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Willmes M, Sturrock AM, Cordoleani F, Hugentobler S, Meek MH, Whitman G, Evans K, Palkovacs EP, Stauffer-Olsen NJ, Johnson RC. Integrating otolith and genetic tools to reveal intraspecific biodiversity in a highly impacted salmon population. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38982714 DOI: 10.1111/jfb.15847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/15/2024] [Accepted: 06/03/2024] [Indexed: 07/11/2024]
Abstract
Intraspecific biodiversity is vital for species persistence in an increasingly volatile world. By embracing methods that integrate information at different spatiotemporal scales, we can directly monitor and reconstruct changes in intraspecific biodiversity. Here we combined genetics and otolith biochronologies to describe the genotypic and phenotypic diversity of Chinook salmon (Oncorhynchus tshawytscha) in the Yuba River, California, comparing cohorts that experienced a range of hydroclimatic conditions. Yuba River salmon have been heavily impacted by habitat loss and degradation, and large influxes of unmarked hatchery fish each year have led to concern about introgression and uncertainty around the viability of its wild populations, particularly the rarer spring-run salmon. Otolith strontium isotopes showed that Yuba River origin fish represented, on average, 42% (range 7%-73%) of spawners across six return years (2009-2011, 2018-2020), with large interannual variability. The remainder of adult Chinook salmon in the river were primarily strays from the nearby Feather River hatchery, and since 2018 from the Mokelumne River hatchery. Among the Yuba-origin spawners, on average, 30% (range 14%-50%) exhibited the spring-run genotype. The Yuba-origin fish also displayed a variety of outmigration phenotypes that differed in the timing and size at which they left the Yuba river. Early-migrating fry dominated the returns (mean 59%, range 33%-89%), and their contribution rates were negatively correlated with freshwater flows. It is unlikely that fry survival rates are elevated during droughts, suggesting that this trend reflects disproportionately low survival of larger later migrating parr, smolts, and yearlings along the migratory corridor in drier years. Otolith daily increments indicated generally faster growth rates in non-natal habitats, emphasizing the importance of continuing upstream restoration efforts to improve in-river growing conditions. Together, these findings show that, despite a long history of habitat degradation and hatchery introgression, the Yuba River maintains intraspecific biodiversity that should be taken into account in future management, restoration, and reintroduction plans. The finding that genotypic spring-run are reproducing, surviving, and returning to the Yuba River every year suggests that re-establishment of an independent population is possible, although hatchery-wild interactions would need to be carefully considered. Integrating methods is critical to monitor changes in key genetic, physiological, and behavioral traits to assess population viability and resilience.
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Affiliation(s)
- Malte Willmes
- Norwegian Institute for Nature Research, Trondheim, Norway
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | - Anna M Sturrock
- Center for Watershed Sciences, University of California Davis, Davis, California, USA
- School of Life Sciences, University of Essex, Colchester, UK
| | - Flora Cordoleani
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
- National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
| | - Sara Hugentobler
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Mariah H Meek
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
- The Wilderness Society, Bozeman, Montana, USA
| | - George Whitman
- Center for Watershed Sciences, University of California Davis, Davis, California, USA
| | - Kimberly Evans
- Center for Watershed Sciences, University of California Davis, Davis, California, USA
| | - Eric P Palkovacs
- Institute of Marine Sciences, University of California Santa Cruz, Santa Cruz, California, USA
| | | | - Rachel C Johnson
- Center for Watershed Sciences, University of California Davis, Davis, California, USA
- National Marine Fisheries Service, Southwest Fisheries Science Center, Santa Cruz, California, USA
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2
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Habibi E, Miller MR, Schreier A, Campbell MA, Hung TC, Gille D, Baerwald M, Finger AJ. Single generation epigenetic change in captivity and reinforcement in subsequent generations in a delta smelt (Hypomesus transpacificus) conservation hatchery. Mol Ecol 2024:e17449. [PMID: 38967124 DOI: 10.1111/mec.17449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/24/2024] [Accepted: 06/14/2024] [Indexed: 07/06/2024]
Abstract
A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations.
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Affiliation(s)
- Ensieh Habibi
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Michael R Miller
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Andrea Schreier
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, California, USA
| | - Tien-Chieh Hung
- Fish Conservation and Culture Laboratory, Biological and Agricultural Engineering Department, University of California Davis, Davis, California, USA
| | - Daphne Gille
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Melinda Baerwald
- California Department of Water Resources, Division of Integrated Science and Engineering, West Sacramento, California, USA
| | - Amanda J Finger
- Department of Animal Science, University of California Davis, Davis, California, USA
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3
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Reed TE, Kane A, McGinnity P, O'Sullivan RJ. Competitive interactions affect introgression and population viability amidst maladaptive hybridization. Evol Appl 2024; 17:e13746. [PMID: 38957310 PMCID: PMC11217556 DOI: 10.1111/eva.13746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 04/03/2024] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
The deliberate release of captive-bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridization, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco-genetic model explicitly focussed on understanding the influence of such competitive interactions on the eco-evolutionary dynamics of wild populations experiencing an influx of foreign/domesticated individuals. The model is applicable to any taxon that experiences natural or human-mediated inputs of locally maladapted genotypes ('intrusion'), in addition to phenotype-dependent competition for a limiting resource (e.g. breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, density-dependent regulation limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under-appreciated interactions between phenotype-dependent competitive interactions and maladaptive hybridization, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self-sustaining wild populations.
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Affiliation(s)
- Thomas Eric Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
| | - Adam Kane
- School of Biology and Environmental Science and Earth InstituteUniversity College DublinDublinIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Environmental Research InstituteUniversity College CorkCorkIreland
- Marine Institute, Furnace, Newport, CoMayoIreland
| | - Ronan James O'Sullivan
- Human Diversity Consortium, Faculty of Physiology and Genetics, Department of BiologyUniversity of TurkuTurkuFinland
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LaCava MEF, Griffiths JS, Ellison L, Carson EW, Hung T, Finger AJ. Loss of plasticity in maturation timing after ten years of captive spawning in a delta smelt conservation hatchery. Evol Appl 2023; 16:1845-1857. [PMID: 38029063 PMCID: PMC10681455 DOI: 10.1111/eva.13611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/16/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Adaptation to captivity in spawning programs can lead to unintentional consequences, such as domestication that results in reduced fitness in the wild. The timing of sexual maturation has been shown to be a trait under domestication selection in fish hatcheries, which affects a fish's access to mating opportunities and aligning their offspring's development with favorable environmental conditions. Earlier maturing fish may be favored in hatchery settings where managers provide artificially optimal growing conditions, but early maturation may reduce fitness in the wild if, for example, there is a mismatch between timing of reproduction and availability of resources that support recruitment. We investigated patterns of maturation timing in a delta smelt (Hypomesus transpacificus) conservation hatchery by quantifying changes to the median age at maturity since the captive spawning program was initiated in 2008. Over the span of a decade, we observed a small, but significant increase in age at maturity among broodstock by 2.2 weeks. This trait had low heritability and was largely controlled by phenotypic plasticity that was dependent on the time of year fish were born. Fish that were born later in the year matured faster, potentially a carryover from selection favoring synchronous spawning in the wild. However, higher DI (domestication index) fish showed a loss of plasticity, we argue, as a result of hatchery practices that breed individuals past peak periods of female ripeness. Our findings suggest that the hatchery setting has relaxed selection pressures for fish to mature quickly at the end of the year and, consequently, has led to a loss of plasticity in age at maturity. Hatchery fish that are re-introduced in the wild may not be able to align maturation with population peaks if their maturation rates are too slow with reduced plasticity, potentially resulting in lower fitness.
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Affiliation(s)
- Melanie E. F. LaCava
- Genomic Variation Laboratory, Department of Animal ScienceUniversity of California, DavisDavisCaliforniaUSA
| | - Joanna S. Griffiths
- Department of Environmental Toxicology and Department of Wildlife, Fish, and Conservation BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Luke Ellison
- Fish Conservation and Culture Laboratory, Department of Biological and Agricultural EngineeringUniversity of California, DavisDavisCaliforniaUSA
| | - Evan W. Carson
- US Fish and Wildlife ServiceSan Francisco Bay‐Delta Fish and Wildlife OfficeSacramentoCaliforniaUSA
| | - Tien‐Chieh Hung
- Fish Conservation and Culture Laboratory, Department of Biological and Agricultural EngineeringUniversity of California, DavisDavisCaliforniaUSA
| | - Amanda J. Finger
- Genomic Variation Laboratory, Department of Animal ScienceUniversity of California, DavisDavisCaliforniaUSA
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5
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Tenger-Trolander A. Environmental and genetic effects of captivity - are there lessons for monarch butterfly conservation? CURRENT OPINION IN INSECT SCIENCE 2023; 59:101088. [PMID: 37500011 DOI: 10.1016/j.cois.2023.101088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/17/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Rearing monarch butterflies in captivity for later release is a popular but contentious activity due to concerns about its potential negative effects on the wild population. In this review, I discuss how captive rearing and breeding could impact monarch fitness in the wild, the current evidence for such impacts in monarchs and other captive-reared/released organisms, and how this should inform our efforts to conserve monarchs and other species.
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Clark FE, Greggor AL, Montgomery SH, Plotnik JM. The endangered brain: actively preserving ex-situ animal behaviour and cognition will benefit in-situ conservation. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230707. [PMID: 37650055 PMCID: PMC10465207 DOI: 10.1098/rsos.230707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/15/2023] [Indexed: 09/01/2023]
Abstract
Endangered species have small, unsustainable population sizes that are geographically or genetically restricted. Ex-situ conservation programmes are therefore faced with the challenge of breeding sufficiently sized, genetically diverse populations earmarked for reintroduction that have the behavioural skills to survive and breed in the wild. Yet, maintaining historically beneficial behaviours may be insufficient, as research continues to suggest that certain cognitive-behavioural skills and flexibility are necessary to cope with human-induced rapid environmental change (HIREC). This paper begins by reviewing interdisciplinary studies on the 'captivity effect' in laboratory, farmed, domesticated and feral vertebrates and finds that captivity imposes rapid yet often reversible changes to the brain, cognition and behaviour. However, research on this effect in ex-situ conservation sites is lacking. This paper reveals an apparent mismatch between ex-situ enrichment aims and the cognitive-behavioural skills possessed by animals currently coping with HIREC. After synthesizing literature across neuroscience, behavioural biology, comparative cognition and field conservation, it seems that ex-situ endangered species deemed for reintroduction may have better chances of coping with HIREC if their natural cognition and behavioural repertoires are actively preserved. Evaluating the effects of environmental challenges rather than captivity per se is recommended, in addition to using targeted cognitive enrichment.
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Affiliation(s)
- Fay E. Clark
- School of Psychological Science, University of Bristol, Bristol, UK
| | | | | | - Joshua M. Plotnik
- Department of Psychology, Hunter College, City University of New York, New York, NY, USA
- Department of Psychology, The Graduate Center, City University of New York, New York, NY, USA
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Gamble MM, Calsbeek RG. Sex-specific heritabilities for length at maturity among Pacific salmonids and their consequences for evolution in response to artificial selection. Evol Appl 2023; 16:1458-1471. [PMID: 37622093 PMCID: PMC10445087 DOI: 10.1111/eva.13579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/18/2023] [Accepted: 06/25/2023] [Indexed: 08/26/2023] Open
Abstract
Artificial selection, whether intentional or coincidental, is a common result of conservation policies and natural resource management. To reduce unintended consequences of artificial selection, conservation practitioners must understand both artificial selection gradients on traits of interest and how those traits are correlated with others that may affect population growth and resilience. We investigate how artificial selection on male body size in Pacific salmon (Oncorhynchus spp.) may influence the evolution of female body size and female fitness. While salmon hatchery managers often assume that selection for large males will also produce large females, this may not be the case-in fact, because the fastest-growing males mature earliest and at the smallest size, and because female age at maturity varies little, small males may produce larger females if the genetic architecture of growth rate is the same in both sexes. We explored this possibility by estimating sex-specific heritability values of and natural and artificial selection gradients on length at maturity in four populations representing three species of Pacific salmon. We then used the multivariate breeder's equation to project how artificial selection against small males may affect the evolution of female length and fecundity. Our results indicate that the heritability of length at maturity is greater within than between the sexes and that sire-daughter heritability values are especially small. Salmon hatchery policies should consider these sex-specific quantitative genetic parameters to avoid potential unintended consequences of artificial selection.
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Affiliation(s)
- Madilyn M. Gamble
- Graduate Program in Ecology, Evolution, Ecosystems, and SocietyDartmouth CollegeHanoverNew HampshireUSA
| | - Ryan G. Calsbeek
- Department of Biological SciencesDartmouth CollegeHanoverNew HampshireUSA
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8
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Venney CJ, Bouchard R, April J, Normandeau E, Lecomte L, Côté G, Bernatchez L. Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: Sex-specificity and intergenerational stability. Mol Ecol Resour 2023. [PMID: 36760032 DOI: 10.1111/1755-0998.13766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/20/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023]
Abstract
Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0 . There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.
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Affiliation(s)
- Clare J Venney
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Raphaël Bouchard
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Julien April
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Laurie Lecomte
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
| | - Guillaume Côté
- Direction de l'expertise sur la faune aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Quebec, Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
- Département de Biologie, Université Laval, Québec, Quebec, Canada
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9
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Evaluating the Potential Fitness Effects of Chinook Salmon ( Oncorhynchus tshawytscha) Aquaculture Using Non-Invasive Population Genomic Analyses of MHC Nucleotide Substitution Spectra. Animals (Basel) 2023; 13:ani13040593. [PMID: 36830380 PMCID: PMC9951711 DOI: 10.3390/ani13040593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Genetic diversity plays a vital role in the adaptability of salmon to changing environmental conditions that can introduce new selective pressures on populations. Variability among local subpopulations may increase the chance that certain advantageous genes are passed down to future generations to mitigate susceptibility to novel diseases, warming oceans, loss of genetic stocks, and ocean acidification. Class I and II genes of the major histocompatibility complex (MHC) are crucial for the fitness of Chinook salmon due to the role they play in disease and pathogen resistance. The objective of this study was to assess the DNA sequence variability among wild and hatchery populations of Alaskan Chinook salmon at the class I α1 and class II β1 exons of the MHC. We hypothesized that the 96 wild samples taken from the Deshka River would display greater levels of observed heterozygosity (Ho) relative to expected heterozygosity (He) in suggesting that individuals with similar phenotypes mate with one another more frequently than would be expected under random mating patterns. Conversely, since no mate selection occurs in the William Jack Hernandez Sport Fish hatchery, we would not expect to see this discrepancy (He = Ho) in the 96 hatchery fish tested in this study. Alternatively, we hypothesized that post-mating selection is driving higher levels of observed heterozygosity as opposed to mate selection. If this is the case, we will observe higher than expected levels of heterozygosity among hatchery salmon. Both populations displayed higher levels of observed heterozygosity than expected heterozygosity at the Class I and II loci but genetic differentiation between the spatially distinct communities was minimal. Class I sequences showed evidence of balancing selection, despite high rates of non-synonymous substitutions observed, specifically at the peptide binding regions of both MHC genes.
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10
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Wąs-Barcz A, Bernaś R. Parentage-based tagging and parentage analyses of stocked sea trout in Vistula River commercial catches. J Appl Genet 2023; 64:341-350. [PMID: 36746881 PMCID: PMC10076402 DOI: 10.1007/s13353-023-00749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/30/2023] [Indexed: 02/08/2023]
Abstract
The longest Baltic River, the Vistula, historically hosted numerous sea trout populations. However, dam construction in the twentieth century drastically reduced the spawning migration rate. Reduced natural reproduction has resulted in a population collapse and, consequentially, a substantial reduction in catches. In response, like other Baltic countries, Poland has initiated an intensive stocking program, mainly involving smolt. Initially, stocking was conducted primarily with offspring of sea trout caught during spawning migration. Currently, due to difficulties in obtaining fish, most stocking involves fish from breeding stocks. Therefore, determining the proportion of fish derived from stocking has become an important issue. Experiments based on traditional tagging did not provide sufficient material for analysis; hence, we decided to use genetic methods based on analysis of relatedness. In this study, we performed parentage-based tagging and an analysis of the origins of parent animals used for artificial spawning in 2013, and offspring returning to the Vistula in subsequent years. We based the analysis on three different algorithms and compared the results, showing that the presented methods were effective for estimating mass stocking success. The study also indicated that a certain level of natural reproduction in the Vistula continues to occur. The proportion of sea trout from spawning in 2013 in Vistula sea trout catches from 2017 to 2018 was approximately 30%.
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Affiliation(s)
- Anna Wąs-Barcz
- National Marine Fisheries Research Institute, Department of Fisheries Resources, Kołłątaja 1, 81-332, Gdynia, Poland
| | - Rafał Bernaś
- National Inland Fisheries Research Institute, Department of Migratory Fish, Rutki 49, 83-330, Żukowo, Poland.
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11
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Beckman AK, Richey BMS, Rosenthal GG. Behavioral responses of wild animals to anthropogenic change: insights from domestication. Behav Ecol Sociobiol 2022. [DOI: 10.1007/s00265-022-03205-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Bouchard R, Wellband K, Lecomte L, Bernatchez L, April J. Effects of stocking at the parr stage on the reproductive fitness and genetic diversity of a wild population of Atlantic salmon ( Salmo salar L.). Evol Appl 2022; 15:838-852. [PMID: 35603030 PMCID: PMC9108320 DOI: 10.1111/eva.13374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/22/2022] [Indexed: 12/03/2022] Open
Abstract
Captive-breeding programs are among the most adopted conservation practices to mitigate the loss of biodiversity, including genetic diversity. However, both genetic and nongenetic changes occurring in captivity can reduce the fitness of supplemented individuals, which complicate rehabilitation efforts. In the case of Atlantic salmon, the intensity of changes that occur in captivity and their impact on fitness will vary with the stocking practice adopted. In this study, we test whether salmon stocked at the parr stage have reduced reproductive success compared with their wild conspecifics and whether they contribute to increase genetic diversity in the targeted population. To do so, we use high-throughput microsatellite sequencing of 38 loci to accurately assign 2381 offspring to a comprehensive set of possible parents from a supplemented Atlantic salmon population in Québec, Canada. Captive-bred salmon stocked at the parr stage had fewer mates than their wild conspecifics, as well as a reduced relative reproductive success (RSS) compared with their wild counterparts. Nonetheless, in comparison with previous studies, stocking at the parr stage significantly improved RSS compared with salmon stocked as smolts and they displayed a reduction in reproductive success similar to salmon stocked as fry, which spend less time in captivity than parr. Moreover, supplementation of captive-bred salmon significantly contributed to increasing genetic diversity. These results should contribute to informing resource managers in determining the best stocking practice to enhance Atlantic salmon populations.
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Affiliation(s)
- Raphaël Bouchard
- Département de BiologieUniversité LavalQuébecQuebecCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Kyle Wellband
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Laurie Lecomte
- Département de BiologieUniversité LavalQuébecQuebecCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Louis Bernatchez
- Département de BiologieUniversité LavalQuébecQuebecCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuebecCanada
| | - Julien April
- Direction de l’expertise sur la faune aquatiqueMinistère des Forêts, de la Faune et des Parcs du QuébecQuébecQuebecCanada
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Hsu TH, Lee HT, Lu HJ, Liao CH, Gong HY, Huang CW. Maintenance of Genetic Diversity of Black Sea Bream despite Unmonitored and Large-Scale Hatchery Releases. BIOLOGY 2022; 11:554. [PMID: 35453753 PMCID: PMC9026629 DOI: 10.3390/biology11040554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/12/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004-2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.
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Affiliation(s)
- Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Hung-Tai Lee
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Hsueh-Jung Lu
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Cheng-Hsin Liao
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
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14
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Besnier F, Ayllon F, Skaala Ø, Solberg MF, Fjeldheim PT, Anderson K, Knutar S, Glover KA. Introgression of domesticated salmon changes life history and phenology of a wild salmon population. Evol Appl 2022; 15:853-864. [PMID: 35603027 PMCID: PMC9108307 DOI: 10.1111/eva.13375] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- F. Besnier
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - F. Ayllon
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - Ø. Skaala
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - M. F. Solberg
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | | | - K. Anderson
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - S. Knutar
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - K. A. Glover
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
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15
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Blouin MS, Wrey MC, Bollmann SR, Skaar JC, Twibell RG, Fuentes C. Offspring of first-generation hatchery steelhead trout (Oncorhynchus mykiss) grow faster in the hatchery than offspring of wild fish, but survive worse in the wild: Possible mechanisms for inadvertent domestication and fitness loss in hatchery salmon. PLoS One 2021; 16:e0257407. [PMID: 34914737 PMCID: PMC8675725 DOI: 10.1371/journal.pone.0257407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/24/2021] [Indexed: 11/18/2022] Open
Abstract
Salmonid fish raised in hatcheries often have lower fitness (number of returning adult offspring) than wild fish when both spawn in the wild. Body size at release from hatcheries is positively correlated with survival at sea. So one explanation for reduced fitness is that hatcheries inadvertently select for trait values that enhance growth rate under the unnatural environment of a hatchery, but that are maladaptive in the wild environment. A simple prediction of this hypothesis is that juveniles of hatchery origin should grow more quickly than fish of wild origin under hatchery conditions, but should have lower survival under wild conditions. We tested that hypothesis using multiple full sibling families of steelhead (Oncorhynchus mykiss) that were spawned using either two wild parents (WxW) or two first-generation hatchery (HxH) parents. Offspring from all the families were grown together under hatchery conditions and under semi-natural conditions in artificial streams. HxH families grew significantly faster in the hatchery, but had significantly lower survival in the streams. That we see this tradeoff after only a single generation of selection suggests that the traits involved are under very strong selection. We also considered one possible alteration to the hatchery environment that might reduce the intensity of selection among families in size at release. Here we tested whether reducing the fat content of hatchery feed would reduce the variance among families in body size. Although fish raised under a low-fat diet were slightly smaller, the variation among families in final size was unchanged. Thus, there is no evidence that reducing the fat content of hatchery feed would reduce the opportunity for selection among families on size at release.
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Affiliation(s)
- Michael S. Blouin
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Madeleine C. Wrey
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - Stephanie R. Bollmann
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, United States of America
| | - James C. Skaar
- Trask Hatchery, Oregon Department of Fish and Wildlife, Tillamook, Oregon, United States of America
| | - Ronald G. Twibell
- Abernathy Fish Technology Center, Longview, Washington, United States of America
| | - Claudio Fuentes
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
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16
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Zhou Y, Li J, Qi H, Yang H, Ban X, Yang J, Du H. Riverbed Substrate Requirements for Natural Reproduction of Gymnocypris przewalskii. Animals (Basel) 2021; 11:ani11113246. [PMID: 34827978 PMCID: PMC8614266 DOI: 10.3390/ani11113246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/09/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Gymnocypris przewalskii (i.e., Qinghai Lake naked carp) is a migratory fish species that lives in highland brackish water. It is important to understand the abiotic environment required by this fish to reproduce naturally so that its habitat can be protected and the wild population can be conserved. Here, artificial simulation and spawning ground substrate transformation experiments were conducted to examine the riverbed substrate requirements for G. przewalskii to naturally reproduce. Using various techniques (in vitro markers, videography, and Ethovision XT behavior tracking), this study systematically investigated the riverbed substrate preferences of G. przewalskii as well as the characteristics and effectiveness of natural reproduction induced by pebble riverbed substrate. The findings can be summarized as follows: (1) the habitat preferences of G. przewalskii differed significantly between various riverbed substrate, with pebble substrate being preferred during natural reproduction, and sand substrate being preferred pre- and post-spawning, and (2) the natural reproduction of G. przewalskii was heavily reliant on pebble riverbed substrate. Specifically, pebble substrate significantly improved spawn quantity and fertilization rate. These findings provide scientific evidence for the improvement and restoration of G. przewalskii spawning grounds, and insights regarding the artificial bionic reproduction of G. przewalskii.
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Affiliation(s)
- Yanghao Zhou
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.Z.); (J.L.); (H.Y.)
- College of Fisheries, Huazhong Agricultural University, Wuhan 430037, China
| | - Junyi Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.Z.); (J.L.); (H.Y.)
| | - Hongfang Qi
- Qinghai Key Laboratory of Breeding and Protection of Naked Carp, Qinghai Lake Naked Carp Rescue Center, Xining 810016, China; (H.Q.); (J.Y.)
| | - Haile Yang
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.Z.); (J.L.); (H.Y.)
| | - Xuan Ban
- Hubei Key Laboratory of Environmental and Disaster Monitoring and Assessment, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430077, China;
| | - Jianxin Yang
- Qinghai Key Laboratory of Breeding and Protection of Naked Carp, Qinghai Lake Naked Carp Rescue Center, Xining 810016, China; (H.Q.); (J.Y.)
| | - Hao Du
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs of China, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China; (Y.Z.); (J.L.); (H.Y.)
- Qinghai Key Laboratory of Breeding and Protection of Naked Carp, Qinghai Lake Naked Carp Rescue Center, Xining 810016, China; (H.Q.); (J.Y.)
- Correspondence:
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Poo S, Bogisich A, Mack M, Lynn BK, Devan‐Song A. Post‐release comparisons of amphibian growth reveal challenges with sperm cryopreservation as a conservation tool. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Sinlan Poo
- Department of Conservation and Research Memphis Zoological Society Memphis Tennessee USA
- Department of Biological Sciences Arkansas State University Jonesboro Arkansas USA
| | - Allison Bogisich
- Department of Conservation and Research Memphis Zoological Society Memphis Tennessee USA
| | - Mariah Mack
- Department of Biology Southern Illinois University Edwardsville Edwardsville Illinois USA
| | - Bryan K. Lynn
- Department of Integrative Biology Oregon State University Corvallis Oregon USA
| | - Anne Devan‐Song
- Department of Integrative Biology Oregon State University Corvallis Oregon USA
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18
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Lavoie C, Wellband K, Perreault A, Bernatchez L, Derome N. Artificial Rearing of Atlantic Salmon Juveniles for Supportive Breeding Programs Induces Long-Term Effects on Gut Microbiota after Stocking. Microorganisms 2021; 9:microorganisms9091932. [PMID: 34576827 PMCID: PMC8465833 DOI: 10.3390/microorganisms9091932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 12/21/2022] Open
Abstract
In supportive breeding programs for wild salmon populations, stocked parr experience higher mortality rates than wild ones. Among other aspects of phenotype, the gut microbiota of artificially raised parr differs from that of wild parr before stocking. Early steps of microbiota ontogeny are tightly dependent upon environmental conditions, both of which exert long-term effects on host physiology. Therefore, our objective was to assess to what extent the resilience capacity of the microbiota of stocked salmon may prevent taxonomic convergence with that of their wild congeners after two months in the same natural environment. Using the 16S SSU rRNA marker gene, we tested the general hypothesis that environmental conditions during the very first steps of microbiota ontogeny imprint a permanent effect on later stages of microbiota recruitment. Our results first showed that gut microbiota composition of stocked and wild parr from the same genetic population, and sharing the same environment, was dependent on the early rearing environment. In contrast, skin microbiota in stocked individuals converged to that of wild individuals. Taxonomic composition and co-occurrence network analyses suggest an impairment of wild bacteria recruitment and a higher instability for the gut microbiota of stocked parr. This study is the first to demonstrate the long-term effect of early microbiota ontogeny in artificial rearing for natural population conservation programs, raising the need to implement microbial ecology.
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Affiliation(s)
- Camille Lavoie
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Kyle Wellband
- Department of Biology, Canadian Rivers Institute, University of New Brunswick, Fredericton, NB E3B 5A3, Canada;
| | - Alysse Perreault
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Louis Bernatchez
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
| | - Nicolas Derome
- Department of Biology, Laval University, Québec, QC G1V 0A6, Canada; (C.L.); (A.P.); (L.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Laval University, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-(418)-656-7726
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19
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Koch IJ, Narum SR. An evaluation of the potential factors affecting lifetime reproductive success in salmonids. Evol Appl 2021; 14:1929-1957. [PMID: 34429740 PMCID: PMC8372082 DOI: 10.1111/eva.13263] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 06/03/2021] [Accepted: 06/06/2021] [Indexed: 01/24/2023] Open
Abstract
Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.
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Affiliation(s)
- Ilana J. Koch
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
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20
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Gazsi G, Ivánovics B, Izabella RB, Szabó T, Daniel Z, Kucska B, Urbányi B, Horváth L, Müller F, Müller T. Artificial sperm insemination in externally fertilised fish as a novel tool for ex situ and in situ conservation of valuable populations. ENDANGER SPECIES RES 2021. [DOI: 10.3354/esr01124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Loss of genetic diversity and accumulation of deleterious mutations may lead to inbreeding depression in captive breeding. To address the problem of maintaining genetic diversity, we developed a new fish spawning method which offers flexibility in crossing diverse species when in vitro fertilisation (IVF) is not available. This method involves the collection of sperm from several males of ovuliparous fish; the sperm mix is then injected by catheter into the ovarian cavity of a female through the oviduct. We demonstrate, using zebrafish as a model for externally fertilised fish, that the sperm survives the ovarian conditions and can fertilise ovulated eggs, which are released from the body cavity during natural spawning. Wild type females were injected with reporter transgenic sperm from homozygous transgenic males before intended spawning with wild type males. The sperm injection method did not have an impact on reproductive parameters such as egg production or fertilisation rate compared to controls. In 25 successful spawning experiments, 20 females produced mixed genotype offspring comprising both transgenic and wild type larvae in varying ratios, indicating that the injected transgenic sperm efficiently competed with sperm released by non-transgenic wild type mating males, and both sperm types contributed to the fertilisation of the released eggs. This experiment provides proof of principle for increasing the genetic base of offspring of fish species, including that of many endangered fish species for which IVF is not available due to lack of timed induction of ovulation or when gametic release cannot be synchronised.
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Affiliation(s)
- G Gazsi
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - B Ivánovics
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - RB Izabella
- Department of Environmental Toxicology, Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - T Szabó
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Department of Aquaculture, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - Z Daniel
- Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Tuwima 10 Str., 10-748 Olsztyn, Poland
| | - B Kucska
- Department of Applied Fish Biology, Institute of Aquaculture and Environmental Safety, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences 7400 Kaposvár, Guba S. u. 40, Hungary
| | - B Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Department of Aquaculture, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - L Horváth
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Department of Aquaculture, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
| | - F Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Vincent Drive, Edgbaston, B15 2TT Birmingham, UK
| | - T Müller
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Szent István Campus, Hungarian University of Agriculture and Life Sciences, 2100 Gödöllő, Páter K. u. 1, Hungary
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21
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Twardek WM, Ekström A, Eliason EJ, Lennox RJ, Tuononen E, Abrams AEI, Jeanson AL, Cooke SJ. Field assessments of heart rate dynamics during spawning migration of wild and hatchery-reared Chinook salmon. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200214. [PMID: 34121459 DOI: 10.1098/rstb.2020.0214] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During spawning, adult Pacific salmonids (Oncorhynchus spp.) complete challenging upriver migrations during which energy and oxygen delivery must be partitioned into activities such as locomotion, maturation and spawning behaviours under the constraints of an individual's cardiac capacity. To advance our understanding of cardiac function in free-swimming fishes, we implanted migrating adult Chinook salmon (Oncorhynchus tshawytscha) collected near the mouth of the Sydenham River, Ontario, with heart rate (fH) biologgers that recorded fH every 3 min until these semelparous fish expired on spawning grounds several days later. Fundamental aspects of cardiac function were quantified, including resting, routine and maximum fH, as well as scope for fH (maximum-resting fH). Predictors of fH were explored using generalized least-squares regression, including water temperature, discharge, fish size and fish origin (wild versus hatchery). Heart rate was positively correlated with water temperature, which aligned closely with daily and seasonal shifts. Wild fish had slower resting heart rates than hatchery fish, which led to significantly higher scope for fH. Our findings suggest that wild salmon may have better cardiac capacity during migration than hatchery fish, potentially promoting migration success in wild fish. This article is part of the theme issue 'Measuring physiology in free-living animals (Part I)'.
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Affiliation(s)
- W M Twardek
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A Ekström
- Department of Biological and Environmental Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - E J Eliason
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA 93106, USA
| | - R J Lennox
- Norwegian Research Centre (NORCE), Laboratory for Freshwater Ecology and Inland Fisheries (LFI), Nygårdsgaten 112, 5008 Bergen, Norway
| | - E Tuononen
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A E I Abrams
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - A L Jeanson
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
| | - S J Cooke
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, Canada K1S 5B6
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Farquharson KA, Hogg CJ, Grueber CE. Offspring survival changes over generations of captive breeding. Nat Commun 2021; 12:3045. [PMID: 34031378 PMCID: PMC8144597 DOI: 10.1038/s41467-021-22631-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/11/2021] [Indexed: 11/28/2022] Open
Abstract
Conservation breeding programs such as zoos play a major role in preventing extinction, but their sustainability may be impeded by neutral and adaptive population genetic change. These changes are difficult to detect for a single species or context, and impact global conservation efforts. We analyse pedigree data from 15 vertebrate species – over 30,000 individuals – to examine offspring survival over generations of captive breeding. Even accounting for inbreeding, we find that the impacts of increasing generations in captivity are highly variable across species, with some showing substantial increases or decreases in offspring survival over generations. We find further differences between dam and sire effects in first- versus multi-generational analysis. Crucially, our multispecies analysis reveals that responses to captivity could not be predicted from species’ evolutionary (phylogenetic) relationships. Even under best-practice captive management, generational fitness changes that cannot be explained by known processes (such as inbreeding depression), are occurring. Captive breeding could prevent species extinctions, but selection for captivity may decrease fitness. Here the authors analyse pedigree data on 15 long-running vertebrate breeding programs and find generational fitness changes that processes such as inbreeding depression cannot explain.
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Affiliation(s)
- Katherine A Farquharson
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Carolyn J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Catherine E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia.
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23
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Koljonen ML, Masuda M, Kallio-Nyberg I, Koskiniemi J, Saloniemi I. Large inter-stock differences in catch size-at-age of mature Atlantic salmon observed by using genetic individual origin assignment from catch data. PLoS One 2021; 16:e0247435. [PMID: 33822799 PMCID: PMC8023481 DOI: 10.1371/journal.pone.0247435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 02/08/2021] [Indexed: 12/02/2022] Open
Abstract
Genetic individual assignment of river stock of origin of mixed stock catch fish offers a tool to analyze size differences among river stocks. Data on the genetically identified river stock of origin of individual fish from commercial mixed stock catches were used to compare the catch size-at-age of mature Atlantic salmon catch fish (Salmo salar) from different rivers in the Baltic Sea. In this application of genetic mixed stock modeling, individual assignments of the river stock of origin were analyzed together with length- and weight-at-age data for individual catch fish. The use of four genetic stock identification based methods was compared for defining the length distributions of caught mature salmon in different river stocks. The catch data included information on maturing salmon in the northern Baltic Sea over the years 2000–2013. DNA microsatellite data on 17 loci and information on the smoltification age were used to assign spawners to their stock of origin. All of the compared methods for using probabilistic stock of origin data in our case yielded very similar estimates of the final mean length distributions of the stocks. The Bayesian mixture model yielded slightly more conservative estimates than the direct probability method, threshold method, or the modified probability method. The catch size between spawners of a same sex and age from river stocks differed significantly and the differences were large. The mean catch weight of 1-sea-winter old mature males in different rivers varied from 1.9 kg to 2.9 kg, from 5.1 kg to 7.5 kg for 2-sea-winter old males, from 5.0 kg to 7.2 kg for 2-sea-winter old females, and from 8.2 kg to 10.8 kg for 3-sea-winter-old females. The mean size of caught wild salmon spawners in each year-class was on average smaller than that of the hatchery-reared and sea ranched stocks.
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Affiliation(s)
- Marja-Liisa Koljonen
- Natural Resources Institute Finland (Luke), Production Systems, Animal Genetics, Helsinki, Finland
- * E-mail:
| | - Michele Masuda
- Auke Bay Laboratories, Alaska Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Juneau, Alaska, United States of America
| | - Irma Kallio-Nyberg
- Natural Resources Institute Finland (Luke), Ecosystems and Ecology, Fish Stocks and Environment, Helsinki, Finland
| | - Jarmo Koskiniemi
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Irma Saloniemi
- Department of Biology, University of Turku, Turku, Finland
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25
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Nilsson E, Sadler-Riggleman I, Beck D, Skinner MK. Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations. ENVIRONMENTAL EPIGENETICS 2021; 7:dvab002. [PMID: 34040807 PMCID: PMC8132314 DOI: 10.1093/eep/dvab002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/09/2021] [Accepted: 03/01/2021] [Indexed: 05/06/2023]
Abstract
Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.
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Affiliation(s)
- Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Ingrid Sadler-Riggleman
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
- Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +1-509-335-1524; E-mail:
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26
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O'Sullivan RJ, Aykanat T, Johnston SE, Rogan G, Poole R, Prodöhl PA, de Eyto E, Primmer CR, McGinnity P, Reed TE. Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity. Proc Biol Sci 2020; 287:20201671. [PMID: 33081620 PMCID: PMC7661298 DOI: 10.1098/rspb.2020.1671] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.
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Affiliation(s)
- Ronan James O'Sullivan
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland
| | | | - Ger Rogan
- Marine Institute, Furnace, Newport, Mayo, Ireland
| | | | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Belfast, UK
| | | | - Craig R Primmer
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014 Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland.,Marine Institute, Furnace, Newport, Mayo, Ireland
| | - Thomas Eric Reed
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
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27
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Tenger-Trolander A, Kronforst MR. Migration behaviour of commercial monarchs reared outdoors and wild-derived monarchs reared indoors. Proc Biol Sci 2020; 287:20201326. [PMID: 32752991 DOI: 10.1098/rspb.2020.1326] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Captive rearing of monarch butterflies is a commercial and personal pursuit enjoyed by many different groups and individuals. However, the practice remains controversial, especially after new evidence showed that both a group of commercially derived monarchs reared outdoors and a group of wild-derived but indoor-reared monarchs failed to orient south, unlike wild-derived monarchs reared outdoors. To more fully characterize the mechanisms responsible for the loss of orientation in both commercial and indoor-reared monarchs, we performed flight simulator experiments to determine (i) whether any fraction of commercial monarchs maintains a southern heading over multiple tests, and (ii) whether indoor conditions with the addition of sunlight can induce southern flight in wild-derived monarchs. Commercial monarchs changed their flight direction more often over the course of multiple tests than wild-derived monarchs. While as a group the commercial monarchs did not fly south on average, a subset of individuals did orient south over multiple tests, potentially explaining the discordance between flight simulator assays and the recovery of tagged commercial monarchs at overwintering locations. We also show that even when raised indoors with sunlight, wild-derived monarchs did not consistently orient south in the flight simulator, though wild-derived monarchs reared outdoors did orient south.
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Affiliation(s)
| | - Marcus R Kronforst
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
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28
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Population Genetic Analysis for Stock Enhancement of Silver Sea Bream (Rhabdosargus sarba) in Taiwan. FISHES 2020. [DOI: 10.3390/fishes5020019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stock enhancement is a method for replenishing depleted wild finfish populations by supplementing them with hatchery-raised fish. In Taiwan, silver sea bream (Rhabdosargus sarba) is a predominant commercial species involved in stock enhancement projects. Although management agencies conduct stock enhancement projects, there are a lot of private releases without records. Stock enhancement is performed by the private aquaculture sector without accurate genetic records, potentially leading to unintended consequences for wild populations. We analyzed the genetics of 459 wild and 701 hatchery-reared specimens from nine batches produced by various hatcheries. Wild and hatchery-reared samples could be considered two separate clades by using a set of stable and informative microsatellite markers including type I (from gene introns and 3′UTR) and type II markers (randomly picked up from genome). Type I microsatellite markers could more sensitively reflect the loss of genetic diversity more than type II markers in the domestication process. All specimens were considered native by using mtDNA COI and microsatellites. The genetic composition of the wild population is relatively simple, and the estimated low contribution rate of the hatchery stock (1.3–10.9%; 6–50/459) indicated a weak but significant genetic effect of stock enhancement. Therefore, establishing standards for the stock enhancement of silver sea bream for more effective supplementation of wild populations is imperative.
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29
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Leinonen T, Piironen J, Koljonen ML, Koskiniemi J, Kause A. Restored river habitat provides a natural spawning area for a critically endangered landlocked Atlantic salmon population. PLoS One 2020; 15:e0232723. [PMID: 32437447 PMCID: PMC7241772 DOI: 10.1371/journal.pone.0232723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/20/2020] [Indexed: 11/19/2022] Open
Abstract
Supplementing endangered fish populations with captive bred individuals is a common practice in conservation management. The aim of supplementary releases from hatchery broodstocks is to maintain the viability of populations by maintaining their genetic diversity. Landlocked Lake Saimaa salmon (Salmo salar m. sebago) has been critically endangered for the past half-century. As a result of anthropogenic disturbance, especially construction of hydroelectric power plants, the Lake Saimaa salmon has become completely dependent on hatchery broodstock. Recently, habitat restoration has been done in one of the former spawning rivers with the aim of creating a new natural spawning ground for the critically endangered population. Hatchery fish releases have also been revised so that in addition to juveniles, adult fish from the hatchery and from the wild have been released into the restored river. We assessed here if a restored river stretch can be used as a natural spawning ground and juvenile production area with the aim of improving genetic diversity of the critically endangered Lake Saimaa salmon. By constructing a pedigree of the released adults, and juveniles sampled from the restored river, we found that the majority of the released adults had produced offspring in the river. We also found that wild-caught spawners that were released into the restored river had much higher reproductive success than hatchery-reared parents that were released into the restored river at the same time. We found no significant differences in genetic diversity between the parent and offspring generations. Meanwhile, relatedness among different groups of adults and juveniles varied a lot. For example, while the hatchery-reared females were on average half-siblings, wild-caught females showed no significant relatedness. This highlights the importance of using pedigree information in planning the conservation and management of endangered populations, especially when artificial propagation is involved.
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Affiliation(s)
- Tuomas Leinonen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- * E-mail:
| | - Jorma Piironen
- Natural Resources Institute Finland (Luke), Joensuu, Finland
| | | | - Jarmo Koskiniemi
- Department of Agricultural Sciences University of Helsinki, Helsinki, Finland
| | - Antti Kause
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
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30
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Bourret V, Albert V, April J, Côté G, Morissette O. Past, present and future contributions of evolutionary biology to wildlife forensics, management and conservation. Evol Appl 2020; 13:1420-1434. [PMID: 32684967 PMCID: PMC7359848 DOI: 10.1111/eva.12977] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022] Open
Abstract
Successfully implementing fundamental concepts into concrete applications is challenging in any given field. It requires communication, collaboration and shared will between researchers and practitioners. We argue that evolutionary biology, through research work linked to conservation, management and forensics, had a significant impact on wildlife agencies and department practices, where new frameworks and applications have been implemented over the last decades. The Quebec government's Wildlife Department (MFFP: Ministère des Forêts, de la Faune et des Parcs) has been proactive in reducing the “research–implementation” gap, thanks to prolific collaborations with many academic researchers. Among these associations, our department's outstanding partnership with Dr. Louis Bernatchez yielded significant contributions to harvest management, stocking programmes, definition of conservation units, recovery of threatened species, management of invasive species and forensic applications. We discuss key evolutionary biology concepts and resulting concrete examples of their successful implementation that derives directly or indirectly from this successful partnership. While old and new threats to wildlife are bringing new challenges, we expect recent developments in eDNA and genomics to provide innovative solutions as long as the research–implementation bridge remains open.
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Affiliation(s)
- Vincent Bourret
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Vicky Albert
- Direction générale de la protection de la faune Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Julien April
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Guillaume Côté
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
| | - Olivier Morissette
- Direction générale de la gestion de la faune et des habitats Ministère des Forêts, de la Faune et des Parcs Québec QC Canada
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31
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Almodóvar A, Leal S, Nicola GG, Hórreo JL, García-Vázquez E, Elvira B. Long-term stocking practices threaten the original genetic diversity of the southernmost European populations of Atlantic salmon Salmo salar. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many Atlantic salmon Salmo salar populations in Europe are threatened by previous stocking with foreign hatchery strains. Temporal patterns of genetic characteristics of salmon from northern Spain, the southernmost European populations, were compared before and after species decline and heavy stocking with specimens from northern Europe. Eleven microsatellite loci were analysed in archival (scales from 1958-1960) and contemporary (2007-2008) samples from the River Sella. Temporal analyses revealed a similar heterozygosity between archival and contemporary samples, despite a drastic decrease in population abundance, while the contemporary sample showed a higher allelic richness due to the occurrence of foreign alleles. Considering only the alleles with at least 4% frequency in the archival sample, 2 alleles exclusive to the River Sella were absent in the contemporary sample, and 14 alleles showed a decrease of at least 4% frequency. Four alleles common in Scotland showed a high occurrence in the contemporary sample, so they are good candidates as markers of introgression of foreign genes. The heavy stocking with non-native Scottish broodstocks between 1970 and 1990 caused the introgression found in the contemporary sample when compared with the pristine population. An abrupt decrease was evident when the estimates of effective number of breeders were adjusted to take into account overlapping generations (NbAdj), effective population size (NeAdj) estimated from NbAdj, and number of breeders estimated using the sibship assignment method (NbSIB). The very low effective size values found in the contemporary sample, together with the detrimental synergy between genetic drift and high rates of introgression, represent a severe risk for the conservation of native salmon.
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Affiliation(s)
- A Almodóvar
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
| | - S Leal
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
| | - GG Nicola
- Department of Environmental Sciences, University of Castilla-La Mancha (UCLM), Toledo 45071, Spain
| | - JL Hórreo
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid 28006, Spain
| | - E García-Vázquez
- Department of Functional Biology, University of Oviedo, Oviedo 33003, Spain
| | - B Elvira
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
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32
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Patterns of reproductive success among reintroduced Atlantic salmon in two Lake Champlain tributaries. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01243-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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33
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Fraser DJ, Walker L, Yates MC, Marin K, Wood JLA, Bernos TA, Zastavniouk C. Population correlates of rapid captive-induced maladaptation in a wild fish. Evol Appl 2019; 12:1305-1317. [PMID: 31417616 PMCID: PMC6691219 DOI: 10.1111/eva.12649] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 04/06/2018] [Accepted: 05/06/2018] [Indexed: 12/31/2022] Open
Abstract
Understanding the extent to which captivity generates maladaptation in wild species can inform species recovery programs and elucidate wild population responses to novel environmental change. Although rarely quantified, effective population size (N e ) and genetic diversity should influence the magnitude of plastic and genetic changes manifested in captivity that reduce wild fitness. Sexually dimorphic traits might also mediate consequences of captivity. To evaluate these relationships, we generated >600 full- and half-sibling families from nine wild brook trout populations, reared them for one generation under common, captive environmental conditions and contrasted several fitness-related traits in wild versus captive lines. We found substantial variation in lifetime success (lifetime survival and reproductive success) and life history traits among wild populations after just one captive generation (fourteen- and threefold ranges across populations, respectively). Populations with lower heterozygosity showed lower captive lifetime success, suggesting that captivity generates maladaptation within one generation. Greater male-biased mortality in captivity occurred in populations having disproportionately higher growth rates in males than females. Wild population N e and allelic diversity had little or no influence on captive trait expression and lifetime success. Our results have four conservation implications: (i) Trait values and lifetime success were highly variable across populations following one generation of captivity. (ii) Maladaptation induced by captive breeding might be particularly intense for the very populations practitioners are most interested in conserving, such as those with low heterozygosity. (iii) Maladaptive sex differences in captivity might be associated with population-dependent growth costs of reproduction. (iv) Heterozygosity can be a good indicator of short-term, intraspecific responses to novel environmental change.
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Affiliation(s)
| | - Lisa Walker
- Institute of ParasitologyMcGill UniversityMontrealQCCanada
| | | | - Kia Marin
- Golder Associés LtéeMontréalQCCanada
| | | | - Thais A. Bernos
- Professionals for Fair DevelopmentProtected Areas ProgramParisFrance
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34
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Wood ZT, Fryxell DC, Robinson RR, Palkovacs EP, Kinnison MT. Phenotypic and community consequences of captive propagation in mosquitofish. J Appl Ecol 2019. [DOI: 10.1111/1365-2664.13391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zachary T. Wood
- School of Biology and Ecology and Ecology and Environmental Sciences Program University of Maine Orono Maine
| | - David C. Fryxell
- Department of Ecology and Evolutionary Biology University of California, Santa Cruz Santa Cruz California
| | - Rebecca R. Robinson
- Department of Ecology and Evolutionary Biology University of California, Santa Cruz Santa Cruz California
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary Biology University of California, Santa Cruz Santa Cruz California
| | - Michael T. Kinnison
- School of Biology and Ecology and Ecology and Environmental Sciences Program University of Maine Orono Maine
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35
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Jonsson B, Jonsson N, Jonsson M. Supportive breeders of Atlantic salmon
Salmo salar
have reduced fitness in nature. CONSERVATION SCIENCE AND PRACTICE 2019. [DOI: 10.1111/csp2.85] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Bror Jonsson
- Department of Landscape EcologyNorwegian Institute for Nature Research Oslo Norway
| | - Nina Jonsson
- Department of Landscape EcologyNorwegian Institute for Nature Research Oslo Norway
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36
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37
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Janowitz‐Koch I, Rabe C, Kinzer R, Nelson D, Hess MA, Narum SR. Long-term evaluation of fitness and demographic effects of a Chinook Salmon supplementation program. Evol Appl 2019; 12:456-469. [PMID: 30828367 PMCID: PMC6383734 DOI: 10.1111/eva.12725] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 09/17/2018] [Accepted: 10/09/2018] [Indexed: 01/02/2023] Open
Abstract
While the goal of supplementation programs is to provide positive, population-level effects for species of conservation concern, these programs can also present an inherent fitness risk when captive-born individuals are fully integrated into the natural population. In order to evaluate the long-term effects of a supplementation program and estimate the demographic and phenotypic factors influencing the fitness of a threatened population of Chinook Salmon (Oncorhynchus tshawytscha), we genotyped tissue samples spanning a 19-year period (1998-2016) to generate pedigrees from adult fish returning to Johnson Creek, Idaho, USA. We expanded upon previous estimates of relative reproductive success (RRS) to include grandparentage analyses and used generalized linear models to determine whether origin (hatchery or natural) or phenotypic traits (timing of arrival to spawning grounds, body length, and age) significantly predicted reproductive success (RS) across multiple years. Our results provide evidence that this supplementation program with 100% natural-origin broodstock provided a long-term demographic boost to the population (mean of 4.56 times in the first generation and mean of 2.52 times in the second generation). Overall, when spawning in nature, hatchery-origin fish demonstrated a trend toward lower RS compared to natural-origin fish (p < 0.05). However, when hatchery-origin fish successfully spawned with natural-origin fish, they had similar RS compared to natural by natural crosses (first-generation mean hatchery by natural cross RRS = 1.11 females, 1.13 males; second-generation mean hatchery by natural cross RRS = 1.03 females, 1.08 males). While origin, return year, and body length were significant predictors of fitness for both males and females (p < 0.05), return day was significant for males but not females (p > 0.05). These results indicate that supplementation programs that reduce the potential for genetic adaptation to captivity can be effective at increasing population abundance while limiting long-term fitness effects on wild populations.
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Affiliation(s)
| | - Craig Rabe
- Department of Fisheries Resources ManagementNez Perce TribeMcCall Field OfficeIdaho
| | - Ryan Kinzer
- Department of Fisheries Resources ManagementNez Perce TribeMcCall Field OfficeIdaho
| | - Doug Nelson
- Department of Fisheries Resources ManagementNez Perce TribeMcCall Field OfficeIdaho
| | | | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIdaho
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38
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Hagen IJ, Jensen AJ, Bolstad GH, Diserud OH, Hindar K, Lo H, Karlsson S. Supplementary stocking selects for domesticated genotypes. Nat Commun 2019; 10:199. [PMID: 30643117 PMCID: PMC6331577 DOI: 10.1038/s41467-018-08021-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023] Open
Abstract
Stocking of hatchery produced fish is common practise to mitigate declines in natural populations and may have unwanted genetic consequences. Here we describe a novel phenomenon arising where broodstock used for stocking may be introgressed with farmed individuals. We test how stocking affects introgression in a wild population of Atlantic salmon (Salmo salar) by quantifying how the number of adult offspring recaptured in a stocked river depend on parental introgression. We found that hatchery conditions favour farmed genotypes such that introgressed broodstock produce up to four times the number of adult offspring compared to non-introgressed broodstock, leading to increased introgression in the recipient spawning population. Our results provide the first empirical evidence that stocking can unintentionally favour introgressed individuals and through selection for domesticated genotypes compromise the fitness of stocked wild populations.
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Affiliation(s)
- Ingerid J Hagen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway.
| | - Arne J Jensen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Geir H Bolstad
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Ola H Diserud
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
| | - Håvard Lo
- Norwegian Veterinary Institute, P.O. Box 5695 Torgarden, 7485, Trondheim, Norway
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, 7485, Trondheim, Norway
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39
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Lavoie C, Courcelle M, Redivo B, Derome N. Structural and compositional mismatch between captive and wild Atlantic salmon ( Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods. Evol Appl 2018; 11:1671-1685. [PMID: 30344635 PMCID: PMC6183451 DOI: 10.1111/eva.12658] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/18/2018] [Accepted: 05/29/2018] [Indexed: 12/17/2022] Open
Abstract
Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.
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Affiliation(s)
- Camille Lavoie
- Biology DepartmentLaval UniversityQuebecQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Laval UniversityQuebecQCCanada
| | - Maxime Courcelle
- Institut des Sciences de l’Évolution (ISEM)Montpellier UniversityMontpellierFrance
| | | | - Nicolas Derome
- Biology DepartmentLaval UniversityQuebecQCCanada
- Institut de Biologie Intégrative et des Systèmes (IBIS)Laval UniversityQuebecQCCanada
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40
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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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Kusche H, Côté G, Hernandez C, Normandeau E, Boivin-Delisle D, Bernatchez L. Characterization of natural variation in North American Atlantic Salmon populations (Salmonidae: Salmo salar) at a locus with a major effect on sea age. Ecol Evol 2017; 7:5797-5807. [PMID: 28808549 PMCID: PMC5550958 DOI: 10.1002/ece3.3132] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/26/2017] [Accepted: 05/10/2017] [Indexed: 12/25/2022] Open
Abstract
Age at maturity is a key life‐history trait of most organisms. In anadromous salmonid fishes such as Atlantic Salmon (Salmo salar), age at sexual maturity is associated with sea age, the number of years spent at sea before the spawning migration. For the first time, we investigated the presence of two nonsynonymous vgll3 polymorphisms in North American Atlantic Salmon populations that relate to sea age in European salmon and quantified the natural variation at these and two additional candidate SNPs from two other genes. A targeted resequencing assay was developed and 1,505 returning adult individuals of size‐inferred sea age and sex from four populations were genotyped. Across three of four populations sampled in Québec, Canada, the late‐maturing component (MSW) of the population of a given sex exhibited higher proportions of SNP genotypes 54Thrvgll3 and 323Lysvgll3 compared to early‐maturing fish (1SW), for example, 85% versus 53% of females from Trinité River carried 323Lysvgll3 (nMSW = 205 vs. n1SW = 30; p < .001). However, the association between vgll3 polymorphism and sea age was more pronounced in females than in males in the rivers we studied. Logistic regression analysis of vgll3 SNP genotypes revealed increased probabilities of exhibiting higher sea age for 54Thrvgll3 and 323Lysvgll3 genotypes compared to alternative genotypes, depending on population and sex. Moreover, individuals carrying the heterozygous vgll3 SNP genotypes were more likely (>66%) to be female. In summary, two nonsynonymous vgll3 polymorphisms were confirmed in North American populations of Atlantic Salmon and our results suggest that variation at those loci correlates with sea age and sex. Our results also suggest that this correlation varies among populations. Future work would benefit from a more balanced sampling and from adding data on juvenile riverine life stages to contrast our data.
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Affiliation(s)
- Henrik Kusche
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada.,Present address: Thünen Institute of Fisheries Ecology Hamburg Germany
| | - Guillaume Côté
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Cécilia Hernandez
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Damien Boivin-Delisle
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Louis Bernatchez
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec QC Canada
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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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Considerations for the Propagation and Conservation of Endangered Lake Suckers of the Western United States. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2017. [DOI: 10.3996/022016-jfwm-011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
Decades of persistent natural and anthropogenic threats coupled with competing water needs have compromised numerous species of freshwater fishes, many of which are now artificially propagated in hatcheries. Low survival upon release is common, particularly in systems with substantial nonnative predator populations. Extensive sampling for Shortnose (Chasmistes brevirostris) and Lost River Suckers (Deltistes luxatus) in the Klamath River Basin on the California–Oregon border have failed to detect any new adult recruitment for at least two decades, prompting an investigation into artificial propagation as an extinction prevention measure. A comprehensive assessment of strategies and successes associated with propagation for conservation restocking has not been performed for any Catostomid. Here, we review available literature for all western lake sucker species to inform propagation and recovery efforts for Klamath suckers and summarize the relevance of these considerations to other endangered fishes.
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Stock enhancement or sea ranching? Insights from monitoring the genetic diversity, relatedness and effective population size in a seeded great scallop population (Pecten maximus). Heredity (Edinb) 2016; 117:142-8. [PMID: 27353046 DOI: 10.1038/hdy.2016.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/10/2016] [Accepted: 04/12/2016] [Indexed: 01/18/2023] Open
Abstract
The mass release of hatchery-propagated stocks raises numerous questions concerning its efficiency in terms of local recruitment and effect on the genetic diversity of wild populations. A seeding program, consisting of mass release of hatchery-produced juveniles in the local naturally occurring population of great scallops (Pecten maximus L.), was initiated in the early 1980s in the Bay of Brest (France). The present study aims at evaluating whether this seeding program leads to actual population enhancement, with detectable effects on genetic diversity and effective population size, or consists of sea ranching with limited genetic consequences on the wild stock. To address this question, microsatellite-based genetic monitoring of three hatchery-born and naturally recruited populations was conducted over a 5-year period. Results showed a limited reduction in allelic richness but a strong alteration of allelic frequencies in hatchery populations, while genetic diversity appeared very stable over time in the wild populations. A temporal increase in relatedness was observed in both cultured stock and wild populations. Effective population size (Ne) estimates were low and variable in the wild population. Moreover, the application of the Ryman-Laikre model suggested a high contribution of hatchery-born scallops to the reproductive output of the wild population. Overall, the data suggest that the main objective of the seeding program, which is stock enhancement, is fulfilled. Moreover, gene flow from surrounding populations and/or the reproductive input of undetected sub-populations within the bay may buffer the Ryman-Laikre effect and ensure the retention of the local genetic variability.
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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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Clarke CN, Fraser DJ, Purchase CF. Lifelong and carry-over effects of early captive exposure in a recovery program for Atlantic salmon (Salmo salar). Anim Conserv 2016. [DOI: 10.1111/acv.12251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- C. N. Clarke
- Fish Evolutionary Ecology Research Group; Environmental Science Graduate Program; Memorial University; St. John's NL Canada
| | - D. J. Fraser
- Department of Biology; Concordia University; Montreal QC Canada
| | - C. F. Purchase
- Department of Biology; Fish Evolutionary Ecology Research Group; Memorial University; St. John's NL Canada
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Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Waples RS, Knudsen CM, Bosch WJ, Naish KA. Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding. Evol Appl 2015; 8:956-71. [PMID: 26640521 PMCID: PMC4662342 DOI: 10.1111/eva.12331] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/02/2015] [Indexed: 12/28/2022] Open
Abstract
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | - Jeffrey J Hard
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | - Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
| | | | | | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric AdministrationSeattle, WA, USA
| | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of WashingtonSeattle, WA, USA
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Neff BD, Garner SR, Fleming IA, Gross MR. Reproductive success in wild and hatchery male coho salmon. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150161. [PMID: 26361548 PMCID: PMC4555853 DOI: 10.1098/rsos.150161] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Salmon produced by hatcheries have lower fitness in the wild than naturally produced salmon, but the factors underlying this difference remain an active area of research. We used genetic parentage analysis of alevins produced by experimentally mixed groups of wild and hatchery coho salmon (Oncorhynchus kisutch) to quantify male paternity in spawning hierarchies. We identify factors influencing paternity and revise previously published behavioural estimates of reproductive success for wild and hatchery males. We observed a strong effect of hierarchy size and hierarchy position on paternity: in two-male hierarchies, the first male sired 63% (±29%; s.d.) of the alevins and the second male 37% (±29%); in three-male hierarchies, the first male sired 64% (±26%), the second male 24% (±20%) and the third male 12% (±10%). As previously documented, hatchery males hold inferior positions in spawning hierarchies, but we also discovered that hatchery males had only 55-84% the paternity of wild males when occupying the same position within a spawning hierarchy. This paternity difference may result from inferior performance of hatchery males during sperm competition, female mate choice for wild males, or differential offspring survival. Regardless of its cause, the combination of inferior hierarchical position and inferior success at a position resulted in hatchery males having only half (51%) the reproductive success of wild males.
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Affiliation(s)
- Bryan D. Neff
- Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Shawn R. Garner
- Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Ian A. Fleming
- Department of Ocean Sciences, Memorial University of Newfoundland, St John's, Newfoundland and Labrador, Canada A1C 5S7
| | - Mart R. Gross
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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Genetic structure of a commercially exploited bivalve, the great scallop Pecten maximus, along the European coasts. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0760-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Effective number of breeders in relation to census size as management tools for Atlantic salmon conservation in a context of stocked populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0758-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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