Abstract
We have compared phylogenies and time estimates for Y-chromosomal lineages based on resequencing ∼9 Mb of DNA and applying the program GENETREE to similar analyses based on the more standard approach of genotyping 26 Y-SNPs plus 21 Y-STRs and applying the programs NETWORK and BATWING. We find that deep phylogenetic structure is not adequately reconstructed after Y-SNP plus Y-STR genotyping, and that times estimated using observed Y-STR mutation rates are several-fold too recent. In contrast, an evolutionary mutation rate gives times that are more similar to the resequencing data. In principle, systematic comparisons of this kind can in future studies be used to identify the combinations of Y-SNP and Y-STR markers, and time estimation methodologies, that correspond best to resequencing data.
Highlights
The combination of its male-specific inheritance, small effective population size and geographical specificity make the Y chromosome the locus of choice for investigating many questions about both forensics [1] and human male history and prehistory [2]
The commonly used Y-STRs are variable in all populations and mutate quickly enough that their mutation rates can be measured in deeprooting families [12] or father–son pairs [13], and refined using information from levels of population variation [14]
The 29 YSNPs were chosen to correspond to those that might have been used if the resequencing data had not been available: they defined common haplogroups and subdivided haplogroups known to be frequent in Africa and Europe, where many of the samples originated
Summary
The combination of its male-specific inheritance, small effective population size and geographical specificity make the Y chromosome the locus of choice for investigating many questions about both forensics [1] and human male history and prehistory [2]. The distribution [3] or sharing [4,5] of a Ychromosomal lineage may itself provide the information sought, but often an estimate of a date or time is an integral part of a study: for example, the time when a lineage originated [6,7,8] or spread [9], or when a population began to expand in numbers [10,11].
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