Conservation genomics of Esox flaviae (Italian pike)

The recent discovery of a novel pike species naturally distributed in the Alpine region, Esox flaviae (“Italian pike”), has fuelled debate on the conservation status of this prized game fish and apex predator. For decades, allochtonous Northern pike (E. lucius, here “European pike”) have been widely used in stocking practices to sustain angling activities. Although the two species differ phenotypically, hybrids are often indistinguishable, and patterns of introgression are becoming increasingly complex to unravel with traditional genetic markers, namely microsatellites. We aim to bypass this obstacle by using Whole Genome Sequence data (WGS) to study population structure and genomic adaptation in the Italian pike, and, ultimately, develop a genotyping tool to aid its conservation. Samples were previously categorized as either Italian (n = 16), European (n = 6) or hybrid (n = 6) based on microsatellites. In this study, the European pike genome was used as reference to align reads, yielding 7.3 million quality-filtered SNPs. Our SNP dataset allowed for successful clustering of individuals at species and subpopulation levels using Principal Component Analysis, as well as a more thorough analysis of hybridization as opposed to microsatellites, using FastSTRUCTURE. Genome- wide selection scans (GWSS) were carried out, which involved calculation of per-locus statistics such as FST, π and α (the rate of adaptive molecular evolution as described by the McDonald-Kreitman test). Several chromosomic regions were identified as candidates for selection. Ongoing analyses will shed further light on the patterns of adaptive variation and the functional consequences of introgressive hybridization.