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Sbiba SE, Quintela M, Øyro J, Dahle G, Jurado-Ruzafa A, Iita K, Nikolioudakis N, Bazairi H, Chlaida M. Genetic investigation of population structure in Atlantic chub mackerel, Scomber colias Gmelin, 1789 along the West African coast. PeerJ 2024; 12:e17928. [PMID: 39247552 PMCID: PMC11380841 DOI: 10.7717/peerj.17928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 07/24/2024] [Indexed: 09/10/2024] Open
Abstract
Sustainable management of transboundary fish stocks hinges on accurate delineation of population structure. Genetic analysis offers a powerful tool to identify potential subpopulations within a seemingly homogenous stock, facilitating the development of effective, coordinated management strategies across international borders. Along the West African coast, the Atlantic chub mackerel (Scomber colias) is a commercially important and ecologically significant species, yet little is known about its genetic population structure and connectivity. Currently, the stock is managed as a single unit in West African waters despite new research suggesting morphological and adaptive differences. Here, eight microsatellite loci were genotyped on 1,169 individuals distributed across 33 sampling sites from Morocco (27.39°N) to Namibia (22.21°S). Bayesian clustering analysis depicts one homogeneous population across the studied area with null overall differentiation (F ST = 0.0001ns), which suggests panmixia and aligns with the migratory potential of this species. This finding has significant implications for the effective conservation and management of S. colias within a wide scope of its distribution across West African waters from the South of Morocco to the North-Centre of Namibia and underscores the need for increased regional cooperation in fisheries management and conservation.
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Affiliation(s)
- Salah Eddine Sbiba
- Biodiversity, Ecology and Genome Laboratory, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- Research and Development Unit on Marine Biology, National Institute of Fisheries Research, Casablanca, Morocco
| | - María Quintela
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Johanne Øyro
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Geir Dahle
- Department of Population Genetics, Institute of Marine Research, Bergen, Norway
| | - Alba Jurado-Ruzafa
- Oceanographic Centre of the Canary Islands, Spanish Institute of Oceanography (IEO-CSIC), Tenerife, Spain
| | - Kashona Iita
- National Marine Information and Research Centre (NATMIRC), Ministry of Fisheries and Marine Resources, Swakopmund, Namibia
| | | | - Hocein Bazairi
- Biodiversity, Ecology and Genome Laboratory, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco
- University of Gibraltar, Europa Point Campus, Natural Sciences and Environment Research Hub, Gibraltar, Gibraltar
| | - Malika Chlaida
- Research and Development Unit on Marine Biology, National Institute of Fisheries Research, Casablanca, Morocco
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2
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Flores AM, Christensen KA, Siah A, Koop BF. Insights from Hi-C data regarding the Pacific salmon louse (Lepeophtheirus salmonis) sex chromosomes. G3 (BETHESDA, MD.) 2024; 14:jkae087. [PMID: 38683737 PMCID: PMC11228835 DOI: 10.1093/g3journal/jkae087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/09/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W chromosome was approximately 800 kb in size, which is ∼30 times smaller than the Z chromosome (24 Mb). The W chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long noncoding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W chromosome. Two genes of interest on the W chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies.
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Affiliation(s)
- Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Ahmed Siah
- British Columbia Centre for Aquatic Health Sciences, Campbell River, BC V9W 2C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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3
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Trombetta E, Jakubiak S, Kutkova S, Lipschutz D, O’Hare A, Enright JA. A modeling study of the impact of treatment policies on the evolution of resistance in sea lice on salmon farms. PLoS One 2023; 18:e0294708. [PMID: 38019751 PMCID: PMC10686416 DOI: 10.1371/journal.pone.0294708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
Salmonid aquaculture is an important source of nutritious food with more than 2 million tonnes of fish produced each year (Food and Agriculture Organisation of the United Nations, 2019). In most salmon producing countries, sea lice represent a major barrier to the sustainability of salmonid aquaculture. This issue is exacerbated by widespread resistance to chemical treatments on both sides of the Atlantic. Regulation for sea lice management mostly involves reporting lice counts and treatment thresholds, which depending on interpretation may encourage preemptive treatments. We have developed a stochastic simulation model of sea lice infestation including the lice life-cycle, genetic resistance to treatment, a wildlife reservoir, salmon growth and stocking practices in the context of infestation, and coordination of treatment between farms. Farms report infestation levels to a central organisation, and may then cooperate or not when coordinated treatment is triggered. Treatment practice then impacts the level of resistance in the surrounding sea lice population. Our simulation finds that treatment drives selection for resistance and coordination between managers is key. We also find that position in the hydrologically-derived network of farms can impact individual farm infestation levels and the topology of this network can impact overall infestation and resistance. We show how coordination and triggering of treatment alongside varying hydrological topology of farm connections affects the evolution of lice resistance, and thus optimise salmon quality within socio-economic and environmental constraints. Network topology drives infestation levels in cages, treatments, and hence treatment-driven resistance. Thus farmer behaviour may be highly dependent on hydrologically position and local level of infestation.
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Affiliation(s)
- Enrico Trombetta
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Sara Jakubiak
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Sara Kutkova
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
| | - Debby Lipschutz
- Usher Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Anthony O’Hare
- Computing Science and Mathematics, University of Stirling, Stirling, United Kingdom
| | - Jessica A. Enright
- School of Computing Science, University of Glasgow, Glasgow, United Kingdom
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4
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Rutle KH, Skern‐Mauritzen R, Nilsen F, Mateos‐Rivera A, Eide AGS, Jansson E, Quintela M, Besnier F, Allyon F, Fjørtoft HB, Glover KA. Aquaculture-driven evolution of the salmon louse mtDNA genome. Evol Appl 2023; 16:1328-1344. [PMID: 37492153 PMCID: PMC10363823 DOI: 10.1111/eva.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
Resistance toward the antiparasitic pyrethroid, deltamethrin, is reported in the Atlantic salmon louse (Lepeophtheirus salmonis salmonis), a persistent ectoparasite of farmed and wild salmonids. The resistance mechanism is linked to mitochondrial DNA (mtDNA), where genetic markers for resistance have been identified. Here, we investigated how widespread pyrethroid use in aquaculture may have influenced mtDNA variation in lice, and the dispersion of resistant haplotypes across the North Atlantic, using historical (2000-2002 "pre-resistance") and contemporary (2014-2017 "post-resistance") samples. To study this, we sequenced ATPase 6 and cytochrome b, genotyped two genetic markers for deltamethrin resistance, and genotyped microsatellites as "neutral" controls of potential population bottlenecks. Overall, we observed a modest reduction in mtDNA diversity in the period 2000-2017, but no reduction in microsatellite variation was observed. The reduction in mtDNA variation was especially distinct in two of the contemporary samples, fixed for one and two haplotypes, respectively. By contrast, all historical samples consisted of close to one mtDNA haplotype per individual. No population genetic structure was detected among the historical samples for mtDNA nor microsatellites. By contrast, significant population genetic differentiation was observed for mtDNA among some of the contemporary samples. However, the observed population genetic structure was tightly linked with the pattern of deltamethrin resistance, and we therefore conclude that it primarily reflects the transient mosaic of pyrethroid usage in time and space. Two historically undetected mtDNA haplotypes dominated in the contemporary samples, both of which were linked to deltamethrin resistance, demonstrating primarily two origins of deltamethrin resistance in the North Atlantic. Collectively, these data demonstrate that the widespread use of pyrethroids in commercial aquaculture has substantially altered the patterns of mtDNA diversity in lice across the North Atlantic, and that long-distance dispersion of resistance is rapid due to high level of genetic connectivity that is observed in this species.
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Affiliation(s)
| | | | - Frank Nilsen
- Department of Biological SciencesUniversity of BergenBergenNorway
| | | | | | | | | | | | | | - Helene Børretzen Fjørtoft
- Department of Biological SciencesUniversity of BergenBergenNorway
- Department of Biological Sciences in AalesundNorwegian University of Science and TechnologyAalesundNorway
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5
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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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6
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Joshi J, Flores AM, Christensen KA, Johnson H, Siah A, Koop BF. An update of the salmon louse (Lepeophtheirus salmonis) reference genome assembly. G3 (BETHESDA, MD.) 2022; 12:jkac087. [PMID: 35404448 PMCID: PMC9157166 DOI: 10.1093/g3journal/jkac087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/04/2022] [Indexed: 11/21/2022]
Abstract
Salmon lice have plagued the salmon farming industry and have negatively impacted salmon populations in the wild. In response, researchers have generated high density genetic maps, genome assemblies, transcriptomes, and whole-genome resequencing data to better understand this parasite. In this study, we used long-read sequencing technology to update the previous genome assemblies of Atlantic Ocean salmon lice with a more contiguous assembly and a more comprehensive gene catalog of Pacific Ocean salmon lice. We were also able to further characterize genomic features previously identified from other studies by using published resequenced genomes of 25 Atlantic and 15 Pacific salmon lice. One example was further characterizing the ZW sex chromosomes. For both the Atlantic and Pacific Ocean salmon lice subspecies, we found that the female W-chromosome is only a small fraction of the Z-chromosome and that the vast majority of the W and Z-chromosome do not contain conserved regions (i.e. pseudoautosomal regions). However, conserved orthologous protein sequences can still be identified between the W- and Z-chromosomes.
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Affiliation(s)
- Jay Joshi
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Anne-Marie Flores
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Kris A Christensen
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Hollie Johnson
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
| | - Ahmed Siah
- British Columbia Centre for Aquatic Health Sciences, Campbell River, BC V9W 2C2, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada
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7
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Wyngaard GA, Skern-Mauritzen R, Malde K, Prendergast R, Peruzzi S. The salmon louse genome may be much larger than sequencing suggests. Sci Rep 2022; 12:6616. [PMID: 35459797 PMCID: PMC9033869 DOI: 10.1038/s41598-022-10585-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/08/2022] [Indexed: 12/30/2022] Open
Abstract
The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.
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Affiliation(s)
- Grace A Wyngaard
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | | | - Ketil Malde
- Institute of Marine Research, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Stefano Peruzzi
- Department of Arctic Marine Biology, UiT-the Arctic University of Norway, Tromsø, Norway.
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8
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Guragain P, Båtnes AS, Zobolas J, Olsen Y, Bones AM, Winge P. IIb-RAD-sequencing coupled with random forest classification indicates regional population structuring and sex-specific differentiation in salmon lice ( Lepeophtheirus salmonis). Ecol Evol 2022; 12:e8809. [PMID: 35414904 PMCID: PMC8986551 DOI: 10.1002/ece3.8809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 11/29/2022] Open
Abstract
The aquaculture industry has been dealing with salmon lice problems forming serious threats to salmonid farming. Several treatment approaches have been used to control the parasite. Treatment effectiveness must be optimized, and the systematic genetic differences between subpopulations must be studied to monitor louse species and enhance targeted control measures. We have used IIb-RAD sequencing in tandem with a random forest classification algorithm to detect the regional genetic structure of the Norwegian salmon lice and identify important markers for sex differentiation of this species. We identified 19,428 single nucleotide polymorphisms (SNPs) from 95 individuals of salmon lice. These SNPs, however, were not able to distinguish the differential structure of lice populations. Using the random forest algorithm, we selected 91 SNPs important for geographical classification and 14 SNPs important for sex classification. The geographically important SNP data substantially improved the genetic understanding of the population structure and classified regional demographic clusters along the Norwegian coast. We also uncovered SNP markers that could help determine the sex of the salmon louse. A large portion of the SNPs identified to be under directional selection was also ranked highly important by random forest. According to our findings, there is a regional population structure of salmon lice associated with the geographical location along the Norwegian coastline.
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Affiliation(s)
- Prashanna Guragain
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Anna Solvang Båtnes
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - John Zobolas
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Yngvar Olsen
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Atle M. Bones
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
| | - Per Winge
- Cell, Molecular Biology and Genomics GroupDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
- Taskforce Salmon LiceDepartment of BiologyNorwegian University of Science and TechnologyTrondheimNorway
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9
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Tschesche C, Bekaert M, Humble JL, Bron JE, Sturm A. Genomic analysis of the carboxylesterase family in the salmon louse (Lepeophtheirus salmonis). Comp Biochem Physiol C Toxicol Pharmacol 2021; 248:109095. [PMID: 34098083 PMCID: PMC8387733 DOI: 10.1016/j.cbpc.2021.109095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022]
Abstract
The pyrethroid deltamethrin and the macrocyclic lactone emamectin benzoate (EMB) are used to treat infestations of farmed salmon by parasitic salmon lice, Lepeophtheirus salmonis. While the efficacy of both compounds against Atlantic populations of the parasite has decreased as a result of the evolution of resistance, the molecular mechanisms of drug resistance in L. salmonis are currently not fully understood. The functionally diverse carboxylesterases (CaE) family includes members involved in pesticide resistance phenotypes of terrestrial arthropods. The present study had the objective to characterize the CaE family in L. salmonis and assess its role in drug resistance. L. salmonis CaE homologues were identified by homology searches in the parasite's transcriptome and genome. The transcript expression of CaEs predicted to be catalytically competent was studied using quantitative reverse-transcription PCR in drug susceptible and multi-resistant L. salmonis. The above strategy led to the identification of 21 CaEs genes/pseudogenes. Phylogenetic analyses assigned 13 CaEs to clades involved in neurodevelopmental signaling and cell adhesion, while three sequences were predicted to encode secreted enzymes. Ten CaEs were identified as being potentially catalytically competent. Transcript expression of acetylcholinesterase (ace1b) was significantly increased in multi-resistant lice compared to drug-susceptible L. salmonis, with transcript abundance further increased in preadult-II females following EMB exposure. In summary, results from the present study demonstrate that L. salmonis possesses fewer CaE gene family members than most arthropods characterized so far. Drug resistance in L. salmonis was associated with overexpression of ace1b.
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Affiliation(s)
- Claudia Tschesche
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom.
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Joseph L Humble
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - James E Bron
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
| | - Armin Sturm
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, United Kingdom
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10
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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: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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.
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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.
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11
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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] [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.
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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
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12
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VanIderstine CR, Poley JD, Whyte SK, Purcell SL, Fast MD. Hydrogen peroxide treatment and its impacts on Lepeophtheirus salmonis originating from the Bay of Fundy, Canada. JOURNAL OF FISH DISEASES 2021; 44:757-769. [PMID: 33146907 DOI: 10.1111/jfd.13299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
Hydrogen peroxide (H2 O2 ) is used to treat sea lice infections of farmed salmonids in the Atlantic and Pacific Oceans and issues with resistance to this treatment, and others are a major threat to the sustainability of the industry. The objectives of this study were to determine how H2 O2 exposure affects survival and antioxidant-related gene expression in salmon lice (Lepeophtheirus salmonis) collected from the Bay of Fundy, New Brunswick. The maximum recommended dose of H2 O2 is 1,800 mg/L, while the EC50 values (with 95% CI) for the population tested were 1,486 (457, 2,515) mg/L for males and 2,126 (984, 3,268) mg/L for females. Neither temperature nor pretreatment with emamectin benzoate (EMB) impacted survival after H2 O2 exposure. RT-qPCR was performed on pre-adult sea lice exposed to H2 O2 and showed that four genes classically involved in the response to oxidative stress were unchanged between treated and control groups. Seven genes were found to be significantly upregulated in males and one in females. This is the first report on the efficacy and molecular responses of Atlantic Canada sea lice to H2 O2 treatment.
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Affiliation(s)
- Carter R VanIderstine
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Jordan D Poley
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Shona K Whyte
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Sara L Purcell
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Mark D Fast
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
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13
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Hamre LA, Oldham T, Oppedal F, Nilsen F, Glover KA. The potential for cleaner fish-driven evolution in the salmon louse Lepeophtheirus salmonis: Genetic or environmental control of pigmentation? Ecol Evol 2021; 11:7865-7878. [PMID: 34188857 PMCID: PMC8216962 DOI: 10.1002/ece3.7618] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/08/2021] [Indexed: 11/25/2022] Open
Abstract
The parasitic salmon louse represents one of the biggest challenges to environmentally sustainable salmonid aquaculture across the globe. This species also displays a high evolutionary potential, as demonstrated by its rapid development of resistance to delousing chemicals. In response, farms now use a range of non-chemical delousing methods, including cleaner fish that eat lice from salmon. Anecdotal reports suggest that in regions where cleaner fish are extensively used on farms, lice have begun to appear less pigmented and therefore putatively less visible to cleaner fish. However, it remains an open question whether these observations reflect a plastic (environmental) or adaptive (genetic) response. To investigate this, we developed a pigment scoring system and conducted complimentary experiments which collectively demonstrate that, a) louse pigmentation is strongly influenced by environmental conditions, most likely light, and b) the presence of modest but significant differences in pigmentation between two strains of lice reared under identical conditions. Based on these data, we conclude that pigmentation in the salmon louse is strongly influenced by environmental conditions, yet there are also indications of underlying genetic control. Therefore, lice could display both plastic and adaptive responses to extensive cleaner fish usage where visual appearance is likely to influence survival of lice.
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Affiliation(s)
- Lars Are Hamre
- Department of Biological SciencesSea Lice Research CentreUniversity of BergenBergenNorway
| | | | | | - Frank Nilsen
- Department of Biological SciencesSea Lice Research CentreUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
| | - Kevin Alan Glover
- Department of Biological SciencesSea Lice Research CentreUniversity of BergenBergenNorway
- Institute of Marine ResearchBergenNorway
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14
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Fjørtoft HB, Nilsen F, Besnier F, Stene A, Tveten AK, Bjørn PA, Aspehaug VT, Glover KA. Losing the 'arms race': multiresistant salmon lice are dispersed throughout the North Atlantic Ocean. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210265. [PMID: 34084551 PMCID: PMC8150044 DOI: 10.1098/rsos.210265] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/23/2021] [Indexed: 06/12/2023]
Abstract
Nothing lasts forever, including the effect of chemicals aimed to control pests in food production. As old pesticides have been compromised by emerging resistance, new ones have been introduced and turned the odds back in our favour. With time, however, some pests have developed multi-pesticide resistance, challenging our ability to control them. In salmonid aquaculture, the ectoparasitic salmon louse has developed resistance to most of the available delousing compounds. The discovery of genetic markers associated with resistance to organophosphates and pyrethroids made it possible for us to investigate simultaneous resistance to both compounds in approximately 2000 samples of salmon lice from throughout the North Atlantic in the years 2000-2016. We observed widespread and increasing multiresistance on the European side of the Atlantic, particularly in areas with intensive aquaculture. Multiresistant lice were also found on wild Atlantic salmon and sea trout, and also on farmed salmonid hosts in areas where delousing chemicals have not been used. In areas with intensive aquaculture, there are almost no lice left that are sensitive to both compounds. These results demonstrate the speed to which this parasite can develop widespread multiresistance, illustrating why the aquaculture industry has repeatedly lost the arms race with this highly problematic parasite.
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Affiliation(s)
- Helene Børretzen Fjørtoft
- Department of Biological Sciences in Aalesund, Norwegian University of Science and Technology, PO Box 1517, 6025 Aalesund, Norway
- Department of Biology, Sea Lice Research Center, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| | - Frank Nilsen
- Department of Biology, Sea Lice Research Center, University of Bergen, PO Box 7803, 5020 Bergen, Norway
| | | | - Anne Stene
- Department of Biological Sciences in Aalesund, Norwegian University of Science and Technology, PO Box 1517, 6025 Aalesund, Norway
| | - Ann-Kristin Tveten
- Department of Biological Sciences in Aalesund, Norwegian University of Science and Technology, PO Box 1517, 6025 Aalesund, Norway
| | - Pål Arne Bjørn
- Institute of Marine Research, PO Box 1870, 5817 Bergen, Norway
| | | | - Kevin Alan Glover
- Department of Biology, Sea Lice Research Center, University of Bergen, PO Box 7803, 5020 Bergen, Norway
- Institute of Marine Research, PO Box 1870, 5817 Bergen, Norway
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15
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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] [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.
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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
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16
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Mladineo I, Hrabar J, Trumbić Ž, Manousaki T, Tsakogiannis A, Taggart JB, Tsigenopoulos CS. Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish. Pathogens 2021; 10:pathogens10020100. [PMID: 33494355 PMCID: PMC7912605 DOI: 10.3390/pathogens10020100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/14/2021] [Accepted: 01/19/2021] [Indexed: 12/28/2022] Open
Abstract
Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.
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Affiliation(s)
- Ivona Mladineo
- Institute of Oceanography and Fisheries, Laboratory of Aquaculture, 21000 Split, Croatia;
- Institute of Parasitology, Biology Centre of Czech Academy of Science, 37005 Ceske Budejovice, Czech Republic
- Correspondence: or
| | - Jerko Hrabar
- Institute of Oceanography and Fisheries, Laboratory of Aquaculture, 21000 Split, Croatia;
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, 21000 Split, Croatia;
| | - Tereza Manousaki
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
| | - Alexandros Tsakogiannis
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
| | - John B. Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK;
| | - Costas S. Tsigenopoulos
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), 71003 Heraklion, Greece; (T.M.); (A.T.); (C.S.T.)
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17
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Bateman AW, Peacock SJ, Krkošek M, Lewis MA. Migratory hosts can maintain the high-dose/refuge effect in a structured host-parasite system: The case of sea lice and salmon. Evol Appl 2020; 13:2521-2535. [PMID: 33294006 PMCID: PMC7691465 DOI: 10.1111/eva.12984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 01/13/2023] Open
Abstract
Migration can reduce parasite burdens in migratory hosts, but it connects populations and can drive disease dynamics in domestic species. Farmed salmon are infested by sea louse parasites, often carried by migratory wild salmonids, resulting in a costly problem for industry and risk to wild populations when farms amplify louse numbers. Chemical treatment can control lice, but resistance has evolved in many salmon-farming regions. Resistance has, however, been slow to evolve in the north-east Pacific Ocean, where large wild-salmon populations harbour large sea louse populations. Using a mathematical model of host-macroparasite dynamics, we explored the roles of domestic, wild oceanic and connective migratory host populations in maintaining treatment susceptibility in associated sea lice. Our results show that a large wild salmon population, unexposed to direct infestation by lice from farms; high levels of on-farm treatment; and a healthy migratory host population are all critical to slowing or stopping the evolution of treatment resistance. Our results reproduce the "high-dose/refuge effect," from the agricultural literature, with the added requirement of a migratory host population to maintain treatment susceptibility. This work highlights the role that migratory hosts may play in shared wildlife/livestock disease, where evolution can occur in ecological time.
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Affiliation(s)
- Andrew W. Bateman
- Pacific Salmon FoundationVancouverBCCanada
- Salmon Coast Field StationSimoom SoundBCCanada
| | - Stephanie J. Peacock
- Salmon Coast Field StationSimoom SoundBCCanada
- Department of Biological SciencesUniversity of CalgaryCalgaryABCanada
| | - Martin Krkošek
- Salmon Coast Field StationSimoom SoundBCCanada
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Mark A. Lewis
- Department of Biological SciencesUniversity of AlbertaEdmontonABCanada
- Department of Mathematical and Statistical SciencesUniversity of AlbertaEdmontonABCanada
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18
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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] [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.
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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
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19
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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] [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.
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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
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20
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Coates A, Phillips BL, Oppedal F, Bui S, Overton K, Dempster T. Parasites under pressure: salmon lice have the capacity to adapt to depth-based preventions in aquaculture. Int J Parasitol 2020; 50:865-872. [PMID: 32652129 DOI: 10.1016/j.ijpara.2020.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 10/23/2022]
Abstract
The evolution of pesticide resistance has driven renewed interest in non-chemical pest controls in agriculture. Spatial manipulations (physical barriers and fallowing, for example) can be an effective method of prevention, but these too might impose selection and cause rapid adaptation in pests. In salmon aquaculture, various non-chemical approaches have emerged to combat parasitic salmon lice (Lepeophtheirus salmonis) - a major pest with clear signs of evolved chemical resistance. 'Depth-based' preventions, now widely implemented, reduce infestation rates by physically segregating salmon from lice in their infective copepodid stage occurring in surface waters. Copepodids distributed deeper in the water column, however, can bypass these barriers and infest farms. If swimming depth is a heritable trait, we may see rapid evolutionary shifts in response to widespread depth-based prevention. We collected lice from Norwegian salmon farms and assayed more than 11,250 of their laboratory-reared offspring across 37 families. The vertical distributions of copepodids were measured using experimental water columns pressurised to simulate conditions at 0, 5 and 10 m depths. We demonstrated that lice respond strongly to hydrostatic pressure: an increase in pressure doubled the number of lice that migrated to the top of columns. There was also a large effect of family on this response, with the percentage of lice ascending to the top of pressurised columns ranging from 17 to 79% across families. Families with a weak swimming response to pressure are expected to occur deeper in the water column and so be more likely to infest farms employing depth-based preventions. If this between-family variation reflects genetic variation, then the parasite population may have the capacity to adapt to preventative measures. Such adaptation would have important commercial and ecological implications.
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Affiliation(s)
- Andrew Coates
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, University of Melbourne, Victoria 3010, Australia; Spatial Ecology and Evolution Lab (SpEEL), School of BioSciences, University of Melbourne, Victoria 3010, Australia
| | - Ben L Phillips
- Spatial Ecology and Evolution Lab (SpEEL), School of BioSciences, University of Melbourne, Victoria 3010, Australia
| | - Frode Oppedal
- Institute of Marine Research, Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Samantha Bui
- Institute of Marine Research, Matre Aquaculture Research Station, 5984 Matredal, Norway
| | - Kathy Overton
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, University of Melbourne, Victoria 3010, Australia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, University of Melbourne, Victoria 3010, Australia.
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Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods Mol Biol 2020; 2090:87-123. [PMID: 31975165 DOI: 10.1007/978-1-0716-0199-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput genomic sequencing allows to disentangle the evolutionary forces acting in populations. Among evolutionary forces, positive selection has received a lot of attention because it is related to the adaptation of populations in their environments, both biotic and abiotic. Positive selection, also known as Darwinian selection, occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps. Such a process leaves traces in genomes that can be detected in a future time point. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular linkage disequilibrium (LD) patterns in the region. A variety of approaches can be used for detecting selective sweeps, ranging from simple implementations that compute summary statistics to more advanced statistical approaches, e.g., Bayesian approaches, maximum-likelihood-based methods, and machine learning methods. In this chapter, we discuss selective sweep detection methodologies on the basis of their capacity to analyze whole genomes or just subgenomic regions, and on the specific polymorphism patterns they exploit as selective sweep signatures. We also summarize the results of comparisons among five open-source software releases (SweeD, SweepFinder, SweepFinder2, OmegaPlus, and RAiSD) regarding sensitivity, specificity, and execution times. Furthermore, we test and discuss machine learning methods and present a thorough performance analysis. In equilibrium neutral models or mild bottlenecks, most methods are able to detect selective sweeps accurately. Methods and tools that rely on linkage disequilibrium (LD) rather than single SNPs exhibit higher true positive rates than the site frequency spectrum (SFS)-based methods under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to build the distribution of the statistic under the null hypothesis. Both LD and SFS-based approaches suffer from decreased accuracy on localizing the true target of selection in bottleneck scenarios. Furthermore, we present an extensive analysis of the effects of gene flow on selective sweep detection, a problem that has been understudied in selective sweep literature.
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Affiliation(s)
- Angelos Koropoulis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Computer Science Department, University of Crete, Crete, Heraklion, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece.
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Humble JL, Carmona-Antoñanzas G, McNair CM, Nelson DR, Bassett DI, Egholm I, Bron JE, Bekaert M, Sturm A. Genome-wide survey of cytochrome P450 genes in the salmon louse Lepeophtheirus salmonis (Krøyer, 1837). Parasit Vectors 2019; 12:563. [PMID: 31775848 PMCID: PMC6880348 DOI: 10.1186/s13071-019-3808-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 11/15/2019] [Indexed: 11/24/2022] Open
Abstract
Background The salmon louse (Lepeophtheirus salmonis) infests farmed and wild salmonid fishes, causing considerable economic damage to the salmon farming industry. Infestations of farmed salmon are controlled using a combination of non-medicinal approaches and veterinary drug treatments. While L. salmonis has developed resistance to most available salmon delousing agents, relatively little is known about the molecular mechanisms involved. Members of the cytochrome P450 (CYP) superfamily are typically monooxygenases, some of which are involved in the biosynthesis and metabolism of endogenous compounds, while others have central roles in the detoxification of xenobiotics. In terrestrial arthropods, insecticide resistance can be based on the enhanced expression of CYPs. The reported research aimed to characterise the CYP superfamily in L. salmonis and assess its potential roles in drug resistance. Methods Lepeophtheirus salmonis CYPs were identified by homology searches of the genome and transcriptome of the parasite. CYP transcript abundance in drug susceptible and multi-resistant L. salmonis was assessed by quantitative reverse transcription PCR, taking into account both constitutive expression and expression in parasites exposed to sublethal levels of salmon delousing agents, ecdysteroids and environmental chemicals. Results The above strategy led to the identification of 25 CYP genes/pseudogenes in L. salmonis, making its CYP superfamily the most compact characterised for any arthropod to date. Lepeophtheirus salmonis possesses homologues of a number of arthropod CYP genes with roles in ecdysteroid metabolism, such as the fruit fly genes disembodied, shadow, shade, spook and Cyp18a1. CYP transcript expression did not differ between one drug susceptible and one multi-resistant strain of L. salmonis. Exposure of L. salmonis to emamectin benzoate or deltamethrin caused the transcriptional upregulation of certain CYPs. In contrast, neither ecdysteroid nor benzo[a]pyrene exposure affected CYP transcription significantly. Conclusions The parasite L. salmonis is demonstrated to possess the most compact CYP superfamily characterised for any arthropod to date. The complement of CYP genes in L. salmonis includes conserved CYP genes involved in ecdysteroid biosynthesis and metabolism, as well as drug-inducible CYP genes. The present study does not provide evidence for a role of CYP genes in the decreased susceptibility of the multiresistant parasite strain studied. ![]()
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Affiliation(s)
- Joseph L Humble
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | | | - Carol M McNair
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - David R Nelson
- Department of Microbiology, University of Tennessee, Memphis, TN, 38163, USA
| | - David I Bassett
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Ingibjørg Egholm
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - James E Bron
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Michaël Bekaert
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Armin Sturm
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
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Vollset KW. Parasite induced mortality is context dependent in Atlantic salmon: insights from an individual-based model. Sci Rep 2019; 9:17377. [PMID: 31758025 PMCID: PMC6874588 DOI: 10.1038/s41598-019-53871-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/04/2019] [Indexed: 11/09/2022] Open
Abstract
An individual-based model was parameterized to explore the impact of a crustacean ectoparasite (sea louse, Lepeophtheirus salmonis & Caligus spp.) on migrating Atlantic salmon smolt. The model explores how environmental and intrinsic factors can modulate the effect of sea lice on survival, growth and maturation of Atlantic salmon at sea. Relative to other effects, the parasite infestation pressure from fish farms and the encounter process emerge as the most important parameters. Although small variations in parasite-induced mortality may be masked by variable environmental effects, episodes of high infestation pressure from fish farms should be observable in wild populations of Atlantic salmon if laboratory studies accurately reflect the physiological effects of sea lice. Increases in temperature in the model negatively influenced fish survival by affecting the development time of the parasite at a rate that was not compensated for by the growth of the host. Discharge from rivers was parameterized to increase migration speed and influenced parasite induced mortality by decreasing time spent in areas with increased infestation pressure. Initial size and growth of the host was inversely related to the impact of the parasite because of size-dependent parasite-induced mortality in the early phase of migration. Overall, the model illustrates how environmental factors modulate effects on the host population by impacting either the parasite load or the relative effect of the parasite. The results suggest that linking population-level effects to parasite infestation pressure across climatic and environmental gradients may be challenging without correctly accounting for these effects.
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Affiliation(s)
- Knut Wiik Vollset
- NORCE Norwegian Research Centre, Laboratory for Freshwater ecology and Inland fisheries, Nygårdsporten 112, 5006, Bergen, Norway.
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25
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Samsing F, Johnsen I, Treml EA, Dempster T. Identifying 'firebreaks' to fragment dispersal networks of a marine parasite. Int J Parasitol 2019; 49:277-286. [PMID: 30660636 DOI: 10.1016/j.ijpara.2018.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/02/2018] [Accepted: 11/03/2018] [Indexed: 10/27/2022]
Abstract
Marine ecosystems are beset by disease outbreaks, and efficient strategies to control dispersal of pathogens are scarce. We tested whether introducing no-farming areas or 'firebreaks' could disconnect dispersal networks of a parasitic disease affecting the world's largest marine fish farming industry (∼1000 farms). Larval salmon lice (Lepeophtheirus salmonis) are released from and transported among salmon farms by ocean currents, creating inter-farm networks of louse dispersal. We used a state-of-the-art biophysical model to predict louse movement along the Norwegian coastline and network analysis to identify firebreaks to dispersal. At least one firebreak that fragmented the network into two large unconnected groups of farms was identified for all seasons. During spring, when wild salmon migrate out into the ocean, and louse levels per fish at farms must be minimised, two effective firebreaks were created by removing 13 and 21 farms (1.3% and 2.2% of all farms in the system) at ∼61°N and 67°N, respectively. We have demonstrated that dispersal models coupled with network analysis can identify no-farming zones that fragment dispersal networks. Reduced dispersal pathways should lower infection pressure at farms, slow the evolution of resistance to parasite control measures, and alleviate infection pressure on wild salmon populations.
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Affiliation(s)
- Francisca Samsing
- School of BioSciences, University of Melbourne, 3010 Victoria, Australia; CSIRO, Castray Esplanade, Hobart 7004 TAS, Australia.
| | - Ingrid Johnsen
- Institute of Marine Research, P.O. Box 1870 Nordnes, N-5817 Bergen, Norway
| | - Eric A Treml
- School of BioSciences, University of Melbourne, 3010 Victoria, Australia; School of Life and Environmental Sciences, Deakin University, Victoria 3220, Australia
| | - Tim Dempster
- School of BioSciences, University of Melbourne, 3010 Victoria, Australia
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26
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Danzmann RG, Norman JD, Rondeau EB, Messmer AM, Kent MP, Lien S, Igboeli O, Fast MD, Koop BF. A genetic linkage map for the salmon louse (Lepeophtheirus salmonis): evidence for high male:female and inter-familial recombination rate differences. Mol Genet Genomics 2018; 294:343-363. [PMID: 30460550 DOI: 10.1007/s00438-018-1513-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 10/15/2018] [Indexed: 01/28/2023]
Abstract
A salmon louse (Lepeophtheirus salmonis salmonis) genetic linkage map was constructed to serve as a genomic resource for future investigations into the biology of this important marine parasitic copepod species, and to provide insights into the inheritance patterns of genetic markers in this species. SNP genotyping of 8 families confirmed the presence of 15 linkage groups based upon the assignment of 93,773 markers. Progeny sample size weight adjusted map sizes in males (with the exception of SL12 and SL15) ranged in size from 96.50 cM (SL11) to 134.61 cM (SL06), and total combined map steps or bins ranged from 143 (SL09) to 203 (SL13). The SL12 male map was the smallest linkage group with a weight-averaged size of 3.05 cM with 6 recombination bins. Male:female specific recombination rate differences are 10.49:1 and represent one of the largest reported sex-specific differences for any animal species. Recombination ratio differences (M:F) ranged from 1.0 (SL12) to 29:1 (SL15). The number of markers exhibiting normal Mendelian segregation within the sex linkage group SL15 was extremely low (N = 80) in comparison to other linkage groups genotyped [range: 1459 (SL12)-10206 markers (SL05)]. Re-evaluation of Mendelian inheritance patterns of markers unassigned to any mapping parent according to hemizygous segregation patterns (models presented) identified matches for many of these markers to hemizygous patterns. The greatest proportion of these markers assigned to SL15 (N increased to 574). Inclusion of the hemizygous markers revised SL15 sex-specific recombination rate differences to 28:1. Recombination hot- and coldspots were identified across all linkage groups with all linkage groups possessing multiple peaks. Nine of 13 linkage groups evaluated possessed adjacent domains with hot-coldspot transitional zones. The most common pattern was for one end of the linkage to show elevated recombination in addition to internal regions. For SL01 and SL06, however, a terminal region with high recombination was not evident while a central domain possessing extremely high-recombination levels was present. High levels of recombination were weakly coupled to higher levels of SNP variation within domains, but this association was very strong for the central domains of SL01 and SL06. From the pooled paternal half-sib lots (several virgin females placed with 1 male), only 1 or two surviving family lots were obtained. Surviving families possessed parents where both the male and female possessed either inherently low or high recombination rates. This study provides insight into the organization of the sea louse genome, and describes large differences in recombination rate that exist among individuals of the same sex, and between the sexes. These differences in recombination rate may be coupled to the capabilities of this species to adapt to environmental and pharmaceutical treatments, given that family survivorship appears to be enhanced when parents have similar recombination levels.
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Affiliation(s)
- Roy G Danzmann
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,The Hospital for Sick Children, 686 Bay St., Toronto, ON, M5G 0A4, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Amber M Messmer
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
| | - Matthew P Kent
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics (CIGENE), Norwegian University of Life Sciences, 1432, As, Norway
| | - Okechukwu Igboeli
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Mark D Fast
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, PEI, C1A 4P3, Canada
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, 3800 Finnerty Road, Victoria, BC, V8W 3N5, Canada
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Øvergård AC, Hamre LA, Grotmol S, Nilsen F. Salmon louse rhabdoviruses: Impact on louse development and transcription of selected Atlantic salmon immune genes. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 86:86-95. [PMID: 29747070 DOI: 10.1016/j.dci.2018.04.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Recently, it has been shown that the salmon louse (Lepeophtheirus salmonis) is commonly infected by one or two vertically transmitted Lepeophtheirus salmonis rhabdoviruses (LsRVs). As shown in the present study, the viruses have limited effect on louse survival, developmental rate and fecundity. Since the LsRVs were confirmed to be present in the louse salivary glands, the salmon cutaneous immune response towards LsRV positive and negative lice was analyzed. In general, L. salmonis increased the expression of IL1β, IL8 and IL4/13A at the attachment site, in addition to the non-specific cytotoxic cell receptor protein 1 (NCCRP-1). Interestingly, LsRV free lice induced a higher skin expression of IL1β, IL8, and NCCRP-1 than the LsRV infected lice. The inflammatory response is important for louse clearance, and the present results suggest that the LsRVs can be beneficial for the louse by dampening inflammation. Further research is, however; needed to ascertain whether this is a direct modulatory effect of secreted virions, or if virus replication is altering the level of louse salivary gland proteins.
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Affiliation(s)
- Aina-Cathrine Øvergård
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Lars Are Hamre
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Sindre Grotmol
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
| | - Frank Nilsen
- SLRC - Sea Lice Research Centre, Department of Biological Sciences, University of Bergen, Thormøhlensgt. 55, Pb. 7803, 5020, Bergen, Norway.
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28
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Fields DM, Skiftesvik AB, Browman HI. Behavioural responses of infective-stage copepodids of the salmon louse (Lepeophtheirus salmonis, Copepoda:Caligidae) to host-related sensory cues. JOURNAL OF FISH DISEASES 2018; 41:875-884. [PMID: 28921570 DOI: 10.1111/jfd.12690] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 05/04/2023]
Abstract
The salmon louse (Lepeophtheirus salmonis [Krøyer]) is an ectoparasitic copepod that causes disease in farmed Atlantic salmon (Salmo salar) and may play a role in the decline of some wild salmonid populations. Controlling lice infestations is a major cost for the salmon industry; this has stimulated the pursuit of alternative approaches to controlling them. One such approach involves determining, and then disrupting, the sensory cues used by the parasite to find its host. In this context, we examined the behavioural responses of lice copepodids to light flicker-simulating light reflecting from the sides of the salmon host and/or the shadows cast by fish passing overhead-and water-soluble chemicals released from the skin of the salmon. From these observations, we estimate that visual cues such as those presented here would operate at relatively long range (metres to tens of metres). A diffuse host-related olfactory cue stimulated swimming, however, it remains unclear whether olfactory cues provide directional information. The observations presented herein could be used to disrupt the link between the parasite and host fish, using a large number of traps deployed at a distance from a salmon farm, for example, thereby reducing sea lice infestation pressure.
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Affiliation(s)
- D M Fields
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - A B Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
| | - H I Browman
- Institute of Marine Research, Austevoll Research Station, Storebø, Norway
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29
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Jackson D, Moberg O, Stenevik Djupevåg EM, Kane F, Hareide H. The drivers of sea lice management policies and how best to integrate them into a risk management strategy: An ecosystem approach to sea lice management. JOURNAL OF FISH DISEASES 2018; 41:927-933. [PMID: 29027681 DOI: 10.1111/jfd.12705] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/20/2017] [Accepted: 07/23/2017] [Indexed: 06/07/2023]
Abstract
The control of sea lice infestations on cultivated Atlantic salmon is a major issue in many regions of the world. The numerous drivers which shape the priorities and objectives of the control strategies vary for different regions/jurisdictions. These range from the animal welfare and economic priorities of the producers, to the mitigation of any potential impacts on wild stocks. Veterinary ethics, environmental impacts of therapeutants, and impacts for organic certification of the produce are, amongst others, additional sets of factors which should be considered. Current best practice in both EU and international environmental law advocates a holistic ecosystem approach to assessment of impacts and risks. The issues of biosecurity and ethics, including the impacts on the stocks of species used as cleaner fish, are areas for inclusion in such a holistic ecosystem assessment. The Drivers, Pressures, State, Impacts, Responses (DPSIR) process is examined as a decision-making framework and potential applications to sea lice management are outlined. It is argued that this is required to underpin any integrated sea lice management (ISLM) strategy to balance pressures and outcomes and ensure a holistic approach to managing the issue of sea lice infestations on farmed stock on a medium to long-term basis.
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Affiliation(s)
| | - O Moberg
- Fisheries Directorate, Oslo, Norway
| | | | - F Kane
- Marine Institute, Galway, Ireland
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Madhun AS, Isachsen CH, Omdal LM, Einen ACB, Maehle S, Wennevik V, Niemelä E, Svåsand T, Karlsbakk E. Prevalence of piscine orthoreovirus and salmonid alphavirus in sea-caught returning adult Atlantic salmon (Salmo salar L.) in northern Norway. JOURNAL OF FISH DISEASES 2018; 41:797-803. [PMID: 29388217 DOI: 10.1111/jfd.12785] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/29/2017] [Accepted: 12/29/2017] [Indexed: 06/07/2023]
Abstract
Heart and skeletal muscle inflammation (HSMI) caused by piscine orthoreovirus (PRV) and pancreas disease (PD) caused by salmonid alphavirus (SAV) are among the most prevalent viral diseases of Atlantic salmon farmed in Norway. There are limited data about the impact of disease in farmed salmon on wild salmon populations. Therefore, the prevalence of PRV and SAV in returning salmon caught in six sea sites was determined using real-time RT-PCR analyses. Of 419 salmon tested, 15.8% tested positive for PRV, while none were positive for SAV. However, scale reading revealed that 10% of the salmon had escaped from farms. The prevalence of PRV in wild salmon (8%) was significantly lower than in farm escapees (86%), and increased with fish length (proxy for age). Sequencing of the S1 gene of PRV from 39 infected fish revealed a mix of genotypes. The observed increase in PRV prevalence with fish age and the lack of phylogeographic structure of the virus could be explained by virus transmission in the feeding areas. Our results highlight the need for studies about the prevalence of PRV and other pathogens in Atlantic salmon in its oceanic phase.
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Affiliation(s)
- A S Madhun
- Institute of Marine Research, Bergen, Norway
| | | | - L M Omdal
- Institute of Marine Research, Bergen, Norway
| | - A C B Einen
- Institute of Marine Research, Bergen, Norway
| | - S Maehle
- Institute of Marine Research, Bergen, Norway
| | - V Wennevik
- Institute of Marine Research, Bergen, Norway
| | - E Niemelä
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - T Svåsand
- Institute of Marine Research, Bergen, Norway
| | - E Karlsbakk
- Institute of Marine Research, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
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31
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Messmer AM, Leong JS, Rondeau EB, Mueller A, Despins CA, Minkley DR, Kent MP, Lien S, Boyce B, Morrison D, Fast MD, Norman JD, Danzmann RG, Koop BF. A 200K SNP chip reveals a novel Pacific salmon louse genotype linked to differential efficacy of emamectin benzoate. Mar Genomics 2018; 40:45-57. [PMID: 29673959 DOI: 10.1016/j.margen.2018.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 02/28/2018] [Accepted: 03/27/2018] [Indexed: 11/28/2022]
Abstract
Antiparasitic drugs such as emamectin benzoate (EMB) are relied upon to reduce the parasite load, particularly of the sea louse Lepeophtheirus salmonis, on farmed salmon. The decline in EMB treatment efficacy for this purpose is an important issue for salmon producers around the world, and particularly for those in the Atlantic Ocean where widespread EMB tolerance in sea lice is recognized as a significant problem. Salmon farms in the Northeast Pacific Ocean have not historically experienced the same issues with treatment efficacy, possibly due to the relatively large population of endemic salmonid hosts that serve to both redistribute surviving lice and dilute populations potentially under selection by introducing naïve lice to farms. Frequent migration of lice among farmed and wild hosts should limit the effect of farm-specific selection pressures on changes to the overall allele frequencies of sea lice in the Pacific Ocean. A previous study using microsatellites examined L. salmonis oncorhynchi from 10 Pacific locations from wild and farmed hosts and found no population structure. Recently however, a farm population of sea lice was detected where EMB bioassay exposure tolerance was abnormally elevated. In response, we have developed a Pacific louse draft genome that complements the previously-released Atlantic louse sequence. These genomes were combined with whole-genome re-sequencing data to design a highly sensitive 201,279 marker SNP array applicable for both subspecies (90,827 validated Pacific loci; 153,569 validated Atlantic loci). Notably, kmer spectrum analysis of the re-sequenced samples indicated that Pacific lice exhibit a large within-individual heterozygosity rate (average of 1 in every 72 bases) that is markedly higher than that of Atlantic individuals (1 in every 173 bases). The SNP chip was used to produce a high-density map for Atlantic sea louse linkage group 5 that was previously shown to be associated with EMB tolerance in Atlantic lice. Additionally, 478 Pacific louse samples from farmed and wild hosts obtained between 2005 and 2014 were also genotyped on the array. Clustering analysis allowed us to detect the apparent emergence of an otherwise rare genotype at a high frequency among the lice collected from two farms in 2013 that had reported elevated EMB tolerance. This genotype was not observed in louse samples collected from the same farm in 2010, nor in any lice sampled from other locations prior to 2013. However, this genotype was detected at low frequencies in louse samples from farms in two locations reporting elevated EMB tolerance in 2014. These results suggest that a rare genotype present in Pacific lice may be locally expanded in farms after EMB treatment. Supporting this hypothesis, 437 SNPs associated with this genotype were found to be in a region of linkage group 5 that overlaps the region associated with EMB resistance in Atlantic lice. Finally, five of the top diagnostic SNPs within this region were used to screen lice that had been subjected to an EMB survival assay, revealing a significant association between these SNPs and EMB treatment outcome. To our knowledge this work is the first report to identify a genetic link to altered EMB efficacy in L. salmonis in the Pacific Ocean.
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Affiliation(s)
- Amber M Messmer
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Eric B Rondeau
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Anita Mueller
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Cody A Despins
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - David R Minkley
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada.
| | - Matthew P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Brad Boyce
- Marine Harvest Canada, Campbell River, BC, Canada.
| | | | - Mark D Fast
- Department of Pathology and Microbiology, University of Prince Edward Island, Charlottetown, PEI C1A 4P3, Canada.
| | - Joseph D Norman
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; Present address: The Hospital for Sick Children, 686 Bay St., Toronto, ON M5G 0A4, Canada.
| | - Roy G Danzmann
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada.
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria V8W 2Y2, BC, Canada; Centre for Biomedical Research, University of Victoria, Victoria, BC V8W 3N5, Canada.
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32
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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33
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Bui S, Dalvin S, Dempster T, Skulstad OF, Edvardsen RB, Wargelius A, Oppedal F. Susceptibility, behaviour, and retention of the parasitic salmon louse (Lepeophtheirus salmonis) differ with Atlantic salmon population origin. JOURNAL OF FISH DISEASES 2018; 41:431-442. [PMID: 28921589 DOI: 10.1111/jfd.12707] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/18/2017] [Accepted: 07/25/2017] [Indexed: 06/07/2023]
Abstract
Atlantic salmon populations across the world have diverse ecological and evolutionary histories, from wild anadromous or landlocked, to domestication and genetic modification. The natural host behaviours confer protection from infestation by ectoparasitic salmon lice Lepeophtheirus salmonis, yet whether genetic origin results in different behaviours and thus susceptibility to infestation is unknown. In common garden experiments, we tested antiparasite behaviours, susceptibility and retention of salmon lice in wild anadromous, wild landlocked, domesticated and genetically modified domesticated strains. Within domesticated strains, we tested two infestation histories (previously infested and naïve) and a new phenotype (albino colouring). Farmed stocks initially acquired 24%-44% higher levels of parasite density than the wild and landlocked strains. Burst swimming and displacement behaviours were higher in the domesticated groups, and jumping was more prevalent in the domesticated strains. At 34 days post-infestation, domesticated strains and the wild anadromous strain did not differ significantly from each other; however, landlocked salmon had increased infestation levels considerably. Domesticated strains lost ~20% (±9.9%-16.5%; 95% CI) of their initial parasite load, while parasite load increased by 5.5% (±30.1%) for wild salmon and 20.1% (±28.5%) in landlocked salmon. This study provides early evidence for diverged host-parasite interactions associated with domestication in this system.
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Affiliation(s)
- S Bui
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, University of Melbourne, Parkville, Vic, Australia
- Institute of Marine Research, Bergen, Norway
| | - S Dalvin
- Institute of Marine Research, Bergen, Norway
| | - T Dempster
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), School of BioSciences, University of Melbourne, Parkville, Vic, Australia
- Institute of Marine Research, Bergen, Norway
| | | | | | - A Wargelius
- Institute of Marine Research, Bergen, Norway
| | - F Oppedal
- Institute of Marine Research, Bergen, Norway
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Faust E, Halvorsen KT, Andersen P, Knutsen H, André C. Cleaner fish escape salmon farms and hybridize with local wrasse populations. ROYAL SOCIETY OPEN SCIENCE 2018; 5:171752. [PMID: 29657779 PMCID: PMC5882703 DOI: 10.1098/rsos.171752] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 06/08/2023]
Abstract
The genetic impact of farmed fish escaping aquaculture is a highly debated issue. However, non-target species, such as cleaner fish used to remove sea lice from farmed fish, are rarely considered. Here, we report that wild corkwing wrasse (Symphodus melops), which are transported long distances to be used as cleaner fish in salmon farms, escape and hybridize with local populations. Recently, increasing numbers of corkwing wrasse have been reported in Flatanger in Norway, north of its described distribution range, an area heavily relying on the import of cleaner fish from Skagerrak. Using genetic markers identified with 2bRAD sequencing, we show that, although the Flatanger population largely is a result of a northward range expansion, there is also evidence of considerable gene flow from southern populations in Skagerrak and Kattegat. Of the 40 corkwing wrasses sampled in Flatanger, we discovered two individuals with clear southern genotypes, one first-generation hybrid, and 12 potential second-generation hybrids. In summary, we provide evidence that corkwing wrasse escape from fish farms and hybridize with local populations at the leading edge of an ongoing range expansion. Although the magnitude and significance of escapees warrant further investigation, these results should be taken into consideration in the use of translocated cleaner fish.
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Affiliation(s)
- Ellika Faust
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296 Strömstad, Sweden
| | | | - Per Andersen
- Marine senior advisor Nord-Trøndelag, 7770 Flatanger, Norway
| | - Halvor Knutsen
- Institute of Marine Research, Flødevigen, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
- Centre for Coastal Research, University of Agder, Kristiansand, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, 45296 Strömstad, Sweden
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35
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Jacobs A, De Noia M, Praebel K, Kanstad-Hanssen Ø, Paterno M, Jackson D, McGinnity P, Sturm A, Elmer KR, Llewellyn MS. Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach. Sci Rep 2018; 8:1203. [PMID: 29352185 PMCID: PMC5775277 DOI: 10.1038/s41598-018-19323-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/17/2017] [Indexed: 12/13/2022] Open
Abstract
Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.
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Affiliation(s)
- A Jacobs
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M De Noia
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - K Praebel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - M Paterno
- Department of Biology, University of Padova, Padova, Italy
| | | | - P McGinnity
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - A Sturm
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - K R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - M S Llewellyn
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK.
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36
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Ljungfeldt LER, Quintela M, Besnier F, Nilsen F, Glover KA. A pedigree-based experiment reveals variation in salinity and thermal tolerance in the salmon louse, Lepeophtheirus salmonis. Evol Appl 2017; 10:1007-1019. [PMID: 29151856 PMCID: PMC5680634 DOI: 10.1111/eva.12505] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 06/05/2017] [Indexed: 11/29/2022] Open
Abstract
The salmon louse is a highly abundant ectoparasitic copepod of salmonids in the North Pacific and Atlantic. Widespread and rapid development of resistance to chemical agents used to delouse salmonids on marine farms is now threatening the continued development of the aquaculture industry and have served as a potent catalyst for the development of alternative pest management strategies. These include freshwater and warm-water treatments to which the louse is sensitive. However, given the well-documented evolutionary capacity of this species, the risk of developing tolerance towards these environmental treatments cannot be dismissed. Two common-garden experiments were performed using full-sibling families of lice identified by DNA parentage testing to investigate whether one of the fundamental premises for evolution, in this context genetic variation in the capacity of coping with fresh or warm water, exists within this species. Significant differences in survival were observed among families in both experiments, although for the salinity experiment, it was not possible to unequivocally disentangle background mortality from treatment-induced mortality. Thus, our data demonstrate genetic variation in tolerance of warm water and are suggestive of genetic variation in salinity tolerance. We conclude that extensive use of these environmental-based treatments to delouse salmonids on commercial farms may drive lice towards increased tolerance.
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Affiliation(s)
| | | | | | - Frank Nilsen
- Sea Lice Research CentreDepartment of BiologyUniversity of BergenBergenNorway
| | - Kevin Alan Glover
- Institute of Marine ResearchBergenNorway
- Sea Lice Research CentreDepartment of BiologyUniversity of BergenBergenNorway
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37
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The Phe362Tyr mutation conveying resistance to organophosphates occurs in high frequencies in salmon lice collected from wild salmon and trout. Sci Rep 2017; 7:14258. [PMID: 29079820 PMCID: PMC5660183 DOI: 10.1038/s41598-017-14681-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/13/2017] [Indexed: 12/02/2022] Open
Abstract
The parasitic salmon louse, and its resistance to chemical delousing agents, represents one of the largest challenges to the salmon aquaculture industry. We genotyped lice sampled from wild salmon and sea trout throughout Norway with the recently identified Phe362Tyr mutation that conveys resistance to organophosphates. These results were compared to data from lice sampled on farmed salmon in the same regions. The resistant (R) allele was observed in salmon lice from wild salmon and sea trout throughout Norway, although its frequency was highest in farming-intense regions. In most regions, the frequency of the R allele was higher in lice collected from wild sea trout than wild Atlantic salmon, and in all regions, the frequency of the R allele was similar in lice collected from wild sea trout and farmed Atlantic salmon. The R allele is only selected for in fish-farms where organophosphates are used for delousing. Therefore, our results suggest extensive exchange of lice between farmed and wild hosts, and indicate that in farming-dense regions in Norway, aquaculture represents a major driver of salmon louse population structure. Finally, these data suggest that the wild hosts within the regions studied will not delay the spread of resistance when organophosphates are used.
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38
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Øvergård AC, Hamre LA, Kongshaug H, Nilsen F. RNAi-mediated treatment of two vertically transmitted rhabdovirus infecting the salmon louse (Lepeophtheirus salmonis). Sci Rep 2017; 7:14030. [PMID: 29070796 PMCID: PMC5656668 DOI: 10.1038/s41598-017-14282-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/06/2017] [Indexed: 12/21/2022] Open
Abstract
Rhabdoviruses are a family of enveloped negative-sense single-stranded RNA viruses infecting a variety of hosts. Recently, two vertically transmitted salmon louse (Lepeophtheirus salmonis) rhabdoviruses (LsRV) have been identified. The prevalence of these viruses was measured along the Norwegian coast and found to be close to 100%, and with the present lack of suitable cell lines to propagate these viruses, it is challenging to obtain material to study their host impact and infection routes. Thus, virus free lice strains were established from virus infected lice carrying one or both LsRVs by treating them with N protein dsRNA twice during development. The viral replication of the N protein was specifically down-regulated following introduction of virus-specific dsRNA, and virus-free lice strains were maintained for several generations. A preliminary study on infection routes suggested that the LsRV-No9 is maternally transmitted, and that the virus transmits from males to females horizontally. The ability to produce virus free strains allows for further studies on transmission modes and how these viruses influences on the L.salmonis interaction with its salmonid host. Moreover, this study provides a general fundament for future studies on how vertically transmitted rhabdoviruses influence the biology of their arthropod hosts.
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Affiliation(s)
- Aina-Cathrine Øvergård
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway.
| | - Lars Are Hamre
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
| | - Heidi Kongshaug
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
| | - Frank Nilsen
- SLCR-Sea Lice Research Centre, Department of Biology, University of Bergen, Thormøhlensgt. 55, Pb. 7803, NO-5020, Bergen, Norway
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39
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The mechanism (Phe362Tyr mutation) behind resistance in Lepeophtheirus salmonis pre-dates organophosphate use in salmon farming. Sci Rep 2017; 7:12349. [PMID: 28955050 PMCID: PMC5617835 DOI: 10.1038/s41598-017-12384-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/07/2017] [Indexed: 11/29/2022] Open
Abstract
The salmon louse is an ectoparasitic copepod of salmonids in the marine environment, and represents a global challenge to salmon aquaculture. A major issue is the reliance of the industry on a limited number of chemicals to delouse salmonids on farms, and the high levels of resistance that lice have developed to all of these agents. However, for most of these chemicals, resistance and dispersal mechanisms are unknown. We recently demonstrated that the Phe362Tyr mutation is the primary cause of organophosphate resistance in lice collected on Norwegian farms. In the present study, we genotyped >2000 lice collected throughout the entire North Atlantic in the period 1998–2016, using Phe362Tyr and nine tightly linked SNPs. Our results showed that the Phe362Tyr mutation is strongly linked to lice survival following chemical treatment on farms located throughout the North Atlantic, demonstrating for the first time, that this mutation represents the primary mechanism for organophosphate resistance in salmon lice across the North Atlantic. Additionally, we observed multiple and diverse high frequency haplotypes linked with the allele conveying resistance to organophosphate. We, therefore, conclude that Phe362Tyr is not a de novo mutation, but probably existed in salmon lice before the introduction of organophosphates in commercial aquaculture.
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40
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Mennerat A, Ugelvik MS, Håkonsrud Jensen C, Skorping A. Invest more and die faster: The life history of a parasite on intensive farms. Evol Appl 2017; 10:890-896. [PMID: 29151880 PMCID: PMC5680424 DOI: 10.1111/eva.12488] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Organisms are expected to respond to alterations in their survival by evolutionary changes in their life history traits. As agriculture and aquaculture have become increasingly intensive in the past decades, there has been growing interest in their evolutionary effects on the life histories of agri‐ and aquacultural pests, parasites, and pathogens. In this study, we used salmon lice (Lepeophtheirus salmonis) to explore how modern farming might have affected life history evolution in parasites. We infected salmon hosts with lice from either farmed or unfarmed locations, and monitored life history traits of those parasites in laboratory conditions. Our results show that compared to salmon lice from areas unaffected by salmon farming, those from farmed areas produced more eggs in their first clutch, and less eggs later on; they achieved higher infestation intensities in early adulthood, but suffered higher adult mortality. These results suggest that salmon lice on farms may have been selected for increased investment in early reproduction, at the expense of later fecundity and survival. This call for further empirical studies of the extent to which farming practices may alter the virulence of agricultural parasites.
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Affiliation(s)
- Adèle Mennerat
- Department of Biology University of Bergen Bergen Norway.,Ecologie et Dynamique des Systèmes Anthropisés (FRE 3498) CNRS/Université de Picardie Jules Verne Amiens France
| | | | | | - Arne Skorping
- Department of Biology University of Bergen Bergen Norway
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41
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Ugelvik MS, Skorping A, Moberg O, Mennerat A. Evolution of virulence under intensive farming: salmon lice increase skin lesions and reduce host growth in salmon farms. J Evol Biol 2017; 30:1136-1142. [DOI: 10.1111/jeb.13082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 01/05/2023]
Affiliation(s)
- M. S. Ugelvik
- Department of Biology; University of Bergen; Bergen Norway
| | - A. Skorping
- Department of Biology; University of Bergen; Bergen Norway
| | - O. Moberg
- Department of Biology; University of Bergen; Bergen Norway
| | - A. Mennerat
- Department of Biology; University of Bergen; Bergen Norway
- Ecologie et Dynamique des Systèmes Anthropisés (FRE 3498); CNRS/Université de Picardie Jules Verne; Amiens France
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42
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Pavlidis P, Alachiotis N. A survey of methods and tools to detect recent and strong positive selection. ACTA ACUST UNITED AC 2017; 24:7. [PMID: 28405579 PMCID: PMC5385031 DOI: 10.1186/s40709-017-0064-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 03/29/2017] [Indexed: 01/25/2023]
Abstract
Positive selection occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and due to genetic hitchhiking the neighboring linked variation diminishes, creating so-called selective sweeps. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular LD patterns in the region. A variety of methods and tools can be used for detecting sweeps, ranging from simple implementations that compute summary statistics such as Tajima's D, to more advanced statistical approaches that use combinations of statistics, maximum likelihood, machine learning etc. In this survey, we present and discuss summary statistics and software tools, and classify them based on the selective sweep signature they detect, i.e., SFS-based vs. LD-based, as well as their capacity to analyze whole genomes or just subgenomic regions. Additionally, we summarize the results of comparisons among four open-source software releases (SweeD, SweepFinder, SweepFinder2, and OmegaPlus) regarding sensitivity, specificity, and execution times. In equilibrium neutral models or mild bottlenecks, both SFS- and LD-based methods are able to detect selective sweeps accurately. Methods and tools that rely on LD exhibit higher true positive rates than SFS-based ones under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to represent the null hypothesis. When the correct (or similar to the correct) demographic model is used instead, the false positive rates are considerably reduced. The accuracy of detecting the true target of selection is decreased in bottleneck scenarios. In terms of execution time, LD-based methods are typically faster than SFS-based methods, due to the nature of required arithmetic.
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Affiliation(s)
- Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, 70013 Crete, Greece
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43
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Øvergård AC, Eichner C, Nilsen F, Dalvin S. Molecular characterization and functional analysis of a salmon louse (Lepeophtheirus salmonis, Krøyer 1838) heme peroxidase with a potential role in extracellular matrixes. Comp Biochem Physiol A Mol Integr Physiol 2017; 206:1-10. [DOI: 10.1016/j.cbpa.2017.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 01/03/2017] [Accepted: 01/08/2017] [Indexed: 01/05/2023]
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Carmona-Antoñanzas G, Humble JL, Carmichael SN, Heumann J, Christie HR, Green DM, Bassett DI, Bron JE, Sturm A. Time-to-response toxicity analysis as a method for drug susceptibility assessment in salmon lice. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2016; 464:570-575. [PMID: 27812230 PMCID: PMC5035062 DOI: 10.1016/j.aquaculture.2016.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 08/01/2016] [Accepted: 08/03/2016] [Indexed: 06/06/2023]
Abstract
UNLABELLED The salmon louse Lepeophtheirus salmonis (Krøyer, 1837) is an ectoparasite causing infections of wild and farmed Atlantic salmon (Salmo salar L.) in the Northern hemisphere. While L. salmonis control at commercial mariculture sites increasingly employs non-medicinal approaches, such as cage designs reducing infection rates and biological control through cleaner fish, anti-parasitic drugs are still a requirement for effective fish health care. With only a limited range of salmon delousing agents available, all of which have been in use for more than a decade, drug resistance formation has been reported for different products. Successful resistance management requires reliable susceptibility assessment, which is usually achieved through L. salmonis bioassays. These tests involve the exposure of parasites to different drug concentrations and require significant numbers of suitable L. salmonis stages. The present study reports an alternative bioassay that is based on time-to-response toxicity analyses and can be carried out with limited parasite numbers. The assay determines the median effective time (ET50), i.e., the time required until impaired swimming and/or attachment behaviour becomes apparent in 50% of parasites, by conducting repeated examinations of test animals starting at the time point where exposure to a set drug concentration commences. This experimental approach further allows the estimation of the apparent drug susceptibility of individual L. salmonis by determining their time to response, which may prove useful in experiments designed to elucidate associations between genetic factors and the drug susceptibility phenotype of parasites. Three laboratory strains of L. salmonis differing in susceptibility to emamectin benzoate were characterised using standard 24 h bioassays and time-to-response toxicity assays. While both the median effective concentration (EC50) and the ET50 showed variability between experimental repeats, both types of bioassay consistently discriminated susceptible and drug-resistant L. salmonis laboratory strains. STATEMENT OF RELEVANCE Infections by sea lice cause significant costs to the global salmon farming industry, which have been estimated to exceed €300 million per year worldwide. Control of sea lice still relies to a significant extent on chemical delousing; however, chemical control is threatened by resistance formation. Resistance can be combated by rotation between different drugs and strategic implementation of non-medicinal strategies. However, resistance management requires reliable and feasible methods of susceptibility assessment. The present study is a technical note introducing a novel approach to susceptibility assessments in sea lice. The method can be applied in susceptibility assessments on farms, where it offers the advantage of a reduced requirement of parasites for testing. In addition, the novel method allows deriving the times of parasite require to show a response after drug treatment has started, thus providing a variable characterizing the drug susceptibility phenotype of individual parasites. Accordingly, the bioassay approach presented here will be useful for studies aiming at unravelling the genetic determinants of drug resistance.
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Affiliation(s)
- Greta Carmona-Antoñanzas
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Joseph L. Humble
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Stephen N. Carmichael
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Jan Heumann
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Hayden R.L. Christie
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Darren M. Green
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - David I. Bassett
- Marine Environmental Research Laboratory, University of Stirling, Machrihanish, Argyll, PA28 6PZ, Scotland, UK
| | - James E. Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Armin Sturm
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
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Aaen SM, Horsberg TE. A screening of multiple classes of pharmaceutical compounds for effect on preadult salmon lice Lepeophtheirus salmonis. JOURNAL OF FISH DISEASES 2016; 39:1213-1223. [PMID: 27037538 DOI: 10.1111/jfd.12463] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 12/22/2015] [Indexed: 06/05/2023]
Abstract
The salmon louse, Lepeophtheirus salmonis Krøyer, is the major obstacle facing a sustainable future for farmers of salmonids in the North Atlantic Ocean. Medicinal compounds have been the most utilized tool to prevent salmon lice infestation; however, the active compounds have become less effective or considered environmentally unfriendly in the past years. Novel medicinal compounds are thus highly desired. In two experiment series, 26 medicinal compounds were screened for their efficacy against salmon lice, in a 30-min exposure and 24-h exposure, respectively. Pyriprole, imidacloprid, cartap and spinetoram were effective at 50 mg L(-1) in the short-time exposure. In the 24-h exposure, pyriprole, propoxur, cartap, imidacloprid, fenoxycarb, pyriproxyfen, nitenpyram, spinetoram, spiromesifen and diflubenzuron induced a high level of immobilization at 5 mg L(-1) . The EC50 values of the effective compounds were calculated in further titration studies for both exposure periods. Several physiological and biochemical pathways were discovered as possible targets for medicinal intervention against the salmon louse.
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Affiliation(s)
- S M Aaen
- NMBU School of Veterinary Science, Sea Lice Research Centre, Oslo, Norway
| | - T E Horsberg
- NMBU School of Veterinary Science, Sea Lice Research Centre, Oslo, Norway
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46
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Øvergård AC, Hamre LA, Harasimczuk E, Dalvin S, Nilsen F, Grotmol S. Exocrine glands ofLepeophtheirus salmonis(Copepoda: Caligidae): Distribution, developmental appearance, and site of secretion. J Morphol 2016; 277:1616-1630. [DOI: 10.1002/jmor.20611] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/19/2016] [Accepted: 08/26/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Aina-Cathrine Øvergård
- Disease and Pathogen Transmission; SLCR-Sea Lice Research Centre, Institute of Marine Research; Nordnesgaten 50, Pb. 1870 Nordnes Bergen NO-5817 Norway
| | - Lars A. Hamre
- Department of Biology; SLCR-Sea Lice Research Centre, University of Bergen; Thormøhlensgt. 55, Pb. 7803 Bergen NO-5020 Norway
| | - Ewa Harasimczuk
- Disease and Pathogen Transmission; SLCR-Sea Lice Research Centre, Institute of Marine Research; Nordnesgaten 50, Pb. 1870 Nordnes Bergen NO-5817 Norway
| | - Sussie Dalvin
- Disease and Pathogen Transmission; SLCR-Sea Lice Research Centre, Institute of Marine Research; Nordnesgaten 50, Pb. 1870 Nordnes Bergen NO-5817 Norway
| | - Frank Nilsen
- Department of Biology; SLCR-Sea Lice Research Centre, University of Bergen; Thormøhlensgt. 55, Pb. 7803 Bergen NO-5020 Norway
| | - Sindre Grotmol
- Department of Biology; SLCR-Sea Lice Research Centre, University of Bergen; Thormøhlensgt. 55, Pb. 7803 Bergen NO-5020 Norway
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Poley JD, Braden LM, Messmer AM, Whyte SK, Koop BF, Fast MD. Cypermethrin exposure induces metabolic and stress-related gene expression in copepodid salmon lice (Lepeophtheirus salmonis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 20:74-84. [PMID: 27612154 DOI: 10.1016/j.cbd.2016.08.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/05/2016] [Accepted: 08/11/2016] [Indexed: 01/12/2023]
Abstract
Cypermethrin has been administered for decades to control salmon lice (Lepeophtheirus salmonis) infestations in Atlantic salmon farming regions globally. However, resistance to cypermethrin and other available therapeutants has threatened the sustainability of this growing industry. To better understand the effects of cypermethrin on L. salmonis, a 38K oligonucleotide microarray and RT-qPCR analyses were applied to pools of copepodid larvae exposed to 1.0ppb cypermethrin or seawater controls for 24h. Phenotypic assessments and global gene expression profiles showed a significant disruption of homeostasis in copepodid L. salmonis exposed to cypermethrin. Multiple degradative enzymes were overexpressed in cypermethrin-treated lice including five trypsin-like serine proteases and three cytochrome p450s CYP3a24 (p=0.03, fold change (FC)=3.8; GenBank accession no. JP326960.1), CYP6w1 (p=0.008, FC=5.3; GenBank accession no. JP317875.1), and CYP6d4 (p=0.01; FC=7.9; GenBank accession no. JP334550.1). These enzymes represent preliminary markers for understanding the physiological response of L. salmonis to cypermethrin exposure. A general stress response was also observed in cypermethrin-treated lice which included differential expression of cell signaling genes involved in the induction of cell growth, solute transport, and metabolism. Lastly, a consensus-based analysis was completed with two previously published L. salmonis transcriptome studies revealing genes that respond to cypermethrin, emamectin benzoate (another delousing agent) and hyposalinity. This included concordant differential expression of heat shock beta-1, ammonium transporter Rh types B, and 72kDa type IV collagenase across different L. salmonis studies. This is currently the most comprehensive transcriptome assessment of chemical exposure on the first infectious stage of L. salmonis, providing novel markers for studying drug resistance and general stress in this important parasite.
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Affiliation(s)
- Jordan D Poley
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Laura M Braden
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Amber M Messmer
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| | - Shona K Whyte
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
| | - Ben F Koop
- Centre for Biomedical Research, Department of Biology, University of Victoria, Victoria, BC, V8W 3N5, Canada.
| | - Mark D Fast
- Hoplite Lab, Department of Pathology & Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE, C1A 4P3, Canada.
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48
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Predicting the effectiveness of depth-based technologies to prevent salmon lice infection using a dispersal model. Prev Vet Med 2016; 129:48-57. [DOI: 10.1016/j.prevetmed.2016.05.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/01/2016] [Accepted: 05/20/2016] [Indexed: 11/19/2022]
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49
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Jansen PA, Grøntvedt RN, Tarpai A, Helgesen KO, Horsberg TE. Surveillance of the Sensitivity towards Antiparasitic Bath-Treatments in the Salmon Louse (Lepeophtheirus salmonis). PLoS One 2016; 11:e0149006. [PMID: 26889677 PMCID: PMC4759459 DOI: 10.1371/journal.pone.0149006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/26/2016] [Indexed: 11/18/2022] Open
Abstract
The evolution of drug resistant parasitic sea lice is of major concern to the salmon farming industry worldwide and challenges sustainable growth of this enterprise. To assess current status and development of L. salmonis sensitivity towards different pesticides used for parasite control in Norwegian salmon farming, a national surveillance programme was implemented in 2013. The programme aims to summarize data on the use of different pesticides applied to control L. salmonis and to test L. salmonis sensitivity to different pesticides in farms along the Norwegian coast. Here we analyse two years of test-data from biological assays designed to detect sensitivity-levels towards the pesticides azamethiphos and deltamethrin, both among the most common pesticides used in bath-treatments of farmed salmon in Norway in later years. The focus of the analysis is on how different variables predict the binomial outcome of the bioassay tests, being whether L. salmonis are immobilized/die or survive pesticide exposure. We found that local kernel densities of bath treatments, along with a spatial geographic index of test-farm locations, were significant predictors of the binomial outcome of the tests. Furthermore, the probability of L. salmonis being immobilized/dead after test-exposure was reduced by odds-ratios of 0.60 (95% CI: 0.42–0.86) for 2014 compared to 2013 and 0.39 (95% CI: 0.36–0.42) for low concentration compared to high concentration exposure. There were also significant but more marginal effects of parasite gender and developmental stage, and a relatively large random effect of test-farm. We conclude that the present data support an association between local intensities of bath treatments along the coast and the outcome of bioassay tests where salmon lice are exposed to azamethiphos or deltamethrin. Furthermore, there is a predictable structure of L. salmonis phenotypes along the coast in the data, characterized by high susceptibility to pesticides in the far north and far south, but low susceptibility in mid Norway. The study emphasizes the need to address local susceptibility to pesticides and the need for restrictive use of pesticides to preserve treatment efficacy.
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Affiliation(s)
- Peder A. Jansen
- Norwegian Veterinary Institute, Oslo, Norway
- Sea Lice Research Centre, Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
| | | | | | - Kari O. Helgesen
- NMBU School of Veterinary Science, Sea Lice Research Centre, Oslo, Norway
| | - Tor Einar Horsberg
- NMBU School of Veterinary Science, Sea Lice Research Centre, Oslo, Norway
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50
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Murray AG. Increased frequency and changed methods in the treatment of sea lice (Lepeophtheirus salmonis) in Scottish salmon farms 2005-2011. PEST MANAGEMENT SCIENCE 2016; 72:322-326. [PMID: 25712895 DOI: 10.1002/ps.3996] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/03/2015] [Accepted: 02/18/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND The sea louse is the most economically and environmentally serious ectoparasite of marine salmonids. Sea lice have been largely controlled by treatment with a variety of medicines. In order to understand the sustainability of medicine usage, an analysis of sea louse treatment data has been carried out for all Scottish salmon farms from 2005 to 2011. RESULTS Overall, there was an increase from 0.156 to 0.282 treatments month(-1) ; treatments could involve one or multiple agents. This increase was mostly in bath treatments (cypermethrin in 2007, largely replaced by deltamethrin and azamethiphos in 2008). Treatments using in-feed treatments (emamectin benzoate and teflubenzuron) increased only slowly. Treatments involving more than one medicine in a single month also increased, as did the probability of follow-up treatments. Treatments were seasonal, with peaks of in-feed treatments in March and August and bath treatments more frequent between August and December. CONCLUSION Frequency of sea louse treatment increased substantially, with an increase in multiagent and follow-up treatments. This increase in treatment activity is expensive to the industry and increases exposure of the neighbouring environment. This indicates that earlier louse control practices were not sustainable and so adapted.
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