Dynamics of gene conversion in human Y-chromosome palindromes

The Male Specific region of the human Y chromosome (MSY) is characterized by the presence of eight massive palindromes. Each palindrome is composed of two large arms separated by a non-duplicated spacer. These elements exhibit an arm-to-arm sequence identity >99.9%, due to gene conversion (GC) events between them. The effect of GC on the genetic diversity of palindromes, as well as its rate and extension, remain largely unexplored. To gain new insights into the evolutionary dynamics of the human Y chromosome palindromes, we analysed by high-coverage next-generation sequencing (>50×) a 30 kb palindrome in 157 samples, chosen to represent the most divergent evolutionary lineages of the MSY. In this analysis we overcame the problem of a non-unique mapping of the sequencing reads, and we performed an analysis of the sequencing depth. The availability of a reliable Y chromosome phylogeny (for the 157 samples), based on the analysis of 3.3 Mb of X-degenerate unique regions, allowed us to identify several GC events and a peculiar mutational pattern within arms. Finally, by mapping GC events across the Y phylogeny, we were able to calculate a precise Y-Y GC rate.