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

Abstract

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 large nonrecombining regions spanning [~]90% of the sex chromosome ([~]618-625 Mb), whereas semi-differentiated Y haplotype retains only a 4.64 Mb Dmrt1-linked sex-determining region, and XX males are genetically indistinguishable from XX females. The large NRRs show limited degeneration, with no evidence of gene loss, Y-linked copy decay, faster-X evolution or enrichment of sex-biased genes, and only modest repeat accumulation. Surprisingly, the coexisting Y haplotypes are neither independent sex-determining systems nor successive stages of a single degeneration trajectory. Instead, they share an ancestral Dmrt1-linked region whose X-Y divergence dates to [~]3.47-5.70 Mya, while present-day Y copies of this region remain nearly identical and the large NRRs have accumulated private mutations independently. We thus propose that the Y chromosome undergoes cyclic dynamics of differentiation: extreme heterochiasmy promotes rapid large NRRs formation, sex-reversed XY females recurrently restore X-Y recombination, gene conversion and/or rare Y-Y recombination may homogenize Y copies at the Dmrt1-linked region, and renewed male transmission drives subsequent Y-specific differentiation. The findings provide a genome-wide resolution to a central paradox in sex chromosome evolution: how sex chromosomes can experience extensive recombination suppression yet remain homomorphic and only weakly degenerated. By showing that heterochiasmy and sex reversal uncouple the physical extent, age, and degeneration of sex-linked regions, our study reframes homomorphic sex chromosomes as dynamic, repeatedly regenerated systems shaped by alternating phases of recombination suppression, restored X-Y recombination and renewed Y differentiation. Significance statementWhy many vertebrate sex chromosomes remain homomorphic despite long-term recombination suppression remains unresolved. Using whole-genome population genomics, doubled-haploid YY genomes, and transcriptomics in the common frog, we show that multiple coexisting Y haplotypes in a single pond share an old Dmrt1-linked sex-determining region but carry younger, independently differentiated Y chromosomes. This genome-wide resolution reveals that extreme heterochiasmy, where recombination is largely restricted to chromosome ends in males, can rapidly generate very large nonrecombining regions, while sex-reversed XY females can restore X-Y recombination and reduce divergence outside the Dmrt1-linked region. These opposing processes generate cyclic dynamics of Y differentiation rather than a directional path towards degeneration. Our study provides a mechanistic explanation for the persistence of co-existing multiple Y haplotypes in one population, maintenance of homomorphic sex chromosomes, and a broadly relevant framework for sex chromosome evolution in lineages with heterochiasmy and sex reversal.