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Besnier F, Ayllon F, Skaala Ø, Solberg MF, Fjeldheim PT, Anderson K, Knutar S, Glover KA. Introgression of domesticated salmon changes life history and phenology of a wild salmon population. Evol Appl 2022; 15:853-864. [PMID: 35603027 PMCID: PMC9108307 DOI: 10.1111/eva.13375] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- F. Besnier
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - F. Ayllon
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - Ø. Skaala
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - M. F. Solberg
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | | | - K. Anderson
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - S. Knutar
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
| | - K. A. Glover
- Institute of Marine Research PO box 1870 Nordnes N‐5817 Norway
- Department of Biological Sciences University of Bergen N‐5020 Bergen Norway
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2
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Bolstad GH, Karlsson S, Hagen IJ, Fiske P, Urdal K, Sægrov H, Florø-Larsen B, Sollien VP, Østborg G, Diserud OH, Jensen AJ, Hindar K. Introgression from farmed escapees affects the full life cycle of wild Atlantic salmon. SCIENCE ADVANCES 2021; 7:eabj3397. [PMID: 34936452 PMCID: PMC8694624 DOI: 10.1126/sciadv.abj3397] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/03/2021] [Indexed: 05/28/2023]
Abstract
After a half a century of salmon farming, we have yet to understand how the influx of genes from farmed escapees affects the full life history of Atlantic salmon (Salmo salar L.) in the wild. Using scale samples of over 6900 wild adult salmon from 105 rivers, we document that increased farmed genetic ancestry is associated with increased growth throughout life and a younger age at both seaward migration and sexual maturity. There was large among-population variation in the effects of introgression. Most saliently, the increased growth at sea following introgression declined with the population’s average growth potential. Variation at two major-effect loci associated with age at maturity was little affected by farmed genetic ancestry and could not explain the observed phenotypic effects of introgression. Our study provides knowledge crucial for predicting the ecological and evolutionary consequences of increased aquaculture production worldwide.
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Affiliation(s)
- Geir H. Bolstad
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Sten Karlsson
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Ingerid J. Hagen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Peder Fiske
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kurt Urdal
- Rådgivende Biologer, NO-5059 Bergen, Norway
| | | | | | | | - Gunnel Østborg
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Ola H. Diserud
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Arne J. Jensen
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), NO-7485 Trondheim, Norway
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3
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Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon. Heredity (Edinb) 2021; 127:455-466. [PMID: 34446857 PMCID: PMC8551234 DOI: 10.1038/s41437-021-00469-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 08/13/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023] Open
Abstract
Populations may counteract lasting temperature changes or recurrent extremes through plasticity or adaptation. However, it remains underexplored how outbreeding, either naturally, unintentionally, or facilitated, may modify a local response potential and whether genotype-by-environment interactions or between-trait correlations can restrict this potential. We quantified population differences and outbreeding effects, within-population genetic variation, and plasticity of these, for thermal performance proxy traits using 32 pedigreed wild, domesticated, and wild-domesticated Atlantic salmon families reared under common-garden conditions. Following exposure to ambient cold (11.6 °C) or ~4° and ~8° warmer summer temperatures, populations differed notably for body length and critical thermal maximum (CTmax) and for thermal plasticity of length, condition, and CTmax, but not for haematocrit. Line-cross analysis suggested mostly additive and some dominant outbreeding effects on means and solely additive outbreeding effects on plasticity. Heritability was detected for all traits. However, with increasing acclimation temperature, differences in CTmax between populations and CTmax heritability diminished, and CTmax breeding values re-ranked. Furthermore, CTmax and body size were negatively correlated at the genetic and phenotypic levels, and there was indirect evidence for a positive correlation between growth potential and thermal performance breadth for growth. Thus, population differences (including those between wild and domesticated populations) in thermal performance and plasticity may present a genetic resource in addition to the within-population genetic variance to facilitate, or impede, thermal adaptation. However, unfavourable genotype-by-environment interactions and negative between-trait correlations may generally hamper joint evolution in response to an increase in average temperature and temporary extremes.
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4
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Perry WB, Kaufmann J, Solberg MF, Brodie C, Coral Medina AM, Pillay K, Egerton A, Harvey A, Phillips KP, Coughlan J, Egan F, Grealis R, Hutton S, Leseur F, Ryan S, Poole R, Rogan G, Ryder E, Schaal P, Waters C, Wynne R, Taylor M, Prodöhl P, Creer S, Llewellyn M, McGinnity P, Carvalho G, Glover KA. Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon ( Salmo salar L.). Evol Appl 2021; 14:2319-2332. [PMID: 34603501 PMCID: PMC8477603 DOI: 10.1111/eva.13297] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 08/24/2021] [Indexed: 11/28/2022] Open
Abstract
Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
- Water Research InstituteSchool of BiosciencesCardiff UniversityCardiffUK
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
| | - Joshka Kaufmann
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | | | - Christopher Brodie
- Ecosystems and Environment Research CentreSchool of Environment and Life SciencesUniversity of SalfordSalfordUK
| | | | - Kirthana Pillay
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Anna Egerton
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Alison Harvey
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
| | - Karl P. Phillips
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Jamie Coughlan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Fintan Egan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Ronan Grealis
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Steve Hutton
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Floriane Leseur
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Sarah Ryan
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | | | - Ger Rogan
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Elizabeth Ryder
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Patrick Schaal
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
- Institute of BiodiversityAnimal Health & Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Catherine Waters
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Robert Wynne
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
| | - Martin Taylor
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Paulo Prodöhl
- Institute for Global Food SecuritySchool of Biological SciencesMedical Biology CentreQueen’s UniversityBelfastUK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Martin Llewellyn
- Institute of BiodiversityAnimal Health & Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Philip McGinnity
- School of Biological, Earth and Environmental SciencesUniversity College CorkCorkIreland
- Marine InstituteFurnace, NewportCo. MayoIreland
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics LaboratorySchool of Biological ScienceBangor UniversityBangor, GwyneddUK
| | - Kevin Alan Glover
- Population Genetics Research GroupInstitute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
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5
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Palińska-Żarska K, Król J, Woźny M, Kamaszewski M, Szudrowicz H, Wiechetek W, Brzuzan P, Fopp-Bayat D, Żarski D. Domestication affected stress and immune response markers in Perca fluviatilis in the early larval stage. FISH & SHELLFISH IMMUNOLOGY 2021; 114:184-198. [PMID: 33940175 DOI: 10.1016/j.fsi.2021.04.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
It is already known that domestication modifies stress and immune responses in juveniles and adults of several fish species. However, there is a lack of information on whether these modulations result from adaptability along the life cycle or if they are pre-determined in very early developmental stages. To shed light on mechanisms that help to explain the process of domestication, a study was conducted to analyze comparatively Eurasian perch larval performance, stress, and immune status between wild and domesticated specimens. Eurasian perch larvae obtained from wild and domesticated (generation F5 reared in recirculating aquaculture systems) spawners were reared in the same conditions during the main rearing trial (MRT) and also subjected to a thermal challenge (TC). During the study, larval performance (including survival, growth performance, swim bladder inflation effectiveness, deformity rate), the expression of genes involved in immune and stress response, and the specific activity of oxidative stress enzymes (during MRT only) were analyzed. No significant differences in hatching rate, deformity rate, or swim bladder inflation effectiveness between wild and domesticated larvae were found, whereas specific growth rate, final total length, and wet body weight were significantly lower in wild larvae. Higher mortality was also observed in wild larvae during both MRT and TC. The data obtained in this study clearly indicated that during domestication, significant modifications in stress and immune response, such as complement component c3, were noted as early as just after hatching. Generally, domesticated fish were characterized by a lower stress response and improved immune response in comparison to the wild fish. This probably resulted from the domesticated larvae being better adapted to the conditions of artificial aquaculture. The data obtained provided information on how domestication affects fish in aquaculture, and they contribute to the development of efficient selective breeding programs of Eurasian perch and other freshwater teleosts.
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Affiliation(s)
- Katarzyna Palińska-Żarska
- Department of Ichthyology, Hydrobiology and Aquatic Ecology, Stanislaw Sakowicz Inland Fisheries Institute, Oczapowskiego 10, 10-719, Olsztyn, Poland.
| | - Jarosław Król
- Department of Salmonid Research, Stanislaw Sakowicz Inland Fisheries Institute, Oczapowskiego 10, 10-719, Olsztyn, Poland
| | - Maciej Woźny
- Department of Environmental Biotechnology, Institute of Engineering and Environment Protection, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Maciej Kamaszewski
- Department of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Hubert Szudrowicz
- Department of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Wiktoria Wiechetek
- Department of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland; Kielanowski Institute of Animal Physiology and Nutrition, Polish Academy of Science, Instytucka 3, 05-110, Jabłonna, Poland
| | - Paweł Brzuzan
- Department of Environmental Biotechnology, Institute of Engineering and Environment Protection, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, ul. Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Dorota Fopp-Bayat
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury in Olsztyn, Oczapowskiego 5, 10-719, Olsztyn, Poland
| | - Daniel Żarski
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
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6
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Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation. Sci Rep 2021; 11:11235. [PMID: 34045615 PMCID: PMC8159941 DOI: 10.1038/s41598-021-90645-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/12/2021] [Indexed: 11/28/2022] Open
Abstract
Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.
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7
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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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8
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Ayllon F, Solberg MF, Besnier F, Fjelldal PG, Hansen TJ, Wargelius A, Edvardsen RB, Glover KA. Autosomal sdY Pseudogenes Explain Discordances Between Phenotypic Sex and DNA Marker for Sex Identification in Atlantic Salmon. Front Genet 2020; 11:544207. [PMID: 33173531 PMCID: PMC7591749 DOI: 10.3389/fgene.2020.544207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/17/2020] [Indexed: 11/13/2022] Open
Abstract
Despite the key role that sex-determination plays in evolutionary processes, it is still poorly understood in many species. In salmonids, which are among the best studied fishes, the master sex-determining gene sexually dimorphic on the Y-chromosome (sdY) has been identified. However, sdY displays unexplained discordance to the phenotypic sex, with a variable frequency of phenotypic females being reported as genetic males. Multiple sex determining loci in Atlantic salmon have also been reported, possibly as a result of recent transposition events in this species. We hypothesized the existence of an autosomal copy of sdY, causing apparent discordance between phenotypic and genetic sex, that is transmitted in accordance with autosomal inheritance. To test this, we developed a qPCR methodology to detect the total number of sdY copies present in the genome. Based on the observed phenotype/genotype frequencies and linkage analysis among 2,025 offspring from 64 pedigree-controlled families of accurately phenotyped Atlantic salmon, we identified both males and females carrying one or two autosomal copies of sdY in addition to the Y-specific copy present in males. Patterns across families were highly consistent with autosomal inheritance. These autosomal sdY copies appear to have lost the ability to function as a sex determining gene and were only occasionally assigned to the actual sex chromosome in any of the affected families.
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Affiliation(s)
| | | | | | | | | | | | | | - Kevin Alan Glover
- Institute of Marine Research, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
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9
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Perry WB, Solberg MF, Brodie C, Medina AC, Pillay KG, Egerton A, Harvey A, Creer S, Llewellyn M, Taylor M, Carvalho G, Glover KA. Disentangling the effects of sex, life history and genetic background in Atlantic salmon: growth, heart and liver under common garden conditions. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200811. [PMID: 33204455 PMCID: PMC7657880 DOI: 10.1098/rsos.200811] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Livestock domestication has long been a part of agriculture, estimated to have first occurred approximately 10 000 years ago. Despite the plethora of traits studied, there is little understanding of the possible impacts domestication has had on internal organs, which are key determinants of survival. Moreover, the genetic basis of observed associated changes in artificial environments is still puzzling. Here we examine impacts of captivity on two organs in Atlantic salmon (Salar salar) that have been domesticated for approximately 50 years: heart and liver, in addition to growth. We studied multiple families of wild, domesticated, F1 and F2 hybrid, and backcrossed strains of S. salar in replicated common garden tanks during the freshwater and marine stages of development. Heart and liver weight were investigated, along with heart morphology metrics examined in just the wild, domesticated and F1 hybrid strains (heart height and width). Growth was positively linked with the proportion of the domesticated strain, and recombination in F2 hybrids (and the potential disruption of co-adapted gene complexes) did not influence growth. Despite the influence of domestication on growth, we found no evidence for domestication-driven divergence in heart or liver morphology. However, sexual dimorphism was detected in heart morphology, and after controlling for body size, females exhibited significantly larger heart weight and heart width when compared with males. Wild females also had an increased heart height when compared with wild males, and this was not observed in any other strain. Females sampled in saltwater showed significantly larger heart height with rounder hearts, than saltwater males. Collectively, these results demonstrate an additive basis of growth and, despite a strong influence of domestication on growth, no clear evidence of changes in heart or liver morphology associated with domestication was identified.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Monica F. Solberg
- Population Genetics Research Group, Institute of Marine Research, PO Box 1870, Nordnes 5817, Bergen, Norway
| | - Christopher Brodie
- Mariani Molecular Ecology Laboratory, School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 5UX, UK
| | - Angela C. Medina
- School of Microbiology, Food Science and Technology Building University College Cork, Cork T12 TP07, Ireland
| | - Kirthana G. Pillay
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Anna Egerton
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Alison Harvey
- Population Genetics Research Group, Institute of Marine Research, PO Box 1870, Nordnes 5817, Bergen, Norway
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological 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 Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Kevin A. Glover
- Population Genetics Research Group, Institute of Marine Research, PO Box 1870, Nordnes 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
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10
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Glover KA, Harvey AC, Hansen TJ, Fjelldal PG, Besnier FN, Bos JB, Ayllon F, Taggart JB, Solberg MF. Chromosome aberrations in pressure-induced triploid Atlantic salmon. BMC Genet 2020; 21:59. [PMID: 32505176 PMCID: PMC7276064 DOI: 10.1186/s12863-020-00864-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/28/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Triploid organisms have three sets of chromosomes. In Atlantic salmon, hydrostatic pressure treatment of newly fertilized eggs has been extensively used to produce triploids which are functionally sterile due to their unpaired chromosomes. These fish often perform poorly on commercial farms, sometimes without explanation. Inheritance patterns in individuals subjected to pressure treatment have not been investigated in Atlantic salmon thus far. However, work on other species suggests that this treatment can result in aberrant inheritance. We therefore studied this in Atlantic salmon by genotyping 16 polymorphic microsatellites in eyed eggs and juveniles which had been subjected to pressure-induction of triploidy. Communally reared juveniles including fish subjected to pressure-induction of triploidy and their diploid siblings were included as a control. RESULTS No diploid offspring were detected in any of the eggs or juveniles which were subjected to hydrostatic pressure; therefore, the induction of triploidy was highly successful. Aberrant inheritance was nevertheless observed in 0.9% of the eggs and 0.9% of the juveniles that had been subjected to pressure treatment. In the communally reared fish, 0.3% of the fish subjected to pressure treatment displayed aberrant inheritance, while their diploid controls displayed 0% aberrant inheritance. Inheritance errors included two eyed eggs lacking maternal DNA across all microsatellites, and, examples in both eggs and juveniles of either the maternal or paternal allele lacking in one of the microsatellites. All individuals displaying chromosome aberrations were otherwise triploid. CONCLUSIONS This is the first study to document aberrant inheritance in Atlantic salmon that have been subjected to pressure-induction of triploidy. Our experiments unequivocally demonstrate that even when induction of triploidy is highly successful, this treatment can cause chromosome aberrations in this species. Based upon our novel data, and earlier studies in other organisms, we hypothesize that in batches of Atlantic salmon where low to modest triploid induction rates have been reported, aberrant inheritance is likely to be higher than the rates observed here. Therefore, we tentatively suggest that this could contribute to the unexplained poor performance of triploid salmon that is occasionally reported in commercial aquaculture. These hypotheses require further investigation.
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Affiliation(s)
- K A Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - A C Harvey
- Institute of Marine Research, Bergen, Norway.
| | - T J Hansen
- Institute of Marine Research, Bergen, Norway
| | | | - F N Besnier
- Institute of Marine Research, Bergen, Norway
| | - J B Bos
- ZEBCARE, Nederweert, The Netherlands
| | - F Ayllon
- Institute of Marine Research, Bergen, Norway
| | | | - M F Solberg
- Institute of Marine Research, Bergen, Norway
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11
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Palińska-Żarska K, Woźny M, Kamaszewski M, Szudrowicz H, Brzuzan P, Żarski D. Domestication process modifies digestion ability in larvae of Eurasian perch (Perca fluviatilis), a freshwater Teleostei. Sci Rep 2020; 10:2211. [PMID: 32042003 PMCID: PMC7010758 DOI: 10.1038/s41598-020-59145-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/20/2020] [Indexed: 11/12/2022] Open
Abstract
To date, a comparative analysis of larval performance and digestion abilities between wild and domesticated Eurasian perch has not yet been performed. Eurasian perch larvae from wild and domesticated spawners were reared in the same conditions and at different development stages, growth performance variables, the expression of genes encoding digestive enzymes and specific enzymatic activity were analysed. No significant differences in hatching rate, deformity rate or swim bladder inflation effectiveness between wild and domesticated larvae were found. Specific growth rate, final total length and wet body weight were significantly lower in wild larvae, whereas higher mortality in wild larvae was observed compared to domesticated larvae. The data obtained in this study clearly indicate that during domestication, significant modification of digestion ability occurs at the very beginning of ontogeny, where domesticated fish are characterised by lower enzymatic activity and lower expression of genes encoding digestive enzymes. This probably results from the low diversity of the food offered in culture conditions, which significantly modified digestion capability. The obtained data provide an understanding of how domestication affects fish in aquaculture and may improve the planning of selective breeding programs of Eurasian perch and other freshwater Teleosts.
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Affiliation(s)
- Katarzyna Palińska-Żarska
- Department of Ichthyology and Aquaculture, University of Warmia and Mazury, Oczapowskiego 5, 10-719, Olsztyn, Poland.
| | - Maciej Woźny
- Department of Environmental Biotechnology, University of Warmia and Mazury, Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Maciej Kamaszewski
- Departament of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Hubert Szudrowicz
- Departament of Ichthyology and Biotechnology in Aquaculture, Institute of Animal Sciences, University of Life Sciences, Ciszewskiego 8, 02-786, Warsaw, Poland
| | - Paweł Brzuzan
- Department of Environmental Biotechnology, University of Warmia and Mazury, Słoneczna 45G, 10-709, Olsztyn, Poland
| | - Daniel Żarski
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748, Olsztyn, Poland.
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12
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Solberg MF, Robertsen G, Sundt-Hansen LE, Hindar K, Glover KA. Domestication leads to increased predation susceptibility. Sci Rep 2020; 10:1929. [PMID: 32029847 PMCID: PMC7005312 DOI: 10.1038/s41598-020-58661-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2020] [Indexed: 12/18/2022] Open
Abstract
Domestication involves adapting animals to the human-controlled environment. Genetic changes occurring during the domestication process may manifest themselves in phenotypes that render domesticated animals maladaptive for life in the wild. Domesticated Atlantic salmon frequently interbreed with wild conspecifics, and their offspring display reduced survival in the wild. However, the mechanism(s) contributing to their lower survival in the wild remains a subject of conjecture. Here, we document higher susceptibility to predation by brown trout in fast-growing domesticated salmon, as compared to their slow-growing wild conspecifics, demonstrating that directional selection for increased growth comes at a cost of decreased survival when under the risk of predation, as predicted by the growth/predation risk trade-off. Despite earlier documentation of altered risk-taking behavior, this study demonstrates for the first time that domestication of Atlantic salmon has lead to increased predation susceptibility, and that this consitutes a mechanism underpinning the observed survial differences in the wild.
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Affiliation(s)
- Monica F Solberg
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.
| | - Grethe Robertsen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Line E Sundt-Hansen
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kjetil Hindar
- Norwegian Institute for Nature Research (NINA), P.O. Box 5685 Torgarden, NO, 7485, Trondheim, Norway
| | - Kevin A Glover
- Institute of Marine Research, P.O. Box 1870 Nordnes, NO, 5817, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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13
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Straume AH, Kjærner-Semb E, Ove Skaftnesmo K, Güralp H, Kleppe L, Wargelius A, Edvardsen RB. Indel locations are determined by template polarity in highly efficient in vivo CRISPR/Cas9-mediated HDR in Atlantic salmon. Sci Rep 2020; 10:409. [PMID: 31941961 PMCID: PMC6962318 DOI: 10.1038/s41598-019-57295-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 12/19/2019] [Indexed: 01/20/2023] Open
Abstract
Precise gene editing such as CRISPR/Cas9-mediated homology directed repair (HDR) can increase our understanding of gene function and improve traits of importance for aquaculture. This fine-tuned technology has not been developed for farmed fish including Atlantic salmon. We performed knock-in (KI) of a FLAG element in the slc45a2 gene in salmon using sense (S), anti-sense (AS) and double-stranded (ds) oligodeoxynucleotide (ODN) templates with short (24/48/84 bp) homology arms. We show in vivo ODN integration in almost all the gene edited animals, and demonstrate perfect HDR rates up to 27% in individual F0 embryos, much higher than reported previously in any fish. HDR efficiency was dependent on template concentration, but not homology arm length. Analysis of imperfect HDR variants suggest that repair occurs by synthesis-dependent strand annealing (SDSA), as we show for the first time in any species that indel location is dependent on template polarity. Correct ODN polarity can be used to avoid 5'-indels interrupting the reading frame of an inserted sequence and be of importance for HDR template design in general.
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Affiliation(s)
- Anne Hege Straume
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Erik Kjærner-Semb
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kai Ove Skaftnesmo
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Hilal Güralp
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Lene Kleppe
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Anna Wargelius
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
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14
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Skaala Ø, Besnier F, Borgstrøm R, Barlaup B, Sørvik AG, Normann E, Østebø BI, Hansen MM, Glover KA. An extensive common-garden study with domesticated and wild Atlantic salmon in the wild reveals impact on smolt production and shifts in fitness traits. Evol Appl 2019; 12:1001-1016. [PMID: 31080511 PMCID: PMC6503829 DOI: 10.1111/eva.12777] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/18/2019] [Accepted: 01/19/2019] [Indexed: 01/15/2023] Open
Abstract
Interactions between domesticated escapees and wild conspecifics represent a threat to the genetic integrity and fitness of native populations. For Atlantic salmon, the recurrent presence of large numbers of domesticated escapees in the wild makes it necessary to better understand their impacts on native populations. We planted 254,400 eggs from 75 families of domesticated, F1-hybrid, and wild salmon in a river containing up- and downstream traps. Additionally, 41,630 hatchery smolts of the same pedigrees were released into the river. Over 8 years, 6,669 out-migrating smolts and 356 returning adults were recaptured and identified to their families of origin with DNA. In comparison with wild salmon, domesticated fish had substantially lower egg to smolt survival (1.8% vs. 3.8% across cohorts), they migrated earlier in the year (11.8 days earlier across years), but they only displayed marginally larger smolt sizes and marginally lower smolt ages. Upon return to freshwater, domesticated salmon were substantially larger at age than wild salmon (2.4 vs. 2.0, 4.8 vs. 3.2, and 8.5 vs. 5.6 kg across sexes for 1, 2, and 3 sea-winter fish) and displayed substantially lower released smolt to adult survival (0.41% vs. 0.94% across releases). Overall, egg-to-returning adult survival ratios were 1:0.76:0.30 and 1:0.44:0.21 for wild:F1-hybrid:domesticated salmon, respectively, using two different types of data. This study represents the most updated and extensive analysis of domesticated, hybrid, and wild salmon in the wild and provides the first documentation of a clear genetic difference in the timing of smolt migration-an adaptive trait presumed to be linked with optimal timing of entry to seawater. We conclude that spawning and hybridization of domesticated escapees can lead to (i) reduced wild smolt output and therefore wild adult abundance, through resource competition in freshwater, (ii) reduced total adult abundance due to freshwater competition and reduced marine survival of domesticated salmon, and (iii) maladaptive changes in phenotypic traits.
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Affiliation(s)
| | | | - Reidar Borgstrøm
- Faculty of Environmental Sciences and Natural Resource ManagementÅsNorway
| | | | | | | | | | - Michael Møller Hansen
- Institute of Marine ResearchNordnes, BergenNorway
- Department of BioscienceAarhus UniversityAarhus CDenmark
| | - Kevin Alan Glover
- Institute of Marine ResearchNordnes, BergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
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15
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Kitada S, Nakajima K, Hamasaki K, Shishidou H, Waples RS, Kishino H. Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat. Sci Rep 2019; 9:5290. [PMID: 30918306 PMCID: PMC6437203 DOI: 10.1038/s41598-019-39050-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/16/2019] [Indexed: 12/16/2022] Open
Abstract
Release of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the size and genetic diversity of wild populations of one of the world’s largest marine stock enhancement programs–the red sea bream (Pagrus major) in Kagoshima Bay, Japan. Our analyses found that the stock enhancement program reduced genetic diversity of the population, but the genetic effect diminished with increased size of the wild population. Increases to the seaweed communities and reduced fishing efforts were the primary factors associated with the wild population recovery; effects of aquaculture were much smaller. Our results represent crucial evidence that hatcheries for enhancement and conservation of populations cannot be successful over the long term unless sufficient efforts are also made to reduce harvest rates and rehabilitate natural habitats.
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Affiliation(s)
- Shuichi Kitada
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan.
| | - Kaori Nakajima
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Katsuyuki Hamasaki
- Tokyo University of Marine Science and Technology, Tokyo, 108-8477, Japan
| | - Hirotoshi Shishidou
- Kagoshima Prefectural Fisheries Technology and Development Center, Kagoshima, 891-0315, Japan
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA, Seattle, WA, 98112, USA
| | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
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16
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Robertsen G, Reid D, Einum S, Aronsen T, Fleming IA, Sundt‐Hansen LE, Karlsson S, Kvingedal E, Ugedal O, Hindar K. Can variation in standard metabolic rate explain context-dependent performance of farmed Atlantic salmon offspring? Ecol Evol 2019; 9:212-222. [PMID: 30680108 PMCID: PMC6342125 DOI: 10.1002/ece3.4716] [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: 11/28/2017] [Revised: 10/18/2018] [Accepted: 10/20/2018] [Indexed: 01/13/2023] Open
Abstract
Escaped farmed Atlantic salmon interbreed with wild Atlantic salmon, leaving offspring that often have lower success in nature than pure wild salmon. On top of this, presence of farmed salmon descendants can impair production of wild-type recruits. We hypothesize that both these effects connect with farmed salmon having acquired higher standard metabolic rates (SMR, the energetic cost of self-maintenance) during domestication. Fitness-related advantages of phenotypic traits associated with both high SMR and farmed salmon (e.g., social dominance) depend on environmental conditions, such as food availability. We hypothesize that farmed offspring have an advantage at high food availability due to, for example, dominance behavior but suffer increased risks of starvation when food is scarce because this behavior is energy-demanding. To test these hypotheses, we first compare embryo SMR of pure farmed, farmed-wild hybrids and pure wild offspring. Next, we test early-life performance (in terms of survival and growth) of hybrids relative to that of their wild half-siblings, as well as their competitive abilities, in semi-natural conditions of high and low food availability. Finally, we test how SMR affects early-life performance at high and low food availability. We find inconclusive support for the hypothesis that domestication has induced increased SMR. Further, wild and hybrid juveniles had similar survival and growth in the semi-natural streams. Yet, the presence of hybrids led to decreased survival of their wild half-siblings. Contrary to our hypothesis about context-dependency, these effects were not modified by food availability. However, wild juveniles with high SMR had decreased survival when food was scarce, but there was no such effect at high food availability. This study provides further proof that farmed salmon introgression may compromise the viability of wild salmon populations. We cannot, however, conclude that this is connected to alterations in the metabolic phenotype of farmed salmon.
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Affiliation(s)
| | - Donald Reid
- School of Life Sciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
| | - Sigurd Einum
- Centre for Biodiversity Dynamics, Department of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Tonje Aronsen
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ian A. Fleming
- Department of Ocean SciencesMemorial University of NewfoundlandSt John’sNewfoundlandCanada
| | | | - Sten Karlsson
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Eli Kvingedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Ola Ugedal
- Norwegian Institute for Nature ResearchTrondheimNorway
| | - Kjetil Hindar
- Norwegian Institute for Nature ResearchTrondheimNorway
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