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Rapid evolution of a Y-chromosome heterochromatin protein underlies sex chromosome meiotic drive

Significance Intragenomic conflict between the sex chromosomes is a strong evolutionary force. It can arise through the evolution of sex chromosome meiotic drive, where selfish genes located on the X chromosome promote their own transmission at the expense of the Y chromosome. Sex chromosome drive occurs in Drosophila simulans, where Paris drive results from segregation failure of the heterochromatic Y chromosome during meiosis II. Here, we show that Paris drive is caused by deficient alleles of the fast-evolving X-linked heterochromatin protein 1 D2 (HP1D2) gene. Our results suggest that dysfunctional HP1D2 alleles promote their own transmission, because they do not prepare the Y chromosome for meiosis. This finding shows that the rapid evolution of genes involved in heterochromatin structure can fuel intragenomic conflict. Sex chromosome meiotic drive, the non-Mendelian transmission of sex chromosomes, is the expression of an intragenomic conflict that can have extreme evolutionary consequences. However, the molecular bases of such conflicts remain poorly understood. Here, we show that a young and rapidly evolving X-linked heterochromatin protein 1 (HP1) gene, HP1D2, plays a key role in the classical Paris sex-ratio (SR) meiotic drive occurring in Drosophila simulans. Driver HP1D2 alleles prevent the segregation of the Y chromatids during meiosis II, causing female-biased sex ratio in progeny. HP1D2 accumulates on the heterochromatic Y chromosome in male germ cells, strongly suggesting that it controls the segregation of sister chromatids through heterochromatin modification. We show that Paris SR drive is a consequence of dysfunctional HP1D2 alleles that fail to prepare the Y chromosome for meiosis, thus providing evidence that the rapid evolution of genes controlling the heterochromatin structure can be a significant source of intragenomic conflicts.