P6 palindrome

About one quarter of the euchromatic portion of the male-specific region of the human Y chromosomeconsists of large duplicated sequences, organized in eight palindromes (termed P1-P8) which undergo arm-toarm gene conversion, a proposed mechanism for maintaining their sequence integrity. Although therelevance of gene conversion in the evolution of palindromes has been profoundly recognized, the dynamicof this mechanism is still nuanced. Here we analysed the genetic diversity of human P6 palindrome (armsand spacer) in order to give new insights into the evolutionary dynamics of this element. We identified 118new paralogous sequence variants and 80 gene conversion events that shaped the diversity of P6 arms duringrecent human history. In contrast to previous studies we demonstrated that: 1) arm-to-arm gene conversion,which occurs at a rate of 6.01 × 10 -6 conversions/base/year, is not biased towards the retention of theancestral state of sequences and 2) the establishment of a mutation/conversion balance drives the evolutionof the diversity between the arms of the palindrome. In addition, we found that the significantly highermutation rate of the spacer (9.16 × 10 -10 mutations/base/year) compared to the arms (6.18 × 10 -10mutations/base/year) may explain the observed (human-chimpanzee) lower divergence between theorthologous duplicated sequences of the palindrome compared to its haploid portion, without invoking anybias of conversion.