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

Human Y-chromosomal short tandem repeat (STR) data provide a potential mode l system for the understanding of autosomal STR mutations in humans and oth er species. Yet, the reconstruction of STR evolution is rarely attempted, b ecause of the absence of an appropriate methodology We here develop and val idate a phylogenetic network approach. We have typed 256 Y chromosomes of i ndigenous descent from Africa, Asia, Europe, Australia, and highland Papua Near 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-153 2 mutations, and the 92R7 mutation. We have used our previously published p edigree 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 l ocus lengths and motif lengths. Reduced-median-network analysis yields a ph ylogeny that is independently supported by the five biallelic mutations, wi th 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 m utation, we estimate a mutation rate of 2.6 x 10(-4) mutations/20 years for slowly mutating Y STRs, similar to 10-fold slower than the published avera ge pedigree rate.