1R.Y.Y. Yong, 1L.S.H. Gan, 2Y. Khripin, 3V.B. Yap, 1E.P.H. Yap
1Defence Medical and Environmental Research Institute, DSO National Laboratories, 27 Medical Drive #12-00, Singapore 117510, 2Marligen Biosciences, 2502 Urbana Pike, Ijamsville, MD 21754, USA, 3Department of Statistics and Applied Probability, National University of Singapore, Block S16 Level 7, Faculty of Science, 6 Science Drive 2, Singapore 117546
The Y chromosome is a potentially useful marker of paternal ancestral origins. Its constitutively haploid state permits unambiguous determination of compound haplogroup or haplotype. The lack of recombination along most of its length has resulted in a sequential accumulation of mutations defining the slowly evolving Y-SNP haplogroup or the faster evolving Y-STR haplotype. Thus, Y chromosomal variation reflects a high degree of geographical structure, usually explained by its low effective population size and sensitivity to genetic drift, and possibly the effect of patrilocality.
In this study, we assessed the possibility and accuracy of inferring paternal ancestry with Y chromosome variation for three main ethnic groups residing in Singapore. 91 Y-SNP potentially classifying 87 haplogroups, and 12 Y-STR loci were genotyped in 564 randomly selected individuals, comprising 209 Chinese, 181 Malay and 174 Indian. A total of 33 haplogroups consisting 14 clades, and 525 unique Y-STR haplotypes were recorded. About 90% and 73% of the Chinese and Malay samples respectively were classified under Clade O, with a dominant haplogroup of O3e1 for Chinese and O2a* for Malay. Indian samples showed a diverse distribution of clades including F, J, H, L and R. Population differentiation tests using AMOVA and exact test both showed significant inter-population differences using either Y-SNP or Y-STR markers. Y-SNPs demonstrated greater variation between populations than Y-STR, confirming it to be better informative marker for population differentiation. Exact tests also confirmed strong association of specific haplogroups to ethnic populations. A method combining both Y-SNP haplogroups and Y-STR haplotypes was devised for ancestry inference. The predictability of ethnic affiliation using this method is estimated to be more than 75% for our present dataset of Singapore populations. Hence chromosome Y markers may be useful in inferring paternal geographical origins within Asian populations.
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