Investigation of sex determination in African cichlids reveals lack of fixed sex chromosomes in wild populations

Sex chromosomes are theorized to stop recombining and become fixed, yet many taxa show ambiguous genomic signals of sex consistent with either continuous recombination or sex chromosome turnover. Elucidating the basis of sex chromosome conservation or alternatively, turnover, requires comparative studies among natural populations with shared evolutionary histories. The African Great Lake radiations of cichlid fishes display an outstanding propensity to rapidly evolve novel sex-linked regions, yet older cichlid lineages external to these radiations seem to show conservation of a few sex chromosomes. Here, we studied sex-determining regions of species uniquely representing two older lineages within Lake Tanganyika; Oreochromis tanganicae (Oreochromini) and Tylochromis polylepis (Tylochromini). Using a combined SNP- and kmer-based approach, we confirm a ZW system on linkage group (LG) 3 in O. tanganicae, but not the previously proposed sex-determining gene. However, in T. polylepis, no clear region of sex-association could be identified, although kmer-based analyses point towards LG12 as a candidate sex chromosome. Additionally, we investigated four other species from older, non-East African radiation lineages and confirmed LG3 to be frequently associated with sex, but also found stronger signals of sex association on different chromosomes not previously discovered. Combined, these results suggest that homomorphic sex chromosomes are a feature of African cichlids at large. LG3 frequently harbours regions of sex-linkage, but is often polygenic with more strongly sex-linked regions on other chromosomes, possibly denoting its ancestral function as sex-determining across African cichlids, that leaves traces as novel sex-determining regions emerge. Our investigation captures this in a phylogenetic context, from emergence to fixation, or turnover to a new sex chromosome.