Genetic admixture between captive-bred and wild individuals affects patterns of dispersal in a brown trout (Salmo trutta) population

Saint‐Pé, Keoni; Blanchet, Simon; Tissot, Laurence; Poulet, Nicolas; Plasseraud, Olivier; Loot, Géraldine; Veyssière, Charlotte; Prunier, Jérôme G.

doi:10.1007/s10592-018-1095-2

Cited by 18 publications

(27 citation statements)

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“…We first compared genetic admixture between wild and captive-bred strains using STRUCTURE 2.3.1 [96] with the admixture model and the correlated allele frequency model, without prior population information. Twenty runs assuming two clusters (K = 2, in order to discriminate between wild and captive-bred individuals, see [94]) were performed with a burn-in period of 200,000 and 200,000 subsequent MCMC repetitions. The ten best runs (highest LnP(D) values) were compiled using CLUMPP [97] to obtain final averaged individual Q-values.…”

Section: Methodsmentioning

confidence: 99%

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

et al. 2019

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Background The brown trout ( Salmo trutta ) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites. Results A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation. Conclusions The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

et al. 2019

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“…For instance, Saint‐Pé et al. () showed that, in a brown trout ( Salmo trutta trutta ) population from a small French watershed stocked for decades, both the emigration propensity and the dispersal destination of individuals were influenced by their individual level of genetic admixture with the domestic strain. Nevertheless, when contemporary individual dispersal events cannot be identified, genetic approaches relying on the spatial distribution of allelic frequencies (e.g., measures of genetic differentiation) must carefully dissociate the influence of between‐site landscape processes (geographic distance and/or landscape resistance) impacting the transience phase from the influence of at‐site landscape processes (local carrying capacity, patch quality, etc.)…”

Section: How To Infer Environmental and Individual Effects On Non‐effmentioning

confidence: 99%

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

et al. 2018

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Dispersal is a central process in ecology and evolution. At the individual level, the three stages of the dispersal process (i.e., emigration, transience and immigration) are affected by complex interactions between phenotypes and environmental factors. Condition- and context-dependent dispersal have far-reaching consequences, both for the demography and the genetic structuring of natural populations and for adaptive processes. From an applied point of view, dispersal also deeply affects the spatial dynamics of populations and their ability to respond to land-use changes, habitat degradation and climate change. For these reasons, dispersal has received considerable attention from ecologists and evolutionary biologists. Demographic and genetic methods allow quantifying non-effective (i.e., followed or not by a successful reproduction) and effective (i.e., with a successful reproduction) dispersal and to investigate how individual and environmental factors affect the different stages of the dispersal process. Over the past decade, demographic and genetic methods designed to quantify dispersal have rapidly evolved but interactions between researchers from the two fields are limited. We here review recent developments in both demographic and genetic methods to study dispersal in wild animal populations. We present their strengths and limits, as well as their applicability depending on study objectives and population characteristics. We propose a unified framework allowing researchers to combine methods and select the more suitable tools to address a broad range of important topics about the ecology and evolution of dispersal and its consequences on animal population dynamics and genetics.

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“…Studies investigating whether and how migratory behavior is affected by hybridization between different migratory forms are scarce. However, Saint-Pé et al (2018) investigated genetic structure and spatial patterns of admixture in brown trout (S. trutta) within a small watershed in France, and report that dispersal was admixture-biased. In conclusion, populations can differentiate rapidly, selection can modify migratory behavior, and admixture between different migratory forms can impact on dispersal probability, population differentiation and genetic structure of migratory fish.…”

Section: Genetic Admixturementioning

confidence: 99%

Ecological and Evolutionary Consequences of Environmental Change and Management Actions for Migrating Fish

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Migration strategies in fishes comprise a rich, ecologically important, and socioeconomically valuable example of biological diversity. The variation and flexibility in migration is evident between and within individuals, populations, and species, and thereby provides a useful model system that continues to inform how ecological and evolutionary processes mold biodiversity and how biological systems respond to environmental heterogeneity and change. Migrating fishes are targeted by commercial and recreational fishing and impact the functioning of aquatic ecosystems. Sadly, many species of migrating fish are under increasing threat by exploitation, pollution, habitat destruction, dispersal barriers, overfishing, and ongoing climate change that brings modified, novel, more variable and extreme conditions and selection regimes. All this calls for protection, sustainable utilization and adaptive management. However, the situation for migrating fishes is complicated further by actions aimed at mitigating the devastating effects of such threats. Changes in river connectivity associated with removal of dispersal barriers such as dams and construction of fishways, together with compensatory breeding, and supplemental stocking can impact on gene flow and selection. How this in turn affects the dynamics, genetic structure, genetic diversity, evolutionary potential, and viability of spawning migrating fish populations remains largely unknown. In this narrative review we describe and discuss patterns, causes, and consequences of variation and flexibility in fish migration that are scientifically interesting and concern key issues within the framework of evolution and maintenance of biological diversity. We showcase how the evolutionary solutions to key questions that define migrating fish-whether or not to migrate, why to migrate, where to migrate, and when to migrate-may depend on individual characteristics and ecological conditions. We explore links between environmental change and migration strategies, and discuss whether and how threats associated with overexploitation, environmental makeovers, and management actions may differently influence vulnerability of individuals, populations, and species depending on the variation and flexibility of their migration strategies. Our goal is to provide a broad overview of knowledge in this emerging area, spur future research, and development of informed management, and ultimately promote sustainable utilization and protection of migrating fish and their ecosystems.

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Genetic admixture between captive-bred and wild individuals affects patterns of dispersal in a brown trout (Salmo trutta) population

Cited by 18 publications

References 88 publications

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics

Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review

Ecological and Evolutionary Consequences of Environmental Change and Management Actions for Migrating Fish

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