Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge (Esox masquinongy) from the St. Lawrence River basin

Abstract

Understanding the genetic and evolutionary impacts of fish stocking on wild populations has long been of interest as negative consequences such as reduced fitness and loss of genetic resources are commonly reported. Nearly five decades of extensive stocking of over a million Muskellunge ( Esox masquinongy) in the Lower St. Lawrence River (Québec, Canada) was implemented by managers in an attempt to sustain a fishery. We investigated the effect of stocking on this native species' genetic structure and allelic diversity in the St. Lawrence river and its tributaries as well as several stocked inland lakes. Using Genotype-By-Sequencing (GBS), we genotyped 643 individuals representing 22 sampling sites and combined this information with forward simulations to investigate the genetic consequences of stocking. Individuals native to the St. Lawrence watershed were genetically divergent from the sources used for stocking and both the St.Lawrence tributaries and inland lakes were also naturally divergent from the main stem. Empirical data and simulations revealed weak effects of stocking on admixture patterns within the St. Lawrence despite intense stocking in the past, whereas footprints of admixture were higher in the smaller stocked populations from tributaries and lakes. Altogether, our data suggests that selection against introgression has been relatively efficient within the large St. Lawrence River. In contrast, the smaller populations from adjacent tributaries and lakes still displayed stocking related admixture which apparently resulted in higher genetic diversity, suggesting that, while stocking stopped at the same time, its impact remained higher in these populations.Finally, the origin of populations from inland lakes that were established by stocking confirmed their close affinity with these source populations. This study illustrates the benefit of combining extensive genomic data with forward simulations for improved inferences regarding outcomes of population enhancement by stocking, as well as its relevance for fishery management decision making.

Genetic population structure of a top predatory fish (northern pike, Esox lucius) covaries with anthropogenic alteration of freshwater ecosystems

“…Our data are in line with genetic structures of pike populations in Denmark at the intra‐specific level (Bekkevold et al., 2015) and Italy at the inter‐specific level (Gandolfi et al., 2017), both of which not always reflected natural catchment barriers and were probably caused by successful pike stock enhancement activities in the past. Similar results exist for muskellunge in North America (Roegemont et al., 2019).…”

“…Humans have facilitated natural migration through human‐made artificial connections among different river basins as well as stocking of economically important fish species. The latter represents an important factor that increases the potential for gene flow between populations naturally separated in space (Arlinghaus et al., 2015) and is known to shape the genetic diversity of the congeneric muskellunge ( Esox masquinongy ) in North America (Roegemont et al., 2019). Both processes are expected to lead to admixed genotypes and may lead to an erosion of population‐specific genetic variance.…”

“…Likewise, relatively low admixture levels were observed in pike populations of the Ems and Weser catchments belonging to the North Sea hydrogeographic region. A possible explanation for the persistence of autochthonous populations is either a low level of local stocking or competitive exclusion of foreign genotypes by better‐adapted native populations (Englbrecht et al., 2002; Eschbach et al., 2014; Gandolfi et al., 2017; Larsen et al., 2005; Möller et al., 2021; Roegemont et al., 2019).…”

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish

“…Both DNA extractions and library preparation were performed following protocols fully described elsewhere (e.g., Moore et al, 2017; Rougemont et al., 2019). The methods are detailed in the methods section.…”

“…SNPs were kept if they displayed a read depth greater than five and less than 70 (based on the mean distribution of read depth computed with vcftools ), the latter being set to control for paralogy and highly repetitive regions. Then, SNPs present in a least 70% in each sampling location and with heterozygosity lower than 0.60 were kept to further control for paralogues and Hardy–Weinberg disequilibrium (Dorant et al., 2019; Rougemont et al., 2019). The resulting vcf file comprised 550,724 SNPs spread over 27,442 loci and was further filtered prior to being used for demographic inferences with ∂a∂i (see filtering details provided in the methods section).…”