1
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Tréhin C, Rivot E, Santanbien V, Patin R, Gregory SD, Lamireau L, Marchand F, Beaumont WRC, Scott LJ, Hillman R, Besnard AL, Boisson PY, Meslier L, King AR, Stevens JR, Nevoux M. A multi-population approach supports common patterns in marine growth and maturation decision in Atlantic salmon (Salmo salar L.) from southern Europe. JOURNAL OF FISH BIOLOGY 2024; 104:125-138. [PMID: 37728039 DOI: 10.1111/jfb.15567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/23/2023] [Accepted: 09/14/2023] [Indexed: 09/21/2023]
Abstract
This study provides a regional picture of long-term changes in Atlantic salmon growth at the southern edge of their distribution, using a multi-population approach spanning 49 years and five populations. We provide empirical evidence of salmon life history being influenced by a combination of common signals in the marine environment and population-specific signals. We identified an abrupt decline in growth from 1976 and a more recent decline after 2005. As these declines have also been recorded in northern European populations, our study significantly expands a pattern of declining marine growth to include southern European populations, thereby revealing a large-scale synchrony in marine growth patterns for almost five decades. Growth increments during their sea sojourn were characterized by distinct temporal dynamics. At a coarse temporal resolution, growth during the first winter at sea seemed to gradually improve over the study period. However, the analysis of finer seasonal growth patterns revealed ecological bottlenecks of salmon life histories at sea in time and space. Our study reinforces existing evidence of an impact of early marine growth on maturation decision, with small-sized individuals at the end of the first summer at sea being more likely to delay maturation. However, each population was characterized by a specific probabilistic maturation reaction norm, and a local component of growth at sea in which some populations have better growth in some years might further amplify differences in maturation rate. Differences between populations were smaller than those between sexes, suggesting that the sex-specific growth threshold for maturation is a well-conserved evolutionary phenomenon in salmon. Finally, our results illustrate that although most of the gain in length occurs during the first summer at sea, the temporal variability in body length at return is buffered against the decrease in post-smolt growth conditions. The intricate combination of growth over successive seasons, and its interplay with the maturation decision, could be regulating body length by maintaining diversity in early growth trajectories, life histories, and the composition of salmon populations.
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Affiliation(s)
- Cécile Tréhin
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
- U3E, Experimental Unit of Aquatic Ecology and Ecotoxicology, INRAE, OFB, Rennes, France
- MIAME- Management of Diadromous Fish in their Environment, OFB, INRAE, Institut Agro, UNIV PAU & PAYS ADOUR/E2S UPPA, Rennes, France
| | - Etienne Rivot
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
- MIAME- Management of Diadromous Fish in their Environment, OFB, INRAE, Institut Agro, UNIV PAU & PAYS ADOUR/E2S UPPA, Rennes, France
| | - Valentin Santanbien
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Rémi Patin
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
- Univ. of Grenoble Alpes, CNRS, Univ. Savoie Mont Blanc, LECA, Grenoble, France
| | - Stephen D Gregory
- Salmon and Trout Research Centre, Game and Wildlife Conservation Trust, River Laboratory, Wareham, UK
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, UK
- Department of Life and Environmental Sciences, Faculty of Science and Technology, Bournemouth University, Poole, UK
| | - Ludivine Lamireau
- U3E, Experimental Unit of Aquatic Ecology and Ecotoxicology, INRAE, OFB, Rennes, France
| | - Frédéric Marchand
- U3E, Experimental Unit of Aquatic Ecology and Ecotoxicology, INRAE, OFB, Rennes, France
| | - William R C Beaumont
- Salmon and Trout Research Centre, Game and Wildlife Conservation Trust, River Laboratory, Wareham, UK
| | - Luke J Scott
- Salmon and Trout Research Centre, Game and Wildlife Conservation Trust, River Laboratory, Wareham, UK
| | | | - Anne-Laure Besnard
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Pierre-Yves Boisson
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Lisa Meslier
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Andrew R King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, Exeter, UK
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, Exeter, UK
| | - Marie Nevoux
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
- MIAME- Management of Diadromous Fish in their Environment, OFB, INRAE, Institut Agro, UNIV PAU & PAYS ADOUR/E2S UPPA, Rennes, France
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2
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Rougemont Q, Perrier C, Besnard AL, Lebel I, Abdallah Y, Feunteun E, Réveillac E, Lasne E, Acou A, Nachón DJ, Cobo F, Evanno G, Baglinière JL, Launey S. Population genetics reveals divergent lineages and ongoing hybridization in a declining migratory fish species complex. Heredity (Edinb) 2022; 129:137-151. [PMID: 35665777 PMCID: PMC9338086 DOI: 10.1038/s41437-022-00547-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 11/08/2022] Open
Abstract
Deciphering the effects of historical and recent demographic processes responsible for the spatial patterns of genetic diversity and structure is a key objective in evolutionary and conservation biology. Using population genetic analyses, we investigated the demographic history, the contemporary genetic diversity and structure, and the occurrence of hybridization and introgression of two species of anadromous fish with contrasting life history strategies and which have undergone recent demographic declines, the allis shad (Alosa alosa) and the twaite shad (Alosa fallax). We genotyped 706 individuals from 20 rivers and 5 sites at sea in Southern Europe at thirteen microsatellite markers. Genetic structure between populations was lower for the nearly semelparous species A. alosa, which disperses greater distances compared to the iteroparous species, A. fallax. Individuals caught at sea were assigned at the river level for A. fallax and at the region level for A. alosa. Using an approximate Bayesian computation framework, we inferred that the most likely long term historical divergence scenario between both species and lineages involved historical separation followed by secondary contact accompanied by strong population size decline. Accordingly, we found evidence for contemporary hybridization and bidirectional introgression due to gene flow between both species and lineages. Moreover, our results support the existence of at least one distinct species in the Mediterrannean sea: A. agone in Golfe du Lion area, and another divergent lineage in Corsica. Overall, our results shed light on the interplay between historical and recent demographic processes and life history strategies in shaping population genetic diversity and structure of closely related species. The recent demographic decline of these species' populations and their hybridization should be carefully considered while implementing conservation programs.
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Affiliation(s)
- Quentin Rougemont
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France.
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
| | - Charles Perrier
- UMR CBGP, INRAE, CIRAD, IRD, Institut Agro, Univ Montpellier, Montpellier, France
| | - Anne-Laure Besnard
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Isabelle Lebel
- Migrateurs Rhône Méditerranée, Arles, France
- Fédération Nationale de la Pêche en France et de la protection du milieu aquatique (FNPF), Paris, France
| | - Yann Abdallah
- Migrateurs Rhône Méditerranée, Arles, France
- SCIMABIO, Thonon-les-Bains, France
| | - Eric Feunteun
- UMS OFB-CNRS-MNHN PatriNat, Station marine du Museum National d'Histoire Naturelle, Dinard, France
| | - Elodie Réveillac
- UMS OFB-CNRS-MNHN PatriNat, Station marine du Museum National d'Histoire Naturelle, Dinard, France
- LIENSs, Univ La Rochelle CNRS, La Rochelle, France
| | - Emilien Lasne
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
- UMS OFB-CNRS-MNHN PatriNat, Station marine du Museum National d'Histoire Naturelle, Dinard, France
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Anthony Acou
- LIENSs, Univ La Rochelle CNRS, La Rochelle, France
- Management of Diadromous Fish in their Environment OFB-INRAE-Institut Agro-UPPA, Rennes, France
| | - David José Nachón
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Fernando Cobo
- Departamento de Zooloxía, Xenética e Antropoloxía Física, Facultade de Bioloxía, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Guillaume Evanno
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Jean-Luc Baglinière
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Sophie Launey
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Finlay R, Poole R, Coughlan J, Phillips KP, Prodöhl P, Cotter D, McGinnity P, Reed TE. Telemetry and genetics reveal asymmetric dispersal of a lake-feeding salmonid between inflow and outflow spawning streams at a microgeographic scale. Ecol Evol 2020; 10:1762-1783. [PMID: 32128115 PMCID: PMC7042748 DOI: 10.1002/ece3.5937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/01/2022] Open
Abstract
The degree of natal philopatry relative to natal dispersal in animal populations has important demographic and genetic consequences and often varies substantially within species. In salmonid fishes, lakes have been shown to have a strong influence on dispersal and gene flow within catchments; for example, populations spawning in inflow streams are often reproductively isolated and genetically distinct from those spawning in relatively distant outflow streams. Less is known, however, regarding the level of philopatry and genetic differentiation occurring at microgeographic scales, for example, where inflow and outflow streams are separated by very small expanses of lake habitat. Here, we investigated the interplay between genetic differentiation and fine-scale spawning movements of brown trout between their lake-feeding habitat and two spawning streams (one inflow, one outflow, separated by <100 m of lake habitat). Most (69.2%) of the lake-tagged trout subsequently detected during the spawning period were recorded in just one of the two streams, consistent with natal fidelity, while the remainder were detected in both streams, creating an opportunity for these individuals to spawn in both natal and non-natal streams. The latter behavior was supported by genetic sibship analysis, which revealed several half-sibling dyads containing one individual that was sampled as a fry in the outflow and another that was sampled as fry in the inflow. Genetic clustering analyses in conjunction with telemetry data suggested that asymmetrical dispersal patterns were occurring, with natal fidelity being more common among individuals originating from the outflow than the inflow stream. This was corroborated by Bayesian analysis of gene flow, which indicated significantly higher rates of gene flow from the inflow into the outflow than vice versa. Collectively, these results reveal how a combination of telemetry and genetics can identify distinct reproductive behaviors and associated asymmetries in natal dispersal that produce subtle, but nonetheless biologically relevant, population structuring at microgeographic scales.
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Affiliation(s)
- Ross Finlay
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | | | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Karl P. Phillips
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Paulo Prodöhl
- Institute for Global Food SecuritySchool of Biological SciencesQueen's University BelfastBelfastIreland
| | | | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
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5
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Rougemont Q, Bernatchez L. The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations. Evolution 2019; 72:1261-1277. [PMID: 29644624 DOI: 10.1111/evo.13486] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/14/2018] [Indexed: 12/18/2022]
Abstract
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps, and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflect the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.
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Affiliation(s)
- Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6 Québec, Canada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6 Québec, Canada
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6
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Genetic diversity in tilapia populations in a freshwater reservoir assayed by randomly amplified polymorphic DNA markers. Saudi J Biol Sci 2019; 26:363-367. [PMID: 31485178 PMCID: PMC6717130 DOI: 10.1016/j.sjbs.2018.11.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 11/06/2018] [Accepted: 11/20/2018] [Indexed: 11/22/2022] Open
Abstract
Genetic variation in fish stocks decreasing due to water pollution in the freshwater rivers, streams and canals. The objective of this study was to determine the genetic diversity and polymorphism in Oreochromis niloticus collected from the Wadi Hanefah Riyadh, Saudi Arabia by using RAPD-PCR. Total thirty fish specimens were harvested from each of four pre-determined locations of the reservoir which were designated as H1, H2, H3, and H4. Five random decamer primers were used to assess the diversity in the stock of O. niloticus. In this fish stock 48 bands were polymorphic and 12 were monomorphic. The maximum polymorphism (100%) was recorded in the fish samples procured from H4, followed by 88.75, 87.33 and 76.12% of the tilapia collected from H3, H2, and H4, respectively. Nei's genetic distance value was ranged as 0.0005 to 0.1006. Maximum and minimum genetic distance was recorded as 0.1006 and 0.005 in tilapia harvested from H1 and H2 locations. Average heterozygosity was ranged from 0.3009 to 0.3744. This information about the genetic polymorphism of O. niloticus may be used by the concerned authorities to evolve strategies to conserve the diversity of tilapia in the country.
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Wennevik V, Quintela M, Skaala Ø, Verspoor E, Prusov S, Glover KA. Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway. Ecol Evol 2019; 9:6901-6921. [PMID: 31380023 PMCID: PMC6662299 DOI: 10.1002/ece3.5258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.
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Affiliation(s)
| | | | | | - Eric Verspoor
- Rivers and Lochs Institute, Inverness CollegeUniversity of the Highlands and IslandsInvernessUK
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO)MurmanskRussia
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López ME, Benestan L, Moore J, Perrier C, Gilbey J, Di Genova A, Maass A, Diaz D, Lhorente J, Correa K, Neira R, Bernatchez L, Yáñez JM. Comparing genomic signatures of domestication in two Atlantic salmon ( Salmo salar L.) populations with different geographical origins. Evol Appl 2019; 12:137-156. [PMID: 30622641 PMCID: PMC6304691 DOI: 10.1111/eva.12689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
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.
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Affiliation(s)
- Maria E. López
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Laura Benestan
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Jean‐Sebastien Moore
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - Charles Perrier
- Centre d’Écologie Fonctionnelle et ÉvolutiveUnité Mixte de Recherche CNRS 5175MontpellierFrance
| | - John Gilbey
- Marine Scotland ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Alex Di Genova
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | - Diego Diaz
- Laboratory of Bioinformatics and Mathematics of the GenomeCenter for Mathematical Modeling (UMI 2807 CNRS) and Center for Genome Regulation (Fondap 15090007)Universidad de ChileSantiagoChile
| | | | | | - Roberto Neira
- Facultad de Ciencias AgronómicasUniversidad de ChileSantiagoChile
| | - Louis Bernatchez
- IBISInstitut de Biologie Intégrative et des SystèmesUniversité LavalQuébec CityQuébecCanada
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y PecuariasUniversidad de ChileSantiagoChile
- AquainnovoPuerto MonttChile
- Núcleo Milenio INVASALConcepciónChile
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9
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Wellband K, Mérot C, Linnansaari T, Elliott JAK, Curry RA, Bernatchez L. Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon. Mol Ecol 2018; 28:1439-1459. [PMID: 30506831 DOI: 10.1111/mec.14965] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/30/2022]
Abstract
Chromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation, we genotyped 728 juvenile salmon using a 50 K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river's two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019), and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250-Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall, our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.
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Affiliation(s)
- Kyle Wellband
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Claire Mérot
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
| | - Tommi Linnansaari
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - J A K Elliott
- Cooke Aquaculture Inc, Oak Bay, New Brunswick, Canada
| | - R Allen Curry
- Canadian Rivers Institute, Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Quebec, Canada
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10
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Castellani M, Heino M, Gilbey J, Araki H, Svåsand T, Glover KA. Modeling fitness changes in wild Atlantic salmon populations faced by spawning intrusion of domesticated escapees. Evol Appl 2018; 11:1010-1025. [PMID: 29928306 PMCID: PMC5999203 DOI: 10.1111/eva.12615] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/11/2018] [Indexed: 12/17/2022] Open
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.
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Affiliation(s)
| | - Mikko Heino
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
- International Institute for Applied Systems Analysis (IIASA)LaxenburgAustria
| | - John Gilbey
- Freshwater Fisheries LaboratoryMarine ScotlandPitlochryUK
| | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | | | - Kevin A. Glover
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
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11
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Rougemont Q, Bernatchez L. The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations. Evolution 2018; 72:1261-1277. [PMID: 29644624 DOI: 10.1101/142372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 03/14/2018] [Indexed: 05/18/2023]
Abstract
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps, and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflect the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an underappreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.
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Affiliation(s)
- Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6 Québec, Canada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6 Québec, Canada
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12
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Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR. Atlantic salmon Salmo salar in the chalk streams of England are genetically unique. JOURNAL OF FISH BIOLOGY 2018; 92:621-641. [PMID: 29385651 DOI: 10.1111/jfb.13538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/14/2017] [Indexed: 06/07/2023]
Abstract
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
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Affiliation(s)
- C Ikediashi
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - J R Paris
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - R A King
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - W R C Beaumont
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - A Ibbotson
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - J R Stevens
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
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13
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Savary R, Dufresnes C, Champigneulle A, Caudron A, Dubey S, Perrin N, Fumagalli L. Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time. Ecol Evol 2017; 7:5201-5211. [PMID: 28770060 PMCID: PMC5528235 DOI: 10.1002/ece3.3073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 01/19/2023] Open
Abstract
Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr (Salvelinus alpinus) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980-1990s, a break of Hardy-Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re-establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation-based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.
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Affiliation(s)
- Romain Savary
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | - Christophe Dufresnes
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | | | - Arnaud Caudron
- UMR CARRTEL INRA-Université de Savoie Mont Blanc Thonon-les-Bains Cedex France.,Science-Management Interface for Biodiversity Conservation Thonon-les-Bains France
| | - Sylvain Dubey
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland.,Hintermann & Weber SA Montreux Switzerland
| | - Nicolas Perrin
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
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14
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Bal G, Montorio L, Rivot E, Prévost E, Baglinière JL, Nevoux M. Evidence for long-term change in length, mass and migration phenology of anadromous spawners in French Atlantic salmon Salmo salar. JOURNAL OF FISH BIOLOGY 2017; 90:2375-2393. [PMID: 28474348 DOI: 10.1111/jfb.13314] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/16/2017] [Indexed: 06/07/2023]
Abstract
This study provides new data on Atlantic salmon Salmo salar life-history traits across France. Using a long-term recreational angling database (1987-2013) covering 34 rivers in three regions (genetic units), a decline in individual length, mass and a delayed adult return to French rivers was reported. Temporal similarities in trait variations between regions may be attributed to common change in environmental conditions at sea. The relative rate of change in phenotypic traits was more pronounced in early maturing fish [1 sea-winter (1SW) fish] than in late maturing fish (2SW fish). Such contrasted response within populations highlights the need to account for the diversity in life histories when exploring mechanisms of phenotypic change in S. salar. Such detailed life-history data on returning S. salar have not previously been reported from France. This study on French populations also contributes to reducing the gap in knowledge by providing further empirical evidence of a global pattern in S. salar across its distribution range. Results are consistent with the hypothesis that the observed changes in life-history traits are primarily associated with environmental changes in the North Atlantic Ocean. They also emphasize the presence of less important, but still significant contrasts between region and life history.
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Affiliation(s)
- G Bal
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042, Rennes, France
- Marine Institute, Oranmore, Co., Galway, Ireland
| | - L Montorio
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042, Rennes, France
| | - E Rivot
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042, Rennes, France
| | - E Prévost
- ECOBIOP, INRA, University Pau & Pays Adour, Aquapôle, Quartier Ibarron, 64310, Saint-Pée-sur-Nivelle, France
- AFB, Pôle GEST'AQUA, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - J-L Baglinière
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042, Rennes, France
- AFB, Pôle GEST'AQUA, 65 rue de Saint-Brieuc, 35042, Rennes, France
| | - M Nevoux
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest, INRA, 35042, Rennes, France
- AFB, Pôle GEST'AQUA, 65 rue de Saint-Brieuc, 35042, Rennes, France
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15
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Côte J, Roussel JM, Le Cam S, Guillaume F, Evanno G. Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations. J Evol Biol 2016; 29:1593-601. [PMID: 27177256 DOI: 10.1111/jeb.12896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
Abstract
In the context of global changes, the long-term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a QST -FST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed-stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. QST was higher than FST in all but one comparison suggesting an important effect of divergent selection. QST was also higher under the high-temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them.
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Affiliation(s)
- J Côte
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France.,UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - J-M Roussel
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - S Le Cam
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - F Guillaume
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - G Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
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16
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Le Cam S, Perrier C, Besnard AL, Bernatchez L, Evanno G. Genetic and phenotypic changes in an Atlantic salmon population supplemented with non-local individuals: a longitudinal study over 21 years. Proc Biol Sci 2016; 282:rspb.2014.2765. [PMID: 25608883 DOI: 10.1098/rspb.2014.2765] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
While introductions and supplementations using non-native and potentially domesticated individuals may have dramatic evolutionary effects on wild populations, few studies documented the evolution of genetic diversity and life-history traits in supplemented populations. Here, we investigated year-to-year changes from 1989 to 2009 in genetic admixture at 15 microsatellite loci and in phenotypic traits in an Atlantic salmon (Salmo salar) population stocked during the first decade of this period with two genetically and phenotypically distinct source populations. We detected a pattern of temporally increasing introgressive hybridization between the stocked population and both source populations. The proportion of fish returning to the river after a single winter at sea (versus several ones) was higher in fish assigned to the main source population than in local individuals. Moreover, during the first decade of the study, both single-sea-winter and multi-sea-winter (MSW) fish assigned to the main source population were smaller than local fish. During the second decade of the study, MSW fish defined as hybrids were lighter and smaller than fish from parental populations, suggesting outbreeding depression. Overall, this study suggests that supplementation with non-local individuals may alter not only the genetic diversity of wild populations but also life-history traits of adaptive significance.
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Affiliation(s)
- Sabrina Le Cam
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France Station Biologique de Roscoff, Place Georges Teissier, Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Roscoff Cedex 29688, France Station Biologique de Roscoff, Place Georges Teissier, CNRS, UMR 7144, Roscoff Cedex 29688, France
| | - Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Anne-Laure Besnard
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, Canada
| | - Guillaume Evanno
- INRA, UMR 0985 Ecology and Health of Ecosystems, Rennes 35042, France Agrocampus Ouest, 65 Rue de Saint-Brieuc, Rennes 35042, France
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17
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Aykanat T, Johnston SE, Orell P, Niemelä E, Erkinaro J, Primmer CR. Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population. Mol Ecol 2015; 24:5158-74. [DOI: 10.1111/mec.13383] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 09/04/2015] [Accepted: 09/09/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Tutku Aykanat
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
| | - Susan E. Johnston
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
- Institute of Evolutionary Biology; University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
| | - Panu Orell
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Eero Niemelä
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Jaakko Erkinaro
- Natural Resources Institute Finland; Utsjoki FI-99980 Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology; Department of Biology; University of Turku; Itäinen Pitkäkatu 4 Turku FI-20520 Finland
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18
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Gagnaire PA, Broquet T, Aurelle D, Viard F, Souissi A, Bonhomme F, Arnaud-Haond S, Bierne N. Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era. Evol Appl 2015; 8:769-86. [PMID: 26366195 PMCID: PMC4561567 DOI: 10.1111/eva.12288] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/05/2015] [Indexed: 12/14/2022] Open
Abstract
Estimating the rate of exchange of individuals among populations is a central concern to evolutionary ecology and its applications to conservation and management. For instance, the efficiency of protected areas in sustaining locally endangered populations and ecosystems depends on reserve network connectivity. The population genetics theory offers a powerful framework for estimating dispersal distances and migration rates from molecular data. In the marine realm, however, decades of molecular studies have met limited success in inferring genetic connectivity, due to the frequent lack of spatial genetic structure in species exhibiting high fecundity and dispersal capabilities. This is especially true within biogeographic regions bounded by well-known hotspots of genetic differentiation. Here, we provide an overview of the current methods for estimating genetic connectivity using molecular markers and propose several directions for improving existing approaches using large population genomic datasets. We highlight several issues that limit the effectiveness of methods based on neutral markers when there is virtually no genetic differentiation among samples. We then focus on alternative methods based on markers influenced by selection. Although some of these methodologies are still underexplored, our aim was to stimulate new research to test how broadly they are applicable to nonmodel marine species. We argue that the increased ability to apply the concepts of cline analyses will improve dispersal inferences across physical and ecological barriers that reduce connectivity locally. We finally present how neutral markers hitchhiking with selected loci can also provide information about connectivity patterns within apparently well-mixed biogeographic regions. We contend that one of the most promising applications of population genomics is the use of outlier loci to delineate relevant conservation units and related eco-geographic features across which connectivity can be measured.
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Affiliation(s)
- Pierre-Alexandre Gagnaire
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Thomas Broquet
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | - Didier Aurelle
- Aix Marseille Université, CNRS-IRD-Avignon Université, IMBE UMR 7263 Marseille, France
| | - Frédérique Viard
- CNRS team Diversity and connectivity of coastal marine landscapes, Station Biologique de Roscoff Roscoff, France ; Sorbonne Universités, UPMC Université Paris 06, UMR 7144, Station Biologique de Roscoff Roscoff, France
| | | | - François Bonhomme
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
| | - Sophie Arnaud-Haond
- Université de Montpellier Montpellier, France ; Ifremer, UMR "Ecosystèmes Marins Exploités" Sète, France
| | - Nicolas Bierne
- Université de Montpellier Montpellier, France ; CNRS - Institut des Sciences de l'Evolution, UMR 5554 UM-CNRS-IRD-EPHE, Station Méditerranéenne de l'Environnement Littoral Sète, France
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19
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Moore JS, Bourret V, Dionne M, Bradbury I, O'Reilly P, Kent M, Chaput G, Bernatchez L. Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci. Mol Ecol 2014; 23:5680-97. [DOI: 10.1111/mec.12972] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Revised: 10/14/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Vincent Bourret
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
- Direction de la Protection de la Faune; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Mélanie Dionne
- Direction de la Faune Aquatique; Ministère des Forêts; de la Faune et des Parcs; Québec Québec G1S 4X4 Canada
| | - Ian Bradbury
- Science Branch; Fisheries and Oceans Canada; 80 East White Road St. John's Newfoundland A1C 5X1 Canada
| | - Patrick O'Reilly
- Science Branch; Fisheries and Oceans Canada; Bedford Institute of Oceanography; 1 Challenger Drive Dartmouth Nova Scotia B2Y 4A2 Canada
| | - Matthew Kent
- Centre for Integrative Genetics (CIGENE); Department of Animal and Aquacultural Sciences (IHA); Norwegian University of Life Sciences; PO Box 5003 1432 Aas Norway
| | - Gérald Chaput
- Fisheries and Oceans Canada; PO Box 5030 Moncton New Brunswick E1C 9B6 Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes; Université Laval; 1030 Avenue de la Médecine Québec Québec G1V 0A6 Canada
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20
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Outbreeding Depression in Atlantic Salmon Revealed by Hypoxic Stress During Embryonic Development. Evol Biol 2014. [DOI: 10.1007/s11692-014-9289-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Valiquette E, Perrier C, Thibault I, Bernatchez L. Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada. Evol Appl 2014; 7:625-44. [PMID: 25067947 PMCID: PMC4105915 DOI: 10.1111/eva.12160] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/17/2014] [Indexed: 11/29/2022] Open
Abstract
Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations.
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Affiliation(s)
- Eliane Valiquette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Isabel Thibault
- Ministère du Développement durable, de l'Environnement de la Faune et des Parcs Québec, QC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
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22
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Origins and genetic diversity among Atlantic salmon recolonizing upstream areas of a large South European river following restoration of connectivity and stocking. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0602-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Glover KA, Pertoldi C, Besnier F, Wennevik V, Kent M, Skaala Ø. Atlantic salmon populations invaded by farmed escapees: quantifying genetic introgression with a Bayesian approach and SNPs. BMC Genet 2013; 14:74. [PMID: 23968202 PMCID: PMC3765417 DOI: 10.1186/1471-2156-14-74] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/15/2013] [Indexed: 11/12/2022] Open
Abstract
Background Many native Atlantic salmon populations have been invaded by domesticated escapees for three decades or longer. However, thus far, the cumulative level of gene-flow that has occurred from farmed to wild salmon has not been reported for any native Atlantic salmon population. The aim of the present study was to investigate temporal genetic stability in native populations, and, quantify gene-flow from farmed salmon that caused genetic changes where they were observed. This was achieved by genotyping historical and contemporary samples from 20 populations covering all of Norway with recently identified single nucleotide polymorphism markers that are collectively diagnostic for farmed and wild salmon. These analyses were combined with analysis of farmed salmon and implementation of Approximate Bayesian computation based simulations. Results Five of the populations displayed statistically significant temporal genetic changes. All five of these populations became more similar to a pool of farmed fish with time, strongly suggesting introgression of farmed fish as the primary cause. The remaining 15 populations displayed weak or non-significant temporal genetic changes. Estimated introgression of farmed fish ranged from 2-47% per population using approximate Bayesian computation. Thus, some populations exhibited high degrees of farmed salmon introgression while others were more or less unaffected. The observed frequency of escapees in each population was moderately correlated with estimated introgression per population R2 = 0.47 P < 0.001. Genetic isolation by distance existed within the historical and contemporary data sets, however, the among-population level of divergence decreased with time. Conclusions This is the first study to quantify cumulative introgression of farmed salmon in any native Atlantic salmon population. The estimations demonstrate that the level of introgression has been population-specific, and that the level of introgression is not solely predicted by the frequency of escapees observed in the population. However, some populations have been strongly admixed with farmed salmon, and these data provide policy makers with unique information to address this situation.
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Affiliation(s)
- Kevin Alan Glover
- Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.
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24
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Perrier C, Guyomard R, Bagliniere JL, Nikolic N, Evanno G. Changes in the genetic structure of Atlantic salmon populations over four decades reveal substantial impacts of stocking and potential resiliency. Ecol Evol 2013; 3:2334-49. [PMID: 23919174 PMCID: PMC3728969 DOI: 10.1002/ece3.629] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/28/2013] [Accepted: 05/06/2013] [Indexed: 01/08/2023] Open
Abstract
While the stocking of captive-bred fish has been occurring for decades and has had substantial immediate genetic and evolutionary impacts on wild populations, its long-term consequences have only been weakly investigated. Here, we conducted a spatiotemporal analysis of 1428 Atlantic salmon sampled from 1965 to 2006 in 25 populations throughout France to investigate the influence of stocking on the neutral genetic structure in wild Atlantic salmon (Salmo salar) populations. On the basis of the analysis of 11 microsatellite loci, we found that the overall genetic structure among populations dramatically decreased over the period studied. Admixture rates among populations were highly variable, ranging from a nearly undetectable contribution from donor stocks to total replacement of the native gene pool, suggesting extremely variable impacts of stocking. Depending on population, admixture rates either increased, remained stable, or decreased in samples collected between 1998 and 2006 compared to samples from 1965 to 1987, suggesting either rising, long-lasting or short-term impacts of stocking. We discuss the potential mechanisms contributing to this variability, including the reduced fitness of stocked fish and persistence of wild locally adapted individuals.
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Affiliation(s)
- Charles Perrier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, Canada ; INRA, UMR 0985 Ecology and Health of Ecosystems 35042, Rennes, France ; Agrocampus Ouest 65 rue de Saint-Brieuc, 35042, Rennes, France ; INRA, UMR 1313 Génétique Animale et Biologie Intégrative F-78350, Jouy-en-Josas, France
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25
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He Q, Edwards DL, Knowles LL. INTEGRATIVE TESTING OF HOW ENVIRONMENTS FROM THE PAST TO THE PRESENT SHAPE GENETIC STRUCTURE ACROSS LANDSCAPES. Evolution 2013; 67:3386-402. [DOI: 10.1111/evo.12159] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 04/26/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Qixin He
- Department of Ecology & Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
| | - Danielle L. Edwards
- Department of Ecology and Evolutionary Biology; Yale University; New Haven Connecticut 06520
| | - L. Lacey Knowles
- Department of Ecology & Evolutionary Biology; University of Michigan; Ann Arbor Michigan 48109
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26
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Vincent B, Dionne M, Kent MP, Lien S, Bernatchez L. LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION. Evolution 2013; 67:3469-87. [DOI: 10.1111/evo.12139] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 03/27/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Bourret Vincent
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Mélanie Dionne
- Direction de la faune aquatique; Ministère du Développement durable; de l'Environnement; de la Faune et des Parcs; Québec G1S 4×4 Canada
| | - Matthew P. Kent
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Louis Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
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27
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Interplay between isolation by distance and genetic clusters in the red coral Corallium rubrum: insights from simulated and empirical data. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0464-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Milot E, Perrier C, Papillon L, Dodson JJ, Bernatchez L. Reduced fitness of Atlantic salmon released in the wild after one generation of captive breeding. Evol Appl 2012; 6:472-85. [PMID: 23745139 PMCID: PMC3673475 DOI: 10.1111/eva.12028] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 10/08/2012] [Indexed: 11/30/2022] Open
Abstract
Salmonids rank among the most socioeconomically valuable fishes and the most targeted species by stocking with hatchery-reared individuals. Here, we used molecular parentage analysis to assess the reproductive success of wild- and hatchery-born Atlantic salmon over three consecutive years in a small river in Québec. Yearly restocking in this river follows a single generation of captive breeding. Among the adults returning to the river to spawn, between 11% and 41% each year were born in hatchery. Their relative reproductive success (RRS) was nearly half that of wild-born fish (0.55). RRS varied with life stage, being 0.71 for fish released at the fry stage and 0.42 for fish released as smolt. The lower reproductive success of salmon released as smolt was partly mediated by the modification of the proportion of single-sea-winter/multi-sea-winter fish. Overall, our results suggest that modifications in survival and growth rates alter the life-history strategies of these fish at the cost of their reproductive success. Our results underline the potential fitness decrease, warn on long-term evolutionary consequences for the population of repeated stocking and support the adoption of more natural rearing conditions for captive juveniles and their release at a younger stage, such as unfed fry.
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Affiliation(s)
- Emmanuel Milot
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec City, QC, Canada
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29
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Côte J, Roussel JM, Le Cam S, Bal G, Evanno G. Population differences in response to hypoxic stress in Atlantic salmon. J Evol Biol 2012; 25:2596-606. [PMID: 23107024 DOI: 10.1111/jeb.12007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 09/03/2012] [Indexed: 01/27/2023]
Abstract
Understanding whether populations can adapt to new environmental conditions is a major issue in conservation and evolutionary biology. Aquatic organisms are increasingly exposed to environmental changes linked with human activities in river catchments. For instance, the clogging of bottom substratum by fine sediments is observed in many rivers and usually leads to a decrease in dissolved oxygen concentrations in gravel beds. Such hypoxic stress can alter the development and even be lethal for Atlantic salmon (Salmo salar) embryos that spend their early life into gravel beds. In this study, we used a common garden experiment to compare the responses to hypoxic stress of four genetically differentiated and environmentally contrasted populations. We used factorial crossing designs to measure additive genetic variation of early life-history traits in each population. Embryos were reared under normoxic and hypoxic conditions, and we measured their survival, incubation time and length at the end of embryonic development. Under hypoxic conditions, embryos had a lower survival and hatched later than in normoxic conditions. We found different hypoxia reaction norms among populations, but almost no population effect in both treatments. We also detected significant sire × treatment interactions in most populations and a tendency for heritability values to be lower under stressful conditions. Overall, these results reveal a high degree of phenotypic plasticity in salmon populations that nevertheless differ in their adaptive potential to hypoxia given the distinct reaction norms observed between and within populations.
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Affiliation(s)
- J Côte
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.
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30
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Glover KA, Quintela M, Wennevik V, Besnier F, Sørvik AGE, Skaala Ø. Three decades of farmed escapees in the wild: a spatio-temporal analysis of Atlantic salmon population genetic structure throughout Norway. PLoS One 2012; 7:e43129. [PMID: 22916215 PMCID: PMC3419752 DOI: 10.1371/journal.pone.0043129] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 07/17/2012] [Indexed: 12/05/2022] Open
Abstract
Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, FST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global FST = 0.038) and contemporary data sets (global FST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global FST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.
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Affiliation(s)
- Kevin A Glover
- Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.
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31
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Perrier C, Baglinière JL, Evanno G. Understanding admixture patterns in supplemented populations: a case study combining molecular analyses and temporally explicit simulations in Atlantic salmon. Evol Appl 2012; 6:218-30. [PMID: 23798972 PMCID: PMC3689348 DOI: 10.1111/j.1752-4571.2012.00280.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 05/07/2012] [Indexed: 12/01/2022] Open
Abstract
Genetic admixture between wild and introduced populations is a rising concern for the management of endangered species. Here, we use a dual approach based on molecular analyses of samples collected before and after hatchery fish introduction in combination with a simulation study to obtain insight into the mechanisms of admixture in wild populations. Using 17 microsatellites, we genotyped pre- and post-stocking samples from four Atlantic salmon populations supplemented with non-native fish to estimate genetic admixture. We also used individual-based temporally explicit simulations based on realistic demographic and stocking data to predict the extent of admixture. We found a low admixture by hatchery stocks within prestocking samples but moderate to high values in post-stocking samples (from 12% to 60%). The simulation scenarios best fitting the real data suggested a 10-25 times lower survival of stocked fish relative to wild individuals. Simulations also suggested relatively high dispersal rates of stocked and wild fish, which may explain some high levels of admixture in weakly stocked populations and the persistence of indigenous genotypes in heavily stocked populations. This study overall demonstrates that combining genetic analyses with simulations can significantly improve the understanding of admixture mechanisms in wild populations.
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Affiliation(s)
- Charles Perrier
- INRA, UMR 0985 Ecology and Health of Ecosystems Rennes, France ; Agrocampus Ouest Rennes, France ; INRA, UMR 1313 Animal Genetics and Integrative Biology, Domaine de Vilvert Jouy-en-Josas, France ; Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec QC, Canada
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LAMAZE FABIENC, SAUVAGE CHRISTOPHER, MARIE AMANDINE, GARANT DANY, BERNATCHEZ LOUIS. Dynamics of introgressive hybridization assessed by SNP population genomics of coding genes in stocked brook charr (Salvelinus fontinalis). Mol Ecol 2012; 21:2877-95. [DOI: 10.1111/j.1365-294x.2012.05579.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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