Parallel and nonparallel genome‐wide divergence among replicate population pairs of freshwater and anadromous<scp>A</scp>tlantic salmon

Perrier, Charles; Bourret, Vincent; Kent, Matthew; Bernatchez, Louis

doi:10.1111/mec.12500

Cited by 71 publications

(90 citation statements)

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“…salar) populations (Perrier et al, 2013). Overall the patterns reflected the microevolutionary processes unfolding in the smaller and isolated freshwater populations: across the genome, freshwater populations had lower genetic diversity and higher interpopulation genetic differentiation compared to the patterns among anadromous populations (Perrier et al, 2013). No evidence of individuals migrating from anadromous to freshwater populations was found, but there was some evidence for a handful of migrants out of freshwater populations (Perrier et al, 2013).…”

Section: Migrationmentioning

confidence: 83%

“…They examined 2336 genetically mapped SNPs among three pairs of North American anadromous and freshwater Atlantic salmon (Sm. salar) populations (Perrier et al, 2013). Overall the patterns reflected the microevolutionary processes unfolding in the smaller and isolated freshwater populations: across the genome, freshwater populations had lower genetic diversity and higher interpopulation genetic differentiation compared to the patterns among anadromous populations (Perrier et al, 2013).…”

Section: Migrationmentioning

confidence: 96%

“…No evidence of individuals migrating from anadromous to freshwater populations was found, but there was some evidence for a handful of migrants out of freshwater populations (Perrier et al, 2013). Genome scans found incomplete parallelism across population pairs, with little evidence that the same genomic regions were responding to selection in the same way across replicate freshwater-anadromous populations (Perrier et al, 2013).…”

Section: Migrationmentioning

confidence: 99%

“…Overall the patterns reflected the microevolutionary processes unfolding in the smaller and isolated freshwater populations: across the genome, freshwater populations had lower genetic diversity and higher interpopulation genetic differentiation compared to the patterns among anadromous populations (Perrier et al, 2013). No evidence of individuals migrating from anadromous to freshwater populations was found, but there was some evidence for a handful of migrants out of freshwater populations (Perrier et al, 2013). Genome scans found incomplete parallelism across population pairs, with little evidence that the same genomic regions were responding to selection in the same way across replicate freshwater-anadromous populations (Perrier et al, 2013).…”

Section: Migrationmentioning

confidence: 99%

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Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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The past few years have seen an absolute revolution in genomic technologies and their potential applications to ecology and evolutionary biology research. Such advances open up a range of opportunities for research on non-model organisms and individuals drawn from wild populations. This has resulted in exciting new research seeking to identify the genetic polymorphisms important in adaptation and speciation and how they are organised within the genome. Building on this, there is great interest in the extent to which similar evolutionary patterns are found across multiple populations, particularly whether consistent genetic mechanisms are associated with recurrent phenotypes. A powerful context for disentangling these mechanisms is to focus on highly diverse radiations, where phenotypes vary in and across environments. Therefore, the high diversity found within and among species of salmonid fishes such as charr (Salvelinus) make for an ideal 'non'-model for genomic research. This paper outlines some of the current approaches available in ecological genomics and highlights some recent advances in salmonid research. It also suggests avenues for the sort of predictions that can be derived from ecological genomics, with the aim of understanding the genetics behind the fantastic diversity of salmonid fishes.Keywords Ecological genomics Á Transcriptomics Á Speciation Á Genetic mapping Á Salmonid fishes Á Charr Recent advances in the field of molecular biology have exciting implications for research on the ecology and evolution of natural populations. Particularly, high throughput 'next-generation' sequencing (NGS) (also known as 'second-generation', or 'massively parallel' sequencing) can generate huge amounts of genomic or transcriptomic data on almost any organism. NGS is dramatically decreasing in cost and the associated tools and pipelines are within reach of even modest research groups. This is therefore becoming an invaluable tool for understanding the origins and maintenance of biodiversity. These exciting new approaches can address long-standing questions in evolutionary biology, such as: What is the genetic basis of adaptations? How do closely related species differ? Why are some lineages more diverse than others?The challenge for 'omics' of non-model organisms now shifts away from raw data generation to focusing on informative evolutionary, ecological, and environmental contexts in order to most efficiently and

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Section: Migrationmentioning

confidence: 83%

Section: Migrationmentioning

confidence: 96%

Section: Migrationmentioning

confidence: 99%

Section: Migrationmentioning

confidence: 99%

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Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Elmer

2016

Hydrobiologia

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“…Recent outlier locus studies of salmonid fishes have primarily compared wild populations at different spatial scales (Freamo, O'Reilly, Berg, Lien, & Boulding, 2011; Vasemägi & Primmer, 2005) or have correlated outlier loci of wild populations with specific environmental variables (Bourret, Kent, et al., 2013; Bourret, Dionne, Kent, Lien, & Bernatchez, 2013; Narum, Campbell, Kozfkay, & Meyer, 2010; Perrier, Bourret, Kent, & Bernatchez et al., 2013). Of more relevance to Atlantic salmon domestication are four outlier studies comparing aquaculture strains with wild populations from the same region as their putative founder population(s) (Gutierrez, Yáñez, & Davidson, 2016; Karlsson, Moen, Lien, Glover, & Hindar, 2011; Mäkinen, Vasemägi, McGinnity, Cross, & Primmer, 2015; Vasemägi, Nilsson, & Primmer, 2005).…”

Section: Introductionmentioning

confidence: 99%

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Liu

Ang

Elliott

et al. 2016

Evolutionary Applications

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Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.

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Spatial and temporal genetic structure of a river‐residentAtlantic salmon (Salmo salar) after millennia of isolation

Sandlund

Karlsson

Thorstad

et al. 2014

Ecology and Evolution

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The river-resident Salmo salar (“småblank”) has been isolated from other Atlantic salmon populations for 9,500 years in upper River Namsen, Norway. This is the only European Atlantic salmon population accomplishing its entire life cycle in a river. Hydropower development during the last six decades has introduced movement barriers and changed more than 50% of the river habitat to lentic conditions. Based on microsatellites and SNPs, genetic variation within småblank was only about 50% of that in the anadromous Atlantic salmon within the same river. The genetic differentiation (FST) between småblank and the anadromous population was 0.24. This is similar to the differentiation between anadromous Atlantic salmon in Europe and North America. Microsatellite analyses identified three genetic subpopulations within småblank, each with an effective population size Ne of a few hundred individuals. There was no evidence of reduced heterozygosity and allelic richness in contemporary samples (2005–2008) compared with historical samples (1955–56 and 1978–79). However, there was a reduction in genetic differentiation between sampling localities over time. SNP data supported the differentiation of småblank into subpopulations and revealed downstream asymmetric gene flow between subpopulations. In spite of this, genetic variation was not higher in the lower than in the upper areas. The meta-population structure of småblank probably maintains genetic variation better than one panmictic population would do, as long as gene flow among subpopulations is maintained. Småblank is a unique endemic island population of Atlantic salmon. It is in a precarious situation due to a variety of anthropogenic impacts on its restricted habitat area. Thus, maintaining population size and avoiding further habitat fragmentation are important.

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Parallel and nonparallel genome‐wide divergence among replicate population pairs of freshwater and anadromousAtlantic salmon

Cited by 71 publications

References 94 publications

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

Spatial and temporal genetic structure of a river‐residentAtlantic salmon (Salmo salar) after millennia of isolation

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