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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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Saint-Pé K, Leitwein M, Tissot L, Poulet N, Guinand B, Berrebi P, Marselli G, Lascaux JM, Gagnaire PA, Blanchet S. Development of a large SNPs resource and a low-density SNP array for brown trout (Salmo trutta) population genetics. BMC Genomics 2019; 20:582. [PMID: 31307373 PMCID: PMC6631668 DOI: 10.1186/s12864-019-5958-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 01/04/2023] Open
Abstract
Background The brown trout (Salmo trutta) is an economically and ecologically important species for which population genetic monitoring is frequently performed. The most commonly used genetic markers for this species are microsatellites and mitochondrial markers that lack replicability among laboratories, and a large genome coverage. An alternative that may be particularly efficient and universal is the development of small to large panels of Single Nucleotide Polymorphism markers (SNPs). Here, we used Restriction site Associated DNA sequences (RADs) markers to identify a set of 12,204 informative SNPs positioned on the brown trout linkage map and suitable for population genetics studies. Then, we used this novel resource to develop a cost-effective array of 192 SNPs (96 × 2) evenly spread on this map. This array was tested for genotyping success in five independent rivers occupied by two main brown trout evolutionary lineages (Atlantic -AT- and Mediterranean -ME-) on a total of 1862 individuals. Moreover, inference of admixture rate with domestic strains and population differentiation were assessed for a small river system (the Taurion River, 190 individuals) and results were compared to a panel of 13 microsatellites. Results A high genotyping success was observed for all rivers (< 1% of non-genotyped loci per individual), although some initially used SNP failed to be amplified, probably because of mutations in primers, and were replaced. These SNPs permitted to identify patterns of isolation-by-distance for some rivers. Finally, we found that microsatellite and SNP markers yielded very similar patterns for population differentiation and admixture assessments, with SNPs having better ability to detect introgression and differentiation. Conclusions The novel resources provided here opens new perspectives for universality and genome-wide studies in brown trout populations. Electronic supplementary material The online version of this article (10.1186/s12864-019-5958-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keoni Saint-Pé
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.
| | - Maeva Leitwein
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.,ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Laurence Tissot
- EDF R and D LNHE - Laboratoire National d'Hydraulique et Environnement, 6 quai Watier, 78401, Chatou Cedex, France
| | - Nicolas Poulet
- Pôle écohydraulique AFB-IMT, allée du Pr Camille Soula, 31400, Toulouse, France
| | - Bruno Guinand
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Patrick Berrebi
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France.,Present address: Genome - Research and Diagnostic, 697 avenue de Lunel, 34400, Saint-Just, France
| | - Geoffrey Marselli
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France
| | | | | | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS), Station d'Ecologie Théorique et Expérimentale, SETE, UMR 5321, 2 route du CNRS, 09200, Moulis, France.,Université de Toulouse, UPS, UMR 5174 (EDB), 118 route de Narbonne, F-31062, Toulouse cedex 4, France
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Lemopoulos A, Prokkola JM, Uusi‐Heikkilä S, Vasemägi A, Huusko A, Hyvärinen P, Koljonen M, Koskiniemi J, Vainikka A. Comparing RADseq and microsatellites for estimating genetic diversity and relatedness - Implications for brown trout conservation. Ecol Evol 2019; 9:2106-2120. [PMID: 30847096 PMCID: PMC6392366 DOI: 10.1002/ece3.4905] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/30/2018] [Accepted: 12/21/2018] [Indexed: 12/24/2022] Open
Abstract
The conservation and management of endangered species requires information on their genetic diversity, relatedness and population structure. The main genetic markers applied for these questions are microsatellites and single nucleotide polymorphisms (SNPs), the latter of which remain the more resource demanding approach in most cases. Here, we compare the performance of two approaches, SNPs obtained by restriction-site-associated DNA sequencing (RADseq) and 16 DNA microsatellite loci, for estimating genetic diversity, relatedness and genetic differentiation of three, small, geographically close wild brown trout (Salmo trutta) populations and a regionally used hatchery strain. The genetic differentiation, quantified as F ST, was similar when measured using 16 microsatellites and 4,876 SNPs. Based on both marker types, each brown trout population represented a distinct gene pool with a low level of interbreeding. Analysis of SNPs identified half- and full-siblings with a higher probability than the analysis based on microsatellites, and SNPs outperformed microsatellites in estimating individual-level multilocus heterozygosity. Overall, the results indicated that moderately polymorphic microsatellites and SNPs from RADseq agreed on estimates of population genetic structure in moderately diverged, small populations, but RADseq outperformed microsatellites for applications that required individual-level genotype information, such as quantifying relatedness and individual-level heterozygosity. The results can be applied to other small populations with low or moderate levels of genetic diversity.
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Affiliation(s)
- Alexandre Lemopoulos
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Department of BiologyUniversity of TurkuTurkuFinland
| | - Jenni M. Prokkola
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Silva Uusi‐Heikkilä
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anti Vasemägi
- Department of BiologyUniversity of TurkuTurkuFinland
- Department of Aquatic Resources, Institute of Freshwater ResearchSwedish University of Agricultural SciencesDrottningholmSweden
- Estonian University of Life SciencesInstitute of Veterinary Medicine and Animal SciencesTartuEstonia
| | - Ari Huusko
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (Luke), Kainuu Fisheries Research StationPaltamoFinland
| | | | - Jarmo Koskiniemi
- Department of Agricultural SciencesUniversity of HelsinkiHelsinkiFinland
| | - Anssi Vainikka
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
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Faulks L, Östman Ö. Genetic Diversity and Hybridisation between Native and Introduced Salmonidae Fishes in a Swedish Alpine Lake. PLoS One 2016; 11:e0152732. [PMID: 27032100 PMCID: PMC4816307 DOI: 10.1371/journal.pone.0152732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 03/18/2016] [Indexed: 01/11/2023] Open
Abstract
Understanding the processes underlying diversification can aid in formulating appropriate conservation management plans that help maintain the evolutionary potential of taxa, particularly under human-induced activities and climate change. Here we assessed the microsatellite genetic diversity and structure of three salmonid species, two native (Arctic charr, Salvelinus alpinus and brown trout, Salmo trutta) and one introduced (brook charr, Salvelinus fontinalis), from an alpine lake in sub-arctic Sweden, Lake Ånn. The genetic diversity of the three species was similar and sufficiently high from a conservation genetics perspective: corrected total heterozygosity, H’T = 0.54, 0.66, 0.60 and allelic richness, AR = 4.93, 5.53 and 5.26 for Arctic charr, brown trout and brook charr, respectively. There were indications of elevated inbreeding coefficients in brown trout (GIS = 0.144) and brook charr (GIS = 0.129) although sibling relationships were likely a confounding factor, as a high proportion of siblings were observed in all species within and among sampling locations. Overall genetic structure differed between species, Fst = 0.01, 0.02 and 0.04 in Arctic charr, brown trout and brook charr respectively, and there was differentiation at only a few specific locations. There was clear evidence of hybridisation between the native Arctic charr and the introduced brook charr, with 6% of individuals being hybrids, all of which were sampled in tributary streams. The ecological and evolutionary consequences of the observed hybridisation are priorities for further research and the conservation of the evolutionary potential of native salmonid species.
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Affiliation(s)
- Leanne Faulks
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Sugadaira Montane Research Centre, University of Tsukuba, Sugadaira-kogen 1278–294, Ueda, Nagano, 386–2204, Japan
- * E-mail:
| | - Örjan Östman
- Department of Ecology and Genetics – Animal Ecology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Department of Aquatic Resources, Institute of Coastal Research, Skolvägen 6, 742 42 Öregrund, Sweden
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Swatdipong A, Vasemägi A, Niva T, Koljonen ML, Primmer CR. Genetic mixed-stock analysis of lake-run brown trout Salmo trutta fishery catches in the Inari Basin, northern Finland: implications for conservation and management. JOURNAL OF FISH BIOLOGY 2013; 83:598-617. [PMID: 23991877 DOI: 10.1111/jfb.12199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2011] [Accepted: 06/14/2013] [Indexed: 06/02/2023]
Abstract
Genetic mixed-stock analysis (MSA) of wild lake-run brown trout Salmo trutta fishery catches (n = 665) from the Inari Basin (northern Finland) between 2006 and 2008 was carried out using a previously characterized baseline with 30 populations (n = 813) and 13 microsatellite loci. Altogether, 12 populations contributed significantly to mixed-stock fisheries, with the Ivalojoki system being the major contributor (70%) to the total catch. When catches were analysed regionally, geographically nearby populations were the main contributors to the local catches, indicating that a large proportion of S. trutta occupy lacustrine areas near the natal river mouth rather than dispersing throughout the lake. Similarly, far upstream populations contributed insignificantly to catches. These findings have important implications for the conservation and sustainable fishery management of the Inari system.
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Affiliation(s)
- A Swatdipong
- Department of Biology, University of Turku, Itäinenpitkäkatu 2, 20014 Turku, Finland
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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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7
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Pukk L, Kuparinen A, Järv L, Gross R, Vasemägi A. Genetic and life-history changes associated with fisheries-induced population collapse. Evol Appl 2013; 6:749-760. [PMID: 29387163 PMCID: PMC5779128 DOI: 10.1111/eva.12060] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 11/30/2022] Open
Abstract
Over the recent years, growing number of studies suggests that intensive size-selective fishing can cause evolutionary changes in life-history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. We detected marked changes in size- and age-distributions and increase in juvenile growth rate. We also observed reduction of age at sexual maturity in males that has frequently been considered to support the hypothesis of fisheries-induced evolution. However, combined individual-based life-history and genetic analyses indicated increased immigration of foreign individuals with different life-history patterns as an alternative mechanism behind the observed phenotypic change. This study demonstrates the value of combining genetic and phenotypic analyses and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.
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Affiliation(s)
- Lilian Pukk
- Department of Aquaculture Estonian University of Life Sciences Estonia
| | - Anna Kuparinen
- Department of Environmental Sciences University of Helsinki Finland.,Ecological Genetics Research Unit Department of Biosciences University of Helsinki Finland
| | - Leili Järv
- Estonian Marine Institute University of Tartu Estonia
| | - Riho Gross
- Department of Aquaculture Estonian University of Life Sciences Estonia
| | - Anti Vasemägi
- Department of Aquaculture Estonian University of Life Sciences Estonia.,Department of Biology University of Turku Finland
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Thaulow J, Borgstrøm R, Heun M. Brown trout population structure highly affected by multiple stocking and river diversion in a high mountain national park. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0438-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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