Investigating genomic and phenotypic parallelism between piscivorous and planktivorous lake trout (Salvelinus namaycush) ecotypes by means of RADseq and morphometrics analyses.

Repeated adaptive ecological diversification has commonly been reported in fish and has often been associated with trophic niche diversity. The main goal of this study was to investigate the extent of parallelism in the genomic and phenotypic divergence between piscivorous and planktivorous lake trout ecotypes from Laurentian Shield lakes, Canada. This was achieved by documenting the extent of morphological differentiation using geometric morphometrics and linear measurements as well as the pattern of genomic divergence by means of RADseq genotyping (3925 filtered SNPs) in 12 lakes. Our results indicate that the two ecotypes evolved distinct body shape and several linear measurements in parallel. Neutral genetic differentiation was pronounced between all isolated populations (Mean FST  = 0.433), indicating no or very limited migration and pronounced genetic drift. Significant genetic differentiation also suggested partial reproductive isolation between ecotypes in the two lakes where they are found in sympatry. Combining different outlier detection methods, we identified 48 SNPs putatively under divergent selection between ecotypes, among which 10 could be annotated and related to functions such as developmental processes and ionic regulation. Finally, our results indicate that parallel morphological divergence is accompanied by both parallel and nonparallel genomic divergence, which is associated with the use of different trophic niches between ecotypes. The results are also discussed in the context of management and conservation of this highly exploited species throughout northern North America.

Bernatchez S ，Laporte M ，Perrier C ，Sirois P ，Bernatchez L ... -  《-》

Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior.

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four lake trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (mean FST  = 0.016) than between ecotypes within sites (mean FST  = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions supports the presence of a continuum of divergence in lake trout.

Perreault-Payette A ，Muir AM ，Goetz F ，Perrier C ，Normandeau E ，Sirois P ，Bernatchez L ... -  《-》

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush.

Baillie SM ，Muir AM ，Hansen MJ ，Krueger CC ，Bentzen P ... -  《BMC EVOLUTIONARY BIOLOGY》

The role of ecotype-environment interactions in intraspecific trophic niche partitioning subsequent to stocking.

Worldwide, stocking of fish represents a valuable tool for conservation and maintenance of species exploited by recreational fishing. Releases of hatchery-reared fish are more and more recognized to have numerous demographic, ecological, and genetic impacts on wild populations. However, consequences on intraspecific trophic relationships have rarely been investigated. In this study, we assessed the impacts of supplementation stocking and resulting introgressive hybridization on the trophic niches occupied by stocked, local, and hybrid lake trout (Salvelinus namaycush) within populations of piscivorous and planktivorous ecotypes stocked from a wild piscivorous source population. We compared trophic niches using stable isotope analysis (δ13 C and δ15 N) and trophic position among the three genetic origins. Putative genetic effects were tested with phenotype-genotype association of "life history" ecological traits (body size, growth rate, condition index, and trophic niche) and genotypes (RADseq SNP markers) using redundant discriminant analysis (RDA). Results showed that sympatry resulting from the stocking of contrasting ecotypes is a risk factor for niche partitioning. Planktivorous populations are more susceptible to niche partitioning, by competitive exclusion of the local fish from a littoral niche to an alternative pelagic/profundal niche. Observed niche partitioning is probably a manifestation of competitive interactions between ecotypes. Our results emphasize that ecotypic variation should be considered for more efficient management and conservation practices and in order to mitigate negative impact of supplementation stocking.

Morissette O ，Sirois P ，Wilson CC ，Laporte M ，Bernatchez L ... -  《ECOLOGICAL APPLICATIONS》

Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish.

Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

Perrier C ，Ferchaud AL ，Sirois P ，Thibault I ，Bernatchez L ... -  《-》