A short tandem repeat-based phylogeny for the human Y chromosome

Abstract

Human Y-chromosomal short tandem repeat (STR) data provide a potential model system for the understanding of autosomal STR mutations in humans and other species. Yet, the reconstruction of STR evolution is rarely attempted, because of the absence of an appropriate methodology. We here develop and validate a phylogenetic-network approach. We have typed 256 Y chromosomes of indigenous descent from Africa, Asia, Europe, Australia, and highland Papua New Guinea, for the STR loci DYS19, DXYS156Y, DYS389, DYS390, DYS392, and DYS393, as well as for five ancient biallelic mutation events: two poly (A) length variants associated with the YAP insertion, two independent SRY-1532 mutations, and the 92R7 mutation. We have used our previously published pedigree data from 11,000 paternity-tested autosomal STR-allele transfers to produce a two-class weighting system for the Y-STR loci that is based on locus lengths and motif lengths. Reduced-median-network analysis yields a phylogeny that is independently supported by the five biallelic mutations, with an error of 6%. We find the earliest branch in our African San (Bushmen) sample. Assuming an age of 20,000 years for the Native American DYS199 T mutation, we estimate a mutation rate of 2.6x10-4 mutations/20 years for slowly mutating Y STRs, approximately 10-fold slower than the published average pedigree rate.

Figure 1

Structure of Y-STR loci typed in the study. The nonrepetitive block of DNA in DYS389 is not to scale.

Figure 2

RM network of 187 Y chromosomes from a global sample. The network contains 45 Y-STR types represented more than once in a sample of 256 Y chromosomes (125 Y types). The STR loci were weighted as follows: DYS19, DYS390n and -p, and DYS393, weight 1; DXYS156Y, DYS389m, and DYS390m, weight 2. The length of an MP tree in this network is estimated at 65 single-repeat mutation steps. Note that the placement of the DYS390p branch is ambiguous, since it depends on the coding of DYS390n, -p, and -q. Links are labeled by loci, with the arrows pointing in the direction of locus lengthening. Parallel links in a reticulation represent the same locus. The area of a given circle is proportional to number of individuals. For clarity, one superfluous node in the cluster of White individuals has been omitted. Single-letter abbreviations are as intable 1. For reference, the Papuan in the center of the network has the following repeat lengths: 15 (DYS19), 12 (DXYS156Y), 5 (DYS389m), 8 (DYS390m), 10 (DYS390n), 1 (DYS390p), and 13 (DYS393).

Figure 3

Superposition of biallelic markers on the STR phylogeny. For orientation, the Y-type nomenclature of Jobling et al. (1997) has been provided. Superfluous links not confirmed by the biallelic markers are denoted by the dotted lines. L = long YAP variant.

Figure 4

Network of Native American Y types, from Bianchi et al. (1998). The network includes all 89 individuals and was calculated by the MJ method (ε = .6), to resolve the high homoplasy caused by DYS392. The weighting scheme was as follows: DYS19, 1; DYS390 (total), .6; DYS391, 1; DYS392, .6; and DYS393, 1. Preprocessing the data with RM before applying MJ produces an identical network.