1
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Miettinen A, Romakkaniemi A, Dannewitz J, Pakarinen T, Palm S, Persson L, Östergren J, Primmer CR, Pritchard VL. Temporal allele frequency changes in large-effect loci reveal potential fishing impacts on salmon life-history diversity. Evol Appl 2024; 17:e13690. [PMID: 38681510 PMCID: PMC11046039 DOI: 10.1111/eva.13690] [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: 08/15/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024] Open
Abstract
Fishing has the potential to influence the life-history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large-effect loci linked with ecologically important life-history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93-year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping-by-sequencing approach (GT-seq), we discovered strong within-season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within-season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life-history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life-history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.
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Affiliation(s)
- Antti Miettinen
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | | | - Johan Dannewitz
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | | | - Stefan Palm
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Lo Persson
- Department of Wildlife, Fish and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Johan Östergren
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
| | - Craig R. Primmer
- Organismal & Evolutionary Biology Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Victoria L. Pritchard
- Institute for Biodiversity & Freshwater ConservationUniversity of the Highlands & IslandsInvernessUK
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2
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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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3
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Willis S, Coykendall DK, Campbell MR, Narum S. Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes. Evol Appl 2024; 17:e13623. [PMID: 38283605 PMCID: PMC10810252 DOI: 10.1111/eva.13623] [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: 09/16/2022] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024] Open
Abstract
Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.
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Affiliation(s)
- Stuart Willis
- Hagerman Genetics LabColumbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
| | | | | | - Shawn Narum
- Hagerman Genetics LabColumbia River Inter‐Tribal Fish CommissionHagermanIdahoUSA
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4
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Fischman RL, Ruhl JB, Forester BR, Lama TM, Kardos M, Rojas GA, Robinson NA, Shirey PD, Lamberti GA, Ando AW, Palumbi S, Wara M, Schwartz MW, Williamson MA, Berger-Wolf T, Beery S, Rolnick D, Kitzes J, Thau D, Tuia D, Rubenstein D, Hickman CR, Thorstenson J, Kaebnick GE, Collins JP, Jayaram A, Deleuil T, Zhao Y. A landmark environmental law looks ahead. Science 2023; 382:1348-1355. [PMID: 38127744 DOI: 10.1126/science.adn3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
In late December 1973, the United States enacted what some would come to call "the pitbull of environmental laws." In the 50 years since, the formidable regulatory teeth of the Endangered Species Act (ESA) have been credited with considerable successes, obliging agencies to draw upon the best available science to protect species and habitats. Yet human pressures continue to push the planet toward extinctions on a massive scale. With that prospect looming, and with scientific understanding ever changing, Science invited experts to discuss how the ESA has evolved and what its future might hold. -Brad Wible.
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Affiliation(s)
| | - J B Ruhl
- Vanderbilt University Law School, Nashville, TN, USA
| | | | - Tanya M Lama
- Department of Biological Sciences, Smith College, Northampton, MA, USA
| | - Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, Seattle, WA, USA
| | - Grethel Aguilar Rojas
- Director General, International Union for the Conservation of Nature (IUCN), Gland, Switzerland
| | - Nicholas A Robinson
- Executive Governor, International Council of Environmental Law (ICEL), New York, NY, USA
| | - Patrick D Shirey
- Department of Geology and Environmental Science, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gary A Lamberti
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Amy W Ando
- Department of Agricultural, Environmental, and Development Economics, The Ohio State University, Columbus, OH, USA
| | - Stephen Palumbi
- Department of Oceans and Department of Biology, Stanford University, Stanford, CA, USA
| | - Michael Wara
- Woods Institute for the Environment, Stanford University, Stanford, CA, USA
| | - Mark W Schwartz
- Department of Environmental Science and Policy, University of California, Davis, CA, USA
| | | | - Tanya Berger-Wolf
- Departments of Computer Science and Engineering, Electrical and Computer Engineering, and Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
- Wild Me, Portland, OR, USA
| | - Sara Beery
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Rolnick
- School of Computer Science, McGill University, Montreal, QC, Canada
- Mila-Quebec AI Institute, Montreal, QC, Canada
| | - Justin Kitzes
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - David Thau
- World Wildlife Fund, San Francisco, CA, USA
| | - Devis Tuia
- School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), Sion, Switzerland
| | - Daniel Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Caleb R Hickman
- Office of Fisheries & Wildlife Management, Eastern Band of Cherokee Indians, Cherokee, NC, USA
| | | | | | - James P Collins
- School for the Future of Innovation in Society, Arizona State University, Tempe, AZ, USA
| | | | | | - Ying Zhao
- CITES Secretariat, Geneva, Switzerland
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5
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Hoelzel AR. Where to now with the evolutionarily significant unit? Trends Ecol Evol 2023; 38:1134-1142. [PMID: 37596130 DOI: 10.1016/j.tree.2023.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
The designation of units for conservation has been a necessary but challenging objective since conservation efforts began. Most species are divided, typically by environment, into populations with independent evolutionary trajectories. There are practical conservation objectives for defining these boundaries. Separate genetic clusters provide future evolutionary potential as environments change, and individuals in isolated populations may lose fitness when population size is reduced. The history of the effort to define units is briefly reviewed here, but I focus on finding a process that may facilitate uniform and effective application at a time when conservation urgency is great. I propose a refinement of the designated unit concept, distinguishing between conservation units (CUs) and evolutionarily sustaining conservation units (ESCUs).
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Affiliation(s)
- A Rus Hoelzel
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE, UK.
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6
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Lehnert SJ, Bradbury IR, Wringe BF, Van Wyngaarden M, Bentzen P. Multifaceted framework for defining conservation units: An example from Atlantic salmon ( Salmo salar) in Canada. Evol Appl 2023; 16:1568-1585. [PMID: 37752960 PMCID: PMC10519414 DOI: 10.1111/eva.13587] [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: 05/01/2023] [Revised: 07/12/2023] [Accepted: 07/26/2023] [Indexed: 09/28/2023] Open
Abstract
Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units is done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed "designatable units"; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet criteria of discreteness and significance, and increasing access to "big data" is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. Here, we develop a framework that uses a multifaceted, weight of evidence approach to incorporate multiple data types, including genetic and genomic data, to inform COSEWIC DUs. We apply this framework to delineate DUs of Atlantic salmon (Salmo salar, L.), an economically, culturally, and ecologically significant species, that is also characterized by complex hierarchical population structure. Specifically, we focus on an in-depth example of how our approach was applied to a previously data limited region of northern Canada that was defined by a single large DU. Application of our framework with newly available genetic and genomic data led to subdividing this DU into three new DUs. Although our approach was developed to meet criteria of COSEWIC, it is widely applicable given similarities in the definitions of a conservation unit.
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Affiliation(s)
- Sarah J. Lehnert
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries CentreFisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Bedford Institute of OceanographyFisheries and Oceans CanadaDartmouthNova ScotiaCanada
| | | | - Paul Bentzen
- Biology DepartmentDalhousie UniversityHalifaxNova ScotiaCanada
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7
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Reid BN, Star B, Pinsky ML. Detecting parallel polygenic adaptation to novel evolutionary pressure in wild populations: a case study in Atlantic cod ( Gadus morhua). Philos Trans R Soc Lond B Biol Sci 2023; 378:20220190. [PMID: 37246382 DOI: 10.1098/rstb.2022.0190] [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: 09/26/2022] [Accepted: 02/13/2023] [Indexed: 05/30/2023] Open
Abstract
Populations can adapt to novel selection pressures through dramatic frequency changes in a few genes of large effect or subtle shifts in many genes of small effect. The latter (polygenic adaptation) is expected to be the primary mode of evolution for many life-history traits but tends to be more difficult to detect than changes in genes of large effect. Atlantic cod (Gadus morhua) were subjected to intense fishing pressure over the twentieth century, leading to abundance crashes and a phenotypic shift toward earlier maturation across many populations. Here, we use spatially replicated temporal genomic data to test for a shared polygenic adaptive response to fishing using methods previously applied to evolve-and-resequence experiments. Cod populations on either side of the Atlantic show covariance in allele frequency change across the genome that are characteristic of recent polygenic adaptation. Using simulations, we demonstrate that the degree of covariance in allele frequency change observed in cod is unlikely to be explained by neutral processes or background selection. As human pressures on wild populations continue to increase, understanding and attributing modes of adaptation using methods similar to those demonstrated here will be important in identifying the capacity for adaptive responses and evolutionary rescue. This article is part of the theme issue 'Detecting and attributing the causes of biodiversity change: needs, gaps and solutions'.
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Affiliation(s)
- Brendan N Reid
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
| | - Bastiaan Star
- Center for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066, Blindern, 0316 Oslo, Norway
| | - Malin L Pinsky
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08540, USA
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8
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Andrews KR, Seaborn T, Egan JP, Fagnan MW, New DD, Chen Z, Hohenlohe PA, Waits LP, Caudill CC, Narum SR. Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout. Mol Ecol 2023; 32:800-818. [PMID: 36478624 PMCID: PMC9905331 DOI: 10.1111/mec.16810] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 11/20/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
Aquatic ectotherms are predicted to harbour genomic signals of local adaptation resulting from selective pressures driven by the strong influence of climate conditions on body temperature. We investigated local adaptation in redband trout (Oncorhynchus mykiss gairdneri) using genome scans for 547 samples from 11 populations across a wide range of habitats and thermal gradients in the interior Columbia River. We estimated allele frequencies for millions of single nucleotide polymorphism loci (SNPs) across populations using low-coverage whole genome resequencing, and used population structure outlier analyses to identify genomic regions under divergent selection between populations. Twelve genomic regions showed signatures of local adaptation, including two regions associated with genes known to influence migration and developmental timing in salmonids (GREB1L, ROCK1, SIX6). Genotype-environment association analyses indicated that diurnal temperature variation was a strong driver of local adaptation, with signatures of selection driven primarily by divergence of two populations in the northern extreme of the subspecies range. We also found evidence for adaptive differences between high-elevation desert vs. montane habitats at a smaller geographical scale. Finally, we estimated vulnerability of redband trout to future climate change using ecological niche modelling and genetic offset analyses under two climate change scenarios. These analyses predicted substantial habitat loss and strong genetic shifts necessary for adaptation to future habitats, with the greatest vulnerability predicted for high-elevation desert populations. Our results provide new insight into the complexity of local adaptation in salmonids, and important predictions regarding future responses of redband trout to climate change.
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Affiliation(s)
- Kimberly R Andrews
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Travis Seaborn
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Joshua P Egan
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA.,Bell Museum of Natural History, University of Minnesota, Saint Paul, Minnesota, USA
| | - Matthew W Fagnan
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Daniel D New
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, Idaho, USA
| | - Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA
| | - Paul A Hohenlohe
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, Idaho, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Christopher C Caudill
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, Idaho, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, Idaho, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, Idaho, USA
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9
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May SA, Hard JJ, Ford MJ, Naish KA, Ward EJ. Assortative mating for reproductive timing affects population recruitment and resilience in a quantitative genetic model. Evol Appl 2023; 16:657-672. [PMID: 36969143 PMCID: PMC10033844 DOI: 10.1111/eva.13524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/12/2022] [Indexed: 01/22/2023] Open
Abstract
Quantitative models that simulate the inheritance and evolution of fitness-linked traits offer a method for predicting how environmental or anthropogenic perturbations can affect the dynamics of wild populations. Random mating between individuals within populations is a key assumption of many such models used in conservation and management to predict the impacts of proposed management or conservation actions. However, recent evidence suggests that non-random mating may be underestimated in wild populations and play an important role in diversity-stability relationships. Here we introduce a novel individual-based quantitative genetic model that incorporates assortative mating for reproductive timing, a defining attribute of many aggregate breeding species. We demonstrate the utility of this framework by simulating a generalized salmonid lifecycle, varying input parameters, and comparing model outputs to theoretical expectations for several eco-evolutionary, population dynamic scenarios. Simulations with assortative mating systems resulted in more resilient and productive populations than those that were randomly mating. In accordance with established ecological and evolutionary theory, we also found that decreasing the magnitude of trait correlations, environmental variability, and strength of selection each had a positive effect on population growth. Our model is constructed in a modular framework so that future components can be easily added to address pressing issues such as the effects of supportive breeding, variable age structure, differential selection by sex or age, and fishery interactions on population growth and resilience. With code published in a public Github repository, model outputs may easily be tailored to specific study systems by parameterizing with empirically generated values from long-term ecological monitoring programs.
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Affiliation(s)
- Samuel A. May
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Jeffrey J. Hard
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
| | - Michael J. Ford
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Eric J. Ward
- NOAA Fisheries Northwest Fisheries Science Center Seattle Washington USA
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10
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Guo C, Zhang X, Li Y, Xie J, Gao P, Hao P, Han L, Zhang J, Wang W, Liu P, Ding J, Chang Y. Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus. BMC Genomics 2023; 24:25. [PMID: 36647018 PMCID: PMC9843871 DOI: 10.1186/s12864-023-09113-x] [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: 08/22/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Apostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown. RESULT In this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses. CONCLUSIONS This study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
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Affiliation(s)
- Chao Guo
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Xianglei Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yuanxin Li
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jiahui Xie
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pingping Gao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Pengfei Hao
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Lingshu Han
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China ,grid.203507.30000 0000 8950 5267Ningbo University, Ningbo, Zhejiang 315211 People’s Republic of China
| | - Jinyuan Zhang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Wenpei Wang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Peng Liu
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Jun Ding
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
| | - Yaqing Chang
- grid.410631.10000 0001 1867 7333Key Laboratory of Mariculture & Stock Enhancement in North China’s Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning 116023 People’s Republic of China
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11
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Genomic divergence of hatchery- and natural-origin Chinook salmon (Oncorhynchus tshawytscha) in two supplemented populations. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01491-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Lowell N, Suhrbier A, Tarpey C, May S, Carson H, Hauser L. Population structure and adaptive differentiation in the sea cucumber Apostichopus californicus and implications for spatial resource management. PLoS One 2023; 18:e0280500. [PMID: 36928497 PMCID: PMC10019739 DOI: 10.1371/journal.pone.0280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/03/2023] [Indexed: 03/18/2023] Open
Abstract
A growing body of evidence suggests that spatial population structure can develop in marine species despite large population sizes and high gene flow. Characterizing population structure is important for the effective management of exploited species, as it can be used to identify appropriate scales of management in fishery and aquaculture contexts. The California sea cucumber, Apostichopus californicus, is one such exploited species whose management could benefit from further characterization of population structure. Using restriction site-associated DNA (RAD) sequencing, we developed 2075 single nucleotide polymorphisms (SNPs) to quantify genetic structure over a broad section of the species' range along the North American west coast and within the Salish Sea, a region supporting the Washington State A. californicus fishery and developing aquaculture production of the species. We found evidence for population structure (global fixation index (FST) = 0.0068) with limited dispersal driving two patterns of differentiation: isolation-by-distance and a latitudinal gradient of differentiation. Notably, we found detectable population differences among collection sites within the Salish Sea (pairwise FST = 0.001-0.006). Using FST outlier detection and gene-environment association, we identified 10.2% of total SNPs as putatively adaptive. Environmental variables (e.g., temperature, salinity) from the sea surface were more correlated with genetic variation than those same variables measured near the benthos, suggesting that selection on pelagic larvae may drive adaptive differentiation to a greater degree than selection on adults. Our results were consistent with previous estimates of and patterns in population structure for this species in other extents of the range. Additionally, we found that patterns of neutral and adaptive differentiation co-varied, suggesting that adaptive barriers may limit dispersal. Our study provides guidance to decision-makers regarding the designation of management units for A. californicus and adds to the growing body of literature identifying genetic population differentiation in marine species despite large, nominally connected populations.
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Affiliation(s)
- Natalie Lowell
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| | - Andy Suhrbier
- Pacific Shellfish Institute, Olympia, Washington, United States of America
| | - Carolyn Tarpey
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Samuel May
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
| | - Henry Carson
- Washington Department of Fish and Wildlife, Olympia, Washington, United States of America
| | - Lorenz Hauser
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, United States of America
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Meek MH, Beever EA, Barbosa S, Fitzpatrick SW, Fletcher NK, Mittan-Moreau CS, Reid BN, Campbell-Staton SC, Green NF, Hellmann JJ. Understanding Local Adaptation to Prepare Populations for Climate Change. Bioscience 2022. [DOI: 10.1093/biosci/biac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.
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Affiliation(s)
- Mariah H Meek
- Department of Integrative Biology, AgBio Research, and the Ecology, Evolution, and Behavior Program Michigan State University , East Lansing, Michigan, United States
| | - Erik A Beever
- Department of Ecology, Montana State University , Bozeman, Montana, United States
| | - Soraia Barbosa
- Department of Fish and Wildlife Sciences, University of Idaho , Moscow, Idaho, United States
| | - Sarah W Fitzpatrick
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
| | - Nicholas K Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
- Department of Biology, University of Maryland , College Park, Maryland, United States
| | - Cinnamon S Mittan-Moreau
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
| | - Brendan N Reid
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology, Evolution, and Natural Resources, Rutgers University , New Brunswick, New Jersey, United States
| | - Shane C Campbell-Staton
- Department of Ecology and Evolutionary Biology, Princeton University , Princeton, New Jersey, United States
| | - Nancy F Green
- US Fish and Wildlife Service, Falls Church , Virginia, United States
| | - Jessica J Hellmann
- Institute of the Environment and Department of Ecology, Evolution, and Behavior, University of Minnesota , Saint Paul, Minnesota, United States
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Xuereb A, Rougemont Q, Dallaire X, Moore J, Normandeau E, Bougas B, Perreault‐Payette A, Koop BF, Withler R, Beacham T, Bernatchez L. Re‐evaluating Coho salmon (
Oncorhynchus kisutch
) conservation units in Canada using genomic data. Evol Appl 2022; 15:1925-1944. [DOI: 10.1111/eva.13489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amanda Xuereb
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
- CEFE, Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175, CNRS, Univ Montpellier, CNRS, EPHE, IRD Univ Paul Valéry Montpellier Montpellier France
| | - Xavier Dallaire
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Jean‐Sébastien Moore
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Eric Normandeau
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Bérénice Bougas
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Alysse Perreault‐Payette
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Ben F. Koop
- Department of Biology University of Victoria Victoria British Columbia Canada
| | - Ruth Withler
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Terry Beacham
- Department of Fisheries and Ocean Pacific Biological Station Nanaimo British Columbia Canada
| | - Louis Bernatchez
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
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