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

Abstract

The relationship between Y-chromosome single-nucleotide polymorphisms (SNPs) registered in the Japanese SNP (JSNP) database (http://snp.ims.u-tokyo.ac.jp) and Y-binary haplogroup lineages was investigated to identify new Y-chromosomal binary haplogroup markers and further refine Y-chromosomal haplogroup classification in the Japanese population. We used SNPs for which it was possible to construct primers to make Y-specific PCR product sizes small enough to obtain amplification products even from degraded DNA, as this would allow their use not only in genetic, but also archeological and forensic studies. The

Confirmation of Y haplogroup tree topologies with newly suggested Y-SNPs for the C2, O2b and O3a subhaplogroups

“…S3). However, JST037852, the mutation frequency of which was 3.4% in Japanese samples from a report by Naitoh et al [20] and as high as 7.9% in the Korean samples in this study, could not be located at a certain clade within the phylogenetic tree composed of the hierarchical arrangement of the JST002611, F11, F238 and F449 markers, because the mutation at JST037852 occurred sporadically both in O3a1c1 and O3a1c2 haplotypes (data not shown). Therefore, JST037852 was excluded for the revision of the Y haplogroup tree.…”

“…The information of selected YSNPs was obtained from ISOGG Y-DNA haplogroup tree version 2013 or 2014 (http://www.isogg.org/tree/index.html), the minimal reference phylogeny for the human Y chromosome (http://www.phylotree.org/Y/tree/index.htm) and related articles [17][18][19][20]. The newly added Y-SNPs for the haplogroup designation are shown in Table 1.…”

“…Since Karafet et al [6], many researchers have reported changes to this Y haplogroup tree, and these changes include the additions of new roots and new basal clades [7][8], modifications of the global backbone [7,9], new descriptions of sub-haplogroups and different phylogenetic topologies within a haplogroup [7,10,20]. Haplogroups C and O, which are prevalent in East Asia, have been updated as well to include these changes [10][11][12][13][14][15][16].…”

“…Haplogroups C and O, which are prevalent in East Asia, have been updated as well to include these changes [10][11][12][13][14][15][16]. Naitoh et al identified new Y chromosome binary markers for sub-haplogroups of the D2a, C2 and O3a haplogroups [20]. Moreover, different namings of Y haplogroups and different phylogenetic topologies within haplogroups were observed between the International Society of Genetic Genealogy (ISOGG) Y-DNA haplogroup tree and the minimal reference phylogeny Y chromosome tree [19]; they have not been coordinated with each other, and thus use different Y-SNPs and different names for haplogroups.…”

“…The JST075888 sequence structure was identified as having two copies of the 9 or 10T repeat region and the variations of JST075888 marker, JST075888-9T/10T and JST075888-9T/9T, existed with frequencies of 0.023 and 0.008 in Japanese samples according to a report by Naitoh et al,respectively[20]. However, in a test with 158 samples of O3a2c1 haplogroups, JST075888 was not observed in Korean samples and complicated the analysis.…”