The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time

Abstract

We estimate an effective mutation rate at an average Y chromosome short-tandem repeat locus as 6.9x10-4 per 25 years, with a standard deviation across loci of 5.7x10-4, using data on microsatellite variation within Y chromosome haplogroups defined by unique-event polymorphisms in populations with documented short-term histories, as well as comparative data on worldwide populations at both the Y chromosome and various autosomal loci. This value is used to estimate the times of the African Bantu expansion, the divergence of Polynesian populations (the Maoris, Cook Islanders, and Samoans), and the origin of Gypsy populations from Bulgaria.

Figure 1

Network of Maori haplotypes (without loci DYS439, DYS388, and DYSA7.2). The number of chromosomes is shown in parentheses (see table 1).

Figure 2

Distribution of mutation rates at Y chromosome STRs. Black columns indicate estimates inferred from the present study; white columns indicate estimates from pedigree and familial studies.

Figure 3

Genetic differentiation among the Polynesian populations. The time between the nodes was computed as ΔT_D=(D^′₁-D^′₁)/2w (Zhivotovsky 2001), where D^′₁ is the average value of D₁ for population pairs (Samoans/Maoris and Samoans/Cook Islanders), and D^′′₁ is for the Maoris/Cook Islanders comparison.

Figure 4

Genetic differentiation among the Bulgarian Gypsy populations. The time between the nodes was computed as for that in figure 3.