Differences in DYF387S1 copy number distribution among haplogroups caused by haplogroup-specific ancestral Y-chromosome mutations

• Published in: Forensic science international : genetics Vol. 48; p. 102315
• Main Authors: Watahiki, Haruhiko, Fujii, Koji, Fukagawa, Takashi, Mita, Yusuke, Kitayama, Tetsushi, Mizuno, Natsuko
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.09.2020
• Subjects: Copy number variant; DYF387S1; Paralogous sequence variant; Y-chromosome haplogroup; Y-STR; Paralogous sequence variant; DYF387S1; Copy number variant; Y-STR; Y-chromosome haplogroup
• ISSN: 1872-4973; 1878-0326
• DOI: 10.1016/j.fsigen.2020.102315

•We found differences in DYF387S1 copy number distribution among haplogroups.•DYF387S1 copy numbers were estimated based on the results with the Yfiler™ Plus kit.•Two DYF387S1 paralogs were typed separately by singleplex PCR amplification.•We suggest that ancestral Y-chromosome mutations cause the differences. DYF387S1 is a major Y-chromosome short tandem repeat (Y-STR) used in forensic genetics that is included in the Y-chromosomal haplotype reference database (YHRD, https://yhrd.org) and it is known as a rapidly mutating Y-STR. DYF387S1 is a multi-locus marker and the two paralogs are within a palindromic sequence which is a region prone to structural chromosome mutation. In this study, we investigated DYF387S1 copy number distribution and separately typed the two DYF387S1 paralogs in a Japanese population. We found different DYF387S1 copy numbers among haplogroups indicating that the differences had been caused by haplogroup-specific ancestral Y-chromosomal mutations, such as deletion, duplication and non-allelic gene conversion. In haplogroup C, it is likely that gene conversion between two DYF387S1 paralogs had occurred in the common ancestral Y-chromosome for paragroup C-M130* and duplication of DYF387S1 had occurred in the common ancestral Y-chromosome for haplogroup C-M131. Meanwhile, in haplogroup D, deletion of the upstream DYF387S1 paralog is likely to have occurred in the common ancestral Y-chromosome for paragroup D-M57* and duplication of the remaining DYF387S1 paralog is indicated in the common ancestral Y-chromosome for haplogroup D-M125. In haplogroup O, structural mutations changing the DYF387S1 copy number had probably not occurred in the common ancestral Y-chromosome. We also suggest that deletion of one DYF387S1 paralog occurred in haplogroup N and that deletion of one DYF387S1 paralog or DYF387S1 gene conversion occurred in haplogroup Q. This is the first study that has separately typed the two DYF387S1 paralogs in a large population dataset. As haplogroups C, D, N, O and Q are also observed in other populations, the ancestral mutation events indicated by this study may have affected DYF387S1 polymorphism in other areas of the world.