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Bekkevold D, Besnier F, Frank‐Gopolos T, Nielsen EE, Glover KA. Introgression affects Salmo trutta juvenile life-history traits generations after stocking with non-native strains. Evol Appl 2024; 17:e13725. [PMID: 38962360 PMCID: PMC11219512 DOI: 10.1111/eva.13725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 07/05/2024] Open
Abstract
Introgression of non-native conspecifics changes the genetic composition of wild populations, potentially leading to loss of local adaptations and fitness declines. However, long-term data from wild populations are still relatively few. Here, we studied the effects of introgression in a Danish brown trout (Salmo trutta, L.) population, subjected to intensive stocking with domesticated hatchery fish of non-native origin. We used wild-caught genetically wild and admixed trout as well as fish from the partly domesticated hatchery strain used for stocking the river up until ~15 years prior to this study, to produce 22 families varying in hatchery/wild admixture. Following a replicated common-garden experiment conducted in fish tanks from first feeding through 23 weeks at 7, 12, and 16°C, we observed a significant positive relationship between family admixture and fish size upon termination, an effect observed through all levels of admixture. Furthermore, the admixture effect was most distinct at the higher rearing temperatures. Although the hatchery strain used for stocking had been in culture for ~7 generations, it had not been deliberately selected for increased growth. These data thus demonstrate: (i) that growth had increased in the hatchery strain even in the absence of deliberate directional selection for this trait, (ii) that the increasing effect of admixture by temperature could represent inadvertent selection for performance in the hatchery strain at higher temperatures, and most significantly, (iii) that despite undergoing up to five generations of natural selection in the admixed wild population, the genetically increased growth potential was still detectable and thus persistent. Our findings suggest that altered growth patterns and potentially their cascading effects are of importance to the severity of hatchery/wild introgression, especially under changing-climate scenarios and are of general significance to conservation practitioners seeking to evaluate long-term effects of intra-specific hybridization including under recovery.
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Affiliation(s)
- Dorte Bekkevold
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | - Thomas Frank‐Gopolos
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | - Einar E. Nielsen
- National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
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Salguero‐Gómez R, Evans DM, Gaillard J, Lancaster L, Sanders NJ, Scandrett K, Meyer J. Time counts in animal ecology. J Anim Ecol 2022; 91:2154-2157. [DOI: 10.1111/1365-2656.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
Affiliation(s)
| | - Darren M. Evans
- School of Natural and Environmental Sciences Newcastle University Newcastle‐upon‐Tyne UK
| | - Jean‐Michel Gaillard
- Mixed Research Unit (UMR 5558) “Biometry & Evolutionary Biology” University Claude Bernard Lyon 1, Campus de la Doua, Bâtiment Mendel Villeurbanne Cedex France
| | - Lesley Lancaster
- School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Nathan J. Sanders
- Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor Michigan USA
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The Ten Commandments of Successful Fishery Management of Wild Brown Trout Salmo trutta Populations in Salmonid Streams in the Bohemian Region (Czech Republic). APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12094602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brown trout Salmo trutta is a fish species that is vulnerable to climate change and anthropogenic activities in its native range. The case studies of successful restoration of brown trout populations are rare. In this study, fishery managers who successfully restored brown trout populations are sharing their know-how and advice about their conservation strategy. Overall, twenty fishery managers were interviewed to give advice about their successful conservation practices of local brown trout populations. Using a qualitative analysis method, ten main recommendations were extracted: (1) assess the status of local brown trout populations, (2) form a union of fisheries managers and work together, (3) support the ability of the streams to retain water, (4) prevent artificial removal of water from the salmonid streams, (5) adjust the brown trout stocking strategy to individual streams, (6) set strict protection of native wild brown trout populations, (7) enforce angling bans and regulations, (8) support the rearing of brown trout in the aquaculture sector, (9) limit brown trout stocking to genetically native fish, and (10) stock smaller 0 + brown trout instead of large adult ones. In conclusion, the fishery managers agreed on the basic management steps that need to be made to conserve brown trout populations.
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Duval E, Skaala Ø, Quintela M, Dahle G, Delaval A, Wennevik V, Glover KA, Hansen MM. Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run. BMC Ecol Evol 2021; 21:143. [PMID: 34256705 PMCID: PMC8276402 DOI: 10.1186/s12862-021-01876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
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Affiliation(s)
- Eloïse Duval
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Theoretical and Experimental Ecology Station, UMR-5321, CNRS, University of Toulouse III Paul Sabatier, 2 route du CNRS, 09200, Moulis, France.
| | - Øystein Skaala
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| | - María Quintela
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Geir Dahle
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Aurélien Delaval
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Vidar Wennevik
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Kevin A Glover
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Michael M Hansen
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
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Rich C, Reilly SB, Sinervo B. Relaxed predation selection on rare morphs of Ensatina salamanders (Caudata: Plethodontidae) promotes a polymorphic population in a novel dune sand habitat. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The ring species Ensatina represents a classic example of locally adapted lineages. The Monterey ensatina (Ensatina eschscholtzii eschscholtzii) is a cryptic subspecies with brown coloration, although a recently discovered polymorphic population within a wind-blown sand region also contains leucistic (pink) and xanthistic (orange) morphs. In the present study, the frequency of leucism/xanthism was mapped across the subspecies’ range, revealing that these morphs are generally rare or absent except within regions containing light-coloured substrate. Attack rates were estimated using clay models of the three morphs, deployed only at the crepuscular period and during the night, on both light and dark substrates at a site within the dune sand region. Model selection found that the interaction between morph and substrate colour best predicted attack rates. Typical morphs had equal attack rates on both substrates while xanthistic and leucistic morphs incurred significantly fewer attacks on light vs. dark substrate, and there was no significant difference in attack rates among morphs on light substrates. These results support the idea that xanthistic and leucistic morphs are poorly adapted for dark substrates compared to typical morphs, but they are more or less equally adapted for light substrates. We suggest that this microgeographic island of relaxed selection on light-coloured morphs helps to explain the existence of this polymorphic population.
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Affiliation(s)
- Caitlyn Rich
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Sean B Reilly
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
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6
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An open-source database model and collections management system for fish scale and otolith archives. ECOL INFORM 2020. [DOI: 10.1016/j.ecoinf.2020.101115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Dermond P, Sperlich N, Brodersen J. Heritable morphological differentiation in salmonids from two distinct stream types. JOURNAL OF FISH BIOLOGY 2019; 95:1215-1222. [PMID: 31418819 DOI: 10.1111/jfb.14121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
We tested for phenotype-to-habitat associations in brown trout Salmo trutta populations from two ecologically different habitat types; i.e., groundwater and surface-water-fed streams. Additionally, we raised captive offspring from two such populations under standardised conditions to test whether potential phenotypic differentiation would be passed on to offspring. We found analogous differentiation by habitat in multiple wild populations. Some of these morphological differences were at least partially inherited by offspring. We suggest that this could have implications for both scientists and fisheries authorities studying or managing trout populations.
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Affiliation(s)
- Philip Dermond
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Nicola Sperlich
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Jakob Brodersen
- Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Centre of Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
- Department of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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8
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Baggio RA, Araujo SB, Ayllón D, Boeger WA. Dams cause genetic homogenization in populations of fish that present homing behavior: Evidence from a demogenetic individual-based model. Ecol Modell 2018. [DOI: 10.1016/j.ecolmodel.2018.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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9
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Ikediashi C, Paris JR, King RA, Beaumont WRC, Ibbotson A, Stevens JR. Atlantic salmon Salmo salar in the chalk streams of England are genetically unique. JOURNAL OF FISH BIOLOGY 2018; 92:621-641. [PMID: 29385651 DOI: 10.1111/jfb.13538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/14/2017] [Indexed: 06/07/2023]
Abstract
Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar.
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Affiliation(s)
- C Ikediashi
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - J R Paris
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - R A King
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
| | - W R C Beaumont
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - A Ibbotson
- Salmon & Trout Research Centre, Game & Wildlife Conservation Trust (GWCT), East Stoke, Wareham, Dorset BH20 6BB, U.K
| | - J R Stevens
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, U.K
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10
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Spatiotemporal genetic structure of anadromous Arctic char (Salvelinus alpinus) populations in a region experiencing pronounced climate change. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1047-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Birnie-Gauvin K, Peiman KS, Larsen MH, Aarestrup K, Gilmour KM, Cooke SJ. Comparison of vegetable shortening and cocoa butter as vehicles for cortisol manipulation in Salmo trutta. JOURNAL OF FISH BIOLOGY 2018; 92:229-236. [PMID: 29194613 DOI: 10.1111/jfb.13513] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 11/06/2017] [Indexed: 06/07/2023]
Abstract
This study demonstrates that vegetable shortening and cocoa butter are two effective vehicles for intraperitoneal cortisol implants in juvenile teleosts, specifically brown trout Salmo trutta, residing in north temperate freshwater environments. Each vehicle showed a different pattern of cortisol elevation. Vegetable shortening was found to be a more suitable vehicle for long-term cortisol elevation [elevated at 3, 6 and 9 days post treatment (dpt)], while cocoa butter may be better suited for short-term cortisol elevation (only elevated at 3 dpt). Additionally, plasma cortisol levels were higher with cortisol-vegetable shortening than with cortisol-cocoa butter implants. Plasma glucose levels were elevated 6 and 9 dpt for fishes injected with cortisol-vegetable shortening, but did not change relative to controls and shams in cortisol-cocoa butter fishes. In conclusion, vegetable shortening and cocoa butter are both viable techniques for cortisol manipulation in fishes in temperate climates, providing researchers with different options depending on study objectives.
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Affiliation(s)
- K Birnie-Gauvin
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - K S Peiman
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - M H Larsen
- Danish Centre for Wild Salmon, Brusgårdsvej 15, 8960 Randers, Denmark
| | - K Aarestrup
- DTU AQUA, National Institute of Aquatic Resources, Section for Freshwater Fisheries and Ecology, Technical University of Denmark, Vejlsøvej 39, 8600 Silkeborg, Denmark
| | - K M Gilmour
- Department of Biology, University of Ottawa, 30 Marie-Curie, Ottawa, ON, K1N 6N5, Canada
| | - S J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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12
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Peiman KS, Birnie-Gauvin K, Larsen MH, Colborne SF, Gilmour KM, Aarestrup K, Willmore WG, Cooke SJ. Morphological, physiological and dietary covariation in migratory and resident adult brown trout (Salmo trutta). ZOOLOGY 2017; 123:79-90. [PMID: 28807503 DOI: 10.1016/j.zool.2017.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 07/06/2017] [Accepted: 07/06/2017] [Indexed: 12/21/2022]
Abstract
The causes and consequences of trait relationships within and among the categories of physiology, morphology, and life-history remain poorly studied. Few studies cross the boundaries of these categories, and recent reviews have pointed out not only the dearth of evidence for among-category correlations but that trait relationships may change depending on the ecological conditions a population faces. We examined changes in mean values and correlations between traits in a partially migrant population of brown trout when migrant sea-run and resident stream forms were breeding sympatrically. Within each sex and life-history strategy group, we used carbon and nitrogen stable isotopes to assess trophic level and habitat use; assessed morphology which reflects swimming and foraging ability; measured circulating cortisol as it is released in response to stressors and is involved in the transition from salt to freshwater; and determined oxidative status by measuring oxidative stress and antioxidants. We found that sea-run trout were larger and had higher values of stable isotopes, cortisol and oxidative stress compared to residents. Most groups showed some correlations between morphology and diet, indicating individual resource specialization was occurring, and we found consistent correlations between morphology and cortisol. Additionally, relationships differed between the sexes (cortisol and oxidative status were related in females but not males) and between life-history strategies (habitat use was related to oxidative status in male sea-run trout but not in either sex of residents). The differing patterns of covariation between the two life-history strategies and between the sexes suggest that the relationships among phenotypic traits are subjected to different selection pressures, illustrating the importance of integrating multiple phenotypic measures across different trait categories and contrasting life-history strategies.
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Affiliation(s)
- Kathryn S Peiman
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, ON, Canada.
| | - Kim Birnie-Gauvin
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, ON, Canada; Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada; DTU AQUA, National Institute of Aquatic Resources, Section for Freshwater Fisheries Ecology, Technical University of Denmark, Silkeborg, Denmark
| | - Martin H Larsen
- DTU AQUA, National Institute of Aquatic Resources, Section for Freshwater Fisheries Ecology, Technical University of Denmark, Silkeborg, Denmark; Danish Centre for Wild Salmon, Randers, Denmark
| | - Scott F Colborne
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | | | - Kim Aarestrup
- DTU AQUA, National Institute of Aquatic Resources, Section for Freshwater Fisheries Ecology, Technical University of Denmark, Silkeborg, Denmark
| | - William G Willmore
- Department of Biology and Institute of Biochemistry, Carleton University, Ottawa, ON, Canada
| | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology and Institute of Environmental Science, Carleton University, Ottawa, ON, Canada
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13
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Harris LN, Palstra FP, Bajno R, Gallagher CP, Howland KL, Taylor EB, Reist JD. Assessing conservation risks to populations of an anadromous Arctic salmonid, the northern Dolly Varden (Salvelinus malma malma), via estimates of effective and census population sizes and approximate Bayesian computation. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0915-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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An assessment of spatio-temporal genetic variation in the South African abalone (Haliotis midae), using SNPs: implications for conservation management. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0879-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Pujolar JM, Vincenzi S, Zane L, Crivelli AJ. Temporal changes in allele frequencies in a small marble trout Salmo marmoratus population threatened by extreme flood events. JOURNAL OF FISH BIOLOGY 2016; 88:1175-1190. [PMID: 26832308 DOI: 10.1111/jfb.12897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/14/2015] [Indexed: 06/05/2023]
Abstract
The effect of extreme floods on the genetic composition of marble trout Salmo marmoratus living in Lipovscek, a tributary of the Soca River in Slovenia, which has been affected by multiple destructive flood events for centuries was investigated. By monitoring genetic variability during the period 2004-2011, apparent signatures of genetic erosion including a decline in observed and expected heterozygosities and allelic richness were observed. Contemporary effective population size was estimated between 11 and 55 individuals, which is congruent with census data. The data suggest asymmetric gene flow between the two sections of the river. The existence of substantial downstream migration (15-19%) was confirmed by paternity analysis. A small (1-3%) upstream migration was also suggested, which was confirmed by tagging data. Overall, low genetic diversity has not prevented the survival of the Lipovscek population, which might be a common feature of salmonid freshwater populations.
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Affiliation(s)
- J M Pujolar
- Department of Bioscience, Aarhus University, DK-8000, Aarhus, Denmark
| | - S Vincenzi
- Center for Stock Assessment Research, Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA, 95064, U.S.A
- Department of Environmental Sciences, University of Parma, 43100, Parma, Italy
| | - L Zane
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - A J Crivelli
- Station Biologique de la Tour du Valat, 13200, Arles, France
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16
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Benavente JN, Seeb LW, Seeb JE, Arismendi I, Hernández CE, Gajardo G, Galleguillos R, Cádiz MI, Musleh SS, Gomez-Uchida D. Temporal Genetic Variance and Propagule-Driven Genetic Structure Characterize Naturalized Rainbow Trout (Oncorhynchus mykiss) from a Patagonian Lake Impacted by Trout Farming. PLoS One 2015; 10:e0142040. [PMID: 26544983 PMCID: PMC4636326 DOI: 10.1371/journal.pone.0142040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/17/2015] [Indexed: 12/30/2022] Open
Abstract
Knowledge about the genetic underpinnings of invasions—a theme addressed by invasion genetics as a discipline—is still scarce amid well documented ecological impacts of non-native species on ecosystems of Patagonia in South America. One of the most invasive species in Patagonia’s freshwater systems and elsewhere is rainbow trout (Oncorhynchus mykiss). This species was introduced to Chile during the early twentieth century for stocking and promoting recreational fishing; during the late twentieth century was reintroduced for farming purposes and is now naturalized. We used population- and individual-based inference from single nucleotide polymorphisms (SNPs) to illuminate three objectives related to the establishment and naturalization of Rainbow Trout in Lake Llanquihue. This lake has been intensively used for trout farming during the last three decades. Our results emanate from samples collected from five inlet streams over two seasons, winter and spring. First, we found that significant intra- population (temporal) genetic variance was greater than inter-population (spatial) genetic variance, downplaying the importance of spatial divergence during the process of naturalization. Allele frequency differences between cohorts, consistent with variation in fish length between spring and winter collections, might explain temporal genetic differences. Second, individual-based Bayesian clustering suggested that genetic structure within Lake Llanquihue was largely driven by putative farm propagules found at one single stream during spring, but not in winter. This suggests that farm broodstock might migrate upstream to breed during spring at that particular stream. It is unclear whether interbreeding has occurred between “pure” naturalized and farm trout in this and other streams. Third, estimates of the annual number of breeders (Nb) were below 73 in half of the collections, suggestive of genetically small and recently founded populations that might experience substantial genetic drift. Our results reinforce the notion that naturalized trout originated recently from a small yet genetically diverse source and that farm propagules might have played a significant role in the invasion of Rainbow Trout within a single lake with intensive trout farming. Our results also argue for proficient mitigation measures that include management of escapes and strategies to minimize unintentional releases from farm facilities.
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Affiliation(s)
- Javiera N Benavente
- Department of Zoology, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile
| | - Lisa W Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195-5020, United States of America
| | - James E Seeb
- School of Aquatic and Fishery Sciences, University of Washington, Box 355020, Seattle, WA, 98195-5020, United States of America
| | - Ivan Arismendi
- Department of Fisheries & Wildlife, Oregon State University, 104 Nash Hall, 2820 SW Campus Way, Corvallis, OR, 97331, United States of America
| | - Cristián E Hernández
- Department of Zoology, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Ricardo Galleguillos
- Department of Oceanography, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile
| | - Maria I Cádiz
- Department of Zoology, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Barrio Universitario s/n, Universidad de Concepcion, Concepcion, Chile
| | - Selim S Musleh
- Department of Zoology, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile.,Department of Oceanography, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile
| | - Daniel Gomez-Uchida
- Department of Zoology, Universidad de Concepcion, Casilla 160-C, Concepcion, Chile.,Interdisciplinary Center for Aquaculture Research (INCAR), Barrio Universitario s/n, Universidad de Concepcion, Concepcion, Chile
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17
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O'Toole CL, Reed TE, Bailie D, Bradley C, Cotter D, Coughlan J, Cross T, Dillane E, McEvoy S, Ó Maoiléidigh N, Prodöhl P, Rogan G, McGinnity P. The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature. Evol Appl 2015; 8:881-900. [PMID: 26495041 PMCID: PMC4610385 DOI: 10.1111/eva.12299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/08/2015] [Indexed: 11/18/2022] Open
Abstract
Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population. Experimental groups did not differ in wild smolt output but a catastrophic flood event may have limited our ability to detect freshwater performance differences, which were evident in a previous study. Foreign parr exhibited higher, and hybrids intermediate, emigration rates from the natal stream relative to local parr, consistent with genetically based behavioural differences. Adult return rates were lower for the foreign compared to the local group. Overall lifetime success of foreigners and hybrids relative to locals was estimated at 31% and 40% (mean of both hybrid groups), respectively. The results imply a genetic basis to fitness differences among populations separated by only 50 km, driven largely by variation in smolt to adult return rates. Hence even if supplementary stocking programs obtain broodstock from neighbouring rivers, the risk of extrinsic outbreeding depression may be high.
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Affiliation(s)
- Ciar L O'Toole
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
| | - Thomas E Reed
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
| | - Deborah Bailie
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Northern Ireland
| | - Caroline Bradley
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Northern Ireland
| | | | - Jamie Coughlan
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
| | - Tom Cross
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
| | - Eileen Dillane
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
| | - Sarah McEvoy
- Marine Institute, Furnace Newport, Co. Mayo, Ireland
| | | | - Paulo Prodöhl
- Institute for Global Food Security, School of Biological Sciences, Medical Biology Centre, Queen's University Belfast, Northern Ireland
| | - Ger Rogan
- Marine Institute, Furnace Newport, Co. Mayo, Ireland
| | - Philip McGinnity
- School of Biological, Earth & Environmental Sciences, University College Cork Cork, Ireland
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18
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Konijnendijk N, Shikano T, Daneels D, Volckaert FAM, Raeymaekers JAM. Signatures of selection in the three-spined stickleback along a small-scale brackish water - freshwater transition zone. Ecol Evol 2015; 5:4174-86. [PMID: 26445666 PMCID: PMC4588664 DOI: 10.1002/ece3.1671] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 07/13/2015] [Accepted: 07/22/2015] [Indexed: 01/31/2023] Open
Abstract
Local adaptation is often obvious when gene flow is impeded, such as observed at large spatial scales and across strong ecological contrasts. However, it becomes less certain at small scales such as between adjacent populations or across weak ecological contrasts, when gene flow is strong. While studies on genomic adaptation tend to focus on the former, less is known about the genomic targets of natural selection in the latter situation. In this study, we investigate genomic adaptation in populations of the three-spined stickleback Gasterosteus aculeatus L. across a small-scale ecological transition with salinities ranging from brackish to fresh. Adaptation to salinity has been repeatedly demonstrated in this species. A genome scan based on 87 microsatellite markers revealed only few signatures of selection, likely owing to the constraints that homogenizing gene flow puts on adaptive divergence. However, the detected loci appear repeatedly as targets of selection in similar studies of genomic adaptation in the three-spined stickleback. We conclude that the signature of genomic selection in the face of strong gene flow is weak, yet detectable. We argue that the range of studies of genomic divergence should be extended to include more systems characterized by limited geographical and ecological isolation, which is often a realistic setting in nature.
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Affiliation(s)
- Nellie Konijnendijk
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Takahito Shikano
- Ecological Genetics Research Unit Department of Biosciences University of Helsinki P.O. Box 65 FI-000 14 Helsinki Finland
| | - Dorien Daneels
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
| | - Joost A M Raeymaekers
- Laboratory of Biodiversity and Evolutionary Genomics University of Leuven Ch. Deberiotstraat 32, B-3000 Leuven Belgium
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19
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20
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Maebe K, Meeus I, Ganne M, De Meulemeester T, Biesmeijer K, Smagghe G. Microsatellite Analysis of Museum Specimens Reveals Historical Differences in Genetic Diversity between Declining and More Stable Bombus Species. PLoS One 2015; 10:e0127870. [PMID: 26061732 PMCID: PMC4464549 DOI: 10.1371/journal.pone.0127870] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 04/21/2015] [Indexed: 11/19/2022] Open
Abstract
Worldwide most pollinators, e.g. bumblebees, are undergoing global declines. Loss of genetic diversity can play an essential role in these observed declines. In this paper, we investigated the level of genetic diversity of seven declining Bombus species and four more stable species with the use of microsatellite loci. Hereto we genotyped a unique collection of museum specimens. Specimens were collected between 1918 and 1926, in 6 provinces of the Netherlands which allowed us to make interspecific comparisons of genetic diversity. For the stable species B. pascuorum, we also selected populations from two additional time periods: 1949-1955 and 1975-1990. The genetic diversity and population structure in B. pascuorum remained constant over the three time periods. However, populations of declining bumblebee species showed a significantly lower genetic diversity than co-occurring stable species before their major declines. This historical difference indicates that the repeatedly observed reduced genetic diversity in recent populations of declining bumblebee species is not caused solely by the decline itself. The historically low genetic diversity in the declined species may be due to the fact that these species were already rare, making them more vulnerable to the major drivers of bumblebee decline.
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Affiliation(s)
- Kevin Maebe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Ivan Meeus
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | - Maarten Ganne
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
| | | | - Koos Biesmeijer
- Naturalis Biodiversity Center, Darwinweg 2, Leiden, the Netherlands
| | - Guy Smagghe
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, Ghent, Belgium
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21
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Berrebi P. Three brown trout Salmo trutta lineages in Corsica described through allozyme variation. JOURNAL OF FISH BIOLOGY 2015; 86:60-73. [PMID: 25353357 DOI: 10.1111/jfb.12534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 08/18/2014] [Indexed: 06/04/2023]
Abstract
The brown trout Salmo trutta is represented by three lineages in Corsica: (1) an ancestral Corsican lineage, (2) a Mediterranean lineage and (3) a recently stocked domestic Atlantic S. trutta lineage (all are interfertile); the main focus of this study was the ancestral Corsican S. trutta, but the other lineages were also considered. A total of 38 samples captured between 1993 and 1998 were analysed, with nearly 1000 individuals considered overall. The Corsican ancestral lineage (Adriatic lineage according to the mitochondrial DNA control region nomenclature, AD) mostly inhabits streams in the southern half of the island; the Mediterranean lineage (ME) is present more in the north, especially in Golu River, but most populations are an admixture of these lineages and the domestic Atlantic S. trutta (AT). Locations where the Corsican ancestral S. trutta is dominant are now protected against stocking and sometimes fishing is also forbidden. The presence of the Corsican S. trutta is unique in France.
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Affiliation(s)
- P Berrebi
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR UM2-CNRS-IRD, cc065, Université Montpellier 2, place Bataillon, 34095 Montpellier cedex 05, France
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22
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Gubili C, Sims DW, Veríssimo A, Domenici P, Ellis J, Grigoriou P, Johnson AF, McHugh M, Neat F, Satta A, Scarcella G, Serra-Pereira B, Soldo A, Genner MJ, Griffiths AM. A tale of two seas: contrasting patterns of population structure in the small-spotted catshark across Europe. ROYAL SOCIETY OPEN SCIENCE 2014; 1:140175. [PMID: 26064555 PMCID: PMC4448844 DOI: 10.1098/rsos.140175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 10/14/2014] [Indexed: 06/04/2023]
Abstract
Elasmobranchs represent important components of marine ecosystems, but they can be vulnerable to overexploitation. This has driven investigations into the population genetic structure of large-bodied pelagic sharks, but relatively little is known of population structure in smaller demersal taxa, which are perhaps more representative of the biodiversity of the group. This study explores spatial population genetic structure of the small-spotted catshark (Scyliorhinus canicula), across European seas. The results show significant genetic differences among most of the Mediterranean sample collections, but no significant structure among Atlantic shelf areas. The data suggest the Mediterranean populations are likely to have persisted in a stable and structured environment during Pleistocene sea-level changes. Conversely, the Northeast Atlantic populations would have experienced major changes in habitat availability during glacial cycles, driving patterns of population reduction and expansion. The data also provide evidence of male-biased dispersal and female philopatry over large spatial scales, implying complex sex-determined differences in the behaviour of elasmobranchs. On the basis of this evidence, we suggest that patterns of connectivity are determined by trends of past habitat stability that provides opportunity for local adaptation in species exhibiting philopatric behaviour, implying that resilience of populations to fisheries and other stressors may differ across the range of species.
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Affiliation(s)
- Chrysoula Gubili
- School of Environment and Life Sciences, University of Salford, Salford, Greater Manchester M5 4WU, UK
| | - David W. Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
| | - Ana Veríssimo
- CIBIO-U.P., Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão 4485-661, Portugal
| | | | - Jim Ellis
- Centre for Environment, Fisheries and Aquaclture Science (CEFAS), Pakefield Road, Lowestoft, Suffolk NR33 0HT, UK
| | - Panagiotis Grigoriou
- Cretaquarium, Thalassocosmos, Hellenic Centre for Marine Research (HCMR), PO Box 2214, Heraklion Crete 71003, Greece
| | - Andrew F. Johnson
- Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography 0202, University of California, 9500 Gilman Drive, San Diego, CA 92083-0202, USA
| | - Matthew McHugh
- Marine and Estuarine Ecology Unit, School of Biological Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Francis Neat
- Marine Scotland—Science, Marine Laboratory, PO Box 101, Aberdeen AB11 9DB, UK
| | - Andrea Satta
- CNR-IAMC Località Sa Mardini, Torregrande 09170, Italy
| | - Giuseppe Scarcella
- ISMAR-CNR—Istituto di Scienze Marine, Consiglio Nazionale delle Ricerche, Largo Fiera della Pesca 2, Ancona 60125, Italy
| | - Bárbara Serra-Pereira
- Departamento do Mar e Recursos Marinhos, IPMA, Instituto Português do Mar e da Atmosfera, Av. Brasilia, Lisboa 1449-006, Portugal
| | - Alen Soldo
- Department of Marine Studies, University of Split, Livanjska 5, Split 21000, Croatia
| | - Martin J. Genner
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Andrew M. Griffiths
- Marine Biological Association of the United Kingdom, The Laboratory, Plymouth PL1 2PB, UK
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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23
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Pattern of genetic variation of yellow catfish Pelteobagrus fulvidraco Richardso in Huaihe river and the Yangtze river revealed using mitochondrial DNA control region sequences. Mol Biol Rep 2014; 41:5593-606. [PMID: 25052185 DOI: 10.1007/s11033-014-3251-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 02/08/2014] [Indexed: 10/25/2022]
Abstract
Genetic variability and population genetic structure of the yellow catfish Pelteobagrus fulvidraco Richardso in the Huaihe river and the Yangtze river was examined with a 810-bp of the mitochondrial DNA control region. A total of 70 haplotypes were identified from 145 samples, which were characterized with high haplotype diversity (h = 0.9832 ± 0.0041) but low nucleotide diversity (π = 0.0415 ± 0.0201). The analysis of molecular variance and phylogenetic reconstructions detected significant geographic structure between Huaihe river and Yangtze with FST = 0.1183 (P = 0.0000). Neighbor-joining (NJ) phylogenetic analyses identified two distinct clades (bootstrap support 99 %). The medium joining network drawn using the complete data set was reticulated and also distinctly split the 70 haplotypes into two groups corresponding to those of the NJ tree. Departures from neutrality were not significant for the Huaihe river and the Yangtze river Pelteobagrus fulvidraco, concordant with the observed multimodal mismatch distributions (P > 0.05), which suggested that the effective size of this species has been large and stable for a long period. The question about the existence of significant genetic differentiation for Pelteobagrus fulvidraco in the Yangtze river and Huaihe river basins remains to be further studied with molecular nuclear markers and larger sample sizes from throughout the river basins.
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24
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Hansen MM, Limborg MT, Ferchaud AL, Pujolar JM. The effects of Medieval dams on genetic divergence and demographic history in brown trout populations. BMC Evol Biol 2014; 14:122. [PMID: 24903056 PMCID: PMC4106231 DOI: 10.1186/1471-2148-14-122] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 05/30/2014] [Indexed: 12/22/2022] Open
Abstract
Background Habitat fragmentation has accelerated within the last century, but may have been ongoing over longer time scales. We analyzed the timing and genetic consequences of fragmentation in two isolated lake-dwelling brown trout populations. They are from the same river system (the Gudenå River, Denmark) and have been isolated from downstream anadromous trout by dams established ca. 600–800 years ago. For reference, we included ten other anadromous populations and two hatchery strains. Based on analysis of 44 microsatellite loci we investigated if the lake populations have been naturally genetically differentiated from anadromous trout for thousands of years, or have diverged recently due to the establishment of dams. Results Divergence time estimates were based on 1) Approximate Bayesian Computation and 2) a coalescent-based isolation-with-gene-flow model. Both methods suggested divergence times ca. 600–800 years bp, providing strong evidence for establishment of dams in the Medieval as the factor causing divergence. Bayesian cluster analysis showed influence of stocked trout in several reference populations, but not in the focal lake and anadromous populations. Estimates of effective population size using a linkage disequilibrium method ranged from 244 to > 1,000 in all but one anadromous population, but were lower (153 and 252) in the lake populations. Conclusions We show that genetic divergence of lake-dwelling trout in two Danish lakes reflects establishment of water mills and impassable dams ca. 600–800 years ago rather than a natural genetic population structure. Although effective population sizes of the two lake populations are not critically low they may ultimately limit response to selection and thereby future adaptation. Our results demonstrate that populations may have been affected by anthropogenic disturbance over longer time scales than normally assumed.
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Affiliation(s)
- Michael M Hansen
- Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
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25
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Valiquette E, Perrier C, Thibault I, Bernatchez L. Loss of genetic integrity in wild lake trout populations following stocking: insights from an exhaustive study of 72 lakes from Québec, Canada. Evol Appl 2014; 7:625-44. [PMID: 25067947 PMCID: PMC4105915 DOI: 10.1111/eva.12160] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/17/2014] [Indexed: 11/29/2022] Open
Abstract
Stocking represents the most important management tool worldwide to increase and sustain commercial and recreational fisheries in a context of overexploitation. Genetic impacts of this practice have been investigated in many studies, which examined population and individual admixture, but few have investigated determinants of these processes. Here, we addressed these questions from the genotyping at 19 microsatellite loci of 3341 adult lake trout (Salvelinus namaycush) from 72 unstocked and stocked lakes. Results showed an increase in genetic diversity and a twofold decrease in the extent of genetic differentiation among stocked populations when compared to unstocked. Stocked populations were characterized by significant admixture at both population and individual levels. Moreover, levels of admixture in stocked populations were strongly correlated with stocking intensity and a threshold value of total homogenization between source and stocked populations was identified. Our results also suggest that under certain scenarios, the genetic impacts of stocking could be of short duration. Overall, our study emphasizes the important alteration of the genetic integrity of stocked populations and the need to better understand determinants of admixture to optimize stocking strategies and to conserve the genetic integrity of wild populations.
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Affiliation(s)
- Eliane Valiquette
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Charles Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
| | - Isabel Thibault
- Ministère du Développement durable, de l'Environnement de la Faune et des Parcs Québec, QC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval Québec, QC, Canada
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26
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Meier K, Hansen MM, Normandeau E, Mensberg KLD, Frydenberg J, Larsen PF, Bekkevold D, Bernatchez L. Local adaptation at the transcriptome level in brown trout: evidence from early life history temperature genomic reaction norms. PLoS One 2014; 9:e85171. [PMID: 24454810 PMCID: PMC3891768 DOI: 10.1371/journal.pone.0085171] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/23/2013] [Indexed: 01/19/2023] Open
Abstract
Local adaptation and its underlying molecular basis has long been a key focus in evolutionary biology. There has recently been increased interest in the evolutionary role of plasticity and the molecular mechanisms underlying local adaptation. Using transcriptome analysis, we assessed differences in gene expression profiles for three brown trout (Salmo trutta) populations, one resident and two anadromous, experiencing different temperature regimes in the wild. The study was based on an F2 generation raised in a common garden setting. A previous study of the F1 generation revealed different reaction norms and significantly higher QST than FST among populations for two early life-history traits. In the present study we investigated if genomic reaction norm patterns were also present at the transcriptome level. Eggs from the three populations were incubated at two temperatures (5 and 8 degrees C) representing conditions encountered in the local environments. Global gene expression for fry at the stage of first feeding was analysed using a 32k cDNA microarray. The results revealed differences in gene expression between populations and temperatures and population × temperature interactions, the latter indicating locally adapted reaction norms. Moreover, the reaction norms paralleled those observed previously at early life-history traits. We identified 90 cDNA clones among the genes with an interaction effect that were differently expressed between the ecologically divergent populations. These included genes involved in immune- and stress response. We observed less plasticity in the resident as compared to the anadromous populations, possibly reflecting that the degree of environmental heterogeneity encountered by individuals throughout their life cycle will select for variable level of phenotypic plasticity at the transcriptome level. Our study demonstrates the usefulness of transcriptome approaches to identify genes with different temperature reaction norms. The responses observed suggest that populations may vary in their susceptibility to climate change.
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Affiliation(s)
- Kristian Meier
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Canada
| | - Karen-Lise D. Mensberg
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Jane Frydenberg
- Department of Bioscience, Aarhus University, Aarhus C, Denmark
| | | | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Canada
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27
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Poćwierz-Kotus A, Bernaś R, Dębowski P, Kent MP, Lien S, Kesler M, Titov S, Leliūna E, Jespersen H, Drywa A, Wenne R. Genetic differentiation of southeast Baltic populations of sea trout inferred from single nucleotide polymorphisms. Anim Genet 2013; 45:96-104. [DOI: 10.1111/age.12095] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2013] [Indexed: 11/28/2022]
Affiliation(s)
- A. Poćwierz-Kotus
- Institute of Oceanology; Polish Academy of Sciences; Powstanców Warszawy 55 81-712 Sopot Poland
| | - R. Bernaś
- Department of Migratory Fishes Synów Pułku 37, 80-298 Gdansk; Inland Fisheries Institute; Olsztyn Poland
| | - P. Dębowski
- Department of Migratory Fishes Synów Pułku 37, 80-298 Gdansk; Inland Fisheries Institute; Olsztyn Poland
| | - M. P. Kent
- Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; Postboks 5003, 1432 Ås Norway
| | - S. Lien
- Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; Postboks 5003, 1432 Ås Norway
| | - M. Kesler
- Estonian Marine Institute; Tartu University; EE-12618 Tallinn Estonia
| | - S. Titov
- State Research Institute on Lake and River Fisheries (GosNIORKH); Makarova emb., 26, St. Petersburg 199053 Russian Federation
| | - E. Leliūna
- Institute of Ecology of Nature Research Centre; Akademijos str. 2 LT-08412 Vilnius-21 Lithuania
| | - H. Jespersen
- Technical and Environmental Services; Municipality of Bornholm; Skovløkken 4, Tejn 3770 Allinge Denmark
| | - A. Drywa
- National Marine Fisheries Research Institute; Kołłataja 1 81-332 Gdynia Poland
| | - R. Wenne
- Institute of Oceanology; Polish Academy of Sciences; Powstanców Warszawy 55 81-712 Sopot Poland
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28
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Song R, Li WX, Wu SG, Zou H, Wang GT. Population genetic structure of the acanthocephalan Acanthosentis cheni in anadromous, freshwater, and landlocked stocks of its fish host, Coilia nasus. J Parasitol 2013; 100:193-7. [PMID: 24224788 DOI: 10.1645/12-144.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The acanthocephalan Acanthosentis cheni was found in anadromous, freshwater, and landlocked stocks of its fish host, Coilia nasus. To examine the genetic variations of the acanthocephalan among the 3 populations with the adaptation of the host to the freshwater, the genetic structure of the helminth was investigated in anadromous (Zhoushan and Chongming islands, and Anqing), freshwater (Anqing, Ezhou, and Poyang Lake), and landlocked (Tian'ezhou Reserve) populations by sequencing intergenic transcribed spacers (ITS) of the ribosomal RNA coding genes. Low Fst values and high gene flow were found among the 7 populations (Fst = 0.0135, P = 0.2723; Nm = 36.48) and the 3 ecotypes of Acanthosentis cheni (Fst = 0.0178, P = 0.1044; Nm = 27.67). On the other hand, significant genetic differentiation of the C. nasus host populations was detected between the upstream and downstream areas of Xiaogu Mountain (Fst = 0.1961, P = 0.0030; Nm = 2.05), which is the farthest location of spawning migration for C. nasus . However, the migration break of the fish host appeared not to cause significant genetic differentiation of A. cheni populations between the upper and lower reaches of Xiaogu Mountain. Other factors might promote genetic exchange of A. cheni populations such as dispersal of the intermediate host by flooding or other fish species serving as the definitive or paratenic hosts. In Anqing, nucleotide diversity of the acanthocephalan was highest in the freshwater population (0.0038) and lower in the anadromous population (0.0026). This suggested that new mutations may have occurred in the freshwater A. cheni population in Anqing when adapting to a freshwater environment.
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Affiliation(s)
- Rui Song
- * The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, and Institute of Hydrobiology, the Chinese Academy of Sciences, Wuhan 430072, China. Correspondence should be sent to:
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29
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Ozerov MY, Veselov AE, Lumme J, Primmer CR. Temporal variation of genetic composition in Atlantic salmon populations from the Western White Sea Basin: influence of anthropogenic factors? BMC Genet 2013; 14:88. [PMID: 24053319 PMCID: PMC3852729 DOI: 10.1186/1471-2156-14-88] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Accepted: 09/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Studies of the temporal patterns of population genetic structure assist in evaluating the consequences of demographic and environmental changes on population stability and persistence. In this study, we evaluated the level of temporal genetic variation in 16 anadromous and 2 freshwater salmon populations from the Western White Sea Basin (Russia) using samples collected between 1995 and 2008. To assess whether the genetic stability was affected by human activity, we also evaluated the effect of fishing pressure on the temporal genetic variation in this region. RESULTS We found that the genetic structure of salmon populations in this region was relatively stable over a period of 1.5 to 2.5 generations. However, the level of temporal variation varied among geographical regions: anadromous salmon of the Kola Peninsula exhibited a higher stability compared to that of the anadromous and freshwater salmon from the Karelian White Sea coast. This discrepancy was most likely attributed to the higher census, and therefore effective, population sizes of the populations inhabiting the rivers of the Kola Peninsula compared to salmon of the Karelian White Sea coast. Importantly, changes in the genetic diversity observed in a few anadromous populations were best explained by the increased level of fishing pressure in these populations rather than environmental variation or the negative effects of hatchery escapees. The observed population genetic patterns of isolation by distance remained consistent among earlier and more recent samples, which support the stability of the genetic structure over the period studied. CONCLUSIONS Given the increasing level of fishing pressure in the Western White Sea Basin and the higher level of temporal variation in populations exhibiting small census and effective population sizes, further genetic monitoring in this region is recommended, particularly on populations from the Karelian rivers.
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Affiliation(s)
- Mikhail Yu Ozerov
- Department of Biology, Division of Genetics and Physiology, University of Turku, 20014 Turku, Finland.
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Vincent B, Dionne M, Kent MP, Lien S, Bernatchez L. LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION. Evolution 2013; 67:3469-87. [DOI: 10.1111/evo.12139] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 03/27/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Bourret Vincent
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
| | - Mélanie Dionne
- Direction de la faune aquatique; Ministère du Développement durable; de l'Environnement; de la Faune et des Parcs; Québec G1S 4×4 Canada
| | - Matthew P. Kent
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences; Centre for Integrative Genetics (CIGENE); Norwegian University of Life Sciences; PO Box 5003, 1432 Aas Norway
| | - Louis Bernatchez
- Département de Biologie; Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; 1030 avenue de la Médecine Québec Québec G1V 0A6 Canada
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31
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Filipe AF, Markovic D, Pletterbauer F, Tisseuil C, De Wever A, Schmutz S, Bonada N, Freyhof J. Forecasting fish distribution along stream networks: brown trout (Salmo trutta) in Europe. DIVERS DISTRIB 2013. [DOI: 10.1111/ddi.12086] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Ana Filipa Filipe
- Grup de Recerca “Freshwater Ecology and Management” (FEM); Department d'Ecologia; Facultat de Biologia; Universitat de Barcelona (UB); Diagonal 643; 08028; Barcelona; Catalonia; Spain
| | - Danijela Markovic
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Müggelseedamm 310; 12587; Berlin; Germany
| | - Florian Pletterbauer
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG); University of Natural Resources and Life Sciences Vienna (BOKU); Max Emanuel Strasse 17; 1180; Vienna; Austria
| | - Clément Tisseuil
- Département Milieux et Peuplements Aquatiques; UMR BOREA-IRD 207/CNRS 7208/MNHN/UPMC; Muséum National d'Histoire Naturelle; Paris; France
| | - Aaike De Wever
- Freshwater Laboratory; Royal Belgian Institute of Natural Sciences; Vautierstraat 29; 1000; Brussels; Belgium
| | - Stefan Schmutz
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG); University of Natural Resources and Life Sciences Vienna (BOKU); Max Emanuel Strasse 17; 1180; Vienna; Austria
| | - Núria Bonada
- Grup de Recerca “Freshwater Ecology and Management” (FEM); Department d'Ecologia; Facultat de Biologia; Universitat de Barcelona (UB); Diagonal 643; 08028; Barcelona; Catalonia; Spain
| | - Jörg Freyhof
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries; Müggelseedamm 310; 12587; Berlin; Germany
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Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array. Mar Genomics 2013; 9:25-32. [DOI: 10.1016/j.margen.2012.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Revised: 08/23/2012] [Accepted: 08/30/2012] [Indexed: 11/20/2022]
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33
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Charlier J, Laikre L, Ryman N. Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population. Heredity (Edinb) 2012; 109:246-53. [PMID: 22828900 PMCID: PMC3464028 DOI: 10.1038/hdy.2012.36] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/16/2012] [Accepted: 04/19/2012] [Indexed: 11/08/2022] Open
Abstract
Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (N(e)) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean N(e) is estimated as 74. We find indications that N(e) varies over time, but there is no obvious temporal trend. We also estimated N(e) using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an N(e) estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (N(b)) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.
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Affiliation(s)
- J Charlier
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
| | - L Laikre
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
| | - N Ryman
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
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34
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Serbezov D, Jorde PE, Bernatchez L, Olsen EM, Vøllestad LA. Life history and demographic determinants of effective/census size ratios as exemplified by brown trout (Salmo trutta). Evol Appl 2012; 5:607-18. [PMID: 23028401 PMCID: PMC3461143 DOI: 10.1111/j.1752-4571.2012.00239.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 12/19/2011] [Indexed: 11/30/2022] Open
Abstract
A number of demographic factors, many of which related to human-driven encroachments, are predicted to decrease the effective population size (N(e)) relative to the census population size (N), but these have been little investigated. Yet, it is necessary to know which factors most strongly impact N(e), and how to mitigate these effects through sound management actions. In this study, we use parentage analysis of a stream-living brown trout (Salmo trutta) population to quantify the effect of between-individual variance in reproductive success on the effective number of breeders (N(b)) relative to the census number of breeders (N(i)). Comprehensive estimates of the N(b)/N ratio were reduced to 0.16-0.28, almost entirely due to larger than binomial variance in family size. We used computer simulations, based on empirical estimates of age-specific survival and fecundity rates, to assess the effect of repeat spawning (iteroparity) on N(e) and found that the variance in lifetime reproductive success was substantially higher for repeat spawners. Random family-specific survival, on the other hand, acts to buffer these effects. We discuss the implications of these findings for the management of small populations, where maintaining high and stable levels of N(e) is crucial to extenuate inbreeding and protect genetic variability.
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Affiliation(s)
- Dimitar Serbezov
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
| | - Per Erik Jorde
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
- Institute of Marine ResearchFlødevigen, Norway
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Pavillon Charles-Eugène Marchand, Université LavalQuébec, QC, Canada
| | - Esben Moland Olsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
- Institute of Marine ResearchFlødevigen, Norway
| | - Leif Asbjørn Vøllestad
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloBlindern, Oslo, Norway
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35
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Effective size and genetic composition of two exploited, migratory whitefish (Coregonus lavaretus lavaretus) populations. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0394-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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36
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MacManes MD, Lacey EA. Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)? PLoS One 2012; 7:e37562. [PMID: 22649541 PMCID: PMC3359288 DOI: 10.1371/journal.pone.0037562] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/25/2012] [Indexed: 12/24/2022] Open
Abstract
Reproductive behavior may play an important role in shaping selection on Major Histocompatibility Complex (MHC) genes. For example, the number of sexual partners that an individual has may affect exposure to sexually transmitted pathogens, with more partners leading to greater exposure and, hence, potentially greater selection for variation at MHC loci. To explore this hypothesis, we examined the strength of selection on exon 2 of the MHC-DQα locus in two species of Peromyscus. While the California mouse (P. californicus) is characterized by lifetime social and genetic monogamy, the deer mouse (P. maniculatus) is socially and genetically promiscuous; consistent with these differences in mating behavior, the diversity of bacteria present within the reproductive tracts of females is significantly greater for P. maniculatus. To test the prediction that more reproductive partners and exposure to a greater range of sexually transmitted pathogens are associated with enhanced diversifying selection on genes responsible for immune function, we compared patterns and levels of diversity at the Class II MHC-DQα locus in sympatric populations of P. maniculatus and P. californicus. Using likelihood based analyses, we show that selection is enhanced in the promiscuous P. maniculatus. This study is the first to compare the strength of selection in wild sympatric rodents with known differences in pathogen milieu.
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Affiliation(s)
- Matthew D MacManes
- Department of Integrative Biology, Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America.
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37
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STELKENS RIKEB, JAFFUEL GEOFFREY, ESCHER MATTHIAS, WEDEKIND CLAUS. Genetic and phenotypic population divergence on a microgeographic scale in brown trout. Mol Ecol 2012; 21:2896-915. [DOI: 10.1111/j.1365-294x.2012.05581.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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Iwamoto EM, Myers JM, Gustafson RG. Resurrecting an extinct salmon evolutionarily significant unit: archived scales, historical DNA and implications for restoration. Mol Ecol 2012; 21:1567-82. [PMID: 22221423 DOI: 10.1111/j.1365-294x.2011.05419.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Archival scales from 603 sockeye salmon (Oncorhynchus nerka), sampled from May to July 1924 in the lower Columbia River, were analysed for genetic variability at 12 microsatellite loci and compared to 17 present-day O. nerka populations-exhibiting either anadromous (sockeye salmon) or nonanadromous (kokanee) life histories-from throughout the Columbia River Basin, including areas upstream of impassable dams built subsequent to 1924. Statistical analyses identified four major genetic assemblages of sockeye salmon in the 1924 samples. Two of these putative historical groupings were found to be genetically similar to extant evolutionarily significant units (ESUs) in the Okanogan and Wenatchee Rivers (pairwise F(ST) = 0.004 and 0.002, respectively), and assignment tests were able to allocate 77% of the fish in these two historical groupings to the contemporary Okanogan River and Lake Wenatchee ESUs. A third historical genetic grouping was most closely aligned with contemporary sockeye salmon in Redfish Lake, Idaho, although the association was less robust (pairwise F(ST) = 0.060). However, a fourth genetic grouping did not appear to be related to any contemporary sockeye salmon or kokanee population, assigned poorly to the O. nerka baseline, and had distinctive early return migration timing, suggesting that this group represents a historical ESU originating in headwater lakes in British Columbia that was probably extirpated sometime after 1924. The lack of a contemporary O. nerka population possessing the genetic legacy of this extinct ESU indicates that efforts to reestablish early-migrating sockeye salmon to the headwater lakes region of the Columbia River will be difficult.
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Affiliation(s)
- Eric M Iwamoto
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd. E, Seattle, WA 98112, USA.
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39
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Barker JSF. Effective population size of natural populations of Drosophila buzzatii, with a comparative evaluation of nine methods of estimation. Mol Ecol 2011; 20:4452-71. [PMID: 21951766 DOI: 10.1111/j.1365-294x.2011.05324.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Allozyme and microsatellite data from numerous populations of Drosophila buzzatii have been used (i) to determine to what degree N(e) varies among generations within populations, and among populations, and (ii) to evaluate the congruence of four temporal and five single-sample estimators of N(e) . Effective size of different populations varied over two orders of magnitude, most populations are not temporally stable in genetic composition, and N(e) showed large variation over generations in some populations. Short-term N(e) estimates from the temporal methods were highly correlated, but the smallest estimates were the most precise for all four methods, and the most consistent across methods. Except for one population, N(e) estimates were lower when assuming gene flow than when assuming populations that were closed. However, attempts to jointly estimate N(e) and immigration rate were of little value because the source of migrants was unknown. Correlations among the estimates from the single-sample methods generally were not significant although, as for the temporal methods, estimates were most consistent when they were small. These single-sample estimates of current N(e) are generally smaller than the short-term temporal estimates. Nevertheless, population genetic variation is not being depleted, presumably because of past or ongoing migration. A clearer picture of current and short-term effective population sizes will only follow with better knowledge of migration rates between populations. Different methods are not necessarily estimating the same N(e) , they are subject to different bias, and the biology, demography and history of the population(s) may affect different estimators differently.
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Affiliation(s)
- J S F Barker
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia.
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40
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Genetic variation at mtDNA and microsatellite loci in Chinese longsnout catfish (Leiocassis longirostris). Mol Biol Rep 2011; 39:4605-17. [PMID: 21947845 DOI: 10.1007/s11033-011-1252-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
Genetic variability and population structure of the Chinese longsnout catfish Leiocassis longirostris Günther in the Yangtze River was examined with mitochondrial control region sequences and nuclear microsatellite markers. A 705-bp segment of the mitochondrial DNA control region was sequenced from 132 samples, which identified a total of 61 haplotypes. The Chinese longsnout catfish in the Yangtze River was characterized with high haplotype diversity (h = 0.9770 ± 0.0041) but low nucleotide diversity (π = 0.0081 ± 0.0043). Median-joining network analysis revealed a star-shaped pattern and mismatch distribution analysis found a smooth unimodal distribution, which suggested that this species in the Yangtze River underwent a population expansion following bottlenecks and/or they originated from a small size of founding population. It was estimated that the possible time of population expansion was 139,000-435,000 years before present, a time period in the middle Pleistocene. The analysis of molecular variance and phylogenetic reconstructions did not detect significant geographic structure between different river sections. This pattern of genetic variation was further evidenced with nuclear microsatellite markers. The genetic differentiation between above and below the Gezhouba Dam and Three Gorges Dam is very small at mitochondrial and nuclear levels, which suggested that these recently developed dams might have not significantly resulted in population genetic fragmentation in the Chinese longsnout catfish. However, the potential exacerbation of genetic structuring by the dams should not be overlooked in the future.
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41
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McElroy TC, Kandl KL, Trexler JC. Temporal population genetic structure of eastern mosquitofish in a dynamic aquatic landscape. ACTA ACUST UNITED AC 2011; 102:678-87. [PMID: 21885573 DOI: 10.1093/jhered/esr088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We analyzed the effect of periodic drying in the Florida Everglades on spatiotemporal population genetic structure of eastern mosquitofish (Gambusia holbrooki). Severe periodic drying events force individuals from disparate sources to mix in dry season relatively deep-water refuges. In 1996 (a wet year) and 1999 (a dry year), we sampled mosquitofish at 20 dry-season refuges distributed in 3 water management regions and characterized genetic variation for 10 allozyme and 3 microsatellite loci. In 1996, most of the ecosystem did not dry, whereas in 1999, many of our sampling locations were isolated by expanses of dried marsh surface. In 1996, most spatial genetic variation was attributed to heterogeneity within regions. In 1999, spatial genetic variation within regions was not significant. In both years, a small but significant amount of variation (less than 1% of the total variation) was partitioned among regions. Variance was consistently greater than zero among long-hydroperiod sites within a region, but not among short-hydroperiod sites within a region, where hydroperiod was measured as time since last marsh surface dry-down forcing fishes into local refuges. In 1996, all sites were in Hardy-Weinberg equilibrium. In 1999, we observed fewer heterozygotes than expected for most loci and sites suggesting a Wahlund effect arising from fish leaving areas that dried and mixing in deep-water refuges.
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Affiliation(s)
- Thomas C McElroy
- Department of Biology and Physics, Kennesaw State University, Kennesaw, GA 30144, USA.
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42
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Gow JL, Tamkee P, Heggenes J, Wilson GA, Taylor EB. Little impact of hatchery supplementation that uses native broodstock on the genetic structure and diversity of steelhead trout revealed by a large-scale spatio-temporal microsatellite survey. Evol Appl 2011; 4:763-82. [PMID: 25568021 PMCID: PMC3352543 DOI: 10.1111/j.1752-4571.2011.00198.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 06/06/2011] [Indexed: 11/30/2022] Open
Abstract
Artificial breeding programs initiated to enhance the size of animal populations are often motivated by the desire to increase harvest opportunities. The introduction of non-native genotypes, however, can have negative evolutionary impacts. These may be direct, such as introgressive hybridization, or indirect via competition. Less is known about the effects of stocking with native genotypes. We assayed variation at nine microsatellite loci in 902 steelhead trout (Oncorhynchus mykiss) from five rivers in British Columbia, Canada. These samples were collected over 58 years, a time period that spanned the initiation of native steelhead trout broodstock hatchery supplementation in these rivers. We detected no changes in estimates of effective population size, genetic variation or temporal genetic structure within any population, nor of altered genetic structure among them. Genetic interactions with nonmigratory O. mykiss, the use of substantial numbers of primarily native broodstock with an approximate 1:1 male-to-female ratio, and/or poor survival and reproductive success of hatchery fish may have minimized potential genetic changes. Although no genetic changes were detected, ecological effects of hatchery programs still may influence wild population productivity and abundance. Their effects await the design and implementation of a more comprehensive evaluation program.
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Affiliation(s)
- Jennifer L Gow
- Department of Zoology, Biodiversity Research Centre and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada
| | - Patrick Tamkee
- Department of Zoology, Biodiversity Research Centre and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada
| | - Jan Heggenes
- Department of Zoology, Biodiversity Research Centre and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada ; Laboratory of Freshwater Ecology, University of Oslo Oslo, Norway
| | - Greg A Wilson
- British Columbia Ministry of Environment Surrey, BC, Canada
| | - Eric B Taylor
- Department of Zoology, Biodiversity Research Centre and Native Fishes Research Group, University of British Columbia Vancouver, BC, Canada
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43
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Farrington HL, Petren K. A century of genetic change and metapopulation dynamics in the Galápagos warbler finches (Certhidea). Evolution 2011; 65:3148-61. [PMID: 22023582 DOI: 10.1111/j.1558-5646.2011.01385.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Populations that are connected by immigrants play an important role in evolutionary and conservation biology, yet we have little direct evidence of how such metapopulations change genetically over evolutionary time. We compared historic (1894-1906) to modern (1988-2006) genetic variation in 11 populations of warbler finches at 14 microsatellite loci. Although several lines of evidence suggest that Darwin's finches may be in decline, we found that the genetic diversity of warbler finches has not generally declined, and broad-scale patterns of variation remained similar over time. Contrary to expectations, inferred population sizes have generally increased over time (6-8%) as have immigration rates (8-16%), which may reflect a recent increase in the frequency and intensity of El Niño events. Individual island populations showed significant declines (18-19%) and also substantial gains (18-20%) in allelic richness over time. Changes in genetic diversity were correlated with changes in immigration rates, but did not correspond to population size or human disturbance. These results reflect the expected stabilizing properties of whole metapopulations over time. However, the dramatic and unpredictable changes observed in individual populations during this short time interval suggests that care should be taken when monitoring individual population fragments with snapshots of genetic variation.
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Affiliation(s)
- Heather L Farrington
- Department of Biological Sciences, University of Cincinnati, OH 45221-0006, USA.
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44
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Goyache F, Álvarez I, Fernández I, Pérez-Pardal L, Royo LJ, Lorenzo L. Usefulness of molecular-based methods for estimating effective population size in livestock assessed using data from the endangered black-coated Asturcón pony1. J Anim Sci 2011; 89:1251-9. [DOI: 10.2527/jas.2010-3620] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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45
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An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci. Heredity (Edinb) 2011; 106:488-99. [PMID: 21224872 DOI: 10.1038/hdy.2010.164] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Local adaptation is considered a paradigm in studies of salmonid fish populations. Yet, little is known about the geographical scale of local adaptation. Is adaptive divergence primarily evident at the scale of regions or individual populations? Also, many salmonid populations are subject to spawning intrusion by farmed conspecifics that experience selection regimes fundamentally different from wild populations. This prompts the question if adaptive differences between wild populations and hatchery strains are more pronounced than between different wild populations? We addressed these issues by analyzing variation at 74 microsatellite loci (including anonymous and expressed sequence tag- and quantitative trait locus-linked markers) in 15 anadromous wild brown trout (Salmo trutta L.) populations, representing five geographical regions, along with two lake populations and two hatchery strains used for stocking some of the populations. F(ST)-based outlier tests revealed more outlier loci between different geographical regions separated by 522 ± 228 km (mean ± s.d.) than between populations within regions separated by 117 ± 79 km (mean ± s.d.). A significant association between geographical distance and number of outliers between regions was evident. There was no evidence for more outliers in comparisons involving hatchery trout, but the loci under putative selection generally were not the same as those found to be outliers between wild populations. Our study supports the notion of local adaption being increasingly important at the scale of regions as compared with individual populations, and suggests that loci involved in adaptation to captive environments are not necessarily the same as those involved in adaptive divergence among wild populations.
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46
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Swatdipong A, Vasemägi A, Niva T, Koljonen ML, Primmer CR. High level of population genetic structuring in lake-run brown trout, Salmo trutta, of the Inari Basin, northern Finland. JOURNAL OF FISH BIOLOGY 2010; 77:2048-2071. [PMID: 21133916 DOI: 10.1111/j.1095-8649.2010.02784.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Rivers draining into (Lake) Inarijärvi, northern Finland, sustain a number of lake-run brown trout, Salmo trutta, populations but, as with most lake-run S. trutta systems, the level of population genetic structuring among populations is unknown. To address this and to assist fish stock management in the region, the population genetic structure of S. trutta collected from 28 sampling sites in rivers flowing into Inarijärvi was studied using 13 microsatellite loci. Populations were clustered into three separate groups, largely corresponding to geographic regions, with between-region F(ST) values ranging from 0·11 to 0·16. The significant differentiation observed between most populations within each region also implies that individual populations should be recognized as separate management units and actions to improve, and subsequently maintain, conditions for natural spawning should be prioritized. The results of this study further indicate that the trout from each of these regions may have different biological characteristics, such as local-lake feeding behaviour among the western populations and strong isolation among the northern stocks. As a consequence, further research is warranted to better understand the level of ecological uniqueness of lake-run S. trutta populations.
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Affiliation(s)
- A Swatdipong
- Department of Biology, University of Turku, Turku, Finland
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47
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Ozerov MY, Veselov AJ, Lumme J, Primmer CR. Genetic structure of freshwater Atlantic salmon (Salmo salar L.) populations from the lakes Onega and Ladoga of northwest Russia and implications for conservation. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0064-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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48
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Massa-Gallucci A, Coscia I, O’Grady M, Kelly-Quinn M, Mariani S. Patterns of genetic structuring in a brown trout (Salmo trutta L.) metapopulation. CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0061-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Griffiths AM, Machado-Schiaffino G, Dillane E, Coughlan J, Horreo JL, Bowkett AE, Minting P, Toms S, Roche W, Gargan P, McGinnity P, Cross T, Bright D, Garcia-Vazquez E, Stevens JR. Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range. BMC Genet 2010; 11:31. [PMID: 20429926 PMCID: PMC2882343 DOI: 10.1186/1471-2156-11-31] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 04/29/2010] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Anadromous migratory fish species such as Atlantic salmon (Salmo salar) have significant economic, cultural and ecological importance, but present a complex case for management and conservation due to the range of their migration. Atlantic salmon exist in rivers across the North Atlantic, returning to their river of birth with a high degree of accuracy; however, despite continuing efforts and improvements in in-river conservation, they are in steep decline across their range. Salmon from rivers across Europe migrate along similar routes, where they have, historically, been subject to commercial netting. This mixed stock exploitation has the potential to devastate weak and declining populations where they are exploited indiscriminately. Despite various tagging and marking studies, the effect of marine exploitation and the marine element of the salmon lifecycle in general, remain the "black-box" of salmon management. In a number of Pacific salmonid species and in several regions within the range of the Atlantic salmon, genetic stock identification and mixed stock analysis have been used successfully to quantify exploitation rates and identify the natal origins of fish outside their home waters - to date this has not been attempted for Atlantic salmon in the south of their European range. RESULTS To facilitate mixed stock analysis (MSA) of Atlantic salmon, we have produced a baseline of genetic data for salmon populations originating from the largest rivers from Spain to northern Scotland, a region in which declines have been particularly marked. Using 12 microsatellites, 3,730 individual fish from 57 river catchments have been genotyped. Detailed patterns of population genetic diversity of Atlantic salmon at a sub-continent-wide level have been evaluated, demonstrating the existence of regional genetic signatures. Critically, these appear to be independent of more commonly recognised terrestrial biogeographical and political boundaries, allowing reporting regions to be defined. The implications of these results on the accuracy of MSA are evaluated and indicate that the success of MSA is not uniform across the range studied; our findings indicate large differences in the relative accuracy of stock composition estimates and MSA apportioning across the geographical range of the study, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the area studied. This result probably reflects the more genetically distinct nature of populations in the database from Spain, northwest France and southern England. Genetic stock identification has been undertaken and validation of the baseline microsatellite dataset with rod-and-line and estuary net fisheries of known origin has produced realistic estimates of stock composition at a regional scale. CONCLUSIONS This southern European database and supporting phylogeographic and mixed-stock analyses of net samples provide a unique tool for Atlantic salmon research and management, in both their natal rivers and the marine environment. However, the success of MSA is not uniform across the area studied, with large differences in the relative accuracy of stock composition estimates and MSA apportioning, with a much higher degree of accuracy achieved when assigning and apportioning to populations in the south of the region. More broadly, this study provides a basis for long-term salmon management across the region and confirms the value of this genetic approach for fisheries management of anadromous species.
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Affiliation(s)
- Andrew M Griffiths
- Hatherly Laboratories, School of Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Gonzalo Machado-Schiaffino
- Departamento Biologia Funcional, Area de Genética, Universidad de Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Eileen Dillane
- Department of Zoology, Ecology and Plant Science/Aquaculture and Fisheries Development Centre, University College Cork, Cork, Ireland
| | - Jamie Coughlan
- Department of Zoology, Ecology and Plant Science/Aquaculture and Fisheries Development Centre, University College Cork, Cork, Ireland
| | - Jose L Horreo
- Departamento Biologia Funcional, Area de Genética, Universidad de Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Andrew E Bowkett
- Hatherly Laboratories, School of Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
| | - Peter Minting
- Ayrshire Rivers Trust, Donald Hendrie Building, Auchincruive Estate, Ayr KA6 5HW, UK
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Simon Toms
- Environment Agency, Cornwall Area Office, Sir John Moore House, Victoria Square, Bodmin PL31 1EB, UK
| | - Willie Roche
- Central Fisheries Board, Swords Business Campus, Balheary Road, Swords, Co. Dublin, Ireland
| | - Paddy Gargan
- Central Fisheries Board, Swords Business Campus, Balheary Road, Swords, Co. Dublin, Ireland
| | - Philip McGinnity
- Department of Zoology, Ecology and Plant Science/Aquaculture and Fisheries Development Centre, University College Cork, Cork, Ireland
| | - Tom Cross
- Department of Zoology, Ecology and Plant Science/Aquaculture and Fisheries Development Centre, University College Cork, Cork, Ireland
| | - Dylan Bright
- Westcountry Rivers Trust, Rain-Charm House, Kyl Cober Parc, Stoke Climsland, Callington, Cornwall PL17 8PH, UK
| | - Eva Garcia-Vazquez
- Departamento Biologia Funcional, Area de Genética, Universidad de Oviedo, C/Julian Claveria s/n, 33006 Oviedo, Spain
| | - Jamie R Stevens
- Hatherly Laboratories, School of Biosciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK
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Launey S, Brunet G, Guyomard R, Davaine P. Role of introduction history and landscape in the range expansion of brown trout (Salmo trutta L.) in the Kerguelen Islands. J Hered 2010; 101:270-83. [PMID: 20133353 DOI: 10.1093/jhered/esp130] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human-mediated biological invasions constitute interesting case studies to understand evolutionary processes, including the role of founder effects. Population expansion of newly introduced species can be highly dependant on barriers caused by landscape features, but identifying these barriers and their impact on genetic structure is a relatively recent concern in population genetics and ecology. Salmonid populations of the Kerguelen Islands archipelago are a favorable model system to address these questions as these populations are characterized by a simple history of introduction, little or no anthropogenic influence, and demographic monitoring since the first introductions. We analyzed genetic variation at 10 microsatellite loci in 19 populations of brown trout (Salmo trutta L.) in the Courbet Peninsula (Kerguelen Islands), where the species, introduced in 3 rivers only, has colonized the whole water system in 40 years. Despite a limited numbers of introductions, trout populations have maintained a genetic diversity comparable with what is found in hatchery or wild populations in Europe, but they are genetically structured. The main factor explaining the observed patterns of genetic diversity is the history of introductions, with each introduced population acting as a source for colonization of nearby rivers. Correlations between environmental and genetic parameters show that within each "source population" group, landscape characteristics (type of coast, accessibility of river mouth, distances between rivers, river length ...) play a role in shaping directions and rates of migration, and thus the genetic structure of the colonizing populations.
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Affiliation(s)
- Sophie Launey
- Institut National de la Recherche Agronomique, Laboratoire de Génétique des Poissons, Domaine de Vilvert, F-78352 Jouy en Josas, France.
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