The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

Admixture is an evolutionary process that enables short-term adaptation. The Creole cattle from Guadeloupe is a tropically adapted breed. Its three-way admixture and long-term isolation offer a unique opportunity for understanding the genetic determinants of adaptive admixture in livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA) and combined our data with sequenced genomes of 99 cattle from 25 breeds representative of European, African and indicine groups to provide the most detailed exploration, to date, of patterns of genetic variation and to detect selection signatures in this population. We detect 17 228 983 single nucleotide polymorphisms (SNPs) and we confirmed the higher level of African and indicine ancestries, compared to the European ancestry, in the GUA genome. We show that, unlike Criollo cattle, GUA population originates directly from West Africa with indicine ancestry inherited via West African ancestors. We relied on consistency of signals across various methods based on excess of haplotype homozygosity, differences in allele frequencies and excess ⁄ deficiency of local ancestry to identify five strong candidate regions showing an excess of indicine ancestry. These encompass immune-, heat-tolerance- and physical exercise-related genes. Moreover, we found that a previously identified horn-related gene, RXFP2 is under strong selective pressure in GUA genome likely owing to human-driven (socio-cultural) pressure. Our study highlights the role played by population admixture for driving rapid adaptive response to local environmental constraints.