Sex chromosome turnover in hybridizing stickleback lineages

Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in Pungitius sticklebacks. Sex chromosomes are highly conserved in mammals and birds but much more labile in other species, such as reptiles, amphibians, and fish. In the species having labile sex chromosomes, even different populations of the same species have the potential to evolve different sex chromosomes and sex-determining systems. In the nine-spined stickleback fish (Pungitius pungitius), the eastern European lineage has heteromorphic sex chromosomes on linkage group 12 (LG12), whereas our study identified the western European lineage to have homomorphic sex chromosomes on LG3, where an 80 kbp region determines sex. Interestingly, although the two lineages have different pairs of sex chromosomes, they mate and reproduce in the Baltic Sea. We show that in the hybrid marine populations, the western lineage's homomorphic sex chromosomes (LG3) are taking over the eastern lineage's heteromorphic sex chromosomes (LG12). This suggests that a transition of sex chromosomes (i.e., sex chromosome turnover) is happening in these populations. This study shows that sex chromosomes can be highly diverse in stickleback fish populations, even within the same species. Lastly, we also show a likely different and uncharacterized sex-determining system in UK populations of nine-spined sticklebacks, which indicates high sex chromosome diversity in Pungitius sticklebacks.