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Ebizur
06-02-2022, 11:13 AM
This is the first new study of Japanese Y-DNA that I recall having seen since Sato et al. (2014).

"Subclassification of Y chromosome haplogroups in Japanese population and application to personal identification." [日本人を対象としたY染色体ハプログループの細分類と個人識別への応用] OCHIAI Eriko, School of Medicine, Tokai University / May 30, 2021

The Tokai University School of Medicine is located at the Isehara campus of Tokai University in Isehara, Kanagawa, Japan.


3.研究の方法
(1)日本人集団におけるY染色体ハプログループの頻度調査
血縁関係のない日本人男性567名について、口腔粘膜細胞から常法にてDNAを抽出し、試料とした。本研究 は東海大学医学部医の倫理委員会の承認を得て行われた。Y-SNPsのプライマーパネルとしてHID-Ion AmpliSeq Identity Panel (Thermo Fisher Scientific)を用い、鋳型DNA 10ngでY-SNP 34座位を同時にPCR増幅した。Ion PGMシーケンサーにて配列解析を行い、型判定の結果からYハプログループを決定した。一部の資料について はサンガー法で型判定を行った。"3. Research methods
(1) Investigation of [the] frequency of Y-chromosome haplogroup[s] in [a] Japanese population
For [our] samples, [we] extracted DNA from oral mucosal cells of 567 unrelated Japanese men through conventional method[s]. This study was conducted with the approval of the Medical Ethics Committee of the Tokai University School of Medicine. Using the HID-Ion AmpliSeq Identity Panel (Thermo Fisher Scientific) as a primer panel for Y-SNPs, 34 Y-SNP loci were simultaneously PCR amplified with 10 ng of template DNA. Sequence analysis was performed with the Ion PGM sequencer, and the Y-chromosome group was determined from the typing results. For some specimens, the type was determined through the Sanger method."


Table 1 Frequency of Y-DNA Haplogroups in the Japanese (n=567)
C-M130 n=57 (10.1%)
D1-M174 n=211 (37.2%)
N-M231 n=2 (0.4%)
O*-P186 n=13 (2.3%)
O1b-M268 n=163 (28.7%)
O2-P198 n=118 (20.8%)
Q-M242 n=3 (0.5%)

The proportions of Y-DNA haplogroups D-M174, O2-P198, and Q-M242 are somewhat greater in this sample than in most previous studies' samples of Japanese, whereas the proportions of haplogroups O1b-M268 and N-M231 are somewhat smaller in this sample than in most previous studies' samples of Japanese. All members of O*-P186 most likely should belong to haplogroup O1a-M119; the frequency of O1a-M119 in this sample should be somewhat greater than the average (≈1%) for previous studies' samples of Japanese. Judging from previous studies of Japanese Y-DNA, about half the members of C-M130 in this sample should turn out to belong to haplogroup C1a1-M8, whereas the other half should turn out to belong to haplogroup C2-M217, but this ought to be confirmed through DNA testing.

MNOPSC1b
06-02-2022, 01:10 PM
Why are the haplogroups in this study only at the top level (most general level) and didn't bother to look at more specific clades? I would expect new studies like this to be much more specific, yet this doesn't seem to be the case. What's the possible cause of this?

O1b-M268 here should predominantly refer to O1b2-M176 or even more specifically O1b2-47z

D1-M174 here should predominantly be D1a2a

Ebizur
06-02-2022, 02:30 PM
Why are the haplogroups in this study only at the top level (most general level) and didn't bother to look at more specific clades? I would expect new studies like this to be much more specific, yet this doesn't seem to be the case. What's the possible cause of this?Intentional preference for basic, manual techniques over automated ones that require proprietary technology? Unintentional tardiness in adopting new methods, or lacking the prerequisite funding? I don't see any point in speculating about such things.


O1b-M268 here should predominantly refer to O1b2-M176 or even more specifically O1b2-47z

D1-M174 here should predominantly be D1a2aThey actually did try out an NGS assay on three of their haplogroup D specimens, and found that they could be assigned to D1a2a2a1-CTS10495, D1a2a1c1a-IMS-JST022456, and D1a2a1a*-M125, respectively.

They did not have such success with subtyping their O1b-M268 specimens using the same NGS assay. However, they did manually type several additional SNPs (O1b2a-IMS-JST022454, O1b2a1a1-CTS713, O1b2a1a1a-CTS1875, O1b2a1a1b-Z24598, O1b2a1a1c-CTS203) as well as STRs for a subset (127/163 = 77.9%) of their O1b-M268 specimens. They reported the results to be as follows:

Figure 2 STR diversity within each haplogroup of the O1b lineage
O1b*-M268 n=8 HD=1.0000 GD=0.560.25 ACDR=15.866.17
O1b2a*-IMS-JST022454 n=34 HD=1.0000 GD=0.360.21 ACDR=7.162.90
O1b2a1a1*-CTS713 n=26 HD=0.9978 GD=0.370.21 ACDR=9.064.05
O1b2a1a1a-CTS1875 n=39 HD=0.9752 GD=0.220.17 ACDR=4.002.25
O1b2a1a1b-Z24598 n=15 HD=0.9709 GD=0.250.21 ACDR=4.571.72
O1b2a1a1c-CTS203 n=5 HD=1.0000 GD=0.190.26 ACDR=3.401.26

HD: Haplotype diversity
GD: Average gene diversity at each locus within each haplogroup
ACDR: Average cumulative number of differences in repeat size in pairwise comparison within each haplogroup

O1b2a1a1-CTS713 is phylogenetically equivalent to O-47z, so at least 85 of their samples should belong to O-47z, which would amount to at least 52.1% (85/163) of all their O1b-M268 samples and at least 15.0% (85/567) of their entire sample set. If the proportion of O-CTS713/47z among the subset of O1b-M268 that they have tested to a higher resolution (85/127 = 66.9%) is the same as the proportion of O-CTS713/47z among all O1b-M268 in the entire sample set, then about 109 individuals (19.2%) should belong to O-CTS713/47z and about 54 individuals (9.5%) should belong to O1b-M268(xCTS713, 47z) in the entire sample set; such figures would not be too far off those that may be found in previously published papers that have included data regarding Japanese Y-DNA.

alchemist223
07-03-2022, 02:22 PM
I've been surprised at how rare maternal haplogroup C is in Japanese populations, being at 0.5% in Tanaka (2004) and 0% in Zheng (2011). I thought it would be significantly more common.

Ebizur
07-03-2022, 03:00 PM
I've been surprised at how rare maternal haplogroup C is in Japanese populations, being at 0.5% in Tanaka (2004) and 0% in Zheng (2011). I thought it would be significantly more common.Yamamoto et al. (2020) have found mtDNA haplogroup C in 0.7% of a large sample (n = 1928) of Japanese, but 0.5% (i.e. approximately 71% of the total 0.7%) has been contributed by people from the Chubu-hokuriku region (a zone in central Honshu that is in many ways transitional between "Western Japan" and "Eastern Japan"), so it might reflect some sort of minor founder effect in some locality in central Honshu. MtDNA haplogroup C is absent or present only sporadically in every other region of Japan according to that study's samples.

MtDNA haplogroup C among the samples of Yamamoto et al. 2020 may be resolved as follows:

C total: 13/1928 = 0.67% or 14/1928 = 0.73%
-C*: 2/1928 = 0.10% [n=1 from the Chubu-hokuriku region + n=1 from the Kinki region]
-C1a: 5/1928 = 0.26% or 6/1928 = 0.31% [n=1 from the Hokkaido region + n=3 or n=4 from the Chubu-hokuriku region + n=1 or n=2 from the Kyushu region]
-C4: 3/1928 = 0.16% or 4/1928 = 0.21% [n=3 or n=4 from the Chubu-hokuriku region]
--C4a1a+195: 1/1928 = 0.05% or 2/1928 = 0.10% [n=1 or n=2 from the Chubu-hokuriku region]
--C4a2a1: 1/1928 = 0.05% or 2/1928 = 0.10% [n=1 or n=2 from the Chubu-hokuriku region]
-C5+16093: 1/1928 = 0.05% or 2/1928 = 0.10% [n=1 or n=2 from the Chubu-hokuriku region]
-C7b: 1/1928 = 0.05% [n=1 from the Hokkaido region]

Haplogroup C was not found in any sampled individual from eastern Honshu (i.e. Kanto-Koshin'etsu & Tohoku) or Okinawa.

MNOPSC1b
07-03-2022, 04:16 PM
I've been surprised at how rare maternal haplogroup C is in Japanese populations, being at 0.5% in Tanaka (2004) and 0% in Zheng (2011). I thought it would be significantly more common.

From my understanding mt haplogroup C is more commonly found among continental Northeast Asian populations like some Siberian peoples, whereas Japanese along with Koreans and Northern Chinese have a high frequency of mt haplogroup D4

Ebizur
07-04-2022, 01:47 PM
From my understanding mt haplogroup C is more commonly found among continental Northeast Asian populations like some Siberian peoples, whereas Japanese along with Koreans and Northern Chinese have a high frequency of mt haplogroup D4MtDNA haplogroup D4 is also very common among populations of Siberia, although such populations (especially Yakuts, Nganasans, Yukaghirs, Evenks, Evens, Tuvans, and Tofalars) tend to have more C than D4.

Furthermore, most members of mtDNA haplogroup D4 among populations of Siberia do not share recent (Holocene) common matrilineal ancestors with most members of mtDNA haplogroup D4 among populations of East Asia. This is reminiscent of the deep genealogical separation between "Siberian" Y-DNA haplogroup C-L1373 and "East Asian" Y-DNA haplogroup C-F1067, or between Y-DNA haplogroup N and Y-DNA haplogroup O. Members of mtDNA haplogroup D4 among populations of the Americas outside the arctic belong to yet another distinctive set of subclades.