Analysis of non-allelic gene conversion in the evolution of human MSY palindromes

The Male-Specific region of Y chromosome (MSY) has long been considered a recombinationally inert genomic element, a view that has been profoundly dismissed by the discovery that the sequence landscape of this region can be actually modulated by inter- and intra- chromosomal recombination. The MSY includes eight large near-identical inverted repeats, palindromes P1-P8, considered to be in a ‘pseudo-diploid’ state. Although these structures originated in a non-recombining context, they evolved a strong self-recombinational activity in the form of non-allelic gene conversion, by which their arm-to-arm similarity exceeds 99.9%. Palindromic sequences contain many genes essential for sperm production and evolved independently on the constitutively haploid sex chromosomes of several taxa belonging to different kingdoms. Thus, it has been hypothesised that gene conversion is a mechanism necessary to counteract new possibly deleterious variants by retaining the ancestral state of gene sequences, in order to preserve their functionality over time. This hypothetical bias towards the retention of the ancestral state has also been proposed to explain the lower human-chimpanzee sequence divergence in the palindrome arms compared to palindrome spacers. Despite the relevance of this mechanism in maintaining genome integrity, it is not clear if the bias towards the ancestral state really exists and little is known about the dynamics of gene conversion in the ampliconic MSY. Moreover, it is still unknown if differences in the conversion dynamics among different palindromes exist. Indeed, P8 palindrome showed evidence of X-to-Y gene conversion, but the interaction between Y-Y and X-Y recombination has never been clarified. To shed light on these issues, we performed a high-depth (>50×) targeted next-generation sequencing (NGS) of palindromes P6, P7 and P8 in 157 samples, which cover the most divergent evolutionary lineages of the human Y chromosome. We reconstructed a stable Y phylogeny of samples to explore gene conversion in an evolutionary context and found a large number of previously undescribed PSVs increasing the possibility to identify gene conversion events occurring during the recent human history. By mapping these events across our phylogeny and comparing the sequences of the three palindromes conserved between human and chimpanzee, we were able to infer the minimum number of conversions, palindrome-specific mutation and gene conversion rates and the direction of the gene conversion mechanism (ancestral/derived, GC-bias). We found no evidence for a bias towards the retention of the ancestral state and that the evolution of different palindromes is governed by independent and complex dynamics. We also observed higher mutation rates in the spacers compared to palindrome arms. This difference in mutation rate may represent the true cause of the previously observed higher human-chimpanzee spacer divergence with respect to the arms, without the need to invoke a Y-Y recombination bias towards the ancestral state.