Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Hemmer‐Hansen, Jakob; Therkildsen, Nina Overgaard; Pujolar, J. M.

doi:10.1086/bblv227n2p117

Cited by 64 publications

(47 citation statements)

References 174 publications

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“…The difficulty of monitoring FIE at the level of molecular markers lies in identifying the genetic basis of specific traits of interest and linking it to fishing pressure (Hemmer- Hansen et al 2014, Vasemägi & Primmer 2005. To overcome this challenge, population genomics and quantitative genetics need to be combined, but performing quantitative genetic tests in natural populations of marine fishes remains difficult (Hemmer-Hansen et al 2014).…”

Section: Genotypic Versus Phenotypic Evidencementioning

confidence: 99%

“…To overcome this challenge, population genomics and quantitative genetics need to be combined, but performing quantitative genetic tests in natural populations of marine fishes remains difficult (Hemmer-Hansen et al 2014). Consequently, molecular genetic approaches are complementing, not replacing, phenotypic approaches to study FIE.…”

Section: Genotypic Versus Phenotypic Evidencementioning

confidence: 99%

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Fisheries-Induced Evolution

Heino

Pauli

Dieckmann

2015

Annu. Rev. Ecol. Evol. Syst.

303

329

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Increased mortality from fishing is expected to favor faster life histories, realized through earlier maturation, increased reproductive investment, and reduced postmaturation growth. There is also direct and indirect selection on behavioral traits. Molecular genetic methods have so far contributed minimally to understanding such fisheries-induced evolution (FIE), but a large body of literature studying evolution using phenotypic methods has suggested that FIE in life-history traits, in particular maturation traits, is commonplace in exploited fish populations. Although no phenotypic study in the wild can individually provide conclusive evidence for FIE, the observed common pattern suggests a common explanation, strengthening the case for FIE. This interpretation is supported by theoretical and experimental studies. Evidence for FIE of behavioral traits is limited from the wild, but strong from experimental studies. We suggest that such evolution is also common, but has so far been overlooked.

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Section: Genotypic Versus Phenotypic Evidencementioning

confidence: 99%

Section: Genotypic Versus Phenotypic Evidencementioning

confidence: 99%

Fisheries-Induced Evolution

Heino

Pauli

Dieckmann

2015

Annu. Rev. Ecol. Evol. Syst.

303

329

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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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“…2010) enabling the discovery of fine-scale genetic variation and thus the deduction of population divergences with drastically increased accuracy (Hemmer-Hansen et al. 2014).…”

Section: Introductionmentioning

confidence: 99%

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

Barth

Damerau

Matschiner

et al. 2017

Genome Biology and Evolution

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Recent developments in the field of genomics have provided new and powerful insights into population structure and dynamics that are essential for the conservation of biological diversity. As a commercially highly valuable species, the yellowfin tuna (Thunnus albacares) is intensely exploited throughout its distribution in tropical oceans around the world, and is currently classified as near threatened. However, conservation efforts for this species have so far been hampered by limited knowledge of its population structure, due to incongruent results of previous investigations. Here, we use whole-genome sequencing in concert with a draft genome assembly to decipher the global population structure of the yellowfin tuna, and to investigate its demographic history. We detect significant differentiation of Atlantic and Indo-Pacific yellowfin tuna populations as well as the possibility of a third diverged yellowfin tuna group in the Arabian Sea. We further observe evidence for past population expansion as well as asymmetric gene flow from the Indo-Pacific to the Atlantic.

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Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

Cited by 64 publications

References 174 publications

Fisheries-Induced Evolution

Fisheries-Induced Evolution

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

Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations

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