1
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Ludwig S, Pimentel JDSM, Cardoso Resende L, Kalapothakis E. Eco-evolutionary factors that influence its demographic oscillations in Prochilodus costatus (Actinopterygii: Characiformes) populations evidenced through a genetic spatial-temporal evaluation. Evol Appl 2023; 16:895-910. [PMID: 37124086 PMCID: PMC10130561 DOI: 10.1111/eva.13544] [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: 06/14/2019] [Revised: 02/10/2020] [Accepted: 03/04/2020] [Indexed: 05/02/2023] Open
Abstract
The human activity impact on wild animal populations is indicated by eco-evolutionary and demographic processes, along with their survival and capacity to evolve; consequently, such data can contribute toward enhancing genetic-based conservation programs. In this context, knowledge on the life-history and the eco-evolutionary processes is required to understand extant patterns of population structure in Prochilodus costatus a Neotropical migratory fish that has been threatened due to loss and fragmentation of its natural habitat since 1960s promoted by the expansion of hydroelectric power plant construction programs. This study evaluated the eco-evolutionary parameters that cause oscillations in the demography and structure of P. costatus populations. An integrated approach was used, including temporal and spatial sampling, next-generation sequencing of eight microsatellite loci, multivariate genetic analysis, and demographic life-history reconstruction. The results provided evidence of the complex interplay of ecological-evolutionary and human-interference events on the life history of this species in the upper basin. In particular, spawning wave behavior might have ecological triggers resulting in an overlapping of distinct genetic generations, and arising distinct migratory and nonmigratory genetic patterns living in the same area. An abrupt decrease in the effective population size of the P. costatus populations in the recent past (1960-80) was likely driven by environment fragmentation promoted by the construction of the Três Marias hydropower dam. The low allelic diversity that resulted from this event is still detected today; thus, active stocking programs are not effective at expanding the genetic diversity of this species in the river basin. Finally, this study highlights the importance of using mixed methods to understand spatial and temporal variation in genetic structure for effective mitigation and conservation programs for threatened species that are directly affected by human actions.
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Affiliation(s)
- Sandra Ludwig
- Departament of Genetics, Ecology and EvolutionFederal University of Minas GeraisBelo HorizonteBrazil
| | | | - Leonardo Cardoso Resende
- Departament of Genetics, Ecology and EvolutionFederal University of Minas GeraisBelo HorizonteBrazil
| | - Evanguedes Kalapothakis
- Departament of Genetics, Ecology and EvolutionFederal University of Minas GeraisBelo HorizonteBrazil
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2
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Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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3
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Klütsch CFC, Maduna SN, Polikarpova N, Forfang K, Beddari B, Gjelland KØ, Aspholm PE, Amundsen PA, Hagen SB. Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population. Sci Rep 2021; 11:17396. [PMID: 34462480 PMCID: PMC8405680 DOI: 10.1038/s41598-021-96681-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/03/2021] [Indexed: 11/10/2022] Open
Abstract
Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (Salmo trutta) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna.
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Affiliation(s)
- Cornelya F C Klütsch
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway.
| | - Simo N Maduna
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | | | - Kristin Forfang
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | - Benedicte Beddari
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | | | - Paul Eric Aspholm
- Division of Forest and Forest Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway
| | - Per-Arne Amundsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Snorre B Hagen
- Division of Environment and Natural Resources, Norwegian Institute of Bioeconomy Research (NIBIO), Svanhovd, Norway.
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4
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Cote D, Van Leeuwen TE, Bath AJ, Gonzales EK, Cote A. Social–ecological management results in sustained recovery of an imperiled salmon population. Restor Ecol 2021. [DOI: 10.1111/rec.13401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- D. Cote
- North Atlantic Fisheries Centre Fisheries and Oceans Canada, 80 East White Hills Road, P.O. Box 5667 St. John's NL A1C 5X1 Canada
| | - T. E. Van Leeuwen
- North Atlantic Fisheries Centre Fisheries and Oceans Canada, 80 East White Hills Road, P.O. Box 5667 St. John's NL A1C 5X1 Canada
| | - A. J. Bath
- Department of Geography Memorial University, Science Building St. John's NL A1B 3X9 Canada
| | - E. K. Gonzales
- Parks Canada 300‐300 West Georgia St. Vancouver BC V6B 6B4 Canada
| | - A.L. Cote
- Parks Canada, Terra Nova National Park General Delivery Glovertown Newfoundland A0G 2L0 Canada
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5
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Östergren J, Palm S, Gilbey J, Spong G, Dannewitz J, Königsson H, Persson J, Vasemägi A. A century of genetic homogenization in Baltic salmon-evidence from archival DNA. Proc Biol Sci 2021; 288:20203147. [PMID: 33878928 PMCID: PMC8059615 DOI: 10.1098/rspb.2020.3147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.
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Affiliation(s)
- Johan Östergren
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden
| | - Stefan Palm
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden
| | - John Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, UK
| | - Göran Spong
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 USA
| | - Johan Dannewitz
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden
| | - Helena Königsson
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-901 83 USA
| | - John Persson
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden
| | - Anti Vasemägi
- Swedish University of Agricultural Sciences, Department of Aquatic Resources, Institute of Freshwater Research, Stångholmsvägen 2, SE-178 93 Drottningholm, Sweden.,Chair of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
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6
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Bootsma ML, Miller L, Sass GG, Euclide PT, Larson WA. The ghosts of propagation past: haplotype information clarifies the relative influence of stocking history and phylogeographic processes on contemporary population structure of walleye ( Sander vitreus). Evol Appl 2021; 14:1124-1144. [PMID: 33897825 PMCID: PMC8061267 DOI: 10.1111/eva.13186] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Stocking of fish is an important tool for maintaining fisheries but can also significantly alter population genetic structure and erode the portfolio of within-species diversity that is important for promoting resilience and adaptability. Walleye (Sander vitreus) are a highly valued sportfish in the midwestern United States, a region characterized by postglacial recolonization from multiple lineages and an extensive history of stocking. We leveraged genomic data and recently developed analytical approaches to explore the population structure of walleye from two midwestern states, Minnesota and Wisconsin. We genotyped 954 walleye from 23 populations at ~20,000 loci using genotyping by sequencing and tested for patterns of population structure with single-SNP and microhaplotype data. Populations from Minnesota and Wisconsin were highly differentiated from each other, with additional substructure found in each state. Population structure did not consistently adhere to drainage boundaries, as cases of high intra-drainage and low inter-drainage differentiation were observed. Low genetic structure was observed between populations from the upper Wisconsin and upper Chippewa river watersheds, which are found as few as 50 km apart and were likely homogenized through historical stocking. Nevertheless, we were able to differentiate these populations using microhaplotype-based co-ancestry analysis, providing increased resolution over previous microsatellite studies and our other single SNP-based analyses. Although our results illustrate that walleye population structure has been influenced by past stocking practices, native ancestry still exists in most populations and walleye populations may be able to purge non-native alleles and haplotypes in the absence of stocking. Our study is one of the first to use genomic tools to investigate the influence of stocking on population structure in a nonsalmonid fish and outlines a workflow leveraging recently developed analytical methods to improve resolution of complex population structure that will be highly applicable in many species and systems.
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Affiliation(s)
- Matthew L. Bootsma
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Loren Miller
- Minnesota Department of Natural ResourcesUniversity of MinnesotaSt. PaulMNUSA
| | - Greg G. Sass
- Office of Applied ScienceWisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWIUSA
| | - Peter T. Euclide
- Wisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
| | - Wesley A. Larson
- U.S. Geological SurveyWisconsin Cooperative Fishery Research UnitCollege of Natural ResourcesUniversity of Wisconsin‐Stevens PointStevens PointWIUSA
- Present address:
Ted Stevens Marine Research InstituteAlaska Fisheries Science CenterNational Marine Fisheries ServiceNational Oceanic and Atmospheric AdministrationJuneauAKUSA
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7
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Pomianowski K, Ocalewicz K. Cytogenetic investigation of Arctic char × brook trout F 1, F 2 and backcross hybrids revealed remnants of the chromosomal rearrangements. J Appl Genet 2020; 62:151-164. [PMID: 33128700 PMCID: PMC7822801 DOI: 10.1007/s13353-020-00584-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 11/25/2022]
Abstract
Arctic char (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) hybridize and their offspring is viable and fertile. This may be a real treat for the native European stocks of Arctic char which gene pools might be unintendedly contaminated with the genetic elements of brook trout. On the other hand, hybrids of these two species are appreciated by customers and have some potential for the aquaculture. Moreover, Salvelinus hybrids and backcross individuals are interesting models in the research focused on influence of hybridization on the genomic organization and chromosome rearrangements. Thus, the main goal of the present study was to examine chromosomes of Arctic char × brook trout F1, F2 hybrids and backcross individuals and compare with genomic information concerning parental species to recognize karyotypic changes provoked by the hybridization events. Application of conventional and molecular (FISH) techniques allow to identify characteristic chromosomes for both parental species in the hybrid progeny and show multiplicity of cytotypes among different types of crosses with variability in structure and number of chromosome (81–85) and chromosome arm (99–101). Chromosome fragment was detected in the karyotype of one F1 and one backcross individual and the presence of one triploid (3n) fish was documented. Occurrence of chromosomes containing internally located telomeric sequences (ITS) inherited after brook trout or both parental species was shown in F1 and backcross progeny. Moreover, additional CMA3-positive signal on chromosome from Arctic char pair no. 2 in F1 fish and interstitially located active NOR visible on subtelo-acrocentric (F2 hybrid) and acrocentric (Sf × H individual) chromosomes were detected. Described polymorphic chromosomes together with specific, interstitial location of CMA3-positive found in F2 and Sf × H hybrids and DAPI-positive regions observed in H × Sa fish at different uniarmed chromosomes pair presumably are remnants of chromosomal rearrangements. Provided results strongly indicate that the hybridization process influenced the genome organization in the Salvelinus hybrid progeny.
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Affiliation(s)
- Konrad Pomianowski
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, ul. Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, Institute of Oceanography University of Gdansk, al. Marszalka Józefa Pilsudskiego 46, 81-378 Gdynia, Poland
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8
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Monk CT, Chéret B, Czapla P, Hühn D, Klefoth T, Eschbach E, Hagemann R, Arlinghaus R. Behavioural and fitness effects of translocation to a novel environment: Whole‐lake experiments in two aquatic top predators. J Anim Ecol 2020; 89:2325-2344. [DOI: 10.1111/1365-2656.13298] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 06/04/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Christopher T. Monk
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - Bernard Chéret
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - Philipp Czapla
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - Daniel Hühn
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | | | - Erik Eschbach
- Thünen Institute of Fisheries Ecology Bremerhaven Germany
| | - Robert Hagemann
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
| | - Robert Arlinghaus
- Department of Biology and Ecology of FishesLeibniz‐Institute of Freshwater Ecology and Inland Fisheries Berlin Germany
- Faculty of Life Sciences and Integrative Research Institute for the Transformation of Human‐Environmental Systems Humboldt‐Universität zu Berlin Berlin Germany
- Division of Integrative Fisheries Management Department of Crop and Animal Sciences Faculty of Life Science Humboldt‐Universität zu Berlin Berlin Germany
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9
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Genotyping-by-sequencing reveals the effects of riverscape, climate and interspecific introgression on the genetic diversity and local adaptation of the endangered Mexican golden trout (Oncorhynchus chrysogaster). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Almodóvar A, Leal S, Nicola GG, Hórreo JL, García-Vázquez E, Elvira B. Long-term stocking practices threaten the original genetic diversity of the southernmost European populations of Atlantic salmon Salmo salar. ENDANGER SPECIES RES 2020. [DOI: 10.3354/esr01029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many Atlantic salmon Salmo salar populations in Europe are threatened by previous stocking with foreign hatchery strains. Temporal patterns of genetic characteristics of salmon from northern Spain, the southernmost European populations, were compared before and after species decline and heavy stocking with specimens from northern Europe. Eleven microsatellite loci were analysed in archival (scales from 1958-1960) and contemporary (2007-2008) samples from the River Sella. Temporal analyses revealed a similar heterozygosity between archival and contemporary samples, despite a drastic decrease in population abundance, while the contemporary sample showed a higher allelic richness due to the occurrence of foreign alleles. Considering only the alleles with at least 4% frequency in the archival sample, 2 alleles exclusive to the River Sella were absent in the contemporary sample, and 14 alleles showed a decrease of at least 4% frequency. Four alleles common in Scotland showed a high occurrence in the contemporary sample, so they are good candidates as markers of introgression of foreign genes. The heavy stocking with non-native Scottish broodstocks between 1970 and 1990 caused the introgression found in the contemporary sample when compared with the pristine population. An abrupt decrease was evident when the estimates of effective number of breeders were adjusted to take into account overlapping generations (NbAdj), effective population size (NeAdj) estimated from NbAdj, and number of breeders estimated using the sibship assignment method (NbSIB). The very low effective size values found in the contemporary sample, together with the detrimental synergy between genetic drift and high rates of introgression, represent a severe risk for the conservation of native salmon.
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Affiliation(s)
- A Almodóvar
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
| | - S Leal
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
| | - GG Nicola
- Department of Environmental Sciences, University of Castilla-La Mancha (UCLM), Toledo 45071, Spain
| | - JL Hórreo
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences (MNCN), Spanish National Research Council (CSIC), Madrid 28006, Spain
| | - E García-Vázquez
- Department of Functional Biology, University of Oviedo, Oviedo 33003, Spain
| | - B Elvira
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid (UCM), Madrid 28040, Spain
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11
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Beer SD, Cornett S, Austerman P, Trometer B, Hoffman T, Bartron ML. Genetic diversity, admixture, and hatchery influence in Brook Trout ( Salvelinus fontinalis) throughout western New York State. Ecol Evol 2019; 9:7455-7479. [PMID: 31346416 PMCID: PMC6635958 DOI: 10.1002/ece3.5237] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/22/2019] [Accepted: 04/16/2019] [Indexed: 02/06/2023] Open
Abstract
Although Brook Trout are distributed across most of eastern North America, population numbers have declined in many regions due to habitat loss, climate change, and competition with non-native species. In New York State, Brook Trout habitat has been substantially reduced, with many areas showing complete extirpation of Brook Trout populations, predominantly in the western portion of the state. Small, fragmented populations are at risk of genetic diversity loss, inbreeding depression, and reduced fitness, leading to a greater potential for local extirpation. Genetic monitoring is a practical tool that can facilitate further conservation-decision making regarding small populations. In this study, we used 12 microsatellite loci to examine 3,436 sampled Brook Trout, representing 75 sites from the Allegheny, Erie/Niagara, Genesee, Oswego, Lake Ontario, and Susquehanna drainage basins throughout western New York State. Three Brook Trout hatchery strains were also genetically characterized to evaluate the degree of hatchery introgression between wild populations and hatchery strains stocked in the region. Overall, estimates of genetic diversity varied widely: Allelic richness ranged from 2.23 to 7.485, and expected heterozygosity ranged from 0.402 to 0.766. As observed for Brook Trout in other regions, we found a high degree of genetic differentiation among populations, with all comparisons except one showing significant F ST values. Hatchery introgression was found to be minimal, with estimates ranging from 1.96% to 3.10% of wild individuals exhibiting membership proportions to a hatchery strain cluster exceeding 10% (q ≥ 0.10). Results from this investigation can be used to prioritize management efforts for Brook Trout in western New York State and act as a baseline to monitor future population trends.
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Affiliation(s)
| | - Scott Cornett
- New York State Department of Environmental ConservationAlleganyNew York
| | - Peter Austerman
- New York State Department of Environmental ConservationAvonNew York
| | - Betsy Trometer
- U.S. Fish and Wildlife ServiceLower Great Lakes Fish and Wildlife Conservation OfficeBasomNew York
| | - Thomas Hoffman
- U.S. Fish and Wildlife ServiceLower Great Lakes Fish and Wildlife Conservation OfficeBasomNew York
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12
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Bruce SA, Daniel PC, Krause MK, Henson FG, Pershyn CE, Wright JJ. A methodological approach to the genetic identification of native Brook Trout (Salvelinus fontinalis) populations for conservation purposes. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00682] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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13
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Horreo JL, Griffiths AM, Machado-Schiaffino G, Stevens JR, Garcia-Vazquez E. Northern areas as refugia for temperate species under current climate warming: Atlantic salmon (Salmo salar L.) as a model in northern Europe. JOURNAL OF FISH BIOLOGY 2019; 95:304-310. [PMID: 30281146 DOI: 10.1111/jfb.13825] [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: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
In this work, patterns of geographical genetic diversity in Atlantic salmon Salmo salar were studied across the whole Atlantic Arc; whether these patterns (and thus genetic population structure) were affected by water temperatures was also evaluated. Salmo salar populations were characterized using microsatellite loci and then analysed with reference to ocean surface temperature data from across the region. Analysis showed the presence of a latitudinal cline of genetic variability (higher in northern areas) and water temperatures (sea surface temperatures) determining genetic population structure (the latter in combination with genetic drift in southern populations). Under the current global change scenario, northern areas of Europe would constitute refugia for diversity in the future. This is effectively the inverse of what appears to have happened in glacial refugia during the last glacial maximum. From this perspective, the still abundant and large northern populations S. salar should be considered as precious as the small almost relict southern ones and given appropriate protection. Careful management of the species, coordinated across countries and latitudes, is needed in order to avoid its extinction in Europe.
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Affiliation(s)
- Jose L Horreo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Andrew M Griffiths
- Department of Biosciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | | | - Jamie R Stevens
- Department of Biosciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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14
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Rougemont Q, Carrier A, Le Luyer J, Ferchaud A, Farrell JM, Hatin D, Brodeur P, Bernatchez L. Combining population genomics and forward simulations to investigate stocking impacts: A case study of Muskellunge ( Esox masquinongy) from the St. Lawrence River basin. Evol Appl 2019; 12:902-922. [PMID: 31080504 PMCID: PMC6503833 DOI: 10.1111/eva.12765] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/17/2018] [Indexed: 01/03/2023] Open
Abstract
Understanding the genetic and evolutionary impacts of stocking on wild fish populations has long been of interest as negative consequences such as reduced fitness and loss of genetic diversity are commonly reported outcomes. In an attempt to sustain a fishery, managers implemented nearly five decades of extensive stocking of over a million Muskellunge (Esox masquinongy), a native species in the Lower St. Lawrence River (Québec, Canada). We investigated the effect of this stocking on population genetic structure and allelic diversity in the St. Lawrence River in addition to tributaries and several stocked inland lakes. Using genotype by sequencing, we genotyped 643 individuals representing 22 locations and combined this information with forward simulations to investigate the genetic consequences of long-term stocking. Individuals native to the St. Lawrence watershed were genetically differentiated from stocking sources and tributaries, and inland lakes were naturally differentiated from the main river. Empirical data and simulations within the St. Lawrence River revealed weak stocking effects on admixture patterns. Our data suggest that the genetic structure associated with stocked fish was diluted into its relatively large effective population size. This interpretation is also consistent with a hypothesis that selection against introgression was in operation and relatively efficient within the large St. Lawrence River system. In contrast, smaller populations from adjacent tributaries and lakes displayed greater stocking-related admixture that resulted in comparatively higher heterozygosity than the St. Lawrence. Finally, individuals from inland lakes that were established by stocking maintained a close affinity with their source populations. This study illustrated a benefit of combining extensive genomic data with forward simulations for improved inference regarding population-level genetic effects of long-term stocking, and its relevance for fishery management decision making.
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Affiliation(s)
- Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Anne Carrier
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - Jeremy Le Luyer
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
- IFREMER, Unité Ressources Marines en Polynésie, Centre Océanologique du PacifiqueTaravao, TahitiFrench Polynesia
| | - Anne‐Laure Ferchaud
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
| | - John M. Farrell
- Department of Environmental and Forest Biology, College of Environmental Science and ForestryState University of New YorkSyracuseNew York
| | - Daniel Hatin
- Ministère des Forêts, de la Faune et des Parcs, Direction de la Gestion de la FauneEstrie‐Montréal‐Montérégie‐LavalLongueuilQuébecCanada
| | - Philippe Brodeur
- Ministère des Forêts, de la Faune et des ParcsDirection de la gestion de la faune de la Mauricie et du Centre‐du‐QuébecTrois‐RivièresQuebecCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQuébecCanada
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15
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Saint-Pé K, Blanchet S, Tissot L, Poulet N, Plasseraud O, Loot G, Veyssière C, Prunier JG. Genetic admixture between captive-bred and wild individuals affects patterns of dispersal in a brown trout (Salmo trutta) population. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1095-2] [Citation(s) in RCA: 3] [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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16
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Létourneau J, Ferchaud A, Le Luyer J, Laporte M, Garant D, Bernatchez L. Predicting the genetic impact of stocking in Brook Charr ( Salvelinus fontinalis) by combining RAD sequencing and modeling of explanatory variables. Evol Appl 2018; 11:577-592. [PMID: 29875804 PMCID: PMC5978948 DOI: 10.1111/eva.12566] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 09/21/2017] [Indexed: 01/15/2023] Open
Abstract
In fisheries management, intensive stocking programs are commonly used to enhance population abundance and maintain stock productivity. However, such practices are increasingly raising concerns as multiple studies documented adverse genetic and evolutionary impacts of stocking on wild populations. Improvement of stocking management relies on a better understanding of the dynamic of introgressive hybridization between wild and domestic population and on assessment of the genetic state of wild populations after stocking cessation. In Québec, Canada, over five million captive-reared Brook Charr (Salvelinus fontinalis) are stocked every year to support recreational fishing activities. Here, we investigated how variation in stocking history and environmental variables, including water temperature, pH, and dissolved oxygen, may influence the impact of stocking practices on the genetic integrity of wild Brook Charr populations. We collected DNA samples (n = 862, average of 30 individuals per lake) from 29 lakes that underwent different stocking intensity through time and also collected environmental parameters for each sampled lake. An average of 4,580 high-quality filtered SNPs was obtained for each population using genotyping by sequencing (GBS), which were then used to quantify the mean domestic membership of each sampled population. An exhaustive process of model selection was conducted to obtain a best-fitted model that explained 56% of the variance observed in mean domestic genetic membership. The number of years since the mean year of stocking was the best explanatory variable to predict variation in mean domestic genetic membership whereas environmental characteristics had little influence on observed patterns of admixture. Our model predictions also revealed that each sampled wild population could potentially return to a wild genetic state (absence of domestic genetic background) after stocking cessation. Overall, our study provides new insights on factors determining level of introgressive hybridization and suggests that stocking impacts could be reversible with time.
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Affiliation(s)
- Justine Létourneau
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Anne‐Laure Ferchaud
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Jérémy Le Luyer
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Martin Laporte
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Dany Garant
- Département de BiologieFaculté des SciencesUniversité de SherbrookeSherbrookeQCCanada
| | - Louis Bernatchez
- Département de BiologieInstitut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
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17
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Canales-Aguirre CB, Seeb LW, Seeb JE, Cádiz MI, Musleh SS, Arismendi I, Gajardo G, Galleguillos R, Gomez-Uchida D. Contrasting genetic metrics and patterns among naturalized rainbow trout ( Oncorhynchus mykiss) in two Patagonian lakes differentially impacted by trout aquaculture. Ecol Evol 2017; 8:273-285. [PMID: 29321870 PMCID: PMC5756871 DOI: 10.1002/ece3.3574] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 11/29/2022] Open
Abstract
Different pathways of propagation and dispersal of non‐native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law. Trout from Lake Llanquihue showed higher genetic diversity, weaker genetic structure, and larger estimates for the effective number of breeders (Nb) than trout from Lake TLS. Trout from Lake TLS were divergent from Lake Llanquihue and showed marked genetic structure and a significant isolation‐by‐distance pattern consistent with secondary contact between documented and undocumented stocking events in opposite shores of the lake. Multiple factors, including differences in propagule pressure, origin of donor populations, lake geomorphology, habitat quality or quantity, and life history, may help explain contrasting genetic metrics and patterns for trout between lakes. We contend that high propagule pressure from aquaculture may not only increase genetic diversity and Nb via demographic effects and admixture, but also may impact the evolution of genetic structure and increase gene flow, consistent with findings from artificially propagated salmonid populations in their native and naturalized ranges.
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Affiliation(s)
- Cristian B Canales-Aguirre
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
| | - Lisa W Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - James E Seeb
- Nucleo Milenio INVASAL Concepción Chile.,School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - María I Cádiz
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile
| | - Selim S Musleh
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile
| | - Ivan Arismendi
- Department of Fisheries and Wildlife Oregon State University Corvallis OR USA
| | - Gonzalo Gajardo
- Laboratorio de Genética, Acuicultura & Biodiversidad Universidad de Los Lagos Osorno Chile
| | - Ricardo Galleguillos
- Laboratorio de Genética y Acuicultura Departamento de Oceanografía Facultad de Ciencias Naturales y Oceanográficas Universidad de Concepción Concepción Chile
| | - Daniel Gomez-Uchida
- Genomics in Ecology, Evolution and Conservation Lab (GEECLAB) Departamento de Zoología Universidad de Concepción Concepción Chile.,Nucleo Milenio INVASAL Concepción Chile.,Centro i-mar Universidad de Los Lagos Camino Chinquihue 6 km Puerto Montt Chile
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18
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Savary R, Dufresnes C, Champigneulle A, Caudron A, Dubey S, Perrin N, Fumagalli L. Stocking activities for the Arctic charr in Lake Geneva: Genetic effects in space and time. Ecol Evol 2017; 7:5201-5211. [PMID: 28770060 PMCID: PMC5528235 DOI: 10.1002/ece3.3073] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 01/19/2023] Open
Abstract
Artificial stocking practices are widely used by resource managers worldwide, in order to sustain fish populations exploited by both recreational and commercial activities, but their benefits are controversial. Former practices involved exotic strains, although current programs rather consider artificial breeding of local fishes (supportive breeding). Understanding the complex genetic effects of these management strategies is an important challenge with economic and conservation implications, especially in the context of population declines. In this study, we focus on the declining Arctic charr (Salvelinus alpinus) population from Lake Geneva (Switzerland and France), which has initially been restocked with allochtonous fishes in the early eighties, followed by supportive breeding. In this context, we conducted a genetic survey to document the evolution of the genetic diversity and structure throughout the last 50 years, before and after the initiation of hatchery supplementation, using contemporary and historical samples. We show that the introduction of exotic fishes was associated with a genetic bottleneck in the 1980-1990s, a break of Hardy-Weinberg Equilibrium (HWE), a reduction in genetic diversity, an increase in genetic structure among spawning sites, and a change in their genetic composition. Together with better environmental conditions, three decades of subsequent supportive breeding using local fishes allowed to re-establish HWE and the initial levels of genetic variation. However, current spawning sites have not fully recovered their original genetic composition and were extensively homogenized across the lake. Our study demonstrates the drastic genetic consequences of different restocking tactics in a comprehensive spatiotemporal framework and suggests that genetic alteration by nonlocal stocking may be partly reversible through supportive breeding. We recommend that conservation-based programs consider local diversity and implement adequate protocols to limit the genetic homogenization of this Arctic charr population.
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Affiliation(s)
- Romain Savary
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | - Christophe Dufresnes
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | | | - Arnaud Caudron
- UMR CARRTEL INRA-Université de Savoie Mont Blanc Thonon-les-Bains Cedex France.,Science-Management Interface for Biodiversity Conservation Thonon-les-Bains France
| | - Sylvain Dubey
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland.,Hintermann & Weber SA Montreux Switzerland
| | - Nicolas Perrin
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
| | - Luca Fumagalli
- Laboratory for Conservation Biology Department of Ecology and Evolution Biophore University of Lausanne Lausanne Switzerland
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19
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Young MK, Isaak DJ, McKelvey KS, Wilcox TM, Pilgrim KL, Carim KJ, Campbell MR, Corsi MP, Horan DL, Nagel DE, Schwartz MK. Climate, Demography, and Zoogeography Predict Introgression Thresholds in Salmonid Hybrid Zones in Rocky Mountain Streams. PLoS One 2016; 11:e0163563. [PMID: 27828980 PMCID: PMC5102351 DOI: 10.1371/journal.pone.0163563] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/11/2016] [Indexed: 11/19/2022] Open
Abstract
Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.S. northern Rocky Mountains. A consensus model performed well (AUC, 0.78–0.86; classification success, 72–82%; 10-fold cross validation, 70–82%) and predicted that rainbow trout introgression was significantly associated with warmer water temperatures, larger streams, proximity to warmer habitats and to recent sources of rainbow trout propagules, presence within the historical range of rainbow trout, and locations further east. Assuming that water temperatures will continue to rise in response to climate change and that levels of introgression outside the historical range of rainbow trout will equilibrate with those inside that range, we applied six scenarios across a 55,234-km stream network that forecast 9.5–74.7% declines in the amount of habitat occupied by westslope cutthroat trout populations of conservation value, but not the wholesale loss of such populations. We conclude that introgression between these taxa is predictably related to environmental conditions, many of which can be manipulated to foster largely genetically intact populations of westslope cutthroat trout and help managers prioritize conservation activities.
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Affiliation(s)
- Michael K. Young
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
- * E-mail:
| | - Daniel J. Isaak
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - Kevin S. McKelvey
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Taylor M. Wilcox
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Kristine L. Pilgrim
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Kellie J. Carim
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
| | - Matthew R. Campbell
- Eagle Fish Genetics Laboratory, Idaho Department of Fish and Game, Eagle, Idaho, United States of America
| | - Matthew P. Corsi
- Idaho Department of Fish and Game, Coeur d'Alene, Idaho, United States of America
| | - Dona L. Horan
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - David E. Nagel
- Rocky Mountain Research Station, USDA Forest Service, Boise, Idaho, United States of America
| | - Michael K. Schwartz
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, USDA Forest Service, Missoula, Montana, United States of America
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20
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Ferchaud AL, Perrier C, April J, Hernandez C, Dionne M, Bernatchez L. Making sense of the relationships between Ne, Nb and Nc towards defining conservation thresholds in Atlantic salmon (Salmo salar). Heredity (Edinb) 2016; 117:268-78. [PMID: 27530910 PMCID: PMC5026759 DOI: 10.1038/hdy.2016.62] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 06/23/2016] [Accepted: 06/29/2016] [Indexed: 01/13/2023] Open
Abstract
Effective population size over a generation (Ne) or over a reproductive cycle (Nb) and the adult census size (Nc) are important parameters in both conservation and evolutionary biology. Ne provides information regarding the rate of loss of genetic diversity and can be tracked back in time to infer demographic history of populations, whereas Nb may often be more easily quantified than Nc for short-term abundance monitoring. In this study, we propose (1) an empirical context to Waples et al. (2014) who introduced a correction to bias due to overlapping generations, and (2) a mathematical relationship between Ne and Nb for direct application in Atlantic salmon populations in Québec, Canada. To achieve this, we investigate the relationships between Ne, Nb and Nc in 10 Atlantic salmon populations, Canada, for which we genotyped 100 randomly sampled young-of-the year individuals for 5 consecutive years. The results show a positive correlation between Ne, Nb and Nc, suggesting that Nb is an indicative parameter for tracking effective population size and abundance of Atlantic salmon. However, our model allows predicting Nc from Nb values at 27% that can be partly explained by high variance in Nb/Nc both among populations (37%) and among years (19%). This result illustrates the need for thorough calibration of Nb/Nc before using Nb in monitoring programs, as well as a full understanding of the limits of such an approach. Finally, we discuss the importance of these results for the management of wild populations.
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Affiliation(s)
- A-L Ferchaud
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - C Perrier
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS), Montpellier, France
| | - J April
- Direction de la Faune Aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Canada
| | - C Hernandez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
| | - M Dionne
- Direction de la Faune Aquatique, Ministère des Forêts, de la Faune et des Parcs du Québec, Québec, Canada
| | - L Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada
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21
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Parentage assignment in the critically endangered European sturgeon (Acipenser sturio) based on a novel microsatellite multiplex assay: a valuable resource for restocking, monitoring and conservation programs. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0538-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Côte J, Roussel JM, Le Cam S, Guillaume F, Evanno G. Adaptive divergence in embryonic thermal plasticity among Atlantic salmon populations. J Evol Biol 2016; 29:1593-601. [PMID: 27177256 DOI: 10.1111/jeb.12896] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
Abstract
In the context of global changes, the long-term viability of populations of endangered ectotherms may depend on their adaptive potential and ability to cope with temperature variations. We measured responses of Atlantic salmon embryos from four populations to temperature variations and used a QST -FST approach to study the adaptive divergence among these populations. Embryos were reared under two experimental conditions: a low temperature regime at 4 °C until eyed-stage and 10 °C until the end of embryonic development and a high temperature regime with a constant temperature of 10 °C throughout embryonic development. Significant variations among populations and population × temperature interactions were observed for embryo survival, incubation time and length. QST was higher than FST in all but one comparison suggesting an important effect of divergent selection. QST was also higher under the high-temperature treatment than at low temperature for length and survival due to a higher variance among populations under the stressful warmer treatment. Interestingly, heritability was lower for survival under high temperature in relation to a lower additive genetic variance under that treatment. Overall, these results reveal an adaptive divergence in thermal plasticity in embryonic life stages of Atlantic salmon suggesting that salmon populations may differentially respond to temperature variations induced by climate change. These results also suggest that changes in temperature may alter not only the adaptive potential of natural populations but also the selection regimes among them.
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Affiliation(s)
- J Côte
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France.,UMR 5174 EDB (Laboratoire Evolution et Diversité Biologique), CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - J-M Roussel
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - S Le Cam
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
| | - F Guillaume
- Institute of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - G Evanno
- INRA, UMR 985 Ecologie et Santé des Ecosystèmes, Rennes, France.,Agrocampus Ouest, UMR ESE, Rennes, France
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23
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Ozerov MY, Gross R, Bruneaux M, Vähä JP, Burimski O, Pukk L, Vasemägi A. Genomewide introgressive hybridization patterns in wild Atlantic salmon influenced by inadvertent gene flow from hatchery releases. Mol Ecol 2016; 25:1275-93. [PMID: 26840557 DOI: 10.1111/mec.13570] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 01/13/2016] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
Abstract
Many salmonid fish populations are threatened by genetic homogenization, primarily due to introgressive hybridization with hatchery-reared conspecifics. By applying genomewide analysis using two molecular marker types (1986 SNPs and 17 microsatellites), we assessed the genetic impacts of inadvertent gene flow via straying from hatchery releases on wild populations of Atlantic salmon in the Gulf of Finland, Baltic Sea, over 16 years (1996-2012). Both microsatellites and SNPs revealed congruent population genetic structuring, indicating that introgression changed the genetic make-up of wild populations by increasing genetic diversity and reducing genetic divergence. However, the degree of genetic introgression varied among studied populations, being higher in the eastern part and lower in the western part of Estonia, which most likely reflects the history of past stocking activities. Using kernel smoothing and permutation testing, we detected considerable heterogeneity in introgression patterns across the genome, with a large number of regions exhibiting nonrandom introgression widely dispersed across the genome. We also observed substantial variation in nonrandom introgression patterns within populations, as the majority of genomic regions showing elevated or reduced introgression were not consistently detected among temporal samples. This suggests that recombination, selection and stochastic processes may contribute to complex nonrandom introgression patterns. Our results suggest that (i) some genomic regions in Atlantic salmon are more vulnerable to introgressive hybridization, while others show greater resistance to unidirectional gene flow; and (ii) the hybridization of previously separated populations leads to complex and dynamic nonrandom introgression patterns that most likely have functional consequences for indigenous populations.
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Affiliation(s)
- M Y Ozerov
- Department of Biology, University of Turku, 20014, Turku, Finland.,Kevo Subarctic Research Institute, University of Turku, 20014, Turku, Finland
| | - R Gross
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - M Bruneaux
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - J-P Vähä
- Department of Biology, University of Turku, 20014, Turku, Finland.,Kevo Subarctic Research Institute, University of Turku, 20014, Turku, Finland
| | - O Burimski
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - L Pukk
- Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014, Tartu, Estonia
| | - A Vasemägi
- Department of Biology, University of Turku, 20014, Turku, Finland.,Department of Aquaculture, Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51014, Tartu, Estonia
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24
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Effective number of breeders in relation to census size as management tools for Atlantic salmon conservation in a context of stocked populations. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0758-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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Origins and genetic diversity among Atlantic salmon recolonizing upstream areas of a large South European river following restoration of connectivity and stocking. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0602-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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