1
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Osmond DR, King RA, Stockley B, Launey S, Stevens JR. A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales. JOURNAL OF FISH BIOLOGY 2023; 102:258-270. [PMID: 36281821 DOI: 10.1111/jfb.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
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Affiliation(s)
- Daniel R Osmond
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - R Andrew King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bruce Stockley
- Westcountry Rivers Trust, Rain-Charm House, Cornwall, UK
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRAe, Rennes, France
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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2
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Crotti M, Bean CW, Gowans ARD, Winfield IJ, Butowska M, Wanzenböck J, Bondarencko G, Praebel K, Adams CE, Elmer KR. Complex and divergent histories gave rise to genome-wide divergence patterns amongst European whitefish (Coregonus lavaretus). J Evol Biol 2021; 34:1954-1969. [PMID: 34653264 PMCID: PMC9251650 DOI: 10.1111/jeb.13948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/31/2022]
Abstract
Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome‐wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (FST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome‐wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto‐nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre‐glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum.
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Affiliation(s)
- Marco Crotti
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Colin W Bean
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK.,NatureScot, Clydebank, UK
| | | | - Ian J Winfield
- Lake Ecosystems Group, UK Centre for Ecology & Hydrology, Lancaster Environment Centre, Bailrigg, UK
| | - Magdalena Butowska
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Josef Wanzenböck
- Research Institute for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | | | - Kim Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Glasgow, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
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3
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Guinand B, Oral M, Tougard C. Brown trout phylogenetics: A persistent mirage towards (too) many species. JOURNAL OF FISH BIOLOGY 2021; 99:298-307. [PMID: 33483952 DOI: 10.1111/jfb.14686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Bruno Guinand
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Münevver Oral
- Faculty of Fisheries and Aquatic Science, Recep Tayyip Erdogan University, Rize, Turkey
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4
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Jonsson B, Jonsson N. Continuous outmigration and sequential encountering of environmental cues are important for successful homing of hatchery-reared, anadromous brown trout Salmo trutta. JOURNAL OF FISH BIOLOGY 2021; 98:1481-1484. [PMID: 33439494 DOI: 10.1111/jfb.14673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
When rehabilitating and reintroducing trout Salmo trutta in rivers, it is a goal that as many as possible survive, home and form self-sustaining populations. Hatchery-reared, anadromous S. trutta have significant lower ability to return to the area where they were raised if (a) transported in a closed tank to sea and released 5 km from the River Imsa, relative to those that were (b) transported when swimming in a partly submerged tank with sea water run-through, while being slowly towed by a boat the same distance or (c) released at the outlet of the River Imsa. Thus, if deprived from environmental cues during part of the way, they lose their ability to home.
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Affiliation(s)
- Bror Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
| | - Nina Jonsson
- Norwegian Institute for Nature Research, Oslo, Norway
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5
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Gargan PG, Økland F, Shephard S, Fitzgerald C, O'Grady M. The spawning location of vulnerable ferox trout (Salmo trutta L.) in the Lough Corrib and Lough Mask catchments, Western Ireland. JOURNAL OF FISH BIOLOGY 2021; 98:485-497. [PMID: 33064311 DOI: 10.1111/jfb.14593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Ferox trout are large, long-lived, piscivorous trout normally found in deep lakes; they are highly prized by trophy anglers. Lough Corrib and Lough Mask, Western Ireland, have recorded the majority of Irish specimen ferox trout since angling records began. Little was known regarding the spawning location of ferox trout relative to sympatric brown trout, and a radio telemetry study was initiated in both catchments in 2005. Over the period 2005-2009, 79 ferox were captured by angling and radio tagged in Lough Corrib, while 55 ferox were tagged in Lough Mask. Manual and helicopter tracking were carried out on all spawning streams entering both lakes over the autumn/winter period to detect tagged fish. Overall, 37 radio-tagged trout (46.8%) were detected in Lough Corrib streams and 21 tagged trout (38.2%) were recorded from Lough Mask streams. Results from radio tracking indicate that the majority (92%) of ferox trout tagged in Lough Corrib spawned in a single spawning stream, the Cong river, while the majority (76%) of ferox trout tagged in Lough Mask spawned in the Cong canal and Cong river. These results suggest that these streams are most likely the principle spawning locations of ferox trout in both lakes. The occurrence of ferox trout predominantly in single spawning rivers in both catchments highlights the vulnerability of the study ferox populations. As a result of these findings, conservation measures were introduced for ferox trout in both catchments.
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Affiliation(s)
| | - Finn Økland
- Norwegian Institute for Nature Research (NINA), Trondheim, Norway
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6
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Gaffaroglu M, Majtánová Z, Symonová R, Pelikánová Š, Unal S, Lajbner Z, Ráb P. Present and Future Salmonid Cytogenetics. Genes (Basel) 2020; 11:E1462. [PMID: 33291343 PMCID: PMC7762217 DOI: 10.3390/genes11121462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 01/04/2023] Open
Abstract
Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved.
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Affiliation(s)
- Muhammet Gaffaroglu
- Department of Molecular Biology and Genetics, Faculty of Science, University of Ahi Evran, Kirsehir 40200, Turkey;
| | - Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, 85354 Freising, Germany
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
| | - Sevgi Unal
- Department of Molecular Biology and Genetics, Faculty of Science, Bartin University, Bartin 74000, Turkey;
| | - Zdeněk Lajbner
- Physics and Biology Unit, Okinawa Institute of Science and Technology, Graduate University, Onna, Okinawa 904 0495, Japan;
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic; (Z.M.); (Š.P.); (P.R.)
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7
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Finlay R, Poole R, Coughlan J, Phillips KP, Prodöhl P, Cotter D, McGinnity P, Reed TE. Telemetry and genetics reveal asymmetric dispersal of a lake-feeding salmonid between inflow and outflow spawning streams at a microgeographic scale. Ecol Evol 2020; 10:1762-1783. [PMID: 32128115 PMCID: PMC7042748 DOI: 10.1002/ece3.5937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/01/2022] Open
Abstract
The degree of natal philopatry relative to natal dispersal in animal populations has important demographic and genetic consequences and often varies substantially within species. In salmonid fishes, lakes have been shown to have a strong influence on dispersal and gene flow within catchments; for example, populations spawning in inflow streams are often reproductively isolated and genetically distinct from those spawning in relatively distant outflow streams. Less is known, however, regarding the level of philopatry and genetic differentiation occurring at microgeographic scales, for example, where inflow and outflow streams are separated by very small expanses of lake habitat. Here, we investigated the interplay between genetic differentiation and fine-scale spawning movements of brown trout between their lake-feeding habitat and two spawning streams (one inflow, one outflow, separated by <100 m of lake habitat). Most (69.2%) of the lake-tagged trout subsequently detected during the spawning period were recorded in just one of the two streams, consistent with natal fidelity, while the remainder were detected in both streams, creating an opportunity for these individuals to spawn in both natal and non-natal streams. The latter behavior was supported by genetic sibship analysis, which revealed several half-sibling dyads containing one individual that was sampled as a fry in the outflow and another that was sampled as fry in the inflow. Genetic clustering analyses in conjunction with telemetry data suggested that asymmetrical dispersal patterns were occurring, with natal fidelity being more common among individuals originating from the outflow than the inflow stream. This was corroborated by Bayesian analysis of gene flow, which indicated significantly higher rates of gene flow from the inflow into the outflow than vice versa. Collectively, these results reveal how a combination of telemetry and genetics can identify distinct reproductive behaviors and associated asymmetries in natal dispersal that produce subtle, but nonetheless biologically relevant, population structuring at microgeographic scales.
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Affiliation(s)
- Ross Finlay
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | | | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Karl P. Phillips
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Paulo Prodöhl
- Institute for Global Food SecuritySchool of Biological SciencesQueen's University BelfastBelfastIreland
| | | | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnaceNewportIreland
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
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8
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Bekkevold D, Höjesjö J, Nielsen EE, Aldvén D, Als TD, Sodeland M, Kent MP, Lien S, Hansen MM. Northern European Salmo trutta (L.) populations are genetically divergent across geographical regions and environmental gradients. Evol Appl 2020; 13:400-416. [PMID: 31993085 PMCID: PMC6976966 DOI: 10.1111/eva.12877] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/22/2019] [Indexed: 12/19/2022] Open
Abstract
The salmonid fish Brown trout is iconic as a model for the application of conservation genetics to understand and manage local interspecific variation. However, there is still scant information about relationships between local and large-scale population structure, and to what extent geographical and environmental variables are associated with barriers to gene flow. We used information from 3,782 mapped SNPs developed for the present study and conducted outlier tests and gene-environment association (GEA) analyses in order to examine drivers of population structure. Analyses comprised >2,600 fish from 72 riverine populations spanning a central part of the species' distribution in northern Europe. We report hitherto unidentified genetic breaks in population structure, indicating strong barriers to gene flow. GEA loci were widely spread across genomic regions and showed correlations with climatic, abiotic and geographical parameters. In some cases, individual loci showed consistent GEA across the geographical regions Britain, Europe and Scandinavia. In other cases, correlations were observed only within a sub-set of regions, suggesting that locus-specific variation was associated with local processes. A paired-population sampling design allowed us to evaluate sampling effects on detection of outlier loci and GEA. Two widely applied methods for outlier detection (pcadapt and bayescan) showed low overlap in loci identified as statistical outliers across sub-sets of data. Two GEA analytical approaches (LFMM and RDA) showed good correspondence concerning loci associated with specific variables, but LFMM identified five times more statistically significant associations than RDA. Our results emphasize the importance of carefully considering the statistical methods applied for the hypotheses being tested in outlier analysis. Sampling design may have lower impact on results if the objective is to identify GEA loci and their population distribution. Our study provides new insights into trout populations, and results have direct management implications in serving as a tool for identification of conservation units.
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Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Johan Höjesjö
- Department of Biological & Environmental SciencesUniversity of GothenburgGothenburgSweden
| | - Einar Eg Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | - Marte Sodeland
- Department of Natural SciencesUniversity of AgderKristiansandNorway
| | | | - Sigbjørn Lien
- Faculty of BiosciencesNorwegian University of Life SciencesÅsNorway
| | - Michael Møller Hansen
- Department of Bioscience – Genetics, Ecology and EvolutionAarhus UniversityAarhusDenmark
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9
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Prodöhl PA, Ferguson A, Bradley CR, Ade R, Roberts C, Keay EJ, Costa AR, Hynes R. Impacts of acidification on brown trout Salmo trutta populations and the contribution of stocking to population recovery and genetic diversity. JOURNAL OF FISH BIOLOGY 2019; 95:719-742. [PMID: 31111501 PMCID: PMC6852074 DOI: 10.1111/jfb.14054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/20/2019] [Indexed: 05/25/2023]
Abstract
Anthropogenic acidification in SW-Scotland, from the early 19th Century onwards, led to the extinction of several loch (lake) brown trout (Salmo trutta) populations and substantial reductions in numbers in many others. Higher altitude populations with no stocking influence, which are isolated above natural and artificial barriers and subjected to the greatest effect of acidification, exhibited the least intrapopulation genetic diversity (34% of the allelic richness of the populations accessible to anadromous S. trutta). These, however, were characterised by the greatest interpopulation divergence (highest pairwise DEST 0.61 and FST 0.53 in contemporary samples) based on 16 microsatellite loci and are among the most differentiated S. trutta populations in NW-Europe. Five lochs above impassable waterfalls, where S. trutta were thought to be extinct, are documented as having been stocked in the late 1980s or 1990s. All five lochs now support self-sustaining S. trutta populations; three as a direct result of restoration stocking and two adjoining lochs largely arising from a small remnant wild population in one, but with some stocking input. The genetically unique Loch Grannoch S. trutta, which has been shown to have a heritable increased tolerance to acid conditions, was successfully used as a donor stock to restore populations in two acidic lochs. Loch Fleet S. trutta, which were re-established from four separate donor sources in the late 1980s, showed differential contribution from these ancestors and a higher genetic diversity than all 17 natural loch populations examined in the area. Genetically distinct inlet and outlet spawning S. trutta populations were found in this loch. Three genetically distinct sympatric populations of S. trutta were identified in Loch Grannoch, most likely representing recruitment from the three main spawning rivers. A distinct genetic signature of Loch Leven S. trutta, the progenitor of many Scottish farm strains, facilitated detection of stocking with these strains. One artificially created loch was shown to have a population genetically very similar to Loch Leven S. trutta. In spite of recorded historical supplemental stocking with Loch Leven derived farm strains, much of the indigenous S. trutta genetic diversity in the area remains intact, aside from the effects of acidification induced bottlenecks. Overall genetic diversity and extant populations have been increased by allochthonous stocking.
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Affiliation(s)
- Paulo A. Prodöhl
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Andrew Ferguson
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Caroline R. Bradley
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Robin Ade
- Dalry, Dumfries & GallowayScotlandUK
| | | | - E. J. Keay
- Marine Scotland, Freshwater Laboratory, FaskallyPitlochryUK
| | - Artur R. Costa
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | - Rosaleen Hynes
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
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10
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Ferguson A, Reed TE, Cross TF, McGinnity P, Prodöhl PA. Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. JOURNAL OF FISH BIOLOGY 2019; 95:692-718. [PMID: 31197849 PMCID: PMC6771713 DOI: 10.1111/jfb.14005] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/09/2019] [Indexed: 05/10/2023]
Abstract
Brown trout Salmo trutta is endemic to Europe, western Asia and north-western Africa; it is a prominent member of freshwater and coastal marine fish faunas. The species shows two resident (river-resident, lake-resident) and three main facultative migratory life histories (downstream-upstream within a river system, fluvial-adfluvial potamodromous; to and from a lake, lacustrine-adfluvial (inlet) or allacustrine (outlet) potamodromous; to and from the sea, anadromous). River-residency v. migration is a balance between enhanced feeding and thus growth advantages of migration to a particular habitat v. the costs of potentially greater mortality and energy expenditure. Fluvial-adfluvial migration usually has less feeding improvement, but less mortality risk, than lacustrine-adfluvial or allacustrine and anadromous, but the latter vary among catchments as to which is favoured. Indirect evidence suggests that around 50% of the variability in S. trutta migration v. residency, among individuals within a population, is due to genetic variance. This dichotomous decision can best be explained by the threshold-trait model of quantitative genetics. Thus, an individual's physiological condition (e.g., energy status) as regulated by environmental factors, genes and non-genetic parental effects, acts as the cue. The magnitude of this cue relative to a genetically predetermined individual threshold, governs whether it will migrate or sexually mature as a river-resident. This decision threshold occurs early in life and, if the choice is to migrate, a second threshold probably follows determining the age and timing of migration. Migration destination (mainstem river, lake, or sea) also appears to be genetically programmed. Decisions to migrate and ultimate destination result in a number of subsequent consequential changes such as parr-smolt transformation, sexual maturity and return migration. Strong associations with one or a few genes have been found for most aspects of the migratory syndrome and indirect evidence supports genetic involvement in all parts. Thus, migratory and resident life histories potentially evolve as a result of natural and anthropogenic environmental changes, which alter relative survival and reproduction. Knowledge of genetic determinants of the various components of migration in S. trutta lags substantially behind that of Oncorhynchus mykiss and other salmonines. Identification of genetic markers linked to migration components and especially to the migration-residency decision, is a prerequisite for facilitating detailed empirical studies. In order to predict effectively, through modelling, the effects of environmental changes, quantification of the relative fitness of different migratory traits and of their heritabilities, across a range of environmental conditions, is also urgently required in the face of the increasing pace of such changes.
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Affiliation(s)
- Andrew Ferguson
- School of Biological SciencesQueen's University BelfastBelfastUK
| | - Thomas E. Reed
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Tom F. Cross
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Paulo A. Prodöhl
- School of Biological SciencesQueen's University BelfastBelfastUK
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11
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Makhrov AA, Bolotov IN. Ecological Causes of High Morphological Plasticity of Members of a Taxon Inhabiting the Center of Its Origin (Exemplified by the Noble Salmons, Genus Salmo). BIOL BULL+ 2019. [DOI: 10.1134/s1062359019010059] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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McLoone P, Shephard S, Delanty K, Rocks K, Feeney R, Kelly F. Coexistence of pike Esox lucius and brown trout Salmo trutta in Irish lakes. JOURNAL OF FISH BIOLOGY 2018; 93:1005-1011. [PMID: 30251249 DOI: 10.1111/jfb.13811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
An environmental study of pike Esox lucius recorded their presence in 522 Irish lakes and that they coexisted with brown trout Salmo trutta in 97 of these. Statistical models, accounting for spatial non-independence among lakes, suggested that lakes with greater area, maximum depth and stream connectivity show a higher probability of coexistence. Introductions of E. lucius are likely to have negative effects on S. trutta stocks in small isolated lakes, but coexistence may be possible in larger systems.
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13
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Jacobs A, Hughes MR, Robinson PC, Adams CE, Elmer KR. The Genetic Architecture Underlying the Evolution of a Rare Piscivorous Life History Form in Brown Trout after Secondary Contact and Strong Introgression. Genes (Basel) 2018; 9:genes9060280. [PMID: 29857499 PMCID: PMC6026935 DOI: 10.3390/genes9060280] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/17/2023] Open
Abstract
Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout (Salmo trutta) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation.
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Affiliation(s)
- Arne Jacobs
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
| | - Martin R Hughes
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow G63 0AW, Scotland, UK.
| | - Paige C Robinson
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
| | - Colin E Adams
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
- Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, Loch Lomond, Glasgow G63 0AW, Scotland, UK.
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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14
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Dočkalová K, Holubcová J, Bacardit M, Bartrons M, Camarero L, Gallego E, Grimalt JO, Hardekopf D, Hořická Z, Rosseland BO, Tátosová J, Stuchlík E. Brown and brook trout populations in the Tatra Mountain lakes (Slovakia, Poland) and contamination by long-range transported pollutants. Biologia (Bratisl) 2015. [DOI: 10.1515/biolog-2015-0052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Boston ESM, Ian Montgomery W, Hynes R, Prodöhl PA. New insights on postglacial colonization in western Europe: the phylogeography of the Leisler's bat (Nyctalus leisleri). Proc Biol Sci 2015; 282:20142605. [PMID: 25716786 DOI: 10.1098/rspb.2014.2605] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Despite recent advances in the understanding of the interplay between a dynamic physical environment and phylogeography in Europe, the origins of contemporary Irish biota remain uncertain. Current thinking is that Ireland was colonized post-glacially from southern European refugia, following the end of the last glacial maximum (LGM), some 20 000 years BP. The Leisler's bat (Nyctalus leisleri), one of the few native Irish mammal species, is widely distributed throughout Europe but, with the exception of Ireland, is generally rare and considered vulnerable. We investigate the origins and phylogeographic relationships of Irish populations in relation to those across Europe, including the closely related species N. azoreum. We use a combination of approaches, including mitochondrial and nuclear DNA markers, in addition to approximate Bayesian computation and palaeo-climatic species distribution modelling. Molecular analyses revealed two distinct and diverse European mitochondrial DNA lineages, which probably diverged in separate glacial refugia. A western lineage, restricted to Ireland, Britain and the Azores, comprises Irish and British N. leisleri and N. azoreum specimens; an eastern lineage is distributed throughout mainland Europe. Palaeo-climatic projections indicate suitable habitats during the LGM, including known glacial refugia, in addition to potential novel cryptic refugia along the western fringe of Europe. These results may be applicable to populations of many species.
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Affiliation(s)
- Emma S M Boston
- Quercus, School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - W Ian Montgomery
- Quercus, School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Rosaleen Hynes
- Quercus, School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Paulo A Prodöhl
- Quercus, School of Biological Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
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16
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Ravinet M, Harrod C, Eizaguirre C, Prodöhl PA. Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization? Ecol Evol 2014; 4:2488-504. [PMID: 25360281 PMCID: PMC4203293 DOI: 10.1002/ece3.853] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/06/2013] [Indexed: 11/24/2022] Open
Abstract
Repeated recolonization of freshwater environments following Pleistocene glaciations has played a major role in the evolution and adaptation of anadromous taxa. Located at the western fringe of Europe, Ireland and Britain were likely recolonized rapidly by anadromous fishes from the North Atlantic following the last glacial maximum (LGM). While the presence of unique mitochondrial haplotypes in Ireland suggests that a cryptic northern refugium may have played a role in recolonization, no explicit test of this hypothesis has been conducted. The three-spined stickleback is native and ubiquitous to aquatic ecosystems throughout Ireland, making it an excellent model species with which to examine the biogeographical history of anadromous fishes in the region. We used mitochondrial and microsatellite markers to examine the presence of divergent evolutionary lineages and to assess broad-scale patterns of geographical clustering among postglacially isolated populations. Our results confirm that Ireland is a region of secondary contact for divergent mitochondrial lineages and that endemic haplotypes occur in populations in Central and Southern Ireland. To test whether a putative Irish lineage arose from a cryptic Irish refugium, we used approximate Bayesian computation (ABC). However, we found no support for this hypothesis. Instead, the Irish lineage likely diverged from the European lineage as a result of postglacial isolation of freshwater populations by rising sea levels. These findings emphasize the need to rigorously test biogeographical hypothesis and contribute further evidence that postglacial processes may have shaped genetic diversity in temperate fauna.
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Affiliation(s)
- Mark Ravinet
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Lovén Centre-Tjärnö, Department of Biology and Environmental Sciences, University of Gothenburg Gothenburg, Sweden
| | - Chris Harrod
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K ; Instituto de Ciencias Naturales Alexander Von Humboldt, Universidad de Antofagasta Chile
| | - Christophe Eizaguirre
- GEOMAR
- Helmholtz Centre for Ocean Research Duesternbrooker weg 20, 24105, Kiel, Germany ; Max Planck Institute for Evolutionary Biology August Thienemannstr. 2, 24306, Ploen, Germany
| | - Paulo A Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast Belfast, U.K
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17
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Keenan K, Bradley CR, Magee JJ, Hynes RA, Kennedy RJ, Crozier WW, Poole R, Cross TF, McGinnity P, Prodöhl PA. Beaufort trout MicroPlex: a high-throughput multiplex platform comprising 38 informative microsatellite loci for use in resident and anadromous (sea trout) brown trout Salmo trutta genetic studies. JOURNAL OF FISH BIOLOGY 2013; 82:1789-1804. [PMID: 23731137 DOI: 10.1111/jfb.12095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Accepted: 02/04/2013] [Indexed: 06/02/2023]
Abstract
A flexible panel consisting of 38 informative microsatellite markers for Salmo trutta is described. These markers were selected from a pool of over 150 candidate loci that can be readily amplified in four multiplex PCR groups but other permutations are also possible. The basic properties of each markers were assessed in six population samples from both the Burrishoole catchment, in the west of Ireland, and Lough Neagh, in Northern Ireland. A method to assess the relative utility of individual markers for the detection of population genetic structuring is also described. Given its flexibility, technical reliability and high degree of informativeness, the use of this panel of markers is advocated as a standard for S. trutta genetic studies.
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Affiliation(s)
- K Keenan
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
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18
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Gowell CP, Quinn TP, Taylor EB. Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in a south-western Alaskan lake. J Evol Biol 2012; 25:2432-48. [PMID: 23110688 DOI: 10.1111/jeb.12011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 08/26/2012] [Accepted: 09/06/2012] [Indexed: 11/28/2022]
Abstract
Ecologically, morphologically and genetically distinct populations within single taxa often coexist in postglacial lakes and have provided important model systems with which to investigate ecological and evolutionary processes such as niche partitioning and ecological speciation. Within the Salmonidae, these species complexes have been well studied, particularly within the Coregonus clupeaformis-C. laveratus (lake and European whitefish, respectively) group, but the phenomenon has been less well documented in the other whitefish genera, Prosopium and Stenodus. Here, we examined the morphology, feeding biology and genetic structure of three putative forms of the pygmy whitefish, Prosopium coulterii (Eigenmann & Eigenmann, 1892), first reported from Chignik Lake, south-western Alaska, over 40 years ago. Field collections and morphological analyses resolved a shallow water (< 5 m depth) low gill raker count form (< 15 first arch gill rakers), a deepwater (> 30 m), low gill raker form and a deepwater, high gill raker count (> 15 gill rakers) form. The two low gill raker count forms fed almost exclusively on benthic invertebrates (mostly chironomids), while the deepwater, high gill raker count form fed almost exclusively on zooplankton; differences in diet were also reflected in differences both in δ(13) C and δ(15) N stable isotopes. All three forms were characterized by the same major mitochondrial DNA clade that has been associated with persistence in, and postglacial dispersal from, a Beringian glacial refugium. Analysis of variation at nine microsatellite DNA loci indicated low, but significant differentiation among forms, especially between the two low gill raker count forms and the high gill raker count form. The extent of differentiation along phenotypic (considerable) and genetic (subtle) axes among the Chignik Lake forms is similar to that found among distinct taxa of Prosopium found in pre-glacial Bear Lake (Utah-Idaho, USA) which is probably at least ten times older than Chignik Lake. Our analyses illustrate the potential for the postglacial differentiation in traits subject to divergent natural selection across variable environments.
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Affiliation(s)
- C P Gowell
- Department of Biology, University of Puget Sound, Tacoma, WA, USA
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19
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Apostolidis AP, Stoumboudi MT, Kalogianni E, Cote G, Bernatchez L. Genetic divergence among native trout Salmo trutta populations from southern Balkans based on mitochondrial DNA and microsatellite variation. JOURNAL OF FISH BIOLOGY 2011; 79:1950-1960. [PMID: 22141897 DOI: 10.1111/j.1095-8649.2011.03136.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The genetic structure and the phylogenetic relationships among five Balkan populations of trout Salmo trutta that have been classified earlier into five different taxa were studied, using microsatellite and mitochondrial DNA (mtDNA) analyses. The pattern of population differentiation observed at microsatellites differed to that depicted by mtDNA variation, yet both methods indicated a very strong partitioning of the genetic variation among sampling locations. Results thus suggest that conservation strategies should be directed towards preserving the genetic integrity and uniqueness of each population.
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Affiliation(s)
- A P Apostolidis
- Lab of Ichthyology and Fisheries, Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Greece.
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