1
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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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2
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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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3
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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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4
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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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5
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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: 31] [Impact Index Per Article: 5.2] [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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6
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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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7
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Piggott CVH, Verspoor E, Greer R, Hooker O, Newton J, Adams CE. Phenotypic and resource use partitioning amongst sympatric, lacustrine brown trout, Salmo trutta. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly032] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Camilla V H Piggott
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
| | - Eric Verspoor
- The Rivers and Lochs Institute, University of the Highlands and Islands, Inverness, UK
| | | | - Oliver Hooker
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
- PR Statistics, Hope Park Crescent, Edinburgh, UK
| | - Jason Newton
- NERC Life Sciences Mass Spectrometry Facility, SUERC, East Kilbride, UK
| | - Colin E Adams
- Scottish Centre for Ecology & the Natural Environment, IBAHCM, University of Glasgow, Rowardennan, Glasgow, UK
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8
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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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9
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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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10
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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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11
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Nichols KM, Kozfkay CC, Narum SR. Genomic signatures among Oncorhynchus nerka ecotypes to inform conservation and management of endangered Sockeye Salmon. Evol Appl 2016; 9:1285-1300. [PMID: 27877206 PMCID: PMC5108219 DOI: 10.1111/eva.12412] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 07/25/2016] [Indexed: 01/04/2023] Open
Abstract
Conservation of life history variation is an important consideration for many species with trade-offs in migratory characteristics. Many salmonid species exhibit both resident and migratory strategies that capitalize on benefits in freshwater and marine environments. In this study, we investigated genomic signatures for migratory life history in collections of resident and anadromous Oncorhynchus nerka (Kokanee and Sockeye Salmon, respectively) from two lake systems, using ~2,600 SNPs from restriction-site-associated DNA sequencing (RAD-seq). Differing demographic histories were evident in the two systems where one pair was significantly differentiated (Redfish Lake, FST = 0.091 [95% confidence interval: 0.087 to 0.095]) but the other pair was not (Alturas Lake, FST = -0.007 [-0.008 to -0.006]). Outlier and association analyses identified several candidate markers in each population pair, but there was limited evidence for parallel signatures of genomic variation associated with migration. Despite lack of evidence for consistent markers associated with migratory life history in this species, candidate markers were mapped to functional genes and provide evidence for adaptive genetic variation within each lake system. Life history variation has been maintained in these nearly extirpated populations of O. nerka, and conservation efforts to preserve this diversity are important for long-term resiliency of this species.
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Affiliation(s)
- Krista M Nichols
- Conservation Biology Division Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle WA USA
| | | | - Shawn R Narum
- Columbia River Intertribal Fish Commission, Hagerman Fish Culture Experiment Station Hagerman ID USA
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12
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Adams CE, Bean CW, Dodd JA, Down A, Etheridge EC, Gowans ARD, Hooker O, Knudsen R, Lyle AA, Winfield IJ, Præbel K. Inter and intra-population phenotypic and genotypic structuring in the European whitefish Coregonus lavaretus, a rare freshwater fish in Scotland. JOURNAL OF FISH BIOLOGY 2016; 88:580-594. [PMID: 26748995 DOI: 10.1111/jfb.12855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/02/2015] [Indexed: 06/05/2023]
Abstract
This study revealed between-lake genetic structuring between Coregonus lavaretus collected from the only two native populations of this species in Scotland, U.K. (Lochs Eck and Lomond) evidenced by the existence of private alleles (12 in Lomond and four in Eck) and significant genetic differentiation (FST = 0·056) across 10 microsatellite markers. Juvenile C. lavaretus originating from eggs collected from the two lakes and reared in a common-garden experiment showed clear phenotypic differences in trophic morphology (i.e. head and body shape) between these populations indicating that these characteristics were, at least partly, inherited. Microsatellite analysis of adults collected from different geographic regions within Loch Lomond revealed detectable and statistically significant but relatively weak genetic structuring (FST = 0·001-0·024) and evidence of private alleles related to the basin structure of the lake. Within-lake genetic divergence patterns suggest three possibilities for this observed pattern: (1) differential selection pressures causing divergence into separate gene pools, (2) a collapse of two formerly divergent gene pools and (3) a stable state maintained by balancing selection forces resulting from spatial variation in selection and lake heterogeneity. Small estimates of effective population sizes for the populations in both lakes suggest that the capacity of both populations to adapt to future environmental change may be limited.
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Affiliation(s)
- C E Adams
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - C W Bean
- Scottish Natural Heritage, Caspian House, Clydebank Business Park, Clydebank, Glasgow G81 2NR, U.K
| | - J A Dodd
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A Down
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - E C Etheridge
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - A R D Gowans
- Environment Agency, Ghyll Mount, Gillan Way, Penrith 40 Business Park, Penrith, Cumbria CA11 9BP, U.K
| | - O Hooker
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - R Knudsen
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - A A Lyle
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Glasgow G63 0AW, U.K
| | - I J Winfield
- Lake Ecosystems Group, Centre for Ecology & Hydrology, Lancaster Environment Centre, Library Avenue, Bailrigg, Lancaster LA1 4AP, U.K
| | - K Præbel
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
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13
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Fourteen additional microsatellite markers for Mussaenda pubescens and cross-species amplification. J Genet 2015. [DOI: 10.1007/s12041-014-0378-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Paris JR, King RA, Stevens JR. Human mining activity across the ages determines the genetic structure of modern brown trout (Salmo trutta L.) populations. Evol Appl 2015; 8:573-85. [PMID: 26136823 PMCID: PMC4479513 DOI: 10.1111/eva.12266] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 04/13/2015] [Indexed: 01/09/2023] Open
Abstract
Humans have exploited the earth's metal resources for thousands of years leaving behind a legacy of toxic metal contamination and poor water quality. The southwest of England provides a well-defined example, with a rich history of metal mining dating to the Bronze Age. Mine water washout continues to negatively impact water quality across the region where brown trout (Salmo trutta L.) populations exist in both metal-impacted and relatively clean rivers. We used microsatellites to assess the genetic impact of mining practices on trout populations in this region. Our analyses demonstrated that metal-impacted trout populations have low genetic diversity and have experienced severe population declines. Metal-river trout populations are genetically distinct from clean-river populations, and also from one another, despite being geographically proximate. Using approximate Bayesian computation (ABC), we dated the origins of these genetic patterns to periods of intensive mining activity. The historical split of contemporary metal-impacted populations from clean-river fish dated to the Medieval period. Moreover, we observed two distinct genetic populations of trout within a single catchment and dated their divergence to the Industrial Revolution. Our investigation thus provides an evaluation of contemporary population genetics in showing how human-altered landscapes can change the genetic makeup of a species.
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Affiliation(s)
- Josephine R Paris
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - R Andrew King
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
| | - Jamie R Stevens
- Biosciences, College of Life and Environmental Sciences, University of Exeter Exeter, UK
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15
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Lemay MA, Russello MA. Genetic evidence for ecological divergence in kokanee salmon. Mol Ecol 2015; 24:798-811. [PMID: 25580953 DOI: 10.1111/mec.13066] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 12/29/2014] [Accepted: 01/06/2015] [Indexed: 01/16/2023]
Abstract
The evolution of locally adapted phenotypes among populations that experience divergent selective pressures is a central mechanism for generating and maintaining biodiversity. Recently, the advent of high-throughput DNA sequencing technology has provided tools for investigating the genetic basis of this process in natural populations of nonmodel organisms. Kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), occurs as two reproductive ecotypes, which differ in spawning habitat (tributaries vs. shorelines); however, outside of the spawning season the two ecotypes co-occur in many lakes and lack diagnostic morphological characteristics. We used restriction site-associated DNA (RAD) sequencing to identify 6145 SNPs and genotype kokanee from multiple spawning sites in Okanagan Lake (British Columbia, Canada). Outlier tests revealed 18 loci putatively under divergent selection between ecotypes, all of which exhibited temporally stable allele frequencies within ecotypes. Six outliers were annotated to sequences in the NCBI database, two of which matched genes associated with early development. There was no evidence for neutral genetic differentiation; however, outlier loci demonstrated significant structure with respect to ecotype and had high assignment accuracy in mixed composition simulations. The absence of neutral structure combined with a small number of highly divergent outlier loci is consistent with theoretical predictions for the early stages of ecological divergence. These outlier loci were then applied to a realistic fisheries scenario in which additional RAD sequencing was used to genotype kokanee collected by trawl in Okanagan Lake, providing preliminary evidence that this approach may be an effective tool for conservation and management.
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Affiliation(s)
- Matthew A Lemay
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, British Columbia, Canada, V1V 1V7
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16
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Lemay MA, Russello MA. Diversity and relative abundance of the bacterial pathogen, Flavobacterium spp., infecting reproductive ecotypes of kokanee salmon. BMC Res Notes 2014; 7:778. [PMID: 25367228 PMCID: PMC4228061 DOI: 10.1186/1756-0500-7-778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/24/2014] [Indexed: 11/28/2022] Open
Abstract
Background Understanding the distribution and abundance of pathogens can provide insight into the evolution and ecology of their host species. Previous research in kokanee, the freshwater form of sockeye salmon (Oncorhynchus nerka), found evidence that populations spawning in streams may experience a greater pathogen load compared with populations that spawn on beaches. In this study we tested for differences in the abundance and diversity of the gram-negative bacteria, Flavobacterium spp., infecting tissues of kokanee in both of these spawning habitats (streams and beaches). Molecular assays were carried out using primers designed to amplify a ~200 nucleotide region of the gene encoding the ATP synthase alpha subunit (AtpA) within the genus Flavobacterium. Using a combination of DNA sequencing and quantitative PCR (qPCR) we compared the diversity and relative abundance of Flavobacterium AtpA amplicons present in DNA extracted from tissue samples of kokanee collected from each spawning habitat. Results We identified 10 Flavobacterium AtpA haplotypes among the tissues of stream-spawning kokanee and seven haplotypes among the tissues of beach-spawning kokanee, with only two haplotypes shared between spawning habitats. Haplotypes occurring in the same clade as F. psychrophilum were the most prevalent (92% of all reads, 60% of all haplotypes), and occurred in kokanee from both spawning habitats (streams and beaches). Subsequent qPCR assays did not find any significant difference in the relative abundance of Flavobacterium AtpA amplicons between samples from the different spawning habitats. Conclusions We confirmed the presence of Flavobacterium spp. in both spawning habitats and found weak evidence for increased Flavobacterium diversity in kokanee sampled from stream-spawning sites. However, the quantity of Flavobacterium DNA did not differ between spawning habitats. We recommend further study aimed at quantifying pathogen diversity and abundance in population-level samples of kokanee combined with environmental sampling to better understand the ecology of pathogen infection in this species. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-778) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Lemay
- University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada.
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