Bimodal allele frequency distribution at Y-STR loci DYS392 and DYS438: no evidence for a deviation from the stepwise mutation model

Abstract

A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise Phi(st) values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise Phi(st) values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.