1
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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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2
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Delomas TA, Willis SC. Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data. BMC Bioinformatics 2023; 24:415. [PMID: 37923981 PMCID: PMC10623847 DOI: 10.1186/s12859-023-05554-z] [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: 07/25/2022] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND Microhaplotypes have the potential to be more cost-effective than SNPs for applications that require genetic panels of highly variable loci. However, development of microhaplotype panels is hindered by a lack of methods for estimating microhaplotype allele frequency from low-coverage whole genome sequencing or pooled sequencing (pool-seq) data. RESULTS We developed new methods for estimating microhaplotype allele frequency from low-coverage whole genome sequence and pool-seq data. We validated these methods using datasets from three non-model organisms. These methods allowed estimation of allele frequency and expected heterozygosity at depths routinely achieved from pooled sequencing. CONCLUSIONS These new methods will allow microhaplotype panels to be designed using low-coverage WGS and pool-seq data to discover and evaluate candidate loci. The python script implementing the two methods and documentation are available at https://www.github.com/delomast/mhFromLowDepSeq .
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Affiliation(s)
- Thomas A Delomas
- Agricultural Research Service, United States Department of Agriculture, National Cold Water Marine Aquaculture Center, 483 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA.
| | - Stuart C Willis
- Hagerman Genetics Laboratory, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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3
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Kurland S, Rafati N, Ryman N, Laikre L. Genomic dynamics of brown trout populations released to a novel environment. Ecol Evol 2022; 12:e9050. [PMID: 35813906 PMCID: PMC9251865 DOI: 10.1002/ece3.9050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/04/2022] [Accepted: 06/04/2022] [Indexed: 11/15/2022] Open
Abstract
Population translocations occur for a variety of reasons, from displacement due to climate change to human‐induced transfers. Such actions have adverse effects on genetic variation and understanding their microevolutionary consequences requires monitoring. Here, we return to an experimental release of brown trout (Salmo trutta) in order to monitor the genomic effects of population translocations. In 1979, fish from each of two genetically (FST = 0.16) and ecologically separate populations were simultaneously released, at one point in time, to a lake system previously void of brown trout. Here, whole‐genome sequencing of pooled DNA (Pool‐seq) is used to characterize diversity within and divergence between the introduced populations and fish inhabiting two lakes downstream of the release sites, sampled 30 years later (c. 5 generations). Present results suggest that while extensive hybridization has occurred, the two introduced populations are unequally represented in the lakes downstream of the release sites. One population, which is ecologically resident in its original habitat, mainly contributes to the lake closest to the release site. The other population, migratory in its natal habitat, is genetically more represented in the lake further downstream. Genomic regions putatively under directional selection in the new habitat are identified, where allele frequencies in both established populations are more similar to the introduced population stemming from a resident population than the migratory one. Results suggest that the microevolutionary consequences of population translocations, for example, hybridization and adaptation, can be rapid and that Pool‐seq can be used as an initial tool to monitor genome‐wide effects.
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Affiliation(s)
- Sara Kurland
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Nima Rafati
- Department of Medical Biochemistry and MicrobiologyNational Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala UniversityUppsalaSweden
| | - Nils Ryman
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
| | - Linda Laikre
- Department of Zoology, Division of Population GeneticsStockholm UniversityStockholmSweden
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4
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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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5
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Salisbury SJ, Ruzzante DE. Genetic Causes and Consequences of Sympatric Morph Divergence in Salmonidae: A Search for Mechanisms. Annu Rev Anim Biosci 2021; 10:81-106. [PMID: 34758272 DOI: 10.1146/annurev-animal-051021-080709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Repeatedly and recently evolved sympatric morphs exhibiting consistent phenotypic differences provide natural experimental replicates of speciation. Because such morphs are observed frequently in Salmonidae, this clade provides a rare opportunity to uncover the genomic mechanisms underpinning speciation. Such insight is also critical for conserving salmonid diversity, the loss of which could have significant ecological and economic consequences. Our review suggests that genetic differentiation among sympatric morphs is largely nonparallel apart from a few key genes that may be critical for consistently driving morph differentiation. We discuss alternative levels of parallelism likely underlying consistent morph differentiation and identify several factors that may temper this incipient speciation between sympatric morphs, including glacial history and contemporary selective pressures. Our synthesis demonstrates that salmonids are useful for studying speciation and poses additional research questions to be answered by future study of this family. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- S J Salisbury
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
| | - D E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada; ,
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6
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Hale MC, Campbell MA, McKinney GJ. A candidate chromosome inversion in Arctic charr (Salvelinus alpinus) identified by population genetic analysis techniques. G3-GENES GENOMES GENETICS 2021; 11:6329827. [PMID: 34568922 PMCID: PMC8473973 DOI: 10.1093/g3journal/jkab267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 11/13/2022]
Abstract
The "genomics era" has allowed questions to be asked about genome organization and genome architecture of non-model species at a rate not previously seen. Analyses of these genome-wide datasets have documented many examples of novel structural variants (SVs) such as chromosomal inversions, copy number variants, and chromosomal translocations, many of which have been linked to adaptation. The salmonids are a taxonomic group with abundant genome-wide datasets due to their importance in aquaculture and fisheries. However, the number of documented SVs in salmonids is surprisingly low and is most likely due to removing loci in high linkage disequilibrium when analyzing structure and gene flow. Here we re-analyze RAD-seq data from several populations of Arctic charr (Salvelinus alpinus) and document a novel ∼1.2 MB SV at the distal end of LG12. This variant contains 15 protein-coding genes connected to a wide-range of functions including cell adhesion and signal transduction. Interestingly, we studied the frequency of this polymorphism in four disjointed populations of charr-one each from Nunavut, Newfoundland, Eastern Russia, and Scotland-and found evidence of the variant only in Nunavut, Canada, suggesting the polymorphism is novel and recently evolved.
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Affiliation(s)
- Matthew C Hale
- Department of Biology, Texas Christian University, Fort Worth, TX 76129, USA
| | - Matthew A Campbell
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA.,University of Alaska Museum, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Garrett J McKinney
- National Research Council Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA
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7
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Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop. J Hered 2021; 111:227-236. [PMID: 32037446 PMCID: PMC7117792 DOI: 10.1093/jhered/esaa001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
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Affiliation(s)
- Amanda Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Donavan Bell
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Tashi Dhendup
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Department of Forest and Park Services, Ugyen Wangchuck Institute for Conservation and Environmental Research, Bumthang, Bhutan
| | - Brooke Kern
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Samuel Pannoni
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Zachary Robinson
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Jeffrey Strait
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Seth Smith
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Brian K Hand
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Gordon Luikart
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
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8
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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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9
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Emami-Khoyi A, Le Roux R, Adair MG, Monsanto DM, Main DC, Parbhu SP, Schnelle CM, van der Lingen CD, Jansen van Vuuren B, Teske PR. Transcriptomic Diversity in the Livers of South African Sardines Participating in the Annual Sardine Run. Genes (Basel) 2021; 12:genes12030368. [PMID: 33806647 PMCID: PMC8001748 DOI: 10.3390/genes12030368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/18/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022] Open
Abstract
During austral winter, the southern and eastern coastlines of South Africa witness one of the largest animal migrations on the planet, the KwaZulu-Natal sardine run. Hundreds of millions of temperate sardines, Sardinops sagax, form large shoals that migrate north-east towards the subtropical Indian Ocean. Recent studies have highlighted the role that genetic and environmental factors play in sardine run formation. In the present study, we used massively parallel sequencing to assemble and annotate the first reference transcriptome from the liver cells of South African sardines, and to investigate the functional content and transcriptomic diversity. A total of 1,310,530 transcripts with an N50 of 1578 bp were assembled de novo. Several genes and core biochemical pathways that modulate energy production, energy storage, digestion, secretory processes, immune responses, signaling, regulatory processes, and detoxification were identified. The functional content of the liver transcriptome from six individuals that participated in the 2019 sardine run demonstrated heterogeneous levels of variation. Data presented in the current study provide new insights into the complex function of the liver transcriptome in South African sardines.
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Affiliation(s)
- Arsalan Emami-Khoyi
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Rynhardt Le Roux
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Matthew G. Adair
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Daniela M. Monsanto
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Devon C. Main
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Shilpa P. Parbhu
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Claudia M. Schnelle
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Carl D. van der Lingen
- Branch: Fisheries Management, Department of Environment, Forestry and Fisheries, Private Bag X2, Vlaeberg 8012, South Africa;
- Department of Biological Sciences and Marine Research Institute, University of Cape Town, Private Bag X3, Rondebosch 7700, South Africa
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
| | - Peter R. Teske
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa; (A.E.-K.); (R.L.R.); (M.G.A.); (D.M.M.); (D.C.M.); (S.P.P.); (C.M.S.); (B.J.v.V.)
- Correspondence:
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10
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Genetic interactions among native and introduced stocks of Oncorhynchus mykiss in the upper Willamette River, Oregon. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01322-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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The Impacts of Dam Construction and Removal on the Genetics of Recovering Steelhead ( Oncorhynchus mykiss) Populations across the Elwha River Watershed. Genes (Basel) 2021; 12:genes12010089. [PMID: 33450806 PMCID: PMC7828262 DOI: 10.3390/genes12010089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 11/25/2022] Open
Abstract
Dam construction and longitudinal river habitat fragmentation disrupt important life histories and movement of aquatic species. This is especially true for Oncorhynchus mykiss that exhibits both migratory (steelhead) and non-migratory (resident rainbow) forms. While the negative effects of dams on salmonids have been extensively documented, few studies have had the opportunity to compare population genetic diversity and structure prior to and following dam removal. Here we examine the impacts of the removal of two dams on the Elwha River on the population genetics of O. mykiss. Genetic data were produced from >1200 samples collected prior to dam removal from both life history forms, and post-dam removal from steelhead. We identified three genetic clusters prior to dam removal primarily explained by isolation due to dams and natural barriers. Following dam removal, genetic structure decreased and admixture increased. Despite large O. mykiss population declines after dam construction, we did not detect shifts in population genetic diversity or allele frequencies of loci putatively involved in migratory phenotypic variation. Steelhead descendants from formerly below and above dammed populations recolonized the river rapidly after dam removal, suggesting that dam construction did not significantly reduce genetic diversity underlying O. mykiss life history strategies. These results have significant evolutionary implications for the conservation of migratory adaptive potential in O. mykiss populations above current anthropogenic barriers.
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12
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Abstract
Diadromy, the predictable movements of individuals between marine and freshwater environments, is biogeographically and phylogenetically widespread across fishes. Thus, despite the high energetic and potential fitness costs involved in moving between distinct environments, diadromy appears to be an effective life history strategy. Yet, the origin and molecular mechanisms that underpin this migratory behavior are not fully understood. In this review, we aim first to summarize what is known about diadromy in fishes; this includes the phylogenetic relationship among diadromous species, a description of the main hypotheses regarding its origin, and a discussion of the presence of non-migratory populations within diadromous species. Second, we discuss how recent research based on -omics approaches (chiefly genomics, transcriptomics, and epigenomics) is beginning to provide answers to questions on the genetic bases and origin(s) of diadromy. Finally, we suggest future directions for -omics research that can help tackle questions on the evolution of diadromy.
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Affiliation(s)
- M. Lisette Delgado
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Daniel E. Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
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13
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Willis SC, Hess JE, Fryer JK, Whiteaker JM, Brun C, Gerstenberger R, Narum SR. Steelhead ( Oncorhynchus mykiss) lineages and sexes show variable patterns of association of adult migration timing and age-at-maturity traits with two genomic regions. Evol Appl 2020; 13:2836-2856. [PMID: 33294026 PMCID: PMC7691471 DOI: 10.1111/eva.13088] [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: 05/18/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age-at-maturity in steelhead (Oncorhynchus mykiss) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead (R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139-0.170; females R 2 = 0.096-0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock-specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.
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Affiliation(s)
- Stuart C. Willis
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Jon E. Hess
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
| | - Jeff K. Fryer
- Fishery Science DepartmentColumbia River Inter‐Tribal Fish CommissionPortlandORUSA
| | - John M. Whiteaker
- Fishery Science DepartmentColumbia River Inter‐Tribal Fish CommissionPortlandORUSA
| | - Chris Brun
- Branch of Natural Resources – Fisheries, Confederated Tribes of Warm SpringsPortlandORUSA
| | - Ryan Gerstenberger
- Branch of Natural Resources – Fisheries, Confederated Tribes of Warm SpringsPortlandORUSA
| | - Shawn R. Narum
- Hagerman Genetics LaboratoryColumbia River Inter‐Tribal Fish CommissionHagermanIDUSA
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14
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Chen Z, Narum SR. Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout. Mol Ecol 2020; 30:162-174. [PMID: 33135227 DOI: 10.1111/mec.15717] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/18/2022]
Abstract
Adaptation to local environments involves evolution of ecologically important traits and underlying physiological processes. Here, we used low coverage whole-genome resequencing (lcWGR) on individuals to identify genome regions involved in thermal adaptation in wild redband trout Oncorhynchus mykiss gairdneri, a subspecies of rainbow trout that inhabits ecosystems ranging from cold montane forests to high elevation deserts. This study includes allele frequency-based analyses for selective sweeps among populations, followed by multiple association tests for specific sets of phenotypes measured under thermal stress (acute and chronic survival/mortality; high or low cardiac performance groups). Depending on the groups in each set of analyses, sequencing reads covered 43%-75% of the genome at ≥15× and each analysis included millions of SNPs across the genome. In tests for selective sweeps among populations, a total of six chromosomal regions were significant. The further association tests for specific phenotypes revealed that the region on chromosome 4 was consistently the most significant and contains the cerk gene (ceramide kinase). This study provides insight into a potential genetic mechanism of local thermal adaptation and suggests cerk may be an important candidate gene. However, further validation of this cerk gene is necessary to determine if the association with cardiac performance results in a functional role to influence thermal performance when exposed to high water temperatures and hypoxic conditions.
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Affiliation(s)
- Zhongqi Chen
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA
| | - Shawn R Narum
- Aquaculture Research Institute, University of Idaho, Hagerman, ID, USA.,Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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15
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Affiliation(s)
- Garrett McKinney
- National Research Council Research Associateship Program, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112, USA.
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16
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The sockeye salmon genome, transcriptome, and analyses identifying population defining regions of the genome. PLoS One 2020; 15:e0240935. [PMID: 33119641 PMCID: PMC7595290 DOI: 10.1371/journal.pone.0240935] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022] Open
Abstract
Sockeye salmon (Oncorhynchus nerka) is a commercially and culturally important species to the people that live along the northern Pacific Ocean coast. There are two main sockeye salmon ecotypes—the ocean-going (anadromous) ecotype and the fresh-water ecotype known as kokanee. The goal of this study was to better understand the population structure of sockeye salmon and identify possible genomic differences among populations and between the two ecotypes. In pursuit of this goal, we generated the first reference sockeye salmon genome assembly and an RNA-seq transcriptome data set to better annotate features of the assembly. Resequenced whole-genomes of 140 sockeye salmon and kokanee were analyzed to understand population structure and identify genomic differences between ecotypes. Three distinct geographic and genetic groups were identified from analyses of the resequencing data. Nucleotide variants in an immunoglobulin heavy chain variable gene cluster on chromosome 26 were found to differentiate the northwestern group from the southern and upper Columbia River groups. Several candidate genes were found to be associated with the kokanee ecotype. Many of these genes were related to ammonia tolerance or vision. Finally, the sex chromosomes of this species were better characterized, and an alternative sex-determination mechanism was identified in a subset of upper Columbia River kokanee.
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17
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Koch IJ, Narum SR. Validation and association of candidate markers for adult migration timing and fitness in Chinook Salmon. Evol Appl 2020; 13:2316-2332. [PMID: 33005226 PMCID: PMC7513726 DOI: 10.1111/eva.13026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 01/02/2023] Open
Abstract
Recent studies have begun to elucidate the genetic basis for phenotypic traits in salmonid species, but many questions remain before these candidate genes can be directly incorporated into conservation management. In Chinook Salmon (Oncorhynchus tshawytscha), a region of major effect for migration timing has been discovered that harbors two adjacent candidate genes (greb1L, rock1), but there has been limited work to examine the association between these genes and migratory phenotypes at the individual, compared to the population, level. To provide a more thorough test of individual phenotypic association within lineages of Chinook Salmon, 33 candidate markers were developed across a 220 Kb region on chromosome 28 previously associated with migration timing. Candidate and neutral markers were genotyped in individuals from representative collections that exhibit phenotypic variation in timing of arrival to spawning grounds from each of three lineages of Chinook Salmon. Association tests confirmed the majority of markers on chromosome 28 were significantly associated with arrival timing and the strongest association was consistently observed for markers within the rock1 gene and the intergenic region between greb1L and rock1. Candidate markers alone explained a wide range of phenotypic variation for Lower Columbia and Interior ocean-type lineages (29% and 78%, respectively), but less for the Interior stream-type lineage (5%). Individuals that were heterozygous at markers within or upstream of rock1 had phenotypes that suggested a pattern of dominant inheritance for early arrival across populations. Finally, previously published fitness estimates from the Interior stream-type lineage enabled tests of association with arrival timing and two candidate markers, which revealed that fish with homozygous mature genotypes had slightly higher fitness than fish with premature genotypes, while heterozygous fish were intermediate. Overall, these results provide additional information for individual-level genetic variation associated with arrival timing that may assist with conservation management of this species.
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Affiliation(s)
- Ilana J Koch
- Columbia River Inter-Tribal Fish Commission Hagerman ID USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman ID USA
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18
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Hess JE, Smith JJ, Timoshevskaya N, Baker C, Caudill CC, Graves D, Keefer ML, Kinziger AP, Moser ML, Porter LL, Silver G, Whitlock SL, Narum SR. Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey. Mol Ecol 2020; 29:3841-3856. [PMID: 32814354 DOI: 10.1111/mec.15605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/26/2020] [Accepted: 08/14/2020] [Indexed: 12/26/2022]
Abstract
High rates of dispersal can breakdown coadapted gene complexes. However, concentrated genomic architecture (i.e., genomic islands of divergence) can suppress recombination to allow evolution of local adaptations despite high gene flow. Pacific lamprey (Entosphenus tridentatus) is a highly dispersive anadromous fish. Observed trait diversity and evidence for genetic basis of traits suggests it may be locally adapted. We addressed whether concentrated genomic architecture could influence local adaptation for Pacific lamprey. Using two new whole genome assemblies and genotypes from 7,716 single nucleotide polymorphism (SNP) loci in 518 individuals from across the species range, we identified four genomic islands of divergence (on chromosomes 01, 02, 04, and 22). We determined robust phenotype-by-genotype relationships by testing multiple traits across geographic sites. These trait associations probably explain genomic divergence across the species' range. We genotyped a subset of 302 broadly distributed SNPs in 2,145 individuals for association testing for adult body size, sexual maturity, migration distance and timing, adult swimming ability, and larval growth. Body size traits were strongly associated with SNPs on chromosomes 02 and 04. Moderate associations also implicated SNPs on chromosome 01 as being associated with variation in female maturity. Finally, we used candidate SNPs to extrapolate a heterogeneous spatiotemporal distribution of these predicted phenotypes based on independent data sets of larval and adult collections. These maturity and body size results guide future elucidation of factors driving regional optimization of these traits for fitness. Pacific lamprey is culturally important and imperiled. This research addresses biological uncertainties that challenge restoration efforts.
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Affiliation(s)
- Jon E Hess
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | | | - Cyndi Baker
- Oregon Department of Fish and Wildlife, Clackamas, OR, USA
| | | | - David Graves
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | | | | | - Laurie L Porter
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | - Greg Silver
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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19
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Collins EE, Hargrove JS, Delomas TA, Narum SR. Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin. Ecol Evol 2020; 10:9486-9502. [PMID: 32953077 PMCID: PMC7487220 DOI: 10.1002/ece3.6641] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 12/05/2022] Open
Abstract
Fish migrations are energetically costly, especially when moving between freshwater and saltwater, but are a viable strategy for Pacific salmon and trout (Oncorhynchus spp.) due to the advantageous resources available at various life stages. Anadromous steelhead (O. mykiss) migrate vast distances and exhibit variation for adult migration phenotypes that have a genetic basis at candidate genes known as greb1L and rock1. We examined the distribution of genetic variation at 13 candidate markers spanning greb1L, intergenic, and rock1 regions versus 226 neutral markers for 113 populations (n = 9,471) of steelhead from inland and coastal lineages in the Columbia River. Patterns of population structure with neutral markers reflected genetic similarity by geographic region as demonstrated in previous studies, but candidate markers clustered populations by genetic variation associated with adult migration timing. Mature alleles for late migration had the highest frequency overall in steelhead populations throughout the Columbia River, with only 9 of 113 populations that had a higher frequency of premature alleles for early migration. While a single haplotype block was evident for the coastal lineage, we identified multiple haplotype blocks for the inland lineage. The inland lineage had one haplotype block that corresponded to candidate markers within the greb1L gene and immediately upstream in the intergenic region, and the second block only contained candidate markers from the intergenic region. Haplotype frequencies had similar patterns of geographic distribution as single markers, but there were distinct differences in frequency between the two haplotype blocks for the inland lineage. This may represent multiple recombination events that differed between lineages where phenotypic differences exist between freshwater entry versus arrival timing as indicated by Micheletti et al. (2018a). Redundancy analyses were used to model environmental effects on allelic frequencies of candidate markers, and significant variables were migration distance, temperature, isothermality, and annual precipitation. This study improves our understanding of the spatial distribution of genetic variation underlying adult migration timing in steelhead as well as associated environmental factors and has direct conservation and management implications.
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Affiliation(s)
| | - John S. Hargrove
- Eagle Fish Genetics LabPacific States Marine Fisheries CommissionEagleIDUSA
| | - Thomas A. Delomas
- Eagle Fish Genetics LabPacific States Marine Fisheries CommissionEagleIDUSA
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish CommissionHagermanIDUSA
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20
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Horn RL, Kamphaus C, Murdoch K, Narum SR. Detecting genomic variation underlying phenotypic characteristics of reintroduced Coho salmon (Oncorhynchus kisutch). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01307-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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21
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Oomen RA, Kuparinen A, Hutchings JA. Consequences of Single-Locus and Tightly Linked Genomic Architectures for Evolutionary Responses to Environmental Change. J Hered 2020; 111:319-332. [PMID: 32620014 PMCID: PMC7423069 DOI: 10.1093/jhered/esaa020] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 06/25/2020] [Indexed: 12/26/2022] Open
Abstract
Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modeling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
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Affiliation(s)
- Rebekah A Oomen
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Jeffrey A Hutchings
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
- Department of Biology, Dalhousie University, Halifax, NS, Canada
- Institute of Marine Research, Flødevigen Marine Research Station, His, Norway
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22
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McKinney G, McPhee MV, Pascal C, Seeb JE, Seeb LW. Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon. G3 (BETHESDA, MD.) 2020; 10:1553-1561. [PMID: 32165371 PMCID: PMC7202013 DOI: 10.1534/g3.119.400972] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/28/2020] [Indexed: 11/26/2022]
Abstract
Many studies exclude loci that exhibit linkage disequilibrium (LD); however, high LD can signal reduced recombination around genomic features such as chromosome inversions or sex-determining regions. Chromosome inversions and sex-determining regions are often involved in adaptation, allowing for the inheritance of co-adapted gene complexes and for the resolution of sexually antagonistic selection through sex-specific partitioning of genetic variants. Genomic features such as these can escape detection when loci with LD are removed; in addition, failing to account for these features can introduce bias to analyses. We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.
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Affiliation(s)
- Garrett McKinney
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Megan V McPhee
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK, 99801
| | - Carita Pascal
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Box 355020, Seattle WA 98195
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23
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Abstract
Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 104-106) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112, USA;
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington 98195-5020, USA;
| | - Craig R Primmer
- Organismal & Evolutionary Biology Research Program and Biotechnology Institute, University of Helsinki, 00014 Helsinki, Finland;
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24
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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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25
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Parker KA, Hess JE, Narum SR, Kinziger AP. Evidence for the genetic basis and epistatic interactions underlying ocean‐ and river‐maturing ecotypes of Pacific Lamprey (
Entosphenus tridentatus
) returning to the Klamath River, California. Mol Ecol 2019; 28:3171-3185. [DOI: 10.1111/mec.15136] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/15/2019] [Accepted: 05/21/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Keith A. Parker
- Department of Fisheries Biology Humboldt State University Arcata California
| | - Jon E. Hess
- Columbia River Inter‐Tribal Fish Commission Portland Oregon
| | - Shawn R. Narum
- Columbia River Inter‐Tribal Fish Commission Hagerman Idaho
| | - Andrew P. Kinziger
- Department of Fisheries Biology Humboldt State University Arcata California
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26
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Weigel D, Koch I, Monzyk F, Sharpe C, Narum S, Caudill CC. Evaluation of a trap-and-transport program for a threatened population of steelhead (Oncorhynchus mykiss). CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01200-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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