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Ebizur
08-26-2021, 01:33 PM
cf. Haihua Bai, Xiaosen Guo, Narisu Narisu, et al. (2018), "Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia." Nature Genetics volume 50, pages 16961704. https://doi.org/10.1038/s41588-018-0250-5

Supplementary Table 6 Y haplogroup distribution of the Mongolians.

Abaga
1/15 Q1
1/15 T
1/15 R
1/15 N
3/15 O
8/15 C3

Buryat
9/14 N
1/14 O
4/14 C3

Horchin
1/16 D3a
1/16 R
1/16 N
8/16 O
5/16 C3

Khalkha
1/14 H1
1/14 J2
1/14 D3a
1/14 N
3/14 O
7/14 C3

Oirat
1/8 J2
2/8 R
1/8 O
4/8 C3

Sonid
1/5 D3a
1/5 N
1/5 O
2/5 C3

Mongol total
1/72 H1
1/72 Q1
1/72 T
2/72 J2
3/72 D3a
4/72 R
13/72 N
17/72 O
30/72 C3

One can use the maximum likelihood phylogenetic trees presented in Supplementary Figure 7 to refine the haplogroup assignments as follows (I have used a question mark to indicate cases in which I have less than 100% confidence in my resolution of the phylogeny):

Abaga

1/15 Q1-M120 ?> Q-Y515 This Abaga individual's Y-DNA forms a clade with HG02134_KHV and HG02116_KHV (Q-Y529) vis--vis HG02696_PJL (Q-FT9308 > Q-Y225388).

1/15 T-M70 > T-L131(xCTS3767) This Abaga individual's Y-DNA forms a clade with members of T-L131 > T-CTS3767 (NA20758_TSI, HG01530_IBS, HG01051_PUR) vis--vis members of T-CTS11451 (NA20520_TSI, HG01190_PUR, NA19655_MXL, HG01133_CLM, NA20527_TSI). However, his Y-DNA is quite distinct from the Y-DNA of members of T-CTS3767. He most likely should belong to T-L131* like YF15081 from Armenia or to the T-Y13244 clade (Arabs, Turkey, Jew, England, etc.).

1/15 R1a-Z93/F992 ?> R1a-Z94 ?> R1a-Y40 This Abaga individual's Y-DNA may very weakly form a clade with members of R-Z96 (NA20796_TSI, NA20539_TSI) vis--vis members of R-Y37 (NA20897_GIH, HG04194_BEB, HG03926_BEB, HG02603_PJL, HG02699_PJL).

1/15 N-Tat ?> N-Y16323 ?> N-F4205 This Abaga individual's Y-DNA weakly forms a clade with the Y-DNA of eight of the present study's haplogroup N Buryat vis--vis the one remaining haplogroup N Buryat, this last Buryat representing the most basal branch of the typically Buryat subclade of haplogroup N-Tat in this study.

1/15 O1a-M119 ?> pre-O-M307 This Abaga individual's Y-DNA is potentially quite interesting. It weakly forms a clade with members of O1a1-M307/P203 vis--vis the Y-DNA of NA18647_CHB (O-Z23193 > O-CTS5726 > O-F14840), but it surely must not share 66 SNPs with the former vis--vis the latter clade. Therefore, it is likely that, if this Abaga individual's Y-DNA data were added to the YFull tree, it would split from the branch between the current O-Z23193 and O-M307 nodes of the phylogenetic tree.

1/15 O2-M122 > O2a1c-JST002611 > O-F11 ?> O-F4062 This Abaga individual's Y-DNA forms a clade with one of the present study's Oirat; the common ancestor of those two then forms a clade with two of the present study's Horchin vis--vis the Y-DNA of HG02047_KHV (O-F11 > O-F4062 > O-Y15976 > O-Y16154 > O-MF6934). Although HG02047_KHV himself is a Vietnamese person from Ho Chi Minh City, most members of the O-F4062 clade seem to have been found in the eastern part of northern China and in surrounding countries (Mongolia, Korea, Japan). This subclade of O-F11 appears to be a candidate for the haplogroup of some individuals or a population who have contributed to the spread of agriculture toward the northeast of the Yellow River basin.

1/15 O2-M122 > O2a2b1a1-M117/Page23 > O-CTS7634 > O-F2188 (most likely O-Y29861) This Abaga individual's Y-DNA may weakly form a clade with HG02122_KHV (O-Y29861*) vis--vis HG01852_KHV (O-Y178119). In any case, it certainly must belong to the O-F2188 clade.

6/16 C2-M217 > C-L1373 Three of these belong to one subclade of C-L1373 alongside three Khalkha, two Buryat, and two Horchin; I suppose this most likely should be C-M504. Another three Abaga belong to a different subclade of C-L1373 alongside three Oirat, two Khalkha, and a Horchin; I suppose this most likely should be C-M86. This latter subclade appears to be further divisible into an Oirat-Khalkha subclade vs. an Abaga-Horchin subclade.

2/16 C2-M217 > C-F2613 ?> C-F845 These two Abaga individuals may weakly form a clade vis--vis a clade formed by NA19079_JPT, HG02141_KHV, HG02373_CDX, and HG02381_CDX.

Buryat

9/14 N All belong to a particular subclade of N-Tat. Eight of these Buryat form a clade vis--vis the single member of N-Tat from the present study's sample of Abaga. The ninth Buryat is basal to all other members of the Mongol subclade of N-Tat in this study.

1/14 O2-M122 > O2a2b1a1-M117/Page23 > O-M133/M1706 > O-CTS7634 May weakly form a clade with HG00592_CHS (O-CTS7634*) vis--vis NA18623_CHB (O-CTS7634 > O-CTS320*). YFull also has YF64936 from Mongolia (Selenge) and YF03969 from Russia in O-CTS7634*, so it appears that the O-CTS7634 clade may have a fairly long history in the South Baikal/North Mongolia region.

4/14 C2-M217 > C-L1373 Two of these form a clade with three Khalkha, three Abaga, and two Horchin. These most likely should be C-M504. The other two Buryat are very closely related to each other and form a clade with a Horchin individual from the present study; these might belong to C-F1756. Surprisingly, none of the present study's Buryat belongs to C-M407.

Horchin

1/16 D3a Shares a very recent common ancestor with the present study's other Mongol members of haplogroup D3a (Khalkha x1, Sonid x1). This Horchin individual appears to form a shallow clade with the Khalkha individual vis--vis the Sonid individual.

1/16 R1a-M459 > R1a-M198 > R1a-M417 > R1a-Z645 > R1a-Z93 > R1a-Z94 > R1a-Z2124 > R1a-Z2125 > R1a-Z2123 ?> R1a-Y934 May weakly form a clade with members of R-Z2123 > R-Y934 > R-SK2031 > R-YP523 > R1a-YP520 (HG03750_STU, HG03743_STU) vis--vis members of R-Z2123 > R-Y47 > R-Y46 (HG04020_ITU, HG03687_STU, NA20864_GIH, HG04131_BEB, HG04096_ITU, HG04023_ITU).

1/16 N-L729 ?> N-F1360* Basal by a great margin to a clade formed by members of N-M128/N-F710 (HG02026_KHV, NA18613_CHB ). The lineage of this Horchin individual appears to derive from a branch between the N-L729 and the N-F710 nodes shortly after the MRCA of N-L729. N-P43 also derives from such a phylogenetic position, but YFull currently has a total of 70 SNPs shared between N-M128 and N-P43 at or downstream of the N-L666 node, and the Y-DNA of this Horchin individual does not appear to share so many SNPs with members of N-M128 downstream of the N-L729 node to justify his belonging to N-L666 > N-P43, so N-F1360* seems more likely.

1/16 O1b1-M95 > O-M1310 > O-M1348 ?> O-F1252(xF2924) Appears to weakly form a clade with members of O-F2924 vis--vis members of O-M1283. Therefore, this Horchin individual most likely belongs to a clade in the same phylogenetic position as O-F5504, which has been found among Miao people in Hunan and in Sichuan Han, Shaanxi, and a pair of closely related individuals from Ryazan Oblast of Russia.

1/16 O1b1-Page59 > O-F779 > O-F2064 May weakly form a clade with HG00634_CHS vis--vis NA18603_CHB and NA18637_CHB, every one of whom has been placed within O-F2064 on the YFull tree.

1/16 O2-M122 > O2b-CTS1754 > O-F953 > O-F1024 Securely forms a clade with HG00559_CHS (O-F953 > O-F1024 > O-Y29783 > O-Y29790 > O-Y173834) vis--vis HG02088_KHV (O-F953 > O-Y238031).

2/16 O2-M122 > O2a1c-JST002611 > O-F11 ?> O-F4062 Form a clade with an Oirat-Abaga lineage vis--vis HG02047_KHV (O-F11 > O-F4062 > O-Y15976 > O-Y16154 > O-MF6934).

1/16 O2-M122 > O2a1c-JST002611 > O-F11 > O-F632 > O-F133 > O-Y20951 Forms a robust clade with NA18629_CHB (O-F133 > O-Y20951 > O-Y20932 > O-BY57897) vis--vis NA18611_CHB (O-F133*) and eight members of O-F133 > O-F17.

1/16 O2-M122 > O2a1c-JST002611 > O-F11 > O-F632 > O-F133 > O-F17 > O-F793 Forms a clade with a Sonid individual from the present study plus HG00445_CHS (O-F17 > O-F793*) vis--vis members of O-F17 > O-F377 (HG00421_CHS, HG00707_CHS, HG00451_CHS, HG00613_CHS, HG00436_CHS).

1/16 O2-M122 > O2a2a-M7 > O-F1863 May weakly form a clade with members of O-M7 > O-F1276 > O-F1863 > O-V3237 (Kinh in Ho Chi Minh City, Vietnam x4) vis--vis a Xishuangbanna Dai (HG01816) who is currently placed in O-F1863*.

4/16 C2-M217 > C-L1373 Two of these Horchin individuals form a very shallow clade at the tip of a branch that may correspond to C-M504. (A Buryat followed closely by an Abaga are the most basal members of this branch.) Another Horchin is basal to a pair of Buryat within a different subclade of C-L1373, perhaps C-F1756. A fourth Horchin belongs to a third subclade of C-L1373 (perhaps C-M86) and forms a clade with three Abaga individuals vis--vis three Oirat plus two Khalkha.

1/16 C2-M217 > C-F2613 > C-Z1300 > C-F1319(?xF3777) Appears to form a clade with members of C-K700 > C-F1319 > C-F3777 (NA18620_CHB, HG03917_BEB ) vis--vis NA18612_CHB (C-K700 > C-CTS3385 > C-FGC45548 > C-PH2194*). One of the present study's Khalkha individuals shares a similar position in the phylogeny, but this Horchin individual may be very slightly basal (by a margin of one SNP or so) to a clade that subsumes this Khalkha individual plus all members of C-F3777.

Khalkha

1/14 D3a Shares a very recent common ancestor with the present study's other Mongol members of haplogroup D3a.

1/14 H1-M52 > H1a-M82 ?> H-Z5870* This Khalkha individual's Y-DNA forms a clade with HG03846_STU and HG03824_BEB vis--vis members of H-M2914 (HG02786_PJL, HG04164_BEB, HG03778_ITU, HG04002_ITU, HG01583_PJL, etc.). All the aforementioned Y-chromosomes form a clade (i.e. H1a-M82) vis--vis members of H-Z4469 i.e. H-M52(xM82) (HG04188_BEB, HG03812_BEB, NA21093_GIH, NA21111_GIH, NA21112_GIH).

1/14 J2a-L559 ?> J2a-PF4610*, some sort of rather basal J2a but not quite so basal as J2a-PF5008 (It appears to form a clade with HG02774_PJL, HG03693_STU, and HG01781_IBS vis--vis HG01589_PJL.)

1/14 N1b1-Z4784/CTS582 > N-Y6374 > N-CTS7324 > N-CTS7324*(xCTS142) Securely forms a clade with NA18558_CHB vis--vis NA18747_CHB.

1/14 O2-M122 > O2a2-P201 > O2a2a-M188 > O-CTS201 ?> O-MF18110 Appears to very weakly form a clade (i.e. O-CTS201/Z25532) with members of O-M159 vis--vis members of O-M7.

1/14 O2-M122 > O2a2b1a1-M117/Page23 > O-M133/M1706 May weakly form a clade with members of O-A9459/F5970 > O-F438 > O-Y17728 (NA18622_CHB, NA18557_CHB ) vis--vis NA18945_JPT (O-F22770 > O-Y206796), NA18624_CHB (O-A9459/F5970 > O-F14249 > O-F14347*), and HG00409_CHS (O-A9459/F5970 > O-F438*).

1/14 O2-M122 > O2a2b1a1-M117/Page23 > O-M133/M1706 > O-A9459/F5970 > O-CTS1642 > O-CTS5308 ?> O-Y34065

5/14 C2-M217 > C-L1373 Three of these belong to one subclade of C-L1373 (most likely C-M504) alongside three Abaga, two Buryat, and two Horchin. The other two belong to a different subclade of C-L1373 (most likely C-M86) alongside three Oirat, three Abaga, and a Horchin. The three Oirat individuals may weakly form a clade with the two Khalkha individuals vis--vis the rest.

1/14 C2-M217 > C-F2613 > C-Z1300 > C-CTS2657 > C-M407 Appears to form a very young clade with two Sonid individuals vis--vis NA19091_JPT.

1/14 C2-M217 > C-F2613 > C-Z1300 > C-K700 > C-F1319(?xF3777)

Oirat

1/8 J2a-M410 > J2a-Z6065 > J2a-Y7687 ?> J2a-M47/M322 Securely forms a clade with a member of J-PF5119 > J-Z6065 > J-Y7687 > J-Y7702 > J2a-M47/M322 > J-Y7715> J-Y7690 > J-Y14675 > J-Y28883 > J-Y28882 > J-Y28880 > J-Y159137 (HG02490_PJL) vis--vis members of J-PF5119 > J-Z6065 > J-Y13341 > J-Z7515 > J-Z7509 > J-Z7507 (HG03018_PJL, HG02724_PJL), members of J-PF5119 > J-CTS4800 > J-L558 > J-Y5014 > J-M319 (HG01991_PEL, HG01781_IBS), and members of J-PF5119 > J-CTS4800 > J-L558 > J-M67 (HG01402_PUR, NA20534_TSI, HG02236_IBS, plus seven other TSI individuals).

1/8 R2a-M124 > R2a-L294 ?> R2a-Y35095 Most likely forms a clade with HG02660_PJL (R-L294 > R-Y35095 > R-Y171695 > R-FT333560) vis--vis members of R-L294 > R-Y1349 (HG03015_PJL, HG04182_BEB, HG03773_ITU, NA20845_GIH, HG04022_ITU).

1/8 R1b-CTS1078 ≈ R1b-Z2103(?xR-Z2106) May weakly form a clade with NA20532_TSI (R-Z2103 > R-M12149 > R-Y4364 > R-Y4366 > R-Y36437*) vis--vis members of R-Z2103 > R-M12149 > R-Z2106 (HG01515_IBS, HG01277_CLM, NA18645_CHB, NA20866_GIH).

1/8 O2-M122 > O2a1c-JST002611 > O-F11 ?> O-F4062

1/8 C2-M217 > C-F2613 > C-Z1300 > C-K700 > C-CTS3385 Appears to weakly form a clade with NA18612_CHB in C-Z1300 > C-K700 > C-CTS3385 > C-PH2194 vis--vis members of C-Z1300 > C-K700 > C-F1319 > C-F3777 (NA18620_CHB, HG03917_BEB ) and members of C-Z1300 > C-CTS2657 (NA18749_CHB, NA19091_JPT).

3/8 C-L1373 Most likely C-M86. These three Oirat individuals appear to form a very young clade with two Khalkha individuals vis--vis three Abaga and one Horchin.

Sonid

1/5 D3a Shares a very recent common ancestor with a Khalkha and a Horchin from the present study. The Sonid individual appears to be slightly basal to the other two.

1/5 N1b2-CTS12473 Appears to be basal to a clade (N-F1486/M1814) formed by HG04015_ITU, HG02138_KHV, and NA18639_CHB.

1/5 O2-M122 > O2a1c-JST002611 > O-F11 > O-F17 > O-F793

2/5 C2-M217 > C-F2613 > C-Z1300 > C-CTS2657 > C-M407 Appear to form a very young clade with a Khalkha individual from the present study vis--vis NA19091_JPT.

One important fact that is apparent in this study's Mongol Y-DNA data is a presence of the O2a1c-JST002611 > O-F11 (and especially its O-F4062 subclade) clade among Mongols. O-F11 has been found in 4/16 (25%) of this study's sample of Horchin (i.e. Khorchin) Mongols (https://en.wikipedia.org/wiki/Khorchin_Mongols), one of the easternmost groups of people who currently speak a Mongolic language. O-F11 also has been found in 1/5 Sonid, 1/8 Oirat, and 1/15 Abaga.

Compare this with the Mongol Y-DNA data from Di Cristofaro et al. (2013):

1/160 = 0.6% O1a-M119 [1/23 Southeast]
1/160 = 0.6% O-M175(xM119, M95, M176, M122) [1/97 Northwest]
1/160 = 0.6% O1b2-M176 [1/20 Northeast]
3/160 = 1.9% O2-M122(xO2a1-KL2, O2a2-P201) [3/97 Northwest]
2/160 = 1.25% O2a2-P201(xM134) [2/97 Northwest]
7/160 = 4.4% O-M134(xM117) [2/23 Southeast, 1/20 Northeast, 4/97 Northwest]
9/160 = 5.6% O-M117 [4/20 Northeast, 1/18 Central, 1/23 Southeast, 3/97 Northwest]
24/160 = 15.0% O-M175 total

Di Cristofaro et al. (2013) have found O-M134(xM117) in 7/160 = 4.4% of their Mongol samples while not finding any case of potential O2a1c-JST002611 among their Mongol samples. In contrast with this, Bai et al. (2018) have found O2a1c-JST002611 > O-F11 in 7/72 = 9.7% of their Mongol samples while not finding any case of O-M134(xM117).

Combining the results of both studies would produce the following estimate of the breakdown of haplogroup O-M175 among Mongols:

2/232 = 0.86% O1a-M119 (Abaga x1, Southeast Mongolia x1)
2/232 = 0.86% O-M175(xM119, M95, M176, M122) (Horchin x1, Northwest Mongolia x1)
1/232 = 0.43% O1b1a1a-M95 (most likely O-F5504) (Horchin x1)
1/232 = 0.43% O1b2-M176 (Northeast Mongolia x1)
4/232 = 1.72% O2-M122(xO2a1-KL2, O2a2-P201) (Northwest Mongolia x3, Horchin x1)
7/232 = 3.02% O2a1c-F11 (Horchin x4, Sonid x1, Oirat x1, Abaga x1)
4/232 = 1.72% O2a2-P201(xM134) (Northwest Mongolia x2, Khalkha x1, Horchin x1)
7/232 = 3.02% O2a2b1-M134(xM117) (Northwest Mongolia x4, Southeast Mongolia x2, Northeast Mongolia x1)
13/232 = 5.60% O2a2b1a1-M117 (Northeast Mongolia x4, Northwest Mongolia x3, Khalkha x2, Buryat x1, Abaga x1, Central Mongolia x1, Southeast Mongolia x1)
41/232 = 17.67% O-M175 total

Lineages of the samples of Bai et al. (2018) that stand out for their potential phylogenetic interest include:

*the O-M119 Abaga, whose lineage would probably split the branch between the current O-Z23193 and O-M307 nodes of the YFull tree
*the O-M95 Horchin, whose lineage most likely should belong to the rare O-F5504 subclade (which also has been found in two individuals from Ryazan Oblast, Russia)
*the O-M188(xCTS800, M7, M159) Khalkha, whose lineage potentially might be related to the curious Korean & Japanese O-FGC50558 clade about which I have written here (https://anthrogenica.com/showthread.php?24293-Population-admixture-structure-and-demographic-history-of-North-East-Asians&p=790733&viewfull=1#post790733), here (https://anthrogenica.com/showthread.php?24293-Population-admixture-structure-and-demographic-history-of-North-East-Asians&p=791999&viewfull=1#post791999), and here (https://anthrogenica.com/showthread.php?24293-Population-admixture-structure-and-demographic-history-of-North-East-Asians&p=792806&viewfull=1#post792806)
*the N-L729 Horchin, whose lineage most likely should belong to N-F1360*, which is currently represented on the YFull tree only by one commercially tested individual with reported origin in Shaanxi

It is also nice to have confirmation of a presence of N1b-F2905 among Mongols: N1b1-Z4784 in 1/14 Khalkha and N1b2-CTS12473 in 1/5 Sonid.

4624146240462434623946242

Ahmed Ali
08-26-2021, 03:29 PM
Fascinating post. Thanks very much for sharing. Just a brief question - I'm interested in the J2a-L559 Khalka sample (1/14):

[1/14 J2a-L559 ?> J2a-PF4610*, some sort of rather basal J2a but not quite so basal as J2a-PF5008 (It appears to form a clade with HG02774_PJL, HG03693_STU, and HG01781_IBS vis--vis HG01589_PJL.]

The reason being that I share the same (obscure) clade as HG01589_PJL but didn't fully comprehend the link between this Khalka sample and the latter's subclade

Ebizur
08-26-2021, 04:58 PM
Fascinating post. Thanks very much for sharing. Just a brief question - I'm interested in the J2a-L559 Khalka sample (1/14):

[1/14 J2a-L559 ?> J2a-PF4610*, some sort of rather basal J2a but not quite so basal as J2a-PF5008 (It appears to form a clade with HG02774_PJL, HG03693_STU, and HG01781_IBS vis--vis HG01589_PJL.]

The reason being that I share the same (obscure) clade as HG01589_PJL but didn't fully comprehend the link between this Khalka sample and the latter's subclade46247

The Khalkha lineage in question is portrayed in the dendrogram in Supplementary Figure 7c of Bai et al. (2018) as deriving from a branch between a Node A (which is equivalent to the J-M410 node on the current YFull tree) and a Node B (which is equivalent to the J-PF4610 node on the current YFull tree).

If one assumes that both the dendrogram in Supplementary Figure 7c of Bai et al. (2018) and the current YFull tree are entirely accurate (which is not necessarily true, and I have noted a few discrepancies between the two), then:

(1) there must be some SNPs that are positive in every member of the J-PF4610 clade but negative in every member of the J-PF5008 clade, and
(2) 880318_Khalkha must be positive for some of those SNPs but negative for others.

Essentially, what would happen on the YFull tree is that there would be a reduction in the number of SNPs regarded as defining Node B i.e. the J-PF4610 node (which would require a renaming of this node if PF4610 happened to be one of the SNPs found to be negative in 880318_Khalkha), with 880318_Khalkha being placed on the YFull tree as "J-xxx*" (in which xxx would be PF4610 or whichever SNP might be chosen as its replacement), and with J-Z6046 and J-L26 being united under a newly created clade immediately below "J-xxx*."

As for the relation of 880318_Khalkha to you personally, he should be no more closely related to you than any member of the J-PF4610 clade on the current version of the YFull tree is related to you. The Y-DNA of 880318_Khalkha should form a clade with J-PF4610 in comparison to your lineage; in other words, you, HG01589_PJL, and all other members of J-PF5008 form an outgroup that should be basal to a clade subsuming the Y-DNA of 880318_Khalkha in addition to all members of the current J-PF4610 clade (which includes an overwhelming majority of members of haplogroup J2a-M410 who are currently tabulated by YFull).

Shuzam87
08-26-2021, 08:53 PM
There was a more recent study on the Chinese Mongols :
Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels
https://doi.org/10.1016/j.fsigen.2021.102565

Abstract
The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.

Shuzam87
08-26-2021, 08:54 PM
Conclusion
We constructed a high-resolution C-M130 Y-SNP SNaPshot panel containing 28 Y-SNPs and a high-resolution N/O/Q complementary Y-SNP SNaPshot panel containing 30 Y-SNPs. The phylogenetic tree built in the previous study was upgraded to a Chinese population high-resolution phylogenetic tree containing 215 Y-SNPs. The typing results of 37 Y-STRs and 215 Y-SNPs in 679 Mongolian individuals indicated that some detected microvariants were associated with specific haplogroups, which provided a theoretical basis for inferring haplogroups via Y-STR haplotypes. The results of haplogroup assignment revealed Mongolian-prevailing haplogroups (C2*-M217, O2*-M122, N*-M231, R*-M207, and O1b*-P31) and low-frequency haplogroups (DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242), which provided genetic evidence for the complex admixture paternal genetic structure of Mongolic-speaking populations. The observations of genetic affinity showed that the fine-scale paternal genetic structure of Chinese populations was highly consistent with geographical division and language classification, and the studied Inner Mongolia Mongolians had close genetic relatedness with reference Mongolic-, Turkic-, and Sinitic-speaking Hui populations. In conclusion, the Chinese population high-resolution phylogenetic tree and genetic evidence from geographically different Mongolic-speaking populations are indispensable for dissecting the population substructure of Chinese Mongolic-speaking people.

vettor
08-26-2021, 10:24 PM
cf. Haihua Bai, Xiaosen Guo, Narisu Narisu, et al. (2018), "Whole-genome sequencing of 175 Mongolians uncovers population-specific genetic architecture and gene flow throughout North and East Asia." Nature Genetics volume 50, pages 1696–1704. https://doi.org/10.1038/s41588-018-0250-5

Supplementary Table 6 Y haplogroup distribution of the Mongolians.

Abaga
1/15 Q1
1/15 T
1/15 R
1/15 N
3/15 O
8/15 C3

Buryat
9/14 N
1/14 O
4/14 C3

Horchin
1/16 D3a
1/16 R
1/16 N
8/16 O
5/16 C3

Khalkha
1/14 H1
1/14 J2
1/14 D3a
1/14 N
3/14 O
7/14 C3

Oirat
1/8 J2
2/8 R
1/8 O
4/8 C3

Sonid
1/5 D3a
1/5 N
1/5 O
2/5 C3

Mongol total
1/72 H1
1/72 Q1
1/72 T
2/72 J2
3/72 D3a
4/72 R
13/72 N
17/72 O
30/72 C3

One can use the maximum likelihood phylogenetic trees presented in Supplementary Figure 7 to refine the haplogroup assignments as follows (I have used a question mark to indicate cases in which I have less than 100% confidence in my resolution of the phylogeny):

Abaga

1/15 Q1-M120 ?> Q-Y515 This Abaga individual's Y-DNA forms a clade with HG02134_KHV and HG02116_KHV (Q-Y529) vis--vis HG02696_PJL (Q-FT9308 > Q-Y225388).

1/15 T-M70 > T-L131(xCTS3767) This Abaga individual's Y-DNA forms a clade with members of T-L131 > T-CTS3767 (NA20758_TSI, HG01530_IBS, HG01051_PUR) vis--vis members of T-CTS11451 (NA20520_TSI, HG01190_PUR, NA19655_MXL, HG01133_CLM, NA20527_TSI). However, his Y-DNA is quite distinct from the Y-DNA of members of T-CTS3767. He most likely should belong to T-L131* like YF15081 from Armenia or to the T-Y13244 clade (Arabs, Turkey, Jew, England, etc.).



Interesting is that this T is my line of T

Ebizur
08-27-2021, 03:48 AM
There was a more recent study on the Chinese Mongols :
Genetic insights into the paternal admixture history of Chinese Mongolians via high-resolution customized Y-SNP SNaPshot panels
https://doi.org/10.1016/j.fsigen.2021.102565

Abstract
The Mongolian people, one of the Mongolic-speaking populations, are native to the Mongolian Plateau in North China and southern Siberia. Many ancient DNA studies recently reported extensive population transformations during the Paleolithic to historic periods in this region, while little is known about the paternal genetic legacy of modern geographically different Mongolians. Here, we genotyped 215 Y-chromosomal single nucleotide polymorphisms (Y-SNPs) and 37 Y-chromosomal short tandem repeats (Y-STRs) among 679 Mongolian individuals from Hohhot, Hulunbuir, and Ordos in North China using the AGCU Y37 kit and our developed eight Y-SNP SNaPshot panels (including two panels first reported herein). The C-M130 Y-SNP SNaPshot panel defines 28 subhaplogroups, and the N/O/Q complementary Y-SNP SNaPshot panel defines 30 subhaplogroups of N1b-F2930, N1a1a1a1a3-B197, Q-M242, and O2a2b1a1a1a4a-CTS4658, which improved the resolution our developed Y-SNP SNaPshot panel set and could be applied for dissecting the finer-scale paternal lineages of Mongolic speakers. We found a strong association between Mongolian-prevailing haplogroups and some observed microvariants among the newly generated Y-STR haplotype data, suggesting the possibility of haplogroup prediction based on the distribution of Y-STR haplotypes. We identified three main ancestral sources of the observed Mongolian-dominant haplogroups, including the local lineage of C2*-M217 and incoming lineages from other regions of southern East Asia (O2*-M122, O1b*-P31, and N1*-CTS3750) and western Eurasia (R1*-M173). We also observed DE-M145, D1*-M174, C1*-F3393, G*-M201, I-M170, J*-M304, L-M20, O1a*-M119, and Q*-M242 at relatively low frequencies (< 5.00%), suggesting a complex admixture history between Mongolians and other incoming Eurasians from surrounding regions. Genetic clustering analyses indicated that the studied Mongolians showed close genetic affinities with other Altaic-speaking populations and Sinitic-speaking Hui people. The Y-SNP haplotype/haplogroup-based genetic legacy not only revealed that the stratification among geographically/linguistically/ethnically different Chinese populations was highly consistent with the geographical division and language classification, but also demonstrated that patrilineal genetic materials could provide fine-scale genetic structures among geographically different Mongolian people, suggesting that our developed high-resolution Y-SNP SNaPshot panels have the potential for forensic pedigree searches and biogeographical ancestry inference.I noticed that that study had been prepublished online last month, but I took little interest in it because even the supplementary materials were behind a paywall.

I will see whether anything changes when the article is officially published in FSI: Genetics next month.

Ebizur
08-27-2021, 11:58 AM
cf. "Supplementary Material: Haplogroup Frequencies for 39 Populations, grouped by Geography" of Michael F. Hammer, Tatiana M. Karafet, Hwayong Park, et al. (2006), "Dual origins of the Japanese: common ground for hunter-gatherer and farmer Y chromosomes." J Hum Genet (2006) 51:47–58. DOI 10.1007/s10038-005-0322-0

Mongolia
51/149 = 34.2% C-M217(xM86)
27/149 = 18.1% C-M86
2/149 = 1.3% D-M15
2/149 = 1.3% D-P47
1/149 = 0.7% G-M201
1/149 = 0.7% H-M69
4/149 = 2.7% J-12f2 (J2-M172 x3, J-12f2(xM172) x1 according to Karafet et al. 2001, who have tested the same sample of Mongolians)
1/149 = 0.7% NO-M214(xM175, LLY22g)
9/149 = 6.0% N-P43
3/149 = 2.0% N-M178
1/149 = 0.7% O-M175(xM119, P31, M122)
4/149 = 2.7% O2-M122(xM134, LINE1)
24/149 = 16.1% O2-M134
6/149 = 4.0% O2-LINE1
1/149 = 0.7% O1a-M119(xM110)
2/149 = 1.3% O1b-P31(xM176, P49, M95)
4/149 = 2.7% Q-P36
6/149 = 4.0% R-M207 (R-UTY2(xR1-M173) x2, R1b-P25 x1, R1a-SRY10831.2 x3 according to Karafet et al. 2001)

------

cf. Tatiana M. Karafet, Ludmila P. Osipova, Olga V. Savina, Brian Hallmark, and Michael F. Hammer (2018), "Siberian genetic diversity reveals complex origins of the Samoyedic-speaking populations." Am J Hum Biol. 2018;e23194. https://doi.org/10.1002/ajhb.23194

Khalkha from Ulaanbaatar, Mongolia (Note that this may be a subset of the aforementioned "Mongolia" sample of Hammer et al. 2006.)
2/75 = 2.7% C2-M217(xC2a-M325, C2b1-P323) [These might belong to C2b2-CTS4660, which is represented on the current version of the YFull tree by ERR1395618=HGDP01308 from the HGDP sample of Dai from China, HG00628 from the 1KGP sample of Han Chinese from Fujian, and YF87890, who is a commercially tested individual with reported origin in Guangdong.]
14/75 = 18.7% C2a-M325(xC2a1a2a-M86, C2a1a1a-P39, C2a1a3-P369) [This potentially may represent the highest frequency of C-F3918(xP39) found in any sample of present-day people. Members of the same clade have been conspicuously common among examined ancient specimens from central and eastern Inner Mongolia and even Bronze Age and Iron Age Houtaomuga in the Songnen Plain.]
16/75 = 21.3% C2a1a2a-M86
12/75 = 16.0% C2a1a3-P369 ["Star Cluster"; this is the most frequently observed Y-DNA haplogroup among members of the Kerey tribe and among members of most tribes of the Senior Juz of Kazakhs]
1/75 = 1.3% C2b1-P323(xM407)
8/75 = 10.7% C2b1a1a1a-M407
53/75 = 70.7% C2-M217 total

1/75 = 1.3% N1a2b1-P63(xP362) [N-P63 should be equivalent to N-B478, a subclade of N-P43 that is currently found with very high frequency among Nenets, Nganasans, and some groups of Khakas, and which also has been found among Selkups, Dolgans, Tuvans, Altaians, Uyghurs, Mongols, Buryats, and Evenks.]
1/75 = 1.3% N1a2b1-P362
1/75 = 1.3% N1a1a-M178(xN1a1a1a-L708/Z1951) [May belong to Manchurian/Japanese/Korean/Chinese/Tibetan N-Y23747 or Khakas/Indian N-Y24317. I infer that this individual should be the one whose Y-DNA has been assigned to NO-M214(xM175, LLY22g) by Hammer et al. 2006, which I think makes it somewhat more likely that he should belong to N-Y23747, because that clade is present in Japan, and six Japanese individuals also have been assigned to NO-M214(xM175, LLY22g) in that study. Perhaps LLY22g may have undergone a reversion in the N-Y23747 lineage. However, Kang Hu et al. (2015) have written, "As described before, although most of the N samples show C/A genotype on LLY22g, we found three genotypes, C/C, C/A, and A/A inside the N2-F2930 clade. Therefore, we suggest that the LLY22g C/C > C/A occurred already before the split of N1 and N2, and the C/C genotype inside Haplogroup N was caused by reverse mutation, or rather likely a gene conversion between the both LLY22g loci, since recurrent de novo mutations are rarely found inside the human Y chromosomal history. All of the a few C/C individuals that we genotyped belong to the N2a1*-F1883(xF846) clade." Yan et al. (2014) have written, "The former defining SNP of Haplogroup N1, LLY22g (double copied, CC > CA) is proved to be prone to recurrent mutation, since the sample YCH142, downstream of F842 clade, has CC genotype at LLY22g, while the other sequenced N samples have CA. The AA genotype was also observed in an N sample (genotyped in this study but not sequenced by next-generation method). It seems that CC and AA genotypes under Haplogroup N were results of homologous recombination of the two copies." N-F842 is currently considered by YFull and ISOGG to be equivalent to N1b2-CTS12473. Perhaps the individual whose Y-DNA has been assigned to O-M175(xM119, P31, M122) by Hammer et al. 2006 has been mistyped and upon further testing has been found to belong to a subclade of N-Tat, or perhaps this sample of Khalkha from Ulaanbaatar is not in fact a subset of the "Mongolians"/"Mongolia" sample examined by Karafet et al. 2001 and Hammer et al. 2006 after all.]
1/75 = 1.3% N1a1a1a-L708(xN1a1a1a1a-L392) [May belong to Udmurt/Komi/Chuvash/Mari/Mordvin/Bashkir/Tatar N-Y9022 or Estonian/Korean/Chinese/Hungarian/Turkish/Yakut N-M2019.]
2/75 = 2.7% N1a1a1a1a3a-P89 [within N1a1a1a1a-L392; predominates among the Buryat members of haplogroup N]
6/75 = 8.0% N-M231 total

1/75 = 1.3% O1a-M119(xO1a1a-P203)
1/75 = 1.3% O1b-P31(xO1b1a1a-M95, O1b2-P49)
1/75 = 1.3% O2a1b-JST002611
1/75 = 1.3% O2a2-P201(xM7, M134)
5/75 = 6.7% O2a2b1-M134
9/75 = 12.0% O-M175 total

2/75 = 2.7% Q1b1a-L54(xQ1b1a1a-M3) [May belong to Q1b1a3-L330, which has been found with high frequency among present-day Kets and Selkups.]
2/75 = 2.7% Q1a2-M25
4/75 = 5.3% Q-M242 total

1/75 = 1.3% R1a1a1-M417/Page7(xP98,Z93,Z282)
1/75 = 1.3% R1a1a1b1a-Z282
1/75 = 1.3% R1a1a1b2-Z93
3/75 = 4.0% R1a total

------

Combining the Mongol Y-DNA data of Di Cristofaro et al. (2013), Bai et al. (2018), and Karafet et al. (2018) results in the following estimate of the composition of the Y-chromosomal gene pool of present-day Mongols:

131/307 = 42.67% C2a-L1373/M325/M532
23/307 = 7.49% C2b1a1a1a-M407 (Khalkha x9, Northwest Mongolia x6, Sonid x2, Northeast Mongolia x2, Southeast Mongolia x2, Southwest Mongolia x1, Central Mongolia x1)
11/307 = 3.58% C2-M217/M386(xC2a-L1373/M325/M532, C2b1a1a1a-M407) (Khalkha x4, Northwest Mongolia x3, Abaga x2, Oirat x1, Horchin x1)
165/307 = 53.75% C2-M217 total

9/307 = 2.93% D3a-P47 (Central Mongolia x2, Southeast Mongolia x2, Sonid x1, Khalkha x1, Horchin x1, Northeast Mongolia x1, Northwest Mongolia x1)

1/307 = 0.33% G1-M285 (Southeast Mongolia x1)

1/307 = 0.33% H1a-M82 ?> H-Z5870* (Khalkha x1)

1/307 = 0.33% I2a1b-M436(xI2a1b1-M223) (Northwest Mongolia x1)

2/307 = 0.65% J1a2a1a2-Page8 (Central Mongolia x1, Northwest Mongolia x1)
3/307 = 0.98% J2a-M410(xPage55) (Northwest Mongolia x2, Khalkha x1)
3/307 = 0.98% J2a-Page55(xM67) (Northwest Mongolia x2, Oirat x1)
1/307 = 0.33% J2a-M67(xM92) (Northwest Mongolia x1)
9/307 = 2.93% J-12f2 total

1/307 = 0.33% N1b1-Z4784/CTS582 (Khalkha x1)
1/307 = 0.33% N1b2-CTS12473 (Sonid x1)
8/307 = 2.61% N-F1360 (Khalkha x2, Northeast Mongolia x2, Horchin x1, Central Mongolia x1, Southeast Mongolia x1, Northwest Mongolia x1)
28/307 = 9.12% N-Tat (Northwest Mongolia x12, Buryat x9, Khalkha x4, Northeast Mongolia x2, Abaga x1)
38/307 = 12.38% N-M231 total

3/307 = 0.98% O1a-M119 (Abaga x1, Khalkha x1, Southeast Mongolia x1)
3/307 = 0.98% O-M175(xM119, M95, M176, M122) (Horchin x1, Khalkha x1, Northwest Mongolia x1)
1/307 = 0.33% O1b1a1a-M95 (Horchin x1)
1/307 = 0.33% O1b2-M176 (Northeast Mongolia x1)
4/307 = 1.30% O2-M122(xO2a1-KL2, O2a2-P201) (Northwest Mongolia x3, Horchin x1)
8/307 = 2.61% O2a1b-JST002611 (Horchin x4, Sonid x1, Oirat x1, Abaga x1, Khalkha x1)
5/307 = 1.63% O2a2-P201(xM134) (Northwest Mongolia x2, Khalkha x2, Horchin x1)
25/307 = 8.14% O2a2b1-M134 (Northwest Mongolia x7, Khalkha x7, Northeast Mongolia x5, Southeast Mongolia x3, Buryat x1, Abaga x1, Central Mongolia x1)
50/307 = 16.29% O-M175 total

2/307 = 0.65% Q-M242(xM120, M25, M346, M378) (Southeast Mongolia x1, Northwest Mongolia x1)
3/307 = 0.98% Q-M120 (Abaga x1, Central Mongolia x1, Northwest Mongolia x1)
3/307 = 0.98% Q1a2-M25 (Khalkha x2, Central Mongolia x1)
7/307 = 2.28% Q-M346 (Northwest Mongolia x5, Khalkha x2)
15/307 = 4.89% Q-M242 total

7/307 = 2.28% R1a-M198/M17 (Khalkha x3, Northwest Mongolia x2, Abaga x1, Horchin x1)
2/307 = 0.65% R1b1a1a2a-L23(xR1b1a1a2a1a-L11) (Oirat x1, Northwest Mongolia x1)
1/307 = 0.33% R1b1a1a2-M269(xR1b1a1a2a-L23) (Southeast Mongolia x1)
5/307 = 1.63% R1b-M478/M73 (Central Mongolia x2, Northwest Mongolia x2, Southeast Mongolia x1)
2/307 = 0.65% R2a-M124 (Southeast Mongolia x1, Oirat x1)
17/307 = 5.54% R-M207 total

1/307 = 0.33% T-L131(xCTS3767) (Abaga x1)

By the way, the sampling locations for the Mongol samples of Bai et al. (2018) have been presented as follows:

*Abaga from Abaga Banner, Xilingol League, Inner Mongolia, China
*Buryat from Evenk Autonomous Banner, Inner Mongolia, China
*Horchin from Hinggan League, Inner Mongolia, China
*Khalkha from Ulaanbaatar, Mongolia
*Oirat from Bortala Mongol Autonomous Prefecture, Xinjiang, China
*Sonid from Sonid Banner, Xilingol League, Inner Mongolia, China

The 75 Mongols examined by Karafet et al. (2018) also have been described as Khalkha from Ulaanbaatar, Mongolia.

Therefore, the geographical/ethnic composition of the n=307 Mongol samples of Di Cristofaro et al. (2013) + Bai et al. (2018) + Karafet et al. (2018) is as follows:

*Mongol from Northwest Mongolia n=97
*Khalkha from Ulaanbaatar, Mongolia n=89
*Mongol from Southeast Mongolia n=23
*Mongol from Northeast Mongolia n=20
*Mongol from Central Mongolia n=18
*Horchin from Hinggan League, Inner Mongolia, China n=16
*Abaga from Abaga Banner, Xilingol League, Inner Mongolia, China n=15
*Buryat from Evenk Autonomous Banner, Inner Mongolia, China n=14
*Oirat from Bortala Mongol Autonomous Prefecture, Xinjiang, China n=8
*Sonid from Sonid Banner, Xilingol League, Inner Mongolia, China n=5
*Mongol from Southwest Mongolia n=2

Shuzam87
09-01-2021, 05:29 AM
deleted

Ebizur
12-18-2021, 03:06 PM
cf. Yang X, Sarengaowa, He G, Guo J, Zhu K, Ma H, Zhao J, Yang M, Chen J, Zhang X, Tao L, Liu Y, Zhang X-F and Wang C-C (2021), "Genomic Insights Into the Genetic Structure and Natural Selection of Mongolians (https://www.frontiersin.org/articles/10.3389/fgene.2021.735786/)." Front. Genet. 12:735786. doi: 10.3389/fgene.2021.735786


Sample Collections
We collected saliva samples from 42 Mongolian individuals from Baotou city of Inner Mongolia Autonomous Region. Each included individual followed the criteria of sampling collection that require people to have long-term resident history and do not have recorded intermarriages with other surrounding populations for at least three generations. Our work was approved by the Medical Ethics Committee of Xiamen University (Approval Number: XDYX2019009). Informed consent was obtained from all participants included in the study.

Genotyping and Data Merging
Genotyping was performed on the Illumina arrays covering genome-wide 600,000 SNPs designed to identify all known paternal Y chromosome and maternal mtDNA lineages. We first analyzed the relatedness of individuals measured by IBD (identified by descent) segments using KING software (Manichaikul et al., 2010); unrelated individuals were identified using the value of kinship < 0.0442. A total of 39 unrelated participants without family relationships were retained for subsequent analysis.


Population Genetic Substructure Showing the West-East Admixture Cline
... To obtain a more elaborate genetic structure of Mongolians, we conducted the IBD (identified by descent) analysis and pairwise f4 statistics of all individuals (Supplementary Figures S2S8). Taking results from PCA, admixture, pairwise IBD, and pairwise f4 statistics into careful consideration, we grouped the Mongolian population into three subgroups for subsequent analysis, marked as Mongolian_inner who clustered with Mongolian speakers in China, Mongolian_mid, and Mongolian_outer clustered with Mongols and closed with Tungusic populations.


The Paternal/Maternal Lineages of Mongolian
We assigned 39 mitochondrial genomes based on 4,198 maternal lineage-informative SNPs and 33 Y-chromosomal genomes based on 22,512 paternal lineage-informative SNPs (Supplementary Table S12). The maternal mtDNA lineages of Mongolians were diverse, with lineages significantly enriched in present-day East Asian populations (A, B4, C4, D4, F1, G, M, and N), showing terminal lineage frequencies ranging from 0.0256 to 0.0513 (G2a5: 2); B4, C4, D4, and F1 were prevalent in the Mongolian population. From the paternal perspective, 24 different terminal paternal lineages with frequencies ranging from 0.0303 to 0.1212 (C2b1a3b∼: 4). Siberian-dominant paternal lineage was detected (C2b1a and C2c1a). In addition, more East Asian Y-chromosomal founding lineages were identified in Mongolians with dominant lineage O2a2b1a2. To further validate the potential sex bias admixture in the Mongolian population, we used qpAdm to estimate the sex bias Z-score. We observed positive Z sex bias scores in different two-way admixture models focused on Mongolians, which suggested a male-dominated admixture of Han-related ancestry.

From Table 12B: The detailed information of mtDNA and Y lineage
Mongolian_outer (n=14)
mtDNA A12a ['16356', '1709', '9754'], Y-DNA NA
mtDNA A12a ['16356', '1709', '9754'], Y-DNA C2b1a3 ['21888793 Y4631']
mtDNA C5b1a1 ['1719'], Y-DNA I2a2a1b1a1a1a~ ['15094173 Y5362']
mtDNA F1a1d ['11380', '16399'], Y-DNA O1b1a1a1a1b1a1 ['7843210 Y14251', '7926414 Y13996', '8798524 Z23853', '13513077 FGC19724', '17018656 Y14013', '18414585 Z23860', '18729756 Z23861', '23140567 Z23866', '23547020 Z23845', '24420336 FGC19713']
mtDNA F1b1 ['4732'], Y-DNA D1a2a1~ ['7048870 CTS852', '8537039 F1287', '8569161 F1317', '8597871 F1335', '14337193 F1771', '14873839 F1852', '15538480 S17259', '17397409 F2465', '18887403 F2886', '18940243 F2904', '19368335 F3030']
mtDNA F1c1a1 ['16266'], Y-DNA NA
mtDNA F2a ['16203'], Y-DNA C2b1a3b~ ['8438277 Y4541', '9397750 F10312', '13832160 F11134', '16236831 F11899', '18689874 F12521', '21104677 FGC16467', '21221551 FGC16470', '21869132 Y4630', '21990058 Y4633', '22814009 FGC16509']
mtDNA D4j9 ['13573'], Y-DNA NA
mtDNA D4o2 ['16093', '9077'], Y-DNA O2a2b1a2a1a3b2b1a ['22794103 FGC23868']
mtDNA H5 ['16304'], Y-DNA C2b1a3b~ ['9397750 F10312', '21104677 FGC16467', '21221551 FGC16470', '21869132 Y4630', '21990058 Y4633', '22814009 FGC16509']
mtDNA M10a1a ['13135'], Y-DNA C2b1a3b~ ['8857950 F10216', '9397750 F10312', '16236831 F11899', '21104677 FGC16467', '21221551 FGC16470', '21869132 Y4630', '21990058 Y4633', '22814009 FGC16509']
mtDNA N9a ['16261', '12358', '12372', '16257'], Y-DNA C2c1a1a1a ['7402264 F3850']
mtDNA R1b1 ['6683', '11122'], Y-DNA C2b1a2a2a~ ['15789078 M7644']
mtDNA Z1a ['151', '16129', '10325'], Y-DNA I2a2a1b1a1a1a~ ['15094173 Y5362']

Mongolian_mid (n=16)
mtDNA A ['16319', '16290', '4824', '235', '4248', '663'], Y-DNA C2c1a2a1a1 ['8616847 F3748', '21423003 F3806']
mtDNA A1a ['16249', '9713'], Y-DNA NA
mtDNA A1a ['16249', '9713'], Y-DNA O2a1c1a1a1a1c ['2815513 F12', '9416046 F196', '18254697 F480', '23771877 PF659.2', '23771902 F660']
mtDNA B4a1c3b ['4907'], Y-DNA Q1b1a3b1a1~ ['7358159 Y7986.2']
mtDNA B4b1c ['14587'], Y-DNA O2a2b1a2a1a2 ['14173991 F242', '14946079 F273', '16932715 CTS6493', '19371700 CTS10286', '19436515 CTS10401', '21127074 F563', '22821767 CTS10888', '23024318 F634', '23136102 CTS11492']
mtDNA B4i1 ['9329', '6497'], Y-DNA C2b1a3b~ ['9397750 F10312', '16236831 F11899', '18689874 F12521', '21104677 FGC16467', '21221551 FGC16470', '21869132 Y4630', '22814009 FGC16509']
mtDNA C4 ['6026', '11969', '15204'], Y-DNA C2c1a1a1a ['7402264 F3850']
mtDNA C4a1'5 ['7999'], Y-DNA O2a2a1a1 ['2805744 CTS201']
mtDNA C4a1c ['15607'], Y-DNA O2a2b1a1a ['2800495 F8', '6840710 F42']
mtDNA C5a1 ['4904'], Y-DNA C2b1a1b1a2a ['8632808 FGC28857', '15716734 F11787', '17150132 FGC28912', '17996604 FGC28922', '22092009 F13142', '22920334 FGC28959', '23243411 FGC28963']
mtDNA F1a ['16172'], Y-DNA O2a2b1a2a1a2 ['14173991 F242', '14946079 F273', '16932715 CTS6493', '19371700 CTS10286', '19436515 CTS10401', '21127074 F563', '22821767 CTS10888', '23024318 F634', '23136102 CTS11492']
mtDNA G1a1a ['4793'], Y-DNA NA
mtDNA M61a ['3438', '8790', '16270', '980'], Y-DNA O2a2b2a2a2 ['17493867 SK1783']
mtDNA N9a2a ['16497'], Y-DNA NA
mtDNA N11a1 ['12634'], Y-DNA O2a1c1a1a1a1e1a1 ['7825563 Y26383', '24451243 Y26387']
mtDNA U5a1 ['16399', '15218'], Y-DNA O2a2b1a2a1a2a1 ['9123362 Z26109', '19529819 Z26110']

Mongolian_inner (n=9)
mtDNA A11 ['9650'], Y-DNA O2a2b1a2b2a ['2764107 F728', '16922949 F2326']
mtDNA B4c1a1 ['16311', '14133'], Y-DNA C2b1a2a2a~ ['15789078 M7644']
mtDNA C4b ['3816'], Y-DNA C2c1b7~ ['6653699 Z45293']
mtDNA D4a3b ['7912'], Y-DNA O2a2b1a2a1a3b2b1 ['2738239 SK1769', '2890963 FGC23844', '6963027 SK1770', '8531327 FGC23850', '15908198 FGC23854', '16835142 FGC23855', '17488850 FGC23856', '17587342 FGC23857', '17821473 F4249', '17911814 FGC23858', '21774947 FGC23862', '22068249 FGC23863', '22183799 FGC23864', '22618007 Y16779', '23280398 FGC23870', '24476155 FGC23873']
mtDNA D4o1 ['16319', '16274', '13500', '9833'], Y-DNA O2a2b1a1a1a1a1 ['8799343 Y20928']
mtDNA F1b1b ['16172', '204'], Y-DNA NA
mtDNA G2a5 ['16234', '14861', '13383', '15562'], Y-DNA C2b1a1b1a2a ['8632808 FGC28857', '15716734 F11787', '17150132 FGC28912', '17996604 FGC28922', '22092009 F13142', '22920334 FGC28959', '23243411 FGC28963']
mtDNA G2a5 ['16234', '14861', '13383', '15562'], Y-DNA O2a2b2b1a ['6677930 SK1776', '8536206 SK1775']
mtDNA M8a3a ['16134'], Y-DNA O2a1c1a1a1a1a1 ['8068096 F110', '8097388 Y21437', '8265546 Z25064', '8417164 F133', '17791467 F434', '21616774 Z25065', '22721792 CTS10716', '23482948 F646']

These ethnic Mongols are from territory that is currently under the jurisdiction of Baotou, Inner Mongolia, PRC. The name of Baotou is said to be a Sinicized form of a Mongolic term for "having deer, being endowed with deer." I am happy to see these data regarding Mongols from the south-central part of "Greater Mongolia"; studies to date have almost exclusively sampled Mongols from the northernmost and/or easternmost parts of Greater Mongolia. The subjects have been separated into "outer," "mid," and "inner" subgroups based on their slightly differing autosomal affinities to certain outgroups.

One of the subjects whose autosomal profile falls into the "outer" cluster appears to belong to Y-DNA haplogroup D-F1771. According to the current version of YFull, D-F1771 has formed 2300 (95% CI 2800 <-> 1850) ybp and has a TMRCA of 1450 (95% CI 1900 <-> 1050) ybp; one member is a Bosniak from Zlatibor District of western Serbia, one member is from East Kazakhstan Region, one member is from Kyrgyzstan, one member is from the Republic of Crimea, and one member is from Turkey. D-F1771 is a young subclade of D-M533; most branches of D-M533 have been found almost exclusively among Tibetans.

The "outer" cluster also includes two members of haplogroup I-Y5362 (https://www.yfull.com/tree/I-Y5362/): formed 3900 (95% CI 4600 <-> 3200) ybp, TMRCA 3500 (95% CI 4200 <-> 2800) ybp according to the current version of YFull.

One subject who has been assigned to the "outer" cluster should belong to Y-DNA haplogroup O-Y13994 (https://www.yfull.com/tree/O-Y13994/): formed 5000 (95% CI 6200 <-> 3900) ybp, TMRCA 3200 (95% CI 4000 <-> 2500) ybp according to the current version of YFull. Other than that individual, all members of haplogroup O-M175 among the present study's subjects belong to subclades of O2a-M324: 5/8 "inner," 8/13 "mid," 1/11 "outer." It appears that the studied population of ethnic Mongols in Baotou may have received a male-biased migration bringing additional Han Chinese-like autosomal ancestry; I suppose many of these Han-like males may have belonged to subclades of O2a-M324.

Shuzam87
12-18-2021, 09:31 PM
One of the subjects whose autosomal profile falls into the "outer" cluster appears to belong to Y-DNA haplogroup D-F1771. According to the current version of YFull, D-F1771 has formed 2300 (95% CI 2800 <-> 1850) ybp and has a TMRCA of 1450 (95% CI 1900 <-> 1050) ybp; one member is a Bosniak from Zlatibor District of western Serbia, one member is from East Kazakhstan Region, one member is from Kyrgyzstan, one member is from the Republic of Crimea, and one member is from Turkey. D-F1771 is a young subclade of D-M533; most branches of D-M533 have been found almost exclusively among Tibetans.

You are talking about D-Y14813, which could possibly be the paternal lineage of the Tangut people. https://www.yfull.com/tree/D-Y14813/

47793

Ebizur
12-19-2021, 12:44 AM
You are talking about D-Y14813, which could possibly be the paternal lineage of the Tangut people. https://www.yfull.com/tree/D-Y14813/

47793The Y14813 SNP is currently considered by YFull to be phylogenetically equivalent to the F1771 SNP. According to the present study's Table S12B, the Y-DNA of this particular Mongol individual from Baotou is positive for the following SNPs:


mtDNA F1b1 ['4732'], Y-DNA D1a2a1~ ['7048870 CTS852', '8537039 F1287', '8569161 F1317', '8597871 F1335', '14337193 F1771', '14873839 F1852', '15538480 S17259', '17397409 F2465', '18887403 F2886', '18940243 F2904', '19368335 F3030']

Among eight SNPs currently considered by YFull to mark the D-Y14813 clade, only the F1771 SNP has been listed in the present study's Table S12B as being found in the derived state in this individual's Y-DNA, so it is uncertain whether this individual may really share the Y14813 SNP with the presumably Turkic and Slavic individuals currently tabulated under D-Y14813 on YFull. It is possible that this Mongol from Baotou might form a basal branch whose TMRCA with the members of D-Y14813 currently tabulated by YFull might be closer to D-Y14813's date of formation, which is currently estimated by YFull to be 2300 (95% CI 2800 <-> 1850) ybp, than to the TMRCA of the currently tabulated members of D-Y14813, which is currently estimated to be TMRCA 1450 (95% CI 1900 <-> 1050) ybp. Since it is only certain according to the published data that this Mongol from Baotou is positive for the F1771 SNP, I chose to use that as the defining SNP when referring to his subclade, i.e. D-F1771.

To make myself clear, I should mention that I have used the modal verb "should" as a marker of uncertainty when writing about the Mongol from Baotou who belongs to Y-DNA haplogroup O1b1 for a similar reason:


One subject who has been assigned to the "outer" cluster should belong to Y-DNA haplogroup O-Y13994: formed 5000 (95% CI 6200 <-> 3900) ybp, TMRCA 3200 (95% CI 4000 <-> 2500) ybp according to the current version of YFull.

In reality, the Y13994 SNP has not been listed as being positive in this individual's Y-DNA. However, ten of a total of twenty-one SNPs currently considered by YFull to mark the O-Y13994 clade have been found in the derived state. In the case of the aforementioned haplogroup D individual, only one of eight markers of a subclade has been reported to be derived, whereas in the case of this haplogroup O1b1 individual, ten of twenty-one markers of a subclade have been reported to be derived. Strictly speaking, it would be more accurate to refer this individual's Y-DNA as belonging to haplogroup O-Y13996 (or haplogroup O-Y14251, haplogroup O-Z23853, etc.) rather than referring to it as belonging to haplogroup O-Y13994.

By the way, there is a discrepancy between the present study's Table S12B, in which Y-DNA haplogroup assignments and end node SNPs have been tabulated for only thirty-two individuals (a total of thirty-nine individuals minus seven whose Y-DNA has been labeled as "NA"; the latter should be female subjects), and Table S12A, according to which a Y-DNA haplogroup has been assigned to thirty-three individuals (a total of thirty-nine individuals minus six whose Y-DNA has been labeled as "NA"). In the body of the article, the authors have stated that they have "assigned...33 Y-chromosomal genomes based on 22,512 paternal lineage-informative SNPs (Supplementary Table S12)":


The Paternal/Maternal Lineages of Mongolian
We assigned 39 mitochondrial genomes based on 4,198 maternal lineage-informative SNPs and 33 Y-chromosomal genomes based on 22,512 paternal lineage-informative SNPs (Supplementary Table S12). The maternal mtDNA lineages of Mongolians were diverse, with lineages significantly enriched in present-day East Asian populations (A, B4, C4, D4, F1, G, M, and N), showing terminal lineage frequencies ranging from 0.0256 to 0.0513 (G2a5: 2); B4, C4, D4, and F1 were prevalent in the Mongolian population. From the paternal perspective, 24 different terminal paternal lineages with frequencies ranging from 0.0303 to 0.1212 (C2b1a3b∼: 4). Siberian-dominant paternal lineage was detected (C2b1a and C2c1a). In addition, more East Asian Y-chromosomal founding lineages were identified in Mongolians with dominant lineage O2a2b1a2. To further validate the potential sex bias admixture in the Mongolian population, we used qpAdm to estimate the sex bias Z-score. We observed positive Z sex bias scores in different two-way admixture models focused on Mongolians, which suggested a male-dominated admixture of Han-related ancestry.

Therefore, it is most likely that the total of thirty-three Y-DNA haplogroup assignments as per Table S12A is correct, and that the Y-DNA of one individual has mistakenly been tabulated as "NA" in Table S12B.

Table S12A indicates a total of fifteen members of haplogroup O2a-M324 among these Mongols from Baotou, whereas Table S12B indicates a total of only fourteen members of haplogroup O2a-M324.

From Table S12A:
O2a1c1a1a1a1a1 1
O2a1c1a1a1a1c 1
O2a1c1a1a1a1e1a1 1
O2a2a1a1 1
O2a2b1a1a 1
O2a2b1a1a1a1a1 1
O2a2b1a2a1a2 2
O2a2b1a2a1a2a1 1
O2a2b1a2a1a3b2b1 2
O2a2b1a2a1a3b2b1a 1
O2a2b1a2b2a 1
O2a2b2a2a2 1
O2a2b2b1a 1

From Table S12B:
O2a1c1a1a1a1a1 ['8068096 F110', '8097388 Y21437', '8265546 Z25064', '8417164 F133', '17791467 F434', '21616774 Z25065', '22721792 CTS10716', '23482948 F646']
O2a1c1a1a1a1c ['2815513 F12', '9416046 F196', '18254697 F480', '23771877 PF659.2', '23771902 F660']
O2a1c1a1a1a1e1a1 ['7825563 Y26383', '24451243 Y26387']
O2a2a1a1 ['2805744 CTS201']
O2a2b1a1a ['2800495 F8', '6840710 F42']
O2a2b1a1a1a1a1 ['8799343 Y20928']
O2a2b1a2a1a2 ['14173991 F242', '14946079 F273', '16932715 CTS6493', '19371700 CTS10286', '19436515 CTS10401', '21127074 F563', '22821767 CTS10888', '23024318 F634', '23136102 CTS11492']
O2a2b1a2a1a2 ['14173991 F242', '14946079 F273', '16932715 CTS6493', '19371700 CTS10286', '19436515 CTS10401', '21127074 F563', '22821767 CTS10888', '23024318 F634', '23136102 CTS11492']
O2a2b1a2a1a2a1 ['9123362 Z26109', '19529819 Z26110']
O2a2b1a2a1a3b2b1 ['2738239 SK1769', '2890963 FGC23844', '6963027 SK1770', '8531327 FGC23850', '15908198 FGC23854', '16835142 FGC23855', '17488850 FGC23856', '17587342 FGC23857', '17821473 F4249', '17911814 FGC23858', '21774947 FGC23862', '22068249 FGC23863', '22183799 FGC23864', '22618007 Y16779', '23280398 FGC23870', '24476155 FGC23873']
O2a2b1a2a1a3b2b1a ['22794103 FGC23868']
O2a2b1a2b2a ['2764107 F728', '16922949 F2326']
O2a2b2a2a2 ['17493867 SK1783']
O2a2b2b1a ['6677930 SK1776', '8536206 SK1775']

More precisely, it can be said that one of the individuals whose Y-DNA has been tabulated as "NA" in Table S12B most likely should have been tabulated as belonging to haplogroup O2a2b1a2a1a3b2b1-F4249.

As for members of haplogroup C2-M217 among these Mongols from Baotou, including six of eleven members (≈55%) of the "outer" cluster, four of thirteen members (≈31%) of the "mid" cluster, three of eight members (37.5%) of the "inner" cluster," and thirteen of thirty-three members (39.4%) of the entire sample, they may be analyzed as follows:

"Outer" cluster
1/11 C2b1a2a2a~ M7644 (I cannot find any information regarding the phylogenetic position of the M7644 SNP, but, since the alphanumeric nomenclature used in the present study appears to be based on that of ISOGG 2017 (https://isogg.org/tree/2017/ISOGG_HapgrpC17.html), the C-M7644 clade should be downstream of C-M86 and maybe also downstream of C2b1a2a2a~ F8473/Y12797 (https://www.yfull.com/tree/C-Y12825/).)
1/11 C2b1a3-Y4631 (https://www.yfull.com/tree/C-M504/) (Y4631 is a synonym for M504, not merely a "phylogenetically equivalent" SNP.)
1/11 C2b1a3b~ Y4633 (https://www.yfull.com/tree/C-Y4633/) (C-Y4633 is downstream of C-M504/Y4631.)
1/11 C2b1a3b~ F10216 (https://www.yfull.com/tree/C-Y8818/) (F10216 is a synonym for Y8818. C-Y8818 is downstream of C-Y4633.)
1/11 C2b1a3b~ Y4541 (https://www.yfull.com/tree/C-Y4541/) (C-Y4541 is downstream of C-Y8818.)
1/11 C2c1a1a1a-F3850 (https://www.yfull.com/tree/C-F3850/) (C-F3850 is downstream of C-M407.)

"Mid" cluster
1/13 C2b1a1b1a2a-FGC28857 (https://www.yfull.com/tree/C-Z603/) (C-FGC28857 is downstream of C-F1756.)
1/13 C2b1a3b~ Y4630 (https://www.yfull.com/tree/C-Y4580/) (C-Y4630 is downstream of C-M504/Y4631 and immediately upstream of C-Y4633.)
1/13 C2c1a1a1a-F3850 (https://www.yfull.com/tree/C-F3850/) (C-F3850 is downstream of C-M407.)
1/13 C2c1a2a1a1-F3748/F3806 (https://www.yfull.com/tree/C-F3735/) (C-F3748/F3806 is downstream of C-K700.)

"Inner" cluster
1/8 C2b1a1b1a2a-FGC28857 (https://www.yfull.com/tree/C-Z603/) (C-FGC28857 is downstream of C-F1756.)
1/8 C2b1a2a2a~ M7644 (Probably downstream of C-M86 and maybe also downstream of C2b1a2a2a~ F8473/Y12797 (https://www.yfull.com/tree/C-Y12825/).)
1/8 C2c1b7~ Z45293 (https://www.yfull.com/tree/C-MF2040/) (C-Z45293 is downstream of C-F845.)

Breakdown of C-M217 among Mongols in Baotou
5/13 (≈ 38.5%) C-M504 (4/11 ≈ 36% "Outer," 1/13 ≈ 7.7% "Mid")
2/13 (≈ 15%) C-F3850 (≈ C-M407) (1/11 "Outer," 1/13 "Mid")
2/13 (≈ 15%) C-M7644 (≈ C-M86) (1/11 "Outer," 1/8 "Inner")
2/13 (≈ 15%) C-FGC28857 (≈ C-F1756) (1/13 "Mid," 1/8 "Inner")
1/13 (≈ 7.7%) C-F3748/F3806 (≈ C-K700) (1/13 "Mid")
1/13 (≈ 7.7%) C-Z45293 (≈ C-F845) (1/8 "Inner")