A deeper look back at Y

Two new studies use large-scale sequencing of the Y chromosome to infer key evolutionary dates. Carlos Bustamante and colleagues sequenced the complete Y chromosome of 69 males from 9 diverse populations (Science 341, 562–565, 2013). They identified 11,640 single-nucleotide variants (SNVs), which they used to construct a maximum-likelihood tree. Using archaeological dating for calibration, the authors estimated a mutation rate of 0.82 × 10⁻⁹ mutations per base pair per year and a Y-chromosome time to most recent common ancestor (t_MRCA) of 120,000–156,000 years ago. The authors also sequenced mitochondrial DNA from the 69 males as well as from 24 females; using a similar analysis, they estimated the mitochondrial DNA t_MRCA at 99,000–148,000 years ago. In a second study, Francesco Cucca and colleagues report low-pass sequencing of the male-specific portion of the Y chromosome (MSY) in 1,204 males from Sardinia (Science 341, 565–569, 2013). They inferred 11,763 phylogenetically informative SNPs and used these to construct a phylogenetic tree. They calibrated against archaeological records, estimating a phylogenetic rate of 0.53 × 10⁻⁹ mutations per base pair per year and a Y-chromosome t_MRCA of ∼180,000–200,000 years ago. Together, these studies suggest an earlier Y-chromosome coalescence time than previous studies and suggest that this coalescence time may overlap with that for mitochondrial DNA.