Genetic Recovery of Two Wild Seatrout Populations Following Long‐Term Stocking with Non‐Native Conspecifics

Predicting the long-term impact of releases and introgression from non-native strains into wild populations remains an important conservation issue, particularly in fishes where stocking and aquaculture escapes have led to widespread genetic admixture between wild and cultured conspecifics. Here, we investigated the genetic response of two wild sea trout, Salmo trutta L., populations following long-term stocking programmes with non-native conspecifics. This included temporal sampling spanning 23 years and genome-wide SNP data from two neighbouring Danish rivers that from the 1970's to 1990's were heavily stocked with partially domesticated, non-local hatchery strains. To estimate wild-hatchery admixture we analysed 3656 SNPs in 195 wild-caught fish, 74 hatchery strain fish, and expanded collections temporally by analysing a subset 288 SNPs in 489 additional fish. Admixture estimates decreased from 46% to 62% input from the stocked strains to 25% seven generations after the last stocking. Introgression varied across the genome, indicative of selection for and against specific hatchery gene variants under wild conditions. For the first time in trout, strong temporal allele frequency changes were observed in a gene region harbouring the maturation gene six6 likely associated with divergent selection on age-at-maturity under hatchery versus wild conditions. The two populations showed low overlap between SNPs identified as under negative (or purifying) selection. Results point to selection against hatchery fish and partial recovery of both populations but also emphasise the role of local dynamics in shaping genetic responses to anthropogenic pressure and support the notion that introgression is likely to incur long-lasting changes to the genetic make-up of wild populations.