1
|
Madhun AS, Karlsbakk E, Skaala Ø, Solberg MF, Wennevik V, Harvey A, Meier S, Fjeldheim PT, Andersen KC, Glover KA. Most of the escaped farmed salmon entering a river during a 5-year period were infected with one or more viruses. J Fish Dis 2024:e13950. [PMID: 38555528 DOI: 10.1111/jfd.13950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/01/2024] [Accepted: 03/14/2024] [Indexed: 04/02/2024]
Abstract
Disease interactions between farmed and wild populations have been poorly documented for most aquaculture species, in part due to the complexities to study this. Here, we tested 567 farmed Atlantic salmon escapees, captured in a Norwegian river during 2014-2018, for five viral infections that are prevalent in global salmonid aquaculture. Over 90% of the escapees were infected with one or more viruses. Overall prevalences were: 75.7% for piscine orthoreovirus (PRV-1), 43.6% for salmonid alphavirus (SAV), 31.2% for piscine myocarditis virus (PMCV), 1.2% for infectious pancreatic necrosis virus (IPNV) and 0.4% for salmon anaemia virus (ISAV). A significantly higher prevalence of PMCV infection was observed in immature compared to mature individuals. The prevalence of both SAV and PMCV infections was higher in fish determined by fatty acid profiling to be 'recent' as opposed to 'early' escapees that had been in the wild for a longer period of time. This is the first study to establish a time-series of viral infection status of escapees entering a river with a native salmon population. Our results demonstrate that farmed escapees represent a continuous source of infectious agents which could potentially be transmitted to wild fish populations.
Collapse
Affiliation(s)
| | - Egil Karlsbakk
- Institute of Marine Research, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Besnier F, Skaala Ø, Wennevik V, Ayllon F, Utne KR, Fjeldheim PT, Andersen-Fjeldheim K, Knutar S, Glover KA. Overruled by nature: A plastic response to environmental change disconnects a gene and its trait. Mol Ecol 2024; 33:e16933. [PMID: 36942798 DOI: 10.1111/mec.16933] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/21/2023] [Accepted: 03/17/2023] [Indexed: 03/23/2023]
Abstract
In Atlantic salmon, age at maturation is a life history trait governed by a sex-specific trade-off between reproductive success and survival. Following environmental changes across large areas of the Northeast Atlantic, many populations currently display smaller size at age and higher age at maturation. However, whether these changes reflect rapid evolution or plasticity is unknown. Approximately 1500 historical and contemporary salmon from the river Etne in Western Norway, genotyped at 50,000 SNPs, revealed three loci associated with age at maturation. These included vgll3 and six6 which collectively explained 36%-50% of the age at maturation variation in the 1983-1984 period. These two loci also displayed sex-specific epistasis, as the effect of six6 was only detected in males bearing two copies of the late maturation allele for vgll3. Strikingly, despite allelic frequencies at vgll3 remaining unchanged, the combined influence of these genes was nearly absent in all samples from 2013 to 2016, and genome-wide heritability strongly declined between the two time-points. The difference in age at maturation between males and females was upheld in the population despite the loss of effect from the candidate loci, which strongly points towards additional causative mechanisms resolving the sexual conflict. Finally, because admixture with farmed escaped salmon was excluded as the origin of the observed disconnection between gene(s) and maturation age, we conclude that the environmental changes observed in the North Atlantic during the past decades have led to bypassing of the influence of vgll3 and six6 on maturation through growth-driven plasticity.
Collapse
|
3
|
Graziano M, Solberg MF, Glover KA, Vasudeva R, Dyrhovden L, Murray D, Immler S, Gage MJG. Pre-fertilization gamete thermal environment influences reproductive success, unmasking opposing sex-specific responses in Atlantic salmon ( Salmo salar). R Soc Open Sci 2023; 10:231427. [PMID: 38094267 PMCID: PMC10716643 DOI: 10.1098/rsos.231427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/16/2023] [Indexed: 01/11/2024]
Abstract
The environment gametes perform in just before fertilization is increasingly recognized to affect offspring fitness, yet the contributions of male and female gametes and their adaptive significance remain largely unexplored. Here, we investigated gametic thermal plasticity and its effects on hatching success and embryo performance in Atlantic salmon (Salmo salar). Eggs and sperm were incubated overnight at 2°C or 8°C, temperatures within the optimal thermal range of this species. Crosses between warm- and cold-incubated gametes were compared using a full-factorial design, with half of each clutch reared in cold temperatures and the other in warm temperatures. This allowed disentangling single-sex interaction effects when pre-fertilization temperature of gametes mismatched embryonic conditions. Pre-fertilization temperature influenced hatch timing and synchrony, and matching sperm and embryo temperatures resulted in earlier hatching. Warm incubation benefited eggs but harmed sperm, reducing the hatching success and, overall, gametic thermal plasticity did not enhance offspring fitness, indicating vulnerability to thermal changes. We highlight the sensitivity of male gametes to higher temperatures, and that gamete acclimation may not effectively buffer against deleterious effects of thermal fluctuations. From an applied angle, we propose the differential storage of male and female gametes as a tool to enhance sustainability within the hatcheries.
Collapse
Affiliation(s)
- Marco Graziano
- Centre for Ecology, Evolution, and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Monica F. Solberg
- Population Genetics Group, Institute of Marine Research, 5817 Bergen, Norway
| | - Kevin A. Glover
- Population Genetics Group, Institute of Marine Research, 5817 Bergen, Norway
| | - Ramakrishnan Vasudeva
- Centre for Ecology, Evolution, and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Lise Dyrhovden
- Population Genetics Group, Institute of Marine Research, 5817 Bergen, Norway
| | - David Murray
- Centre for Ecology, Evolution, and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
- Centre for Environment Fisheries and Aquaculture Science (CEFAS), Lowestoft NR33 0HT, UK
| | - Simone Immler
- Centre for Ecology, Evolution, and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Matthew J. G. Gage
- Centre for Ecology, Evolution, and Conservation, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| |
Collapse
|
4
|
Jansson E, Faust E, Bekkevold D, Quintela M, Durif C, Halvorsen KT, Dahle G, Pampoulie C, Kennedy J, Whittaker B, Unneland L, Post S, André C, Glover KA. Global, regional, and cryptic population structure in a high gene-flow transatlantic fish. PLoS One 2023; 18:e0283351. [PMID: 36940210 PMCID: PMC10027230 DOI: 10.1371/journal.pone.0283351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/21/2023] Open
Abstract
Lumpfish (Cyclopterus lumpus) is a transatlantic marine fish displaying large population sizes and a high potential for dispersal and gene-flow. These features are expected to result in weak population structure. Here, we investigated population genetic structure of lumpfish throughout its natural distribution in the North Atlantic using two approaches: I) 4,393 genome wide SNPs and 95 individuals from 10 locations, and II) 139 discriminatory SNPs and 1,669 individuals from 40 locations. Both approaches identified extensive population genetic structuring with a major split between the East and West Atlantic and a distinct Baltic Sea population, as well as further differentiation of lumpfish from the English Channel, Iceland, and Greenland. The discriminatory loci displayed ~2-5 times higher divergence than the genome wide approach, revealing further evidence of local population substructures. Lumpfish from Isfjorden in Svalbard were highly distinct but resembled most fish from Greenland. The Kattegat area in the Baltic transition zone, formed a previously undescribed distinct genetic group. Also, further subdivision was detected within North America, Iceland, West Greenland, Barents Sea, and Norway. Although lumpfish have considerable potential for dispersal and gene-flow, the observed high levels of population structuring throughout the Atlantic suggests that this species may have a natal homing behavior and local populations with adaptive differences. This fine-scale population structure calls for consideration when defining management units for exploitation of lumpfish stocks and in decisions related to sourcing and moving lumpfish for cleaner fish use in salmonid aquaculture.
Collapse
Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, Nordnes, Bergen, Norway
| | - Ellika Faust
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | | | - Caroline Durif
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | | | - Geir Dahle
- Institute of Marine Research, Nordnes, Bergen, Norway
| | | | - James Kennedy
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | - Benjamin Whittaker
- Department of Biosciences, Centre for Sustainable Aquatic Research, Swansea University, Swansea, United Kingdom
| | | | - Søren Post
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - Carl André
- Department of Marine Sciences - Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | | |
Collapse
|
5
|
Skern-Mauritzen R, Malde K, Eichner C, Dondrup M, Furmanek T, Besnier F, Komisarczuk AZ, Nuhn M, Dalvin S, Edvardsen RB, Klages S, Huettel B, Stueber K, Grotmol S, Karlsbakk E, Kersey P, Leong JS, Glover KA, Reinhardt R, Lien S, Jonassen I, Koop BF, Nilsen F. The salmon louse genome: Copepod features and parasitic adaptations. Genomics 2021; 113:3666-3680. [PMID: 34403763 DOI: 10.1016/j.ygeno.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022]
Abstract
Copepods encompass numerous ecological roles including parasites, detrivores and phytoplankton grazers. Nonetheless, copepod genome assemblies remain scarce. Lepeophtheirus salmonis is an economically and ecologically important ectoparasitic copepod found on salmonid fish. We present the 695.4 Mbp L. salmonis genome assembly containing ≈60% repetitive regions and 13,081 annotated protein-coding genes. The genome comprises 14 autosomes and a ZZ-ZW sex chromosome system. Assembly assessment identified 92.4% of the expected arthropod genes. Transcriptomics supported annotation and indicated a marked shift in gene expression after host attachment, including apparent downregulation of genes related to circadian rhythm coinciding with abandoning diurnal migration. The genome shows evolutionary signatures including loss of genes needed for peroxisome biogenesis, presence of numerous FNII domains, and an incomplete heme homeostasis pathway suggesting heme proteins to be obtained from the host. Despite repeated development of resistance against chemical treatments L. salmonis exhibits low numbers of many genes involved in detoxification.
Collapse
Affiliation(s)
| | - Ketil Malde
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Christiane Eichner
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Dondrup
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Tomasz Furmanek
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Anna Zofia Komisarczuk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Michael Nuhn
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Sussie Dalvin
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Rolf B Edvardsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway
| | - Sven Klages
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Kurt Stueber
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sindre Grotmol
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Egil Karlsbakk
- Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Paul Kersey
- EMBL-The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway
| | - Richard Reinhardt
- Max Planck Genome Centre Cologne, Carl von Linné Weg 10, D-50829 Köln, Germany
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Oluf Thesens vei 6, 1433 Ås, Norway
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Thormøhlens Gate 55, 5008 Bergen, Norway
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Frank Nilsen
- Institute of Marine Research, Postboks 1870 Nordnes, 5817 Bergen, Norway; Sea Lice Research Centre. Department of Biological Sciences, University of Bergen, Thormøhlens Gate 53, 5006 Bergen, Norway.
| |
Collapse
|
6
|
Duval E, Skaala Ø, Quintela M, Dahle G, Delaval A, Wennevik V, Glover KA, Hansen MM. Long-term monitoring of a brown trout (Salmo trutta) population reveals kin-associated migration patterns and contributions by resident trout to the anadromous run. BMC Ecol Evol 2021; 21:143. [PMID: 34256705 PMCID: PMC8276402 DOI: 10.1186/s12862-021-01876-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In species showing partial migration, as is the case for many salmonid fishes, it is important to assess how anthropogenic pressure experienced by migrating individuals affects the total population. We focused on brown trout (Salmo trutta) from the Guddal River in the Norwegian Hardanger Fjord system, which encompasses both resident and anadromous individuals. Aquaculture has led to increased anthropogenic pressure on brown trout during the marine phase in this region. Fish traps in the Guddal River allow for sampling all ascending anadromous spawners and descending smolts. We analyzed microsatellite DNA markers from all individuals ascending in 2006-2016, along with all emigrating smolts in 2017. We investigated (1) if there was evidence for declines in census numbers and effective population size during that period, (2) if there was association between kinship and migration timing in smolts and anadromous adults, and (3) to what extent resident trout were parents of outmigrating smolts. RESULTS Census counts of anadromous spawners showed no evidence for a decline from 2006 to 2016, but were lower than in 2000-2005. Estimates of effective population size also showed no trends of declines during the study period. Sibship reconstruction of the 2017 smolt run showed significant association between kinship and migration timing, and a similar association was indicated in anadromous spawners. Parentage assignment of 2017 smolts with ascending anadromous trout as candidate parents, and assuming that unknown parents represented resident trout, showed that 70% of smolts had at least one resident parent and 24% had two resident parents. CONCLUSIONS The results bear evidence of a population that after an initial decline has stabilized at a lower number of anadromous spawners. The significant association between kinship and migration timing in smolts suggests that specific episodes of elevated mortality in the sea could disproportionally affect some families and reduce overall effective population size. Finally, the results based on parentage assignment demonstrate a strong buffering effect of resident trout in case of elevated marine mortality affecting anadromous trout, but also highlight that increased mortality of anadromous trout, most of which are females, may lower overall production in the system.
Collapse
Affiliation(s)
- Eloïse Duval
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Theoretical and Experimental Ecology Station, UMR-5321, CNRS, University of Toulouse III Paul Sabatier, 2 route du CNRS, 09200, Moulis, France.
| | - Øystein Skaala
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| | - María Quintela
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Geir Dahle
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Aurélien Delaval
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Faculty of Biosciences and Aquaculture, Nord University, 8049, Bodø, Norway
| | - Vidar Wennevik
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
| | - Kevin A Glover
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway
- Institute of Biology, University of Bergen, Bergen, Norway
| | - Michael M Hansen
- Department of Biology, Aarhus University, Ny Munkegade 114, 8000, Aarhus C, Denmark.
- Department of Aquaculture, Institute of Marine Research, Nordnes, P.O. Box 1870, 5817, Bergen, Norway.
| |
Collapse
|
7
|
Faust E, Jansson E, André C, Halvorsen KT, Dahle G, Knutsen H, Quintela M, Glover KA. Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range. Evol Appl 2021; 14:1572-1587. [PMID: 34178105 PMCID: PMC8210792 DOI: 10.1111/eva.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
Collapse
Affiliation(s)
- Ellika Faust
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
| |
Collapse
|
8
|
Quintela M, Richter‐Boix À, Bekkevold D, Kvamme C, Berg F, Jansson E, Dahle G, Besnier F, Nash RDM, Glover KA. Genetic response to human-induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway. Ecol Evol 2021; 11:1691-1718. [PMID: 33613998 PMCID: PMC7882954 DOI: 10.1002/ece3.7160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/21/2022] Open
Abstract
Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a self-recruiting population in barely few decades. Landvikvannet sprat proved to be genetically isolated from the three main populations described for this species; that is, Norwegian fjords, Baltic Sea, and the combination of North Sea, Kattegat, and Skagerrak. This distinctness was depicted by an accuracy self-assignment of 89% and a highly significant F ST between the lake sprat and each of the remaining samples (average of ≈0.105). The correlation between genetic and environmental variation indicated that salinity could be an important environmental driver of selection (3.3% of the 91 SNPs showed strong associations). Likewise, Isolation by Environment was detected for salinity, although not for temperature, in samples not adhering to an Isolation by Distance pattern. Neighbor-joining tree analysis suggested that the source of the lake sprat is in the Norwegian fjords, rather than in the Baltic Sea despite a similar salinity profile. Strongly drifted allele frequencies and lower genetic diversity in Landvikvannet compared with the Norwegian fjords concur with a founder effect potentially associated with local adaptation to low salinity. Genetic differentiation (F ST) between marine and brackish sprat is larger in the comparison Norway-Landvikvannet than in Norway-Baltic, which suggests that the observed divergence was achieved in Landvikvannet in some 65 generations, that is, 132 years, rather than gradually over thousands of years (the age of the Baltic Sea), thus highlighting the pace at which human-driven evolution can happen.
Collapse
Affiliation(s)
| | - Àlex Richter‐Boix
- CREAFCampus de BellaterraAutonomous University of BarcelonaBarcelonaSpain
| | - Dorte Bekkevold
- DTU‐Aqua National Institute of Aquatic ResourcesTechnical University of DenmarkSilkeborgDenmark
| | | | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | | | - Richard D. M. Nash
- Centre for EnvironmentFisheries and Aquaculture Science (Cefas)LowestoftUK
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
| |
Collapse
|
9
|
Johansen T, Besnier F, Quintela M, Jorde PE, Glover KA, Westgaard J, Dahle G, Lien S, Kent MP. Genomic analysis reveals neutral and adaptive patterns that challenge the current management regime for East Atlantic cod Gadus morhua L. Evol Appl 2020; 13:2673-2688. [PMID: 33294016 PMCID: PMC7691467 DOI: 10.1111/eva.13070] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/12/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
Challenging long-held perceptions of fish management units can help to protect vulnerable stocks. When a fishery consisting of multiple genetic stocks is managed as a single unit, overexploitation and depletion of minor genetic units can occur. Atlantic cod (Gadus morhua) is an economically and ecologically important marine species across the North Atlantic. The application of new genomic resources, including SNP arrays, allows us to detect and explore novel structure within specific cod management units. In Norwegian waters, coastal cod (i.e. those not undertaking extensive migrations) are divided into two arbitrary management units defined by ICES: one between 62° and 70°N (Norwegian coastal cod; NCC) and one between 58° and 62°N (Norwegian coastal south; NCS). Together, these capture a fishery area of >25,000 km2 containing many spawning grounds. To assess whether these geographic units correctly represent genetic stocks, we analysed spawning cod of NCC and NCS for more than 8,000 SNPs along with samples of Russian White Sea cod, north-east Arctic cod (NEAC: the largest Atlantic stock), and outgroup samples representing the Irish and Faroe Sea's. Our analyses revealed large differences in spatial patterns of genetic differentiation across the genome and revealed a complex biological structure within NCC and NCS. Haplotype maps from four chromosome sets show regional specific SNP indicating a complex genetic structure. The current management plan dividing the coastal cod into only two management units does not accurately reflect the genetic units and needs to be revised. Coastal cod in Norway, while highly heterogenous, is also genetically distinct from neighbouring stocks in the north (NEAC), west (Faroe Island) and the south. The White Sea cod are highly divergent from other cod, possibly yielding support to the earlier notion of subspecies rank.
Collapse
Affiliation(s)
| | | | | | | | - Kevin A. Glover
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | | | - Geir Dahle
- Institute of Marine Research (IMR)BergenNorway
- Department of BiologyUniversity of BergenBergenNorway
| | - Sigbjørn Lien
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| | - Matthew P. Kent
- Department of Animal and Aquaculture SciencesFaculty of BiosciencesCentre for Integrative GeneticsNorwegian University of Life SciencesÅsNorway
| |
Collapse
|
10
|
Fjelldal PG, Hansen TJ, Wargelius A, Ayllon F, Glover KA, Schulz RW, Fraser TWK. Development of supermale and all-male Atlantic salmon to research the vgll3 allele - puberty link. BMC Genet 2020; 21:123. [PMID: 33183224 PMCID: PMC7664053 DOI: 10.1186/s12863-020-00927-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Farmed Atlantic salmon are one of the most economically significant global aquaculture products. Early sexual maturation of farmed males represents a significant challenge to this industry and has been linked with the vgll3 genotype. However, tools to aid research of this topic, such as all-male and clonal fish, are still lacking. The present 6-year study examined if all-male production is possible in Atlantic salmon, a species with heteromorphic sex chromosomes (males being XY, females XX), and if all-male fish can be applied to further explore the vgll3 contribution on the likelihood of early maturation. RESULTS Estrogen treatment of mixed sex yolk sac larvae gave rise to one sexually mature hermaphrodite with a male genotype (XY) that was used to produce both self-fertilized offspring and androgenetic double haploid (dh) offspring following egg activation with UV treated sperm and pressure shock to block the first mitotic division. There were YY supermales among both offspring types, which were crossed with dh females. Between 1 and 8% of the putative all-male offspring from the eight crosses with self-fertilized supermales were found to have ovaries, and 95% of these phenotypic females were also genetically female. None of the offspring from the one dh supermale cross had ovaries. When assessing the general contribution of the vgll3 locus on the likelihood of early post-smolt sexual maturation (jacking) in the all-male populations we found individuals that were homozygous for the early maturing genotype (97%) were more likely to enter puberty than individuals that were homozygous for the late maturing genotype (26%). However, the likelihood of jacking within individuals with an early/late heterozygous genotype was higher when the early allele came from the dam (94%) compared to the sire (45%). CONCLUSIONS The present results show that supermale Atlantic salmon are viable and fertile and can be used as a research tool to study important aspects of sexual maturation, such as to further explore the sex dependent parental genetic contribution to age at puberty in Atlantic salmon. In addition, we report the production of viable double haploid supermale fish.
Collapse
Affiliation(s)
- Per Gunnar Fjelldal
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Tom J. Hansen
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Anna Wargelius
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Fernando Ayllon
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), PO Box 1870, Nordnes, 5817 Bergen, Norway
| | - Rüdiger W. Schulz
- Reproductive Biology Group, Division Developmental Biology, Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, The Netherlands
| | - Thomas W. K. Fraser
- Institute of Marine Research (IMR), Matre Aquaculture Research Station, 5984 Matredal, Norway
| |
Collapse
|
11
|
Jansson E, Besnier F, Malde K, André C, Dahle G, Glover KA. Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations. BMC Genet 2020; 21:118. [PMID: 33036553 PMCID: PMC7547435 DOI: 10.1186/s12863-020-00921-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022] Open
Abstract
Background Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestris) is a heavily exploited species due to its importance as a cleaner-fish in commercial salmonid aquaculture. However, at the present, the population genetic structure of this species is still largely unresolved. Here, full-genome sequencing was used to produce the first genomic reference for this species, to study population-genomic divergence among four geographically distinct populations, and, to identify informative SNP markers for future studies. Results After construction of a de novo assembly, the genome was estimated to be highly polymorphic and of ~600Mbp in size. 33,235 SNPs were thereafter selected to assess genomic diversity and differentiation among four populations collected from Scandinavia, Scotland, and Spain. Global FST among these populations was 0.015–0.092. Approximately 4% of the investigated loci were identified as putative global outliers, and ~ 1% within Scandinavia. SNPs showing large divergence (FST > 0.15) were picked as candidate diagnostic markers for population assignment. One hundred seventy-three of the most diagnostic SNPs between the two Scandinavian populations were validated by genotyping 47 individuals from each end of the species’ Scandinavian distribution range. Sixty-nine of these SNPs were significantly (p < 0.05) differentiated (mean FST_173_loci = 0.065, FST_69_loci = 0.140). Using these validated SNPs, individuals were assigned with high probability (≥ 94%) to their populations of origin. Conclusions Goldsinny wrasse displays a highly polymorphic genome, and substantial population genomic structure. Diversifying selection likely affects population structuring globally and within Scandinavia. The diagnostic loci identified now provide a promising and cost-efficient tool to investigate goldsinny wrasse populations further.
Collapse
Affiliation(s)
- Eeva Jansson
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Francois Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Ketil Malde
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Carl André
- Department of Marine Sciences-Tjärnö, University of Gothenburg, 45296, Strömstad, Sweden
| | - Geir Dahle
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, 5817, Bergen, Norway.,Institute of Biology, University of Bergen, P. O. Box 7803, 5020, Bergen, Norway
| |
Collapse
|
12
|
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. R Soc Open Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
13
|
Otterå H, Johansen T, Folkvord A, Dahle G, Solvang Bingh MK, Westgaard JI, Glover KA. The pantophysin gene and its relationship with survival in early life stages of Atlantic cod. R Soc Open Sci 2020; 7:191983. [PMID: 33204437 PMCID: PMC7657904 DOI: 10.1098/rsos.191983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
Collapse
Affiliation(s)
- Håkon Otterå
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Arild Folkvord
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| | - Geir Dahle
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | | | - Jon-Ivar Westgaard
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Kevin A. Glover
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| |
Collapse
|
14
|
Quintela M, Kvamme C, Bekkevold D, Nash RDM, Jansson E, Sørvik AG, Taggart JB, Skaala Ø, Dahle G, Glover KA. Genetic analysis redraws the management boundaries for the European sprat. Evol Appl 2020; 13:1906-1922. [PMID: 32908594 PMCID: PMC7463317 DOI: 10.1111/eva.12942] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 02/03/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Sustainable fisheries management requires detailed knowledge of population genetic structure. The European sprat is an important commercial fish distributed from Morocco to the Arctic circle, Baltic, Mediterranean, and Black seas. Prior to 2018, annual catch advice on sprat from the International Council for the Exploration of the Sea (ICES) was based on five putative stocks: (a) North Sea, (b) Kattegat-Skagerrak and Norwegian fjords, (c) Baltic Sea, (d) West of Scotland-southern Celtic Seas, and (e) English Channel. However, there were concerns that the sprat advice on stock size estimates management plan inadequately reflected the underlying biological units. Here, we used ddRAD sequencing to develop 91 SNPs that were thereafter used to genotype approximately 2,500 fish from 40 locations. Three highly distinct and relatively homogenous genetic groups were identified: (a) Norwegian fjords; (b) Northeast Atlantic including the North Sea, Kattegat-Skagerrak, Celtic Sea, and Bay of Biscay; and (c) Baltic Sea. Evidence of genetic admixture and possibly physical mixing was detected in samples collected from the transition zone between the North and Baltic seas, but not between any of the other groups. These results have already been implemented by ICES with the decision to merge the North Sea and the Kattegat-Skagerrak sprat to be assessed as a single unit, thus demonstrating that genetic data can be rapidly absorbed to align harvest regimes and biological units.
Collapse
Affiliation(s)
| | | | - Dorte Bekkevold
- DTU-Aqua National Institute of Aquatic Resources Technical University of Denmark Silkeborg Denmark
| | | | | | | | - John B Taggart
- Institute of Aquaculture School of Natural Sciences University of Stirling Stirling UK
| | | | - Geir Dahle
- Institute of Marine Research Bergen Norway
| | - Kevin A Glover
- Institute of Marine Research Bergen Norway
- Institute of Biology University of Bergen Bergen Norway
| |
Collapse
|
15
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
16
|
Seljestad GW, Quintela M, Faust E, Halvorsen KT, Besnier F, Jansson E, Dahle G, Knutsen H, André C, Folkvord A, Glover KA. "A cleaner break": Genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse ( Labrus bergylta). Ecol Evol 2020; 10:6120-6135. [PMID: 32607218 PMCID: PMC7319121 DOI: 10.1002/ece3.6404] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022] Open
Abstract
Capture and long-distance translocation of cleaner fish to control lice infestations on marine salmonid farms has the potential to influence wild populations via overexploitation in source regions, and introgression in recipient regions. Knowledge of population genetic structure is therefore required. We studied the genetic structure of ballan wrasse, a phenotypically diverse and extensively used cleaner fish, from 18 locations in Norway and Sweden, and from Galicia, Spain, using 82 SNP markers. We detected two very distinct genetic groups in Scandinavia, northwestern and southeastern. These groups were split by a stretch of sandy beaches in southwest Norway, representing a habitat discontinuity for this rocky shore associated benthic egg-laying species. Wrasse from Galicia were highly differentiated from all Scandinavian locations, but more similar to northwestern than southeastern locations. Distinct genetic differences were observed between sympatric spotty and plain phenotypes in Galicia, but not in Scandinavia. The mechanisms underlying the geographic patterns between phenotypes are discussed, but not identified. We conclude that extensive aquaculture-mediated translocation of ballan wrasse from Sweden and southern Norway to western and middle Norway has the potential to mix genetically distinct populations. These results question the sustainability of the current cleaner fish practice.
Collapse
Affiliation(s)
- Gaute W. Seljestad
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | | - Ellika Faust
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Kim T. Halvorsen
- Institute of Marine ResearchAustevoll Research StationStorebøNorway
| | | | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchFlødevigenNorway
- Centre for Coastal ResearchUniversity of AgderKristiansandNorway
| | - Carl André
- Department of Marine Sciences—TjärnöUniversity of GothenburgStrömstadSweden
| | - Arild Folkvord
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Department of Biological SciencesUniversity of BergenBergenNorway
| |
Collapse
|
17
|
Bicskei B, Taggart JB, Bron JE, Glover KA. Transcriptomic comparison of communally reared wild, domesticated and hybrid Atlantic salmon fry under stress and control conditions. BMC Genet 2020; 21:57. [PMID: 32471356 PMCID: PMC7257211 DOI: 10.1186/s12863-020-00858-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/12/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Domestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour life in the domesticated environment are unlikely to be advantageous in the wild. Elucidation of the differences between wild and domesticated Atlantic salmon may provide insights into some of the genomic changes occurring during domestication, and, help to predict the evolutionary consequences of farmed salmon escapees interbreeding with wild conspecifics. In this study the transcriptome of the offspring of wild and domesticated Atlantic salmon were compared using a common-garden experiment under standard hatchery conditions and in response to an applied crowding stressor. RESULTS Transcriptomic differences between wild and domesticated crosses were largely consistent between the control and stress conditions, and included down-regulation of environmental information processing, immune and nervous system pathways and up-regulation of genetic information processing, carbohydrate metabolism, lipid metabolism and digestive and endocrine system pathways in the domesticated fish relative to their wild counterparts, likely reflective of different selection pressures acting in wild and cultured populations. Many stress responsive functions were also shared between crosses and included down-regulation of cellular processes and genetic information processing and up-regulation of some metabolic pathways, lipid and energy in particular. The latter may be indicative of mobilization and reallocation of energy resources in response to stress. However, functional analysis indicated that a number of pathways behave differently between domesticated and wild salmon in response to stress. Reciprocal F1 hybrids permitted investigation of inheritance patterns that govern transcriptomic differences between these genetically divergent crosses. Additivity and maternal dominance accounted for approximately 42 and 25% of all differences under control conditions for both hybrids respectively. However, the inheritance of genes differentially expressed between crosses under stress was less consistent between reciprocal hybrids, potentially reflecting maternal environmental effects. CONCLUSION We conclude that there are transcriptomic differences between the domesticated and wild salmon strains studied here, reflecting the different selection pressures operating on them. Our results indicate that stress may affect certain biological functions differently in wild, domesticated and hybrid crosses and these should be further investigated.
Collapse
Affiliation(s)
- Beatrix Bicskei
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - John B. Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - James E. Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA UK
| | - Kevin A. Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| |
Collapse
|
18
|
Harvey AC, Glover KA, Wennevik V, Skaala Ø. Atlantic salmon and sea trout display synchronised smolt migration relative to linked environmental cues. Sci Rep 2020; 10:3529. [PMID: 32103141 PMCID: PMC7044379 DOI: 10.1038/s41598-020-60588-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/14/2020] [Indexed: 11/09/2022] Open
Abstract
Anadromous salmon and sea trout smolts face challenging migrations from freshwater to the marine environment characterised by high mortality. Therefore, the timing of smolt migration is likely to be critical for survival. Time-series comparing migration of Atlantic salmon and sea trout smolts in the same river, and their response to the same environmental cues, are scarce. Here, we analysed migration timing of ~41 000 Atlantic salmon and sea trout smolts over a 19-year period from the river Guddalselva, western Norway. Trout displayed a longer migration window in earlier years, which decreased over time to become more similar to the salmon migration window. On average, salmon migrated out of the river earlier than trout. Migration of both species was significantly influenced by river water temperature and water discharge, but their relative influence varied across the years. On average, body-length of smolts of both species overlapped, however, size differences were observed within the migration period and among the years. We conclude that salmon and trout smolts in this river are highly synchronised and migrate in response to the same range of linked environmental cues.
Collapse
Affiliation(s)
| | - Kevin A Glover
- Institute of Marine Research (IMR), Bergen, Norway.,Institute of Biology, University of Bergen, Bergen, Norway
| | | | | |
Collapse
|
19
|
Besnier F, Solberg MF, Harvey AC, Carvalho GR, Bekkevold D, Taylor MI, Creer S, Nielsen EE, Skaala Ø, Ayllon F, Dahle G, Glover KA. Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface. BMC Genet 2020; 21:13. [PMID: 32033538 PMCID: PMC7006396 DOI: 10.1186/s12863-020-0816-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 01/28/2020] [Indexed: 12/23/2022] Open
Abstract
Background Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Results After rearing fish in common-garden experiments under aquaculture conditions, we performed a variance component analysis in four mapping populations totaling ~ 7000 individuals from six wild, two domesticated and three F1 wild/domesticated hybrid strains. Across the four independent datasets, genome-wide significant quantitative trait loci (QTLs) associated with weight and length were detected on a total of 18 chromosomes, reflecting the polygenic nature of growth. Significant QTLs correlated with both length and weight were detected on chromosomes 2, 6 and 9 in multiple datasets. Significantly, epistatic QTLs were detected in all datasets. Discussion The observed interactions demonstrated that the phenotypic effect of inheriting an allele deviated between half-sib families. Gene-by-gene interactions were also suggested, where the combined effect of two loci resulted in a genetic effect upon phenotypic variance, while no genetic effect was detected when the two loci were considered separately. To our knowledge, this is the first documentation of epistasis in a quantitative trait in Atlantic salmon. These novel results are of relevance for breeding programs, and for predicting the evolutionary consequences of domestication-introgression in wild populations.
Collapse
Affiliation(s)
- Francois Besnier
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - Monica F Solberg
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Alison C Harvey
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Gary R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Dorte Bekkevold
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Einar E Nielsen
- Section for Marine Living Resources, National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, 8600, Silkeborg, Denmark
| | - Øystein Skaala
- 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
| | - Geir Dahle
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| | - Kevin A Glover
- Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
| |
Collapse
|
20
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
21
|
Helle K, Quintela M, Taggart JB, Seliussen B, Dahle G, Glover KA, Johansen T. Development of SNP for the deep-sea fish blue ling, Molva dypterygia (Pennant, 1784) from ddRAD sequencing data. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01107-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
22
|
Wennevik V, Quintela M, Skaala Ø, Verspoor E, Prusov S, Glover KA. Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway. Ecol Evol 2019; 9:6901-6921. [PMID: 31380023 PMCID: PMC6662299 DOI: 10.1002/ece3.5258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.
Collapse
Affiliation(s)
| | | | | | - Eric Verspoor
- Rivers and Lochs Institute, Inverness CollegeUniversity of the Highlands and IslandsInvernessUK
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO)MurmanskRussia
| | | |
Collapse
|
23
|
Ayllon F, Solberg MF, Glover KA, Mohammadi F, Kjærner-Semb E, Fjelldal PG, Andersson E, Hansen T, Edvardsen RB, Wargelius A. The influence of vgll3 genotypes on sea age at maturity is altered in farmed mowi strain Atlantic salmon. BMC Genet 2019; 20:44. [PMID: 31060499 PMCID: PMC6501413 DOI: 10.1186/s12863-019-0745-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/25/2019] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND In Atlantic salmon in the wild, age at maturity is strongly influenced by the vgll3 locus. Under farming conditions, light, temperature and feeding regimes are known significantly advance or delay age at maturity. However, the potential influence of the vgll3 locus on the maturation of salmon reared under farming conditions has been rarely investigated, especially in females. RESULTS Here, we reared domesticated salmon (mowi strain) with different vgll3 genotypes under standard farming conditions until they matured at either one, two or more than two sea winters. Interestingly, and in contrast to previous findings in the wild, we were not able to identify a link between vgll3 and age at maturity in females when reared under farming conditions. For males however, we found that the probability of delaying maturation from one to two sea winters was significantly lower in fish homozygous for the early allele compared to homozygous fish for the late allele, while the probability for heterozygous fish was intermediate. These data also contrast to previous findings in the wild where the early allele has been reported as dominant. However, we found that the probability of males delaying maturation from two to three sea winters was regulated in the same manner as the wild. CONCLUSIONS Collectively, our data suggest that increased growth rates in mowi salmon, caused by high feed intake and artificial light and temperature regimes together with other possible genetic/epigenetic components, may significantly influence the impact that the vgll3 locus has on age at maturity, especially in females. In turn, our results show that the vgll3 locus can only to a large extent be used in selective breeding to control age at maturation in mowi males. In summary, we here show that in contrast to the situation in wild salmon, under farming conditions vgll3 does not seem to influence age at maturity in mowi females whereas in mowi males, maturing as one or two sea winters it alters the early allele effect from dominant to intermediate.
Collapse
Affiliation(s)
- Fernando Ayllon
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Monica F Solberg
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Institute of Biology, University of Bergen, Bergen, Norway
| | - Faezeh Mohammadi
- 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
| | - Per Gunnar Fjelldal
- Institute of Marine research (IMR), Matre Aquaculture Research Station, 5984, Matredal, Norway
| | - Eva Andersson
- Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - Tom Hansen
- Institute of Marine research (IMR), Matre Aquaculture Research Station, 5984, Matredal, Norway
| | - Rolf B Edvardsen
- 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.
| |
Collapse
|
24
|
Harvey AC, Skilbrei OT, Besnier F, Solberg MF, Sørvik AGE, Glover KA. Implications for introgression: has selection for fast growth altered the size threshold for precocious male maturation in domesticated Atlantic salmon? BMC Evol Biol 2018; 18:188. [PMID: 30558529 PMCID: PMC6298023 DOI: 10.1186/s12862-018-1294-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 11/16/2018] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Mature male parr (MMP) represent an important alternative life-history strategy in Atlantic salmon populations. Previous studies indicate that the maturation size threshold for male parr varies among wild populations and is influenced by individual growth, environmental conditions, and genetics. More than ten generations of breeding have resulted in domesticated salmon displaying many genetic differences to wild salmon, including greatly increased growth rates. This may have resulted in domesticated fish with the potential to outgrow the size threshold for early maturation, or evolution of the size threshold of the trait itself. To investigate this, we performed a common-garden experiment under farming conditions using 4680 salmon from 39 families representing four wild, two wild-domesticated hybrid, and two domesticated strains. RESULTS Domesticated salmon outgrew wild salmon 2-5-fold, and hybrids displayed intermediate growth. Overall, the numbers of MMP varied greatly among families and strains: averaging 4-12% in domesticated, 18-25% in hybrid, and 43-74% in the wild populations. However, when the influence of growth was accounted for, by dividing fish into lower and upper size modes, no difference in the incidence of MMP was detected among domesticated and wild strains in either size mode. In the lower size mode, hybrids displayed significantly lower incidences of mature males than their wild parental strains. No consistent differences in the body size of MMP, connected to domestication, was detected. CONCLUSIONS Our data demonstrate: 1- no evidence for the evolution of the size threshold for MMP in domesticated salmon, 2- the vastly lower incidence of MMP in domesticated strains under aquaculture conditions is primarily due to their genetically increased growth rate causing them to outgrow the size threshold for early maturation, 3- the incidence of MMP is likely to overlap among domesticated and wild salmon in the natural habitat where they typically display overlapping growth, although hybrid offspring may display lower incidences of mature male parr. These results have implications for wild salmon populations that are exposed to introgression from domesticated escapees.
Collapse
Affiliation(s)
- A C Harvey
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - O T Skilbrei
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - F Besnier
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - A-G E Sørvik
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Department of Biology, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
| |
Collapse
|
25
|
Jørgensen KM, Wennevik V, Eide Sørvik AG, Unneland L, Prusov S, Ayllon F, Glover KA. Investigating the frequency of triploid Atlantic salmon in wild Norwegian and Russian populations. BMC Genet 2018; 19:90. [PMID: 30285613 PMCID: PMC6171226 DOI: 10.1186/s12863-018-0676-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/19/2018] [Indexed: 12/18/2022] Open
Abstract
Background Fish may display variations in ploidy, including three sets of chromosomes, known as triploidy. A recent study revealed a frequency of ~ 2% spontaneous (i.e., non-intentional) triploidy in domesticated Atlantic salmon produced in Norwegian aquaculture in the period 2007–2014. In contrast, the frequency of triploidy in wild salmon populations has not been studied thus far, and in wild populations of other organisms, it has been very rarely studied. In population genetic data sets, individuals that potentially display chromosome abnormalities, such as triploids with three alleles, are typically excluded on the premise that they may reflect polluted or otherwise compromised samples. Here, we critically re-investigated the microsatellite genetic profile of ~ 6000 wild Atlantic salmon sampled from 80 rivers in Norway and Russia, to investigate the frequency of triploid individuals in wild salmon populations for the first time. Results We detected a single triploid salmon, and five individuals displaying three alleles at one of the loci, thus regarded as putatively trisomic. This gave an overall frequency of triploid and putatively trisomic individuals in the data set of 0.017 and 0.083% respectively. The triploid salmon was an adult female, and had spent 2 years in freshwater and 2 years in the sea. Conclusions We conclude that the frequency of naturally-occurring triploid Atlantic salmon in wild Norwegian and Russian populations is very low, and many-fold lower than the frequency of spontaneous triploids observed in aquaculture. Our results suggest that aquaculture rearing conditions substantially increase the probability of triploidy to develop, and/or permits greater survival of triploid individuals, in comparison to the wild. Electronic supplementary material The online version of this article (10.1186/s12863-018-0676-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | - Vidar Wennevik
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | | | - Laila Unneland
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO), Murmansk, 183038, Russia
| | - Fernando Ayllon
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, Postboks 1870 Nordnes, N-5817, Bergen, Norway.,Sea lice Research Centre, Department of Biology, University of Bergen, N-5020, Bergen, Norway
| |
Collapse
|
26
|
Glover KA, Solberg MF, Besnier F, Skaala Ø. Cryptic introgression: evidence that selection and plasticity mask the full phenotypic potential of domesticated Atlantic salmon in the wild. Sci Rep 2018; 8:13966. [PMID: 30228303 PMCID: PMC6143624 DOI: 10.1038/s41598-018-32467-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/03/2018] [Indexed: 01/13/2023] Open
Abstract
Domesticated Atlantic salmon grow much faster than wild salmon when reared together in fish tanks under farming conditions (size ratios typically 1:2-3). In contrast, domesticated salmon only display marginally higher growth than wild salmon when reared together in rivers (size ratios typically 1:1-1.2). This begs the question why? Is this a difference in the plastic response driven by divergent energy budgets between the two environments, or is it a result of selection, whereby domesticated salmon that display the greatest growth-potential are those at greatest risk of mortality in the wild? We reared domesticated, hybrid and wild salmon in a river until they smoltified at age 2 or 4, and thereafter in fish tanks for a further 2 years. In the river, there was no difference in the mean size between the groups. In contrast, after being transferred from the river to fish tanks, the domesticated salmon significantly outgrew the wild salmon (maximum size ratio of ~1:1.8). This demonstrates that selection alone cannot be responsible for the lack of growth differences observed between domesticated and wild salmon in rivers. Nevertheless, the final size ratios observed after rearing in tanks were lower than expected in that environment, thus suggesting that plasticity, as for selection, cannot be the sole mechanism. We therefore conclude that a combination of energy-budget plasticity, and selection via growth-potential mortality, cause the differences in growth reaction norms between domesticated and wild salmon across these contrasting environments. Our results imply that if phenotypic changes are not observed in wild populations following introgression of domesticated conspecifics, it does not mean that functional genetic changes have not occurred in the admixed population. Clearly, under the right environmental conditions, the underlying genetic changes will manifest themselves in the phenotype.
Collapse
Affiliation(s)
- Kevin A Glover
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway. .,University of Bergen, Department of Biology, P.O. Box 7803, N-5020, Bergen, Norway.
| | - Monica F Solberg
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
| | - Øystein Skaala
- Institute of Marine Research, P.O. Box 1870, N-5817, Bergen, Norway
| |
Collapse
|
27
|
Dahle G, Quintela M, Johansen T, Westgaard JI, Besnier F, Aglen A, Jørstad KE, Glover KA. Analysis of coastal cod (Gadus morhua L.) sampled on spawning sites reveals a genetic gradient throughout Norway's coastline. BMC Genet 2018; 19:42. [PMID: 29986643 PMCID: PMC6036686 DOI: 10.1186/s12863-018-0625-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 05/18/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated. We sampled > 4000 cod from 55 spawning sites. All fish were genotyped with 6 microsatellite markers and Pan I (Dataset 1). A sub-set of the samples (1295 fish from 17 locations) were also genotyped with an additional 9 microsatellites (Dataset 2). Otoliths were read in order to exclude North East Arctic Cod (NEAC) from the analyses, as and where appropriate. RESULTS We found no difference in genetic diversity, measured as number of alleles, allelic richness, heterozygosity nor effective population sizes, in the north-south gradient. In both data sets, weak but significant population genetic structure was revealed (Dataset 1: global FST = 0.008, P < 0.0001. Dataset 2: global FST = 0.004, P < 0.0001). While no clear genetic groups were identified, genetic differentiation increased among geographically-distinct samples. Although the locus Gmo132 was identified as a candidate for positive selection, possibly through linkage with a genomic region under selection, overall trends remained when this locus was excluded from the analyses. The most common allele in loci Gmo132 and Gmo34 showed a marked frequency change in the north-south gradient, increasing towards the frequency observed in NEAC in the north. CONCLUSION We conclude that Norwegian coastal cod displays significant population genetic structure throughout its entire range, that follows a trend of isolation by distance. Furthermore, we suggest that a gradient of genetic introgression between NEAC and NCC contributes to the observed population genetic structure. The current management regime for coastal cod in Norway, dividing it into two stocks at 62°N, represents a simplification of the level of genetic connectivity among coastal cod in Norway, and needs revision.
Collapse
Affiliation(s)
- Geir Dahle
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - María Quintela
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research (IMR), Postbox 6404, N-9019 Tromsø, Norway
| | | | - François Besnier
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Asgeir Aglen
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Knut E. Jørstad
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research (IMR), Postbox 1870, N-5817 Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| |
Collapse
|
28
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
29
|
Harvey AC, Tang Y, Wennevik V, Skaala Ø, Glover KA. Timing is everything: Fishing-season placement may represent the most important angling-induced evolutionary pressure on Atlantic salmon populations. Ecol Evol 2017; 7:7490-7502. [PMID: 28944033 PMCID: PMC5606871 DOI: 10.1002/ece3.3304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 06/01/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023] Open
Abstract
Fisheries‐induced evolution can change the trajectory of wild fish populations by selectively targeting certain phenotypes. For important fish species like Atlantic salmon, this could have large implications for their conservation and management. Most salmon rivers are managed by specifying an angling season of predetermined length based on population demography, which is typically established from catch statistics. Given the circularity of using catch statistics to estimate demographic parameters, it may be difficult to quantify the selective nature of angling and its evolutionary impact. In the River Etne in Norway, a recently installed trap permits daily sampling of fish entering the river, some of which are subsequently captured by anglers upstream. Here, we used 31 microsatellites to establish an individual DNA profile for salmon entering the trap, and for many of those subsequently captured by anglers. These data permitted us to investigate time of rod capture relative to river entry, potential body size‐selective harvest, and environmental variables associated with river entry. Larger, older fish entered the river earlier than smaller, younger fish of both sexes, and larger, older females were more abundant than males and vice versa. There was good agreement between the sizes of fish harvested by angling, and the size distribution of the population sampled on the trap. These results demonstrate that at least in this river, and with the current timing of the season, the angling catch reflects the population's demographics and there is no evidence of size‐selective harvest. We also demonstrated that the probability of being caught by angling declines quickly after river entry. Collectively, these data indicate that that the timing of the fishing season, in relation to the upstream migration patterns of the different demographics of the population, likely represents the most significant directional evolutionary force imposed by angling.
Collapse
Affiliation(s)
| | - Yongkai Tang
- Freshwater Fisheries Research Center Chinese Academy of Fishery Sciences Wuxi China
| | | | | | - Kevin A Glover
- Institute of Marine Research Bergen Norway.,Department of Biology Sea Lice Research Centre University of Bergen Bergen Norway
| |
Collapse
|
30
|
Harvey AC, Fjelldal PG, Solberg MF, Hansen T, Glover KA. Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set. BMC Genet 2017; 18:34. [PMID: 28399816 PMCID: PMC5387229 DOI: 10.1186/s12863-017-0502-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/06/2017] [Indexed: 12/30/2022] Open
Abstract
Background The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid performance often show contrasting results. Studies have identified dosage and dosage-compensation effects for gene expression between triploid and diploid salmonids, but no study has investigated how ploidy and parent-origin effects interact on a polygenic trait in divergent lines of Atlantic salmon (i.e. slow growing wild versus fast growing domesticated phenotype). This study utilised two experiments relating to the freshwater growth of diploid and triploid groups of pure wild (0% domesticated genome), pure domesticated (100% domesticated genome), and F1 reciprocal hybrid (33%, 50% or 66% domesticated genome) salmon where triploidy was either artificially induced (experiment 1) or naturally developed/spontaneous (experiment 2). Results In both experiments, reciprocal hybrid growth was influenced by the dosage effect of the second maternal chromosome, with growth increasing as ploidy level increased in individuals with a domesticated dam (from 50% to 66% domesticated genome), and the inverse in individuals with a wild dam (from 50% to 33% domesticated genome). Conclusions We demonstrate that the combined effect of ploidy and parent-origin on growth, a polygenic trait, is regulated in an additive pattern. Therefore, in order to maximise growth potential, the aquaculture industry should consider placing more emphasis on the breeding value of the dam than the sire when producing triploid families for commercial production. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0502-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- A C Harvey
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.
| | - P G Fjelldal
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - T Hansen
- Institute of Marine Research (IMR), Matre Research Station, NO-5984, Matredal, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway.,Department of Biology, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
| |
Collapse
|
31
|
Malde K, Seliussen BB, Quintela M, Dahle G, Besnier F, Skaug HJ, Øien N, Solvang HK, Haug T, Skern-Mauritzen R, Kanda N, Pastene LA, Jonassen I, Glover KA. Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics 2017; 18:76. [PMID: 28086785 PMCID: PMC5237217 DOI: 10.1186/s12864-016-3416-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/12/2016] [Indexed: 11/24/2022] Open
Abstract
Background In the marine environment, where there are few absolute physical barriers, contemporary contact between previously isolated species can occur across great distances, and in some cases, may be inter-oceanic. An example of this can be seen in the minke whale species complex. Antarctic minke whales are genetically and morphologically distinct from the common minke found in the north Atlantic and Pacific oceans, and the two species are estimated to have been isolated from each other for 5 million years or more. Recent atypical migrations from the southern to the northern hemisphere have been documented and fertile hybrids and back-crossed individuals between both species have also been identified. However, it is not known whether this represents a contemporary event, potentially driven by ecosystem changes in the Antarctic, or a sporadic occurrence happening over an evolutionary time-scale. We successfully used whole genome resequencing to identify a panel of diagnostic SNPs which now enable us address this evolutionary question. Results A large number of SNPs displaying fixed or nearly fixed allele frequency differences among the minke whale species were identified from the sequence data. Five panels of putatively diagnostic markers were established on a genotyping platform for validation of allele frequencies; two panels (26 and 24 SNPs) separating the two species of minke whale, and three panels (22, 23, and 24 SNPs) differentiating the three subspecies of common minke whale. The panels were validated against a set of reference samples, demonstrating the ability to accurately identify back-crossed whales up to three generations. Conclusions This work has resulted in the development of a panel of novel diagnostic genetic markers to address inter-oceanic and global contact among the genetically isolated minke whale species and sub-species. These markers, including a globally relevant genetic reference data set for this species complex, are now openly available for researchers interested in identifying other potential whale hybrids in the world’s oceans. The approach used here, combining whole genome resequencing and high-throughput genotyping, represents a universal approach to develop similar tools for other species and population complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3416-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ketil Malde
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway.,Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | | | - María Quintela
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Geir Dahle
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Francois Besnier
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Hans J Skaug
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway.,Department of Mathematics, University of Bergen, N-5020, Bergen, Norway
| | - Nils Øien
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Hiroko K Solvang
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway
| | - Tore Haug
- Institute of Marine Research, PO box 6404, N-9294, Tromsø, Norway
| | | | - Naohisa Kanda
- Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, Tokyo, 104-0055, Japan.,Japan NUS Co., Ltd, Nishi-Shinjuku Kimuraya Bldg 5F, 7-5-25, Nishi-Shinjuku, 160-0023, Japan
| | - Luis A Pastene
- Institute of Cetacean Research, Toyomi-cho 4-5, Chuo-ku, Tokyo, 104-0055, Japan
| | - Inge Jonassen
- Department of Informatics, University of Bergen, N-5020, Bergen, Norway
| | - Kevin A Glover
- Institute of Marine Research, PO box 1870, Nordnes, N-5817, Bergen, Norway. .,Department of Biology, University of Bergen, N-5020, Bergen, Norway.
| |
Collapse
|
32
|
Quintela M, Danielsen EA, Lopez L, Barreiro R, Svåsand T, Knutsen H, Skiftesvik AB, Glover KA. Is the ballan wrasse (Labrus bergylta) two species? Genetic analysis reveals within-species divergence associated with plain and spotted morphotype frequencies. Integr Zool 2016; 11:162-72. [PMID: 26748687 PMCID: PMC5123583 DOI: 10.1111/1749-4877.12186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ballan wrasse (Labrus bergylta) is a marine fish belonging to the family Labridae characterized by 2 main morphotypes that occur in sympatry: spotty and plain. Previous studies have revealed differences in their life‐history traits, such as growth and maturation; however, the genetic relationship between forms is presently unknown. Using 20 recently developed microsatellite markers, we conducted a genetic analysis of 41 and 48 spotty and plain ballan wrasse collected in Galicia (northwest Spain). The 2 morphotypes displayed highly significant genetic differences to each other (FST = 0.018, P < 0.0001). A similar degree of genetic differentiation (FST = 0.025, P < 0.0001) was shown using the STRUCTURE clustering approach with no priors at K = 2. In this case, the frequency of spotty and plain morphotypes was significantly different (χ2 = 9.46, P = 0.002). It is concluded that there is significant genetic heterogeneity within this species, which appears to be highly associated with the spotty and plain forms, but not completely explained by them. Given the previously demonstrated biological differences between morphotypes, and the present genetic analyses, we speculate about the convenience of a taxonomic re‐evaluation of this species.
Collapse
Affiliation(s)
| | | | - Lua Lopez
- Grupo de investigación BIOCOST, University of A Coruña, Spain
| | | | | | - Halvor Knutsen
- Institute of Marine Research, Bergen, Norway.,Centre for Ecological and Evolutionary Synthesis, Department of Biology, University of Oslo, Oslo, Norway.,University of Agder, Kristiansand, Norway
| | | | | |
Collapse
|
33
|
Harvey AC, Solberg MF, Glover KA, Taylor MI, Creer S, Carvalho GR. Plasticity in response to feed availability: Does feeding regime influence the relative growth performance of domesticated, wild and hybrid Atlantic salmon Salmo salar parr? J Fish Biol 2016; 89:1754-1768. [PMID: 27460446 DOI: 10.1111/jfb.13076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Growth of farmed, wild and F1 hybrid Atlantic salmon parr Salmo salar was investigated under three contrasting feeding regimes in order to understand how varying levels of food availability affects relative growth. Treatments consisted of standard hatchery feeding (ad libitum), access to feed for 4 h every day, and access to feed for 24 h on three alternate days weekly. Mortality was low in all treatments, and food availability had no effect on survival of all groups. The offspring of farmed S. salar significantly outgrew the wild S. salar, while hybrids displayed intermediate growth. Furthermore, the relative growth differences between the farmed and wild S. salar did not change across feeding treatments, indicating a similar plasticity in response to feed availability. Although undertaken in a hatchery setting, these results suggest that food availability may not be the sole driver behind the observed reduced growth differences found between farmed and wild fishes under natural conditions.
Collapse
Affiliation(s)
- A C Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - M F Solberg
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
| | - K A Glover
- Institute of Marine Research, P. O. Box 1870, Nordnes, NO-5817, Bergen, Norway
- Department of Biology, Sea Lice Research Centre, University of Bergen, P. O. Box 7803, N-5020, Bergen, Norway
| | - M I Taylor
- School of Biological Sciences, University of East Anglia, NR4 7TJ, Norwich, U.K
| | - S Creer
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| | - G R Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, U.K
| |
Collapse
|
34
|
Kjærner-Semb E, Ayllon F, Furmanek T, Wennevik V, Dahle G, Niemelä E, Ozerov M, Vähä JP, Glover KA, Rubin CJ, Wargelius A, Edvardsen RB. Atlantic salmon populations reveal adaptive divergence of immune related genes - a duplicated genome under selection. BMC Genomics 2016; 17:610. [PMID: 27515098 PMCID: PMC4982270 DOI: 10.1186/s12864-016-2867-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/30/2016] [Indexed: 12/31/2022] Open
Abstract
Background Populations of Atlantic salmon display highly significant genetic differences with unresolved molecular basis. These differences may result from separate postglacial colonization patterns, diversifying natural selection and adaptation, or a combination. Adaptation could be influenced or even facilitated by the recent whole genome duplication in the salmonid lineage which resulted in a partly tetraploid species with duplicated genes and regions. Results In order to elucidate the genes and genomic regions underlying the genetic differences, we conducted a genome wide association study using whole genome resequencing data from eight populations from Northern and Southern Norway. From a total of ~4.5 million sequencing-derived SNPs, more than 10 % showed significant differentiation between populations from these two regions and ten selective sweeps on chromosomes 5, 10, 11, 13–15, 21, 24 and 25 were identified. These comprised 59 genes, of which 15 had one or more differentiated missense mutation. Our analysis showed that most sweeps have paralogous regions in the partially tetraploid genome, each lacking the high number of significant SNPs found in the sweeps. The most significant sweep was found on Chr 25 and carried several missense mutations in the antiviral mx genes, suggesting that these populations have experienced differing viral pressures. Interestingly the second most significant sweep, found on Chr 5, contains two genes involved in the NF-KB pathway (nkap and nkrf), which is also a known pathogen target that controls a large number of processes in animals. Conclusion Our results show that natural selection acting on immune related genes has contributed to genetic divergence between salmon populations in Norway. The differences between populations may have been facilitated by the plasticity of the salmon genome. The observed signatures of selection in duplicated genomic regions suggest that the recently duplicated genome has provided raw material for evolutionary adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2867-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Erik Kjærner-Semb
- Institute of Marine Research, Bergen, Norway. .,Department of Biology, University of Bergen, Bergen, Norway.
| | | | | | | | - Geir Dahle
- Institute of Marine Research, Bergen, Norway
| | - Eero Niemelä
- Natural Resources Institute Finland, Helsinki, Finland
| | - Mikhail Ozerov
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland
| | - Juha-Pekka Vähä
- Kevo Subarctic Research Institute, University of Turku, Turku, Finland.,Association for Water and Environment of Western Uusimaa, Uusimaa, Finland
| | - Kevin A Glover
- Institute of Marine Research, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Carl J Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | |
Collapse
|
35
|
Harvey AC, Juleff G, Carvalho GR, Taylor MI, Solberg MF, Creer S, Dyrhovden L, Matre IH, Glover KA. Does density influence relative growth performance of farm, wild and F1 hybrid Atlantic salmon in semi-natural and hatchery common garden conditions? R Soc Open Sci 2016; 3:160152. [PMID: 27493772 PMCID: PMC4968464 DOI: 10.1098/rsos.160152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The conditions encountered by Atlantic salmon, Salmo salar L., in aquaculture are markedly different from the natural environment. Typically, farmed salmon experience much higher densities than wild individuals, and may therefore have adapted to living in high densities. Previous studies have demonstrated that farmed salmon typically outgrow wild salmon by large ratios in the hatchery, but these differences are much less pronounced in the wild. Such divergence in growth may be explained partly by the offspring of wild salmon experiencing higher stress and thus lower growth when compared under high-density farming conditions. Here, growth of farmed, wild and F1 hybrid salmon was studied at contrasting densities within a hatchery and semi-natural environment. Farmed salmon significantly outgrew hybrid and wild salmon in all treatments. Importantly, however, the reaction norms were similar across treatments for all groups. Thus, this study was unable to find evidence that the offspring of farmed salmon have adapted more readily to higher fish densities than wild salmon as a result of domestication. It is suggested that the substantially higher growth rate of farmed salmon observed in the hatchery compared with wild individuals may not solely be caused by differences in their ability to grow in high-density hatchery scenarios.
Collapse
Affiliation(s)
- Alison C. Harvey
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gareth Juleff
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Gary R. Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | - Martin I. Taylor
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
- Biological Sciences, University of East Anglia, Norwich, UK
| | | | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2DG, UK
| | | | | | - Kevin A. Glover
- Havforskningsinstituttet, Bergen, Norway
- Sea Lice Research Centre, Universitetet i Bergen Institutt for Biologi, Bergen, Norway
| |
Collapse
|
36
|
Bicskei B, Taggart JB, Glover KA, Bron JE. Comparing the transcriptomes of embryos from domesticated and wild Atlantic salmon (Salmo salar L.) stocks and examining factors that influence heritability of gene expression. Genet Sel Evol 2016; 48:20. [PMID: 26987528 PMCID: PMC4797325 DOI: 10.1186/s12711-016-0200-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Due to selective breeding, domesticated and wild Atlantic salmon are genetically diverged, which raises concerns about farmed escapees having the potential to alter the genetic composition of wild populations and thereby disrupting local adaptation. Documenting transcriptional differences between wild and domesticated stocks under controlled conditions is one way to explore the consequences of domestication and selection. We compared the transcriptomes of wild and domesticated Atlantic salmon embryos, by using a custom 44k oligonucleotide microarray to identify perturbed gene pathways between the two stocks, and to document the inheritance patterns of differentially-expressed genes by examining gene expression in their reciprocal hybrids. RESULTS Data from 24 array interrogations were analysed: four reciprocal cross types (W♀ × W♂, D♀ × W♂; W♀ × D♂, D♀ × D♂) × six biological replicates. A common set of 31,491 features on the microarrays passed quality control, of which about 62 % were assigned a KEGG Orthology number. A total of 6037 distinct genes were identified for gene-set enrichment/pathway analysis. The most highly enriched functional groups that were perturbed between the two stocks were cellular signalling and immune system, ribosome and RNA transport, and focal adhesion and gap junction pathways, relating to cell communication and cell adhesion molecules. Most transcripts that were differentially expressed between the stocks were governed by additive gene interaction (33 to 42 %). Maternal dominance and over-dominance were also prevalent modes of inheritance, with no convincing evidence for a stock effect. CONCLUSIONS Our data indicate that even at this relatively early developmental stage, transcriptional differences exist between the two stocks and affect pathways that are relevant to wild versus domesticated environments. Many of the identified differentially perturbed pathways are involved in organogenesis, which is expected to be an active process at the eyed egg stage. The dominant effects are more largely due to the maternal line than to the origin of the stock. This finding is particularly relevant in the context of potential introgression between farmed and wild fish, since female escapees tend to have a higher spawning success rate compared to males.
Collapse
Affiliation(s)
- Beatrix Bicskei
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK.
| | - John B Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Kevin A Glover
- Institute of Marine Research, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - James E Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| |
Collapse
|
37
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
38
|
Ayllon F, Kjærner-Semb E, Furmanek T, Wennevik V, Solberg MF, Dahle G, Taranger GL, Glover KA, Almén MS, Rubin CJ, Edvardsen RB, Wargelius A. The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males. PLoS Genet 2015; 11:e1005628. [PMID: 26551894 PMCID: PMC4638356 DOI: 10.1371/journal.pgen.1005628] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022] Open
Abstract
Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation, which varies between 1-5 years. Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability, thus suggesting a polygenic or complex nature of this trait. The aim of this study was to identify associated genetic loci, genes and ultimately specific sequence variants conferring sea age at maturity in salmon. We performed a genome wide association study (GWAS) using a pool sequencing approach (20 individuals per river and phenotype) of male salmon returning to rivers as sexually mature either after one sea winter (2009) or three sea winters (2011) in six rivers in Norway. The study revealed one major selective sweep, which covered 76 significant SNPs in which 74 were found in a 370 kb region of chromosome 25. Genotyping other smolt year classes of wild and domesticated salmon confirmed this finding. Genotyping domesticated fish narrowed the haplotype region to four SNPs covering 2386 bp, containing the vgll3 gene, including two missense mutations explaining 33-36% phenotypic variation. A single locus was found to have a highly significant role in governing sea age at maturation in this species. The SNPs identified may be both used as markers to guide breeding for late maturity in salmon aquaculture and in monitoring programs of wild salmon. Interestingly, a SNP in proximity of the VGLL3 gene in humans (Homo sapiens), has previously been linked to age at puberty suggesting a conserved mechanism for timing of puberty in vertebrates.
Collapse
Affiliation(s)
| | - Erik Kjærner-Semb
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | | | | | | | - Geir Dahle
- Institute of Marine Research, Bergen, Norway
| | | | - Kevin A. Glover
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Markus Sällman Almén
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl J Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | |
Collapse
|
39
|
Castellani M, Heino M, Gilbey J, Araki H, Svåsand T, Glover KA. IBSEM: An Individual-Based Atlantic Salmon Population Model. PLoS One 2015; 10:e0138444. [PMID: 26383256 PMCID: PMC4575158 DOI: 10.1371/journal.pone.0138444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 08/31/2015] [Indexed: 11/22/2022] Open
Abstract
Ecology and genetics can influence the fate of individuals and populations in multiple ways. However, to date, few studies consider them when modelling the evolutionary trajectory of populations faced with admixture with non-local populations. For the Atlantic salmon, a model incorporating these elements is urgently needed because many populations are challenged with gene-flow from non-local and domesticated conspecifics. We developed an Individual-Based Salmon Eco-genetic Model (IBSEM) to simulate the demographic and population genetic change of an Atlantic salmon population through its entire life-cycle. Processes such as growth, mortality, and maturation are simulated through stochastic procedures, which take into account environmental variables as well as the genotype of the individuals. IBSEM is based upon detailed empirical data from salmon biology, and parameterized to reproduce the environmental conditions and the characteristics of a wild population inhabiting a Norwegian river. Simulations demonstrated that the model consistently and reliably reproduces the characteristics of the population. Moreover, in absence of farmed escapees, the modelled populations reach an evolutionary equilibrium that is similar to our definition of a ‘wild’ genotype. We assessed the sensitivity of the model in the face of assumptions made on the fitness differences between farm and wild salmon, and evaluated the role of straying as a buffering mechanism against the intrusion of farm genes into wild populations. These results demonstrate that IBSEM is able to capture the evolutionary forces shaping the life history of wild salmon and is therefore able to model the response of populations under environmental and genetic stressors.
Collapse
Affiliation(s)
- Marco Castellani
- Institute of Marine Research, P.O. Box 1870, Nordnes, N-5817, Bergen, Norway
- School of Mechanical Engineering, University of Birmingham, B15 2TT, Birmingham, United Kingdom
- * E-mail: (MC); (KG)
| | - Mikko Heino
- Institute of Marine Research, P.O. Box 1870, Nordnes, N-5817, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- International Institute for Applied Systems Analysis (IIASA), Laxenburg, Austria
| | - John Gilbey
- Marine Scotland Science, Freshwater Laboratory, Faskally, Pitlochry, PH16 5LB, Scotland, United Kingdom
| | - Hitoshi Araki
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060–8589, Japan
| | - Terje Svåsand
- Institute of Marine Research, P.O. Box 1870, Nordnes, N-5817, Bergen, Norway
| | - Kevin A. Glover
- Institute of Marine Research, P.O. Box 1870, Nordnes, N-5817, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail: (MC); (KG)
| |
Collapse
|
40
|
Glover KA, Madhun AS, Dahle G, Sørvik AGE, Wennevik V, Skaala Ø, Morton HC, Hansen TJ, Fjelldal PG. The frequency of spontaneous triploidy in farmed Atlantic salmon produced in Norway during the period 2007-2014. BMC Genet 2015; 16:37. [PMID: 25884873 PMCID: PMC4396060 DOI: 10.1186/s12863-015-0193-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 03/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spontaneous triploidy has been reported in a number of fish species, and is often linked with in vivo or in vitro ageing of eggs post ovulation. Here, we provide the first investigation into the frequency of spontaneous triploidy in farmed Atlantic salmon by analysing more than 4000 fish from 55 farms, and approximately 1000 recaptured escapees, all sampled in the period 2007-2014. In addition, we compare microsatellite genotyping against flow cytometry and red blood cell diameter in a set of 45 putatively diploid and 45 putatively triploid Atlantic salmon. RESULTS The three methods implemented for ploidy determination gave consistent results, thus validating the methods used here. Overall, 2.0% spontaneous triploids were observed in salmon sampled on farms. The frequency of spontaneous triploids varied greatly among sea cages (0-28%), but they were observed in similar frequencies among the three primary breeding companies (1.8-2.4%). Spontaneous triploids were observed in all farming regions in Norway, and in all years sampled. Spontaneous triploids were also observed among the escapees recaptured in both the marine environment and in rivers. CONCLUSIONS Spontaneous triploidy in commercially produced Atlantic salmon is likely to be a result of the practices employed by the industry. For logistical reasons, there is sometimes a pause of hours, and in some cases overnight, between killing the female broodfish, removal of her eggs, and fertilization. This gives the eggs time to age post ovulation, and increases the probability of duplication of the maternal chromosome set by inhibition of the second polar body release after normal meiosis II in the oocyte.
Collapse
Affiliation(s)
- Kevin A Glover
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Abdullah S Madhun
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Geir Dahle
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Anne G E Sørvik
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Vidar Wennevik
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Øystein Skaala
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - H Craig Morton
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Tom J Hansen
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| | - Per G Fjelldal
- Institute of Marine Research, PO Box 1870, Nordnes, 5817, Bergen, Norway.
| |
Collapse
|
41
|
Skilbrei OT, Espedal PG, Nilsen F, Garcia EP, Glover KA. Evaluation of emamectin benzoate and substance EX against salmon lice in sea-ranched Atlantic salmon smolts. Dis Aquat Organ 2015; 113:187-194. [PMID: 25850396 DOI: 10.3354/dao02832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Experimental releases of Atlantic salmon smolts treated with emamectin benzoate (EB) against salmon lice have previously been used to estimate the significance of salmon lice on the survival of migrating smolts. In recent years, the salmon louse has developed reduced sensitivity to EB, which may influence the results of such release experiments. We therefore tested the use of 2 anti-lice drugs: EB was administered to salmon smolts in high doses by intra-peritoneal injection and the prophylactic substance EX (SubEX) was administered by bathing. A third, untreated control group was also established. Salmon were challenged with copepodids of 2 strains of salmon lice (1 EB-sensitive strain and 1 with reduced EB-sensitivity) in mixed-group experimental tanks. At 31 d post-challenge, the numbers of pre-adult lice on treated fish were around 20% compared with the control fish, with minor or no differences between the 2 treatments and lice strains. Both treatments therefore appeared to give the smolts a high degree of protection against infestation of copepodids of salmon lice. However, significantly lower growth of the EB-treatment group indicates that bathing the fish in SubEX is less stressful for smolts than intra-peritoneal injection of EB.
Collapse
|
42
|
Madhun AS, Karlsbakk E, Isachsen CH, Omdal LM, Eide Sørvik AG, Skaala Ø, Barlaup BT, Glover KA. Potential disease interaction reinforced: double-virus-infected escaped farmed Atlantic salmon, Salmo salar L., recaptured in a nearby river. J Fish Dis 2015; 38:209-19. [PMID: 24467305 PMCID: PMC4303929 DOI: 10.1111/jfd.12228] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/03/2013] [Accepted: 12/05/2013] [Indexed: 05/26/2023]
Abstract
The role of escaped farmed salmon in spreading infectious agents from aquaculture to wild salmonid populations is largely unknown. This is a case study of potential disease interaction between escaped farmed and wild fish populations. In summer 2012, significant numbers of farmed Atlantic salmon were captured in the Hardangerfjord and in a local river. Genetic analyses of 59 of the escaped salmon and samples collected from six local salmon farms pointed out the most likely source farm, but two other farms had an overlapping genetic profile. The escapees were also analysed for three viruses that are prevalent in fish farming in Norway. Almost all the escaped salmon were infected with salmon alphavirus (SAV) and piscine reovirus (PRV). To use the infection profile to assist genetic methods in identifying the likely farm of origin, samples from the farms were also tested for these viruses. However, in the current case, all the three farms had an infection profile that was similar to that of the escapees. We have shown that double-virus-infected escaped salmon ascend a river close to the likely source farms, reinforcing the potential for spread of viruses to wild salmonids.
Collapse
Affiliation(s)
- A S Madhun
- Institute of Marine ResearchBergen, Norway
| | | | | | - L M Omdal
- Institute of Marine ResearchBergen, Norway
| | | | - Ø Skaala
- Institute of Marine ResearchBergen, Norway
| | | | - K A Glover
- Institute of Marine ResearchBergen, Norway
| |
Collapse
|
43
|
Besnier F, Kent M, Skern-Mauritzen R, Lien S, Malde K, Edvardsen RB, Taylor S, Ljungfeldt LER, Nilsen F, Glover KA. Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis. BMC Genomics 2014; 15:937. [PMID: 25344698 PMCID: PMC4223847 DOI: 10.1186/1471-2164-15-937] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/16/2014] [Indexed: 12/23/2022] Open
Abstract
Background The salmon louse, Lepeophtheirus salmonis, is an ectoparasite of salmonids that causes huge economic losses in salmon farming, and has also been causatively linked with declines of wild salmonid populations. Lice control on farms is reliant upon a few groups of pesticides that have all shown time-limited efficiency due to resistance development. However, to date, this example of human-induced evolution is poorly documented at the population level due to the lack of molecular tools. As such, important evolutionary and management questions, linked to the development and dispersal of pesticide resistance in this parasite, remain unanswered. Here, we introduce the first Single Nucleotide Polymorphism (SNP) array for the salmon louse, which includes 6000 markers, and present a population genomic scan using this array on 576 lice from twelve farms distributed across the North Atlantic. Results Our results support the hypothesis of a single panmictic population of lice in the Atlantic, and importantly, revealed very strong selective sweeps on linkage groups 1 and 5. These sweeps included candidate genes potentially connected to pesticide resistance. After genotyping a further 576 lice from 12 full sibling families, a genome-wide association analysis established a highly significant association between the major sweep on linkage group 5 and resistance to emamectin benzoate, the most widely used pesticide in salmonid aquaculture for more than a decade. Conclusions The analysis of conserved haplotypes across samples from the Atlantic strongly suggests that emamectin benzoate resistance developed at a single source, and rapidly spread across the Atlantic within the period 1999 when the chemical was first introduced, to 2010 when samples for the present study were obtained. These results provide unique insights into the development and spread of pesticide resistance in the marine environment, and identify a small genomic region strongly linked to emamectin benzoate resistance. Finally, these results have highly significant implications for the way pesticide resistance is considered and managed within the aquaculture industry. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-937) contains supplementary material, which is available to authorized users.
Collapse
|
44
|
Bicskei B, Bron JE, Glover KA, Taggart JB. A comparison of gene transcription profiles of domesticated and wild Atlantic salmon (Salmo salar L.) at early life stages, reared under controlled conditions. BMC Genomics 2014; 15:884. [PMID: 25301270 PMCID: PMC4210632 DOI: 10.1186/1471-2164-15-884] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 09/29/2014] [Indexed: 01/16/2023] Open
Abstract
Background Atlantic salmon have been subject to domestication for approximately ten generations, beginning in the early 1970s. This process of artificial selection will have created various genetic differences between wild and farmed stocks. Each year, hundreds of thousands of farmed fish escape into the wild. These escapees may interbreed with wild conspecifics raising concerns for both the fish-farming industry and fisheries managers. Thus, a better understanding of the interactions between domesticated and wild salmon is essential to the continued sustainability of the aquaculture industry and to the maintenance of healthy wild stocks. Results We compared the transcriptomes of a wild Norwegian Atlantic salmon population (Figgjo) and a Norwegian farmed strain (Mowi) at two life stages: yolk sac fry and post first-feeding fry. The analysis employed 44 k oligo-microarrays to analyse gene expression of 36 farmed, wild and hybrid (farmed dam x wild sire) individuals reared under identical hatchery conditions. Although some of the transcriptional differences detected overlapped between sampling points, our results highlighted the importance of studying various life stages. Compared to the wild population, the Mowi strain displayed up-regulation in mRNA translation-related and down regulation in nervous and immune system -related pathways in the sac fry, whereas up-regulation of digestive and endocrine activities, carbohydrate, energy, amino acid and lipid metabolism and down-regulation of environmental information processing and immune system pathways were evident in the feeding fry. Differentially regulated pathways that were common among life stages generally belonged to environmental information processing and immune system functional groups. In addition, we found indications of strong maternal effects, reinforcing the importance of including reciprocal hybrids in the analysis. Conclusions In agreement with previous studies we showed that domestication has caused changes in the transcriptome of wild Atlantic salmon and that many of the affected pathways are life-stage specific We highlighted the importance of reciprocal hybrids to the deconvolution of maternal/paternal effects and our data support the view that the genetic architecture of the strains studied highly influences the genes differentially expressed between wild and domesticated fish. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-884) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Beatrix Bicskei
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | | | | | | |
Collapse
|
45
|
Frenzl B, Migaud H, Fjelldal PG, Shinn AP, Taylor JF, Richards RH, Glover KA, Cockerill D, Bron JE. Triploid and diploid Atlantic salmon show similar susceptibility to infection with salmon lice Lepeophtheirus salmonis. Pest Manag Sci 2014; 70:982-988. [PMID: 23983154 DOI: 10.1002/ps.3639] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/29/2013] [Accepted: 08/23/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Sea lice infection is the most expensive disease factor for Atlantic salmon sea-cage farming. For triploid salmon to be accepted as a commercial possibility, investigation of susceptibility of triploid salmon to sea lice infection is a fundamental milestone. The susceptibility of diploid and triploid salmon to infection with Lepeophtheirus salmonis was examined in a tank trial in Scotland, a tank trial in Norway and a cage trial in Scotland. RESULTS Following a single infection challenge, results indicated a significant correlation between fish size and the number of attached sea lice. Triploid fish were larger than diploids at the smolt stage. In the tank trials, no difference was found between infection levels on diploids and triploids after a single infection challenge. The tank trial in Scotland continued with a second infection challenge of the same fish, which also showed no infection differences between ploidies. A borderline correlation between first infection and re-infection intensity was found for PIT-tagged diploid salmon examined after each challenge. No significant difference in louse infection between diploid and triploid salmon (∼2 kg) was found in the cage trial undertaken under commercial conditions. CONCLUSION This study concludes that triploid Atlantic salmon are not more susceptible to sea louse infection than diploid fish.
Collapse
Affiliation(s)
- Benedikt Frenzl
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Besnier F, Glover KA. ParallelStructure: a R package to distribute parallel runs of the population genetics program STRUCTURE on multi-core computers. PLoS One 2013; 8:e70651. [PMID: 23923012 PMCID: PMC3726640 DOI: 10.1371/journal.pone.0070651] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Accepted: 06/20/2013] [Indexed: 11/18/2022] Open
Abstract
This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to automatically distribute STRUCTURE jobs among multiple processors. It also consists of additional functions to divide analyses among combinations of populations within a single data set without the need to manually produce multiple projects, as it is currently the case in STRUCTURE. The package consists of two main functions: MPI_structure() and parallel_structure() as well as an example data file. We compared the performance in computing time for this example data on two computer architectures and showed that the use of the present functions can result in several-fold improvements in terms of computation time. ParallelStructure is freely available at https://r-forge.r-project.org/projects/parallstructure/.
Collapse
Affiliation(s)
- Francois Besnier
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway.
| | | |
Collapse
|
47
|
Glover KA, Kanda N, Haug T, Pastene LA, Øien N, Seliussen BB, Sørvik AGE, Skaug HJ. Hybrids between common and Antarctic minke whales are fertile and can back-cross. BMC Genet 2013; 14:25. [PMID: 23586609 PMCID: PMC3637290 DOI: 10.1186/1471-2156-14-25] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 04/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Minke whales are separated into two genetically distinct species: the Antarctic minke whale found in the southern hemisphere, and the common minke whale which is cosmopolitan. The common minke whale is further divided into three allopatric sub-species found in the North Pacific, southern hemisphere, and the North Atlantic. Here, we aimed to identify the genetic ancestry of a pregnant female minke whale captured in the North Atlantic in 2010, and her fetus, using data from the mtDNA control region, 11 microsatellite loci and a sex determining marker. RESULTS All statistical parameters demonstrated that the mother was a hybrid displaying maternal and paternal contribution from North Atlantic common and Antarctic minke whales respectively. Her female fetus displayed greater genetic similarity to North Atlantic common minke whales than herself, strongly suggesting that the hybrid mother had paired with a North Atlantic common minke whale. CONCLUSION This study clearly demonstrates, for the first time, that hybrids between minke whale species may be fertile, and that they can back-cross. Whether contact between these species represents a contemporary event linked with documented recent changes in the Antarctic ecosystem, or has occurred at a low frequency over many years, remains open.
Collapse
Affiliation(s)
- Kevin A Glover
- Institute of Marine Research, PO box 1870, Nordnes N-5817, Bergen, Norway.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Solberg MF, Kvamme BO, Nilsen F, Glover KA. Effects of environmental stress on mRNA expression levels of seven genes related to oxidative stress and growth in Atlantic salmon Salmo salar L. of farmed, hybrid and wild origin. BMC Res Notes 2012; 5:672. [PMID: 23217180 PMCID: PMC3598671 DOI: 10.1186/1756-0500-5-672] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 11/22/2012] [Indexed: 11/25/2022] Open
Abstract
Background Ten generations of domestication selection has caused farmed Atlantic salmon Salmo salar L. to deviate from wild salmon in a range of traits. Each year hundreds of thousands of farmed salmon escape into the wild. Thus, interbreeding between farmed escapees and wild conspecifics represents a significant threat to the genetic integrity of wild salmon populations. In a previous study we demonstrated how domestication has inadvertently selected for reduced responsiveness to stress in farmed salmon. To complement that study, we have evaluated the expression of seven stress-related genes in head kidney of salmon of farmed, hybrid and wild origin exposed to environmentally induced stress. Results In general, the crowding stressor used to induce environmental stress did not have a strong impact on mRNA expression levels of the seven genes, except for insulin-like growth factor-1 (IGF-1) that was downregulated in the stress treatment relative to the control treatment. mRNA expression levels of glutathione reductase (GR), Cu/Zn superoxide dismutase (Cu/Zn SOD), Mn superoxide dismutase (Mn SOD), glutathione peroxidase (GP) and IGF-1 were affected by genetic origin, thus expressed significantly different between the salmon of farmed, hybrid or wild origin. A positive relationship was detected between body size of wild salmon and mRNA expression level of the IGF-1 gene, in both environments. No such relationship was observed for the hybrid or farmed salmon. Conclusion Farmed salmon in this study displayed significantly elevated mRNA levels of the IGF-1 gene relative to the wild salmon, in both treatments, while hybrids displayed a non additive pattern of inheritance. As IGF-1 mRNA levels are positively correlated to growth rate, the observed positive relationship between body size and IGF-1 mRNA levels detected in the wild but neither in the farmed nor the hybrid salmon, could indicate that growth selection has increased IGF-1 levels in farmed salmon to the extent that they may not be limiting growth rate.
Collapse
Affiliation(s)
- Monica F Solberg
- Section of Population Genetics and Ecology, Institute of Marine Research, Nordnes, Bergen, Norway.
| | | | | | | |
Collapse
|
49
|
Glover KA, Quintela M, Wennevik V, Besnier F, Sørvik AGE, Skaala Ø. Three decades of farmed escapees in the wild: a spatio-temporal analysis of Atlantic salmon population genetic structure throughout Norway. PLoS One 2012; 7:e43129. [PMID: 22916215 PMCID: PMC3419752 DOI: 10.1371/journal.pone.0043129] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 07/17/2012] [Indexed: 12/05/2022] Open
Abstract
Each year, hundreds of thousands of domesticated farmed Atlantic salmon escape into the wild. In Norway, which is the world’s largest commercial producer, many native Atlantic salmon populations have experienced large numbers of escapees on the spawning grounds for the past 15–30 years. In order to study the potential genetic impact, we conducted a spatio-temporal analysis of 3049 fish from 21 populations throughout Norway, sampled in the period 1970–2010. Based upon the analysis of 22 microsatellites, individual admixture, FST and increased allelic richness revealed temporal genetic changes in six of the populations. These changes were highly significant in four of them. For example, 76% and 100% of the fish comprising the contemporary samples for the rivers Vosso and Opo were excluded from their respective historical samples at P = 0.001. Based upon several genetic parameters, including simulations, genetic drift was excluded as the primary cause of the observed genetic changes. In the remaining 15 populations, some of which had also been exposed to high numbers of escapees, clear genetic changes were not detected. Significant population genetic structuring was observed among the 21 populations in the historical (global FST = 0.038) and contemporary data sets (global FST = 0.030), although significantly reduced with time (P = 0.008). This reduction was especially distinct when looking at the six populations displaying temporal changes (global FST dropped from 0.058 to 0.039, P = 0.006). We draw two main conclusions: 1. The majority of the historical population genetic structure throughout Norway still appears to be retained, suggesting a low to modest overall success of farmed escapees in the wild; 2. Genetic introgression of farmed escapees in native salmon populations has been strongly population-dependent, and it appears to be linked with the density of the native population.
Collapse
Affiliation(s)
- Kevin A Glover
- Section of Population Genetics and Ecology, Institute of Marine Research, Bergen, Norway.
| | | | | | | | | | | |
Collapse
|
50
|
Krasnov A, Skugor S, Todorcevic M, Glover KA, Nilsen F. Gene expression in Atlantic salmon skin in response to infection with the parasitic copepod Lepeophtheirus salmonis, cortisol implant, and their combination. BMC Genomics 2012; 13:130. [PMID: 22480234 PMCID: PMC3338085 DOI: 10.1186/1471-2164-13-130] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 04/05/2012] [Indexed: 11/23/2022] Open
Abstract
Background The salmon louse is an ectoparasitic copepod that causes major economic losses in the aquaculture industry of Atlantic salmon. This host displays a high level of susceptibility to lice which can be accounted for by several factors including stress. In addition, the parasite itself acts as a potent stressor of the host, and outcomes of infection can depend on biotic and abiotic factors that stimulate production of cortisol. Consequently, examination of responses to infection with this parasite, in addition to stress hormone regulation in Atlantic salmon, is vital for better understanding of the host pathogen interaction. Results Atlantic salmon post smolts were organised into four experimental groups: lice + cortisol, lice + placebo, no lice + cortisol, no lice + placebo. Infection levels were equal in both treatments upon termination of the experiment. Gene expression changes in skin were assessed with 21 k oligonucleotide microarray and qPCR at the chalimus stage 18 days post infection at 9°C. The transcriptomic effects of hormone treatment were significantly greater than lice-infection induced changes. Cortisol stimulated expression of genes involved in metabolism of steroids and amino acids, chaperones, responses to oxidative stress and eicosanoid metabolism and suppressed genes related to antigen presentation, B and T cells, antiviral and inflammatory responses. Cortisol and lice equally down-regulated a large panel of motor proteins that can be important for wound contraction. Cortisol also suppressed multiple genes involved in wound healing, parts of which were activated by the parasite. Down-regulation of collagens and other structural proteins was in parallel with the induction of proteinases that degrade extracellular matrix (MMP9 and MMP13). Cortisol reduced expression of genes encoding proteins involved in formation of various tissue structures, regulators of cell differentiation and growth factors. Conclusions These results suggest that cortisol-induced stress does not affect the level of infection of Atlantic salmon with the parasite, however, it may retard repair of skin. The cortisol induced changes are in close concordance with the existing concept of wound healing cascade.
Collapse
Affiliation(s)
- Aleksei Krasnov
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, P,O, Box 5010, Ås N-1430 Bergin, Norway.
| | | | | | | | | |
Collapse
|