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Conservation Genetics of Mediterranean Brown Trout in Central Italy (Latium): A Multi-Marker Approach. WATER 2022. [DOI: 10.3390/w14060937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Brown trout is considered a complex of incipient species, including several phylogenetic lineages, whose natural distribution in the Mediterranean area has been altered, since the beginning of the 1900s, by massive introductions of domestic strains of Atlantic origin to support fisheries. Introduced trout naturalize in new suitable environments and extensively hybridize with native populations. Here, we characterized putatively neutral and adaptive genetic variability and population structure of Mediterranean brown trout from six river catchments in central peninsular Italy, as revealed by both mitochondrial (Control Region) and nuclear (microsatellites, LDH-C1, major histocompatibility complex) markers. We quantified the admixture of wild populations with hatchery strains and evaluated the effects of domestic trout introductions on shaping population genetics. Our analyses indicated: (1) a composite picture of genetic variability in the area, with the presence of all native Mediterranean trout mitochondrial lineages (“Adriatic”, “Mediterranean”, “marmoratus”), various frequencies of allochthonous genotypes and different rates of introgression among sampling sites; (2) asymmetric mito-nuclear introgression; (3) increasing nuclear marker diversity with increasing levels of admixture across populations; (4) strong population structure coupled with relatively low effective population size. Data allowed the identification of five management units and we propose specific actions to support ongoing and future conservation strategies within the examined area.
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Markevich GN, Izvekova EI, Anisimova LA, Mugue NS, Bonk TV, Esin EV. Annual Temperatures and Dynamics of Food Availability are Associated with the Pelagic-Benthic Diversification in a Sympatric Pair of Salmonid Fish. Evol Biol 2022. [DOI: 10.1007/s11692-022-09560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Gilbey J, Soshnina VA, Volkov AA, Zelenina DA. Comparative genetic variability of pink salmon from different parts of their range: native Pacific, artificially introduced White Sea and naturally invasive Atlantic Scottish rivers. JOURNAL OF FISH BIOLOGY 2022; 100:549-560. [PMID: 34837402 DOI: 10.1111/jfb.14966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 06/13/2023]
Abstract
Trans-oceanic movement, stocking and subsequent establishment of Pacific pink salmon (Oncorhynchus gorbuscha) into the Atlantic White Sea area have resulted in their spreading further across the northern Atlantic, with spawning being reported in a number of regions within this area. Such expansions of non-native species bring potential risks to the ecosystems in question. It has not yet been established if the spawning events of pink salmon observed are the result of self-sustaining populations in these areas, or are because of repeated invasions of strayers from the White Sea stocks. In 2017 pink salmon were observed in a number of Scottish rivers in historically large numbers. This study set out to examine genetic variation in these fish and compare this to fish in Pacific founder regions and the White Sea translocated populations. A total of 286 samples from Scotland, the Atlantic White Sea, the Pacific Okhotsk region and Northern Pacific Bering Sea were screened using a 1018 bp sequenced region of the Cytochrome b mtDNA gene and 205 of these samples for 13 microsatellites. Significant bottleneck and founder effects were observed in the White Sea stocks in both mitochondrial and nuclear DNA, including loss of diversity and changes in haplotype and allele proportions. Scottish fish were indistinguishable from White Sea populations and as such it was not possible to determine if the fish were strayers from this region or returning fish from previous spawning events in Scotland. Therefore, although the fish caught in Scotland have their origins in the White Sea population, it may not be easy to determine whether self-sustaining populations have, or are becoming, established in the UK using genetic analysis and other techniques may need to be used.
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Affiliation(s)
- John Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Pitlochry, UK
| | - Valeriia A Soshnina
- Russian Federal Institute for Fisheries and Oceanography, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Alexander A Volkov
- Russian Federal Institute for Fisheries and Oceanography, Moscow, Russia
| | - Daria A Zelenina
- Russian Federal Institute for Fisheries and Oceanography, Moscow, Russia
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Berrebi P, Jesenšek D, Laporte M, Crivelli AJ. Restoring marble trout genes in the Soča River (Slovenia). CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01430-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bielikova ОY, Mariutsa AE, Mruk AI, Tarasjuk SI, Romanenko VM. Genetic structure of rainbow trout Oncorhynchus mykiss (Salmoniformes, Salmonidae) from aquaculture by DNA-markers. BIOSYSTEMS DIVERSITY 2021. [DOI: 10.15421/012104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The rational use of valuable fish species from aquaculture is difficult to implement without knowledge of the state of the genetic structure of local stocks. Different types of DNA markers can be used to achieve the goals of selection and breeding work. The genetic structure of a local stock of rainbow trout (Oncorhynchus mykiss Walbaum, 1792) (Salmoniformes, Salmonidae) farmed in Ukraine was studied using DNA-markers: microsatellite (SSR-markers – simple-sequence repeats-markers) and intermicrosatellite (ISSR – inter-simple sequence repeat). Five fragments of trinucleotide microsatellite motifs with a single anchor nucleotide at the 3'-end were used as a primer for analysis by the ISSR-PCR method. Totally, 85 amplicons were obtained across the five loci, of which 92.9% were polymorphic. The total number of alleles ranged from 10 (marker (ACC)₆G) to 23 (marker (AGC)₆G). The following monomorphic amplicons were determined for the studied local stock of rainbow trout: according to marker (CTC)₆C – 770 and 520 bp bands, for the marker (GAG)₆C – 345, 295 and 260 bp, and for the marker (AGC)₆C – 350 bp. The average number of polymorphic bands per locus was 15.8. The selected ISSR primers had a level of polymorphic information content above the average. The most effective markers for molecular-genetic analysis of rainbow trout were (AGC)₆G and (AGC)₆C according to the percentage of polymorphic bands, marker index, effective multiplex ratio and resolving power. The selected ISSR loci allow the genetic structure of the studied local stock to be characterized using the total and the effective number of alleles per locus (Na and Ne were 1.9 and 1.4, respectively), the Shannon index (average value I was 0.4) and the unbiased expected heterozygosity (mean uHe = 0.3). Microsatellite-based analysis showed features of the genetic structure of the local stock of rainbow trout at six microsatellite loci (OMM 1032, OMM 1077, OMM 1088, Str 15, Str 60, Str 73). Allelic diversity was established and alleles with the highest frequency and most typical for the given stock were identified. The Shannon index and unbiased expected heterozygosity were determined using SSR-markers and were 1.42 and 0.79, respectively. This depicts the complexity of the population structure, a high level of genetic diversity and indicates a high level of heterozygosity of local stock. The “gene pool profile” established as a result of ISSR-PCR in the future will help to differentiate local stocks of rainbow trout in aquaculture of Ukraine. Microsatellite markers provide the ability to determine individual features of genetic variation of local populations and to conduct the management of genetic resources on fish farms.
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Škraba Jurlina D, Marić A, Mrdak D, Kanjuh T, Špelić I, Nikolić V, Piria M, Simonović P. Alternative Life-History in Native Trout (Salmo spp.) Suppresses the Invasive Effect of Alien Trout Strains Introduced Into Streams in the Western Part of the Balkans. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ősz Á, Horváth Á, Hoitsy G, Kánainé Sipos D, Keszte S, Sáfrány AJ, Marić S, Palkó C, Tóth B, Urbányi B, Kovács B. The genetic status of the Hungarian brown trout populations: exploration of a blind spot on the European map of Salmo trutta studies. PeerJ 2018; 6:e5152. [PMID: 30258703 PMCID: PMC6152457 DOI: 10.7717/peerj.5152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/11/2018] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Analyses of the control region sequences of European brown trout populations' mitrochondrial DNA have revealed five main evolutionary lineages (Atlantic, Danubian, Mediterranean, Adriatic, Marble) mostly relating to the main water basins; however, the hybridization between lineages were increasingly reported. Due to the hydrogeography of Hungary, wild populations should theoretically belong to the Danubian lineage, however, this has not been verified by genetic studies. METHODS In our study multiple molecular marker sets (mitochondrial sequence, microsatellites, PCR-RFLP of nuclear markers and sex marker) were used to investigate the genetic composition and population genetics of the brown trout populations in two broodstocks, six wild streams in Hungary and one Serbian population. RESULTS The admixture of Atlantic and Danubian lineages in these populations, except the Serbian population with pure Danubian origin, was observed by control region sequences of mitochondrial DNA and PCR-RFLP markers in the nuclear genome, and one unpublished Danubian haplotype was found in Hungarian populations. A sex-specific marker revealed equal gender ratio in broodstocks and Kemence stream, whereas in other wild streams the proportion of female individuals were less than 50%. Structure and principal component analyses based on the alleles of microsatellite loci also revealed overlapping populations, however the populations were still significantly different from each other and were mostly in Hardy-Weinberg equilibrium. DISCUSSION Stocking and migration can have a significant genetic impact on trout populations of wild streams, however there are no guidelines or common practices for stocking of small streams in Hungary, thus the genetic background of these populations should be considered when developing conservation actions.
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Affiliation(s)
- Ágnes Ősz
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Ákos Horváth
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | | | - Dóra Kánainé Sipos
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Szilvia Keszte
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Anna Júlia Sáfrány
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Saša Marić
- Institute of Zoology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Csaba Palkó
- Department of Animal Nutrition, Institute of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, Mosonmagyaróvár, Hungary
| | - Balázs Tóth
- Danube-Ipoly National Park Directorate, Budapest, Hungary
| | - Béla Urbányi
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
| | - Balázs Kovács
- Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, Gödöllő, Hungary
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Jagiełło K, Dobosz S, Zalewski T, Polonis M, Ocalewicz K. Developmental competence of eggs produced by rainbow trout Doubled Haploids (DHs) and generation of the clonal lines. Reprod Domest Anim 2018; 53:1176-1183. [PMID: 29956409 DOI: 10.1111/rda.13223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/23/2018] [Accepted: 05/10/2018] [Indexed: 11/27/2022]
Abstract
Poor quality eggs produced by the fully homozygous doubled haploids (DHs) may impair generation of clonal lines in fish species. In the present research, gynogenetic development of rainbow trout (Oncorhynchus mykiss) was induced in eggs originated from the DH females. Eggs were activated with the UV-irradiated grayling (Thymallus thymallus) spermatozoa and subjected to the high hydrostatic pressure (HHP) shock to provide diploid clonal individuals. Only two of four DH females produced eggs that were successfully activated by the irradiated spermatozoa and subsequently developed into the gynogenetic embryos. Survival rates of rainbow trout from the clonal lines equalled 21.5% and 19.8% during embryogenesis and decreased after hatching to 18.6% and 14.9%, respectively. Some of the dead rainbow trout clones collected between hatching and swim-up stage were emaciated and exhibited spinal deformities including scoliosis. Provided results confirmed limited developmental competences of eggs produced by rainbow trout DH females. Clonal rainbow trout developing in such eggs exhibited reduced survival and increased frequency of the body abnormalities.
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Affiliation(s)
- Krzysztof Jagiełło
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Stefan Dobosz
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Żukowo, Poland
| | - Tomasz Zalewski
- Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Żukowo, Poland
| | - Marcin Polonis
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
| | - Konrad Ocalewicz
- Faculty of Oceanography and Geography, Department of Marine Biology and Ecology, Institute of Oceanography, University of Gdansk, Gdynia, Poland
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Lehnert SJ, Pitcher TE, Devlin RH, Heath DD. Red and white Chinook salmon: genetic divergence and mate choice. Mol Ecol 2016; 25:1259-74. [DOI: 10.1111/mec.13560] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/17/2015] [Accepted: 01/15/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Sarah J. Lehnert
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Trevor E. Pitcher
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON N9B 3P4 Canada
- Department of Biological Sciences; University of Windsor; Windsor ON N9B 3P4 Canada
| | - Robert H. Devlin
- Center for Aquaculture and Environmental Research, Fisheries and Oceans Canada; 4160 Marine Drive West Vancouver BC V7V 1N6 Canada
| | - Daniel D. Heath
- Great Lakes Institute for Environmental Research; University of Windsor; Windsor ON N9B 3P4 Canada
- Department of Biological Sciences; University of Windsor; Windsor ON N9B 3P4 Canada
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May-McNally SL, Quinn TP, Taylor EB. Low levels of hybridization between sympatric Arctic char (Salvelinus alpinus) and Dolly Varden char (Salvelinus malma) highlights their genetic distinctiveness and ecological segregation. Ecol Evol 2015; 5:3031-45. [PMID: 26356310 PMCID: PMC4559047 DOI: 10.1002/ece3.1583] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/02/2015] [Accepted: 06/03/2015] [Indexed: 11/07/2022] Open
Abstract
Understanding the extent of interspecific hybridization and how ecological segregation may influence hybridization requires comprehensively sampling different habitats over a range of life history stages. Arctic char (Salvelinus alpinus) and Dolly Varden (S. malma) are recently diverged salmonid fishes that come into contact in several areas of the North Pacific where they occasionally hybridize. To better quantify the degree of hybridization and ecological segregation between these taxa, we sampled over 700 fish from multiple lake (littoral and profundal) and stream sites in two large, interconnected southwestern Alaskan lakes. Individuals were genotyped at 12 microsatellite markers, and genetic admixture (Q) values generated through Bayesian-based clustering revealed hybridization levels generally lower than reported in a previous study (<0.6% to 5% of samples classified as late-generation hybrids). Dolly Varden and Arctic char tended to make different use of stream habitats with the latter apparently abandoning streams for lake habitats after 2-3 years of age. Our results support the distinct biological species status of Dolly Varden and Arctic char and suggest that ecological segregation may be an important factor limiting opportunities for hybridization and/or the ecological performance of hybrid char.
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Affiliation(s)
- Shannan L May-McNally
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia 6270 University Ave., Vancouver, BC, Canada, V6T 1Z4
| | - Thomas P Quinn
- School of Aquatic and Fishery Sciences, University of Washington Seattle, Washington, 98195
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Beaty Biodiversity Museum, University of British Columbia 6270 University Ave., Vancouver, BC, Canada, V6T 1Z4
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Gratton P, Allegrucci G, Sbordoni V, Gandolfi A. The evolutionary jigsaw puzzle of the surviving trout (Salmo trutta L. complex) diversity in the Italian region. A multilocus Bayesian approach. Mol Phylogenet Evol 2014; 79:292-304. [PMID: 24997330 DOI: 10.1016/j.ympev.2014.06.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 10/25/2022]
Abstract
Mediterranean trout populations display a diversity of phenotypes, representing a valuable model for the study of adaptation and a puzzling dilemma for taxonomists and biogeographers, which is further entangled by the widespread introgression of allochthonous genes. In this paper we analysed DNA polymorphism at multiple loci (sequence variation of the mitochondrial control region and eight nuclear fragments and length variation at eleven nuclear microsatellite loci) in representative samples of the autochthonous taxonomic diversity described in Italian trout populations (Salmo marmoratus, S. carpio, S. cenerinus, S. cettii and S. fibreni) and in samples from hatchery-originated strains of Atlantic S. trutta. We employed model-based clustering and Approximate Bayesian Computation in order to: (i) describe the phylogeographic structure of Italian autochthonous trout populations; (ii) evaluate a set of evolutionary/biogeographic models. The inclusion of hatchery-originated strains allowed to account for man-mediated allochthonous introgression in Italian populations. Our results (i) showed that the analysed sample consists of two main autochthonous evolutionary lineages, including the marble trout populations on one side ('marble' lineage) and the three peninsular populations of S. cettii, S. cenerinus and S. fibreni on the other side ('peninsular' lineage); (ii) indicated that S. carpio originated from a 'peninsular' population, with a possible, limited contribution from the 'marble' lineage; (iii) pointed out that the 'marble' lineage started diverging before the separation of the 'peninsular' lineage from Atlantic S. trutta; (iv) suggested that a model of divergence involving gene flow from the 'peninsular' population into the ancestral gene pool of 'marble' trout is most consistent with the genetic data; (v) provided evidence that the autochthonous trout gene pools in the Tyrrhenian and Adriatic basins of the Italian peninsula started diverging very recently (most likely after the last glacial maximum).
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Affiliation(s)
- Paolo Gratton
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, I-38010 S. Michele all'Adige, Italy; Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00133 Roma, Italy.
| | - Giuliana Allegrucci
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00133 Roma, Italy
| | - Valerio Sbordoni
- Department of Biology, University of Rome "Tor Vergata", Via della Ricerca Scientifica, I-00133 Roma, Italy
| | - Andrea Gandolfi
- Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, I-38010 S. Michele all'Adige, Italy
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Berrebi P, Tougard C, Dubois S, Shao Z, Koutseri I, Petkovski S, Crivelli AJ. Genetic diversity and conservation of the Prespa trout in the Balkans. Int J Mol Sci 2013; 14:23454-70. [PMID: 24287917 PMCID: PMC3876056 DOI: 10.3390/ijms141223454] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/11/2013] [Accepted: 11/19/2013] [Indexed: 11/30/2022] Open
Abstract
The Balkans are known to have a high level of biodiversity and endemism. No less than 15 taxa have been recorded in salmonids of the Salmo genus. Among them, the Prespa trout is found in only four river systems flowing into Lake Macro Prespa, three in the Former Yugoslav Republic of Macedonia and one in Greece. This is the first comprehensive survey of all streams located within the Macro Prespa Basin, encompassing the whole taxon range. A large genetic sample of 536 Prespa trout was collected mainly between 2005 and 2007. The sampling included 59 individuals from the Golema river system, 93 from the Kranska, 260 from the Brajcinska, 119 from the Agios Germanos, and five individuals from the lake itself. These specimens were analyzed with six microsatellite markers and by sequencing the mitochondrial control region. Nuclear data were examined through multidimensional analysis and assignment tests. Five clusters were detected by assignment: Golema, Kranska, Brajcinska upstream, Rzanska Brajcinska tributary and Brajcinska downstream. Most of these river systems thus hosted differentiated Prespa trout populations (with past gene flows likely dating before the construction of dams), except Agios Germanos, which was found to be composed of 5% to 32% of each cluster. Among the five trout individuals from the lake, four originated from Kranska River and one was admixed. Supported parsimonious hypotheses are proposed to explain these specificities. Conservation of this endemic taxon should take these results into account. No translocation should be performed between different tributaries of the lake and preservation of the Brajcinska populations should address the upstream-downstream differentiation described.
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Affiliation(s)
- Patrick Berrebi
- Institut des Sciences de l’Evolution, UMR 5554 CNRS/UM2/IRD, Université Montpellier 2, cc065, Place Eugène Bataillon, Montpellier cedex 05 34095, France; E-Mails: (C.T.); (S.D.); (Z.S.)
| | - Christelle Tougard
- Institut des Sciences de l’Evolution, UMR 5554 CNRS/UM2/IRD, Université Montpellier 2, cc065, Place Eugène Bataillon, Montpellier cedex 05 34095, France; E-Mails: (C.T.); (S.D.); (Z.S.)
| | - Sophie Dubois
- Institut des Sciences de l’Evolution, UMR 5554 CNRS/UM2/IRD, Université Montpellier 2, cc065, Place Eugène Bataillon, Montpellier cedex 05 34095, France; E-Mails: (C.T.); (S.D.); (Z.S.)
| | - Zhaojun Shao
- Institut des Sciences de l’Evolution, UMR 5554 CNRS/UM2/IRD, Université Montpellier 2, cc065, Place Eugène Bataillon, Montpellier cedex 05 34095, France; E-Mails: (C.T.); (S.D.); (Z.S.)
| | - Irene Koutseri
- Society for the Protection of Prespa, Agios Germanos, Prespa 530 77, Greece; E-Mail:
| | - Svetozar Petkovski
- Society for the Investigation and Conservation of Biodiversity and the Sustainable Development of Natural Ecosystems-BIOECO, Briselska 12, Skopje 1000, FYR of Macedonia; E-Mail:
| | - Alain J. Crivelli
- Station Biologique de la Tour du Valat, Le Sambuc, Arles 13200, France; E-Mail:
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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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Consuegra S, Phillips N, Gajardo G, de Leaniz CG. Winning the invasion roulette: escapes from fish farms increase admixture and facilitate establishment of non-native rainbow trout. Evol Appl 2011; 4:660-71. [PMID: 25568013 PMCID: PMC3352532 DOI: 10.1111/j.1752-4571.2011.00189.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2010] [Accepted: 04/19/2011] [Indexed: 11/19/2022] Open
Abstract
Aquaculture is a major source of invasive aquatic species, despite the fact that cultured organisms often have low genetic diversity and tend to be maladapted to survive in the wild. Yet, to what extent aquaculture escapees become established by means of high propagule pressure and multiple origins is not clear. We analysed the genetic diversity of 15 established populations and four farmed stocks of non-native rainbow trout in Chile, a species first introduced for recreational fishing around 1900, but which has in recent decades escaped in large numbers from fish farms and become widespread. Aquaculture propagule pressure was a good predictor of the incidence of farm escapees, which represented 16% of all free-ranging rainbow trout and were present in 80% of the study rivers. Hybrids between farm escapes and established trout were present in all rivers at frequencies ranging between 7 and 69%, and population admixture was positively correlated with genetic diversity. We suggest that non-native salmonids introduced into the Southern Hemisphere could benefit from admixture because local adaptations may not have yet developed, and there may be initially little fitness loss resulting from outbreeding depression.
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Affiliation(s)
- Sofia Consuegra
- IBERS, Aberystwyth University, Penglais Campus Aberystwyth SY23 3DA, UK
| | - Nia Phillips
- IBERS, Aberystwyth University, Penglais Campus Aberystwyth SY23 3DA, UK
| | - Gonzalo Gajardo
- Laboratorio de Genética, Biodiversidad & Acuicultura, Universidad de Los Lagos Osorno, Chile
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Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon. CONSERV GENET 2010. [DOI: 10.1007/s10592-009-0034-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Rexroad CE, Vallejo RL. Estimates of linkage disequilibrium and effective population size in rainbow trout. BMC Genet 2009; 10:83. [PMID: 20003428 PMCID: PMC2800115 DOI: 10.1186/1471-2156-10-83] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/14/2009] [Indexed: 12/19/2022] Open
Abstract
Background The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout. Results We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures. Conclusions Our results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia 25430, USA.
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Johnson MA, Banks MA. Interlocus variance of FST provides evidence for directional selection over an olfactory receptor gene in Coho salmon (Oncorhynchus kisutch) populations. Mar Genomics 2009; 2:127-31. [DOI: 10.1016/j.margen.2009.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 07/21/2009] [Indexed: 11/25/2022]
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Glover KA. Genetic characterisation of farmed rainbow trout in Norway: intra- and inter-strain variation reveals potential for identification of escapees. BMC Genet 2008; 9:87. [PMID: 19087266 PMCID: PMC2640418 DOI: 10.1186/1471-2156-9-87] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2008] [Accepted: 12/16/2008] [Indexed: 11/25/2022] Open
Abstract
Background The rainbow trout (Oncorhynchus mykiss) is one of the most important aquaculture species in the world, and Norway is one of the largest producers. The present study was initiated in response to a request from the Norwegian police authority to identify the farm of origin for 35 escaped rainbow trout captured in a fjord. Eleven samples, each consisting of approximately 47 fish, were collected from the three farms operating in the fjord where the escapees were captured. In order to gain a better general understanding of the genetic structure of rainbow trout strains used in Norwegian aquaculture, seven samples (47 fish per sample) were collected from six farms located outside the region where the escapees were captured. All samples, including the escapees, were genotyped with 12 microsatellite loci. Results All samples displayed considerable genetic variability at all loci (mean number of alleles per locus per sample ranged from 5.4–8.6). Variable degrees of genetic differentiation were observed among the samples, with pair-wise FST values ranging from 0–0.127. Self-assignment tests conducted among the samples collected from farms outside the fjord where the escapees were observed gave an overall correct assignment of 82.5%, demonstrating potential for genetic identification of escapees. In the "real life" assignment of the 35 captured escapees, all were excluded from two of the samples included as controls in the analysis, and 26 were excluded from the third control sample. In contrast, only 1 of the escapees was excluded from the 11 pooled samples collected on the 3 farms operating in the fjord. Conclusion Considerable genetic variation exists within and among rainbow trout strains farmed in Norway. Together with modern statistical methods, this will provide commercial operators with a tool to monitor breeding and fish movements, and management authorities with the ability to identify the source of escapees. The data generated in this study were used by the Norwegian police to initiate an investigation of the company operating the three farms in the fjord where escapees were observed.
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Rexroad CE, Palti Y, Gahr SA, Vallejo RL. A second generation genetic map for rainbow trout (Oncorhynchus mykiss). BMC Genet 2008; 9:74. [PMID: 19019240 PMCID: PMC2605456 DOI: 10.1186/1471-2156-9-74] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 11/19/2008] [Indexed: 11/14/2022] Open
Abstract
Background Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species. Results A genetic map ordering 1124 microsatellite loci spanning a sex-averaged distance of 2927.10 cM (Kosambi) and having 2.6 cM resolution was constructed by genotyping 10 parents and 150 offspring from the National Center for Cool and Cold Water Aquaculture (NCCCWA) reference family mapping panel. Microsatellite markers, representing pairs of loci resulting from an evolutionarily recent whole genome duplication event, identified 180 duplicated regions within the rainbow trout genome. Microsatellites associated with genes through expressed sequence tags or bacterial artificial chromosomes produced comparative assignments with tetraodon, zebrafish, fugu, and medaka resulting in assignments of homology for 199 loci. Conclusion The second generation NCCCWA genetic map provides an increased microsatellite marker density and quantifies differences in recombination rate between the sexes in outbred populations. It has the potential to integrate with cytogenetic and other physical maps, identifying paralogous regions of the rainbow trout genome arising from the evolutionarily recent genome duplication event, and anchoring a comparative map with the zebrafish, medaka, tetraodon, and fugu genomes. This resource will facilitate the identification of genes affecting traits of interest through fine mapping and positional cloning of candidate genes.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia, USA.
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Jia ZY, Zhang YY, Shi LY, Bai QL, Jin SB, Mou ZB. Amplification of rainbow trout microsatellites in Brachymystax lenok. Mol Ecol Resour 2008; 8:1520-1. [PMID: 21586095 DOI: 10.1111/j.1755-0998.2008.02310.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Brachymystax lenok is a cold freshwater fish accustomed to inhabit relatively high concentration of dissolved oxygen and clean upper streams. Here we present 13 polymorphic microsatellite primer pairs from rainbow trout to amplify in 32 B. lenok individuals from Ussuri River of China. The number of alleles ranged from two to seven with an average of 3.9 per locus. Observed heterozygosity ranged from 0.0625 to 0.9677. One locus showed significant deviation from Hardy-Weinberg equilibrium. These 13 loci will provide a good basis for investigation of B. lenok population structure and genetic diversity in different distribution region.
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Affiliation(s)
- Z Y Jia
- Key Laboratory of Bioengineering Breeding of Northern Fishing, Ministry of Agriculture, Heilongjiang River Fishery Research Institute, Chinese Academy of Fishery Sciences, Harbin 150070, China, Biotechnology Department, Chengdong College of Northeast Agriculture University, Harbin 150030, China
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Khrustaleva AM, Zelenina DA. Seasonal and interannual variations of sockeye salmon (Oncorhynchus nerka) microsatellite DNA in two Kamchatka lake-river systems. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408070107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Williamson KS, Phillips R, May B. Characterization of a chromosomal rearrangement responsible for producing "apparent" XY-female fall-run Chinook salmon in California. J Hered 2008; 99:483-90. [PMID: 18504255 DOI: 10.1093/jhered/esn038] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) was used to identify the X and Y chromosomes of offspring produced by normal and "apparent" XY-female fall-run Chinook salmon (Oncorhynchus tshawytscha) from California. FISH experiments were performed using probes to 2 sex-linked loci, growth hormone pseudogene (GH-Psi), and OtY1, as well as a probe to a sex-linked microsatellite (Omy7INRA). Comparison of FISH staining patterns between the offspring produced by normal and apparent XY-females revealed that the apparent XY-female examined transmitted a "Y-like" chromosome with an attenuated OtY1 and GH-Psi signal to half of its offspring. Segregation analysis of microsatellites derived from rainbow trout (Oncorhynchus mykiss) with respect to phenotypic sex was carried out for 2 normal and 2 apparent XY-female Chinook salmon families. Inheritance patterns of Omy7INRA were consistent with this locus being closely linked to GH-Psi in males and in apparent XY-females carrying the Y-like chromosome. Another microsatellite locus (Omm1077) was closely linked to the primary sex-determining locus (SEX) in males but not to GH-Psi/OtY1 in apparent XY-females. The FISH analyses suggest that apparent XY-female fall-run Chinook salmon in California are not the product of a Y chromosome to autosome translocation. Despite the combined FISH and inheritance analyses, we were unable to differentiate between 2 alternative explanations for apparent XY-females, namely, recombination of markers between the sex chromosomes, or a Y chromosome with a dysfunctional or missing sex-determining region.
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Affiliation(s)
- Kevin S Williamson
- National Marine Fisheries Service, Northwest Fisheries Science Center, Conservation Biology Division, 2725 Montlake Boulevard East, Seattle, WA 98112, USA.
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Genetic variation of the major histocompatibility complex (MHC class II β gene) in the threatened Gila trout, Oncorhynchus gilae gilae. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9336-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Zelenina DA. Comparative study of the population structure and population assignment of sockeye salmon Oncorhynchus nerka from West Kamchatka based on RAPD-PCR and microsatellite polymorphism. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406050140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Anim Genet 2003; 34:102-15. [PMID: 12648093 DOI: 10.1046/j.1365-2052.2003.00957.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Androgenetic doubled haploid progeny produced from a cross between the Oregon State University and Arlee clonal rainbow trout (Oncorhynchus mykiss) lines, used for a previous published rainbow trout map, were used to update the map with the addition of more amplified fragment length polymorphic (AFLP) markers, microsatellites, type I and allozyme markers. We have added more than 900 markers, bringing the total number to 1359 genetic markers and the sex phenotype including 799 EcoRI AFLPs, 174 PstI AFLPs, 226 microsatellites, 72 VNTR, 38 SINE markers, 29 known genes, 12 minisatellites, five RAPDs, and four allozymes. Thirty major linkage groups were identified. Synteny of linkage groups in our map with the outcrossed microsatellite map has been established for all except one linkage group in this doubled haploid cross. Putative homeologous relationships among linkage groups, resulting from the autotetraploid nature of the salmonid genome, have been revealed based on the placement of duplicated microsatellites and type I loci.
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Affiliation(s)
- K M Nichols
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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