Y‐chromosomal Binary Haplogroups in the Japanese Population and their Relationship to 16 Y‐STR Polymorphisms

Abstract

SummaryWe investigated Y chromosomal binary and STR polymorphisms in 263 unrelated male individuals from the Japanese population and further examined the relationships between the two separate types of data. Using 47 biallelic markers we distinguished 20 haplogroups, four of which (D2b1/-022457, O3/-002611 * , O3/-LINE1 del, and O3/-021354 * ) were newly defined in this study. Most haplogroups in the Japanese population are found in one of the three major clades, C, D, or O. Among these, two major lineages, D2b and O2b, account for 66% of Japanese Y chromosomes. Haplotype diversity of binary markers was calculated at 86.3%. The addition of 16 Y-STR markers increased the number of haplotypes to 225, yielding a haplotype diversity of 99.40%. A comparison of binary haplogroups and Y-STR type revealed a close association between certain binary haplogroups and Y-STR allelic or conformational differences, such as those at the DXYS156Y, DYS390m, DYS392, DYS437, DYS438 and DYS388 loci. Based on our data on the relationships between binary and STR polymorphisms, we estimated the binary haplogroups of individuals from STR haplotypes and frequencies of binary haplogroups in other Japanese, Korean and Taiwanese Han populations. The present data will enable researchers to connect data from binary haplogrouping in anthropological studies and Y-STR typing in forensic studies in East Asian populations, especially those in and around Japan.

An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4

“…[1][2][3] The dominant group of Y chromosome in Eastern Eurasia is Haplogroup O-M175, comprising roughly 75% of the Chinese [4][5][6] and more than half of the Japanese population. [7][8][9] Albeit the huge population of Haplogroup O, its phylogeny 10 is much less adequately resolved than those of Haplogroup R and E, despite the improvements of O tree made during the recent years. [10][11][12] The most important part of potential interest was the paragroup O3a*-M324(xM121, M159, M164, M7, M134), which comprises a substantial part of Chinese population (typically 15-50% of Han Chinese) but could not be further resolved in the last few years.…”

“…For example, a novel clade defined by IMS-JST002611 (in short, 002611) may count for up to 21% of the East Asians. 4,8 From the HapMap project, several SNPs were recognized under Haplogroup O-P191 (rs16980601). One of them, rs17269396, was reported as L127.1 on FamilyTreeDNA (https://www.familytreedna.…”

Refined phylogenetic structure of an abundant East Asian Y-chromosomal haplogroup O*-M134

“…Despite the prevalence of O-F444 across East Asian and Southeast Asian populations, 12,[15][16][17][18][19] this haplogroup has also been found with moderate frequency in Qiangic populations (~5%). 28 The Qiangic populations might participate in the establishing of the Sino-Tibetan populations based on recent genetic evidences.…”

“…[12][13][14] O-M134 is one of the most frequent sub-lineages of O-M175, which represent~30 million people in East Asia (Supplementary Figure S1). The frequency of O*-M134(xM117) varies in different regions, namely China (~11.4%), 12 Japan (~3.6%), 15 Korea (~9.6%), 16 Mongolia (~4.1%), 17 Thailand (~11.6%) 18 and Khasi in India (~16.6%). 17 This paragroup also has been found at high frequency in some Kazakhs (26.1%).…”

Assignment of Y-chromosomal SNPs found in Japanese population to Y-chromosomal haplogroup tree

“…Our group has already described the most detailed Y-chromosomal haplogroup classification in the Japanese population by expanding the YCC tree of 2003, assigning 5 new JSNP markers. 15 These markers have now been included in the YCC tree of 2008. 7 In the present study, we further searched for new Y-chromosomal binary haplogroup markers in the JSNP database 16,17 to classify Japanese Y-chromosomal haplogroups in greater detail.…”