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The survival of Atlantic salmon (Salmo salar), an increasingly rare anadromous species, has declined dramatically during its marine phase, with disproportionate impacts on the poorly understood early post‐smolt period. Logistical constraints on collecting oceanic data to inform this issue pose a formidable obstacle. To advance understanding of post‐smolt distributional ecology in the North‐east Atlantic, a comprehensive analysis of existing information was undertaken. Data were synthesized from 385 marine cruises, 10,202 individual trawls, and 9,269 captured post‐smolts, spanning three decades and ~4.75 million km2 of ocean, with 3,423 individuals genetically assigned to regional phylogeographic origin. The findings confirm major migrational post‐smolt aggregations on the continental shelf‐edge off Ireland, Scotland and Norway, and an important marine foraging area in the Norwegian Sea. Genetic analysis shows that aggregational stock composition does not simply reflect distance to natal rivers, with northern phylogeographic stock groups significantly under‐represented in sampled high‐seas aggregations. It identifies a key foraging habitat for southern European post‐smolts located in international waters immediately west of the Vøring Plateau escarpment, potentially exposing them to a high by‐catch mortality from extra‐territorial pelagic fisheries. Evidence of the differential distribution of regional stocks points to fundamental differences in their migration behaviours and may lead to inter‐stock variation in responses to environmental change and marine survival. The study shows that understanding of post‐smolt marine ecology, as regards to stock‐specific variations in habitat utilization, biological performance and exposure to mortality factors, can be significantly advanced by data integration across studies and exploiting genetic approaches. [ABSTRACT FROM AUTHOR]

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self‐assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI. [ABSTRACT FROM AUTHOR]

Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population‐specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps. [ABSTRACT FROM AUTHOR]

Abstract: Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco‐genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%–10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%–50% escapees) were clear changes visible in this period. Our modeling also revealed that genetic changes in phenotypic and demographic characteristics were greater in situations where strayers originating from a neighboring wild population were domestication‐admixed and changed in parallel with the focal wild population, as opposed to nonadmixed. While recovery in the phenotypic and demographic characteristics was observed in many instances after domesticated salmon intrusion was halted, in the most extreme intrusion scenario, the population went extinct. Based upon results from these simulations, together with existing knowledge, we suggest that a combination of reduced spawning success of domesticated escapees, natural selection purging maladapted phenotypes/genotypes from the wild population, and phenotypic plasticity, buffer the rate and magnitude of change in phenotypic and demographic characteristics of wild populations subject to spawning intrusion of domesticated escapees. The results of our simulations also suggest that under specific conditions, natural straying among wild populations may buffer genetic changes in phenotypic and demographic characteristics resulting from introgression of domesticated escapees and that variation in straying in time and space may contribute to observed differences in domestication‐driven introgression among native populations. [ABSTRACT FROM AUTHOR]

Aim We constructed an independent phylogeographical hypothesis ( IPH) for Atlantic salmon ( Salmo salar L.) in Scotland and adjacent northern England and tested if the distribution of contemporary microsatellite variation accorded with the IPH. Location NW Europe. Methods Knowledge of post-Last Glacial Maximum ( LGM) landscape development and salmon biology were used to define a temporal sequence of late Quaternary ecological niche models and, combined with the central-marginal ( CM) model of diversity evolution, to formulate an IPH. Observed microsatellite locus variation for salmon from 102 rivers in Scotland and northern England was tested for agreement with the IPH. Results The IPH postulated (1) initial colonization ( c. 17 ka bp) of multiple isolated deglaciating coastal regions by long-distance dispersal, predominantly from SW Europe via the Atlantic, (2) intra-region colonization dominated by local range expansion, (3) differentiation by founder effects/genetic drift, in line with CM, until deglaciation complete and regions merged ( c. 10 ka bp). IPH regions were weakly but significantly differentiated, showed broad agreement with genetically defined regions, and genetic diversity within them positively correlated with time post-deglaciation, conforming to the CM model. The greatest differentiation was seen for the most recently diverged populations, with evidence that accumulating homoplastic mutations muted older regional phylogeographical signatures. Main conclusions Microsatellite differentiation in Scottish Atlantic salmon is significantly but weakly conditioned by post- LGM deglaciation, with a mosaic of regional groups and a temporal cascade of within-region CM effects caused by local range expansion as patches became deglaciated. Colonization was predominantly or exclusively from the south-western European LGM refugium. Accumulating homoplastic mutations have increasingly reduced regional differentiation. [ABSTRACT FROM AUTHOR]