur said...

Kristiina wrote,

"That M9 in the Lell study should not be O3 as they specifically say that ”Interestingly, none of the Y chromosomes analyzed in the present study contained the M122 marker, which has been shown to represent a large proportion of northern Chinese and East Asian Y chromosomes”. So O2b-SRY465(xO2b1-DXYS5Y) seems to be the most plausible option. In that case, O2b (and O2b1) would be a clear link between Koreans and Japanese, on one hand, and Udegey, Nivkh, Ulchi, on the other, if this M9 is now O2b in all these Okhotsk groups."

Nice find regarding the lack of M122 in the samples of Lell et al. 2002. That means that their "M9" category is actually K-M9(xN1c1-Tat, O1a-M119, O3-M122, P-M45).
They have reported detecting such Y-DNA in their samples of Udegey (5/20 = 25%), Ulchi/Nanai (8/53 = 15.1%), and Nivkh (2/17 = 11.8%) from the lower Amur region, and Brib[r]i/Cabecar from Costa Rica (1/13 = 7.7%). The Brib[r]i/Cabecar sample from Costa Rica also contains some sort of apparent African admixture (Y*(xDE-YAP, C-RPS4Y, F-M89)), so I would guess that the K-M9(xN1c1-Tat, O1a-M119, O3-M122, P-M45) Y-DNA in their case is probably T1a-M70 from Southern Europe or vicinity.
In the case of the indigenous populations of the lower Amur region, K-M9(xN1c1-Tat, O1a-M119, O3-M122, P-M45) could be any sort of N-M231(xN1c1-Tat), such as N1c2a-M128 (formerly N1 > N1a), N1c2b-P43 (formerly N2 > N1b), or any of the diverse varieties of N*. It could be any sort of O2-P31, such as O2a1-M95, O2b-SRY465, or O2*-P31. There is even an off chance that some or all of it could be L-M20, which has been detected in some nearby populations (e.g. Koreans).
Pending further information, I bet that it should turn out to be some assortment of N-M231(xN1c1-Tat) and O2b-SRY465, with perhaps an occasional instance of O2*-P31.

Consider the Hezhe (PRC Nanai) data of Xue et al. 2006 for comparison:

Hezhe (Xue et al. 2006)
3/45 = 6.7% C-RPS4Y(xC1-M8, C3-M217)
5/45 = 11.1% C3-M217(xC3c-M48)
5/45 = 11.1% C3c-M48
1/45 = 2.2% NO-M214(xN1-LLY22g, O-M175)
8/45 = 17.8% N1c2b-P43
1/45 = 2.2% O2-P31(xO2a1-M95, O2b-SRY465)
2/45 = 4.4% O2b-SRY465(xO2b1a-47z)
7/45 = 15.6% O3-M122(xO3a2a-M159, O3a2b-M7, O3a2c1-M134) [LINE1 -]
4/45 = 8.9% O3-M122(xO3a2a-M159, O3a2b-M7, O3a2c1-M134) [LINE1 +]
2/45 = 4.4% O3a2c1-M134(xO3a2c1a-M117)
7/45 = 15.6% O3a2c1a-M117

12/45 = 26.7% K-M9(xN1c1-Tat, O1a-M119, O3-M122, P-M45) [8 N1c2b-P43 + 2 O2b-SRY465(xO2b1a-47z) + 1 NO-M214(xN1-LLY22g, O-M175) + 1 O2-P31(xO2a1-M95, O2b-SRY465)]

Even with the extremely high frequency of O3-M122 (20/45 = 44.4%) in this sample of Nanais from China, the types equivalent to the K-M9(xN1c1-Tat, O1a-M119, O3-M122, P-M45) category of Lell et al. 2002 are still found in about one quarter of the sample.

Kristiina wrote,

"In a study on Nivkh ydna (Tajima et al.) they have used the formula 28.6% of O-AS1(xO3-M122, O1a-M119)."

The O-AS1 category of Tajima et al. 2004 seems to be equivalent to NO-M214 of the present ISOGG tree. That would explain why "O-AS1" was found in all this study's samples, including 6/61 = 9.8% "Buryat" and 11/49 = 22.4% "Northern Han," whereas K-M9(xAS1, P-P27) was found only in "Philippine (Tagalog language group)" (5/50 = 10.0%) and "ordinary Malay near Kuala Lumpur" (1/12 = 8.3%).

Ebizur said...

Sorry for the double post.

Kristiina wrote,

"That P-M45(xR1a1a-M17, Q1a3a-M3) could, in fact, be R1b or R1a, if Udegey have some western mtdna haplogroups as it seems on the basis of this summary (http://onlinelibrary.wiley.com/doi/10.1002/ajpa.21232/abstract)."

Lell et al. 2002
Lower Amur/Okhotsk Coast:
P-M45(xM17, M3)
6/17 = 35.3% Nivkh
2/20 = 10.0% Udegey
2/53 = 3.8% Ulchi/Nanai
0/16 Okhotsk Evenk
0/10 Upriver Negidal
0/7 Downriver Negidal

Kamchatka:
P-M45(xM17, M3)
5/27 = 18.5% Koryak
0/18 Itelmen

Figure 3
3 M45(xM17, M3, M173) [Okhotsk/Amur]
5 M45(xM17, M3, M173) [Okhotsk/Amur]
3 R1-M173(xM17) [2 Kamchatka + 1 Okhotsk/Amur]
15 R1-M173(xM17) [14 North/Central America + 1 Okhotsk/Amur]

Eight of the ten P-M45(xM17, M3) Y-chromosomes from the Amur/Okhotsk samples of Lell et al. must be negative for M173, and therefore Q(xQ1a2a1a1-M3), R(xR1-M173), or (an otherwise unconfirmed as far as I know) P*-M45(xQ, R). However, two of them are definitely R1-M173(xR1a1a-M17), so probably some sort of R1b. The Udegey sample of Lell et al. 2002 and the Nivkh sample of Tajima et al. 2004 contain some R1a1 Y-chromosomes, so I suspect some sort of Western admixture here (either recent Slavic or ancient Indo-Iranian).
In any case, subtracting the two R1-M173(xR1a1a-M17) individuals from Lell's pool of Lower Amur/Okhotsk Coast samples leaves 8/123 = 6.5% P-M45(xR1-M173, Q1a2a1a1-M3) in this region, so some sort of Q or R2 is definitely present in some members of these populations, especially the Nivkhs. However, it is impossible to deduce whether the two Udegeys are P-M45(xR1-M173, Q1a2a1a1-M3) or R1-M173(xR1a1a-M17).

Kristiina wrote,

"I got acces to the data in “Genetic Diversity of Two Haploid Markers in the Udegey Population From Southeastern Siberia” (Jin et al. 2009). It seems that they share a strange Y*(xC, DE, K) line at a frequency of 1/21 = 4.8% with at least the following groups: Beijing Han (the highest frequency), Koreans, Buryats, Khalk, Yunnan, Philippines, Thais."
Where did you obtain that study? Do you have paid access to it?

Anyway, this Y*(xC, DE, K) is probably a catch-all for various F-M89(xK-M9) derivatives, which generally have been found to belong to typical South Asian (e.g. H-M69) or West Asian/European (e.g. J-M304, I-P19, G-M201) haplogroups upon further testing.

Kristiina wrote,

"They also share with the same groups K-M9(xO) that should not be R or Q as they say-that “in addition, unlike on the maternal side, very little contribution from European Y chromosome haplogroups was observed in the Udegeys studied here, although non-differentiated Y chromosomes (e.g., haplogroups Y* and K-M9) need further analysis of their classification."
It could easily be Q or N, since most researchers do not assume that either of these haplogroups represents "contribution from European Y-chromosome haplogroups." Frankly, it could even be some sort of haplogroup R for all we know. It is just not O-M175.

Kristiina said...

In that other study, Jin etal., they use the following typings (with Udegey frequencies):
y*(xC/DE/K) 4.8%
C-RPS4Y 66.7%
DE-YAP 0%
K-M9 (xO) 9,5%
N/O-M124 (xO-M175) 0%
O-M175 (xO-M119/P31/M122) 0%
O*-M119 0%
O-P31 (xO-M95/SRY+465) 0%
O*-M95 0%
O-SRY+465 (xO-DXYS5Y) 9.5%
O*-DXYS5Y 0%
O-M122 (xO-LINE1) 4.8%
O*LINE1 4.8%

Am I right that based on the above, Udegey K-M9 in Jin paper cannot be N-M231(xN1c1-Tat) or any other upstream NO line. On the basis of above, it should not be O2-P31 either. So, what is left for this K-M9, seems to be either Q, R or L. According to Malyarchuk et al. study, Buryats, Koryaks and Tungusic Evens and Evenks and Koreans have the following frequencies:
Buryats R2-M124 2.7%, R1b1b2-M269 0.7%
Koryaks Q1a*-MEH2 10.3%
Evenks R1b1b2-M269 2.4%
Evens Q1a3a-M3 3.2%
Koreans 0% all
The typings were the following: Q1a*-MEH2, Q1a2-M25, Q1a3*M346, Q1a3a-M3, R2-M124, R1b1b1-M73, R1b1b2-M269.

According to Zhong et al. 2010 study, Heilongjang Han have 1.5 % of R1b-M269. In China R1b-M73 is found in Gansu and Shanxi Han and Heilongjang Mongolians. However, also Q is found in China: Q1a1-M120, Q1a2-M25, Q1a3-M346. Liaoning and Heilongjang Man seem to have Q1a1-M120, and they are not that far from Amur area
So Udegey K-M9 could then be R2-M124, R1b-M73 or R1b1b2-M269 or Q1a lines. Anyway, the comment according to which ”very little contribution from European Y chromosome haplogroups was observed” could have been clearer and they could have said that K-M9 is actually (in part) haplogroup R, if that is the case

As for this Y*(xC, DE, K), according to this same Zhong et al. paper, Gansu Han, Shandong Han, Heilongjang Han, Ningxia Hui and Inner Mongolians have J2. Henan Han, Liaoning Han, Ningxia Hui and Mongolians have G2. Ningxia Hui have also H. Interestingly, L3 has been detected in Heilongjang Han and Ningxia Hui. I would vote for J, as it has the highest frequencies.

Ebizur said...

Thank you for additional information from the Jin et al. 2009 paper, Kristiina.

At the risk of being importunate, I repeat my previous question: where did you obtain that study (Jin et al. 2009)? I do not have access to it, so I can only refer to people's comments that I have found online.

Kristiina said...

Ebizur, we both have a Google account, so is it possible that you send me a personal email. I can then send you the PDF. If it is not working that way, can you accept me in your "circle". (I do not understand very well how this Google profile works and my profile is not complete!)

Ebizur said...

Kristiina,

If it would not be too much trouble, may I ask you to send the Jin et al. 2009, Zhong et al. 2010, and the Malyarchuk et al. study to which you have referred to daikun083@gmail.com? I would be very grateful.

By the way, in the meanwhile, I have noticed that the mtDNA haplogroup M individuals in Starikovskaya's Udegey sample have been defined more precisely as M7 (9/46 = 19.6%, three different but apparently closely related haplotypes) and M9 (4/46 = 8.7%). Two different M7 haplotypes, which are not shared with the Udegeys, also have been found in the nearby and linguistically related Ulchis (2/87 = 2.3%). Starikovskaya's sample of Tuvans from south-central Siberia also contains two different M7 haplotypes (3/95 = 3.2%), shared with neither the Udegeys nor the Ulchis. From another paper, I recall that the M* found in this sample of Mansis from western Siberia also belongs to M7 (1/98 = 1.0%). M7 is generally a coastal East Asian haplogroup, prevalent in populations from Japan, eastern China (and Taiwan, including the aborigines of that island), and Vietnam. I suppose that the Udegeys and Ulchis represent the northernmost extension of this haplogroup along the eastern coast of Asia; maybe its presence in these two populations is somehow connected with the spread of O-M175, which also seems to find its northern terminus in the same populations (excepting singletons that have been reported from some samples of Koryaks and Yukagirs). M7 in the Tuvans is probably indicative of a secondary East Asian influence on this population, related to the East Asian influence(s) on their Southern Altayan, Kazakh, and Mongol neighbors (also reflected by e.g. Y-DNA haplogroups O3 and D3), and is probably separate from the East Asian influence on populations of the Amur River basin/Greater Manchuria.

M9 was found only in this study's sample of Udegeys. It is most common in Tibet, but also found with low frequency elsewhere in continental East Asia and Central Asia, and it is related to haplogroup E, which is common in Austronesians from Taiwan, the Malay Archipelago, and the Mariana Islands.