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

Elmer, Kathryn R.

doi:10.1007/s10750-015-2614-5

Cited by 44 publications

(46 citation statements)

References 128 publications

(178 reference statements)

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“…In fish‐related research, the combined use of RADseq data in genome scans with the aim of identifying targets of selection in freshwater, anadromous and marine species has been increasingly popular, such that it is nearly impossible to provide an exhaustive list of all published studies. References to less recent studies can be found in several review papers (Hemmer‐Hansen et al , ; Pujolar et al , , ; Ulrik et al , ; Willette et al , ; Gaither et al , ; Guo et al , ; Elmer, ; Picq et al , , as well as references in the next section as examples of the most recent studies). In contrast, fewer fish studies have used a landscape genomic framework to detecting selection by finding statistical associations between local allele frequencies and environmental variables and those have mainly been performed on salmonids (Zueva et al , ; Hecht et al , ; Hand et al , ).…”

Section: Modern Approaches To Study Genomics Of Local Adaptationmentioning

confidence: 99%

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

Bernatchez

2016

Journal of Fish Biology

208

216

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The first goal of this paper was to overview modern approaches to local adaptation, with a focus on the use of population genomics data to detect signals of natural selection in fishes. Several mechanisms are discussed that may enhance the maintenance of genetic variation and evolutionary potential, which have been overlooked and should be considered in future theoretical development and predictive models: the prevalence of soft sweeps, polygenic basis of adaptation, balancing selection and transient polymorphisms, parallel evolution, as well as epigenetic variation. Research on fish population genomics has provided ample evidence for local adaptation at the genome level. Pervasive adaptive evolution, however, seems to almost never involve the fixation of beneficial alleles. Instead, adaptation apparently proceeds most commonly by soft sweeps entailing shifts in frequencies of alleles being shared between differentially adapted populations. One obvious factor contributing to the maintenance of standing genetic variation in the face of selective pressures is that adaptive phenotypic traits are most often highly polygenic, and consequently the response to selection should derive mostly from allelic co-variances among causative loci rather than pronounced allele frequency changes. Balancing selection in its various forms may also play an important role in maintaining adaptive genetic variation and the evolutionary potential of species to cope with environmental change. A large body of literature on fishes also shows that repeated evolution of adaptive phenotypes is a ubiquitous evolutionary phenomenon that seems to occur most often via different genetic solutions, further adding to the potential options of species to cope with a changing environment. Moreover, a paradox is emerging from recent fish studies whereby populations of highly reduced effective population sizes and impoverished genetic diversity can apparently retain their adaptive potential in some circumstances. Although more empirical support is needed, several recent studies suggest that epigenetic variation could account for this apparent paradox. Therefore, epigenetic variation should be fully integrated with considerations pertaining to role of soft sweeps, polygenic and balancing selection, as well as repeated adaptation involving different genetic basis towards improving models predicting the evolutionary potential of species to cope with a changing world.

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Section: Modern Approaches To Study Genomics Of Local Adaptationmentioning

confidence: 99%

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

Bernatchez

2016

Journal of Fish Biology

208

216

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“…The very high-resolution approach that is now realistically possible through ''next-generation sequencing'' is starting to allow us to disentangle the patterns of phenotypic variation we see among Salvelinus populations in the wild at the genetic level (Elmer, 2016). In addition, new RNAseq techniques examine messenger RNA and are thus beginning to give us some ideas of which, how and when, genes are being expressed.…”

Section: Evolutionary Studiesmentioning

confidence: 99%

“…Of particular relevance for those of us interested in Salvelinus spp. as evolutionary models is the insight we gain when closely related, recently divergent ecotypes differentially express genes (Elmer, 2016). It is not just the molecular techniques that have developed with time.…”

Section: Evolutionary Studiesmentioning

confidence: 99%

The role of Salvelinus in contemporary studies of evolution, trophic ecology and anthropogenic change

et al. 2016

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“…Salmonids have been a focus of intensive efforts to characterize variation associated with life-history traits (Waples et al, 2004;Miller et al, 2012;Dodson et al, 2013;Brieuc et al, 2015;Elmer, 2016;Phillis et al, 2016). From this, several examples have emerged that provide strong evidence for single genes or genomic regions that have a strong influence on specific phenotypic traits with clear conservation and management implications.…”

Section: Examples Of Agv In Salmonid Life Historiesmentioning

confidence: 99%

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

Pearse

2016

Journal of Fish Biology

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As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.

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

Cited by 44 publications

References 128 publications

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

The role of Salvelinus in contemporary studies of evolution, trophic ecology and anthropogenic change

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

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