Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females

The Y chromosome and the mitochondrial genome have been used to estimate when the common patrilineal and matrilineal ancestors of humans lived. We sequenced the genomes of 69 males from nine populations, including two in which we find basal branches of the Y-chromosome tree. We identify ancient phylogenetic structure within African haplogroups and resolve a long-standing ambiguity deep within the tree. Applying equivalent methodologies to the Y chromosome and the mitochondrial genome, we estimate the time to the most recent common ancestor (TMRCA) of the Y chromosome to be 120 to 156 thousand years and the mitochondrial genome TMRCA to be 99 to 148 thousand years. Our findings suggest that, contrary to previous claims, male lineages do not coalesce significantly more recently than female lineages. The Y chromosome contains the longeststretch of nonrecombining DNA in thehuman genome and is therefore a pow-erful tool with which to study human history. Estimates of the time to the most recent common ancestor (TMRCA) of the Y chromosome have dif-fered by a factor of about 2 from TMRCA estimates for the mitochondrial genome. Y-chromosom