Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char

Abstract

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild.Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic.Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise F ST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian Computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in non-breeding years.Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in non-model organisms in logistically challenging environments such as the Arctic.

Population structure and genomic evidence for local adaptation to freshwater and marine environments in anadromous Arctic Char (Salvelinus alpinus) throughout Nunavik, Québec, Canada

“…Since Arctic Char populations in Nunavik support mainly small-scale subsistence fisheries, stocks are managed on a river-by-river basis, on the premise that each river contains a single and distinct population (Johnson, 1980). However, our results add to the evidence for the prevalence of mixed stocks of Arctic Char in adjacent rivers (Boguski, Gallagher, Howland & Harris, 2016; Moore, Lewis & Tallman, 2014; Moore et al, 2017). While most pairs of sampled rivers sharing an estuary had very low genetic differentiation, we found evidence of substructure within those systems, suggesting that genomic tools could be used for stock assignment of adult fish (e.g.…”

“…While most pairs of sampled rivers sharing an estuary had very low genetic differentiation, we found evidence of substructure within those systems, suggesting that genomic tools could be used for stock assignment of adult fish (e.g. Meek et al, 2016; Moore et al 2017). The evidence we found for local adaptation to marine environments is in concordance with the neutral genetic structure at a broader scale, as major oceanographic basins around Nunavik are contrasted both in their environments and ancestry of their Arctic Char populations.…”

“…Arctic Char is known for its higher straying rates than other salmonids, but many studies argue that this dispersal does not necessarily lead to gene flow, as individuals are more prone to straying when overwintering than when breeding (Moore et al, 2013; Moore et al 2017; Sévigny, Harris, Normandeau, Cayuela, Gilbert & Moore, in prep). This case of reproductive isolation with migration could explain our clustering results for some pairs of sites sharing an estuary.…”

“…Anadromous individuals spend 3 to 9 years in cold oligotrophic freshwater at birth (Johnson, 1980), then complete annual migrations between marine habitats for summer foraging and lakes for overwintering. Although straying (i.e., an upstream migration in a non-natal river system) can occur, several studies have shown that Arctic Char maintained philopatric behaviour during reproductive years, limiting effective dispersal (Gyselman, 1994; Moore, Harris, Tallman & Taylor, 2013; Moore et al 2017). Moore et al (2013) also argued that gene flow could be sufficiently low to allow for local adaptation among populations of eastern Baffin Island in the Canadian Arctic, while Moore et al (2017) provided some genomic evidence for local adaptation to natal rivers at a fine spatial scale.…”

Adaptive and maladaptive genetic diversity in small populations; insights from the Brook Charr (Salvelinus fontinalis)case study

“…Although natural selection 44 may increase the frequency of adaptive mutations and remove deleterious alleles at the same time 45 (Whitlock et al 2003), deleterious variants may also hitchhike with advantageous mutations to high 46 frequencies if they have intermediate fitness costs (Chun and Fay 2011). Additionally, 47 recombination facilitates the removal of maladaptive alleles from a population (Felsenstein 1974), 48 and genomic regions of low recombination are more likely to accumulate deleterious alleles as the 49 including salmonids (Bernatchez & Dodson, 1987), which can drive local adaptation of life history 90 traits (Pearse et al 2014, Moore et al 2017), including in Brook Charr (Fraser and Bernatchez (2005); 91…”