1
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Kobayashi KM, Bond RM, Reid K, Garza JC, Kiernan JD, Palkovacs EP. Genetic divergence and one-way gene flow influence contemporary evolution and ecology of a partially migratory fish. Evol Appl 2024; 17:e13712. [PMID: 38911264 PMCID: PMC11192968 DOI: 10.1111/eva.13712] [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: 11/22/2023] [Revised: 04/05/2024] [Accepted: 04/14/2024] [Indexed: 06/25/2024] Open
Abstract
Recent work has revealed the importance of contemporary evolution in shaping ecological outcomes. In particular, rapid evolutionary divergence between populations has been shown to impact the ecology of populations, communities, and ecosystems. While studies have focused largely on the role of adaptive divergence in generating ecologically important variation among populations, much less is known about the role of gene flow in shaping ecological outcomes. After divergence, populations may continue to interact through gene flow, which may influence evolutionary and ecological processes. Here, we investigate the role of gene flow in shaping the contemporary evolution and ecology of recently diverged populations of anadromous steelhead and resident rainbow trout (Oncorhynchus mykiss). Results show that resident rainbow trout introduced above waterfalls have diverged evolutionarily from downstream anadromous steelhead, which were the source of introductions. However, the movement of fish from above to below the waterfalls has facilitated gene flow, which has reshaped genetic and phenotypic variation in the anadromous source population. In particular, gene flow has led to an increased frequency of residency, which in turn has altered population density, size structure, and sex ratio. This result establishes gene flow as a contemporary evolutionary process that can have important ecological outcomes. From a management perspective, anadromous steelhead are generally regarded as a higher conservation priority than resident rainbow trout, even when found within the same watershed. Our results show that anadromous and resident O. mykiss populations may be connected via gene flow, with important ecological consequences. Such eco-evolutionary processes should be considered when managing recently diverged populations connected by gene flow.
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Affiliation(s)
- Katie M. Kobayashi
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Rosealea M. Bond
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - Kerry Reid
- Area of Ecology and Biodiversity, School of Biological SciencesUniversity of Hong KongHong KongHong Kong, SAR
| | - J. Carlos Garza
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Joseph D. Kiernan
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Collaborative Program, Institute of Marine SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
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2
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Lázari C, Riva-Rossi C, Ciancio J, Pascual M, Clemento AJ, Pearse DE, Garza JC. Ancestry and genetic structure of resident and anadromous rainbow trout (Oncorhynchus mykiss) in Argentina. JOURNAL OF FISH BIOLOGY 2024; 104:1972-1989. [PMID: 38556852 DOI: 10.1111/jfb.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 12/21/2023] [Accepted: 02/25/2024] [Indexed: 04/02/2024]
Abstract
Since the first introduction from North America more than a century ago, rainbow trout (Oncorhynchus mykiss) have rapidly established self-sustaining populations in major river basins of Patagonia. Many generations later, only the freshwater resident life history is expressed in the Chubut and Negro rivers of northern Argentinian Patagonia, whereas both the resident and anadromous life histories are found in the Santa Cruz River of southern Argentina. Despite previous studies that have tried to identify the sources of these introduced populations, uncertainty still exists. Here we combined data from many single-nucleotide polymorphisms and microsatellite loci in O. mykiss populations from Argentina and North America to evaluate putative source populations, gene flow between Argentinian river basins, and genetic diversity differences between Argentinian and North American populations. We found that populations from northern and southern Patagonia are highly differentiated and have limited gene flow between them. Phylogeographic analysis also confirmed that they have separate origins, with the northern populations most closely related to the domesticated rainbow trout strains that are raised worldwide and the Santa Cruz River populations most closely related to North American populations from California and Oregon that have an anadromous component. In addition, fish with different life histories in the Santa Cruz River were found to constitute a single interbreeding population. No evidence was found of reduced genetic variation in introduced rainbow trout, suggesting multiple contributing sources. In spite of these advances in understanding, significant questions remain regarding the origins and evolution of the introduced O. mykiss in Patagonia.
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Affiliation(s)
- Carolina Lázari
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
| | - Carla Riva-Rossi
- Instituto de Diversidad y Evolución Austral (IDEAus-CONICET), Puerto Madryn, Argentina
| | - Javier Ciancio
- Centro para el Estudio de Sistemas Marinos (CESIMAR-CONICET), Puerto Madryn, Argentina
| | - Miguel Pascual
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC-CONICET), Puerto Madryn, Argentina
| | - Anthony J Clemento
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - Devon E Pearse
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - John Carlos Garza
- Ocean Sciences Department, University of California Santa Cruz, Santa Cruz, California, USA
- Southwest Fisheries Science Center, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
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3
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Goetz LC, Nuetzel H, Vendrami DLJ, Beulke AK, Anderson EC, Garza JC, Pearse DE. Genetic parentage reveals the (un)natural history of Central Valley hatchery steelhead. Evol Appl 2024; 17:e13681. [PMID: 38516205 PMCID: PMC10956469 DOI: 10.1111/eva.13681] [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: 08/11/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Populations composed of individuals descended from multiple distinct genetic lineages often feature significant differences in phenotypic frequencies. We considered hatchery production of steelhead, the migratory anadromous form of the salmonid species Oncorhynchus mykiss, and investigated how differences among genetic lineages and environmental variation impacted life history traits. We genotyped 23,670 steelhead returning to the four California Central Valley hatcheries over 9 years from 2011 to 2019, confidently assigning parentage to 13,576 individuals to determine age and date of spawning and rates of iteroparity and repeat spawning within each year. We found steelhead from different genetic lineages showed significant differences in adult life history traits despite inhabiting similar environments. Differences between coastal and Central Valley steelhead lineages contributed to significant differences in age at return, timing of spawning, and rates of iteroparity among programs. In addition, adaptive genomic variation associated with life history development in this species varied among hatchery programs and was associated with the age of steelhead spawners only in the coastal lineage population. Environmental variation likely contributed to variations in phenotypic patterns observed over time, as our study period spanned both a marine heatwave and a serious drought in California. Our results highlight evidence of a strong genetic component underlying known phenotypic differences in life history traits between two steelhead lineages.
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Affiliation(s)
- Laura C. Goetz
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - Hayley Nuetzel
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Present address:
Columbia River Inter‐Tribal Fish CommissionPortlandOregonUSA
| | - David L. J. Vendrami
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
- Present address:
Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
| | - Anne K. Beulke
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Eric C. Anderson
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCaliforniaUSA
| | - Devon E. Pearse
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCaliforniaUSA
- Fisheries Ecology Division, Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCaliforniaUSA
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4
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Beulke AK, Abadía-Cardoso A, Pearse DE, Goetz LC, Thompson NF, Anderson EC, Garza JC. Distinct patterns of inheritance shape life-history traits in steelhead trout. Mol Ecol 2023; 32:6896-6912. [PMID: 37942651 DOI: 10.1111/mec.17182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
Life-history variation is the raw material of adaptation, and understanding its genetic and environmental underpinnings is key to designing effective conservation strategies. We used large-scale genetic pedigree reconstruction of anadromous steelhead trout (Oncorhynchus mykiss) from the Russian River, CA, USA, to elucidate sex-specific patterns of life-history traits and their heritability. SNP data from adults returning from sea over a 14-year period were used to identify 13,474 parent-offspring trios. These pedigrees were used to determine age structure, size distributions and family sizes for these fish, as well as to estimate the heritability of two key life-history traits, spawn date and age at maturity (first reproduction). Spawn date was highly heritable (h2 = 0.73) and had a cross-sex genetic correlation near unity. We provide the first estimate of heritability for age at maturity in ocean-going fish from this species and found it to be highly heritable (h2 from 0.29 to 0.62, depending on sex and method), with a much lower genetic correlation across sexes. We also evaluated genotypes at a migration-associated inversion polymorphism and found sex-specific correlations with age at maturity. The significant heritability of these two key reproductive traits in these imperiled fish, and their patterns of inheritance in the two sexes, is consistent with predictions of both natural and sexually antagonistic selection (sexes experience opposing selection pressures). This emphasizes the importance of anthropogenic factors, including hatchery practices and ecosystem modifications, in shaping the fitness of this species, thus providing important guidance for management and conservation efforts.
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Affiliation(s)
- Anne K Beulke
- Department of Ocean Sciences, University of California, California, Santa Cruz, USA
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - Alicia Abadía-Cardoso
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Devon E Pearse
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
| | - Laura C Goetz
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, USA
| | - Neil F Thompson
- Pacific Shellfish Breeding Center, Agricultural Research Service, US Department of Agriculture, Newport, Oregon, USA
| | - Eric C Anderson
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
| | - John Carlos Garza
- Department of Ocean Sciences, University of California, California, Santa Cruz, USA
- Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, California, USA
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5
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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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6
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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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7
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Wedekind C, Vonlanthen P, de Guttry C, Stadelmann R, Stadelmann N, Pirat A, Perroud G. Persistent high hatchery recruitment despite advanced reoligotrophication and significant natural spawning in a whitefish. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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8
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Waples RS, Ford MJ, Nichols K, Kardos M, Myers J, Thompson TQ, Anderson EC, Koch IJ, McKinney G, Miller MR, Naish K, Narum SR, O'Malley KG, Pearse DE, Pess GR, Quinn TP, Seamons TR, Spidle A, Warheit KI, Willis SC. Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon. J Hered 2022; 113:121-144. [PMID: 35575083 DOI: 10.1093/jhered/esab069] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
The increasing feasibility of assembling large genomic datasets for non-model species presents both opportunities and challenges for applied conservation and management. A popular theme in recent studies is the search for large-effect loci that explain substantial portions of phenotypic variance for a key trait(s). If such loci can be linked to adaptations, 2 important questions arise: 1) Should information from these loci be used to reconfigure conservation units (CUs), even if this conflicts with overall patterns of genetic differentiation? 2) How should this information be used in viability assessments of populations and larger CUs? In this review, we address these questions in the context of recent studies of Chinook salmon and steelhead (anadromous form of rainbow trout) that show strong associations between adult migration timing and specific alleles in one small genomic region. Based on the polygenic paradigm (most traits are controlled by many genes of small effect) and genetic data available at the time showing that early-migrating populations are most closely related to nearby late-migrating populations, adult migration differences in Pacific salmon and steelhead were considered to reflect diversity within CUs rather than separate CUs. Recent data, however, suggest that specific alleles are required for early migration, and that these alleles are lost in populations where conditions do not support early-migrating phenotypes. Contrasting determinations under the US Endangered Species Act and the State of California's equivalent legislation illustrate the complexities of incorporating genomics data into CU configuration decisions. Regardless how CUs are defined, viability assessments should consider that 1) early-migrating phenotypes experience disproportionate risks across large geographic areas, so it becomes important to identify early-migrating populations that can serve as reliable sources for these valuable genetic resources; and 2) genetic architecture, especially the existence of large-effect loci, can affect evolutionary potential and adaptability.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Michael J Ford
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Krista Nichols
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Jim Myers
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | | | - Eric C Anderson
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Ilana J Koch
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Garrett McKinney
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | | | - Kerry Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | | | - Devon E Pearse
- Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - George R Pess
- Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA, USA
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WAUSA
| | - Todd R Seamons
- Washington Department of Fish and Wildlife, Olympia, WA, USA
| | - Adrian Spidle
- Northwest Indian Fisheries Commission, Olympia, WA, USA
| | | | - Stuart C Willis
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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9
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Beacham TD, Wallace CG, Jonsen K, McIntosh B, Candy JR, Horst K, Lynch C, Willis D, Luedke W, Kearey L, Rondeau EB. Parentage-based tagging combined with genetic stock identification is a cost-effective and viable replacement for coded-wire tagging in large-scale assessments of marine Chinook salmon fisheries in British Columbia, Canada. Evol Appl 2021; 14:1365-1389. [PMID: 34025773 PMCID: PMC8127719 DOI: 10.1111/eva.13203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 11/26/2022] Open
Abstract
Wild Pacific salmon, including Chinook salmon Oncorhynchus tshawytscha, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest, mitigation for hydroelectric development, and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. For policy implementation, a new approach to the assessment and management of Chinook salmon and the associated hatchery production and fisheries management are needed. Implementation of genetic stock identification (GSI) and parentage-based tagging (PBT) for marine fisheries assessment may overcome problems associated with coded-wire tag-based (CWT) assessment and management of Chinook salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. GSI and PBT were used to identify Chinook salmon sampled in 2018 and 2019 marine fisheries (18,819 individuals genotyped) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 391 single nucleotide polymorphisms via direct sequencing of amplicons. Very high accuracy of assignment to population and age (>99.5%) via PBT was observed for 1994 Chinook salmon of ages 2-4 years, with a 105,722-individual, 380-population baseline available for assignment. Application of a GSI-PBT system of identification to individuals in 2019 fisheries provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, with fishery exploitation rates directly comparable to those provided by CWTs for 13 populations. GSI and PBT provide an alternate, cheaper, and more effective method in the assessment and management of Canadian-origin Chinook salmon relative to CWTs, and an opportunity for a genetics-based system to replace the current CWT system for salmon assessment.
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Affiliation(s)
- Terry D. Beacham
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Colin G. Wallace
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Kim Jonsen
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Brenda McIntosh
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - John R. Candy
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Katherine Horst
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
| | - Cheryl Lynch
- Fisheries and Oceans CanadaRegional HeadquartersVancouverBritish ColumbiaCanada
| | - David Willis
- Fisheries and Oceans CanadaRegional HeadquartersVancouverBritish ColumbiaCanada
| | - Wilf Luedke
- Fisheries and Oceans CanadaSouth Coast Stock Assessment DivisionNanaimoBritish ColumbiaCanada
| | - Lee Kearey
- Fisheries and Oceans CanadaSouth Coast Stock Assessment DivisionNanaimoBritish ColumbiaCanada
| | - Eric B. Rondeau
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBritish ColumbiaCanada
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10
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Waters CD, Clemento A, Aykanat T, Garza JC, Naish KA, Narum S, Primmer CR. Heterogeneous genetic basis of age at maturity in salmonid fishes. Mol Ecol 2021; 30:1435-1456. [PMID: 33527498 DOI: 10.1111/mec.15822] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/07/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications in conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains underexplored. Here, we address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmonids (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait-Chinook Salmon, Coho Salmon, Sockeye Salmon, and Steelhead Trout. We tested for associations in all four species between age at maturity and two genome regions, six6 and vgll3, that are strongly associated with the same trait in Atlantic Salmon (Salmo salar). We also conducted a genome-wide association analysis in Steelhead to assess whether additional regions were associated with this trait. We found the genetic basis of age at maturity to be heterogeneous across salmonid species. Significant associations between six6 and age at maturity were observed in two of the four species, Sockeye and Steelhead, with the association in Steelhead being particularly strong in both sexes (p = 4.46 × 10-9 after adjusting for genomic inflation). However, no significant associations were detected between age at maturity and the vgll3 genome region in any of the species, despite its strong association with the same trait in Atlantic Salmon. We discuss possible explanations for the heterogeneous nature of the genetic architecture of this key life-history trait, as well as the implications of our findings for conservation and management.
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Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Anthony Clemento
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Tutku Aykanat
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - John Carlos Garza
- Institute of Marine Sciences, University of California, Santa Cruz, CA, USA.,Santa Cruz Laboratory, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Santa Cruz, CA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Shawn Narum
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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11
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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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12
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Pepping MY, O’Rourke SM, Huang C, Katz JVE, Jeffres C, Miller MR. Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids. PLoS One 2020; 15:e0239221. [PMID: 33175847 PMCID: PMC7657533 DOI: 10.1371/journal.pone.0239221] [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: 03/26/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022] Open
Abstract
Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.
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Affiliation(s)
- Michelle Y. Pepping
- Department of Animal Science, University of California, Davis, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Sean M. O’Rourke
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Connie Huang
- Department of Animal Science, University of California, Davis, California, United States of America
| | - Jacob V. E. Katz
- California Trout, San Francisco, California, United States of America
| | - Carson Jeffres
- Center for Watershed Sciences, University of California, Davis, California, United States of America
| | - Michael R. Miller
- Department of Animal Science, University of California, Davis, California, United States of America
- Center for Watershed Sciences, University of California, Davis, California, United States of America
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13
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Thompson NF, Anderson EC, Clemento AJ, Campbell MA, Pearse DE, Hearsey JW, Kinziger AP, Garza JC. A complex phenotype in salmon controlled by a simple change in migratory timing. Science 2020; 370:609-613. [DOI: 10.1126/science.aba9059] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Neil F. Thompson
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
| | - Eric C. Anderson
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Anthony J. Clemento
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
| | - Matthew A. Campbell
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Devon E. Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - James W. Hearsey
- Department of Fisheries Biology, Humboldt State University, Arcata, CA 95521, USA
| | - Andrew P. Kinziger
- Department of Fisheries Biology, Humboldt State University, Arcata, CA 95521, USA
| | - John Carlos Garza
- Department of Ocean Sciences, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- University of California, Santa Cruz, Institute of Marine Sciences, Santa Cruz, CA 95064, USA
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA 95060, USA
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14
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Makhrov AA, Artamonova VS. Instability Stabilized: Mechanisms of Evolutionary Stasis and Genetic Diversity Accumulation in Fishes and Lampreys from Environments with Unstable Abiotic Factors. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425520040083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Sard NM, Smith SR, Homola JJ, Kanefsky J, Bravener G, Adams JV, Holbrook CM, Hrodey PJ, Tallon K, Scribner KT. RAPTURE (RAD capture) panel facilitates analyses characterizing sea lamprey reproductive ecology and movement dynamics. Ecol Evol 2020; 10:1469-1488. [PMID: 32076528 PMCID: PMC7029094 DOI: 10.1002/ece3.6001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/18/2022] Open
Abstract
Genomic tools are lacking for invasive and native populations of sea lamprey (Petromyzon marinus). Our objective was to discover single nucleotide polymorphism (SNP) loci to conduct pedigree analyses to quantify reproductive contributions of adult sea lampreys and dispersion of sibling larval sea lampreys of different ages in Great Lakes tributaries. Additional applications of data were explored using additional geographically expansive samples. We used restriction site-associated DNA sequencing (RAD-Seq) to discover genetic variation in Duffins Creek (DC), Ontario, Canada, and the St. Clair River (SCR), Michigan, USA. We subsequently developed RAD capture baits to genotype 3,446 RAD loci that contained 11,970 SNPs. Based on RAD capture assays, estimates of variance in SNP allele frequency among five Great Lakes tributary populations (mean F ST 0.008; range 0.00-0.018) were concordant with previous microsatellite-based studies; however, outlier loci were identified that contributed substantially to spatial population genetic structure. At finer scales within streams, simulations indicated that accuracy in genetic pedigree reconstruction was high when 200 or 500 independent loci were used, even in situations of high spawner abundance (e.g., 1,000 adults). Based on empirical collections of larval sea lamprey genotypes, we found that age-1 and age-2 families of full and half-siblings were widely but nonrandomly distributed within stream reaches sampled. Using the genomic scale set of SNP loci developed in this study, biologists can rapidly genotype sea lamprey in non-native and native ranges to investigate questions pertaining to population structuring and reproductive ecology at previously unattainable scales.
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Affiliation(s)
- Nicholas M. Sard
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Biology DepartmentSUNY OswegoOswegoNew York
| | - Seth R. Smith
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | - Jeannette Kanefsky
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
| | | | - Jean V. Adams
- Great Lakes Science CenterU.S. Geological SurveyAnn ArborMichigan
| | - Christopher M. Holbrook
- Great Lakes Science CenterHammond Bay Biological StationU.S. Geological SurveyMillersburgMichigan
| | | | - Kevin Tallon
- Fisheries and Oceans CanadaSault Ste. MarieONCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichigan
- Department of Integrative BiologyState UniversityEast LansingMichigan
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16
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Pearse DE, Barson NJ, Nome T, Gao G, Campbell MA, Abadía-Cardoso A, Anderson EC, Rundio DE, Williams TH, Naish KA, Moen T, Liu S, Kent M, Moser M, Minkley DR, Rondeau EB, Brieuc MSO, Sandve SR, Miller MR, Cedillo L, Baruch K, Hernandez AG, Ben-Zvi G, Shem-Tov D, Barad O, Kuzishchin K, Garza JC, Lindley ST, Koop BF, Thorgaard GH, Palti Y, Lien S. Sex-dependent dominance maintains migration supergene in rainbow trout. Nat Ecol Evol 2019; 3:1731-1742. [DOI: 10.1038/s41559-019-1044-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/18/2019] [Indexed: 11/09/2022]
Abstract
AbstractMales and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.
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17
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Ferguson A, Reed TE, Cross TF, McGinnity P, Prodöhl PA. Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. JOURNAL OF FISH BIOLOGY 2019; 95:692-718. [PMID: 31197849 PMCID: PMC6771713 DOI: 10.1111/jfb.14005] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/09/2019] [Indexed: 05/10/2023]
Abstract
Brown trout Salmo trutta is endemic to Europe, western Asia and north-western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river-resident, lake-resident) and three main facultative migratory life histories (downstream-upstream within a river system, fluvial-adfluvial potamodromous; to and from a lake, lacustrine-adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River-residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial-adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine-adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold-trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non-genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river-resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr-smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration-residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
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Affiliation(s)
- Andrew Ferguson
- School of Biological SciencesQueen's University BelfastBelfastUK
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Tom F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Paulo A. Prodöhl
- School of Biological SciencesQueen's University BelfastBelfastUK
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18
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Tillotson MD, Barnett HK, Bhuthimethee M, Koehler ME, Quinn TP. Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change. Evol Appl 2019; 12:1344-1359. [PMID: 31417619 PMCID: PMC6691210 DOI: 10.1111/eva.12730] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/05/2018] [Accepted: 10/22/2018] [Indexed: 01/13/2023] Open
Abstract
The timing of breeding migration and reproduction links generations and substantially influences individual fitness. In salmonid fishes, such phenological events (seasonal return to freshwater and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Changing reproductive phenology has been observed in many populations of Atlantic and Pacific salmon and is sometimes attributed to adaptive responses to climate change. The sockeye salmon spawning in the Cedar River near Seattle, Washington, USA, have displayed dramatic changes in spawning timing over the past 50 years, trending later through the early 1990s, and becoming earlier since then. We explored the patterns and drivers of these changes using generalized linear models and mathematical simulations to identify possible environmental correlates of the changes, and test the alternative hypothesis that hatchery propagation caused inadvertent selection on timing. The trend toward later spawning prior to 1993 was partially explained by environmental changes, but the rapid advance in spawning since was not. Instead, since its initiation in 1991, the hatchery has, on average, selected for earlier spawning, and, depending on trait heritability, could have advanced spawning by 1-3 weeks over this period. We estimated heritability of spawning date to be high (h 2 ~0.8; 95% CI: 0.5-1.1), so the upper end of this range is not improbable, though at lower heritabilities a smaller effect would be expected. The lower reproductive success of early spawners and relatively low survival of early emerging juveniles observed in recent years suggest that artificial and natural selection are acting in opposite directions. The fitness costs of early spawning may be exacerbated by future warming; thus, the artificially advanced phenology could reduce the population's productivity. Such artificial selection is known in many salmon hatcheries, so there are broad consequences for the productivity of wild populations comingled with hatchery-produced fish.
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Affiliation(s)
| | | | | | | | - Thomas P. Quinn
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashington
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19
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Evans ML, Hard JJ, Black AN, Sard NM, O’Malley KG. A quantitative genetic analysis of life-history traits and lifetime reproductive success in reintroduced Chinook salmon. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01174-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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20
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Flanagan SP, Jones AG. The future of parentage analysis: From microsatellites to SNPs and beyond. Mol Ecol 2019; 28:544-567. [PMID: 30575167 DOI: 10.1111/mec.14988] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/30/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022]
Abstract
Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next-generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next-generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next-generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP-based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100-500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next-generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next-generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.
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Affiliation(s)
- Sarah P Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
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21
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Beacham TD, Wallace C, Jonsen K, McIntosh B, Candy JR, Willis D, Lynch C, Moore J, Bernatchez L, Withler RE. Comparison of coded-wire tagging with parentage-based tagging and genetic stock identification in a large-scale coho salmon fisheries application in British Columbia, Canada. Evol Appl 2019; 12:230-254. [PMID: 30697336 PMCID: PMC6346672 DOI: 10.1111/eva.12711] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 01/13/2023] Open
Abstract
Wild Pacific salmon, including Coho salmon Onchorynchus kisutch, have been supplemented with hatchery propagation for over 50 years in support of increased ocean harvest and conservation of threatened populations. In Canada, the Wild Salmon Policy for Pacific salmon was established with the goal of maintaining and restoring healthy and diverse Pacific salmon populations, making conservation of wild salmon and their habitats the highest priority for resource management decision-making. A new approach to the assessment and management of wild coho salmon, and the associated hatchery production and fishery management is needed. Implementation of parentage-based tagging (PBT) may overcome problems associated with coded-wire tag-based (CWT) assessment and management of coho salmon fisheries, providing at a minimum information equivalent to that derived from the CWT program. PBT and genetic stock identification (GSI) were used to identify coho salmon sampled in fisheries (8,006 individuals) and escapements (1,692 individuals) in British Columbia to specific conservation units (CU), populations, and broodyears. Individuals were genotyped at 304 single nucleotide polymorphisms (SNPs) via direct sequencing of amplicons. Very high accuracy of assignment to population (100%) via PBT for 543 jack (age 2) assigned to correct age and collection location and 265 coded-wire tag (CWT, age 3) coho salmon assigned to correct age and release location was observed, with a 40,774-individual, 267-population baseline available for assignment. Coho salmon from un-CWTed enhanced populations contributed 65% of the catch in southern recreational fisheries in 2017. Application of a PBT-GSI system of identification to individuals in 2017 fisheries and escapements provided high-resolution estimates of stock composition, catch, and exploitation rate by CU or population, providing an alternate and more effective method in the assessment and management of Canadian-origin coho salmon relative to CWTs, and an opportunity for a genetic-based system to replace the current CWT system for coho salmon assessment.
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Affiliation(s)
- Terry D. Beacham
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Colin Wallace
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Kim Jonsen
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - Brenda McIntosh
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - John R. Candy
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
| | - David Willis
- Fisheries and Oceans CanadaRegional HeadquartersVancouverBCCanada
| | - Cheryl Lynch
- Fisheries and Oceans CanadaRegional HeadquartersVancouverBCCanada
| | - Jean‐Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Ruth E. Withler
- Fisheries and Oceans CanadaPacific Biological StationNanaimoBCCanada
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22
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Anadromy Redux? Genetic Analysis to Inform Development of an Indigenous American River Steelhead Broodstock. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2019. [DOI: 10.3996/072018-jfwm-063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The construction of dams and water diversions has severely limited access to spawning habitat for anadromous fishes. To mitigate for these impacts, hatchery programs rear and release millions of juvenile salmonids, including steelhead, the anadromous ecotype of the species Oncorhynchus mykiss. These programs sometimes use nonindigenous broodstock sources that may have negative effects on wild populations. In California, however, only one anadromous fish hatchery program currently uses nonnative broodstock: the steelhead program at Nimbus Fish Hatchery on the American River, a tributary of the Sacramento River in the California Central Valley. The goal of this study was to determine if potentially appropriate sources to replace the broodstock for the Nimbus Hatchery steelhead program exist in the Upper American River, above Nimbus and Folsom dams. We show that all Upper American River O. mykiss sampled share ancestry with other populations in the Central Valley steelhead distinct population segment, with limited introgression from out-of-basin sources in some areas. Furthermore, some Upper American River populations retain adaptive genomic variation associated with a migratory life history, supporting the hypothesis that these populations display adfluvial migratory behavior. Together, these results provide insights into the evolution of trout populations above barrier dams. We conclude that some Upper American River O. mykiss populations represent genetically appropriate sources from which fisheries managers could potentially develop a new broodstock for the Nimbus Hatchery steelhead program to reestablish a native anadromous population in the Lower American River and contribute to recovery of the threatened Central Valley steelhead distinct population segment.
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23
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Microhaplotypes provide increased power from short‐read
DNA
sequences for relationship inference. Mol Ecol Resour 2017; 18:296-305. [DOI: 10.1111/1755-0998.12737] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/19/2017] [Accepted: 11/01/2017] [Indexed: 12/17/2022]
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24
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Pearse DE. Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. JOURNAL OF FISH BIOLOGY 2016; 89:2697-2716. [PMID: 27723095 DOI: 10.1111/jfb.13168] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.
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Affiliation(s)
- D E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA, 95060, U.S.A
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25
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Leitwein M, Garza JC, Pearse DE. Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout ( Oncorhynchus mykiss) in the San Francisco bay area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evol Appl 2016; 10:56-67. [PMID: 28035235 PMCID: PMC5192794 DOI: 10.1111/eva.12416] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/10/2016] [Indexed: 01/01/2023] Open
Abstract
The streams draining of into San Francisco Bay, California, have been impacted by habitat alteration for over 150 years, and roads, dams, water diversions, and other impediments now block the paths of many aquatic migratory species. These changes can affect the genetic structure of fish populations, as well as driving adaptive evolution to novel environmental conditions. Here, we determine the evolutionary relationships of San Francisco Bay Area steelhead/rainbow trout (Oncorhynchus mykiss) populations and show that (i) they are more closely related to native coastal steelhead than to the California Central Valley lineage, with no evidence of introgression by domesticated hatchery rainbow trout, (ii) populations above and below barriers within watersheds are each other's closest relatives, and (iii) adaptive genomic variation associated with migratory life-history traits in O. mykiss shows substantial evolutionary differences between fish above and below dams. These findings support continued habitat restoration and protection of San Francisco Bay Area O. mykiss populations and demonstrate that ecological conditions in novel habitats above barriers to anadromy influence life-history evolution. We highlight the importance of considering the adaptive landscape in conservation and restoration programs for species living in highly modified habitats, particularly with respect to key life-history traits.
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Affiliation(s)
- Maeva Leitwein
- Technopôle Brest-Iroiserue Dumont d'Urville Institut Universitaire Européen de la Mer (IUEM) University of Brest Plouzané France; Institute of Marine Sciences University of California Santa Cruz CA USA; Present address: Institut des Sciences de l'Evolution de Montpellier (ISEM) UMR 5554 Université de ´Montpellier Montpellier Cedex 5 France
| | - John Carlos Garza
- Institute of Marine Sciences University of California Santa Cruz CA USA; Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service Santa Cruz CA USA
| | - Devon E Pearse
- Institute of Marine Sciences University of California Santa Cruz CA USA; Fisheries Ecology Division Southwest Fisheries Science Center National Marine Fisheries Service Santa Cruz CA USA
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Ackerman MW, Hand BK, Waples RK, Luikart G, Waples RS, Steele CA, Garner BA, McCane J, Campbell MR. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead. Evol Appl 2016; 10:146-160. [PMID: 28127391 PMCID: PMC5253425 DOI: 10.1111/eva.12433] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 01/21/2023] Open
Abstract
Effective population size (Ne) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region.
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Affiliation(s)
- Michael W Ackerman
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA; Present address: Michael W. Ackerman, Quantitative Consultants, Inc.705 S 8th St.Boise ID 83702 USA
| | - Brian K Hand
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Gordon Luikart
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Robin S Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
| | - Craig A Steele
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA
| | - Brittany A Garner
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Jesse McCane
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA
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Abadía-Cardoso A, Pearse DE, Jacobson S, Marshall J, Dalrymple D, Kawasaki F, Ruiz-Campos G, Garza JC. Population genetic structure and ancestry of steelhead/rainbow trout (Oncorhynchus mykiss) at the extreme southern edge of their range in North America. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0814-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Phillis CC, Moore JW, Buoro M, Hayes SA, Garza JC, Pearse DE. Shifting Thresholds: Rapid Evolution of Migratory Life Histories in Steelhead/Rainbow Trout, Oncorhynchus mykiss. J Hered 2015; 107:51-60. [PMID: 26585381 DOI: 10.1093/jhered/esv085] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 10/07/2015] [Indexed: 11/13/2022] Open
Abstract
Expression of phenotypic plasticity depends on reaction norms adapted to historic selective regimes; anthropogenic changes in these selection regimes necessitate contemporary evolution or declines in productivity and possibly extinction. Adaptation of conditional strategies following a change in the selection regime requires evolution of either the environmentally influenced cue (e.g., size-at-age) or the state (e.g., size threshold) at which an individual switches between alternative tactics. Using a population of steelhead (Oncorhynchus mykiss) introduced above a barrier waterfall in 1910, we evaluate how the conditional strategy to migrate evolves in response to selection against migration. We created 9 families and 917 offspring from 14 parents collected from the above- and below-barrier populations. After 1 year of common garden-rearing above-barrier offspring were 11% smaller and 32% lighter than below-barrier offspring. Using a novel analytical approach, we estimate that the mean size at which above-barrier fish switch between the resident and migrant tactic is 43% larger than below-barrier fish. As a result, above-barrier fish were 26% less likely to express the migratory tactic. Our results demonstrate how rapid and opposing changes in size-at-age and threshold size contribute to the contemporary evolution of a conditional strategy and indicate that migratory barriers may elicit rapid evolution toward the resident life history on timescales relevant for conservation and management of conditionally migratory species.
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Affiliation(s)
- Corey C Phillis
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis).
| | - Jonathan W Moore
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Mathieu Buoro
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Sean A Hayes
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - John Carlos Garza
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
| | - Devon E Pearse
- From the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95060 (Phillis, Moore, and Pearse); Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada (Phillis and Moore); Department of Environmental Science, Policy, & Management, University of California, Berkeley, 130 Mulford Hall, Berkeley, CA 94720 (Buoro); Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Rd., Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); Institute of Marine Sciences, University of California, Santa Cruz, CA 95060 (Hayes, Garza, and Pearse); and Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, 2725 Montlake Blvd. East, Seattle, WA 98112 (Phillis)
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Parallel evolution of the summer steelhead ecotype in multiple populations from Oregon and Northern California. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0769-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Quantitative genetics of migration-related traits in rainbow and steelhead trout. G3-GENES GENOMES GENETICS 2015; 5:873-89. [PMID: 25784164 PMCID: PMC4426373 DOI: 10.1534/g3.114.016469] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Rainbow trout (Oncorhynchus mykiss) exhibit remarkable life history diversity throughout their native range, and among the most evident is variation in migratory propensity. Although some populations and ecotypes will remain resident in freshwater habitats throughout their life history, others have the ability to undertake tremendous marine migrations. Those that migrate undergo a suite of behavioral, morphological, and physiological adaptations in a process called smoltification. We describe a quantitative genetic analysis of 22 growth, size, and morphological traits in addition to overall life history classification (resident or migrant) over the temporal process of smoltification in a large multi-generation experimental pedigree (n = 16,139) of migratory and resident rainbow trout derived from a wild population, which naturally segregates for migratory propensity. We identify significant additive genetic variance and covariance among the suite of traits that make up a component of the migratory syndrome in this species. Additionally, we identify high heritability estimates for the life history classifications and observe a strong negative genetic correlation between the migratory and resident life history trajectories. Given the large heritability estimates of all of the traits that segregate between migratory and resident rainbow trout, we conclude that these traits can respond to selection. However, given the high degree of genetic correlation between these traits, they do not evolve in isolation, but rather as a suite of coordinated characters in a predictable manner.
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31
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Morbey YE, Jensen EL, Russello MA. Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive life span. Ecol Evol 2014; 4:3714-22. [PMID: 25478160 PMCID: PMC4224543 DOI: 10.1002/ece3.1214] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 11/23/2022] Open
Abstract
Seasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort.
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Affiliation(s)
- Yolanda E Morbey
- Department of Biology, Western University London, Ontario, N6A 5B7, Canada
| | - Evelyn L Jensen
- Department of Biology, University of British Columbia, Okanagan Campus Kelowna, British Columbia, V1V 1V7, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus Kelowna, British Columbia, V1V 1V7, Canada
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32
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Small MP, Johnson TH, Bowman C, Martinez E. Genetic assessment of a summer chum salmon metapopulation in recovery. Evol Appl 2014; 7:266-85. [PMID: 24567747 PMCID: PMC3927888 DOI: 10.1111/eva.12118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 09/16/2013] [Indexed: 11/30/2022] Open
Abstract
Programs to rebuild imperiled wild fish populations often include hatchery-born fish derived from wild populations to supplement natural spawner abundance. These programs require monitoring to determine their demographic, biological, and genetic effects. In 1990s in Washington State, the Summer Chum Salmon Conservation Initiative developed a recovery program for the threatened Hood Canal summer chum salmon Evolutionarily Significant Unit (ESU) (the metapopulation) that used in-river spawners (wild fish) for each respective supplementation broodstock in six tributaries. Returning spawners (wild-born and hatchery-born) composed subsequent broodstocks, and tributary-specific supplementation was limited to three generations. We assessed impacts of the programs on neutral genetic diversity in this metapopulation using 16 microsatellite loci and a thirty-year dataset spanning before and after supplementation, roughly eight generations. Following supplementation, differentiation among subpopulations decreased (but not significantly) and isolation by distance patterns remained unchanged. There was no decline in genetic diversity in wild-born fish, but hatchery-born fish sampled in the same spawning areas had significantly lower genetic diversity and unequal family representation. Despite potential for negative effects from supplementation programs, few were detected in wild-born fish. We hypothesize that chum salmon natural history makes them less vulnerable to negative impacts from hatchery supplementation.
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Affiliation(s)
- Maureen P Small
- Washington Department of Fish and Wildlife, Molecular Genetics Laboratory Olympia, WA, USA
| | | | - Cherril Bowman
- Washington Department of Fish and Wildlife, Molecular Genetics Laboratory Olympia, WA, USA
| | - Edith Martinez
- Washington Department of Fish and Wildlife, Molecular Genetics Laboratory Olympia, WA, USA
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