1
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Euclide PT, Larson WA, Shi Y, Gruenthal K, Christensen KA, Seeb J, Seeb L. Conserved islands of divergence associated with adaptive variation in sockeye salmon are maintained by multiple mechanisms. Mol Ecol 2023. [PMID: 37695544 DOI: 10.1111/mec.17126] [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: 05/09/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023]
Abstract
Local adaptation is facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. The mechanisms that create and maintain these islands and how they contribute to adaptive divergence is an active research topic. Here, we use sockeye salmon as a model to investigate both the mechanisms responsible for creating islands of divergence and the patterns of differentiation at these islands. Previous research suggested that multiple islands contributed to adaptive radiation of sockeye salmon. However, the low-density genomic methods used by these studies made it difficult to fully elucidate the mechanisms responsible for islands and connect genotypes to adaptive variation. We used whole genome resequencing to genotype millions of loci to investigate patterns of genetic variation at islands and the mechanisms that potentially created them. We discovered 64 islands, including 16 clustered in four genomic regions shared between two isolated populations. Characterisation of these four regions suggested that three were likely created by structural variation, while one was created by processes not involving structural variation. All four regions were small (< 600 kb), suggesting low recombination regions do not have to span megabases to be important for adaptive divergence. Differentiation at islands was not consistently associated with established population attributes. In sum, the landscape of adaptive divergence and the mechanisms that create it are complex; this complexity likely helps to facilitate fine-scale local adaptation unique to each population.
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Affiliation(s)
- Peter T Euclide
- Department of Forestry and Natural Resources, Illinois-Indiana Sea Grant, Purdue University, West Lafayette, Indiana, USA
| | - Wesley A Larson
- National Oceanographic and Atmospheric Administration, National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay Laboratories, Juneau, Alaska, USA
| | - Yue Shi
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Juneau, Alaska, USA
| | - Kristen Gruenthal
- Alaska Department of Fish and Game, Juneau, Alaska, USA
- Office of Applied Science, Wisconsin Department of Natural Resources, Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, Wisconsin, USA
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
| | - Jim Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
| | - Lisa Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA
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2
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Revolinski SR, Maughan PJ, Coleman CE, Burke IC. Preadapted to adapt: underpinnings of adaptive plasticity revealed by the downy brome genome. Commun Biol 2023; 6:326. [PMID: 36973344 PMCID: PMC10042881 DOI: 10.1038/s42003-023-04620-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023] Open
Abstract
Bromus tectorum L. is arguably the most successful invasive weed in the world. It has fundamentally altered arid ecosystems of the western United States, where it now found on an excess of 20 million hectares. Invasion success is related to avoidance of abiotic stress and human management. Early flowering is a heritable trait utilized by B. tectorum, enabling the species to temporally monopolize limited resources and outcompete the native plant community. Thus, understanding the genetic underpinning of flowering time is critical for the design of integrated management strategies. To study flowering time traits in B. tectorum, we assembled a chromosome scale reference genome for B. tectorum. To assess the utility of the assembled genome, 121 diverse B. tectorum accessions are phenotyped and subjected to a genome wide association study (GWAS). Candidate genes, representing homologs of genes that have been previously associated with plant height or flowering phenology traits in related species are located near QTLs we identified. This study uses a high-resolution GWAS to identify reproductive phenology genes in a weedy species and represents a considerable step forward in understanding the mechanisms underlying genetic plasticity in one of the most successful invasive weed species.
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Affiliation(s)
- Samuel R Revolinski
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Peter J Maughan
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Craig E Coleman
- Department of Plant & Wildlife Science, Brigham Young University, Provo, UT, USA
| | - Ian C Burke
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.
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3
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Tigano A, Russello MA. The genomic basis of reproductive and migratory behaviour in a polymorphic salmonid. Mol Ecol 2022; 31:6588-6604. [PMID: 36208020 DOI: 10.1111/mec.16724] [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: 06/20/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Recent ecotypic differentiation provides unique opportunities to investigate the genomic basis and architecture of local adaptation, while offering insights into how species form and persist. Sockeye salmon (Oncorhynchus nerka) exhibit migratory and resident ("kokanee") ecotypes, which are further distinguished into shore-spawning and stream-spawning reproductive ecotypes. Here, we analysed 36 sockeye (stream-spawning) and kokanee (stream- and shore-spawning) genomes from a system where they co-occur and have recent common ancestry (Okanagan Lake/River in British Columbia, Canada) to investigate the genomic basis of reproductive and migratory behaviour. Examination of the genomic landscape of differentiation, differences in allele frequencies and genotype-phenotype associations revealed three main blocks of sequence differentiation on chromosomes 7, 12 and 20, associated with migratory behaviour, spawning location and spawning timing. Structural variants identified in these same areas suggest they could contribute to ecotypic differentiation directly as causal variants or via maintenance of their genomic architecture through recombination suppression mechanisms. Genes in these regions were related to spatial memory and swimming endurance (SYNGAP, TPM3), as well as eye and brain development (including SIX6), potentially associated with differences in migratory behaviour and visual habitats across spawning locations, respectively. Additional genes (GREB1L, ROCK1) identified here have been associated with timing of migration in other salmonids and could explain variation in timing of O. nerka spawning. Together, these results based on the joint analysis of sequence and structural variation represent a significant advance in our understanding of the genomic landscape of ecotypic differentiation at different stages in the speciation continuum.
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Affiliation(s)
- Anna Tigano
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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4
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Stronen AV, Norman AJ, Vander Wal E, Paquet PC. The relevance of genetic structure in ecotype designation and conservation management. Evol Appl 2022; 15:185-202. [PMID: 35233242 PMCID: PMC8867706 DOI: 10.1111/eva.13339] [Citation(s) in RCA: 5] [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: 07/30/2020] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/28/2022] Open
Abstract
The concept of ecotypes is complex, partly because of its interdisciplinary nature, but the idea is intrinsically valuable for evolutionary biology and applied conservation. The complex nature of ecotypes has spurred some confusion and inconsistencies in the literature, thereby limiting broader theoretical development and practical application. We provide suggestions for how incorporating genetic analyses can ease confusion and help define ecotypes. We approach this by systematically reviewing 112 publications across taxa that simultaneously mention the terms ecotype, conservation and management, to examine the current use of the term in the context of conservation and management. We found that most ecotype studies involve fish, mammals and plants with a focus on habitat use, which at 60% was the most common criterion used for categorization of ecotypes. Only 53% of the studies incorporated genetic analyses, and major discrepancies in available genomic resources among taxa could have contributed to confusion about the role of genetic structure in delineating ecotypes. Our results show that the rapid advances in genetic methods, also for nonmodel organisms, can help clarify the spatiotemporal distribution of adaptive and neutral genetic variation and their relevance to ecotype designations. Genetic analyses can offer empirical support for the ecotype concept and provide a timely measure of evolutionary potential, especially in changing environmental conditions. Genetic variation that is often difficult to detect, including polygenic traits influenced by small contributions from several genes, can be vital for adaptation to rapidly changing environments. Emerging ecotypes may signal speciation in progress, and findings from genome-enabled organisms can help clarify important selective factors driving ecotype development and persistence, and thereby improve preservation of interspecific genetic diversity. Incorporation of genetic analyses in ecotype studies will help connect evolutionary biology and applied conservation, including that of problematic groups such as natural hybrid organisms and urban or anthropogenic ecotypes.
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Affiliation(s)
- Astrid V. Stronen
- Department of BiologyBiotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
- Department of Biotechnology and Life SciencesInsubria UniversityVareseItaly
- Department of Chemistry and BioscienceAalborg UniversityAalborgDenmark
| | - Anita J. Norman
- Department of Fish, Wildlife and Environmental StudiesSwedish University of Agricultural SciencesUmeåSweden
| | - Eric Vander Wal
- Department of BiologyMemorial University of NewfoundlandSt. John’sNLCanada
| | - Paul C. Paquet
- Department of GeographyUniversity of VictoriaVictoriaBCCanada
- Raincoast Conservation FoundationSidneyBCCanada
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5
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Chang SL, Ward HGM, Russello MA. Genotyping-in-Thousands by sequencing panel development and application to inform kokanee salmon (Oncorhynchus nerka) fisheries management at multiple scales. PLoS One 2021; 16:e0261966. [PMID: 34941943 PMCID: PMC8699693 DOI: 10.1371/journal.pone.0261966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 12/14/2021] [Indexed: 11/19/2022] Open
Abstract
The ability to differentiate life history variants is vital for estimating fisheries management parameters, yet traditional survey methods can be inaccurate in mixed-stock fisheries. Such is the case for kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka), which exhibits various reproductive ecotypes (stream-, shore-, deep-spawning) that co-occur with each other and/or anadromous O. nerka in some systems across their pan-Pacific distribution. Here, we developed a multi-purpose Genotyping-in-Thousands by sequencing (GT-seq) panel of 288 targeted single nucleotide polymorphisms (SNPs) to enable accurate kokanee stock identification by geographic basin, migratory form, and reproductive ecotype across British Columbia, Canada. The GT-seq panel exhibited high self-assignment accuracy (93.3%) and perfect assignment of individuals not included in the baseline to their geographic basin, migratory form, and reproductive ecotype of origin. The GT-seq panel was subsequently applied to Wood Lake, a valuable mixed-stock fishery, revealing high concordance (>98%) with previous assignments to ecotype using microsatellites and TaqMan® SNP genotyping assays, while improving resolution, extending a long-term time-series, and demonstrating the scalability of this approach for this system and others.
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Affiliation(s)
- Sarah L. Chang
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Hillary G. M. Ward
- British Columbia Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Penticton, BC, Canada
| | - Michael A. Russello
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
- * E-mail:
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6
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Samad-Zada F, Nakayama K, Russello MA. Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution. J Hered 2021; 112:602-613. [PMID: 34618898 DOI: 10.1093/jhered/esab060] [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: 03/25/2021] [Accepted: 10/01/2021] [Indexed: 11/14/2022] Open
Abstract
Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 m. The latter has only been detected in 5 locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9721 single nucleotide polymorphisms distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed 6 distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggests the deep-spawning ecotype independently evolved on the 2 continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep- and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.
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Affiliation(s)
- Farida Samad-Zada
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Kouji Nakayama
- Division of Applied Biosciences, Kyoto University, Kyoto, Japan
| | - Michael A Russello
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
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7
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Setzke C, Wong C, Russello MA. Genome-wide assessment of kokanee salmon stock diversity, population history and hatchery representation at the northern range margin. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01418-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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8
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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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9
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Samad‐zada F, van Poorten BT, Harris S, Godbout L, Russello MA. Genome-wide analysis reveals demographic and life-history patterns associated with habitat modification in landlocked, deep-spawning sockeye salmon ( Oncorhynchus nerka). Ecol Evol 2021; 11:13186-13205. [PMID: 34646462 PMCID: PMC8495803 DOI: 10.1002/ece3.8040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/11/2022] Open
Abstract
Human-mediated habitat fragmentation in freshwater ecosystems can negatively impact genetic diversity, demography, and life history of native biota, while disrupting the behavior of species that are dependent on spatial connectivity to complete their life cycles. In the Alouette River system (British Columbia, Canada), dam construction in 1928 impacted passage of anadromous sockeye salmon (Oncorhynchus nerka), with the last records of migrants occurring in the 1930s. Since that time, O. nerka persisted as a resident population in Alouette Reservoir until experimental water releases beginning in 2005 created conditions for migration; two years later, returning migrants were observed for the first time in ~70 years, raising important basic and applied questions regarding life-history variation and population structure in this system. Here, we investigated the genetic distinctiveness and population history of Alouette Reservoir O. nerka using genome-wide SNP data (n = 7,709 loci) collected for resident and migrant individuals, as well as for neighboring anadromous sockeye salmon and resident kokanee populations within the Fraser River drainage (n = 312 individuals). Bayesian clustering and principal components analyses based on neutral loci revealed five distinct clusters, largely associated with geography, and clearly demonstrated that Alouette Reservoir resident and migrant individuals are genetically distinct from other O. nerka populations in the Fraser River drainage. At a finer level, there was no clear evidence for differentiation between Alouette Reservoir residents and migrants; although we detected eight high-confidence outlier loci, they all mapped to sex chromosomes suggesting that differences were likely due to uneven sex ratios rather than life history. Taken together, these data suggest that contemporary Alouette Reservoir O. nerka represents a landlocked sockeye salmon population, constituting the first reported instance of deep-water spawning behavior associated with this life-history form. This finding punctuates the need for reassessment of conservation status and supports ongoing fisheries management activities in Alouette Reservoir.
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Affiliation(s)
| | - Brett T. van Poorten
- Applied Freshwater Ecology Research UnitBritish Columbia Ministry of Environment and Climate Change StrategyVancouverBCCanada
- School of Resource and Environmental ManagementSimon Fraser UniversityBurnabyBCCanada
| | - Shannon Harris
- Applied Freshwater Ecology Research UnitBritish Columbia Ministry of Environment and Climate Change StrategyVancouverBCCanada
| | - Lyse Godbout
- Pacific Biological Station, Fisheries and Oceans CanadaNanaimoBCCanada
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10
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Clemens BJ, Schreck CB. An assessment of terminology for intraspecific diversity in fishes, with a focus on "ecotypes" and "life histories". Ecol Evol 2021; 11:10772-10793. [PMID: 34429881 PMCID: PMC8366897 DOI: 10.1002/ece3.7884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/03/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022] Open
Abstract
Understanding and preserving intraspecific diversity (ISD) is important for species conservation. However, ISD units do not have taxonomic standards and are not universally recognized. The terminology used to describe ISD is varied and often used ambiguously. We compared definitions of terms used to describe ISD with use in recent studies of three fish taxa: sticklebacks (Gasterosteidae), Pacific salmon and trout (Oncorhynchus spp., "PST"), and lampreys (Petromyzontiformes). Life history describes the phenotypic responses of organisms to environments and includes biological parameters that affect population growth or decline. Life-history pathway(s) are the result of different organismal routes of development that can result in different life histories. These terms can be used to describe recognizable life-history traits. Life history is generally used in organismal- and ecology-based journals. The terms paired species/species pairs have been used to describe two different phenotypes, whereas in some species and situations a continuum of phenotypes may be expressed. Our review revealed overlapping definitions for race and subspecies, and subspecies and ecotypes. Ecotypes are genotypic adaptations to particular environments, and this term is often used in genetic- and evolution-based journals. "Satellite species" is used for situations in which a parasitic lamprey yields two or more derived, nonparasitic lamprey species. Designatable Units, Evolutionary Significant Units (ESUs), and Distinct Population Segments (DPS) are used by some governments to classify ISD of vertebrate species within distinct and evolutionary significant criteria. In situations where the genetic or life-history components of ISD are not well understood, a conservative approach would be to call them phenotypes.
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Affiliation(s)
| | - Carl B. Schreck
- Department of Fisheries and WildlifeOregon State UniversityCorvallisORUSA
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11
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Discovery of out-of-basin introgression in Pettit Lake Sockeye Salmon: management implications for native genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01386-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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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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14
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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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15
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Weinstein SY, Thrower FP, Nichols KM, Hale MC. A large-scale chromosomal inversion is not associated with life history development in rainbow trout from Southeast Alaska. PLoS One 2019; 14:e0223018. [PMID: 31539414 PMCID: PMC6754156 DOI: 10.1371/journal.pone.0223018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/11/2019] [Indexed: 01/12/2023] Open
Abstract
In studying the causative mechanisms behind migration and life history, the salmonids-salmon, trout, and charr-are an exemplary taxonomic group, as life history development is known to have a strong genetic component. A double inversion located on chromosome 5 in rainbow trout (Oncorhynchus mykiss) is associated with life history development in multiple populations, but the importance of this inversion has not been thoroughly tested in conjunction with other polymorphisms in the genome. To that end, we used a high-density SNP chip to genotype 192 F1 migratory and resident rainbow trout and focused our analyses to determine whether this inversion is important in life history development in a well-studied population of rainbow trout from Southeast Alaska. We identified 4,994 and 436 SNPs-predominantly outside of the inversion region-associated with life history development in the migrant and resident familial lines, respectively. Although F1 samples showed genomic patterns consistent with the double inversion on chromosome 5 (reduced observed and expected heterozygosity and an increase in linkage disequilibrium), we found no statistical association between the inversion and life history development. Progeny produced by crossing resident trout and progeny produced by crossing migrant trout both consisted of a mix of migrant and resident individuals, irrespective of the individuals' inversion haplotype on chromosome 5. This suggests that although the inversion is present at a low frequency, it is not strongly associated with migration as it is in populations of Oncorhynchus mykiss from lower latitudes.
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Affiliation(s)
- Spencer Y. Weinstein
- Department of Biology, Texas Christian University, Fort Worth, United States of America
| | - Frank P. Thrower
- Ted Stevens Marine Research Institute, Alaska Fisheries Center, NOAA, Juneau, AK, United States of America
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, Seattle, WA, United States of America
| | - Matthew C. Hale
- Department of Biology, Texas Christian University, Fort Worth, United States of America
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16
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Association Mapping Based on a Common-Garden Migration Experiment Reveals Candidate Genes for Migration Tendency in Brown Trout. G3-GENES GENOMES GENETICS 2019; 9:2887-2896. [PMID: 31289024 PMCID: PMC6723140 DOI: 10.1534/g3.119.400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A better understanding of the environmental and genetic contribution to migratory behavior and the evolution of traits linked to migration is crucial for fish conservation and fisheries management. Up to date, a few genes with unequivocal influence on the adoption of alternative migration strategies have been identified in salmonids. Here, we used a common garden set-up to measure individual migration distances of generally highly polymorphic brown trout Salmo trutta from two populations. Fish from the assumedly resident population showed clearly shorter migration distances than the fish from the assumed migratory population at the ages of 2 and 3 years. By using two alternative analytical pipelines with 22186 and 18264 SNPs obtained through RAD-sequencing, we searched for associations between individual migration distance, and both called genotypes and genotype probabilities. None of the SNPs showed statistically significant individual effects on migration after correction for multiple testing. By choosing a less stringent threshold, defined as an overlap of the top 0.1% SNPs identified by the analytical pipelines, GAPIT and Angsd, we identified eight candidate genes that are potentially linked to individual migration distance. While our results demonstrate large individual and population level differences in migration distances, the detected genetic associations were weak suggesting that migration traits likely have multigenic control.
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17
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Zhang Y, Zhou Y, Liu X, Yu H, Li D, Zhang Y. Genetic diversity of the Sichuan snub-nosed monkey (Rhinopithecus roxellana) in Shennongjia National Park, China using RAD-seq analyses. Genetica 2019; 147:327-335. [DOI: 10.1007/s10709-019-00073-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/12/2019] [Indexed: 12/30/2022]
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18
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Zhang BD, Xue DX, Li YL, Liu JX. RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the northwestern Pacific Ocean. PeerJ 2019; 7:e7242. [PMID: 31309001 PMCID: PMC6612258 DOI: 10.7717/peerj.7242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/02/2019] [Indexed: 01/08/2023] Open
Abstract
Exploring factors shaping genetic structure of marine fish is challenging due to fewer barriers to gene flow in the ocean. However, genome-wide sequence data can greatly enhance our ability to delineate previously unidentified population structure as well as potential adaptive divergence. The small yellow croaker (Larimichthys polyactis) is a commercially important fish species with high gene flow and its overwintering populations experience heterogeneous environment, suggesting possible population differentiation and adaptive divergence. To delineate patterns of population structure as well as test for signatures of local adaptation, a total of 68,666 quality filtered SNP markers were identified for 80 individuals from four overwintering populations by using restriction site-associated DNA sequencing (RAD-seq). Significant genetic differentiation among overwintering populations from the Central Yellow Sea, the South Yellow Sea and the North East China Sea were detected (Pair-wise FST: 0.00036–0.00390), which were consistent with population division of overwintering groups inferred from traditional ecological approaches. In addition, a total of 126 unique SNPs were detected to be significantly associated with environmental parameters (temperature, salinity and turbidity). These candidate SNPs were involved in multiple pathways such as energy metabolism and phagocytosis, suggesting they may play key roles in growth and innate immunity. Our results suggested the existence of hitherto unrecognized cryptic population structure and local adaptation in this high gene flow marine fish and thus gain new insights into the design of management strategies.
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Affiliation(s)
- Bai-Dong Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Dong-Xiu Xue
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yu-Long Li
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Jin-Xian Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
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19
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Larson WA, Dann TH, Limborg MT, McKinney GJ, Seeb JE, Seeb LW. Parallel signatures of selection at genomic islands of divergence and the major histocompatibility complex in ecotypes of sockeye salmon across Alaska. Mol Ecol 2019; 28:2254-2271. [DOI: 10.1111/mec.15082] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/21/2019] [Accepted: 03/20/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Wesley A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Tyler H. Dann
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
- Gene Conservation Laboratory Alaska Department of Fish and Game Anchorage Alaska
| | - Morten T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington
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20
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Whitaker JM, Welsh AB, Hondorp DW, Boase JC, Merovich GT, Welsh S, Krueger C. Variation in DNA methylation is associated with migratory phenotypes of lake sturgeon Acipenser fulvescens in the St. Clair River, MI, USA. JOURNAL OF FISH BIOLOGY 2018; 93:942-951. [PMID: 30246341 DOI: 10.1111/jfb.13804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 09/17/2018] [Indexed: 06/08/2023]
Abstract
Lake sturgeon Acipenser fulvescens populations show a variety of movement patterns that are poorly understood. To compare two migratory phenotypes of A. fulvescens in the St. Clair River, MI, USA, multiple data types were analysed. Individual fish were classified into migratory phenotypes based on acoustic telemetry data collected 2012-2015. Acipenser fulvescens consistently showed movement from the St. Clair River upriver into Lake Huron or downriver into Lake St. Clair. The two migratory phenotypes were then compared for differences in morphometrics, genetics and epigenetics. Morphological differences based on linear measurements were not detected between phenotypes. Microsatellite data from 11 loci suggested one population with no genetic differentiation between migratory phenotypes. Our epigenetic results indicated that the migratory phenotypes are differentially methylated (P < 0.05), thus epigenetics may be associated with migratory differences in A. fulvescens. Only one restriction site was identified to be driving the differential methylation (P < 0.05). While little evidence at neutral loci occurred for genetic differentiation of A. fulvescens, DNA methylation may play a role in the observed movement pattern variation. When combined with microsatellite and morphometric analyses, our results suggested that different migratory patterns may reflect phenotypic plasticity, allowing A. fulvescens to acclimate to short-term environmental variability. Without an integrated approach, the role of epigenetics in the migratory phenotype of A. fulvescens may have been overlooked. Further characterization of migratory phenotypes could be important for management to conserve behavioural variation across the distribution of A. fulvescens and for design of stocking guidelines.
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Affiliation(s)
- Justine M Whitaker
- School of Natural Resources, West Virginia University, Morgantown, West Virginia
| | - Amy B Welsh
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, West Virginia
| | - Darryl W Hondorp
- U.S. Geological Survey - Great Lakes Science Center, Ann Arbor, Michigan
| | - James C Boase
- U.S. Fish and Wildlife Service - Alpena Fish and Wildlife Conservation Office, Alpena, Michigan
| | - George T Merovich
- Department of Environmental Science, Fisheries and Aquatic Sciences Program, Juniata College, Huntingdon, Pennsylvania
| | - Stuart Welsh
- US Geological Survey, West Virginia Cooperative Fish and Wildlife Research Unit, School of Natural Resources, Morgantown, West Virginia
| | - Charles Krueger
- Department of Fisheries and Wildlife, Michigan State University, Center for Systems Integration and Sustainability, East Lansing, Michigan
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21
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Lemopoulos A, Uusi-Heikkilä S, Huusko A, Vasemägi A, Vainikka A. Comparison of Migratory and Resident Populations of Brown Trout Reveals Candidate Genes for Migration Tendency. Genome Biol Evol 2018; 10:1493-1503. [PMID: 29850813 PMCID: PMC6007540 DOI: 10.1093/gbe/evy102] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
Candidate genes associated with migration have been identified in multiple taxa: including salmonids, many of whom perform migrations requiring a series of physiological changes associated with the freshwater–saltwater transition. We screened over 5,500 SNPs for signatures of selection related to migratory behavior of brown trout Salmo trutta by focusing on ten differentially migrating freshwater populations from two watersheds (the Koutajoki and the Oulujoki). We found eight outlier SNPs potentially associated with migratory versus resident life history using multiple (≥3) outlier detection approaches. Comparison of three migratory versus resident population pairs in the Koutajoki watershed revealed seven outlier SNPs, of which three mapped close to genes ZNF665-like, GRM4-like, and PCDH8-like that have been previously associated with migration and smoltification in salmonids. Two outlier SNPs mapped to genes involved in mucus secretion (ST3GAL1-like) and osmoregulation (C14orf37-like). The last two strongly supported outlier SNPs mapped to thermally induced genes (FNTA1-like, FAM134C-like). Within the Oulujoki, the only consistent outlier SNP mapped close to a gene (EZH2) that is associated with compensatory growth in fasted trout. Our results suggest that a relatively small yet common set of genes responsible for physiological functions associated with resident and migratory life histories is evolutionarily conserved.
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Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Department of Biology, University of Turku, Finland
| | - Silva Uusi-Heikkilä
- Department of Biology, University of Turku, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Finland
| | - Ari Huusko
- Aquatic population dynamics, Natural Resources Institute Finland (Luke), Paltamo, Finland
| | - Anti Vasemägi
- Department of Biology, University of Turku, Finland.,Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.,Department of Aquatic Resources, Institute of Freshwater Research, Swedish University of Agricultural Sciences, Drottningholm, Sweden.,These authors shared senior authorship
| | - Anssi Vainikka
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,These authors shared senior authorship
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22
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Waters CD, Hard JJ, Brieuc MSO, Fast DE, Warheit KI, Knudsen CM, Bosch WJ, Naish KA. Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies. Evol Appl 2018; 11:853-868. [PMID: 29928295 PMCID: PMC5999212 DOI: 10.1111/eva.12599] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
A novel application of genomewide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad-scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated-and potentially adaptive-loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.
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Affiliation(s)
- Charles D. Waters
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
| | - Jeffrey J. Hard
- Conservation Biology DivisionNorthwest Fisheries Science CenterNational Oceanic and Atmospheric AdministrationSeattleWAUSA
| | - Marine S. O. Brieuc
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
- Department of BiosciencesCentre for Ecological and Evolutionary Synthesis (CEES)University of OsloOsloNorway
| | | | | | | | | | - Kerry A. Naish
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWAUSA
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23
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Pritchard VL, Mäkinen H, Vähä JP, Erkinaro J, Orell P, Primmer CR. Genomic signatures of fine-scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence-related genes. Mol Ecol 2018; 27:2560-2575. [DOI: 10.1111/mec.14705] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/30/2018] [Accepted: 04/02/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hannu Mäkinen
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute; University of Turku; Turku Finland
| | | | - Panu Orell
- Natural Resources Institute Finland (LUKE); Oulu Finland
| | - Craig R. Primmer
- Department of Biology; University of Turku; Turku Finland
- Department of Biosciences; University of Helsinki; Helsinki Finland
- Institute of Biotechnology; University of Helsinki; Helsinki Finland
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24
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Brieuc MSO, Waters CD, Drinan DP, Naish KA. A practical introduction to Random Forest for genetic association studies in ecology and evolution. Mol Ecol Resour 2018; 18:755-766. [PMID: 29504715 DOI: 10.1111/1755-0998.12773] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/08/2018] [Accepted: 02/17/2018] [Indexed: 12/25/2022]
Abstract
Large genomic studies are becoming increasingly common with advances in sequencing technology, and our ability to understand how genomic variation influences phenotypic variation between individuals has never been greater. The exploration of such relationships first requires the identification of associations between molecular markers and phenotypes. Here, we explore the use of Random Forest (RF), a powerful machine-learning algorithm, in genomic studies to discern loci underlying both discrete and quantitative traits, particularly when studying wild or nonmodel organisms. RF is becoming increasingly used in ecological and population genetics because, unlike traditional methods, it can efficiently analyse thousands of loci simultaneously and account for nonadditive interactions. However, understanding both the power and limitations of Random Forest is important for its proper implementation and the interpretation of results. We therefore provide a practical introduction to the algorithm and its use for identifying associations between molecular markers and phenotypes, discussing such topics as data limitations, algorithm initiation and optimization, as well as interpretation. We also provide short R tutorials as examples, with the aim of providing a guide to the implementation of the algorithm. Topics discussed here are intended to serve as an entry point for molecular ecologists interested in employing Random Forest to identify trait associations in genomic data sets.
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Affiliation(s)
- Marine S O Brieuc
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA.,Center for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Daniel P Drinan
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
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25
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Veale AJ, Russello MA. Genomic Changes Associated with Reproductive and Migratory Ecotypes in Sockeye Salmon (Oncorhynchus nerka). Genome Biol Evol 2017; 9:2921-2939. [PMID: 29045601 PMCID: PMC5737441 DOI: 10.1093/gbe/evx215] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2017] [Indexed: 12/12/2022] Open
Abstract
Mechanisms underlying adaptive evolution can best be explored using paired populations displaying similar phenotypic divergence, illuminating the genomic changes associated with specific life history traits. Here, we used paired migratory [anadromous vs. resident (kokanee)] and reproductive [shore- vs. stream-spawning] ecotypes of sockeye salmon (Oncorhynchus nerka) sampled from seven lakes and two rivers spanning three catchments (Columbia, Fraser, and Skeena) in British Columbia, Canada to investigate the patterns and processes underlying their divergence. Restriction-site associated DNA sequencing was used to genotype this sampling at 7,347 single nucleotide polymorphisms, 334 of which were identified as outlier loci and candidates for divergent selection within at least one ecotype comparison. Sixty-eight of these outliers were present in two or more comparisons, with 33 detected across multiple catchments. Of particular note, one locus was detected as the most significant outlier between shore and stream-spawning ecotypes in multiple comparisons and across catchments (Columbia, Fraser, and Snake). We also detected several genomic islands of divergence, some shared among comparisons, potentially showing linked signals of differential selection. The single nucleotide polymorphisms and genomic regions identified in our study offer a range of mechanistic hypotheses associated with the genetic basis of O. nerka life history variation and provide novel tools for informing fisheries management.
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Affiliation(s)
- Andrew J. Veale
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
- Present address: Department of Environmental and Animal Sciences, Unitec, 139 Carrington Rd, Auckland, New Zealand
| | - Michael A. Russello
- Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada
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26
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Beacham TD, Withler RE. Population structure of sea-type and lake-type sockeye salmon and kokanee in the Fraser River and Columbia River drainages. PLoS One 2017; 12:e0183713. [PMID: 28886033 PMCID: PMC5590831 DOI: 10.1371/journal.pone.0183713] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/09/2017] [Indexed: 01/02/2023] Open
Abstract
Population structure of three ecotypes of Oncorhynchus nerka (sea-type Sockeye Salmon, lake-type Sockeye Salmon, and Kokanee) in the Fraser River and Columbia River drainages was examined with microsatellite variation, with the main focus as to whether Kokanee population structure within the Fraser River drainage suggested either a monophyletic or polyphyletic origin of the ecotype within the drainage. Variation at 14 microsatellite loci was surveyed for sea-type and lake-type Sockeye Salmon and Kokanee sampled from 121 populations in the two river drainages. An index of genetic differentiation, FST, over all populations and loci was 0.087, with individual locus values ranging from 0.031 to 0.172. Standardized to an ecotype sample size of 275 individuals, the least genetically diverse ecotype was sea-type Sockeye Salmon with 203 alleles, whereas Kokanee displayed the greatest number of alleles (260 alleles), with lake-type Sockeye Salmon intermediate (241 alleles). Kokanee populations from the Columbia River drainage (Okanagan Lake, Kootenay Lake), the South Thompson River (a major Fraser River tributary) drainage populations, and the mid-Fraser River populations all clustered together in a neighbor-joining analysis, indicative of a monophyletic origin of the Kokanee ecotype in these regions, likely reflecting the origin of salmon radiating from a refuge after the last glaciation period. However, upstream of the mid-Fraser River populations, there were closer relationships between the lake-type Sockeye Salmon ecotype and the Kokanee ecotype, indicative of the Kokanee ecotype evolving independently from the lake-type Sockeye Salmon ecotype in parallel radiation. Kokanee population structure within the entire Fraser River drainage suggested a polyphyletic origin of the ecotype within the drainage. Studies employing geographically restricted population sampling may not outline accurately the phylogenetic history of salmonid ecotypes.
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Affiliation(s)
- Terry D. Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, B. C. Canada
- * E-mail:
| | - Ruth E. Withler
- Fisheries and Oceans Canada, Pacific Biological Station, Nanaimo, B. C. Canada
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27
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Limborg MT, Larson WA, Seeb LW, Seeb JE. Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome. Mol Ecol 2017; 26:4509-4522. [DOI: 10.1111/mec.14201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 04/03/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Morten T. Limborg
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Wesley A. Larson
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Lisa W. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - James E. Seeb
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
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28
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Macqueen DJ, Primmer CR, Houston RD, Nowak BF, Bernatchez L, Bergseth S, Davidson WS, Gallardo-Escárate C, Goldammer T, Guiguen Y, Iturra P, Kijas JW, Koop BF, Lien S, Maass A, Martin SAM, McGinnity P, Montecino M, Naish KA, Nichols KM, Ólafsson K, Omholt SW, Palti Y, Plastow GS, Rexroad CE, Rise ML, Ritchie RJ, Sandve SR, Schulte PM, Tello A, Vidal R, Vik JO, Wargelius A, Yáñez JM. Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics 2017; 18:484. [PMID: 28655320 PMCID: PMC5488370 DOI: 10.1186/s12864-017-3862-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 06/14/2017] [Indexed: 11/21/2022] Open
Abstract
We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance.
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Affiliation(s)
- Daniel J. Macqueen
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ UK
| | - Craig R. Primmer
- Department of Biology, University of Turku, 20014 Turku, Finland
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, TAS Australia
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, G1V 0A6 Canada
| | - Steinar Bergseth
- The Research Council of Norway, Drammensveien 288, P.O. Box 564, NO-1327 Lysaker, Norway
| | - William S. Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research, Department of Oceanography, Universidad de Concepción, 4030000 Concepción, Chile
| | - Tom Goldammer
- Leibniz Institute for Farm Animal Biology, Institute for Genome Biology, Fish Genetics Unit, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Yann Guiguen
- INRA, UR1037 Fish Physiology and Genomics, Rennes, France
| | - Patricia Iturra
- Human Genetics Program ICBM Faculty of Medicine, University of Chile, Santiago, Chile
| | | | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 3N5 Canada
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Alejandro Maass
- Center for Mathematical Modelling, Department of Mathematical Engineering, University of Chile, 8370456 Santiago, Chile
- Center for Genome Regulation, University of Chile, 8370456 Santiago, Chile
| | - Samuel A. M. Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 2TZ UK
| | - Philip McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Martin Montecino
- Center for Biomedical Research, Universidad Andres Bello, 8370146 Santiago, Chile
- FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, 8370146 Santiago, Chile
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA 98195 USA
| | - Krista M. Nichols
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle, WA 98112 USA
| | | | - Stig W. Omholt
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
- NTNU - Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, USDA ARS, 11861 Leetown Road, Kearneysville, WV 25430 USA
| | - Graham S. Plastow
- Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Caird E. Rexroad
- Office of National Programs, USDA ARS, 5601 Sunnyside Avenue, Beltsville, MD 20705-5148 USA
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John’s, NL A1C 5S7 Canada
| | - Rachael J. Ritchie
- Genome British Columbia, Suite 400 – 575, West 8th Avenue, Vancouver, BC V5Z 0C4 Canada
| | - Simen R. Sandve
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Patricia M. Schulte
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4 Canada
| | - Alfredo Tello
- Instituto Tecnológico del Salmón S.A., INTESAL de SalmonChile, Puerto Montt, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics, and Evolutionary Studies, Department of Biology, University of Santiago, 9170022 Santiago, Chile
| | - Jon Olav Vik
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, NO-1432 Ås, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - José Manuel Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile, Av. Santa Rosa 11735, Santiago, Chile & Aquainnovo, Cardonal s/n, Puerto Montt, Chile
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29
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Veale AJ, Russello MA. An ancient selective sweep linked to reproductive life history evolution in sockeye salmon. Sci Rep 2017; 7:1747. [PMID: 28496186 PMCID: PMC5431894 DOI: 10.1038/s41598-017-01890-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/05/2017] [Indexed: 11/09/2022] Open
Abstract
Study of parallel (or convergent) phenotypic evolution can provide important insights into processes driving sympatric, ecologically-mediated divergence and speciation, as ecotype pairs may provide a biological replicate of the underlying signals and mechanisms. Here, we provide evidence for a selective sweep creating an island of divergence associated with reproductive behavior in sockeye salmon (Oncorhynchus nerka), identifying a series of linked single nucleotide polymorphisms across a ~22,733 basepair region spanning the leucine-rich repeat-containing protein 9 gene exhibiting signatures of divergent selection associated with stream- and shore-spawning in both anadromous and resident forms across their pan-Pacific distribution. This divergence likely occurred ~3.8 Mya (95% HPD = 2.1–6.03 Mya), after sockeye separated from pink (O. gorbuscha) and chum (O. keta) salmon, but prior to the Pleistocene glaciations. Our results suggest recurrent evolution of reproductive ecotypes across the native range of O. nerka is at least partially associated with divergent selection of pre-existing genetic variation within or linked to this region. As sockeye salmon are unique among Pacific salmonids in their flexibility to spawn in lake-shore benthic environments, this region provides great promise for continued investigation of the genomic basis of O. nerka life history evolution, and, more broadly, for increasing our understanding of the heritable basis of adaptation of complex traits in novel environments.
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Affiliation(s)
- Andrew J Veale
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.,Department of Zoology, University of Otago, 340 Great King Street, Dunedin, 9016, New Zealand
| | - Michael A Russello
- Department of Biology, The University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, British Columbia, V1V 1V7, Canada.
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