1
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Langille BL, Kess T, Brachmann M, Nugent CM, Messmer A, Duffy SJ, Holborn MK, Van Wyngaarden M, Knutsen TM, Kent M, Boyce D, Gregory RS, Gauthier J, Fairchild EA, Pietrak M, Eddy S, de Leaniz CG, Consuegra S, Whittaker B, Bentzen P, Bradbury IR. Fine-scale environmentally associated spatial structure of lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic. Evol Appl 2023; 16:1619-1636. [PMID: 37752959 PMCID: PMC10519416 DOI: 10.1111/eva.13590] [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: 01/09/2023] [Revised: 07/10/2023] [Accepted: 08/14/2023] [Indexed: 09/28/2023] Open
Abstract
Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms-a process which involves both the domestication and the transfer of lumpfish between geographic regions. At present, little is known regarding population structure and diversity of wild lumpfish in Atlantic Canada, limiting attempts to assess the potential impacts of escaped lumpfish individuals from salmon pens on currently at-risk wild populations. Here, we characterize the spatial population structure and genomic-environmental associations of wild populations of lumpfish throughout the Northwest Atlantic using both 70K SNP array data and whole-genome re-sequencing data (WGS). At broad spatial scales, our results reveal a large environmentally associated genetic break between the southern populations (Gulf of Maine and Bay of Fundy) and northern populations (Newfoundland and the Gulf of St. Lawrence), linked to variation in ocean temperature and ice cover. At finer spatial scales, evidence of population structure was also evident in a distinct coastal group in Newfoundland and significant isolation by distance across the northern region. Both evidence of consistent environmental associations and elevated genome-wide variation in F ST values among these three regional groups supports their biological relevance. This study represents the first extensive description of population structure of lumpfish in Atlantic Canada, revealing evidence of broad and fine geographic scale environmentally associated genomic diversity. Our results will facilitate the commercial use of lumpfish as a cleaner fish in Atlantic salmon aquaculture, the identification of lumpfish escapees, and the delineation of conservation units of this at-risk species throughout Atlantic Canada.
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Affiliation(s)
- Barbara L. Langille
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Tony Kess
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Matthew Brachmann
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Cameron M. Nugent
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Amber Messmer
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Steven J. Duffy
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Melissa K. Holborn
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Mallory Van Wyngaarden
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | | | - Matthew Kent
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Danny Boyce
- Department of Ocean Sciences, Ocean Sciences CentreMemorial University of NewfoundlandSt John'sNewfoundland and LabradorCanada
| | - Robert S. Gregory
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
| | - Johanne Gauthier
- Maurice Lamontagne Institute, Fisheries and Oceans CanadaQuebecCanada
| | | | - Michael Pietrak
- USDA, Agricultural Research ServiceNational Cold Water Marine Aquaculture CenterFranklinMaineUSA
| | - Stephen Eddy
- University of Maine Center for Cooperative Aquaculture ResearchFranklinMaineUSA
| | | | - Sofia Consuegra
- Centre for Sustainable Aquatic Research, Swansea UniversitySwanseaUK
| | - Ben Whittaker
- Centre for Sustainable Aquatic Research, Swansea UniversitySwanseaUK
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Ian R. Bradbury
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans CanadaSt. John'sNewfoundland and LabradorCanada
- Marine Gene Probe Laboratory, Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
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2
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Zheng S, Zhang T, Tu K, Li L, Liu Z, Wu B, Zhou L, Sun X. Population Genetics of Manila Clam ( Ruditapes philippinarum) in China Inferred from Microsatellite Markers. BIOLOGY 2023; 12:biology12040557. [PMID: 37106757 PMCID: PMC10135866 DOI: 10.3390/biology12040557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023]
Abstract
The Manila clam (Ruditapes philippinarum) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (Ne). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (Ho) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (He) was calculated to be varying from 0.587 to 0.700. Fst values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all Fst values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.
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Affiliation(s)
- Sichen Zheng
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Tianshi Zhang
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Kang Tu
- Putian Institute of Aquaculture Science of Fujian Province, Putian 351100, China
| | - Li Li
- National Oceanographic Center, Marine Science Research Institute of Shandong Province, Qingdao 266104, China
| | - Zhihong Liu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Biao Wu
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Liqing Zhou
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiujun Sun
- National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
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3
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Bradbury IR, Lehnert SJ, Kess T, Van Wyngaarden M, Duffy S, Messmer A, Wringe B, Karoliussen S, Dempson JB, Fleming IA, Solberg MF, Glover KA, Bentzen P. Genomic evidence of recent European introgression into North American farmed and wild Atlantic Salmon. Evol Appl 2022; 15:1436-1448. [PMID: 36187183 PMCID: PMC9488674 DOI: 10.1111/eva.13454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/10/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Gene flow between wild and domestic populations has been repeatedly demonstrated across a diverse range of taxa. Ultimately, the genetic impacts of gene flow from domestic into wild populations depend both on the degree of domestication and the original source of the domesticated population. Atlantic salmon, Salmo salar, used in North American aquaculture are ostensibly of North American origin. However, evidence of European introgression into North American aquaculture salmon has accumulated in recent decades, even though the use of diploid European salmon has never been approved in Canada. The full extent of such introgression as well as the potential impacts on wild salmon in the Northwest Atlantic remains uncertain. Here, we extend previous work comparing North American and European wild salmon (n = 5799) using a 220 K SNP array to quantify levels of recent European introgression into samples of domestic salmon, aquaculture escapees, and wild salmon collected throughout Atlantic Canada. Analysis of North American farmed salmon (n = 403) and escapees (n = 289) displayed significantly elevated levels of European ancestry by comparison with wild individuals (p < 0.001). Of North American farmed salmon sampled between 2011 and 2018, ~17% had more than 10% European ancestry and several individuals exceeded 40% European ancestry. Samples of escaped farmed salmon similarly displayed elevated levels of European ancestry, with two individuals classified as 100% European. Analysis of juvenile salmon collected in rivers proximate to aquaculture locations also revealed evidence of elevated European ancestry and larger admixture tract in comparison to individuals collected at distance from aquaculture. Overall, our results demonstrate that even though diploid European salmon have never been approved for use in Canada, individuals of full and partial European ancestry have been in use over the last decade, and that some of these individuals have escaped and hybridized in the wild.
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Affiliation(s)
- I. R. Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - S. J. Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - T. Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - M. Van Wyngaarden
- Biology Department Dalhousie University 1355 Oxford Street Halifax Nova Scotia
| | - S. Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - A. Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - B. Wringe
- Bedford Institute of Oceanography Fisheries and Oceans Canada Dartmouth NS Canada
| | - S. Karoliussen
- Centre for Integrative Genetics Norwegian University of Life Sciences Ås Norway
| | - J. B. Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd St. John’s, Newfoundland, A1C 5X1 Canada
| | - I. A. Fleming
- Department of Ocean Sciences, Ocean Sciences Centre Memorial University of Newfoundland St John’s, NL, A1C 5S7 Canada
| | - M. F. Solberg
- Institute of Marine Research Population Genetics Research Group PO Box 1870, Nordnes, N‐5817 Bergen Norway
| | - K. A. Glover
- Institute of Marine Research Population Genetics Research Group PO Box 1870, Nordnes, N‐5817 Bergen Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
| | - P. Bentzen
- Biology Department Dalhousie University 1355 Oxford Street Halifax Nova Scotia
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4
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Holt RD, Barfield M, Peniston JH. Temporal variation may have diverse impacts on range limits. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210016. [PMID: 35184591 PMCID: PMC8861856 DOI: 10.1098/rstb.2021.0016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/24/2022] [Indexed: 01/16/2023] Open
Abstract
Environmental fluctuations are pervasive in nature, but the influence of non-directional temporal variation on range limits has received scant attention. We synthesize insights from the literature and use simple models to make conceptual points about the potentially wide range of ecological and evolutionary effects of temporal variation on range limits. Because organisms respond nonlinearly to environmental conditions, temporal variation can directionally alter long-term growth rates, either to shrink or to expand ranges. We illustrate this diversity of outcomes with a model of competition along a mortality gradient. Temporal variation can permit transitions between alternative states, potentially facilitating range expansion. We show this for variation in dispersal, using simple source-sink population models (with strong Allee effects, or with gene flow hampering local adaptation). Temporal variation enhances extinction risk owing to demographic stochasticity, rare events, and loss of genetic variation, all tending to shrink ranges. However, specific adaptations to exploit variation (including dispersal) may permit larger ranges than in similar but constant environments. Grappling with temporal variation is essential both to understand eco-evolutionary dynamics at range limits and to guide conservation and management strategies. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Robert D. Holt
- Department of Biology, The University of Florida, Gainesville, FL 32611, USA
| | - Michael Barfield
- Department of Biology, The University of Florida, Gainesville, FL 32611, USA
| | - James H. Peniston
- Department of Biology, The University of Florida, Gainesville, FL 32611, USA
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5
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Hsu TH, Lee HT, Lu HJ, Liao CH, Gong HY, Huang CW. Maintenance of Genetic Diversity of Black Sea Bream despite Unmonitored and Large-Scale Hatchery Releases. BIOLOGY 2022; 11:554. [PMID: 35453753 PMCID: PMC9026629 DOI: 10.3390/biology11040554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/12/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004-2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful.
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Affiliation(s)
- Te-Hua Hsu
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Hung-Tai Lee
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Hsueh-Jung Lu
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Cheng-Hsin Liao
- Department of Environmental Biology and Fisheries Science, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.L.); (H.-J.L.); (C.-H.L.)
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Chang-Wen Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (T.-H.H.); (H.-Y.G.)
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
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6
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Wacker S, Aronsen T, Karlsson S, Ugedal O, Diserud OH, Ulvan EM, Hindar K, Næsje TF. Selection against individuals from genetic introgression of escaped farmed salmon in a natural population of Atlantic salmon. Evol Appl 2021; 14:1450-1460. [PMID: 34025778 PMCID: PMC8127704 DOI: 10.1111/eva.13213] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/14/2021] [Accepted: 02/26/2021] [Indexed: 11/27/2022] Open
Abstract
The viability of wild Atlantic salmon populations is threatened by genetic introgression from escaped farmed salmon. Farmed Atlantic salmon are genetically improved for important commercial traits and a life in captivity but are poorly adapted to the natural environment. The rate of gene flow from escaped farmed to wild salmon depends on their spawning success and on offspring survival at various life stages. We here investigate relative survival of introgressed juvenile Atlantic salmon (parr) in a river in northern Norway. The studied population has experienced genetic introgression from farmed salmon for about four generations (20 years). We followed two cohorts of parr from the year of hatching (0+) to the age of 2 years (2+). Farmed genetic introgression was quantified at the individual level and on a continuous scale using diagnostic SNPs. Population-level genetic introgression decreased from 0+ to 2+ by 64% (2011 cohort) and 37% (2013 cohort). This change was driven by a 70% (2011 cohort) and 49% (2013 cohort) lower survival from age 0+ to 2+ in introgressed parr compared to parr of wild origin. Our observations show that there is natural selection against genetic introgression with a potential cost of lower productivity.
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Affiliation(s)
| | - Tonje Aronsen
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Sten Karlsson
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ola Ugedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | | | - Eva M. Ulvan
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Kjetil Hindar
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Tor F. Næsje
- Norwegian Institute for Nature ResearchTrondheimNorway
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7
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Biologia Futura: integrating freshwater ecosystem health in water resources management. Biol Futur 2020; 71:337-358. [DOI: 10.1007/s42977-020-00031-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/20/2020] [Indexed: 11/26/2022]
Abstract
AbstractSustainable water use implies the simultaneous protection of water quality and quantity. Beyond their function to support human needs such as drinking water provision, transportation and recreation freshwater bodies are also habitats. Conceiving them as water users on their own with respective biological, physico-chemical and morphological requirements could help maintaining their healthy state. Healthy freshwater ecosystems are also attractive for high-value human uses. Dwindling per capita availability of water, increasing demands, human well-being and climate change lead to competition for, and pressures on freshwater ecosystems. This has been conceptualized through the modification of the drivers–pressures–state–impacts–responses framework. This distinguishes between pressures, associated with the achievement of human well-being, and stressors, which are defined as the negative effect of excessive pressures or combination thereof on aquatic ecosystems. Guidelines usually specify threshold values to classify water bodies as appropriate for certain utilitarian uses. However, only few guidelines focus on freshwater ecosystem health. Eight guidelines for monitoring of freshwater ecosystem health were analysed in the UNEP-funded project “International Water Quality Guidelines for Ecosystems”. Based on this review, general benchmark values are proposed for key physico-chemical indicators. Furthermore, adaptive pathways towards improved monitoring and protection of the health of freshwater ecosystems are recommended. In this paper, we review the main findings of the report and also review its recent uptake. Water quality guidelines for freshwater ecosystems cannot be conceived without societal consensus and vision. Different climatic, geographical and socioeconomic contexts are to be considered too. Their development is embedded in an adaptive cycle. Its multiple phases and steps indicate a long-term approach including reassessment and potential revisions.
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8
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Population Genetic Analysis for Stock Enhancement of Silver Sea Bream (Rhabdosargus sarba) in Taiwan. FISHES 2020. [DOI: 10.3390/fishes5020019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stock enhancement is a method for replenishing depleted wild finfish populations by supplementing them with hatchery-raised fish. In Taiwan, silver sea bream (Rhabdosargus sarba) is a predominant commercial species involved in stock enhancement projects. Although management agencies conduct stock enhancement projects, there are a lot of private releases without records. Stock enhancement is performed by the private aquaculture sector without accurate genetic records, potentially leading to unintended consequences for wild populations. We analyzed the genetics of 459 wild and 701 hatchery-reared specimens from nine batches produced by various hatcheries. Wild and hatchery-reared samples could be considered two separate clades by using a set of stable and informative microsatellite markers including type I (from gene introns and 3′UTR) and type II markers (randomly picked up from genome). Type I microsatellite markers could more sensitively reflect the loss of genetic diversity more than type II markers in the domestication process. All specimens were considered native by using mtDNA COI and microsatellites. The genetic composition of the wild population is relatively simple, and the estimated low contribution rate of the hatchery stock (1.3–10.9%; 6–50/459) indicated a weak but significant genetic effect of stock enhancement. Therefore, establishing standards for the stock enhancement of silver sea bream for more effective supplementation of wild populations is imperative.
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9
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Atalah J, Sanchez-Jerez P. Global assessment of ecological risks associated with farmed fish escapes. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2019.e00842] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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10
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Xia S, Baskett ML, Powell JR. Quantifying the efficacy of genetic shifting in control of mosquito-borne diseases. Evol Appl 2019; 12:1552-1568. [PMID: 31462914 PMCID: PMC6708429 DOI: 10.1111/eva.12802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/11/2019] [Indexed: 01/07/2023] Open
Abstract
Many of the world's most prevalent diseases are transmitted by animal vectors such as dengue transmitted by mosquitoes. To reduce these vector-borne diseases, a promising approach is "genetic shifting": selective breeding of the vectors to be more resistant to pathogens and releasing them to the target populations to reduce their ability to transmit pathogens, that is, lower their vector competence. The efficacy of genetic shifting will depend on possible counterforces such as natural selection against low vector competence. To quantitatively evaluate the potential efficacy of genetic shifting, we developed a series of coupled genetic-demographic models that simulate the changes of vector competence during releases of individuals with low vector competence. We modeled vector competence using different genetic architectures, as a multilocus, one-locus, or two-locus trait. Using empirically determined estimates of model parameters, the model predicted a reduction of mean vector competence of at least three standard deviations after 20 releases, one release per generation, and 10% of the size of the target population released each time. Sensitivity analysis suggested that release efficacy depends mostly on the vector competence of the released population, release size, release frequency, and the survivorship of the released individuals, with duration of the release program less important. Natural processes such as density-dependent survival and immigration from external populations also strongly influence release efficacy. Among different sex-dependent release strategies, releasing blood-fed females together with males resulted in the highest release efficacy, as these females mate in captivity and reproduce when released, thus contributing a greater proportion of low-vector-competence offspring. Conclusions were generally consistent across three models assuming different genetic architectures of vector competence, suggesting that genetic shifting could generally apply to various vector systems and does not require detailed knowledge of the number of loci contributing to vector competence.
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Affiliation(s)
- Siyang Xia
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
| | - Marissa L. Baskett
- Department of Environmental Science and PolicyUniversity of California, DavisDavisCalifornia
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11
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Peniston JH, Barfield M, Holt RD. Pulsed Immigration Events Can Facilitate Adaptation to Harsh Sink Environments. Am Nat 2019; 194:316-333. [PMID: 31553211 DOI: 10.1086/704608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In nature, rates of dispersal vary greatly over time, yet most theoretical explorations of ecological and evolutionary dynamics to date have assumed constant movement rates. Here we examine how a particular pattern of temporal variation-periodic pulses of immigration-influences adaptation to a harsh environment, in which a species experiences conditions outside its niche requirements. Using both deterministic models and stochastic individual-based simulations, we show that for many ecological and genetic scenarios, temporally spacing out immigration events increases the probability that local adaptation is sufficient for persistence (i.e., niche evolution). When immigration events are too frequent, gene flow can hamper local adaptation in sexual species, but sufficiently infrequent pulses of immigration allow for repeated opportunities for adaptation with temporary escapes from gene flow during which local selection is unleashed. We develop versions of our models with and without density dependence for three different assumptions about the genetics underlying fitness (haploid, diploid, and quantitative genetic variation) so that our results may be applicable to a wide range of natural systems. Our study adds to a growing body of literature showing that temporal variation in migration rates can have significant effects on local adaptation and is among the first to show how such variation affects niche evolution.
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12
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Cossu P, Scarpa F, Sanna D, Lai T, Dedola GL, Curini-Galletti M, Mura L, Fois N, Casu M. Influence of genetic drift on patterns of genetic variation: The footprint of aquaculture practices in Sparus aurata (Teleostei: Sparidae). Mol Ecol 2019; 28:3012-3024. [PMID: 31125994 DOI: 10.1111/mec.15134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 11/30/2022]
Abstract
Aquaculture finfish production based on floating cage technology has raised increasing concerns regarding the genetic integrity of natural populations. Accidental mass escapes can induce the loss of genetic diversity in wild populations by increasing genetic drift and inbreeding. Farm escapes probably represent an important issue in the gilthead sea bream (Sparus aurata), which accounted for 76.4% of total escapees recorded in Europe during a 3-year survey. Here, we investigated patterns of genetic variation in farmed and wild populations of gilthead sea bream from the Western Mediterranean, a region of long gilthead sea bream farming. We focused on the role that genetic drift may play in shaping these patterns. Results based on microsatellite markers matched those observed in previous studies. Farmed populations showed lower levels of genetic diversity than wild populations and were genetically divergent from their wild counterparts. Overall, farmed populations showed the smallest effective population size and increased levels of relatedness compared to wild populations. The small broodstock size coupled with breeding practices that may favour the variance in individual reproductive success probably boosted genetic drift. This factor appeared to be a major driver of the genetic patterns observed in the gilthead sea bream populations analysed in the present study. These results further stress the importance of recommendations aimed at maintaining broodstock sizes as large as possible and equal sex-ratios among breeders, as well as avoiding unequal contributions among parents.
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Affiliation(s)
- Piero Cossu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Fabio Scarpa
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Tiziana Lai
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Gian Luca Dedola
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy
| | - Marco Curini-Galletti
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Laura Mura
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Nicola Fois
- AGRIS Sardegna, Servizio Ricerca Prodotti Ittici, Olmedo, Italy
| | - Marco Casu
- Department of Sciences for Nature and Environmental Resources, University of Sassari, Sassari, Italy.,Department of Veterinary Medicine, University of Sassari, Sassari, Italy
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13
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Yang L, Waples RS, Baskett ML. Life history and temporal variability of escape events interactively determine the fitness consequences of aquaculture escapees on wild populations. Theor Popul Biol 2019; 129:93-102. [PMID: 31028784 DOI: 10.1016/j.tpb.2018.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 11/27/2018] [Accepted: 12/27/2018] [Indexed: 10/27/2022]
Abstract
Domesticated individuals are likely to be maladaptive in the wild due to adaptation to captivity. Escaped aquaculture fish can cause unintended fitness and demographic consequences for their wild conspecifics through interbreeding and competition. Escape events from different sources exhibit great heterogeneity in their frequencies and magnitudes, ranging from rare but large spillover during a storm, to continuous low-level leakage caused by operational errors. The timescale of escape events determines the distribution of gene flow from aquaculture to the wild. The evolutionary consequences of this variation in timescale will depend on the degree of generation overlap and the focal species' life history attributes, especially those under selection in aquaculture (e.g., growth rate, which can influence additional demographically important traits such as age at maturity). To evaluate the effects of variable escape both within and across generations, we construct an age-structured model of coupled genetic and demographic dynamics and parameterize it for species with contrasting life history characteristics (Salmo salar and Gadus morhua). Our results are consistent with earlier discrete-generation models that constant, low-level spillover can have a greater impact than rare, large pulses of leakage, even after accounting for the averaging effects of overlapping generations. The age-structured model also allows detailed evaluation of the role of different life history traits, which reveals that species with longer generation times might experience greater fitness consequences of aquaculture spillover but are less sensitive to variability in spillover. Additionally, environment-induced earlier maturity of escapees can increase the fitness effects on wild fish, especially those with shorter generation times. Our results suggest that effective management to minimize the unintended fitness consequences of aquaculture releases might require extensive monitoring efforts on constant, low-level spillover and assessment of the focal species' life history characteristics.
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Affiliation(s)
- Luojun Yang
- Department of Environmental Science and Policy, University of California, Davis, One Shields Avenue, Davis, CA 95616-5270, USA; School of Life Sciences, Nanjing University, 163 Xianlin Road, Qixia District, Nanjing, Jiangsu Province, 210023, PR China.
| | - Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard East, Seattle, WA 98112-2097, USA
| | - Marissa L Baskett
- Department of Environmental Science and Policy, University of California, Davis, One Shields Avenue, Davis, CA 95616-5270, USA
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14
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Perry WB, Solberg MF, Besnier F, Dyrhovden L, Matre IH, Fjelldal PG, Ayllon F, Creer S, Llewellyn M, Taylor MI, Carvalho G, Glover KA. Evolutionary drivers of kype size in Atlantic salmon ( Salmo salar): domestication, age and genetics. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190021. [PMID: 31183145 PMCID: PMC6502380 DOI: 10.1098/rsos.190021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
The diversity of reproduction and associated mating patterns in Atlantic salmon (Salmo salar) has long captivated evolutionary biologists. Salmo salar exhibit strategies involving migration, bold mating behaviours and radical morphological and physiological change. One such radical change is the elongation and curvature of the lower jaw in sexually mature males into a hook-like appendage called the kype. The kype is a secondary sexual characteristic used in mating hierarchies and a prime candidate for sexual selection. As one of the core global aquaculture fish species, however, mate choice, and thus sexual selection, has been replaced by industrial artificial fertilization seeking to develop more commercially viable strains. Removal of mate choice provides a unique opportunity to examine the kype over successive generations in the absence of sexual selection. Here we use a large-scale common-garden experiment, incorporating six experimental strains (wild, farmed and wild × farmed hybrids), experiencing one to three sea winters, to assess the impact of age and genetic background. After controlling for allometry, fork length-adjusted kype height (AKH) was significantly reduced in the domesticated strain in comparison to two wild strains. Furthermore, genetic variation at a locus on linkage group SSA1 was associated with kype height, and a locus on linkage group SSA23 was associated with fork length-adjusted kype length (AKL). The reduction in fork length-AKH in domesticated salmon suggests that the kype is of importance in mate choice and that it has decreased due to relaxation of sexual selection. Fork length-AKL showed an increase in domesticated individuals, highlighting that it may not be an important cue in mate choice. These results give us insight into the evolutionary significance of the kype, as well as implications of genetic induced phenotypic change caused by domesticated individuals escaping into the natural environment.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Monica Favnebøe Solberg
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Francois Besnier
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Lise Dyrhovden
- Matre Research Station, Institute of Marine Research, Matredal, Norway
| | - Ivar Helge Matre
- Matre Research Station, Institute of Marine Research, Matredal, Norway
| | - Per Gunnar Fjelldal
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Fernando Ayllon
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Martin Llewellyn
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Martin I. Taylor
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kevin Alan Glover
- Population Genetics Research Group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817 Bergen, Norway
- Institute of Biology, University of Bergen, N-5020 Bergen, Norway
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15
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Willoughby JR, Christie MR. Long-term demographic and genetic effects of releasing captive-born individuals into the wild. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:377-388. [PMID: 30168872 DOI: 10.1111/cobi.13217] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/20/2018] [Accepted: 08/28/2018] [Indexed: 05/20/2023]
Abstract
Because of continued habitat destruction and species extirpations, the need to use captive breeding for conservation purposes has been increasing steadily. However, the long-term demographic and genetic effects associated with releasing captive-born individuals with varied life histories into the wild remain largely unknown. To address this question, we developed forward-time, agent-based models for 4 species with long-running captive-breeding and release programs: coho salmon (Oncorhynchus kisutch), golden lion tamarin (Leontopithecus rosalia), western toad (Anaxyrus boreas), and Whooping Crane (Grus americana). We measured the effects of supplementation by comparing population size and neutral genetic diversity in supplemented populations to the same characteristics in unaltered populations 100 years after supplementation ended. Releasing even slightly less fit captive-born individuals to supplement wild populations typically resulted in reductions in population sizes and genetic diversity over the long term when the fitness reductions were heritable (i.e., due to genetic adaptation to captivity) and populations continued to be regulated by density-dependent mechanisms over time. Negative effects for species with longer life spans and lower rates of population replacement were smaller than for species with shorter life spans and higher rates of population replacement. Programs that released captive-born individuals over fewer years or that avoided breeding individuals with captive ancestry had smaller reductions in population size and genetic diversity over the long term. Relying on selection in the wild to remove individuals with reduced fitness mitigated some negative demographic effects, but at a substantial cost to neutral genetic diversity. Our results suggest that conservation-focused captive-breeding programs should take measures to prevent even small amounts of genetic adaptation to captivity, quantitatively determine the minimum number of captive-born individuals to release each year, and fully account for the interactions among genetic adaptation to captivity, population regulation, and life-history variation.
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Affiliation(s)
- Janna R Willoughby
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, U.S.A
| | - Mark R Christie
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, U.S.A
- Department of Forestry and Natural Resources, Purdue University, 715 W. State Street, West Lafayette, IN 47907-2054, U.S.A
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16
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Sylvester EVA, Wringe BF, Duffy SJ, Hamilton LC, Fleming IA, Castellani M, Bentzen P, Bradbury IR. Estimating the relative fitness of escaped farmed salmon offspring in the wild and modelling the consequences of invasion for wild populations. Evol Appl 2019; 12:705-717. [PMID: 30976304 PMCID: PMC6439497 DOI: 10.1111/eva.12746] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/09/2018] [Accepted: 11/14/2018] [Indexed: 12/25/2022] Open
Abstract
Throughout their native range, wild Atlantic salmon populations are threatened by hybridization and introgression with escapees from net-pen salmon aquaculture. Although domestic-wild hybrid offspring have shown reduced fitness in laboratory and field experiments, consequential impacts on population abundance and genetic integrity remain difficult to predict in the field, in part because the strength of selection against domestic offspring is often unknown and context-dependent. Here, we follow a single large escape event of farmed Atlantic salmon in southern Newfoundland and monitor changes in the in-river proportions of hybrids and feral individuals over time using genetically based hybrid identification. Over a three-year period following the escape, the overall proportion of wild parr increased consistently (total wild proportion of 71.6%, 75.1% and 87.5% each year, respectively), with subsequent declines in feral (genetically pure farmed individuals originating from escaped, farmed adults) and hybrid parr. We quantify the strength of selection against parr of aquaculture ancestry and explore the genetic and demographic consequences for populations in the region. Within-cohort changes in the relative proportions of feral and F1 parr suggest reduced relative survival compared to wild individuals over the first (0.15 and 0.81 for feral and F1, respectively) and second years of life (0.26, 0.83). These relative survivorship estimates were used to inform an individual-based salmon eco-genetic model to project changes in adult abundance and overall allele frequency across three invasion scenarios ranging from short-term to long-term invasion and three relative survival scenarios. Modelling results indicate that total population abundance and time to recovery were greatly affected by relative survivorship and predict significant declines in wild population abundance under continued large escape events and calculated survivorship. Overall, this work demonstrates the importance of estimating the strength of selection against domestic offspring in the wild to predict the long-term impact of farmed salmon escape events on wild populations.
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Affiliation(s)
- Emma V. A. Sylvester
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Brendan F. Wringe
- Science Branch, Department of Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Steven J. Duffy
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
| | - Lorraine C. Hamilton
- Aquatic Biotechnology Laboratory, Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ian A. Fleming
- Memorial University of NewfoundlandDepartment of Ocean SciencesSt. John’sNewfoundland and LabradorCanada
| | - Marco Castellani
- Department of Mechanical EngineeringUniversity of BirminghamBirminghamUK
| | - Paul Bentzen
- Marine Gene Probe Laboratory, Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
| | - Ian R. Bradbury
- Science Branch, Fisheries and Oceans CanadaSt. John’sNewfoundland and LabradorCanada
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17
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Castellani M, Heino M, Gilbey J, Araki H, Svåsand T, Glover KA. Modeling fitness changes in wild Atlantic salmon populations faced by spawning intrusion of domesticated escapees. Evol Appl 2018; 11:1010-1025. [PMID: 29928306 PMCID: PMC5999203 DOI: 10.1111/eva.12615] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 02/11/2018] [Indexed: 12/17/2022] Open
Abstract
Genetic interaction between domesticated escapees and wild conspecifics represents a persistent challenge to an environmentally sustainable Atlantic salmon aquaculture industry. We used a recently developed eco-genetic model (IBSEM) to investigate potential changes in a wild salmon population subject to spawning intrusion from domesticated escapees. At low intrusion levels (5%-10% escapees), phenotypic and demographic characteristics of the recipient wild population only displayed weak changes over 50 years and only at high intrusion levels (30%-50% escapees) were clear changes visible in this period. Our modeling also revealed that genetic changes in phenotypic and demographic characteristics were greater in situations where strayers originating from a neighboring wild population were domestication-admixed and changed in parallel with the focal wild population, as opposed to nonadmixed. While recovery in the phenotypic and demographic characteristics was observed in many instances after domesticated salmon intrusion was halted, in the most extreme intrusion scenario, the population went extinct. Based upon results from these simulations, together with existing knowledge, we suggest that a combination of reduced spawning success of domesticated escapees, natural selection purging maladapted phenotypes/genotypes from the wild population, and phenotypic plasticity, buffer the rate and magnitude of change in phenotypic and demographic characteristics of wild populations subject to spawning intrusion of domesticated escapees. The results of our simulations also suggest that under specific conditions, natural straying among wild populations may buffer genetic changes in phenotypic and demographic characteristics resulting from introgression of domesticated escapees and that variation in straying in time and space may contribute to observed differences in domestication-driven introgression among native populations.
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Affiliation(s)
| | - Mikko Heino
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
- International Institute for Applied Systems Analysis (IIASA)LaxenburgAustria
| | - John Gilbey
- Freshwater Fisheries LaboratoryMarine ScotlandPitlochryUK
| | - Hitoshi Araki
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | | | - Kevin A. Glover
- Department of Biological SciencesUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
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18
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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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19
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Tufto J. Domestication and fitness in the wild: A multivariate view. Evolution 2017; 71:2262-2270. [DOI: 10.1111/evo.13307] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/30/2017] [Accepted: 07/01/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Jarle Tufto
- Centre for Biodiversity Dynamics/Department of Mathematical Sciences; Norwegian University of Science and Technology; 7491 Trondheim Norway
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20
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Bolstad GH, Hindar K, Robertsen G, Jonsson B, Sægrov H, Diserud OH, Fiske P, Jensen AJ, Urdal K, Næsje TF, Barlaup BT, Florø-Larsen B, Lo H, Niemelä E, Karlsson S. Gene flow from domesticated escapes alters the life history of wild Atlantic salmon. Nat Ecol Evol 2017; 1:124. [PMID: 28812692 DOI: 10.1038/s41559-017-0124] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/23/2017] [Indexed: 11/09/2022]
Abstract
Interbreeding between domesticated and wild animals occurs in several species. This gene flow has long been anticipated to induce genetic changes in life-history traits of wild populations, thereby influencing population dynamics and viability. Here, we show that individuals with high levels of introgression (domesticated ancestry) have altered age and size at maturation in 62 wild Atlantic salmon Salmo salar populations, including seven ancestral populations to breeding lines of the domesticated salmon. This study documents widespread changes to life-history traits in wild animal populations following gene flow from selectively bred, domesticated conspecifics. The continued high abundance of escaped, domesticated Atlantic salmon thus threatens wild Atlantic salmon populations by inducing genetic changes in fitness-related traits. Our results represent key evidence and a timely warning concerning the potential ecological impacts of the globally increasing use of domesticated animals.
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Affiliation(s)
- Geir H Bolstad
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Grethe Robertsen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Bror Jonsson
- Norwegian Institute for Nature Research (NINA), NO-0349 Oslo, Norway
| | | | - Ola H Diserud
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Peder Fiske
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Arne J Jensen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kurt Urdal
- Radgivende Biologer, NO-5003 Bergen, Norway
| | - Tor F Næsje
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | | | | | - Håvard Lo
- Norwegian Veterinary Institute, NO-7485 Trondheim, Norway
| | - Eero Niemelä
- Natural Resources Institute Finland, FI-90014 Oulu, Finland
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
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21
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Waples RS, Hindar K, Karlsson S, Hard JJ. Evaluating the Ryman-Laikre effect for marine stock enhancement and aquaculture. Curr Zool 2016; 62:617-627. [PMID: 29491949 PMCID: PMC5804264 DOI: 10.1093/cz/zow060] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/04/2016] [Indexed: 01/06/2023] Open
Abstract
The Ryman-Laikre (R-L) effect is an increase in inbreeding and a reduction in total effective population size (NeT ) in a combined captive-wild system, which arises when a few captive parents produce large numbers of offspring. To facilitate evaluation of the R-L effect for scenarios that are relevant to marine stock enhancement and aquaculture, we extended the original R-L formula to explicitly account for several key factors that determine NeT , including the numbers of captive and wild adults, the ratio of captive to wild Ne/N (β), productivity of captive and wild breeders, and removal of individuals from the wild for captive breeding. We show how to provide quantitative answers to questions such as: What scenarios lead to no loss of effective size? What is the maximum effective size that can be achieved? and What scenarios insure that NeT will be no smaller than a specified value? Important results include the following: (1) For large marine populations, the value of β becomes increasingly important as the captive contribution increases. Captive propagation will sharply reduce NeT unless the captive contribution is very small or β is very large (∼103 or higher). (2) Very large values of β are only possible if wild Ne/N is tiny. Therefore, large wild populations undergoing captive enhancement at even modest levels will suffer major reductions in effective size unless wild Ne is a tiny fraction of the census size (about 10-4 or lower).
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Affiliation(s)
- Robin S. Waples
- National Marine Fisheries Service, Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), Trondheim 7485, Norway
| | - Jeffrey J. Hard
- National Marine Fisheries Service, Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
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22
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Harvey AC, Glover KA, Taylor MI, Creer S, Carvalho GR. A common garden design reveals population-specific variability in potential impacts of hybridization between populations of farmed and wild Atlantic salmon, Salmo salar L. Evol Appl 2016; 9:435-49. [PMID: 26989435 PMCID: PMC4778114 DOI: 10.1111/eva.12346] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 11/13/2015] [Indexed: 11/30/2022] Open
Abstract
Released individuals can have negative impacts on native populations through various mechanisms, including competition, disease transfer and introduction of maladapted gene complexes. Previous studies indicate that the level of farmed Atlantic salmon introgression in native populations is population specific. However, few studies have explored the potential role of population diversity or river characteristics, such as temperature, on the consequences of hybridization. We compared freshwater growth of multiple families derived from two farmed, five wild and two F1 hybrid salmon populations at three contrasting temperatures (7°C, 12°C and 16°C) in a common garden experiment. As expected, farmed salmon outgrew wild salmon at all temperatures, with hybrids displaying intermediate growth. However, differences in growth were population specific and some wild populations performed better than others relative to the hybrid and farmed populations at certain temperatures. Therefore, the competitive balance between farmed and wild salmon may depend both on the thermal profile of the river and on the genetic characteristics of the respective farmed and wild strains. While limited to F1 hybridization, this study shows the merits in adopting a more complex spatially resolved approach to risk management of local populations.
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Affiliation(s)
- Alison C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | | | - Martin I Taylor
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK; School of Biological Sciences University of East Anglia Norwich UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory School of Biological Sciences Bangor University Bangor UK
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23
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Segovia-Viadero M, Serrão EA, Canteras-Jordana JC, Gonzalez-Wangüemert M. Do hatchery-reared sea urchins pose a threat to genetic diversity in wild populations? Heredity (Edinb) 2016; 116:378-83. [PMID: 26758187 DOI: 10.1038/hdy.2015.109] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 09/30/2015] [Accepted: 11/18/2015] [Indexed: 11/09/2022] Open
Abstract
In salmonids, the release of hatchery-reared fish has been shown to cause irreversible genetic impacts on wild populations. However, although responsible practices for producing and releasing genetically diverse, hatchery-reared juveniles have been published widely, they are rarely implemented. Here, we investigated genetic differences between wild and early-generation hatchery-reared populations of the purple sea urchin Paracentrotus lividus (a commercially important species in Europe) to assess whether hatcheries were able to maintain natural levels of genetic diversity. To test the hypothesis that hatchery rearing would cause bottleneck effects (that is, a substantial reduction in genetic diversity and differentiation from wild populations), we compared the levels and patterns of genetic variation between two hatcheries and four nearby wild populations, using samples from both Spain and Ireland. We found that hatchery-reared populations were less diverse and had diverged significantly from the wild populations, with a very small effective population size and a high degree of relatedness between individuals. These results raise a number of concerns about the genetic impacts of their release into wild populations, particularly when such a degree of differentiation can occur in a single generation of hatchery rearing. Consequently, we suggest that caution should be taken when using hatchery-reared individuals to augment fisheries, even for marine species with high dispersal capacity, and we provide some recommendations to improve hatchery rearing and release practices. Our results further highlight the need to consider the genetic risks of releasing hatchery-reared juveniles into the wild during the establishment of restocking, stock enhancement and sea ranching programs.
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Affiliation(s)
- M Segovia-Viadero
- CCMAR, Universidade do Algarve, Gambelas, Faro, Portugal.,Departamento de Ciencias del Mar y Biología Aplicada, Universidad de Alicante, Campus de San Vicente de Raspeig, Alicante, Spain
| | - E A Serrão
- CCMAR, Universidade do Algarve, Gambelas, Faro, Portugal
| | - J C Canteras-Jordana
- Departamento de Ciencias y Técnicas del Agua y del Medio Ambiente, Universidad de Cantabria, ETS de Ingenieros de Caminos, Canales y Puertos, Santander, Spain
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Burgess SC, Nickols KJ, Griesemer CD, Barnett LAK, Dedrick AG, Satterthwaite EV, Yamane L, Morgan SG, White JW, Botsford LW. Beyond connectivity: how empirical methods can quantify population persistence to improve marine protected-area design. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2014; 24:257-70. [PMID: 24689139 DOI: 10.1890/13-0710.1] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Demographic connectivity is a fundamental process influencing the dynamics and persistence of spatially structured populations. Consequently, quantifying connectivity is essential for properly designing networks of protected areas so that they achieve their core ecological objective of maintaining population persistence. Recently, many empirical studies in marine systems have provided essential, and historically challenging to obtain, data on patterns of larval dispersal and export from marine protected areas (MPAs). Here, we review the empirical studies that have directly quantified the origins and destinations of individual larvae and assess those studies' relevance to the theory of population persistence and MPA design objectives. We found that empirical studies often do not measure or present quantities that are relevant to assessing population persistence, even though most studies were motivated or contextualized by MPA applications. Persistence of spatial populations, like nonspatial populations, depends on replacement, whether individuals reproduce enough in their lifetime to replace themselves. In spatial populations, one needs to account for the effect of larval dispersal on future recruitment back to the local population through local retention and other connectivity pathways. The most commonly reported descriptor of larval dispersal was the fraction of recruitment from local origin (self-recruitment). Self-recruitment does not inform persistence-based MPA design because it is a fraction of those arriving, not a fraction of those leaving (local retention), so contains no information on replacement. Some studies presented connectivity matrices, which can inform assessments of persistence with additional knowledge of survival and fecundity after recruitment. Some studies collected data in addition to larval dispersal that could inform assessments of population persistence but which were not presented in that way. We describe how three pieces of empirical information are needed to fully describe population persistence in a network of MPAs: (1) lifetime fecundity, (2) the proportion of larvae that are locally retained (or the full connectivity matrix), and (3) survival rate after recruitment. We conclude by linking theory and data to provide detailed guidance to empiricists and practitioners on field sampling design and data presentation that better informs the MPA objective of population persistence.
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