Estimating the Y chromosome point mutation rate in extended patrilineal pedigrees

Mutations are the fundamental source of biological variation. The Y chromosome is mostly haploid and as such it evolves mainly through accumulation of mutations. It is therefore useful in population genetics as well as in forensics, medicine and evolutionary biology. It is often used as a molecular clock and as such it needs calibration. Here we try to calibrate that clock by presenting the point mutation rate for the human Y chromosome. We used 753 whole-genome sequenced males grouped into 274 patrilines to estimate the point mutation rate for the male specific region of the Y chromosome, taking into account that the Y chromosome is a mosaic of different sequence classes. Most striking was the difference between the palindromic regions and other regions of the male specific Y chromosome. The mutation rate for regions excluding palindromes was 8.71 × 10-10 (95% CI = 8.03 × 10−10 to 9.43 × 10−10) per position per year but in palindromes it was 7.37 × 10-10 (6.41 × 10−10 to 8.48 × 10−10) per position per year. We propose that this difference is due to gene conversion that is able to repair damaged nucleotides that would otherwise give rise to mutations in the palindromes but not in other parts of the Y chromosome.Rannís R11-103