Coexisting Y haplotypes reveal cyclic sex chromosome differentiation around a shared sex-determining region

Sex chromosome evolution is often viewed as a unidirectional process in which recombination suppression expands around a sex-determining locus, leading eventually to Y-chromosome degeneration. Yet many vertebrates, including frogs, retain homomorphic sex chromosomes and polymorphic differentiation despite long-term recombination suppression, which is quite puzzling. Here, we combine pooled whole-genome resequencing, doubled-haploid YY genomes, and RNA-seq to understand the dynamics of homomorphic sex chromosome evolution in a Swiss Alpine population of the common frog, Rana temporaria, where multiple Y haplotypes coexist. We show that two fully differentiated Y haplotypes carry exceptionally