We have developed a literature database in order to determine the state of omics applications in fisheries science. The publications below are relevant to Canadian and US fishery managers in government, NGOs, and Indigenous groups. Date last updated: 28-Apr-2026.
Omics Literature Database
| Omics Type | Management Concern | Summary | Citation | Date Published | DOI | Keywords | Paper Type | Applied/Theoretical | Capacity/Scale | Cost | Salinity | Locality | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Proteomics | Animal protein; Aqua food; Aquaculture; Omics; Safety and quality; Sustainable | This paper reviews basic to advanced proteomics technologies in the context of aquaculture. The authors cover sample preparation to bioinformatic ressources used for data analysis. The content and breadth of this review would be of interest to fisheries managers as this review includes studies that have applied proteomics to determine food quality and safety. Further, it also highlights the development of protein-based markers that could be used to track the healthy growth of the fish. Such monitoring could help managers and aquaculture farmers take necessary actions and improve sustainability of fisheries. | Nissa, MU; Pinto, N; Parkar, H; Goswami, M; Srivastava, S. (2021). Proteomics in fisheries and aquaculture: An approach for food security. FOOD CONTROL, 127(). http://dx.doi.org/10.1016/j.foodcont.2021.108125 | 1-Apr-2021 | http://dx.doi.org/10.1016/j.foodcont.2021.108125 | HEMOLYMPH VITELLOGENIN LEVELS; FRESH-WATER PRAWN; OVARIAN DEVELOPMENT; MARINE RESERVES; MACROBRACHIUM-ROSENBERGII; GENE-EXPRESSION; DECAPODA; CRUSTACEA; SEQUENCE; RESTRICTIONS | Opinion / Review | Theoretical | NA | Global | |||
| Transcriptomics | This paper is a review of proteomic and transcriptomic approaches to elucidate the effects of various effluent sources on Atlantic cod. The authors focus their review on early life stages (egg, larvae) and tissue-level responses to effluents and single contaminants. Their objective is to identify transcriptional and translational biomarkers that can be used in environmental monitoring and risk assessment. | Karlsen, OA; Bjorneklett, S; Berg, K; Brattås, M; Bohne-Kjersem, A; Grosvik, BE; Goksoyr, A. (2011). Integrative Environmental Genomics of Cod (Gadus morhua): The Proteomics Approach. J TOXICOL ENV HEAL A, 74(7-9). http://dx.doi.org/10.1080/15287394.2011.550559 | 9-Mar-2011 | http://dx.doi.org/10.1080/15287394.2011.550559 | BROWN ADIPOSE-TISSUE; PACIFIC BLUEFIN TUNA; PHYLOGENETIC ANALYSIS; GENE TREES; NUCLEAR INTROGRESSION; MUSCLE TEMPERATURES; CONCATENATED DATA; METABOLIC-RATE; BIGEYE TUNA; MITOCHONDRIAL | Opinion / Review | Theoretical | SW | Europe | ||||
| Genomics - Whole-Genome | aquaculture; genomics; marine biodiversity; next-generation sequencing, proteomics | This paper reviews omics approaches in marine aquaculture and fisheries. This review also briefly describes a research and training initiative in Central America that is building a genome archive, and the policy-level challenges that they have encountered. This review focused on the application of genomic methods for understanding biodiversity and aquaculture. Highlights the need for Science policies to confront the challenges faced by small nations in this domain. | Huete-Pérez, JA; Quezada, F. (2013). Genomic Approaches in Marine Biodiversity and Aquaculture. BIOL RES, 46(4). http://dx.doi.org/10.4067/S0716-97602013000400007 | 17-Oct-2013 | http://dx.doi.org/10.4067/S0716-97602013000400007 | EARLY-LIFE STAGES; NORTH-SEA-OIL; DIETARY METHYLMERCURY; RAINBOW-TROUT; 2-DIMENSIONAL ELECTROPHORESIS; POLYCHLORINATED-BIPHENYLS; FISH; TOXICOLOGY; BIOMARKER; EXPOSURE | Opinion / Review | Theoretical | Some discussion | SW | Global | ||
| Genomics - Genome-Wide | Research surveys; Bottom trawl; Data Collection; genomic methods; Fish stock assessment | This opinion paper provides background on the use of trawl surveys for marine fish stock assessment and an overview of four potential genomic applications to complement the trawl surveys. Abundance can be estimated using close-kin mark and recapture, while eDNA can give relative abundance. The authors describe using DNA modification to age fish (not proven yet) and to use genome sequencing to assess stock structure more acurately than using a few markers. | Rodríguez-Mendoza R and Saborido-Rey F (2023) The potential use of genomic methods in bottom trawl surveys to improve stock assessments in Europe. Front. Mar. Sci. 10:1095171. doi: 10.3389/fmars.2023.1095171 | 29-May-2023 | https://doi.org/10.3389/fmars.2023.1095171 | DNA methylation; Reproduction; Marine fisheries; Fish; Otoliths; Marine fish; Stock assessment; Surveys; Fishery data; Marine ecosystems; Age; Epigenetics; Marine fishes; Bottom trawling; Working groups; Research; Fisheries; Ecosystems; Genomics; Data collection; Fishery resources; Hydroacoustics; Stocks; Fish stocks; Benthos collecting devices; Methods; Fishing; Commercial fishing; Polls & surveys; Fisheries management | Opinion / Review | Theoretical | Member States of the European Union | Some discussion | SW | Europe | |
| Transcriptomics | Atlantic cod; Aquaculture; Climate Change; fransicella; IPCC; temperature | This data based paper focusses on cod aquaculture and the effects and interactions of elevated water tempertaure and pathogen infection. Likely of limited applicability in wild fishery management except as an example of transcriptomics applications. | Ytteborg E, Falconer L, Krasnov A, Johansen L-H, Timmerhaus G, Johansson GS, Afanasyev S, Høst V, Hjøllo SS, Hansen ØJ and Lazado CC (2023) Climate change with increasing seawater temperature will challenge the health of farmed Atlantic Cod (Gadus morhua L.). Front. Mar. Sci. 10:1232580. doi: 10.3389/fmars.2023.1232580 | 20-Sep-2023 | https://doi.org/10.3389/fmars.2023.1232580 | Chemical analysis; Aquaculture; Seawater; Spleen; Fish; Heat shock proteins; Scanning electron microscopy; Fisheries; Cold shock proteins; Intergovernmental Panel on Climate Change; Food production; Temperature; Hydrogen peroxide; Climate change; Polyculture (aquaculture); Electron microscopy; Explants; Proteins; Oxidative stress; Immunoglobulins; Pathogens; RNA-binding protein; Transcription activation; Immunohistochemistry; Gene expression; Whitefish; Proliferation; High temperature; Pathology; Granulomas; Biological stress; Histology; Genes; Biopsy; Migrations; Water analysis; Vulnerability; Transcriptomics; Skin; Marine fishes; Heat shock; Cod; Thermal stress; Fish skin; Gadus morhua | Technical / Data | Applied | SW | Europe | |||
| Genomics - Genome-Wide | CKMR; SNP markers; genotyping; Kinship analysis; fisheries assessments | This paper provides a review of the close-kin mark recapture method of stock assessment using genomic data to determine relatedness with high accuracy. The paper gives a good description of the power of using kin relatedness of randomly captured fish to assess stock size and other demographic parameters, as well as giving an overview of how this method can be used in stock assessment models. | Casas L and Saborido-Rey F (2023) A review of genomics methods and bioinformatics tools for the analysis of close-kin mark-recapture. Front. Mar. Sci. 10:1113870. doi: 10.3389/fmars.2023.1113870 | 7-Jul-2023 | https://doi.org/10.3389/fmars.2023.1113870 | Fishery sciences; Parameters; Genotyping; Fisheries; Fish; Bioinformatics; Stocks; Fish stocks; Uptake; Stock assessment; Tracking; Uncertainty; Genomes; Statistical methods; Genomics; Probability theory; Capture-recapture studies | Opinion / Review | Theoretical | Fishery | Some discussion | NA | NA | |
| Genomics - Genome-Wide | Genome; global change; candidate genes; Environmental challenges; Benguela hake | This paper is primarily a technical report of a genome sequence developed for one species of exploited hake. It would have limited value for a non-technical fishery managers, although it represents basic genomics studies that contribute to the background data necessary for future management applications | Mateo JL, Blanco-Fernandez C, Garcia-Vazquez E and Machado-Schiaffino G (2023) A new Merluccius polli reference genome to investigate the effects of global change in West African waters. Front. Mar. Sci. 10:1111107. doi: 10.3389/fmars.2023.1111107 | 24-Apr-2023 | https://doi.org/10.3389/fmars.2023.1111107 | Metals; Genes; Geographical distribution; Pollutants; Marine fisheries; Fish; Global warming; Fisheries; Marine fish; Genomes; Hypoxia; Species diversity; Climate change; Contaminants; Nucleotide sequence; Marine fishes; Pollution; Temperature gradients; Consortia; Taxonomy; Heavy metals; Single-nucleotide polymorphism; Fishing; Heterozygosity; Sequencing; Merluccius polli | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | Conservation genomics; Fisheries management; Harvesting; Hybridization; Next-generation sequencing; Simulations | This paper describes the value of testing for hybridization effects in fish raised in captivity for release into the wild for stocking. The authors provide a strong rationale for the use of large scale genomic data to detect such hybridization with a strong test case. However, the actual impact of hybridization on the health and performance of the wild fish is not explored. Where hybridization between closely-related species or among stocks is a potential problem, genomic detection and quanitification of the hybrids is well decsribed here | Attard Catherine, R. M., Sandoval-Castillo, J., Gilligan, D. M., Unmack, P. J., Faulks, L. K., & Beheregaray, L. B. (2022). Genomics outperforms genetics to manage mistakes in fisheries stocking of threatened species. Biodiversity & Conservation, 31(3), 895-908. doi:https://doi.org/10.1007/s10531-022-02369-x | 8-Apr-2022 | https://doi.org/10.1007/s10531-022-02369-x | Lake basins; Fish; Fisheries; Fish stocking; Fingerlings; Biodiversity; Genetic variation; Hatcheries; Fish hatcheries; Genomics; Genomes; Hybridization; Genetic diversity; Threatened species; Nucleotides; Impoundments; Wildlife conservation; Basins; Outbreeding; Inland waters; Microsatellites; Stocking; Lakes; Breeding stock; Fisheries management; Endangered & extinct species; Genetics; Restocking; Single-nucleotide polymorphism; Datasets; Macquaria ambigua | Technical / Data | Applied | FW | Australia | |||
| Genomics - Whole-Genome | Biomarker; Marine fish; Conservation physiology; Management; Climate change | Pablo, B., Cooke, S. J., Quentin, S., Trenkel, V. M., Philippe, S., & Christophe, L. (2021). Physiological biomarkers and fisheries management. Reviews in Fish Biology and Fisheries, 31(4), 797-819. doi:https://doi.org/10.1007/s11160-021-09677-5 | 29-Sep-2021 | https://doi.org/10.1007/s11160-021-09677-5 | Physiology; Climate change; Fishery sciences; Warning systems; Fisheries; Marine fisheries; Fish; Wildlife management; Marine fish; Surveys; Fisheries surveys; Life history; Biomarkers; Prediction models; Fish populations; Species; Fisheries management; Fishery management; Wildlife conservation; Data collection; Recovery plans; Momentum; Fish stocks; Marine fishes | Opinion / Review | Theoretical | SW | NA | ||||
| Genomics - Whole-Genome | Largemouth bass; Whole-genome | This paper describes a whole genome analysis of Largemouth Bass strains that have been domesticated (genetically selected) to improve their performance. The authors show strong evidence for selection acting to change the genome of the selected strains. While this is an interesting paper documenting the genomic signals of selection, it would have litte relevance for wild stock management unless genetically altered strains were being considered for release to address special environmental challenges (e.g., low oxtgen and heat stress) | Sun, C., Zhang, X., Dong, J., You, X., Tian, Y., Gao, F., . . . Ye, X. (2023). Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass (micropterus salmoides). Zoological Research, 44(1), 78-8. doi:https://doi.org/10.24272/j.issn.2095-8137.2022.274 | 18-Jan-2023 | https://doi.org/10.24272/j.issn.2095-8137.2022.274 | Genes; Signal analysis; Genetic analysis; Fish; Phylogenetics; Bass; Domestication; Fisheries; Animals; Breeding; Genetic variation; Genomes; Nucleotide sequence; Genetic diversity; Population structure; Genomics; Population genetics; Bcl-6 protein; Nucleotides; Populations; Whitefish; Fishing; Freshwater fishes; Micropterus salmoides | Technical / Data | Theoretical | FW | North America; Asia | |||
| Genomics - Genome-Wide | ship sturgeon; genome re-sequencing; effective population size; Ili River; China | This paper describes a restricted whole genome analysis of a highly endangered sturgeon species with the goal of determining when the species experienced a population bottleneck and how severe that bottleneck was. This application of genomics is very relevant for extreme at risk species, where captive breeding is being considered as a conservation/management option. Not very relevant for most exploited species. | Hu, G., Chen, F., Zhang, Y., Luan, P., Luo, Z., Niu, J., . . . Ji, F. (2023). Estimates of the effective population size and genetic structure of the critically endangered ship sturgeon (acipenser nudiventris) in the chinese section of the ili river. Fishes, 8(7), 354. doi:https://doi.org/10.3390/fishes8070354 | 7-Jul-2023 | https://doi.org/10.3390/fishes8070354 | Nature conservation; Software; Fish conservation; Fish; Endangered species; Aquaculture techniques; Rare species; Rivers; Genomes; Genetic structure; Genomics; Wildlife conservation; Genetic testing; Reproductive techniques; Threatened species; Sturgeon; Conservation; Endangered animals; Coefficients; Population genetics; Endangered & extinct species; Induced breeding; Ships; Single-nucleotide polymorphism; Fishing; Commercial fishing; Population number; Population decline; Freshwater fishes; Fisheries management; Acipenser nudiventris | Technical / Data | Theoretical | FW | Asia | |||
| Genomics - Whole-Genome | Next-generation sequencing; Shortfin mako shark; Single nucleotide polymorphism; Marine omics | This paper is primarily a technical report of a genome and transcriptome sequence analysis for one exploited shark species with little metadata on their biology available. By itself, it would have limited value for a non-technical fishery managers, although it provides valuable genetic markers for population health and demographic assessments Such studies would be valuable for any exploited species with limited demographic and biological data, but requires very specialized skills to develop and interpret, especially for practical management applications. | Domingues, R. R., Mastrochirico-Filho, V., Mendes, N. J., Hashimoto, D. T., Coelho, R., Antunes, A., . . . Mendonça, F. F. (2022). Gene-associated markers as a genomic and transcriptomic resource for a highly migratory and apex predator shark (isurus oxyrinchus). Marine Biology, 169(9) doi:https://doi.org/10.1007/s00227-022-04094-z | 5-Aug-2022 | https://doi.org/10.1007/s00227-022-04094-z | Genes; Analysis; Sharks; DNA sequencing; Oceans; Fisheries; Pelagic fisheries; Locomotion; Molecular evolution; Predators; Transcriptomics; Annotations; Genotyping; Genomics; Biology; Polymorphism; Nucleotides; Gene sequencing; DNA sequence; RNA sequencing; Deoxyribonucleic acid--DNA; Biomarkers; Single-nucleotide polymorphism; Nucleotide sequence; Longline fishing; Marine fishes; Isurus; Isurus oxyrinchus | Technical / Data | Theoretical | SW | Global | |||
| Transcriptomics | aquaculture; differentially expressed genes; mahseer; quantitative polymerase chain reaction; transcriptome | Shahi, N., Singh, B., Mallik, S. K., Sarma, D., & Surachetpong, W. (2023). RNA-seq reveals differential gene expression patterns related to reproduction in the golden mahseer. Fishes, 8(7), 352. doi:https://doi.org/10.3390/fishes8070352 | 5-Jul-2023 | https://doi.org/10.3390/fishes8070352 | Genes; Software; Hormones; Ribonucleic acid--RNA; Aquaporin 1; Economic importance; Fish; Nucleic acids; Domestication; Bioinformatics; Brain; Ontology; RNA; Aquaculture; Gene expression; Reproduction; Sexual maturity; Down-regulation; Genomics; Males; Complementary DNA; Gonads; Polyculture (aquaculture); Females; Endangered animals; PCR; Fishing; Coding; Annotations; Nucleotide sequence; Homology; Endangered species | Technical / Data | Theoretical | FW | Asia | ||||
| Transcriptomics | HPG/HPI axis; maturation; photoperiod; Scomber japonicus; stress response; wavelength | This paper describes an experimental manipulation of photoperiod using captive mackerel to assess possible sexual maturation control. The work includes gene transcription profiling; however it includes only a few very targted genes. This work is primarily aimed at aquaculture applications and is of limited relevance for fishery applications. | Choi, Y. J., Seul Gi Na Ra, P., A-Hyun, J., & Jun-Hwan, K. (2023). Physiological effect of extended photoperiod and green wavelength on the pituitary hormone, sex hormone and stress response in chub mackerel, scomber japonicus. Fishes, 8(2), 77. doi:https://doi.org/10.3390/fishes8020077 | 16-May-2023 | https://doi.org/10.3390/fishes8020077 | Aquaculture; Physiology; Pituitary; Behavior; Hormones; Fish; Environmental effects; Follicle-stimulating hormone; Sex hormones; Plasma levels; Wavelength; Gonadotropin-releasing hormone; Pituitary gland; Sexual maturity; Metabolism; Testosterone; Photoperiods; Enzyme-linked immunosorbent assay; Immunoassays; Stress response; Photoperiodicity; Fatty acids; Gene expression; Luteinizing hormone; ELISA; Pituitary (anterior); Light effects; Trout; Steroids; Gonadotropins; Pituitary hormones; PCR; 17β-Estradiol; Nucleotide sequence; Light; Wavelengths; Biological stress; Marine fishes; Scomber japonicus | Technical / Data | Theoretical | SW | Asia | |||
| Transcriptomics | Chinese tongue sole (Cynoglossus semilaevis) · Sexual size dimorphism (SSD) · Estradiol · Testosterone | Zhang, M., Yang, Q., Shi, R., Wang, J., Zhang, Z., Yang, Y., . . . Wang, N. (2022). Effects of long-term sex steroid hormones (estradiol and testosterone)–supplemented feeds on the growth performance of chinese tongue sole (cynoglossus semilaevis). Fish Physiology and Biochemistry, 48(5), 1365-1375. doi:https://doi.org/10.1007/s10695-022-01125-w | 20-Sep-2022 | https://doi.org/10.1007/s10695-022-01125-w | Insulin; Receptors; Steroid hormones; Hormones; Steroids; Muscles; Growth hormone; Sex; Dimorphism; Testosterone; Insects; Amphibians; Growth; Estrogens; Growth factors; Insulin-like growth factor I; Proteins; Thyroid; Myostatin; Sexual dimorphism; Reptiles; Insulin-like growth factors; Insulin-like growth factor II; Sex hormones; Genes; Leptin; Reductases; Amphibia; Aquatic reptiles; Gonads; Estrogen receptors; Sexes; Somatostatin; Oestrogens; Growth hormone-releasing hormone; 17β-Estradiol; Marine fishes; Cynoglossus semilaevis | Technical / Data | Theoretical | SW | Asia | ||||
| Genomics - Whole-Genome | Salmonidae; Mexican golden trout; Nelson’s trout; mitochondrial genome; taxonomic status; fish | This paper reports on the results of whole mitochondrial genome sequencing for two species of trout. While these data will be useful for possible fishery-related genomic applications, it is not relevant to non-technical readers. It does, however, add to the growing database of mitochondrial and nuclear genomes in freshwater fishes. | Colín, A., Del Río-Portilla, M.,A., Lafarga-De la Cruz, F., Genoveva Ingle-De, l. M., & García-De León, F.,J. (2023). Assembly, characterization, and phylogenetic relationships of mitogenomes of two species of mexican trout (oncorhynchus chrysogaster and O. mykiss nelsoni). Fishes, 8(4), 178. doi:https://doi.org/10.3390/fishes8040178 | 27-Mar-2023 | https://doi.org/10.3390/fishes8040178 | rRNA; Genes; Phylogenetics; tRNA; Genomes; Cladistics; Genomics; Mitochondria; Mitochondrial DNA; Servers; Replication origins; Phylogeny; Radiation; Trout; Salmon; Genetic engineering; Native species; Taxonomy; Sibling species; Freshwater fishes; Synteny; Oncorhynchus chrysogaster; Oncorhynchus mykiss nelsoni | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Whole-Genome | Chondrichthyes; chimaeras; elasmobranchs; omics; transcriptome; review | This paper used existing RNA sequence data for sharks to assess the depth of that database and possible applications for management and conservation. No new data is generated. The paper provides good background on how RNA sequence (transcriptome) data may be useful for fisheries management; however, no such applications are provided. Good background information. | Seixas, M. J., Domingues, R. R., & Antunes, A. (2023). Decoding the transcriptome of sharks, rays, and chimaeras: Insights into their physiology, morphology, evolution, and biomedical applications. Fishes, 8(5), 271. doi:https://doi.org/10.3390/fishes8050271 | 19-May-2023 | https://doi.org/10.3390/fishes8050271 | Opinion / Review | Theoretical | SW | Global | ||||
| Genomics - Genome-Wide | population genomics, Engraulis japonicus, single nucleotide polymorphism, RAD-seq, genetic structures | This paper describes an analysis of genome-wide genetic markers to detect subpopulation structure in E. japonicus (a fished species) in the North Pacific. The authors note that genome-wide markers can detect subtle population structure and provide evidence for local adaptation. Although this case study may have limited relevance for most fishery managers, it provides a framework for how such genomic data can be used in complex stock or subpopulation situations. | Zhang, B., Li, Y., Xue, D., & Liu, J. (2020). Population genomics reveals shallow genetic structure in a connected and ecologically important fish from the northwestern pacific ocean. Frontiers in Marine Science, doi:https://doi.org/10.3389/fmars.2020.00374 | 28-May-2020 | https://doi.org/10.3389/fmars.2020.00374 | Population; DNA sequencing; Economic importance; Fish; Pelagic fisheries; Ocean currents; Cytochrome; Animal behavior; Commercial fishing; Adaptation; Pelagic fish; Gene flow; Genetic structure; Genomics; Mitochondrial DNA; Natural selection; Genomes; Fish populations; Genetic diversity; Fisheries management; Fishery management; Population genetics; Dispersal; Economics; Deoxyribonucleic acid--DNA; Single-nucleotide polymorphism; Fishing; DNA; Population studies; Nucleotides; Marine fish; Stock assessment | Technical / Data | Theoretical | SW | Asia | |||
| Genomics - Whole-Genome | Fish Immune response; omics; Genomics; Transcriptomics; Proteomics; Metabolomics | This is a review and synthesis of how 'omics can be used to assess disease/pathogen responses in fishes. The primary focus is on captive rearing, specifically aquaculture, but the background information on the nature of the different 'omics data is valuable. May be of specific interest formanagers charged with hatchey production for reintroduction or supplementation. | Natnan, M. E., Low, C., Chong, C., Bunawan, H., & Baharum, S. N. (2021). Integration of omics tools for understanding the fish immune response due to microbial challenge. Frontiers in Marine Science, doi:https://doi.org/10.3389/fmars.2021.668771 | 21-Jun-2021 | https://doi.org/10.3389/fmars.2021.668771 | Aquaculture; Fish; Mortality; Fish culture; Infectious diseases; Cytokines; Skin; Genomics; Peptides; Fishery products; Granulocytes; Biomarkers; Adaptive immunity; Defence mechanisms; Aquatic animals; Proteomics; Proteins; Immune response; Biology; Thymus gland; Spleen; Gene expression; Viruses; Medical treatment; Pathogens; Economics; Infections; Lymphocytes; Parasites; Agricultural production; Lectins; Immunoglobulins; Immunity; Genes; Antibodies; Disease; Metabolomics; Sustainable aquaculture; Nutrition; Immune system; Antigens; Fish hatcheries | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | Marine fish; Population genomics; RAD sequencing; SNP; Tropical tuna; Tuna fishery | This is a strong paper describing using whole-genome genetic markers to detect population structure across the global range of yellowfin tuna. While the specific results reported here may be of limited interest to fishery managers in general, the approach and conclusion are of value. This paper adds to growing body of published litertaure that indicates whole-genome genetic markers are needed to detect subtle population structure | Pecoraro, C., Babbucci, M., Villamor, A., Franch, R., Papetti, C., Leroy, B., . . . Cariani, A. (2016). Methodological assessment of 2b-RAD genotyping technique for population structure inferences in yellowfin tuna (thunnus albacares). Marine Genomics, 25, 43-48. doi:https://doi.org/10.1016/j.margen.2015.12.002 | 1-Feb-2016 | https://doi.org/10.1016/j.margen.2015.12.002 | Biological surveys; Marine fish; Genetics; Population genetics; Migratory Fish; Stock assessment; Population structure; Pipelines; Stacks; Tuna fisheries; Differentiation; Single-nucleotide polymorphism; Scales; Running; Oceans; Genotyping; Fisheries; Recruitment; Dispersal; Thunnus albacares; Marine | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Whole-Genome | conservation physiology; fisheries management; genomics; field physiology; climate change | This paper is a review of progress made in using physiological and genomic tools to help with the complex challenges of salmonid conservation and management. The paper provides a good theoretical background with examples from the authors past resercah. This paper is valuable for managers facing declining stock issues where the cause is not obvious. | Cooke, S. J., Hinch, S. G., Donaldson, M. R., Clark, T. D., Eliason, E. J., Crossin, G. T., . . . Farrell, A. P. (2012). Conservation physiology in practice: How physiological knowledge has improved our ability to sustainably manage pacific salmon during up-river migration. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences, 367(1596), 1757-1769. doi:https://doi.org/10.1098/rstb.2012.0022 | 19-Jun-2012 | https://doi.org/10.1098/rstb.2012.0022 | Migrations; Rivers; Temperature effects; Fitness; Mortality; Reviews; Telemetry; Fisheries; Conservation; genomics; Migration; Models; Salmonidae | Opinion / Review | Applied | FW | North America | |||
| Genomics - Whole-Genome | Genomics; Genetics; Fisheries; Mariculture; Quantitative trait loci; Fish; Oyster | This paper provides a good overview of potential applications of genomics and transcriptomics in fisheries science and management; however, the specific technologies discussed are dated. Nevertheless, this review would be valuable for someone with little technical background as a primer, since it focusses on fishery and aquaculture applications. | Wenne, R., Boudry, P., Hemmer-Hansen, J., Lubieniecki, K. P., Was, A., & Kause, A. (2007). What role for genomics in fisheries management and aquaculture? Aquatic Living Resources, 20(3), 241-255. doi:https://doi.org/10.1051/alr:2007037 | 28-Aug-2007 | https://doi.org/10.1051/alr:2007037 | Scientific research; DNA sequencing; Fishery management; Chemical oxygen demand; genomics; Aquaculture; DNA microarrays; expressed sequence tags; oysters; Reviews; Physiology; DNA; Shellfish; Fish; fishery management; Technology; Dicentrarchus labrax; Tilapia; Salmonidae | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | control, costs, enforcement, genetics, genomics, marine resource management | Martinsohn, J. T., Raymond, P., Knott, T., Glover, K. A., Nielsen, E. E., Lars, B. E., . . . Guillen, J. (2019). DNA‐analysis to monitor fisheries and aquaculture: Too costly? Fish and Fisheries, 20(2), 391-401. doi:https://doi.org/10.1111/faf.12343 | 1-Mar-2019 | https://doi.org/10.1111/faf.12343 | Aquaculture; Cost assessments; Legislation; Fisheries; Genetic analysis; Fish; Costs; Fishing; Enforcement; Cost analysis; Crime; Control; Illegal fishing; Fraud; Wildlife; Deoxyribonucleic acid--DNA; DNA; Supply chains; Compliance; Species identification | Opinion / Review | Theoretical | Significant discussion | SW | Global | |||
| Genomics - Genome-Wide | A tlantic cod; divergent selection; genome scan; outlier loci; population genomics; single nucleotide polymorphism | This highly technical paper provides an excellent example of applied genomics in an exploted stock of conservation concern (Atlantic cod). While it is of most relevance for marine fish stocks, the approach and concepts explored are relevant for any exploited fish that is also of conservation concern. | Bradbury, I. R., Hubert, S., Higgins, B., Bowman, S., Borza, T., Paterson, I. G., . . . Bentzen, P. (2013). Genomic islands of divergence and their consequences for the resolution of spatial structure in an exploited marine fish. Evolutionary Applications, 6(3), 450-461. doi:https://doi.org/10.1111/eva.12026 | 1-Apr-2013 | https://doi.org/10.1111/eva.12026 | Genomes; Genetics; Population genetics; Environmental impact; Conservation; Population structure; Divergence; Biopolymorphism; Nucleotides; Differentiation; Adaptations; Islands; Single-nucleotide polymorphism; Nucleotide sequence; Fisheries; genomics | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Whole-Genome | anthropogenic impacts; pacific salmonids; telemetry; genomics; enzymes; ions; impacts anthropiques; salmonides du Pacifique; telemetrie; genomique; enzymes; ions | This paper is a focussed review of the integrated use of multiple disciplines within "conservation physiology" to evaluate the impacts of hydrological manipulation (primarily hydopower dams) on fish stocks. With a focus on management options, this review provides a lot of information; however, the assessment of genomics is not a particular goal of the authors. This paper does give a good overview of sub-organismal biomarker use in fish management and conservation. | Hasler, C. T., Pon, L. B., Roscoe, D. W., Mossop, B., Patterson, D. A., Hinch, S. G., & Cooke, S. J. (2009). Expanding the 'toolbox' for studying the biological responses of individual fish to hydropower infrastructure and operating strategies. Environmental Reviews, 17, 179-197. doi:https://doi.org/10.1139/A09-008 | 15-Jul-2009 | https://doi.org/10.1139/A09-008 | Turbines; Community composition; Fishways; Fish physiology; Bioenergetics; Stock assessment; Irrigation; Migrations; Sustainable development; Freshwater fish; Rivers; Community structure; Forensic science; Conservation; genomics; Habitat; Drinking water; Migration; migration; anthropogenic factors; Physiology; hydroelectric power; irrigation water; case studies; Reviews; Fisheries; Fish; infrastructure; River Regulations; Drinking Water; Assessments; Hydroelectric Plants; Fish Populations; Benefits; Freshwater | Opinion / Review | Theoretical | FW | ||||
| Genomics - Genome-Wide | Seascape genetics · Genomics · Connectivity · Marine population genetics · Gene flow · Dispersal · Landscape genetics | This paper is a broad review of advances in population genetic applications to defining patterns of connectrivity among stocks or populations of (mostly) marine fishes. While most of the challenges identified are confined to marine fish management, the concepts explored here are valuable for any exploited fish stock of uncertain strock structure. | Selkoe, K. A., D'aloia, C.,C., Crandall, E. D., Iacchei, M., Liggins, L., Puritz, J. B., . . . Toonen, R. J. (2016). A decade of seascape genetics: Contributions to basic and applied marine connectivity. Marine Ecology Progress Series, 554, 1-19. doi:https://doi.org/10.3354/meps11792 | 28-Jul-2016 | https://doi.org/10.3354/meps11792 | Ecology; Temperature effects; Population genetics; Genetics; Resource management; Climate change; Marine parks; Geography; Ecosystem disturbance; Adaptations; Statistics; Data processing; Climatic changes; Statistical analysis; Oceanography; Demography; Reviews; Fisheries; Conservation; genomics; Sampling; Geographic information systems; Marine; Brackish | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Whole-Genome | Comparative genomics; Convergent mapping; Fish; Growth QTL; Linkage map; Marker assisted selection | This paper focusses on gene discovery for production-related traits in sea bass. While this aquaculture-related application of genomics is robust and interesting, it would be of little value to fisheries managers unless genomic modifications to improve performance in released fish were to be considered for extreme conservation action. | Louro, B., Kuhl, H., Tine, M., de Koning, D., Batargias, C., Volckaert, F. A. M., . . . Power, D. M. (2016). Characterization and refinement of growth related quantitative trait loci in european sea bass (dicentrarchus labrax) using a comparative approach. Aquaculture, 455, 8-21. doi:https://doi.org/10.1016/j.aquaculture.2016.01.004 | 20-Mar-2016 | https://doi.org/10.1016/j.aquaculture.2016.01.004 | Genomes; Marine fish; Bibliographic information; Population genetics; Growth; Taxonomy; Hormones; Fish culture; New species; Insulin-like growth factor I; Quantitative trait loci; Evolutionary conservation; Synteny; MAP kinase; Growth hormone; Data processing; Farms; Aquaculture; Insulin; Body weight; Breeding; Genetic markers; genomics; Gene mapping; Signal transduction; Feasibility studies; Proteins; Fish; Mapping; Dicentrarchus labrax; Teleostei; Marine | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Whole-Genome | Comparative genomics; Genome mapping; Teleost fish; Quantitative trait loci; Aquaculture | This paper describes a comparitive approach to use genomic data from "model" species (such as puffer fish or zerbrafish) to build genomic resources for exploited non-model species. However, given the huge reduction is genome sequencing costs and difficulty, the relevance of this work for fishery managers is low. | Sarropoulou, E., & Fernandes, J. M. O. (2011). Comparative genomics in teleost species: Knowledge transfer by linking the genomes of model and non-model fish species. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 6(1), 92-102. doi:https://doi.org/10.1016/j.cbd.2010.09.003 | 1-Mar-2011 | https://doi.org/10.1016/j.cbd.2010.09.003 | Phylogeny; Genomes; Population genetics; Fish physiology; Commercial species; Evolution; Modelling; Quantitative trait loci; Economics; proteomics; genomics; Gene mapping; Models; Teleostei; Pan troglodytes | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Whole-Genome | EST; gene expression; genetic linkage map; genomics; microarray; Pleuronectiformes | This paper provides a now somewhat dated review of 'omics data applied to flatfish biology. The concepts and approcahes decsribed are still relevant to groups of understudied fishes; however specific applications to practical management options are weak. This would be of limited value to most fishery managers today. | Cerda, J., Douglas, S., & Reith, M. (2010). Genomic resources for flatfish research and their applications. Journal of Fish Biology, 77(5), 1045-1070. doi:https://doi.org/10.1111/j.1095-8649.2010.02695.x | 30-Jun-2010 | https://doi.org/10.1111/j.1095-8649.2010.02695.x | Gene expression; Genomes; Marine fish; Fishery management; Fish physiology; Offshore structures; Fish culture; Databases; Data processing; Genetic control; genomics; Aquaculture; DNA microarrays; Gene mapping; Reviews; Physiology; Fish; Technology; Organizations; Construction; Fish Populations; Maps; Productivity; Teleostei; Marine | Opinion / Review | Theoretical | SW | Global | |||
| Transcriptomics | Functional genomics; gene expression; microarrays; transcriptomics | Goetz, F. W., & MacKenzie, S. (2008). Functional genomics with microarrays in fish biology and fisheries. Fish and Fisheries, 9(4), 378-395. doi:https://doi.org/10.1111/j.1467-2979.2008.00301.x | 24-Nov-2008 | https://doi.org/10.1111/j.1467-2979.2008.00301.x | Gene expression; Anadromous species; Commercial availability; Fisheries; DNA; Genetic diversity; Natural populations; Speciation; Host-pathogen interactions; genomics; DNA microarrays; Evolution; Salmonidae; Marine | Opinion / Review | Theoretical | SW | Global | ||||
| Genomics - Genome-Wide | fisheries; genomics; next-generation sequencing; fisheries management; adaptive diversity; outlier loci | This review advocates for a role of genomic analyses in fisherie science primarily through identification of adaptive genomic regions and the potential for environmental stressors and fishing to drive maladaptive changes in the genome. The authors also note other potential genomic applications in fisheries (such as sample origin identification for fishery forensics). A good review of genomic technologies in fishery science. | Valenzuela-Quiñonez, F. (2016). How fisheries management can benefit from genomics? BRIEFINGS IN FUNCTIONAL GENOMICS, 15(5). http://dx.doi.org/10.1093/bfgp/elw006 | 19-Mar-2016 | http://dx.doi.org/10.1093/bfgp/elw006 | COD GADUS-MORHUA; POPULATION-STRUCTURE; INDUCED EVOLUTION; EUROPEAN HAKE; SNP DISCOVERY; ATLANTIC COD; GENETIC-STRUCTURE; FISH; CONSERVATION; SELECTION; Biotechnology & Applied Microbiology; Genetics & Heredity | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | ddRAD; Fishery; Genomic; Dispersal; MPA | This paper proposes genomic applications in the assessment of the efficacy of marine protected areas (MPAs); however their ideas are relevant for any fishery management action involving protected areas to preserve stocks. The authors note that patterns of connectivity and recruitment are critical for MPAs to serve their intended function. While some of the technical details may not be helpful to fishery managers, the basic message is sound - population structure quantification is a powerful applictaion of genomics. | Willis, SC; Hollenbeck, CM; Puritz, JB; Portnoy, DS. (2022). Genetic recruitment patterns are patchy and spatiotemporally unpredictable in a deep-water snapper (Lutjanus vivanus) sampled in fished and protected areas of western Puerto Rico CONSERVATION GENETICS, 23(3). http://dx.doi.org/10.1007/s10592-021-01426-2 | 29-Jan-2022 | http://dx.doi.org/10.1007/s10592-021-01426-2 | EFFECTIVE POPULATION-SIZE; RED SNAPPER; SPATIAL AUTOCORRELATION; MARINE POPULATIONS; LARVAL DISPERSAL; CONNECTIVITY; CONSERVATION; RETENTION; DYNAMICS; SINKS; Biodiversity & Conservation; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | population genomics; fisheries; Scombridae; migratory; pelagic; fish | This paper provides a case study of Atlantic mackerel population genetic analysis using genome-wide genetic markers. Two groups of mackerel spawn in different jurisdicions, hence identifying the fish to source is important for management of the fishery in this declining species. The technical components of this paper may not be very useful for managers, but the application of genome-wide markers to detect subtle population structure in an exploited species is valuable. | Bourret, A; Smith, A; Van Beveren, E; Plourde, S; Curti, KL; Jansen, T; Richardson, DE; Castonguay, M; Rodriguez-Ezpeleta, N; Parent, GJ. (2023). Quantifying genetic differentiation and population assignment between two contingents of Atlantic mackerel (Scomber scombrus) in the Northwest Atlantic CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES, (). http://dx.doi.org/10.1139/cjfas-2022-0232 | 23-Mar-2023 | http://dx.doi.org/10.1139/cjfas-2022-0232 | VARIANT CALL FORMAT; NORDIC SEAS; R-PACKAGE; TOOL SET; NUMBER; PHYLOGEOGRAPHY; MANAGEMENT; INFERENCE; SOFTWARE; GENOMICS; Fisheries; Marine & Freshwater Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | whole genome sequencing; Muskellunge; population genomics; Fisheries; inbreeding | This paper describes a population genetic analysis of genome-wide marker variation using data from a limited number of breeder muskellunge in Iowa and pre-existing data for >600 Canadian fish. The authors report population structure and and genetic markers showing evidence for local selection and inbreeding in some populations. While this paper demonstrates the power of whole-genome marker analyses, the outcomes are of limited practical value for fishery management. | Chinchilla-Vargas, J; Meerbeek, JR; Rothschild, MF; Bertolini, F. (2021). Signatures of Selection and Genomic Diversity of Muskellunge (Esox masquinongy) from Two Populations in North America GENES, 12(7). http://dx.doi.org/10.3390/genes12071021 | 30-Jun-2021 | http://dx.doi.org/10.3390/genes12071021 | SITE FIDELITY; GENETIC-STRUCTURE; PIKE; DISCOVERY; SALMON; TROUT; MODEL; LAKE; SET; Genetics & Heredity | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | adaptive genetic variation; biophysical models; fisheries management; population genomics | This paper describes the potential for combining biophysical modelling and population genomics to better identify functional population connectivity and locally adaptive gene regions. The authors argue that the proposed approach provides a framework for evolutionary fisheries management. However, the practical outcomes of the evolutionary framework, in terms of management action, are not clear. | Baltazar-Soares, M; Hinrichsen, HH; Eizaguirre, C. (2018). Food for Thought Integrating population genomics and biophysical models towards evolutionary-based fisheries management ICES JOURNAL OF MARINE SCIENCE, 75(4). http://dx.doi.org/10.1093/icesjms/fsx244 | 6-Jan-2018 | http://dx.doi.org/10.1093/icesjms/fsx244 | TOOTHFISH DISSOSTICHUS-MAWSONI; ANCHOVY ENGRAULIS-ENCRASICOLUS; HERRING CLUPEA-HARENGUS; EARLY-LIFE HISTORY; COD GADUS-MORHUA; NORTH-SEA COD; MARINE FISHES; ATLANTIC COD; ANTARCTIC TOOTHFISH; LOCAL ADAPTATION; Fisheries; Marine & Freshwater Biology; Oceanography | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | European fisheries; genomics; marine conservation; renewable resources; stock assessments | This paper is a critical review of the application of genetics (genomics) technology in fishery management, primarily marine fisheries. The authors note that developing new genomic tools for fishery management and conservation is not by itself helpful and the goal should be to define fishery-focussed needs, then determine if genomics can provide useful input. Very relevant for fishery managers, and not too technical. | Casey, J; Jardim, E; Martinsohn, JT. (2016). The role of genetics in fisheries management under the EU common fisheries policy JOURNAL OF FISH BIOLOGY, 89(6). http://dx.doi.org/10.1111/jfb.13151 | 19-Oct-2016 | http://dx.doi.org/10.1111/jfb.13151 | EUROPEAN HAKE; STOCK CONCEPT; POPULATION; CONSERVATION; MARKERS; Fisheries; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | fisheries; genomics; stock assessment; high throughput sequencing; research surveys | This is an overview of a special issue of a journal. It just summarizes the papers in the issue, I'm not sure how relevant it is for this database. | Casas, L; Hanel, R; Piferrer, F; Saborido-Rey, F. (2023). Prospects and challenges for the implementation of HTS genetic methods in fisheries research surveys and stock assessments FRONTIERS IN MARINE SCIENCE, 10(). http://dx.doi.org/10.3389/fmars.2023.1238133 | 13-Jul-2013 | http://dx.doi.org/10.3389/fmars.2023.1238133 | ; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Applied | NA | Global | |||
| Genomics - Genome-Wide | conservation; deep-sea; fisheries management; orange roughy; population genomics | This is a data based study that uses ~4K genetic markers to examine the potential for genomic divergence in a species of marine fish. They found a lack of differentiation between the groups. The study is put in the context of how genomics approaches can be used to inform populations that can help restore overharvested populations. | da Silva, AG; Appleyard, SA; Upston, J. (2015). Establishing the evolutionary compatibility of potential sources of colonizers for overfished stocks: a population genomics approach MOLECULAR ECOLOGY, 24(3). http://dx.doi.org/10.1111/mec.13046 | 17-Dec-2014 | http://dx.doi.org/10.1111/mec.13046 | ROUGHY HOPLOSTETHUS-ATLANTICUS; MULTILOCUS GENOTYPE DATA; TELEOST ORANGE ROUGHY; COD GADUS-MORHUA; GENE FLOW; MITOCHONDRIAL-DNA; FISHERIES MANAGEMENT; MIGRATION RATES; ADAPTIVE VARIATION; CONTINENTAL-SLOPE; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | comparative genomics; marine fisheries; microsatellite; stock structure; threatened species | This is a data based paper that uses laregly out of date methods to assess population differences between groups of species. This was likely fine at the time, however there are more cost-effective and high-throughput methods that can be used now to address these questions. | Buonaccorsi, VP; Kimbrell, CA; Lynn, EA; Hyde, JR. (2012). Comparative Population Genetic Analysis of Bocaccio Rockfish Sebastes paucispinis Using Anonymous and Gene-Associated Simple Sequence Repeat Loci JOURNAL OF HEREDITY, 103(3). http://dx.doi.org/10.1093/jhered/ess002 | 4-Apr-2012 | http://dx.doi.org/10.1093/jhered/ess002 | MICROSATELLITES; SELECTION; ATLANTIC; SSRS; DIFFERENTIATION; ADAPTATION; MUTATIONS; PATTERNS; MARKERS; HEART; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | conservation genomics; fisheries management; native brook trout; SNP panels | This is a data based paper that uses reduced representation sequencing to identify 24K genetic markers that are useful for characterizing population structure of brook trout. They use these markers to discuss how this approach can be used to develop targetted panels for future population genetics work. This would be a valuable approach for setting up long term monitoring programs for species of interest. | Mamoozadeh, NR; Whiteley, AR; Letcher, BH; Kazyak, DC; Tarsa, C; Meek, MH. (2023). A new genomic resource to enable standardized surveys of SNPs across the native range of brook trout (Salvelinus fontinalis) MOLECULAR ECOLOGY RESOURCES, (). http://dx.doi.org/10.1111/1755-0998.13853 | 16-Aug-2023 | http://dx.doi.org/10.1111/1755-0998.13853 | GENETIC DIVERSITY; POPULATION ASSIGNMENT; PARENTAGE ASSIGNMENT; ASCERTAINMENT BIAS; R-PACKAGE; CONSERVATION; HATCHERY; CHARR; MANAGEMENT; PATTERNS; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | North America | ||||
| Genomics - Genome-Wide | ecology; ecotype divergence; fisheries management; genomics; population genetics; recruitment | This is a data based study that uses reduced representation sequencing and a targetted 62 marker panel to characterize genomic differentiation of 2 sympatric ecotypes of a marine fish. They are able to find genetic differences related to ecotype and potential habitat use. This is a good example of how genomics data can help understand habitat use and management of fish in mixed-stock fisheries. | Henriksson, S; Pereyra, RT; Sodeland, M; Ortega-Martinez, O; Knutsen, H; Wennhage, H; André, C. (2023). Mixed origin of juvenile Atlantic cod (Gadus morhua) along the Swedish west coast ICES JOURNAL OF MARINE SCIENCE, 80(1). http://dx.doi.org/10.1093/icesjms/fsac220 | 15-Dec-2022 | http://dx.doi.org/10.1093/icesjms/fsac220 | R-PACKAGE; NORTH-SEA; DIVERGENCE; RECRUITMENT; ADAPTATION; LANDSCAPE; DEPLETION; ECOTYPES; STOCKS; Fisheries; Marine & Freshwater Biology; Oceanography | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | adaptive divergence; fisheries; management; population genomics; SNP panel; temporal stability | This is a data based paper that uses a relatively small number of genetic markers to compare populations of a marine species that spawn at different times of year. They are able to establish genetic differences between the different spawning groups despite using a limited number of markers. | Kerr, Q; Fuentes-Pardo, AP; Kho, J; McDermid, JL; Ruzzante, DE. (2019). Temporal stability and assignment power of adaptively divergent genomic regions between herring (Clupea harengus) seasonal spawning aggregations ECOLOGY AND EVOLUTION, 9(1). http://dx.doi.org/10.1002/ece3.4768 | 11-Dec-2018 | http://dx.doi.org/10.1002/ece3.4768 | COD GADUS-MORHUA; GENE-FLOW; POPULATION DIVERSITY; SNP ANALYSIS; ATLANTIC; SELECTION; DIFFERENTIATION; HYBRIDIZATION; EVOLUTIONARY; STRATEGIES; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | fisheries genetics; Pool-Seq; genomic diversity; marine biodiversity; stock structure | This is a data based paper that uses 40K genetic markers to characterize population structure of a fish species. They used a pool-seq approach, which is a cost-effective sequencing strategy for only population-level assessments (i.e., the individual doesn't matter). | Schulze, MJ; von der Heyden, S; Japp, D; Singh, L; Durholtz, D; Kapula, VK; Ndjaula, HON; Henriques, R. (2020). Supporting Fisheries Management With Genomic Tools: A Case Study of Kingklip (Genypterus capensis) Off Southern Africa FRONTIERS IN MARINE SCIENCE, 7(). http://dx.doi.org/10.3389/fmars.2020.557146 | 24-Sep-2020 | http://dx.doi.org/10.3389/fmars.2020.557146 | HIGH GENE FLOW; R-PACKAGE; ADAPTIVE DIFFERENTIATION; POPULATION-GENETICS; MOLECULAR MARKERS; LOCAL ADAPTATION; NEXT-GENERATION; READ ALIGNMENT; FRESH-WATER; MARINE; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | comparative genomics; fisheries; Pacific halibut; RAD; sex determination; sex identification | This is a data based paper that uses reduced representation sequencing to identity sex-linked genomic differences in male and females of a marine species. They take advantage of assembled reference genomes of closely related species to attempt to link some of the genetic markers with sex chromosomes. This demonstrates how to rapidly develop sex-link markers that can be used to quantify sex ratios in commercial catches. | Drinan, DP; Loher, T; Hauser, L. (2018). Identification of Genomic Regions Associated With Sex in Pacific Halibut JOURNAL OF HEREDITY, 109(3). http://dx.doi.org/10.1093/jhered/esx102 | 9-Nov-2017 | http://dx.doi.org/10.1093/jhered/esx102 | FLATFISH; FISH; PLEURONECTIFORMES; LOCI; EVOLUTION; ALIGNMENT; GENETICS; STACKS; GROWTH; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Whole-Genome | population genomics; whole-genome sequencing; demography; conservation; tuna; fisheries management | This is a data based paper that uses whole genome sequencing from populations of a marine species to charaacterize population structure at a global scale. They also assembled a species-specific reference genome to facilitate population genetics studies for this species in the future. This is an example of the importance of developing genomic resources for species of importance. | Barth, JMI; Damerau, M; Matschiner, M; Jentoft, S; Hanel, R. (2017). Genomic Differentiation and Demographic Histories of Atlantic and Indo-Pacific Yellowfin Tuna (Thunnus albacares) Populations GENOME BIOLOGY AND EVOLUTION, 9(4). http://dx.doi.org/10.1093/gbe/evx067 | 1-Apr-2017 | http://dx.doi.org/10.1093/gbe/evx067 | BIGEYE TUNA; KATSUWONUS-PELAMIS; MARINE FISHES; MISSING DATA; R-PACKAGE; FRAMEWORK; INFERENCE; ALIGNMENT; OBESUS; CONSEQUENCES; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | conservation genomics; fisheries management; genomic diversity; Pool-Seq; population dynamics | This is a data based paper that uses a pool-seq strategy to characterize population structure in 2 species of fishes. Pool-seq is a cost-effective sequencing strategy for only population-level assessments (i.e., the individual doesn't matter). | Forde, S; von der Heyden, S; Le Moan, A; Nielsen, ES; Durholtz, D; Kainge, P; Kathena, JN; Lipinski, MR; Ndjaula, HON; Matthee, CA; Henriques, R. (2023). Management and conservation implications of cryptic population substructure for two commercially exploited fishes (Merluccius spp.) in southern Africa MOLECULAR ECOLOGY RESOURCES, (). http://dx.doi.org/10.1111/1755-0998.13820 | 8-Jun-2023 | http://dx.doi.org/10.1111/1755-0998.13820 | GENETIC DIVERSITY; LOCAL SELECTION; M. PARADOXUS; DIFFERENTIATION; CAPENSIS; ATLANTIC; DNA; BENGUELA; HISTORY; COMPLEX; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | SW | Africa | |||
| Genomics - Genome-Wide | ddrad; fisheries management; marine biogeography; marine teleost; population genomics; stock delineation | This is a data based paper that uses reduced representation sequencing to characterize population structure in a marine species. This paper demonstrates how genomics can be used to identify population units for fishery management. | Bertram, A; Bell, J; Brauer, CJ; Fowler, A; Hamer, P; Sandoval-Castillo, J; Stewart, J; Wellenreuther, M; Beheregaray, LB. (2023). Biogeographic provinces and genomically delineated stocks are congruent in snapper (Chrysophrys auratus) from southeastern Australia ICES JOURNAL OF MARINE SCIENCE, 80(5). http://dx.doi.org/10.1093/icesjms/fsad068 | 29-Apr-2023 | http://dx.doi.org/10.1093/icesjms/fsad068 | POPULATION-STRUCTURE; MARINE BIOGEOGRAPHY; SOUTHERN AUSTRALIA; PAGRUS-AURATUS; LIFE-HISTORY; CONNECTIVITY; TEMPERATURE; RECRUITMENT; SPARIDAE; GENETICS; Fisheries; Marine & Freshwater Biology; Oceanography | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | Coaster brook trout; Lake Superior; Population genomics; Native trout; Fisheries management | This is a data based paper that uses ~8k genetic markers to compare genetic structure of several tributaries, hatcheries and a species ecotype of brook trout in the Great Lakes. They are able to use the genomic patterns to determine which river populations act as source populations for the lake (i.e., coaster) ecotype. This is an effective example that shows how genomics can inform conservation strategies for large lake ecosystems. | Mamoozadeh, N; Goldsworthy, C; Miller, L; Peterson, N; Meek, M. (2023). Sources of coaster brook trout (Salvelinus fontinalis) revealed by genomic analysis of brook trout populations along Minnesota's shoreline with Lake Superior JOURNAL OF GREAT LAKES RESEARCH, 49(4). http://dx.doi.org/10.1016/j.jglr.2023.06.005 | 1-Aug-2023 | http://dx.doi.org/10.1016/j.jglr.2023.06.005 | LINKAGE DISEQUILIBRIUM; GENETIC-STRUCTURE; R-PACKAGE; PROJECTED IMPACTS; PACIFIC SALMON; CLIMATE-CHANGE; LIFE-HISTORY; 50/500 RULES; N-E; CONSERVATION; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | demographic models; fishery management; population genomics; related species; Sebastes; spatial ecology | This is a data based paper that uses 24K markers to characterize population structure of 2 marine species. They are able to show that the large number of markers that are used in genomics can be successfully used to characterize differences between cryptic species. This work shows how population genomics approaches can inform management units for commercially harvested species. | Benestan, LM; Rougemont, Q; Senay, C; Normandeau, E; Parent, E; Rideout, R; Bernatchez, L; Lambert, Y; Audet, C; Parent, GJ. (2021). Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus) EVOLUTIONARY APPLICATIONS, 14(2). http://dx.doi.org/10.1111/eva.13143 | 30-Sep-2020 | http://dx.doi.org/10.1111/eva.13143 | GENETIC-STRUCTURE; GENUS SEBASTES; GEOMETRIC MORPHOMETRICS; CONSERVATION GENOMICS; ATLANTIC; INTROGRESSION; DIVERGENCE; ASSIGNMENT; MICROSATELLITES; DIVERSIFICATION; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | ddRADseq; fisheries management; marine connectivity; marine teleost; population genomics; stock structure | This is a data based study that uses reduced representation sequencing to characterize population structure of a marine fish across a large geographical area. They used ~11K markers to show that the genomic differences between regions do not match the fishery management regions. This is a useful example of how population genomics approaches can help inform and re-structure managment zones for fisheries species. | Bertram, A; Fairclough, D; Sandoval-Castillo, J; Brauer, C; Fowler, A; Wellenreuther, M; Beheregaray, LB. (2022). Fisheries genomics of snapper (Chrysophrys auratus) along the west Australian coast EVOLUTIONARY APPLICATIONS, 15(7). http://dx.doi.org/10.1111/eva.13439 | 20-Jun-2022 | http://dx.doi.org/10.1111/eva.13439 | SPATIAL AUTOCORRELATION ANALYSIS; PAGRUS-AURATUS; LEEUWIN CURRENT; GENE FLOW; POPULATION-STRUCTURE; SPAWNING AGGREGATIONS; LARVAL DISPERSAL; CURRENT SYSTEM; LIFE-HISTORY; ATLANTIC COD; Evolutionary Biology | Technical / Data | Theoretical | SW | Australia | |||
| Genomics - Genome-Wide | fisheries-induced evolution; population genomics; genetic diversity; selective sweeps; historical DNA | This is a data based paper that uses whole genome sequencing to examine the effects of fishing pressure on a wild marine fish. They compare samples from 2 locations sampled years apart from each other and use >300k markers for the analyses, which would be needed to detect subtle changes in the genomes of these populations. This study shows that populations can maintain genetic diversity over time despite heavy fishing pressure and that phenotypic changes can occur in fished populations in the absence of large-scale genomic changes. | Pinsky, ML; Eikeset, AM; Helmerson, C; Bradbury, IR; Bentzen, P; Morris, C; Gondek-Wyrozemska, AT; Baalsrud, HT; Brieuc, MSO; Kjesbu, OS; Godiksen, JA; Barth, JMI; Matschiner, M; Stenseth, NC; Jakobsen, KS; Jentoft, S; Star, B. (2021). Genomic stability through time despite decades of in cod on both sides of the Atlantic PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(15). http://dx.doi.org/10.1073/pnas.2025453118 | 7-Apr-2021 | http://dx.doi.org/10.1073/pnas.2025453118 | FISHERIES-INDUCED EVOLUTION; EFFECTIVE POPULATION-SIZE; GENE-EXPRESSION; LOCAL ADAPTATION; SIGNATURES; REVEALS; HISTORY; SEQUENCE; SHIFTS; YIELDS; Science & Technology - Other Topics | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | deep sea; fisheries; fjords; genomics; ling; Molva dypterygia; Molva molva; SNPs | This is a data based study that uses reduced representation DNA sequencing to characterize population structure of two species in the marine environment. This approach uses genotyping by sequencing, which effectively uses the results of the sequencing to determine the population of origin for an individual based on genetic similarity. This is a useful approach for mixed stock fisheries or situations where different populations occupy similar habitats at very stages of their life-histories. | McGill, L; McDevitt, AD; Hellemans, B; Neat, F; Knutsen, H; Mariani, S; Christiansen, H; Johansen, T; Volckaert, FAM; Coscia, I. (2023). Population structure and connectivity in the genus Molva in the Northeast Atlantic ICES JOURNAL OF MARINE SCIENCE, 80(4). http://dx.doi.org/10.1093/icesjms/fsad040 | 17-Mar-2023 | http://dx.doi.org/10.1093/icesjms/fsad040 | DEEP-WATER; R-PACKAGE; MANAGEMENT; FISH; FISHERIES; EVOLUTION; SELECTION; PATTERNS; FUTURE; SAITHE; Fisheries; Marine & Freshwater Biology; Oceanography | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | Arctic; conservation; fish migration; fishery management; genotyping by sequencing; population genomics; RADseq | This is a data based paper that uses reduced representation DNA sequencing to characterize population structure in a migratory species. This study combines non-lethal tissue sampling and telemetry tagging to related genetic structure to migration patterns. This is a great example of how genomics analyses can improve our understanding of fish behavior and habitat use in the wild. | Moore, JS; Harris, LN; Le Luyer, J; Sutherland, BJG; Rougemont, Q; Tallman, RF; Fisk, AT; Bernatchez, L. (2017). Genomics and telemetry suggest a role for migration harshness in determining overwintering habitat choice, but not gene flow, in anadromous Arctic Char MOLECULAR ECOLOGY, 26(24). http://dx.doi.org/10.1111/mec.14393 | 31-Oct-2017 | http://dx.doi.org/10.1111/mec.14393 | SALMON ONCORHYNCHUS-TSHAWYTSCHA; SALVELINUS-ALPINUS; ATLANTIC SALMON; PROVIDES INSIGHTS; SOCKEYE-SALMON; LINKAGE MAP; R-PACKAGE; ADAPTATION; LOCI; EVOLUTION; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | fishery management; genomic differentiation; Lates angustifrons; Lates mariae; Lates microlepis; Lates stappersii | This is a data based paper that uses reduced representation DNA sequencing to characterize population structure in 4 species of fish in a single large lake system. This study highlights how using genomic data with a large number of markers can help detect subtle population divergence between populations. | Rick, JA; Junker, J; Kimirei, IA; Sweke, EA; Mosille, JB; Dinkel, C; Mwaiko, S; Seehausen, O; Wagner, CE. (2022). The Genetic Population Structure of Lake Tanganyika's Lates Species Flock, an Endemic Radiation of Pelagic Top Predators JOURNAL OF HEREDITY, 113(2). http://dx.doi.org/10.1093/jhered/esab072 | 5-Dec-2021 | http://dx.doi.org/10.1093/jhered/esab072 | VARIANT CALL FORMAT; LARVAL DURATION; NILE PERCH; READ ALIGNMENT; NORTHERN PART; TOOL SET; MANAGEMENT; FISHERIES; FISH; ATLANTIC; Evolutionary Biology; Genetics & Heredity | Technical / Data | Theoretical | FW | Africa | |||
| Genomics - Genome-Wide | age and growth analysis; bioinformatic filtering; fisheries harvest; population genomics; RADseq; walleye | The paper is a response to another study that re-analyzed the genomic data to a different study and drew different conclusions about the potential for rapid fisheries induced evolution. The authors stress the importance of large sample sizes for drawing conclusions about rapid genomic changes in wild populations. This paper disagreeing with the orginal paper highlight how differences in analysis approaches can lead to different conclusions despite using the same data sets. | Larson, WA; Isermann, DA; Feiner, ZS. (2021). Incomplete bioinformatic filtering and inadequate age and growth analysis lead to an incorrect inference of harvested-induced changes EVOLUTIONARY APPLICATIONS, 14(2). http://dx.doi.org/10.1111/eva.13122 | 12-Sep-2020 | http://dx.doi.org/10.1111/eva.13122 | WALLEYE SANDER-VITREUS; NORTHERN WISCONSIN; POPULATION; SIZE; MATURATION; MORTALITY; DENSITY; EXPLOITATION; RECRUITMENT; MANAGEMENT; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | Acanthocybium solandri; connectivity; demographic inference; fisheries management; population genomics; population structure; wahoo | This is a data based study that uses reduced representation DNA sequencing to examine population structure between different ocean basins. It uses a process known as pool seq, which effectively pools all individuals from a single collection location in preparing the samples for sequencing, therefore the inferences that can be made are only at the level of the population (i.e., the variation between individuals is ignored). This is a cost effective method for examining genomic divergence between populations. | Haro-Bilbao, I; Riginos, C; Baldwin, JD; Zischke, M; Tibbetts, IR; Thia, JA. (2021). Global connections with some genomic differentiation occur between Indo-Pacific and Atlantic Ocean wahoo, a large circumtropical pelagic fish JOURNAL OF BIOGEOGRAPHY, 48(8). http://dx.doi.org/10.1111/jbi.14135 | 24-May-2021 | http://dx.doi.org/10.1111/jbi.14135 | TUNA THUNNUS-ALBACARES; ACANTHOCYBIUM-SOLANDRI; REPRODUCTIVE-BIOLOGY; MITOCHONDRIAL-DNA; GENETIC-STRUCTURE; NEXT-GENERATION; BLUEFIN TUNA; POPULATION; CONSERVATION; EASTERN; Environmental Sciences & Ecology; Physical Geography | Technical / Data | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | fish; fisheries management; genomics; proteomics; invasive species; landscape genetics; population genetics - empirical | This is a data based paper that uses reduced representation sequencing to characterize genetic variation in multiple species of riverine fish separated by an upstream migration barrier. They are able to determine that in the presence of a migration barrier, there was evidence of unidirectional gene flow between populations and that genetic diversity increased below the barrier. This is a useful study for understanding the role of unidirectional gene flow in the genetic variation detected in wild populations. | Lujan, NK; Weir, JT; Noonan, BP; Lovejoy, NR; Mandrak, NE. (2020). Is Niagara Falls a barrier to gene flow in riverine fishes? A test using genome-wide SNP data from seven native species MOLECULAR ECOLOGY, 29(7). http://dx.doi.org/10.1111/mec.15406 | 23-Mar-2020 | http://dx.doi.org/10.1111/mec.15406 | FRESH-WATER MUSSEL; POPULATION-GENETICS; SPATIAL-PATTERNS; DIVERSITY; DISPERSAL; RANGE; PHYLOGEOGRAPHY; RECESSION; MOVEMENT; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | ancient DNA; archaeology; fish; fisheries; genomics; high-throughput sequencing; next-generation sequencing | This is a conceptual paper that describes the potential for the use of ancient DNA in contemporary fisheries studies. Ancient DNA involves extracting DNA from archived or museam samples. This is an interesting approach to be able to observe genetic change in wild populations during periods of intense human influence. | Oosting, T; Star, B; Barrett, JH; Wellenreuther, M; Ritchie, PA; Rawlence, NJ. (2019). Unlocking the potential of ancient fish DNA in the genomic era EVOLUTIONARY APPLICATIONS, 12(8). http://dx.doi.org/10.1111/eva.12811 | 9-May-2019 | http://dx.doi.org/10.1111/eva.12811 | EFFECTIVE POPULATION-SIZE; SPECIES IDENTIFICATION; DIONISIO POINT; PACIFIC SALMON; CLIMATE-CHANGE; ATLANTIC COD; SNP ANALYSIS; FISHERIES; REVEALS; FUTURE; Evolutionary Biology | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | forage fishes; Arctic; genotype-environment association analyses; population genomics; metadata; fisheries management | This is a meta-analysis that attempts to relate genomics data to environmental conditions in marine species. This work addresses the concept of seascape genomics, which is a term to describe genome and environment relationships between populations along a continuous gradient (i.e., the aquatic version of landscape genomics). This paper describes the metadata needs for papers submitted to journals that would help facilitate these types of studies in the future. | Timm, LE; Tucker, N; Rix, A; Labua, S; López, JA; Boswell, KM; Glass, JR. (2023). The untapped potential of seascape genomics in the North Pacific FRONTIERS IN CONSERVATION SCIENCE, 4(). http://dx.doi.org/10.3389/fcosc.2023.1249551 | 14-Sep-2023 | http://dx.doi.org/10.3389/fcosc.2023.1249551 | GENETICS; Biodiversity & Conservation; Environmental Sciences & Ecology | Opinion / Review | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | high-throughput sequencing; genomics; species distribution model (SDMs); fisheries applications; evolutionary ecology | This is a conceptual paper that discusses how genomics data can be incorporated into species distribution models. The authors suggest that incorporating genomics data into these models will help predict range shifts in the future. | Baltazar-Soares, M; Lima, ARA; Silva, G; Gaget, E. (2023). Towards a unified eco-evolutionary framework for fisheries management: Coupling advances in next-generation sequencing with species distribution modelling FRONTIERS IN MARINE SCIENCE, 9(). http://dx.doi.org/10.3389/fmars.2022.1014361 | 6-Jan-2023 | http://dx.doi.org/10.3389/fmars.2022.1014361 | LOCAL ADAPTATION; CLIMATE-CHANGE; GENE-EXPRESSION; MARINE FISH; RANGE; GENOMICS; MICROSATELLITES; POPULATIONS; INFECTION; INFERENCE; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | biodiversity; conservation genetics; fisheries; molecular population genetics; genomics; SNP; selection; aquatic organisms | This is a review paper that discusses the utility of genetic markers that can be identified using modern DNA sequencing approaches (i.e., SNPs). This paper discusses the applications for wild fishes and highlights the advantages of using a higher resolution SNP appraoch over traditional genetic markers. | Wenne, R. (2023). Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations ANIMALS, 13(6). http://dx.doi.org/10.3390/ani13061089 | 18-Mar-2023 | http://dx.doi.org/10.3390/ani13061089 | COD GADUS-MORHUA; SALMON ONCORHYNCHUS-TSHAWYTSCHA; PARALLEL ADAPTIVE EVOLUTION; GENOME-WIDE DISCOVERY; ATLANTIC COD; SNP DISCOVERY; GENETIC DIFFERENTIATION; CHINOOK SALMON; INTROGRESSIVE HYBRIDIZATION; MARINE FISH; Agriculture; Veterinary Sciences; Zoology | Opinion / Review | Theoretical | NA | Global | |||
| Genomics - Genome-Wide | Atlantic cod (Gadus morhua); conservation; evolution; fisheries management; genetics; genomics; marine fishes | This is a data based paper that used 438 genetic markers to develop a 39 marker panel for genetic stock ID in a wild commercial species. This paper demonstrates how genetic ID can be incorporated into managine mixed-stock fisheries. | Hemmer-Hansen, J; Hüssy, K; Baktoft, H; Huwer, B; Bekkevold, D; Haslob, H; Herrmann, JP; Hinrichsen, HH; Krumme, U; Mosegaard, H; Nielsen, EE; Reusch, TBH; Storr-Paulsen, M; Velasco, A; von Dewitz, B; Dierking, J; Eero, M. (2019). Genetic analyses reveal complex dynamics within a marine fish management area EVOLUTIONARY APPLICATIONS, 12(4). http://dx.doi.org/10.1111/eva.12760 | 30-Dec-2018 | http://dx.doi.org/10.1111/eva.12760 | COD GADUS-MORHUA; WESTERN BALTIC COD; MIXED-STOCK ANALYSIS; POPULATION-STRUCTURE; GEOGRAPHIC ORIGIN; EGG BUOYANCY; REAL-TIME; BELT SEA; ATLANTIC; CONSERVATION; Evolutionary Biology | Technical / Data | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | cryptic species; ecological speciation; genomics; mixed-stock fishery; otolith; Platichthys flesus; Platichthys solemdali | This is a synthesis paper that discusses how genomics have contributed to an increased understanding of the genetic differentiation between cryptic species that are harvested in a mixed-fishery. This is an example of how genomics can contribute to a better understanding of watch species are harvested and therefore can be used for managing the fishery. | Jokinen, H; Momigliano, P; Merilä, J. (2019). From ecology to genetics and back: the tale of two flounder species in the Baltic Sea ICES JOURNAL OF MARINE SCIENCE, 76(7). http://dx.doi.org/10.1093/icesjms/fsz151 | 21-Aug-2019 | http://dx.doi.org/10.1093/icesjms/fsz151 | PLATICHTHYS-FLESUS; MARINE FISHES; POPULATION-STRUCTURE; SPECIATION; ATLANTIC; SALINITY; GENOMICS; ADAPTATION; DIVERGENCE; RECOMBINATION; Fisheries; Marine & Freshwater Biology; Oceanography | Opinion / Review | Theoretical | SW | Europe | |||
| Genomics - Genome-Wide | adaptation; conservation genetics; fisheries management; genomics; life history evolution; natural selection; pop`ulation genetics | This is a perspectives paper that discusses how genomics data can be used to understand the genetic basis of specific traits in species. This paper then discusses how this information can be used to inform conservation strategies by resource managers. | Waples, RS; Lindley, ST. (2018). Genomics and conservation units: The genetic basis of adult migration timing in Pacific salmonids EVOLUTIONARY APPLICATIONS, 11(9). http://dx.doi.org/10.1111/eva.12687 | 1-Aug-2018 | http://dx.doi.org/10.1111/eva.12687 | CHINOOK SALMON; EVOLUTIONARY PROCESSES; POPULATION GENOMICS; PARALLEL EVOLUTION; DIVERSITY; ADAPTATION; STEELHEAD; HISTORY; DIVERGENCE; STRATEGIES; Evolutionary Biology | Opinion / Review | Theoretical | FW | North America | |||
| Genomics - Genome-Wide | fisheries management; heterogeneous genomic divergence; latitudinal cline; Northeast Pacific Ocean; population genomics; RAD sequencing | This is a data based paper that uses reduced representation DNA sequencing to identify distinct genetic clusters of a species of concern across a substantial latitudinal gradient. This paper describes genetics methods useful for characterizing population units for managing wild species. | Longo, GC; Lam, L; Basnett, B; Samhouri, J; Hamilton, S; Andrews, K; Williams, G; Goetz, G; McClure, M; Nichols, KM. (2020). Strong population differentiation in lingcod (Ophiodon elongatus) is driven by a small portion of the genome EVOLUTIONARY APPLICATIONS, 13(10). http://dx.doi.org/10.1111/eva.13037 | 7-Jun-2020 | http://dx.doi.org/10.1111/eva.13037 | GENE FLOW; R-PACKAGE; RANGE SIZE; ROAD MAP; SPECIATION; ROCKFISH; CONSERVATION; MANAGEMENT; PROGRAM; FISHES; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | Indigenous knowledge; Western science; fisheries; population monitoring; genomics; life history; practices for weaving knowledge systems | This is a theoretical paper that compares traditional knowledge of Indigenous communites and genetics approaches for understanding fish populations. The authors state that the approaches are complimentary and they discuss when one approach may be more useful for a particular fisheries question. | Bowles, E; Jeon, HB; Marin, K; MacLeod, P; Fraser, DJ. (2022). Freshwater fisheries monitoring in northern ecosystems using Indigenous ecological knowledge, genomics, and life history: Insights for community decision-making FACETS, 7(). http://dx.doi.org/10.1139/facets-2021-0049 | 8-Sep-2022 | http://dx.doi.org/10.1139/facets-2021-0049 | EFFECTIVE POPULATION-SIZE; SCIENCE; MARINE; MODEL; Science & Technology - Other Topics | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | body size; fisheries-induced evolution; genomics; harvesting; Indigenous knowledge; Sander vitreus; size-at-age; walleye | This is a data based paper that uses 9K genetic markers to attempt to quantify the effects of harvest on wild fish populations. This paper demonstrates that genetic effects of harvest can happen quickly leading to potential fisheries induced evolution. | Bowles, E; Marin, K; Mogensen, S; MacLeod, P; Fraser, DJ. (2020). Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest? EVOLUTIONARY APPLICATIONS, 13(6). http://dx.doi.org/10.1111/eva.12987 | 28-Apr-2020 | http://dx.doi.org/10.1111/eva.12987 | FISHERIES-INDUCED EVOLUTION; TRADITIONAL ECOLOGICAL KNOWLEDGE; GROWING DEGREE-DAY; GENETIC-STRUCTURE; R-PACKAGE; LINKAGE DISEQUILIBRIUM; INDUCED SELECTION; N-E; MODEL; ADAPTATION; Evolutionary Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Whole-Genome | Biological invasion; conservation genomics; exotic species; fisheries; hybridization; Japan Sea stickleback; next-generation sequencer; rapid evolution | This is a data based paper that using whole genome sequencing to understand how some non-native species can become successful invaders despite the potential for genetic bottlenecks associated with colonizing new habitats. This paper demonstrates how hybridization with other species can maintain genetic diversity in an invasive population. This paper provides a potential mechanism for how invasive species can maintain genetic diversity after colonization. | Yoshida, K; Miyagi, R; Mori, S; Takahashi, A; Makino, T; Toyoda, A; Fujiyama, A; Kitano, J. (2016). Whole-genome sequencing reveals small genomic regions of introgression in an introduced crater lake population of threespine stickleback ECOLOGY AND EVOLUTION, 6(7). http://dx.doi.org/10.1002/ece3.2047 | 2-Mar-2016 | http://dx.doi.org/10.1002/ece3.2047 | ADAPTIVE EVOLUTION; GENETIC-VARIATION; BIOLOGICAL INVASION; PARALLEL EVOLUTION; CONSERVATION; HYBRIDIZATION; ADAPTATION; DIVERGENCE; GASTEROSTEUS; MORPHOLOGY; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Theoretical | FW | Asia | |||
| Genomics - Whole-Genome | adaptive differentiation; allochronic reproduction; Atlantic cod; chromosomal inversions; fisheries management; heat shock proteins; population genomics; whole-genome resequencing | This is a data based paper that uses whole-genome sequencing to understand genetic differentiation between populations. This paper provides useful methodology for characterizing the genetic basis of local adaptation in wild fishes. | Clucas, GV; Lou, RN; Therkildsen, NO; Kovach, AI. (2019). Novel signals of adaptive genetic variation in northwestern Atlantic cod revealed by whole-genome sequencing EVOLUTIONARY APPLICATIONS, 12(10). http://dx.doi.org/10.1111/eva.12861 | 29-Aug-2019 | http://dx.doi.org/10.1111/eva.12861 | GADUS-MORHUA; LOCAL ADAPTATION; STOCK IDENTIFICATION; STATIONARY ECOTYPES; SPATIAL STRUCTURE; RAINBOW-TROUT; SNP ANALYSIS; US WATERS; DIVERGENCE; MARINE; Evolutionary Biology | Technical / Data | Theoretical | SW | North America | |||
| Genomics - Genome-Wide | genome-wide association studies; fisheries genomics; aquaculture; teleost; ddRAD; reduced genome representation; ecological genomics; genomic prediction; GenPred; shared data resource | This is a data based paper that uses reduced representation DNA sequencing to identify genetic markers associated with growth in fish in a captivity. This paper describes genetics methods that would be useful for generating optimal traits for captive rearing conditions. | Sandoval-Castillo, J; Beheregaray, LB; Wellenreuther, M. (2022). Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus) G3-GENES GENOMES GENETICS, 12(3). http://dx.doi.org/10.1093/g3journal/jkac015 | 20-Jan-2022 | http://dx.doi.org/10.1093/g3journal/jkac015 | QUANTITATIVE TRAIT LOCI; WIDE ASSOCIATION; GENE-EXPRESSION; LIFE-HISTORY; FISH; TEMPERATURE; VARIANT; GWAS; DOMESTICATION; SIGNATURES; Genetics & Heredity | Technical / Data | Theoretical | SW | Australia | |||
| Transcriptomics | aquaculture; climate change; fisheries management; phenotypic plasticity; transcriptomics | This is a transcriptomics paper. | Valenza-Troubat, N., Davy, M., Storey, R., Wylie, M. J., Hilario, E., Ritchie, P., & Wellenreuther, M. (2022). Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus). Evolutionary Applications, 15, 237–248. https://doi.org/10.1111/eva.13332 | 7-Dec-2021 | https://doi-org.ledproxy2.uwindsor.ca/10.1111/eva.13332 | LIFE-HISTORY TRAITSCLIMATE-CHANGEGENE-EXPRESSIONYELLOWTAIL KINGFISHGROWTH-HORMONEDOMESTICATIONPERFORMANCEADAPTATIONEVOLUTIONIMPACTS | Technical / Data | Theoretical | SW | Australia | |||
| Transcriptomics | Gene-expression; Fish health; Genomics toolkit; Adaptive capacity; Innovative technology; Case study | This is a transcriptomics paper. | Semeniuk, CAD; Jeffries, KM; Li, T; Bettles, CM; Cooke, SJ; Dufour, BA; Halfyard, EA; Heath, JW; Keeshig, K; Mandrak, NE; Muir, AJ; Postma, L; Heath, DD. (2022). Innovating transcriptomics for practitioners in freshwater fish management and conservation: best practices across diverse resource-sector users. REV FISH BIOL FISHER, 32(3). http://dx.doi.org/10.1007/s11160-022-09715-w | 14-May-2022 | http://dx.doi.org/10.1007/s11160-022-09715-w | GENE-EXPRESSION; ENVIRONMENTAL-CHANGE; PREDICT MIGRATION; SELENIUM TOXICITY; CLIMATE-CHANGE; RNA-SEQ; FISHERIES; RESPONSES; STRESS; GENOMICS | Opinion / Review | Applied | FW | North America | |||
| Transcriptomics | This paper describes the de novo assembly and transcriptome analysis of liver, testes, and head kidney from two captive red drum males. The addtional transcriptomic data for this estuarine fish of high commercial value may help improve aquaculture practices and stock enhancement of wild populations. | Sherwood, TA; Main, KL; Wetzel, DL. (2019). De novo assembly and transcriptome dataset of liver, testis and head kidney from red drum (Sciaenops ocellatus). DATA BRIEF, 22(). http://dx.doi.org/10.1016/j.dib.2019.01.011 | 11-Jan-2019 | http://dx.doi.org/10.1016/j.dib.2019.01.011 | Technical / Data | Theoretical | SW | North America | |||||
| Transcriptomics | RNA-seq; transcriptional plasticity; non-model fish; non-lethal sampling; environmental stress | This paper applies a transcriptomics approach to determine which populations are experiencing stress in the wild. Using the transcriptional profiles from non-lethal gill samples, the authors identified sites where fish are experiencing environmental stressors, including low oxygen conditions. This example of a successful application of non-lethal sampling and transcriptomics may be of use to conservation managers wanting to assess the physiological status of wild fish. | Jeffrey, JD; Thorstensen, MJ; Enders, EC; Treberg, JR; Jeffries, KM. (2023). Using transcriptomics to examine the physiological status of wild-caught walleye (Sander vitreus). FACETS, 8(). http://dx.doi.org/10.1139/facets-2022-0177 | 21-Aug-2023 | http://dx.doi.org/10.1139/facets-2022-0177 | TROUT ONCORHYNCHUS-MYKISS; MASS-SPECTROMETRY; PROTEIN COMPLEXES; GENE-EXPRESSION; MUSCLE-TISSUE; FISH; QUALITY; IDENTIFICATION; AUTHENTICATION; SEAFOOD | Technical / Data | Applied | FW | North America (Canada) | |||
| Transcriptomics | Functional genomics; gene expression; microarrays; transcriptomics | Goetz, FW; MacKenzie, S. (2008). Functional genomics with microarrays in fish biology and fisheries. FISH FISH, 9(4). http://dx.doi.org/10.1111/j.1467-2979.2008.00301.x | 24-Nov-2008 | http://dx.doi.org/10.1111/j.1467-2979.2008.00301.x | RNA-SEQ DATA; TISSUES; CLAM | Opinion / Review | Theoretical | ||||||
| Genomics - Whole-Genome | This paper reviews the use of molecular markers in the regulatory oversight of natural ressources in the forestry and fishery sectors. Although omics terms are mentioned, this review focusses largely on the use of DNA barcoding to enhance the reliability of certification programs to prevent fraud and mislabeling of consumer products. | Migone, A; Howlett, M. (2012). From Paper Trails to DNA Barcodes: Enhancing Traceability in Forest and Fishery Certification. NAT RESOUR J, 52(2). | 22-Sep-2012 | https://digitalrepository.unm.edu/cgi/viewcontent.cgi?article=1096&context=nrj | RETINOID-X-RECEPTOR; MESSENGER-RNA EXPRESSION; CRUSTACEAN HYPERGLYCEMIC HORMONE; SHRIMP LITOPENAEUS-VANNAMEI; CDNA-ENCODING VITELLOGENIN; PACIFIC WHITE SHRIMP; CRAB CARCINUS-MAENAS; CHINESE MITTEN CRAB; MOLECULAR CHARACTERIZATION; KURUMA PRAWN | Opinion / Review | Theoretical | Some discussion | NA | Global | |||
| Transcriptomics | endothermy; thermogenesis; phylogenomics; RNA-sequencing; transcriptomics; introgression; positive selection; mitochondrial-nuclear discordance | Ciezarek, AG; Osborne, OG; Shipley, ON; Brooks, EJ; Tracey, SR; McAllister, JD; Gardner, LD; Sternberg, MJE; Block, B; Savolainen, V. (2019). Phylotranscriptomic Insights into the Diversification of Endothermic Thunnus Tunas. MOL BIOL EVOL, 36(1). http://dx.doi.org/10.1093/molbev/msy198 | 26-Oct-2018 | http://dx.doi.org/10.1093/molbev/msy198 | CHINESE MITTEN CRAB; DIFFERENTIALLY EXPRESSED GENES; VASA-LIKE GENE; MUD CRAB; MOLECULAR CHARACTERIZATION; TRANSCRIPTOME ANALYSIS; CYCLIN B; SCYLLA; OVARY; VITELLOGENIN | Technical / Data | Theoretical | ||||||
| Genomics - Genome-Wide | Hypophthalmichthys nobilis; Single nucleotide polymorphism (SNP); Transcriptome | An, R; Fu, JJ; Jiang, BJ; Zhu, WB; Wang, LM; Luo, MK; Dong, ZJ. (2020). Development of SNP markers for the bighead carp (Hypophthalmichthys nobilis) by using transcriptomic sequences. CONSERV GENET RESOUR, 12(3). http://dx.doi.org/10.1007/s12686-020-01133-z | 18-Feb-2020 | http://dx.doi.org/10.1007/s12686-020-01133-z | GENE-EXPRESSION; LAKE WINNIPEG; FRESH-WATER; PREDICT MIGRATION; R-PACKAGE; FISH; STRESS; IDENTIFICATION; HYPOXIA; CONSERVATION | Technical / Data | Theoretical | ||||||
| Transcriptomics | This paper provides high-coverage liver RNA-seq datasets for four species of high commercial value in European fisheries. The authors describe a workflow for de novo transcriptome assembly and annotation which would require prior experience with bioinformatics to carry out. | Machado, AM; Muñoz-Merida, A; Fonseca, E; Veríssimo, A; Pinto, R; Felício, M; da Fonseca, RR; Froufe, E; Castro, LFC. (2020). Liver transcriptome resources of four commercially exploited teleost species. SCI DATA, 7(1). http://dx.doi.org/10.1038/s41597-020-0565-9 | 7-Jul-2020 | http://dx.doi.org/10.1038/s41597-020-0565-9 | HEMATOPOIETIC NECROSIS VIRUS; TROUT SALMO-TRUTTA; FLOUNDER PARALICHTHYS-OLIVACEUS; MUMMICHOG FUNDULUS-HETEROCLITUS; HEMORRHAGIC SEPTICEMIA VIRUS; PAIRS COREGONUS SP.; GENE-EXPRESSION; ATLANTIC SALMON; RAINBOW-TROUT; JAPANESE FLOUNDER | Technical / Data | Theoretical | SW | Europe | ||||
| Transcriptomics | antibiotics; fish microbiome; host–microbe interactions; probiotics; transcriptome | This paper uses transcriptional changes during early developmental processes to understand mechanisms leading to abnormal development in a non-model species. RNA-seq data identified changes in the expression of key genes that coincide with developmental milestones. This paper provides an example of how developmental transcriptomics could be used to determine which processes are disrupted in abnormal embryos. | Sorhus, E; Incardona, JP; Furmanek, T; Jentoft, S; Meier, S; Edvardsen, RB. (2016). Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates. DEV BIOL, 411(2). http://dx.doi.org/10.1016/j.ydbio.2016.02.012 | 15-Mar-2016 | http://dx.doi.org/10.1016/j.ydbio.2016.02.012 | ORIENTAL RIVER PRAWN; CALLINECTES-SAPIDUS; BLUE-CRAB; MOLECULAR CHARACTERIZATION; GENE; EYESTALK; SEQUENCE; STIMPSON; PEPTIDE; BIOLOGY | Technical / Data | Theoretical | SW | Europe | |||
| Transcriptomics | Colouration; Next-generation sequencing; Ornamental fish; Transcriptomics; Unigene | This paper describes the use of next-generation sequencing to determine the molecular basis of pigmentation in a cyprinid. They identified key genes involved in colouration differences between wild and cultured individuals. This paper is of limited use for fisheries management, but may be of interest for ornamental fish production. | Mandal, SC; Tripathy, PS; Khatei, A; Behera, DU; Ghosh, A; Pandey, PK; Parhi, J. (2020). Genetics of colour variation in wild versus cultured queen loath, Botia dario (Hamilton, 1822). GENOMICS, 112(5). http://dx.doi.org/10.1016/j.ygeno.2020.06.012 | 10-Jun-2020 | http://dx.doi.org/10.1016/j.ygeno.2020.06.012 | GLOBAL ENVIRONMENTAL GOVERNANCE; MITOCHONDRIAL-DNA; GENETIC IDENTIFICATION; NORTH-AMERICAN; PUBLIC-HEALTH; FOOD SAFETY; PRODUCTS; STEWARDSHIP; GENOMICS; SCIENCE | Technical / Data | Theoretical | FW | Asia | |||
| Transcriptomics | Larimichthys polyactis; Transcriptome; Illumina HiSeq 2500; Functional annotation | This paper describes de novo transcriptome assemblies for eight tissues from wild-caught small yellow croaker. Tissue-specific transcriptomic data from this commercially important fish in eastern Asia can be used for gene expression and functional studies. | Liu, LW; Sui, YZ; Zhu, WB; Guo, A; Xu, KD; Zhou, YD. (2017). In-depth transcriptome analysis of Larimichthys polyactis, de novo assembly, functional annotation. MAR GENOM, 33(). http://dx.doi.org/10.1016/j.margen.2017.02.002 | 1-Jun-2017 | http://dx.doi.org/10.1016/j.margen.2017.02.002 | DISCOVERY; ABUNDANCE; RIVER | Technical / Data | Theoretical | SW | Asia | |||
| Transcriptomics | 17 beta-oestradiol; largemouth bass; microarrays; pyrosequencing technology | This paper describes the development of a microarray for a non-model species. The microarray was validated by measuring the transcriptional response in the liver and gonads of male largemouth bass injected with 17β-oestradiol, an estrogenic compound. Before the advent of high-throughput sequencing, microarrays were commonly used for transcriptional profiling. | Garcia-Reyero, N; Griffitt, RJ; Liu, L; Kroll, KJ; Farmerie, WG; Barber, DS; Denslow, ND. (2008). Construction of a robust microarray from a non-model species largemouth bass, Micropterus salmoides (Lacepede), using pyrosequencing technology. J FISH BIOL, 72(9). http://dx.doi.org/10.1111/j.1095-8649.2008.01904.x | 28-Jun-2008 | http://dx.doi.org/10.1111/j.1095-8649.2008.01904.x | GENERATION; PROTEIN; FISH | Technical / Data | Theoretical | FW | North America | |||
| Genomics - Whole-Genome | Food security; Genomics; Metabolomics; Metagenomics; Proteomics; Transcriptomics | This paper is a review of high-throughput techniques to assess microbial communities in aquaculture. This review includes genomic, transcriptomic, proteomic, and metabolomic approaches in the context of pathogen detection and identification, and biomarker discovery. | Cancellas, ALB; Costa, WF; Freitas-Silva, J; Lopes, IR; de Oliveira, BFR; Laport, MS. (2022). In sickness and in health: Insights into the application of omics in aquaculture settings under a microbiological perspective. AQUACULTURE, 554(). http://dx.doi.org/10.1016/j.aquaculture.2022.738132 | 28-Jun-2008 | http://dx.doi.org/10.1016/j.aquaculture.2022.738132 | CRUDE-OIL; GENE-EXPRESSION; CATHEPSIN-K; ZEBRAFISH; GROWTH; IDENTIFICATION; LOCALIZATION; MECHANISMS; CHANNELS; PROTEIN | Opinion / Review | Theoretical | NA | Global | |||
| Transcriptomics | Flatfish; Larvae; Transcriptome assembly; Illumina; Roche/454 | This paper decribes the de novo assembly of the senegalese sole transcriptome using published data from larvae at different developmental stages. The authors used TransFlow, an automated assembly workflow, to select the "best" transcriptome. | Córdoba-Caballero, J; Seoane-Zonjic, P; Manchado, M; Claros, MG. (2019). De novo Transcriptome Assembly of Solea senegalensis v5.0 Using TransFlow. LECT N BIOINFORMAT, 11465(). http://dx.doi.org/10.1007/978-3-030-17938-0_5 | 13-Apr-2019 | http://dx.doi.org/10.1007/978-3-030-17938-0_5 | TRANSCRIPTION FACTOR MITF; CAROTENOID COLORATION; CYPRINUS-CARPIO; READ ALIGNMENT; PIGMENTATION; FISH; EXPRESSION; PROTEIN; GROWTH; ALPHA | Technical / Data | Theoretical | Aquaculture | SW | Europe | ||
| Genomics - Whole-Genome | Bioinformatics; Aquaculture; Challenges; Gene | Rather, MA; Agarwal, D; Bhat, TA; Khan, IA; Zafar, I; Kumar, S; Amin, A; Sundaray, JK; Qadri, T. (2023). Bioinformatics approaches and big data analytics opportunities in improving fisheries and aquaculture. INT J BIOL MACROMOL, 233(). http://dx.doi.org/10.1016/j.ijbiomac.2023.123549 | 1-Apr-2023 | http://dx.doi.org/10.1016/j.ijbiomac.2023.123549 | CHINESE MITTEN CRAB; FRESH-WATER CRAYFISH; OVARIAN DEVELOPMENT; HOMARUS-AMERICANUS; MOLECULAR-CLONING; PROCAMBARUS-CLARKII; DECAPOD CRUSTACEANS; PROTEIN-KINASES; REPRODUCTION; ANNOTATION | Opinion / Review | Applied | ||||||
| Genomics - Genome-Wide | Coilia nasus; De novo transcriptome; SSR markers; Illumina sequencing | This paper describes the assembly and annotation of the brain transcriptome for coilia nasus, an anadromous fish found in the Yangtze River, China. The authors also identified simple sequence repeats that may be used to assess genetic variation within and among samples. | Fang, DA; Zhou, YF; Duan, JR; Zhang, MY; Xu, DP; Liu, K; Xu, P; Wei, Q. (2015). Screening potential SSR markers of the anadromous fish Coilia nasus by de novo transcriptome analysis using Illumina sequencing. GENET MOL RES, 14(4). http://dx.doi.org/10.4238/2015.November.13.1 | 13-Nov-2015 | http://dx.doi.org/10.4238/2015.November.13.1 | VIRAL ENCEPHALOPATHY; COAT PROTEIN; QUANTIFICATION; BETANODAVIRUS; SEQUENCE; GENOME; FAMILY; CELLS; RNA | Technical / Data | Theoretical | FW | Asia | |||
| Transcriptomics | CRISPR/Cas9; Petromyzon marinus; Genetic biocontrol; Lamprey; Genome editing | This paper is a review of genetic tools used to study lamprey biology and the application of genomic technologies to control invasive sea lamprey in the North American Great Lakes. Much of this review discusses the use of CRISPR/Cas9 genome editing technologies to target invasive sea lamprey without negative impacts to non-target organisms. This paper would be of interest to fisheries managers wanting to develop alternate management strategies for sea lamprey control. | York, JR; Thresher, RE; McCauley, DW. (2021). Applying functional genomics to the study of lamprey development and sea lamprey population control. J GREAT LAKES RES, 47(). http://dx.doi.org/10.1016/j.jglr.2020.03.010 | 1-Dec-2021 | http://dx.doi.org/10.1016/j.jglr.2020.03.010 | BIVALVES CRASSOSTREA-VIRGINICA; OCEAN ACIDIFICATION; ELEVATED-TEMPERATURE; OXIDATIVE STRESS; CO2 LEVELS; RNA-SEQ; HEMOCYTES; IMPACTS; MUSSEL; FERTILIZATION | Opinion / Review | Theoretical | FW | North America | |||
| Transcriptomics | Transcriptome; Alkalinity; Oxidative stress; Inflammation; Immune | This paper analysed the spleen transcriptome of bulatmai barbel to determine the effects of exposure to high-alkalinity water. The authors found that fish exposed to high alkalinity differentially regulated genes involved in inflammation and immune function compared to control fish. | Shang, XC; Geng, LW; Yang, J; Zhang, YT; Xu, W. (2021). Transcriptome analysis reveals the mechanism of alkalinity exposure on spleen oxidative stress, inflammation and immune function of Luciobarbus capito. ECOTOX ENVIRON SAFE, 225(). http://dx.doi.org/10.1016/j.ecoenv.2021.112748 | 3-Sep-2021 | http://dx.doi.org/10.1016/j.ecoenv.2021.112748 | OYSTER CRASSOSTREA-GIGAS; MUSSEL MYTILUS-GALLOPROVINCIALIS; DOUBLY UNIPARENTAL INHERITANCE; IN-SITU HYBRIDIZATION; SINGLE NUCLEOTIDE POLYMORPHISMS; 2-DOMAIN ARGININE KINASES; BYSSUS RETRACTOR MUSCLE; MOLLUSK DONAX-TRUNCULUS; AMINO-ACID-SEQUENCE; DEPENDENT SEX-RATIO | Technical / Data | Theoretical | SW | Asia | |||
| Genomics - Genome-Wide | adaptive variation; gene flow; outlier loci; population genomics; transcriptomics | Thorstensen, MJ; Jeffrey, JD; Treberg, JR; Watkinson, DA; Enders, EC; Jeffries, KM. (2020). Genomic signals found using RNA sequencing show signatures of selection and subtle population differentiation in walleye (Sander vitreus) in a large freshwater ecosystem. ECOL EVOL, 10(14). http://dx.doi.org/10.1002/ece3.6418 | 13-Jun-2020 | http://dx.doi.org/10.1002/ece3.6418 | YELLOW SEA; CHINA; BLEEKER; LENGTH | Technical / Data | Applied | ||||||
| Transcriptomics | Thermal stress; Metabonomics; NMR; Multivariate analysis; Brachymystax lenok | This is a laboratory study that uses metabonomic and transcriptomic appoaches to assess effects of sublethal high temperatures on juvenile lenok, a coldwater fish. This approach identified metabolic pathways that are activated due to thermal stress and can be used to identify novel biomarkers. | Liu, Y; Liu, JS; Ye, SW; Bureau, DP; Liu, HB; Yin, JS; Mou, ZB; Lin, H; Hao, FH. (2019). Global metabolic responses of the lenok (Brachymystax lenok) to thermal stress. COMP BIOCHEM PHYS D, 29(). http://dx.doi.org/10.1016/j.cbd.2019.01.006 | 15-Jan-2019 | http://dx.doi.org/10.1016/j.cbd.2019.01.006 | EXPRESSION ANALYSIS; OVARIAN DEVELOPMENT; GLUTATHIONE-PEROXIDASE; MOLECULAR-CLONING; DYNAMIC ACTION; RNA-SEQ; PROTEIN; IDENTIFICATION; TESTIS; PCNA | Technical / Data | Theoretical | Aquaculture | FW | Asia | ||
| Proteomics | Authentication; Cod; Greenland halibut; Fishery products; Seafood substitution; SWATH-MS; Proteomics; Chemometrics | The study focused on the development and validation of protein biomarkers for accurate identification of Alaska pollock, Atlantic cod, and Greenland halibut. These markers can also used to identify the mislabelling of these three species. | Chien, HJ; Huang, YH; Zheng, YF; Wang, WC; Kuo, CY; Wei, GJ; Lai, CC. (2022). Proteomics for species authentication of cod and corresponding fishery products. FOOD CHEM, 374(). http://dx.doi.org/10.1016/j.foodchem.2021.131631 | 16-Apr-2022 | http://dx.doi.org/10.1016/j.foodchem.2021.131631 | COMMERCIAL HAKE; IDENTIFICATION; MUSCLE; PARVALBUMIN; PROTEINS; MYOSIN; CHAIN | Technical / Data | Theoretical | |||||
| Proteomics | Biomarker; fishery; food quality; mass spectrometry; proteomics; safety; seafood; traceability | This review summarizes the high-throughput advanced instruments available for the identification of proteomics-based biomarkers. Using these advanced instruments could aid in reducing the biomarker identification time. | Tedesco, S; Mullen, W; Cristobal, S. (2014). High-Throughput Proteomics: A New Tool for Quality and Safety in Fishery Products. CURR PROTEIN PEPT SC, 15(2). http://dx.doi.org/10.2174/1389203715666140221120219 | 1-Mar-2014 | http://dx.doi.org/10.2174/1389203715666140221120219 | ELECTROPHORESIS-MASS-SPECTROMETRY; MUSSELS MYTILUS-EDULIS; CAPILLARY-ELECTROPHORESIS; ZONE-ELECTROPHORESIS; BIOACTIVE PEPTIDES; CHAMAELEA-GALLINA; BIVALVE MOLLUSKS; CROSS-REACTIVITY; COMMERCIAL HAKE; MAJOR ALLERGEN | Opinion / Review | Theoretical | |||||
| Proteomics | Proteomics; Mass spectrometry; Fish authentication; Allergen detection; Bacteria; Quality and safety | This review highlights the studies where proteomics was successfully applied to identifying species and microbial contamination. How proteomics could help to identify the quality of fish during storage and processing. | Carrera, M; Cañas, B; Gallardo, JM. (2013). Proteomics for the assessment of quality and safety of fishery products. FOOD RES INT, 54(1). http://dx.doi.org/10.1016/j.foodres.2012.10.027 | 1-Nov-2013 | http://dx.doi.org/10.1016/j.foodres.2012.10.027 | MUSCLE PROTEIN-DEGRADATION; MASS-SPECTROMETRY; 2-DIMENSIONAL ELECTROPHORESIS; MAJOR ALLERGEN; SPECIES IDENTIFICATION; CROSS-REACTIVITY; COMMERCIAL HAKE; PARVALBUMIN; PEPTIDES; BACTERIA | Opinion / Review | Applied | |||||
| Proteomics | Collagen fingerprinting; Swordfish; Marlin; Tuna; Proteomics; Coastal archaeology; Historical ecology | Rick, T; Harvey, VL; Buckley, M. (2019). Collagen fingerprinting and the Chumash billfish fishery, Santa Barbara Channel, California, USA. ARCHAEOL ANTHROP SCI, 11(12). http://dx.doi.org/10.1007/s12520-019-00930-4 | 21-Nov-2019 | http://dx.doi.org/10.1007/s12520-019-00930-4 | SPECIES IDENTIFICATION; REMAINS | Technical / Data | Theoretical | ||||||
| Proteomics | Adulteration; Food safety; Labeling regulations; Food authentication | Mohanty, BP; Barik, S; Mahanty, A; Mohanty, S. (2013). Food Safety, Labeling Regulations and Fish Food Authentication. NATL ACAD SCI LETT, 36(3). http://dx.doi.org/10.1007/s40009-013-0139-x | 26-Jun-2013 | http://dx.doi.org/10.1007/s40009-013-0139-x | IDENTIFICATION; PROTEOMICS; HAKE; HPLC | Opinion / Review | Theoretical | ||||||
| Proteomics | Fishes capita; Species identification; Feed conversion efficiency; Reproductive fitness; Matrix-assisted laser desorption; ionization; Abiotic stress | This review highlights how proteomics could be used in various applications (e.g., food safety, pathology, disease diagnosis, reproductive fitness, stress management). This review also highlights possiblity of development of proteomic-based user-friendly assays for performing field tests | Jaiswal, S; Rasal, KD; Chandra, T; Prabha, R; Iquebal, MA; Rai, A; Kumar, D. (2023). Proteomics in fish health and aquaculture productivity management: Status and future perspectives. AQUACULTURE, 566(). http://dx.doi.org/10.1016/j.aquaculture.2022.739159 | 15-Mar-2023 | http://dx.doi.org/10.1016/j.aquaculture.2022.739159 | ZEBRAFISH DANIO-RERIO; BREAM SPARUS-AURATA; GILTHEAD SEA BREAM; SALMON SALMO-SALAR; COD GADUS-MORHUA; IONIZATION MASS-SPECTROMETRY; DIFFERENTIALLY EXPRESSED PROTEINS; LASER-DESORPTION/IONIZATION-TIME; GOLDFISH CARASSIUS-AURATUS; MINNOW GOBIOCYPRIS-RARUS | Opinion / Review | Theoretical | |||||
| Proteomics | attenuated vaccines; bony fish; DNA vaccines; inactivated vaccines; recombinant vaccines; viral vaccines | This review focuses on the status of current vaccines (DNA-based or subunit-based) for bony fish. Their advantages and limitations | Salgado-Miranda, C; Loza-Rubio, E; Rojas-Anaya, E; García-Espinosa, G. (2013). Viral vaccines for bony fish: past, present and future. EXPERT REV VACCINES, 12(5). http://dx.doi.org/10.1586/ERV.13.38 | 9-Jan-2014 | http://dx.doi.org/10.1586/ERV.13.38 | PANCREATIC NECROSIS VIRUS; SALMO-SALAR L.; TROUT ONCORHYNCHUS-MYKISS; RED-SEA BREAM; RAINBOW-TROUT; DNA VACCINES; IMMUNE-RESPONSES; ATLANTIC SALMON; BACTERIAL-DNA; CPG MOTIFS | Opinion / Review | Theoretical | |||||
| Proteomics | Temperature; Larvae; Sparus aurata; Proteome; Climate change | This study focused on how increasing temperature could impact the larval fish (Sparus aurata) survival. Authors concluded that S. aurata could not fully acclimate to increased temperature and climate change could adversely affect S. aurata growth and survival. | Madeira, D; Araújo, JE; Vitorino, R; Capelo, JL; Vinagre, C; Diniz, MS. (2016). Ocean warming alters cellular metabolism and induces mortality in fish early life stages: A proteomic approach. ENVIRON RES, 148(). http://dx.doi.org/10.1016/j.envres.2016.03.030 | 1-Jul-2016 | http://dx.doi.org/10.1016/j.envres.2016.03.030 | HEAT-SHOCK PROTEINS; BREAM SPARUS-AURATA; CLIMATE-CHANGE; GENE-EXPRESSION; MARINE ORGANISMS; THERMAL TOLERANCE; MYTILUS-GALLOPROVINCIALIS; GILLICHTHYS-MIRABILIS; MOLECULAR CHAPERONES; TEMPERATURE STRESS | Technical / Data | Theoretical | |||||
| Proteomics | comparative proteomics; fish embryo; mass spectrometry; two-dimensional electrophoresis | Zheng, L; Tanaka, H; Abe, S. (2011). Proteomic analysis of inviable salmonid hybrids between female masu salmon Oncorhynchus masou masou and male rainbow trout Oncorhynchus mykiss during early embryogenesis. J FISH BIOL, 78(5). http://dx.doi.org/10.1111/j.1095-8649.2011.02958.x | 3-May-2011 | http://dx.doi.org/10.1111/j.1095-8649.2011.02958.x | INTERMEDIATE-FILAMENTS; TRIPLOID HYBRIDS; EXPRESSION; CRYOPRESERVATION; ACTIVATION; PROTEINS; GAPDH | Technical / Data | Theoretical | ||||||
| Proteomics | Proteomics; Blood biomarker; Great Lakes; Parasite-host relationship; Ecosystem management; Fisheries | This lab study focused on the identification of proteomics-based biomarkers for fish wound assessment caused by Sea lamprey. Male siscowet lake charr was parasitized in a lab setting for four days and after that sea lamprey was removed. Blood samples were collected from the Male siscowet lake charr immediately and 7 months later. The study concluded that modified blood clot assays could provide an accurate estimate of wound damage caused by Sea lampreys. | Bullingham, OMN; Firkus, TJ; Goetz, FW; Murphy, CA; Alderman, SL. (2022). Lake charr (Salvelinus namaycush) clotting response may act as a plasma biomarker of sea lamprey (Petromyzon marinus) parasitism: Implications for management and wound assessment. J GREAT LAKES RES, 48(1). http://dx.doi.org/10.1016/j.jglr.2021.11.005 | 1-Feb-2022 | http://dx.doi.org/10.1016/j.jglr.2021.11.005 | BUCCAL GLAND SECRETION; GREAT-LAKES; PROTEOMIC ANALYSIS; BLOOD-COAGULATION; TROUT; FIBRINOGEN; PURIFICATION; SISCOWET; BIOLOGY; MORPHOTYPES | Technical / Data | Applied | |||||
| Proteomics | peptides; fermentation; ocnsortium; waste streams | This study focuses on the conversion of fish and dairy waste into useful products by fermentation. They characterized the peptides produced with and without the addition of lactic acid bacteria and concluded that rapid acidification of food waste is better. Results are preliminary and later could be used for the ferementation industry. | Mayta-Apaza, AC; Rocha-Mendoza, D; García-Cano, I; Jiménez-Flores, R. (2022). Characterization and Evaluation of Proteolysis Products during the Fermentation of Acid Whey and Fish Waste and Potential Applications. ACS FOOD SCI TECHNOL, 2(9). http://dx.doi.org/10.1021/acsfoodscitech.2c00157 | 2-Sep-2022 | http://dx.doi.org/10.1021/acsfoodscitech.2c00157 | ENZYMATIC-HYDROLYSIS; PROTEIN HYDROLYSATE; BY-PRODUCTS; BACTERIA; SILAGE; STRAINS; TRENDS; GUT | Technical / Data | Theoretical | |||||
| Proteomics | anthropogenic; Atlantic sturgeon; mucus; proteins; proteomics; stress | This study identified biomarkers for monitoring stress in Atlantic sturgeon using epidermal mucus (skin mucus) protease activity. This is a non-invasive method and could potentially improve conservation regulations. | Murphy, AE; Stokesbury, MJW; Easy, RH. (2020). Exploring epidermal mucus protease activity as an indicator of stress in Atlantic sturgeon (Acipenser oxyrinchusoxyrhinchus). J FISH BIOL, 97(5). http://dx.doi.org/10.1111/jfb.14489 | 12-Aug-2020 | http://dx.doi.org/10.1111/jfb.14489 | OXYRINCHUS MITCHILL; RAINBOW-TROUT; UNITED-STATES; SKIN MUCUS; FISH; RESPONSES; POPULATIONS; MORTALITY; PATHWAY; ROLES | Technical / Data | Theoretical | |||||
| Proteomics | EAA; Growth performance; Immunity; Nutrition; Proteome; Sparus aurata | This study focused on the addition of Tryptophan in plant-based fish meals and concluded that the addition of Tryptophan does not impact growth, however, it enhances immune response. This study was conducted on Gilthead seabream juveniles. | Cerqueira, M; Schrama, D; Silva, TS; Colen, R; Engrola, SAD; Conceiçao, LEC; Rodrigues, PML; Farinha, AP. (2020). How tryptophan levels in plant-based aquafeeds affect fish physiology, metabolism and proteome. J PROTEOMICS, 221(). http://dx.doi.org/10.1016/j.jprot.2020.103782 | 15-Jun-2020 | http://dx.doi.org/10.1016/j.jprot.2020.103782 | WINTER THERMAL-STRESS; BREAM SPARUS-AURATA; DICENTRARCHUS-LABRAX; AMINO-ACIDS; DIETS; MEAL; REPLACEMENT; REQUIREMENT; METHIONINE; CYTOSCAPE | Technical / Data | Theoretical | |||||
| Proteomics | calcium carbonate; endolymph; extracellular serine/threonine protein kinase FAM20C; LC-MS/MS; reverse-phase HPLC; teleost | This study focused on identifying the Black beam (Acanthopagrus butcheri) proteins and molecular mechanisms involved in the otolith formation. | Thomas, ORB; Swearer, SE; Kapp, EA; Peng, P; Tonkin-Hill, GQ; Papenfuss, A; Roberts, A; Bernard, P; Roberts, BR. (2019). The inner ear proteome of fish. FEBS J, 286(1). http://dx.doi.org/10.1111/febs.14715 | 6-Dec-2018 | http://dx.doi.org/10.1111/febs.14715 | OTOLITH MATRIX PROTEINS; ACANTHOPAGRUS-BUTCHERI SPARIDAE; TROUT ONCORHYNCHUS-MYKISS; RAINBOW-TROUT; BLACK BREAM; IMMUNOHISTOCHEMICAL LOCALIZATION; CARBONIC-ANHYDRASE; MOLECULAR-CLONING; ESTUARINE FISH; CICHLID FISH | Technical / Data | Theoretical | |||||
| Proteomics | Aquaculture animals; Proteomics; Immunology; Microbiology; Innate immunity | This review highlights the proteomics-based methodologies available for studying the fish response to bacterial and viral infections. | Peng, XX. (2013). Proteomics and its applications to aquaculture in China: Infection, immunity, and interaction of aquaculture hosts with pathogens. DEV COMP IMMUNOL, 39(1-2). http://dx.doi.org/10.1016/j.dci.2012.03.017 | 1-Jan-2013 | http://dx.doi.org/10.1016/j.dci.2012.03.017 | SPOT SYNDROME VIRUS; OUTER-MEMBRANE PROTEINS; FENNEROPENAEUS-CHINENSIS RESPONSE; AYU PLECOGLOSSUS-ALTIVELIS; EXCESSIVE FLUORIDE; MOLECULAR RESPONSE; PUFFER FISH; EXPRESSION PROFILE; EDWARDSIELLA-TARDA; ENVELOPE PROTEINS | Opinion / Review | Theoretical | |||||
| Proteomics | A high-throughput proteomics-based method was developed to identify the fish at the species level. Validation was done using 51 species. | Bi, HY; Zhong, CY; Shao, MK; Wang, CY; Yi, J; Qiao, L; Zhang, JB. (2019). Differentiation and authentication of fishes at the species level through analysis of fish skin by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUN MASS SP, 33(16). http://dx.doi.org/10.1002/rcm.8474 | 29-Apr-2019 | http://dx.doi.org/10.1002/rcm.8474 | PROTEIN PROFILES; IDENTIFICATION; BACTERIA; PROTEOMICS; PRODUCTS | Technical / Data | Theoretical | ||||||
| Proteomics | Otolith; biomineralization; proteomics; inner ear; endolymph | Thomas, ORB; Swearer, SE. (2019). Otolith Biochemistry-A Review. REV FISH SCI AQUAC, 27(4). http://dx.doi.org/10.1080/23308249.2019.1627285 | 17-Jul-2019 | http://dx.doi.org/10.1080/23308249.2019.1627285 | TROUT ONCORHYNCHUS-MYKISS; MUTATIONS AFFECTING DEVELOPMENT; TURBOT PSETTA-MAXIMA; ZEBRAFISH INNER-EAR; RAINBOW-TROUT; CARBONIC-ANHYDRASE; MATRIX PROTEINS; SACCULAR EPITHELIUM; SOLUBLE-MATRIX; HAIR-CELLS | Opinion / Review | Theoretical | ||||||
| Proteomics | Animal proteomics; Energy metabolism; Flatfish; Larval development; Metamorphosis; Structural proteins | This is a lab-based study on flat fish larvae growth. Authors suggested understanding molecular changes occurring during its developmental stages could help in improving fish larval quality and increase juvenile disease resistance. This study focused on identifying proteins that change at developmental stages in many biological functions including stress response, and energy metabolism. | Chicano-Gálvez, E; Asensio, E; Cañavate, JP; Alhama, J; López-Barea, J. (2015). Proteomic analysis through larval development of Solea senegalensis flatfish. PROTEOMICS, 15(23-24). http://dx.doi.org/10.1002/pmic.201500176 | 14-Sep-2015 | http://dx.doi.org/10.1002/pmic.201500176 | HALIBUT HIPPOGLOSSUS-HIPPOGLOSSUS; DIFFERENTIAL GENE-EXPRESSION; ACID-BINDING PROTEIN; GROWTH-FACTOR-I; MOLECULAR CHARACTERIZATION; THYROID-HORMONES; MARINE FISH; POSTTRANSLATIONAL SYNTHESIS; PARALICHTHYS-OLIVACEUS; JAPANESE FLOUNDER | Technical / Data | Theoretical | |||||
| Proteomics | Spring viremia of carp virus; 2-DE; Pathogenesis; Proteomic analysis | Liu, LY; Li, Q; Lin, L; Wang, M; Lu, YN; Wang, WM; Yuan, JF; Li, LJ; Liu, XQ. (2013). Proteomic analysis of epithelioma papulosum cyprini cells infected with spring viremia of carp virus. FISH SHELLFISH IMMUN, 35(1). http://dx.doi.org/10.1016/j.fsi.2013.03.367 | 1-Jul-2013 | http://dx.doi.org/10.1016/j.fsi.2013.03.367 | IONIZATION-MASS-SPECTROMETRY; ACTIN-BASED MOTILITY; PYRUVATE-KINASE M2; REVERSE-TRANSCRIPTASE; STATISTICAL-MODEL; VACCINIA VIRUS; IN-VITRO; PROTEIN; PROTEASOME; EXPRESSION | Technical / Data | Theoretical | ||||||
| Proteomics | aquaculture; protein expression; mass spectrometry; Rohu; PTM | This is a proteomics-based study, the study of all proteins for Labeo rohita (important fish in aquaculture). This study has detailed the protein makeup of various tissues in L.rohita, identifying around 26% of its proteins and mapping out where these proteins are expressed and how they are modified. This information was made accessible via a new online resource, which could further help in aquaculture research. | Nissa, MU; Pinto, N; Mukherjee, A; Reddy, PJ; Ghosh, B; Sun, Z; Ghantasala, S; Chetanya, C; Shenoy, SV; Moritz, RL; Goswami, M; Srivastava, S. (2022). Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo rohita. J PROTEOME RES, 21(2). http://dx.doi.org/10.1021/acs.jproteome.1c00759 | 28-Dec-2021 | http://dx.doi.org/10.1021/acs.jproteome.1c00759 | MASS-SPECTROMETRY; IMMUNOLOGICAL CHARACTERIZATION; EXPRESSION ANALYSIS; LYSINE ACETYLATION; ANTEMORTEM STRESS; COLOR STABILITY; PROTEINS; PHOSPHORYLATION; POSTMORTEM; ROHU | Technical / Data | Theoretical | |||||
| Proteomics | differential expression proteomics; 2D-gel electrophoresis; isotope coded affinity tagging; ICAT; 2D-LC MS/MS; infectious hematopoietic necrosis virus (IHNV); natural killer cell enhancing factor (NKEF); bacterial kidney disease (BKD) | This study was focused on using advanced protein analysis techniques to understand fish diseases that cause significant financial losses in aquaculture and fisheries. By comparing proteins in healthy and diseased Atlantic salmon, they have identified several that are involved in the fish's response to infectious diseases, providing insights that could lead to more effective treatments or vaccines for conditions like infectious hematopoietic necrosis and bacterial kidney disease. | Booy, AT; Haddow, JD; Ohlund, LB; Hardie, DB; Olafson, RW. (2005). Application of isotope coded affinity tag (ICAT) analysis for the identification of differentially expressed proteins following infection of Atlantic salmon (Salmo salar) with infectious hematopoietic necrosis virus (IHNV) or Renibacterium salmoninarum (BKD). J PROTEOME RES, 4(2). http://dx.doi.org/10.1021/pr049840t | 22-Jan-2005 | http://dx.doi.org/10.1021/pr049840t | BACTERIAL KIDNEY-DISEASE | Technical / Data | Applied | |||||
| Proteomics | Ion trap; High intensity focused ultrasound; Tandem mass spectrometry; Shrimps; SMIM; Species identification | Selecetd tandem mass spectrometry(SMIM) is a precise method for indentiifying known peptides in complex mixtures usin an ion-trap mass spectrometry. This study used SMIM to quickly authenticate seven dfferent closely related speceis of Decapoda shrimps, ensuring accurate labelling and safety in seafood products. | Ortea, I; Cañas, B; Gallardo, JM. (2011). Selected tandem mass spectrometry ion monitoring for the fast identification of seafood species. J CHROMATOGR A, 1218(28). http://dx.doi.org/10.1016/j.chroma.2011.05.032 | 15-Jul-2011 | http://dx.doi.org/10.1016/j.chroma.2011.05.032 | LENGTH POLYMORPHISM METHOD; DNA-BASED METHODS; PROTEIN IDENTIFICATION; ARGININE KINASE; COMMERCIAL FISH; FOOD INTEREST; AUTHENTICATION; PEPTIDES; PRODUCTS | Technical / Data | Theoretical | |||||
| Proteomics | Fish authentication; Proteomics; Mass spectrometry; Molecular profiling; Fish frauds | This is a review article focused on the application of proteomics for seafood authentication. This article summarizes the most relevant proteomic methods developed to efficiently identify authentic seas food products and detect mislabelling, offering a reliable solution for food quality and safety controls. | Mazzeo, MF; Siciliano, RA. (2016). Proteomics for the authentication of fish species. J PROTEOMICS, 147(). http://dx.doi.org/10.1016/j.jprot.2016.03.007 | 16-Sep-2016 | http://dx.doi.org/10.1016/j.jprot.2016.03.007 | IONIZATION MASS-SPECTROMETRY; PCR-RFLP ANALYSIS; MALDI-TOF-MS; FOOD AUTHENTICATION; FAST IDENTIFICATION; COMMERCIAL HAKE; TECHNOLOGY; PEPTIDES; PRODUCTS; PARVALBUMIN | Opinion / Review | Theoretical | |||||
| Transcriptomics | This is a transcriptomics paper in the very early stages of sequencing. | Salem, M; Rexroad, CE; Wang, JN; Thorgaard, GH; Yao, JB. (2010). Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC GENOMICS, 11(). http://dx.doi.org/10.1186/1471-2164-11-564 | 13-Oct-2010 | http://dx.doi.org/10.1186/1471-2164-11-564 | MODEL; DUPLICATION; MICROARRAY; GENERATION; DATABASE; LIBRARY; GENOME; LINES; FISH | Technical / Data | Theoretical | ||||||
| Proteomics | acclimation; global change; fish; phenotypic plasticity; proteome; temperature | This is a one-month laboratory study, that found that juvenile gilt-head sea breams can acclimate to a moderate temperature increase from 18 to 24 C, adjusting their muscle proteome to maintain metabolic processes, but struggle to survive at higher heat wave temperatures (30 C), Showing significant changes in protein expression related to stress response, inflammation and energy metabolism. The findings in the manuscript suggest that the recruitment of key fisheries species like the sea bream could be at risk due to ocean warming, emphasizing the necessity for better fish stock management strategies. | Madeira, D; Araújo, JE; Vitorino, R; Costa, PM; Capelo, JL; Vinagre, C; Diniz, MS. (2017). Molecular Plasticity under Ocean Warming: Proteomics and Fitness Data Provides Clues for a Better Understanding of the Thermal Tolerance in Fish. FRONT PHYSIOL, 8(). http://dx.doi.org/10.3389/fphys.2017.00825 | 22-Oct-2017 | http://dx.doi.org/10.3389/fphys.2017.00825 | GOBY GILLICHTHYS-MIRABILIS; HEAT-SHOCK PROTEINS; CREATINE-KINASE; STRESS-RESPONSE; CLIMATE-CHANGE; TEMPERATURE-ACCLIMATION; MARINE ORGANISMS; GENE-EXPRESSION; SPARUS-AURATA; MUSCLE-TISSUE | Technical / Data | Theoretical | |||||
| Proteomics | Larimichthys polyactis; Heat stress; Liver response; Transcriptomic analysis; Proteomic analysis | This is a laboratory study conducted on Small yellow croaker fish. This study investigated how the Small yellow croaker fish responds to heat stress by analyzing changes in genes and proteins in its liver after exposure to high temperatures. They found some key metabolic pathways are key to the fish's response to heat. Improving understanding of those key processes could help address the problems of stress and diseases in fish farming. | Liu, F; Zhang, TL; He, Y; Zhan, W; Xie, QP; Lou, B. (2023). Integration of transcriptome and proteome analyses reveals the regulation mechanisms of Larimichthys polyactis liver exposed to heat stress. FISH SHELLFISH IMMUN, 135(). http://dx.doi.org/10.1016/j.fsi.2023.108704 | 1-Apr-2023 | http://dx.doi.org/10.1016/j.fsi.2023.108704 | OXIDATIVE STRESS; TEMPERATURE; FISH; RESPONSES; BLOOD; COLD; HISTOPATHOLOGY; METABOLISM; EXPRESSION; INTESTINE | Technical / Data | Theoretical | |||||
| Proteomics | Aeromonas salmonicida; Furunculosis; Type-three secretion system; T3SS; Vaccine; AcrV; Inhibition of immune protection | This is a laboratory study conducted on Rainbow trout to understand how vaccines function to control a disease caused by Aeromonas salmonids. A. salmonids cause a serious disease in fish called furunculosis, which is typically controlled by vaccines, but how these vaccines work is not well understood. This study found that removing a specific part of the bacteria known as the type three secretion system (T3SS) before making the vaccine increased the survival rates of vaccinated fish, suggesting that this system may interfere with the vaccine effectiveness, and further studies are required to understand the best way to protect fish against the disease. | Vanden Bergh, P; Burr, SE; Benedicenti, O; von Siebenthal, B; Frey, J; Wahli, T. (2013). Antigens of the type-three secretion system of Aeromonas salmonicida subsp salmonicida prevent protective immunity in rainbow trout. VACCINE, 31(45). http://dx.doi.org/10.1016/j.vaccine.2013.08.057 | 25-Oct-2013 | http://dx.doi.org/10.1016/j.vaccine.2013.08.057 | YERSINIA-PESTIS; V-ANTIGEN; EXPERIMENTAL FURUNCULOSIS; SALVELINUS-FONTINALIS; ATTENUATED VIRULENCE; ANTIBODY-RESPONSES; EFFECTOR PROTEIN; BROOK TROUT; IMMUNIZATION; MACROPHAGES | Technical / Data | Theoretical | |||||
| Proteomics | This paper is focused on the identification of potential targets for new vaccines against fish disease furunculosis. In this study, comparisons were performed between the proteins released by highly virulent strains of the bacterium Aeromonas salmonicida and a less virulent strain that lacks a key system for causing disease. | Vanden Bergh, P; Heller, M; Braga-Lagache, S; Frey, J. (2013). The Aeromonas salmonicida subsp salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis. PROTEOME SCI, 11(). http://dx.doi.org/10.1186/1477-5956-11-44 | 15-Oct-2013 | http://dx.doi.org/10.1186/1477-5956-11-44 | OUTER-MEMBRANE VESICLES; PEPTIDYLPROLYL ISOMERASE ACTIVITY; III SECRETION SYSTEM; PROTECTIVE IMMUNITY; VIRULENCE FACTORS; IDENTIFICATION; LOCALIZATION; PROTEOME; TRANSLOCATION; PLASMINOGEN | Technical / Data | Theoretical | ||||||
| Metabolomics | Biomarkers; Formaldehyde; Harpodon nehereus; metabolomic | This study focused on identifying the differences between naturally occurring and illegally added formaldehyde in Bombay duck fish. They used a technique called proton NMR to identify changes in specific chemicals. They found that three substances, trimethylamine oxide, trimethylamine, and lysine can act as markers to differentiate between natural and artificial formaldehyde in the fish. | Barokah, GR; Nurhayati, T; Januar, HI; Jacoeb, A. (2023). Identification of Endogenous and Artificial Formaldehyde Biomarkers in Bombay Duck (Harpodon nehereus) Using 1H NMR-Based Metabolomics Approach. J AQUAT FOOD PROD T, (). http://dx.doi.org/10.1080/10498850.2023.2259364 | 21-Sep-2023 | http://dx.doi.org/10.1080/10498850.2023.2259364 | TRIMETHYLAMINE OXIDE; FROZEN STORAGE; FOOD SAFETY; FISH; DIMETHYLAMINE; PRODUCTS; FRESHNESS; PROTEINS; FILLETS; SQUID | Technical / Data | Theoretical | |||||
| Metabolomics | European sea bass; By-products; Growth; Metabolomics; Gut microbiota | This is a laboratory diet study conducted on European sea bass. This study showed that by using by-products from fisheries and aquaculture instead of wild-caught fishmeal and fish oil, the health and growth of the fish were not greatly affected and this replacement might even boost the fish's immune system and disease resistance, suggesting a viable alternative for sustainable fish farming practices. | Marchi, A; Bonaldo, A; Di Biase, A; Cerri, R; Scicchitano, D; Nanetti, E; Candela, M; Picone, G; Capozzi, F; Dondi, F; Gatta, PP; Parma, L. (2023). Towards a free wild-caught fishmeal, fish oil and soy protein in European sea bass diet using by-products from fishery and aquaculture. AQUACULTURE, 573(). http://dx.doi.org/10.1016/j.aquaculture.2023.739571 | 30-Aug-2023 | http://dx.doi.org/10.1016/j.aquaculture.2023.739571 | NUCLEAR-MAGNETIC-RESONANCE; PLANT PROTEIN; PRODUCTION PERFORMANCE; INDUCED ENTERITIS; ATLANTIC SALMON; WHEAT GLUTEN; FATTY-ACIDS; GROWTH; METABOLOMICS; SUPPLEMENTATION | Technical / Data | Theoretical | |||||
| Metabolomics | Metabolomics; High-resolution H-1 NMR; Highly migratory large pelagic fish; Purse seine tuna fisheries; Western Indian Ocean; Raw white and red muscles | This study focused on the development of methods for effectively differentiating Tunas from other species, tuna sizes, tuna storage conditions, and also the geographical origin of wild tropical tuna by analyzing the molecular components of their muscle tissues. This method proved to be a powerful tool in ensuring the traceability of tuna products in the market, protecting consumers and aiding in the conservation of tuna stocks | Bodin, N; Amiel, A; Fouché, E; Sardenne, F; Chassot, E; Debrauwer, L; Guillou, H; Tremblay-Franco, M; Canlet, C. (2022). NMR-based metabolic profiling and discrimination of wild tropical tunas by species, size category, geographic origin, and on-board storage condition. FOOD CHEM, 371(). http://dx.doi.org/10.1016/j.foodchem.2021.131094 | 1-Mar-2022 | http://dx.doi.org/10.1016/j.foodchem.2021.131094 | AMINO-ACIDS; L-HISTIDINE; C-13 NMR; FISH; MUSCLE; SALMON; BIOCHEMISTRY; CARNOSINE; FISHERIES; SPOILAGE | Technical / Data | Theoretical | |||||
| Metabolomics | Katsuwonus pelamis; Microplastics; Molecular docking; Metabolomics; Health risk | Wu, LJ; Dai, XJ; Xu, J; Ou, DY; Wang, L; Lin, H; He, WY; Lin, HT; Du, RP; Huang, H; Li, WW; Pan, Z. (2023). Assessment of microplastic contamination in an eastern Pacific tuna (Katsuwonus pelamis) and evaluation of its health risk implication through molecular docking and metabolomics studies. FOOD CHEM, 426(). http://dx.doi.org/10.1016/j.foodchem.2023.136507 | 15-Nov-2023 | http://dx.doi.org/10.1016/j.foodchem.2023.136507 | REVEALS | Technical / Data | Theoretical | ||||||
| Metabolomics | Fish; food preservative; formaldehyde; metabolomics; Saurida tumbil | This study focused on differentiating between the naturally occurring formaldehyde and that were artificially added to preserve fish in Indonesia using metabolomics. The research found specific chemical markers, Trimethylamine oxide, trimethylamine that can indicate whether formaldehyde has been added to fish, paving the way for a new method to screen for artificial preservation in seafood. | Anissah, U; Ariyani, F; Barokah, G; Januar, HI. (2021). NMR Metabolomics of Saurida tumbil Fish Treated with Formaldehyde Solution as Misconduct Food Preservation Method. J AQUAT FOOD PROD T, 30(3). http://dx.doi.org/10.1080/10498850.2021.1880510 | 8-Feb-2021 | http://dx.doi.org/10.1080/10498850.2021.1880510 | Technical / Data | Theoretical | ||||||
| Metabolomics | PFBS; Probiotic; Metabolome; DNA methylation; Bile acid; Zebrafish larvae | Probiotics (Lactobacillus rhamnosus) have been found to treat and counteract the harmful development effects caused by the pollutant PFBS in zebrafish larvae. This is a laboratory study conducted on Zebra fish and used a metabolomics approach to understand the role of probiotics in controlling the developmental toxicity of perfluorobutane sulfonate (PFBS) pollutants. They found that probiotics altered metabolic processes decreased stress responses and abnormal behavior induced by PFBS, and promoted gut health, suggesting probiotics could be a beneficial, eco-friendly addition to aquaculture and fisheries. | Hu, CY; Huang, ZL; Sun, BL; Liu, MY; Tang, LZ; Chen, LG. (2022). Metabolomic profiles in zebrafish larvae following probiotic and perfluorobutanesulfonate coexposure. ENVIRON RES, 204(). http://dx.doi.org/10.1016/j.envres.2021.112380 | 1-Mar-2022 | http://dx.doi.org/10.1016/j.envres.2021.112380 | DNA METHYLATION; BILE-ACIDS; PERFLUOROALKYL; TOXICITY | Technical / Data | Theoretical | |||||
| Metabolomics | Blue carbon; Seagrass; Mangroves; Saltmarsh; Stable isotopes; Metabolomics | In a study of castal ecosystem in northern Austrialia, reseerchers used various biomarker techniques, including stable isotope ratios and fatty acid analysis, to examine the connections between vegetation in river catchments and the cabon-based food sources for local crabs and fish. They found that the diets of these marine animals are influneced by the type of plants growing along the river banks, with different plant leaving distinct biochemical sigantures in the animals that conusme them. | Gorman, D; Beale, DJ; Crosswell, J; Stephenson, SA; Shah, RM; Hillyer, KE; Steven, ADL. (2023). Multiple-biomarkers show the importance of blue carbon to commercially important fishery species. SCI TOTAL ENVIRON, 881(). http://dx.doi.org/10.1016/j.scitotenv.2023.163162 | 10-Jul-2023 | http://dx.doi.org/10.1016/j.scitotenv.2023.163162 | ORGANIC-MATTER SOURCES; STABLE-ISOTOPE RATIO; FATTY-ACID; FLAT ECOSYSTEM; FOOD-WEB; MANGROVE; SEAGRASS; TRACERS; SEDIMENTS; ESTUARY | Technical / Data | Theoretical | |||||
| Metabolomics | Water flow; Fishery resources supplementation; LC-MS; MS metabolomics; Glutathione; Sebastes schlegelii | The study examined in labouratory on how black rockfish, a speceis that prefers specific habitat conditions responded to different water flow rates over 45 days. It was found that the fish grew better in moving water than in still water, with the best growth at a flow rate of .5 body lengths per second. The study also revealed that water flow affects teh fish's metabolism amd immune response and indentified potential indicators of stress duw o high water flow. These inshights could help in mamanging black rockfish in both aquaculture and conservation efforts to ensure healthier fish and improved survival rates. | Ma, Z; Wang, J; Zhang, J; Ren, XZ; Zhang, X; Liu, Y; Shi, XT. (2023). Effect of water flow on growth and metabolism in Sebastes schlegelii. AQUACULTURE, 571(). http://dx.doi.org/10.1016/j.aquaculture.2023.739485 | 30-Jun-2023 | http://dx.doi.org/10.1016/j.aquaculture.2023.739485 | SALMON SALMO-SALAR; JUVENILE BLACK ROCKFISH; SWIMMING EXERCISE; PERFORMANCE; RESISTANCE; FITNESS; STRESS; IMPACT; OXYGEN; SERUM | Technical / Data | Theoretical | |||||
| Metabolomics | Zebrafish; Tetracycline; Metabolism; Lipid accumulation; Gut microbiome | This is a study conducted on juvenile zebrafish in the laboratory by exposing them to common antibiotic levels found in the environment. Results found that significant weight gain without a change in body length, affected liver health, and altered important bodily functions and gut bacteria when exposed to antibiotics. It highlights how antibiotics like tetracycline in water systems can impact aquatic life even at levels considered environmentally relevant. | Keerthisinghe, TP; Wang, F; Wang, MJ; Yang, Q; Li, JW; Yang, JF; Xi, L; Dong, W; Fang, ML. (2020). Long-term exposure to TET increases body weight of juvenile zebrafish as indicated in host metabolism and gut microbiome. ENVIRON INT, 139(). http://dx.doi.org/10.1016/j.envint.2020.105705 | 1-Jun-2020 | http://dx.doi.org/10.1016/j.envint.2020.105705 | ANTIBIOTICS; TETRACYCLINE; OBESITY; IMPACT; MASS; CONSUMPTION; EXTRACTION; RESPONSES | Technical / Data | Applied | |||||
| Metabolomics | REIMS; Real time; No sample preparation; Fish; Species identification; Catch method | Black, C; Chevallier, OP; Haughey, SA; Balog, J; Stead, S; Pringle, SD; Riina, MV; Martucci, F; Acutis, PL; Morris, M; Nikolopoulos, DS; Takats, Z; Elliott, CT. (2017). A real time metabolomic profiling approach to detecting fish fraud using rapid evaporative ionisation mass spectrometry. METABOLOMICS, 13(12). http://dx.doi.org/10.1007/s11306-017-1291-y | 2-Nov-2017 | http://dx.doi.org/10.1007/s11306-017-1291-y | DNA BARCODING REVEALS; MEAT-PRODUCTS; FOOD FRAUD; SEAFOOD; IDENTIFICATION; AUTHENTICATION; SUBSTITUTION; MARKET; QUALITY; RATES | Technical / Data | Theoretical | ||||||
| Metabolomics | Habitat; Metabolites; Hilsa; Liver; Metabolomics; Transcriptomics | The study reveals that Tenualosa ilisha fish, a valuable food source from eh Padma and Hooghly rivers in India, shows differences in nutritional content based on their habitat, with a focus on fatty acids and amino acids, This is determined by analyzing the fish's metabolic processes and genetic responses to their environments. | Ganguly, S; Mitra, T; Mahanty, A; Mohanty, S; Mohanty, BP. (2020). A comparative metabolomics study on anadromous clupeid Tenualosa ilisha for better understanding the influence of habitat on nutritional composition. METABOLOMICS, 16(3). http://dx.doi.org/10.1007/s11306-020-01655-5 | 25-Feb-2020 | http://dx.doi.org/10.1007/s11306-020-01655-5 | FATTY-ACID-METABOLISM; GENE-EXPRESSION; RNA-SEQ; TRANSCRIPTOME; PROTEIN; HILSA; 2ND-MESSENGER; QUALITY; LIVER; PCR | Technical / Data | Applied | |||||
| Metabolomics | cross-species; epidermal mucus; metabolomics; monitoring; non-invasive | This study focused on using non-invasive metabolomics-based methods, by analyzing fish mucus, to study various eight freshwater fish species and asses their health and relationships. This approach can help identify specific biological markers for monitoring fish well-being without harming them, and this particular study found unique patterns of metabolites across different fish that could lead to new ways of protecting and tracking the health of fish populations. | Ekman, DR; Evich, MG; Mosley, JD; Doering, JA; Fay, KA; Ankley, GT; Collette, TW. (2023). Expanding non-invasive approaches for fish-health monitoring: A survey of the epidermal mucous metabolomes of phylogenetically diverse freshwater fish species. J FISH BIOL, (). http://dx.doi.org/10.1111/jfb.15512 | 26-Jul-2023 | http://dx.doi.org/10.1111/jfb.15512 | NONNEURONAL CHOLINERGIC SYSTEM; MASS-SPECTROMETRY; SKIN MUCUS; ACETYLCHOLINE; EXPOSURE; IMPACTS | Technical / Data | Theoretical | |||||
| Metabolomics | Saline-alkaline stress; Fish; Liver; Biochemical analysis; Metabolomics; Transcriptomics | This is laboratory study conducted on how crucian carp, a type of freshwater fish, respond to stress caused by exposure to sodium bicarbonate in water, which mimics saline-alkaline environments. The research involves a 30-day experiment measuring changes in the fish's liver enzymes, metabolites, and gene expression, finding that sodium bicarbonate exposure affects liver function, lipid metabolism, and energy balance, but the fish may adapt by adjusting their metabolism and boosting their antioxidant and immune responses. These findings offer a new understanding f how freshwater fish like crucian crap cope with saline-alkaline conditions, which could inform strategies for managing fisheries in these environments. | Wei, XF; Liu, YJ; Li, SW; Ding, L; Han, SC; Chen, ZX; Lu, H; Wang, P; Sun, YC. (2023). Stress response and tolerance mechanisms of NaHCO3 exposure based on biochemical assays and multi-omics approach in the liver of crucian carp (Carassius auratus). ECOTOX ENVIRON SAFE, 253(). http://dx.doi.org/10.1016/j.ecoenv.2023.114633 | 15-Mar-2023 | http://dx.doi.org/10.1016/j.ecoenv.2023.114633 | KETONE-BODIES; METABOLOMICS; BIOMARKERS; METABOLITE; DISCOVERY | Technical / Data | Theoretical | |||||
| Metabolomics | Tilapia; Polyethylene microplastics; Dietary exposure; Growth; Gut microbiota; Metabolism; Gene expressions | This is a 9-week laboratory experimental study conducted on juvenile genetically improved farmed tilapia to understand how different-sized microplastics impact. Results showed that microplastics cause negative effects on fish growth, digestive enzymes, gut bacteria, liver metabolism, and brain gene expression with large particles more likely to be excreted and smaller ones accumulating in the intestines. The microplastics disrupt normal biological functions and pathways, demonstrating that the size and amount of microplastics are important factors in their harmful effects on fish health. | Lu, X; Zhang, JX; Zhang, L; Wu, D; Tian, J; Yu, LJ; He, L; Zhong, S; Du, H; Deng, DF; Ding, YZ; Wen, H; Jiang, M. (2022). Comprehensive understanding the impacts of dietary exposure to polyethylene microplastics on genetically improved farmed tilapia (Oreochromis niloticus): tracking from growth, microbiota, metabolism to gene expressions. SCI TOTAL ENVIRON, 841(). http://dx.doi.org/10.1016/j.scitotenv.2022.156571 | 1-Oct-2022 | http://dx.doi.org/10.1016/j.scitotenv.2022.156571 | FRESH-WATER ECOSYSTEMS; MASS-SPECTROMETRY; JUVENILE FISH; GUT; INFLAMMATION; ENVIRONMENT; CYTOSCAPE | Technical / Data | Theoretical | |||||
| Genomics - Genome-Wide | fish; genomics; fishery; stock management; sustainability | This article proposes a roadmap for the use of population genetics in promoting sustainable fisheries. The authors propose that the use of SNPs may be a cost effective tool used in fishery stock assessment and management. | Andersson, L., Bekkevold, D., Berg, F., Farrell, E. D., Felkel, S., Ferreira, M. S., ... & Pettersson, M. (2024). How fish population genomics can promote sustainable fisheries: a road map. Annual Review of Animal Biosciences, 12(1), 1-20. | 15-Feb-24 | https://doi.org/10.1146/annurev-animal-021122-102933 | COD GADUS-MORHUA; LOCAL ADAPTATION; MARINE FISH; ATLANTIC; DIVERGENCE; EVOLUTION; MANAGEMENT; SELECTION; HARENGUS; POWER; Agriculture; Biotechnology & Applied Microbiology; Veterinary Sciences; Zoology | Opinion / Review | Theoretical | SW | North Atlantic region/Atlantic Sea/Baltic sea | |||
| Genomics - Genome-Wide | fisheries genetics; Gadus morhua; genetic tagging; genomics; Oncorhynchus nerka; policy; real-time management; Thunnus maccoyii | This review article explores the use of 'omics' technologies in marine fishery management, and discusses the disconnect that exists between geneticists and practitioners responsible for policy implementation. | Carvalho, G. R. (2025). Genes, fish and fisheries: translating science into policy. Journal of Fish Biology. | 3-Aug-25 | http://dx.doi.org/10.1111/jfb.70153 | COD GADUS-MORHUA; POPULATION GENOMICS; NORTH-SEA; REAL-TIME; MOLECULAR-GENETICS; ENVIRONMENTAL DNA; MITOCHONDRIAL-DNA; ATLANTIC COD; MARINE FISH; MANAGEMENT; Fisheries; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | North Norwegian waters; Bristol Bay, Alaska | |||
| Genomics - Genome-Wide | data; ecosystems; fisheries; genomics; renewables | This opinion paper outlines the emerging challenges in fisheries science, including advances in genomics tool implementation, and stresses the importance of collaboration among scientists, managers and stakeholders to address issues affecting sustainable fisheries. | Murray, D. S., Campón‐Linares, V., O'Brien, C. M., Thorpe, R. B., Vieira, R. P., & Gilmour, F. (2024). Emerging issues in fisheries science by fisheries scientists. Journal of Fish Biology, 105(2), 557-563. | 16-Apr-24 | http://dx.doi.org/10.1111/jfb.15683 | FISH; Fisheries; Marine & Freshwater Biology | Opinion / Review | Theoretical | SW | ||||
| Genomics - Genome-Wide | Marine science; monitoring; management | This review article discusses machine learning applications by combining ML with genomics techniques to assess fish stocks and promote sustainable harvesting. The authors discuss the benefits of ML here, such as reducing labour-intensive and costly nature of fisheries science | Kühn, B., Cayetano, A., Fincham, J. I., Moustahfid, H., Sokolova, M., Trifonova, N., ... & Uusitalo, L. (2025). Machine learning applications for fisheries—at scales from genomics to ecosystems. Reviews in Fisheries Science & Aquaculture, 33(2), 334-357. | 9-Nov-24 | https://doi.org/10.1080/23308249.2024.2423189 | BAYESIAN BELIEF NETWORKS; LIFE-HISTORY PARAMETERS; ECOLOGICAL BIG DATA; SPECIES IDENTIFICATION; SEASCAPE GENETICS; CROSS-VALIDATION; CLIMATE-CHANGE; ATLANTIC COD; FISH; MODEL; Fisheries | Opinion / Review | Applied | SW | Global | |||
| Genomics - Genome-Wide | Atlantic salmon; fishery conservation and management; life-history tactics; mixed-stock fishery; population genomics; subsistence harvesting | This study uses population genomics (GBS and SNPs) to assess the genomic structure of Nunavik Atlantic salmon populations, and identifies the source populations of individuals sampled in a mixed-stock fishery. | Carbonneau, A., April, J., Normandeau, E., Ferchaud, A. L., Nadeau, V., & Bernatchez, L. (2024). Population genomics, life‐history tactics, and mixed‐stock subsistence fisheries in the northernmost American Atlantic salmon populations. Evolutionary Applications, 17(2), e13654. | 22-Feb-24 | https://doi.org/10.1111/eva.13654 | SIGNIFICANT GENETIC DIFFERENTIATION; EVOLUTIONARILY-SIGNIFICANT-UNITS; BROWN TROUT; ONCORHYNCHUS-MYKISS; PARTIAL ANADROMY; ARCTIC CHARR; R PACKAGE; TOOL SET; SALAR L.; RESIDENT; Evolutionary Biology | Technical / Data | Applied | SW | North America | |||
| Genomics - Genome-Wide | bocaccio; California Conservation Genomics Project; CCGP; rockfish; Sebastes | This study offers the first genome assembly of the bocaccio rockfish. This species was previously overfished and suffered from population decline along the Pacific coast. The authors suggest that their work can be used to further develop genomic resources to assist in stock assessment/recovery, and ultimately guide population management plans. | De-Kayne, R., Li, S., Escalona, M., Lou, R. N., Owens, G. L., Kolora, S. R. R., ... & Sudmant, P. H. (2025). A haplotype-resolved genome assembly of the bocaccio rockfish, Sebastes paucispinis. Journal of Heredity, esaf026. | 5-May-25 | https://doi.org/10.1093/jhered/esaf026 | QUALITY ASSESSMENT; CALIFORNIA; Evolutionary Biology; Genetics & Heredity | Technical / Data | Applied | SW | North America | |||
| Genomics - Genome-Wide | Target-enrichment sequencing; Mitochondrial genome; Comparative genomics; Genome structure; Conservation genomics; Fisheries management | This study sequenced the complete mitochondrial genomes of 70 species, contributing to molecular databases of several Latin-American species that were previously under-represented in the literature. The authors state that the sequences they developed and phylogenetic gaps they addressed will allow for identification of species/populations in the Atlantic South, which will ultimately help promote conservation efforts. | Alvarenga, M., D’Elia, A. K. P., Rocha, G., Arantes, C. A., Henning, F., de Vasconcelos, A. T. R., & Solé-Cava, A. M. (2024). Mitochondrial genome structure and composition in 70 fishes: a key resource for fisheries management in the South Atlantic. BMC genomics, 25(1), 215. | 27-Feb-24 | https://doi.org/10.1186/s12864-024-10035-5 | ADAPTIVE EVOLUTION; IDENTIFICATION; PHYLOGENY; TAXONOMY; ANNOTATION; DIVERSITY; ALIGNMENT; PRODUCTS; ACCURATE; SHARK; Biotechnology & Applied Microbiology; Genetics & Heredity | Technical / Data | Applied | SW | South America | |||
| Genomics - Whole-Genome | Alosidae; California current; Clupeiformes; fisheries genomics; population structure | This study used low coverage whole-genome sequencing (lcWGS) to evaluate pacific sardines following the coastline (~4000 km) from Oregon to the Gulf of California. The authors found that there were no genetically distinct populations of Pacific sardines, and therefore, there is a mismatch between current management strategies and actual biology of the species. | Longo, G. C., D′ Amelio, K., Larson, W., Enciso, C. E., Torre, J., Minich, J. J., ... & Craig, M. T. (2025). Population Genomics Reveals Panmixia in Pacific Sardine (Sardinops sagax) of the North Pacific. Evolutionary Applications, 18(9), e70154. | 4-Sep-25 | https://doi.org/10.1111/eva.70154 | CALIFORNIA; PHYLOGEOGRAPHY; VARIABILITY; RETENTION; TRANSPORT; ATLANTIC; CAERULEA; ANCHOVY; STOCKS; Evolutionary Biology | Technical / Data | Applied | SW | North America | |||
| Genomics - Genome-Wide | Global survey; fisheries genetics and genomics; Opinion comparison; Lifelong learning; Developing countries; Molecular tools | Authors conducted a global survey to compare the awareness of genetic applications in fisheries management and the overall willingness to implement these strategies. They found lower implementation of genetic tools across African fisheries, which the authors attributed to limited resources. This paper discusses the steps that can be taken to leverage the knowlege and implementation of genetic tools in fisheries management worldwide. | Milec, L. J., Hugé, J., Raeymaekers, J. A., Van Schoubroeck, S., Van Steenberge, M., & Vanhove, M. P. (2025). High expectation, low implementation: perceptions of African fish and fisheries experts on genetic indicators in fisheries management. Environmental and Sustainability Indicators, 100772. | 9-Jul-25 | https://doi.org/10.1016/j.indic.2025.100772 | FRESH-WATER; TRADE-OFFS; CONSERVATION; BIODIVERSITY; CHALLENGES; EDUCATION; SCIENCE; OPPORTUNITIES; POPULATION; DIVERSITY; Environmental Sciences & Ecology | Technical / Data | Applied | SW/FW | Global | |||
| Genomics - Whole-Genome | fisheries-induced evolution; genetic variation; population genomics; size-selection; whole-genome sequencing | This article uses zebrafish to simulate how size-selective harvesting in fisheries can lead to a reduction in genetic biodiversity | Sadler, D. E., Sävilammi, T., van Dijk, S. N., Watts, P. C., & Uusi‐Heikkilä, S. (2024). Size‐selective harvesting drives genomic shifts in a harvested population. Journal of Fish Biology, 105(6), 1562-1571. | 8-Aug-24 | https://doi.org/10.1111%2Fjfb.15901 | FISHERIES-INDUCED EVOLUTION; COD GADUS-MORHUA; NORTH-SEA; GENETIC DIVERSITY; FISH POPULATIONS; N-E; STABILITY; CONSERVATION; Fisheries; Marine & Freshwater Biology | Technical / Data | Applied | NA | India | |||
| Genomics - Genome-Wide | Sociotechnical imaginaries; Cumulative visioning; Fisheries management; Food security; Genomics | This author conducted interviews with stakeholders involved in salmon farming management, and identifies the main visions of salmon production. This article describes the uses of genomics in salmon production (e.g., selevtive breeding programs), and that genetic applications contribute to emerging visions. Note that no genomic data is analyzed here. | Berseth, V. (2025). Salmon imaginaries: accumulating competing sociotechnical visions in artificial breeding programs. Agriculture and Human Values, 1-16. | 6-May-25 | https://doi.org/10.1007/s10460-025-10737-w | GENETIC ADAPTATION; ATLANTIC SALMON; HATCHERY FISH; CONSERVATION; BIOPOLITICS; DISCOURSE; CAPTIVITY; HABITATS; POLITICS; SCIENCE; Agriculture; History & Philosophy of Science; Sociology | Technical / Data | Applied | SW | North America | |||
| Genomics - Whole-Genome | Acanthopagrus schlegelii; Whole-genome resequencing; Stock enhancement; Population genomics; Paternity analysis | This study used whole-genome sequencing to evaluate stock enhancement in blackhead seabream. The authors argue that genetic tools should be used during breeding and rearing to avoid inbreeding and maintain stock genetic diversity. | Wang, X., Yang, Y., Zhang, H., Shi, Y., Xu, A., Zhang, X., & Song, N. (2025). The stock enhancement for blackhead seabream (Acanthopagrus schlegelii): Insights from whole-genome resequencing. Available at SSRN 4969130. | 1-Jul-25 | https://doi.org/10.1016/j.rsma.2025.104142 | POPULATION-STRUCTURE; GENETIC DIVERSITY; COASTAL FISHERIES; RECAPTURED FISH; SEA; HATCHERY; PROGRAM; WILD; PERCIFORMES; RESTOCKING; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Applied | SW | Asia | |||
| Genomics - Genome-Wide | effective population size; fisheries genomics; fisheries management; genetic diversity; overfishing | This study utilized genome-wide SNPs to estimate genetic effective size of the Australasian snapper. This article highlights the challenges associated with estimating genetic effective size in large, iteroparous populations and suggests that the authors' approach can serve as a guide for assessing effective size in other important fisheries species. | Bertram, A., Bell, J., Brauer, C., Fairclough, D., Hamer, P., Sandoval‐Castillo, J., ... & Beheregaray, L. B. (2024). Estimation of effective number of breeders and effective population size in an abundant and heavily exploited marine teleost. Evolutionary Applications, 17(7), e13758. | 22-Jul-24 | https://doi.org/10.1111/eva.13758 | SNAPPER CHRYSOPHRYS-AURATUS; LINKAGE DISEQUILIBRIUM; INTERANNUAL VARIATION; N-E; CONTEMPORARY; CONSERVATION; EVOLUTION; GENETICS; PATTERNS; SPARIDAE; Evolutionary Biology | Technical / Data | Applied | SW | Australia | |||
| Genomics - Genome-Wide | Aquaculture; conservation; genomics; mitogenome; Pangasiidae | This review article addresses the current state of genomic research on Pangasiid catfish. The authors argue that the implementation of genomics techniques in catfish farming will make for sustainable production, aid in selective breeding programs, and help inform conservation measures | Abdul-Halim, S. A. A., Esa, Y., Duong, T. Y., Syukri, F., Rajandas, H., Parimannan, S., & Mohd-Nor, S. A. (2024). A Review of Pangasiid Catfish Genomics for Conservation and Aquaculture: Current Status and Way Forward. Pertanika Journal of Tropical Agricultural Science, 47(4). | 29-Nov-24 | http://dx.doi.org/10.47836/pjtas.47.4.11 | MEKONG GIANT CATFISH; PANGASIANODON-GIGAS; ASIAN CATFISH; PHYLOGENETIC-RELATIONSHIPS; MITOCHONDRIAL GENOME; FISHES; PERSPECTIVE; DIVERSITY; Agriculture | Opinion / Review | Applied | FW | Asia | |||
| Genomics - Genome-Wide | Harengula; Clupeidae; fishery genomics; genetic diversity; marine protected areas | This study combines ecological niche modeling with population genomics to address the genetic diversity of an under-studied but overexploited species of sardines along the Brazilian coast. The authors found two distinct genetic lineages, indicating that the island population should be managed separately from the coastal population, and they propose protection measures to protect both groups | Coelho, J. F. R., Mendes, L. D. F., Di Dario, F., Carvalho, P. H., Dias, R. M., Lima, S. M. Q., ... & Pereira, R. J. (2024). Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species. Proceedings of the Royal Society B, 291(2018), 20232746. | 13-Mar-24 | http://dx.doi.org/10.1098/rspb.2023.2746 | FISHERIES MANAGEMENT; MODEL; BIODIVERSITY; DIVERSITY; ATLANTIC; COASTAL; Life Sciences & Biomedicine - Other Topics; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | SW | Southwest Atlantic | |||
| Genomics - Genome-Wide | Etelis oculatus; Genetic diversity; Caribbean Fisheries; Genomics | This study used RAD-Seq to generate a large SNP dataset to assess the genetic diversity of the queen snapper, a commercially important deep-sea species. | González-García, M. D. P., García-Sais, J. R., García-Moliner, G., & Schizas, N. V. (2025). RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico. Marine Life Science & Technology, 1-12. | 12-May-25 | http://dx.doi.org/10.1007/s42995-025-00289-7 | LARVAL DISPERSAL; INDO-PACIFIC; TOOL SET; CONNECTIVITY; GENOMICS; GENETICS; LUTJANIDAE; MANAGEMENT; VISUALIZE; FISHERIES; Marine & Freshwater Biology | Technical / Data | Applied | SW | Caribbean (Puerto Rico) | |||
| Genomics - Genome-Wide | Baltic salmon; fisheries management; fisheries-induced evolution; genetic stock identification; SNP; temporal genomics | This study analyzed nearly 100 years of Atlantic salmon samples collected through fisheries monitoring programs. By genotyping these samples and linking them to life-history traits, the authors showed that early-season fishing can directly shift allele frequencies in key maturation genes. | Miettinen, A., Romakkaniemi, A., Dannewitz, J., Pakarinen, T., Palm, S., Persson, L., ... & Pritchard, V. L. (2024). Temporal allele frequency changes in large‐effect loci reveal potential fishing impacts on salmon life‐history diversity. Evolutionary applications, 17(4), e13690. | 25-Apr-24 | http://dx.doi.org/10.1111/eva.13690 | ATLANTIC SALMON; BALTIC SEA; GENETIC-STRUCTURE; WILD; SALAR; RIVER; AGE; ADAPTATION; MANAGEMENT; SIZE; Evolutionary Biology | Technical / Data | Applied | SW/FW | Europe (northern Baltic Sea) | |||
| Genomics - Genome-Wide | genomics; salmonids; brook trout; GT-seq; population structure; mixed-stock | This study used GT-Seq SNP data and georeferencing to investigate the population structure, spatial distributions and harvest contributions of brook trout in three Quebec lakes. By identifying which brook trout populations contribute most to the harvest, the authors argue changes in these populations should be closely monitored to ensure fishery stability over time. | Chamlian, B., Michaelides, S., Gibelli, J., Won, H., Jeon, H. B., & Fraser, D. J. (2025). Mixed-stock analysis reveals long-distance movements and few populations with large harvest contributions in lake-migratory brook trout. Canadian Journal of Fisheries and Aquatic Sciences, 82, 1-25. | 22-May-25 | http://dx.doi.org/10.1139/cjfas-2024-0258 | SALMON SALMO-SALAR; ATLANTIC SALMON; SALVELINUS-ALPINUS; GENETIC DIVERSITY; FISHERIES; DIVERGENCE; PACIFIC; IMPACT; SIZE; DNA; Fisheries; Marine & Freshwater Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | population genetics; fishery management; conservation; microsatellite DNA; Eastern Highlands | This article used microsatellite DNA to assess genetic differentiation, random genetic drift, and evidence of inbreeding among walleye populations, highlighting the effects of glacial refugia. The authors argue that their findings will help to inform management and conservation planning | Harris, S. C., Palmer, G., Stepien, C. A., & Hallerman, E. M. (2023). Population genetic differentiation of walleye (Sander vitreus) across the Eastern Highlands of the United States. Fishes, 9(1), 15. | 29-Dec-23 | http://dx.doi.org/10.3390/fishes9010015 | STIZOSTEDION-VITREUM; CONSERVATION GENOMICS; SPAWNING PHILOPATRY; RIVER; DIVERSITY; SOFTWARE; PHYLOGEOGRAPHY; CONNECTIVITY; VICARIANCE; PATTERNS; Fisheries; Marine & Freshwater Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | conservation management; ecological genomics; fisheries genomics; genetic rescue; genomic offset; range edge effects | This study measured the genomic vulnerability of Australian Golden Perch. Using SNPs to detect genotype-environment associations, the authors identified populations that may be more or less vulnerable to warming water temperatures as a result of climate change, predicting how much genetic change would be required for adaptation. Their findings have applications for management and stocking, as some populations may require greater protection than others. | Booth, E. J., Brauer, C. J., Sandoval‐Castillo, J., Harrisson, K., Rourke, M. L., Attard, C. R., ... & Beheregaray, L. B. (2024). Genomic Vulnerability to Climate Change of an Australian Migratory Freshwater Fish, the Golden Perch (Macquaria ambigua). Molecular Ecology, 33(23), e17570. | 4-Nov-24 | http://dx.doi.org/10.1111/mec.17570 | MURRAY-DARLING BASIN; HIGH GENE FLOW; PAIRWISE RELATEDNESS; ADAPTIVE DIVERGENCE; DRYLAND RIVER; ARID ZONE; R PACKAGE; ADAPTATION; DISPERSAL; FUTURE; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | FW | Australia | |||
| Genomics - Whole-Genome | fisheries management; genetic monitoring; genomics; otolith; single-nucleotide polymorphisms (SNPs); whole-genome resequencing | Recognizing that fish ear bones are routinely collected in fisheries, the authors demonstrated that they can serve as valuable sources of genomic DNA for fish stock research and monitoring. They performed whole-genome sequencing to identify SNPs from archived samples, with the goal of building a large, reliable genomic dataset. This resource can be applied to fisheries management to investigate genetic structure, adaptive pressure, and demographic history. | Caccavo, J. A., Arantes, L. S., Celemín, E., Mbedi, S., Sparmann, S., & Mazzoni, C. J. (2024). Whole‐genome resequencing improves the utility of otoliths as a critical source of DNA for fish stock research and monitoring. Molecular Ecology Resources, 24(8), e14013. | 5-Sep-24 | http://dx.doi.org/10.1111/1755-0998.14013 | TOOTHFISH DISSOSTICHUS-MAWSONI; COD GADUS-MORHUA; EFFECTIVE POPULATION-SIZE; TARGET-ENRICHMENT; CHEMICAL-COMPOSITION; GENETIC-STRUCTURE; AGE ESTIMATION; EXTRACTION; MITOCHONDRIAL; ADAPTATION; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | FW | Global | |||
| Genomics - Genome-Wide | Atlantic bonito; ddRadSeq; Population genomics; Atlantic -mediterranean transition; Fishery management; Pelagic; Genetics; Conservation | This paper used SNPs to identify two genetically differentiated populations of Atlantic bonito, which historically, were treated as a single stock. The authors argue that given their findings, there should be separate management units in charge of stock assessment and conservation. | Ollé-Vilanova, J., Hajjej, G., Macias, D., Saber, S., Lino, P. G., Muñoz-Lechuga, R., ... & Vinas, J. (2024). Atlantic bonito (Sarda sarda) genomic analysis reveals population differentiation across Northeast Atlantic and mediterranean locations: Implications for fishery management. Marine Environmental Research, 196, 106408. | 1-Apr-24 | http://dx.doi.org/10.1016/j.marenvres.2024.106408 | R-PACKAGE; AUXIS-ROCHEI; CONNECTIVITY; SELECTION; PATTERNS; SIZE; PHYLOGEOGRAPHY; RADSEQ; MODEL; SEA; Environmental Sciences & Ecology; Marine & Freshwater Biology; Toxicology | Technical / Data | Applied | SW | Northeast Atlantic/Mediterranean | |||
| Genomics - Genome-Wide | fisheries; genetics; taxonomy and systematics | The authors highlight the potential of historical, formalin-preserved fish specimens as a source of DNA for genetic and phylogenetic studies. They tested multiple DNA extraction methods on different tissues to optimize yields and improve DNA quality for downstream genomic analyses. | Brino, E. E., Schumann, D. A., Rezac, C. R., Ellwanger, R. J., & Osmundson, T. W. (2023). Unlocking the genomes of formalin‐fixed freshwater fish specimens: An assessment of factors influencing DNA extraction quantity and quality. North American Journal of Fisheries Management, 43(6), 1596-1609. | 27-Jul-23 | http://dx.doi.org/10.1002/nafm.10935 | NATURAL-HISTORY COLLECTIONS; MUSEUM SPECIMENS; CONSERVATION; TAXONOMY; AMPLIFICATION; PRESERVATION; EVOLUTION; REVEALS; Fisheries | Technical / Data | Applied | FW | ||||
| Genomics - Genome-Wide | fishery management; groundfish; Merlucciidae; RADseq; stock structure | This study assessed the population structure of coastal Pacific Hake and found that there is no genetic differentiation within the coastal stock. They also found that there was clear genetic differentiation between the coastal and Salish Sea stocks, which are already recognized as separate management units. Overall, their findings are consistent with the current management unit designations used in annual stock assessment reports. | Longo, G. C., Head, M. A., Parker‐Stetter, S. L., Taylor, I. G., Tuttle, V. J., Billings, A. A., ... & Nichols, K. M. (2024). Population genomics of coastal Pacific Hake. North American Journal of Fisheries Management, 44(1), 222-234. | 5-Feb-24 | http://dx.doi.org/10.1002/nafm.10969 | MERLUCCIUS-PRODUCTUS; R-PACKAGE; SELECTION; MARKERS; NUMBER; Fisheries | Technical / Data | Applied | SW | North America | |||
| Genomics - Genome-Wide | conservation genetics; conservation management; fish; fisheries genomics; fisheries management; wildlife management | This study applied otolith chemistry and genomic analyses to golden perch to assess how hatchery stocking has influenced wild population structure. This is rather novel as most previous studies that used this combined method focused on salmonids. Overall, the authors found higher relatedness among the stocked perch, highlighting the need for hatcheries to make informed choices as to not collect previously stocked fish as broodstock and reduce risk of inbreeding. | Harrisson, K. A., Beheregaray, L. B., Bice, C. M., Booth, E. J., Brauer, C. J., Butler, G. L., Dawson D, Dudchenko O, Fanson BG, Hackett G, Harris A, Jones MJ, Kaur P, Koster WM, Krusic-Golub K, Aiden EL, Lieschke JA, Lyon J, Morrongiello JR, Murphy NP, O'Dwyer J, Raymond SMC, Rourke ML, Strawbridge A, Thiem JD, Tonkin Z, Yen JDL, & Zampatti, B. P. (2025). Otolith and Genomic Data Reveal Temporal Insights Into Stocking Across a Large River Basin in a Mobile, Long‐Lived Australian Freshwater Fish Species. Molecular Ecology, 34(7), e17714. | 5-Mar-25 | http://dx.doi.org/10.1111/mec.17714 | EFFECTIVE POPULATION-SIZE; PERCH MACQUARIA-AMBIGUA; GENETIC DIVERSITY; LINKAGE DISEQUILIBRIUM; INBREEDING DEPRESSION; REPRODUCTIVE SUCCESS; COHO SALMON; RECRUITMENT; MANAGEMENT; MURRAY; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | FW | Australia | |||
| Genomics - Genome-Wide | acoustic telemetry; low-coverage whole genome; migration; northern cod | This is an interdisciplinary study that combines acoustic telemetry with whole-genome resequencing to track migratory patterns of northern cod off the coast of newfoundland. The results show that identifying distinct sub-groups and tracking their migrations can provide valuable information for conservation and fisheries management. | Delgado, M. L., Smith, N., Whoriskey, F., Devitt, S., Novaczek, E., Morris, C. J., ... & Ruzzante, D. E. (2025). Northern Cod (Gadus morhua) movement: insights from acoustic telemetry and genomics. Journal of Fish Biology. | 4-Aug-25 | http://dx.doi.org/10.1111/jfb.70167 | ATLANTIC COD; GENETIC DIFFERENTIATION; NEWFOUNDLAND; MIGRATION; INSHORE; BAY; LABRADOR; AREA; Fisheries; Marine & Freshwater Biology | Technical / Data | Applied | SW | North America | |||
| Genomics - Genome-Wide | Genetic structure; Percichthyidae; Phylogeny; Phylogenetic networks; Population genomics; River blackfish; Two-spined blackfish | This is a data-based paper that used SNPs to assess species boundaries and phylogenetic relationships within the Gadopsis genus. The authors identified seven candidate species and developed a SNP dataset that can support conservation applications, such as population and species identification. | Campbell, M. A., Hammer, M. P., Adams, M., Raadik, T. A., & Unmack, P. J. (2024). Evolutionary relationships and fine-scale geographic structuring in the temperate percichthyid genus Gadopsis (blackfishes) to support fisheries and conservation management. Molecular Phylogenetics and Evolution, 199, 108159. | 18-Jul-24 | http://dx.doi.org/10.1016/j.ympev.2024.108159 | RIVER BLACKFISH; PHYLOGENETIC NETWORKS; MITOCHONDRIAL-DNA; GENETIC-STRUCTURE; R-PACKAGE; WATER; TELEOSTEI; FISH; CAPTURE; PHYLOGEOGRAPHY; Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity | Technical / Data | Applied | FW | Australia | |||
| Genomics - Genome-Wide | Genomics; Microhaplotypes; Genotyping; Oncorhynchus mykiss; Phylogeography | This data paper developed a microhaplotype panel comprised of neutral loci (presumed), a sex-determination locus, and ten loci associated with adaptive traits. This panel provided insight into the phylogeography and population structure California rainbow trout. The data generated and markers developed can be used in population monitoring and fisheries management. | Le Gall, R., Barthelemy, N., Clemento, A. J., Columbus, C. D., Campbell, E., Correa, E. C., ... & Pearse, D. E. (2025). Development of a microhaplotype panel for steelhead/rainbow trout (Oncorhynchus mykiss) and application for phylogenetic analysis in California. Conservation Genetics Resources, 17(1), 17-29. | 28-Nov-24 | http://dx.doi.org/10.1007/s12686-024-01374-2 | SINGLE-NUCLEOTIDE POLYMORPHISMS; POPULATION-STRUCTURE; RAINBOW-TROUT; INTROGRESSIVE HYBRIDIZATION; GENETIC-MARKER; CONSERVATION; SEQUENCE; EVOLUTION; PARENTAGE; ANCESTRY; Biodiversity & Conservation; Genetics & Heredity | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | adaptive capacity; conservation genomics; fisheries management; inversion; marine protected areas; structural variation | This is a review article that looks at the benefits of chromosomal inversions in mitigating conservation risks and maintaining locally adapted gene combinations. Inversion data may be helpful in stock assessments and conservation planning by preserving adaptive diversity and reducing loss of adaptive variation. | Schneller, N. M., Strugnell, J. M., Field, M. A., Johannesson, K., & Cooke, I. (2025). Putting Structural Variants Into Practice: The Role of Chromosomal Inversions in the Management of Marine Environments. Molecular Ecology, e17776. | 8-May-25 | http://dx.doi.org/10.1111/mec.17776 | EVOLUTIONARILY-SIGNIFICANT-UNITS; LOCAL ADAPTATION; CLIMATE-CHANGE; DROSOPHILA-MELANOGASTER; THREESPINE STICKLEBACK; GENOMIC DIVERGENCE; ATLANTIC; POLYMORPHISM; SELECTION; RESCUE; | Opinion / Review | Applied | SW | Global | |||
| Genomics - Genome-Wide | Blackspot seabream; Fish stock assessment; Pagellus bogaraveo; Genotyping-by-sequencing | This is a data-based paper that used genotype-by-sequencing (GBS) to assess the population structures of blackspot seabream in the Northeast Atlantic. Their results showed genetic clustering that previous molecular techniques had not revealed, thus highlighting the importance of genomic tools in stock delineation and fisheries management. | Cunha, R. L., Robalo, J. I., Francisco, S. M., Farias, I., Castilho, R., & Figueiredo, I. (2024). Genomics goes deeper in fisheries science: The case of the blackspot seabream (Pagellus bogaraveo) in the northeast Atlantic. Fisheries Research, 270, 106891. | 24-Feb | https://doi.org/10.1016/j.fishres.2023.106891 | R-PACKAGE; MEDITERRANEAN OUTFLOW; POPULATION-STRUCTURE; GENETIC DIVERSITY; OSTEICHTHYES; PARAMETERS; PATTERNS; MARKERS; SCANS; Fisheries | Technical / Data | Applied | SW | Northeast Atlantic | |||
| Genomics - Genome-Wide | Genetics; SNP; Fishery; Stock structure; Stock identification | This data-based paper used SNPs to assess the population structure of three commonly harvested fish species (L. sebae, L. malabaricus, and P. multidens) off the Australian coast. The results showed high levels of genetic connectivity alongside isolation-by-distance patterns. While their results do not support a revision of management boundaries, the authors do emphasize that declines in one stock may have broader impacts across the population network. | Payet, S. D., Underwood, J., Berry, O., Saunders, T., Travers, M. J., Wakefield, C. B., ... & Newman, S. J. (2024). Population genomics informs the management of harvested snappers across north-western Australia. Scientific Reports, 14(1), 26598. | 4-Nov-24 | https://doi.org/10.1038/s41598-024-77424-4 | PELAGIC LARVAL DURATION; PRISTIPOMOIDES-MULTIDENS; STOCK STRUCTURE; REEF FISH; R-PACKAGE; OTOLITH MICROCHEMISTRY; GENETIC SUBDIVISION; OCEAN CIRCULATION; LEEUWIN CURRENT; LIFE-HISTORY; Science & Technology - Other Topics | Technical / Data | Applied | SW | Australia | |||
| Genomics - Genome-Wide | Stock identification; Micromesistius poutassou; Fishery management; Northeast Atlantic | This is a review paper that examines the population structure of the blue whiting in the Northeast Atlantic. Although the blue whitings are currently treated as a single population, the authors present possible evidence for multiple subpopulations, along with mixing zones, that should be recognized to improve fisheries management practices. | Lee, B., Ólafsdóttir, A. H., Post, S., Jacobsen, J. A., Høines, Å., Gonçalves, P., & Randhawa, H. S. (2025). Unravelling the stock structure of blue whiting in the Northeast Atlantic: navigating contradictions towards resolution. Reviews in Fish Biology and Fisheries, 1-20. | 28-Jul-25 | http://dx.doi.org/10.1007/s11160-025-09976-1 | MICROMESISTIUS-POUTASSOU RISSO; PARTIAL MIGRATION; SPAWNING DISTRIBUTION; TROPHIC ECOLOGY; PORCUPINE BANK; SUBPOLAR GYRE; POPULATION; FISH; LARVAE; DIET; Fisheries; Marine & Freshwater Biology | Opinion / Review | Applied | SW | Europe | |||
| Genomics - Genome-Wide | This is a review article that looks at how hatchery reared chinook salmon interact with wild populations in BC, and examines the effectiveness of hatchery programs managed by the DFO. The authors discuss the ecological and genetic implications of hatchery production and emphasize the need for improved management to support wild salmon conservation as natural populations decline under climate change. | Riddell, B. E., Pearsall, I., & Rosenberger, A. (2024). A review of Pacific salmon hatcheries in British Columbia, Canada, and interactions with natural populations. Fisheries, 49(7), 303-318. | 30-Apr-24 | https://doi.org/10.1002/fsh.11091 | CHINOOK SALMON; FITNESS; IDENTIFICATION; TRAITS; Fisheries | Opinion / Review | Applied | FW | North America | ||||
| Genomics - Genome-Wide | adaptation; genetic sex determination; population genetics; Reinhardtius hippoglossoides; sex-biasses | This data-based paper used SNPs to examine how sex influences the genetic structure of Greenland halibut in the North Atlantic. The authors found that sex-linked genetic variation can bias population structure analyses. Resultantly, they advise that fisheries managers include sex-associated loci when developing SNP panels for stock assessment to avoid misassignments and ensure accurate management decisions. | Estévez‐Barcia, D., Roy, D., Vihtakari, M., Gíslason, D., Lindegren, M., Christensen, A., ... & Johansen, T. (2025). Sex Influences the Genetic Structure of Greenland Halibut in the North Atlantic. Ecology and Evolution, 15(2), e70822. | 10-Feb-25 | https://doi.org/10.1002/ece3.70822 | REINHARDTIUS-HIPPOGLOSSOIDES WALBAUM; POPULATION GENOMICS; SELECTION; COD; DIFFERENTIATION; CONNECTIVITY; FISHERIES; SOFTWARE; PATTERNS; PACKAGE; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | SW | North Atlantic | |||
| Genomics - Genome-Wide | fisheries; genomics; hybrid detection; hybrids; morphometrics; research bias | This is a review article that emphasizes the importance of testing and accounting for hybridization in wild populations, particularly pelagix and deep-water species. The authors discuss how unrecognized hybrid individuals can bias population/stock assessments, and potentially affect reproduction estimates and management decisions. Accounting for hybridization can help fisheries managers implement sustainable practices. | Pecoraro, C., Papetti, C., & Fruciano, C. (2024). Hidden in the ocean: The importance of detecting hybridisation in pelagic and deep‐water fishes. Fish and Fisheries, 25(1), 97-113. | 5-Oct-23 | http://dx.doi.org/10.1111/faf.12794 | ANGLERFISH LOPHIUS-BUDEGASSA; BODY SHAPE DIFFERENCES; PARTIAL LEAST-SQUARES; INTROGRESSIVE HYBRIDIZATION; POPULATION-STRUCTURE; SEBASTES-FASCIATUS; INDO-PACIFIC; S-MENTELLA; GENE FLOW; PHYLOGENETIC-RELATIONSHIPS; Fisheries | Opinion / Review | Theoretical | SW | Global | |||
| Genomics - Genome-Wide | This is a short perspective paper that summarizes work done by Zbinden et al. (2023). The original study examined multi-species landscape genomics, rather than a single-species (which most studies focus on). The authors in this perspective paper state that taking on a comparative approach of analyzing multiple species in the same landscape can reveal general patterns of how landscapes shape genetic structure. Ultimately, integration of this approach will help to inform conservation and management strategies that seek to preserve genetic diversity in freshwater aquatic ecosystems. | Riginos, C., & Jahnke, M. (2023). Comparative landscape genomics has arrived with a splash. Molecular Ecology, 32(24), 6725-6728. | 17-Nov-23 | http://dx.doi.org/10.1111/mec.17204 | Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Opinion / Review | Theoretical | FW | North America | ||||
| Genomics - Genome-Wide | brook trout; genomics; habitat fragmentation; phenotype; supplementation | This data-based paper used over 16-thousand SNP markers to assess how anthropogenic activities, such as stocking and dams, affect genetic patterns. The authors compared wild and captive-bred brook trout, examined the effect of dams on gene flow, and tested whether genetic divergence in wild brook trout is reflected in thier morphology. Overall, the authors argue that their results will help inform management decisions that aim to conserve genetic diversity in wild brook trout. | Michaelides, S. N., Pelletier, C., Frawley, C. J., Forrester, G., Libby, A., & McGreevy Jr, T. (2025). Minimal Introgression but Restricted Gene Flow: How Stocking and Dams Influence Wild Brook Trout (Salvelinus fontinalis) Genetics and Morphology. Freshwater Biology, 70(4), e70033. | 11-Apr-25 | http://dx.doi.org/10.1111/fwb.70033 | POPULATION-STRUCTURE; HABITAT FRAGMENTATION; PACIFIC SALMON; R PACKAGE; CHARR; SHAPE; SCALE; PERFORMANCE; DIVERSITY; MIGRATION; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | brook trout; fisheries management; genomics; hatchery introgression; salmonid; simulation | This is a data-based paper that used RAD (restriction-site associated DNA) sequencing to assess how hatchery-reared fish are affecting the population structure of wild brook trout. They found that rapid genetic divergence between hatchery and wild fish can potentially lead to an underestimation of introgression levels. The genomic methods used in this study can improve the accuracy of introgression estimates and support conservation and management of stocked and wild brook trout populations. | Erdman, B., Larson, W., Mitro, M. G., Griffin, J. D., Rowe, D., Haglund, J., ... & Kinnison, M. T. (2024). Complications of Estimating Hatchery Introgression in the Face of Rapid Divergence: A Case Study in Brook Trout (Salvelinus fontinalis). Evolutionary applications, 17(12), e70026. | 16-Dec-24 | http://dx.doi.org/10.1111/eva.70026 | EFFECTIVE POPULATION-SIZE; R-PACKAGE; GENETIC INTEGRITY; ATLANTIC SALMON; TOOL SET; N-E; WILD; STOCKING; FISH; CONSERVATION; Evolutionary Biology | Technical / Data | Applied | FW | North America | |||
| Genomics - Genome-Wide | eye lens; fisheries; life history diversity; migration; otolith; Salmonid | This is a data-based paper that used both SNP genotyping and stable isotope analysis of various tissues to characterize brown trout maternal life histories as either anadromous or freshwater-residents. | Jones, J. I., King, R. A., Sturrock, A. M., Wei, H., Stevens, J. R., & Lauridsen, R. B. (2025). Anadromous Brown Trout (Salmo trutta) Contribute Disproportionally to Recruitment: Insights From Genomics and Multi‐Tissue Stable Isotope Chemistry. Freshwater Biology, 70(8), e70078. | 7-Aug-25 | http://dx.doi.org/10.1111/fwb.70078 | ATLANTIC SALMON; MATERNAL ORIGIN; L.; CARBON; MIGRATION; PROGRAM; SALAR; RIVER; SIZE; DIET; Environmental Sciences & Ecology; Marine & Freshwater Biology | Technical / Data | Applied | FW | Europe | |||
| Genomics - Genome-Wide | dispersal; fisheries; genome; lcWGS; Pacific Sardine; range shift | This is a data-based paper that assembled full mitochondrial genomes in sardines from the northeastern Pacific. These results provide the first genetic evidence of the presence of Japanese sardines occuring in the Califormia Current Large Marine Ecosystem. These findings suggest that dispersial or mixing between sardine populations could be occurring across the Pacific. The authors also note that their findings may have implications for the management of coastal pelagic species along the west coast. | Longo, G. C., Minich, J. J., Allsing, N., James, K., Adams‐Herrmann, E. S., Larson, W., ... & Craig, M. T. (2024). Crossing the Pacific: Genomics Reveals the Presence of Japanese Sardine (Sardinops melanosticta) in the California Current Large Marine Ecosystem. Molecular Ecology, 33(22), e17561. | 23-Oct-24 | http://dx.doi.org/10.1111/mec.17561 | CLIMATE-DRIVEN CHANGES; SEQUENCE; IMPACTS; VISUALIZATION; FLUCTUATIONS; CLUPEIFORMES; POLYMORPHISM; ANNOTATION; HISTORIES; ALIGNMENT; Biochemistry & Molecular Biology; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | SW | North America | |||
| Genomics - Whole-Genome | fisheries management; genomics/proteomics; population genetics - empirical | This data paper used whole-genome sequencing to examine the genomic patterns of differentiation in steelhead (anadromous rainbow trout) populations. The authors compared neutral genetic variation with variation at major effect loci assiociated with life history traits. Overall, they were able to distinguish between natural selection and anthropogenic effects that drove the genomic variaton. | Willis, S., Coykendall, D. K., Campbell, M. R., & Narum, S. (2024). Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes. Evolutionary Applications, 17(1), e13623. | 11-Dec-23 | https://doi.org/10.1111/eva.13623 | ADAPTIVE GENOMIC VARIATION; TROUT ONCORHYNCHUS-MYKISS; SEX-DEPENDENT DOMINANCE; LIFE-HISTORY DIVERSITY; LOCAL ADAPTATION; LANDSCAPE FEATURES; CONSERVATION; MIGRATION; COLUMBIA; GENETICS; Evolutionary Biology | Technical / Data | Applied | FW | North America | |||
| Transcriptomics | Atlantic halibut; Crude oil exposure; Transcriptomics; Organogenesis; Pathway analysis; Downstream effects | Recognizing that oil spills have detrimental and lasting effects on fisheries, this data-based paper sought to assess how a commercially valuable species, Atlantic halibut, transcriptionally responds to this stressor using RNA-Seq. That is, they performed an experiment where they looked at whole-halibut larvae and tissue-specific responses to oil exposure. Several days after exposure, they observed inhibition of reparative and inflammatory pathways, and activation of pathways assiociated with neuronal pathways. | Sørhus, E., Lie, K. K., Meier, S., Furmanek, T., Norberg, B., & Perrichon, P. (2025). Transcriptomics uncover inhibition of repair and wound healing pathways in Atlantic halibut (Hippoglossus hippoglossus) after crude oil exposure. Ecotoxicology and Environmental Safety, 296, 118151. | 25-May | http://dx.doi.org/10.1016/j.ecoenv.2025.118151 | TISSUE-REPAIR; AROMATIC-HYDROCARBONS; EXXON-VALDEZ; TOXICITY; MECHANISMS; IMPACTS; SPILLS; LARVAE; Environmental Sciences & Ecology; Toxicology | Technical / Data | Applied | SW | Europe | |||
| Transcriptomics | climate change; fish; adaptation; egg; ovarian follicle; intergenerational; spawning; maternal-effect genes | This data-based paper used RNA-Seq to examine the effect of elevated temperatures on the deposition of maternal mRNAs on Atlantic cod ovarian follicles and fertilized eggs. The authors found that warmer maternal temperatures altered the maternal mRNA profiles in the eggs, which suggests that elevated ocean temperatures may alter developmental outcomes in the offspring. | Skjærven, K. H., Alix, M., Kleppe, L., Fernandes, J. M., Whatmore, P., Nedoluzhko, A., ... & Kjesbu, O. S. (2024). Ocean warming shapes embryonic developmental prospects of the next generation in Atlantic cod. ICES Journal of Marine Science, 81(4), 733-747. | 8-Mar-24 | http://dx.doi.org/10.1093/icesjms/fsae025 | ZYGOTIC TRANSITION; CLIMATE-CHANGE; TEMPERATURE; IDENTIFICATION; EMBRYOGENESIS; TRANSPORTER; OOGENESIS; MAGNESIUM; FISHERIES; PATHWAYS; Fisheries; Marine & Freshwater Biology; Oceanography | Technical / Data | Applied | SW | Europe | |||
| Transcriptomics | genomic lineages; local adaptation; transcriptomic divergence | This is a data-based paper that used RNA-Seq to identify differences in gene transcription and molecular markers (e.g., SNPs) distinguishing two genomic lineages of silver catfish. | Ríos, N., Pardo, B. G., Fernández, C., Alvarez‐Dios, J. A., Martínez, P., Bouza, C., & García, G. (2025). Transcriptomic divergence and associated markers between genomic lineages of silver catfish (Rhamdia quelen). Ecology and Evolution, 15(3), e71021. | 13-Mar-25 | http://dx.doi.org/10.1002/ece3.71021 | GENE-EXPRESSION; POPULATIONS; ADAPTATION; ANNOTATION; METABOLISM; PATHWAY; Environmental Sciences & Ecology; Evolutionary Biology | Technical / Data | Applied | FW | South America | |||
| Transcriptomics | salinity adaptation; teleost fish; osmoregulation; gut microbiota; metabolomics | This is a multidisciplinary review article that uses an evolutionary perspective of teleosts to assess how transcriptomics, metabolomics and the gut microbiome contribute to acclimitization through osmoregulatory processes under salinity stress | Mkulo, E. M., Iddrisu, L., Yohana, M. A., Zheng, A., Zhong, J., Jin, M., ... & Wang, Z. (2025). Exploring salinity adaptation in teleost fish, focusing on omics perspectives on osmoregulation and gut microbiota. Frontiers in Marine Science, 12, 1559871. | 19-May-25 | http://dx.doi.org/10.3389/fmars.2025.1559871 | KILLIFISH FUNDULUS-HETEROCLITUS; FRESH-WATER; METABOLIC-RESPONSES; OXYGEN-CONSUMPTION; EURYHALINE TELEOST; HORMONAL-CONTROL; ATLANTIC SALMON; GENE-EXPRESSION; RECENT PROGRESS; TIGHT JUNCTION; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Applied | SW/FW | Global | |||
| Transcriptomics | marine heatwaves; oxidative stress; immune function; energy metabolism; Seriola dumerili | This is a data-based paper that used RNA-Seq (with qPCR validation) to assess how juvenile Greater Amberjack transcriptionally respond to short-term and repeated elevated temperatures, simulating the marine heat waves that they experience in their natural habitat. The authors reported DEGs involved in several pathways such as temperature response, metabolism, oxidative stress, and immune function. They found a strong response of these genes under the short-term exposure treatment, but the response diminished with the longer/repeated heat exposure. | Tian, Y., Li, L., Long, H., Zhang, D., Wang, C., Hao, R., ... & Zhu, C. (2025). Transcriptome Analyses Reveal the Molecular Response of Juvenile Greater Amberjack (Seriola dumerili) to Marine Heatwaves. Animals, 15(13), 1871. | 15-Apr-25 | http://dx.doi.org/10.3390/ani15131871 | ENDOPLASMIC-RETICULUM; OXIDATIVE STRESS; HEAT-STRESS; IMMUNE-RESPONSE; FISH; TEMPERATURE; EXPRESSION; TOLERANCE; HSP70; METABOLISM; Agriculture; Veterinary Sciences; Zoology | Technical / Data | Applied | SW | Asia | |||
| Transcriptomics | Pseudorasbora parva; invasive species; gill transcriptome; saline-alkali stress; environmental adaptation | This is a data-based paper that used RNA-Seq to perform de novo transcriptome assembly and analysis on the globally invasive species Wild Topmouth Gudgeon, which originated in Asia. Although this is primarily a freshwater species, it has successfully invaded high-salinity waters. Thus, the authors compared the gill transcriptomes of fish from freshwater and saline-alkaline populations to identify the genes involved in acclimatization. | Liu, L., Duan, Y., Liu, X., Huo, B., Liu, J., Tang, R., & Li, D. (2025). Transcriptional Differences in Gills Provide Insights into the Environmental Acclimatization of Wild Topmouth Gudgeon (Pseudorasbora parva) from Freshwater Invasion to Saline–Alkali Waters. Water, 17(12), 1794. | 15-Jun-25 | http://dx.doi.org/10.3390/w17121794 | MITOCHONDRION-RICH CELLS; TIME QUANTITATIVE PCR; CARBONIC-ANHYDRASE; GYMNOCYPRIS-PRZEWALSKII; APICAL MEMBRANE; R PACKAGE; EXPRESSION; FISH; GENES; OSMOREGULATION; Environmental Sciences & Ecology; Water Resources | Technical / Data | Applied | FW | Asia | |||
| Transcriptomics | climate change; CO2; conservation; fish; fit-chips; food deprivation; genetic biomarkers; ion regulation | This data-based paper used 96 qPCR assays to develop biomarkers for CO2 and starvation stress in Chum salmon (Oncorhynchus keta). The authors note that the assays they developed to identify biomarkers of these stressors can be integrated into the pre-existing "Fit Chips" used by the DFO to monitor salmon health. | Frommel, A. Y., Akbarzadeh, A., Chalifoux, V., Ming, T. J., Collicutt, B., Rolheiser, K., ... & Hunt, B. P. (2025). High sensitivity to ocean acidification in wild out‐migrating juvenile Pacific salmon is not impacted by feeding success. Ecological Applications, 35(5), e70058. | 11-Jul-25 | http://dx.doi.org/10.1002/eap.70058 | PINK SALMON; ONCORHYNCHUS-NERKA; NORTHEAST PACIFIC; SURVIVAL; CO2; CLIMATE; VARIABILITY; ECOSYSTEM; SMOLTS; GROWTH; Environmental Sciences & Ecology | Technical / Data | Applied | FW | North America | |||
| Transcriptomics | Machine learning; Genome; Growth; Fish; Striped bass; Metabolomics; Transcriptomics | This is a data-based paper that used both metabolomic and transcriptomic data to identify the key metabolites and genes that contribute to growth in hybrid striped bass, by comparing "good-growth" vs. "poor-growth" individuals. The authors also incorporated machine learning into their methodology to recognize patterns of gene transcripts and metabolites. Overall, the tools and findings in this paper can be used to improve growth and productivity in aquaculture practices. | Rajab, S. A., Andersen, L. K., Kenter, L. W., Berlinsky, D. L., Borski, R. J., McGinty, A. S., ... & Reading, B. J. (2024). Combinatorial metabolomic and transcriptomic analysis of muscle growth in hybrid striped bass (female white bass Morone chrysops x male striped bass M. saxatilis). BMC genomics, 25(1), 580. | 10-Jun-24 | http://dx.doi.org/10.1186/s12864-024-10325-y | IGF BINDING PROTEIN-1; FATTY-ACID OXIDATION; C VIRUS-INFECTION; HYPERTROPHIC GROWTH; FIBER RECRUITMENT; MYOTOMAL MUSCLE; FARMED FISH; PPAR-GAMMA; T-CELLS; QUALITY; Biotechnology & Applied Microbiology; Genetics & Heredity | Technical / Data | Applied | FW | North America | |||
| Transcriptomics | RNA-seq; High temperature; DNA damage; Hepatic response; Oxidative stress; De novo assembly | This is a data-based paper that used RNA-Seq to perform a de novo assembly of the cusk-eel transcriptome, with a view to determine the effect of thermal stress in this species. The authors note that their findings could be useful in the development of aquaculture for this species. | Dettleff, P., Fuentes, M., Gonzalez, P., Aedo, J., Zuloaga, R., Estrada, J. M., ... & Valdes, J. A. (2025). Generating transcriptomic resources in the teleost fish black cusk-eel (Genypterus maculatus) to evaluate thermal stress in the liver under a climate change scenario. Fish Physiology and Biochemistry, 51(2), 1-16. | 28-Mar-25 | http://dx.doi.org/10.1007/s10695-025-01486-y | OXIDATIVE STRESS; HEAT-STRESS; HIGH-TEMPERATURE; ANNOTATION; CHILENSIS; APOPTOSIS; RESPONSES; REPAIR; Biochemistry & Molecular Biology; Fisheries; Physiology | Technical / Data | Applied | SW | South America | |||
| Transcriptomics | Thamnaconus modestus; Transcriptome analysis; Immune response; poly (I:C); LPS | The Black scraper (Thamnaconus modestus) is an important commercial species in Asia, and has suffered greatly from pathogen infections. This data-based study used both RNA-Seq and qRT-PCR to investigate the immune response of the T. modestus following injections of Poly (I:C) and LPS, which simulate viral and bacterial infections, respectively. | Xu, A., Han, F., Zhang, Y., Chen, S., Bian, L., & Gao, T. (2024). Transcriptomic profiling reveals the immune response mechanism of the Thamnaconus modestus induced by the poly (I: C) and LPS. Gene, 897, 148065. | 1-Mar-24 | http://dx.doi.org/10.1016/j.gene.2023.148065 | UP-REGULATION; EXPRESSION; AQUACULTURE; SYSTEM; CELLS; PHOSPHORYLATION; PERSISTENCE; PROTEIN; GROWTH; TRAF2; Genetics & Heredity | Technical / Data | Applied | SW | Asia | |||
| Transcriptomics | developmental plasticity; thermal plasticity; non-coding RNAs; myogenesis; somatic growth; aquaculture | In this study, researchers were interested in the effect of temperature on the expression of circRNA in fast muscle of Nile tilapia, a common aquaculture species. Specifically, they subjected embryos to different temperature treatments and identified temperature-dependent regulation of circRNA in the muscle tissue, which the authors note may impact development. Although this paper does not explicitly discuss aquaculture applications, these findings could inform hatchery and rearing practices by highlighting the lasting effects of embryonic temperature exposure. | Rbbani, G., Murshed, R., Siriyappagouder, P., Sharko, F., Nedoluzhko, A., Joshi, R., ... & Fernandes, J. M. (2024). Embryonic temperature has long-term effects on muscle circRNA expression and somatic growth in Nile tilapia. Frontiers in Cell and Developmental Biology, 12, 1369758. | 31-Jul-24 | http://dx.doi.org/10.3389/fcell.2024.1369758 | CIRCULAR RNAS; SENEGALESE SOLE; SKELETAL-MUSCLE; INCUBATION-TEMPERATURE; GENE-EXPRESSION; CELL-MIGRATION; TELEOST; MICRORNA; ENVIRONMENT; PROTEIN; Cell Biology; Developmental Biology | Technical / Data | Applied | FW | Africa | |||
| Proteomics | Fish; Histochemistry; Techniques; Tissues | This paper reviews the various histopathological staining techniques that may be used to assess fish health and accurately detect disease. This paper does not go into detail about the use of proteomics in aquaculture, but the authors say that it can complement other methods. | Eissa, E. S. H., Gaafar, A. Y., Mathew, R. T., Al-Shahari, E. A., Okon, E. M., Eissa, M. E., & Abd El-Aziz, Y. M. (2025). The role of histological stains in aquaculture and fisheries development technology. Aquaculture International, 33(4), 283. | 16-Apr-25 | http://dx.doi.org/10.1007/s10499-025-01932-x | DIGITAL PATHOLOGY; FISH; STANDARDIZATION; DYES; HISTOPATHOLOGY; DIAGNOSIS; LESIONS; GILLS; TRACT; Fisheries | Opinion / Review | Applied | FW/SW | Global | |||
| Proteomics | MALDI-TOF MS; Bacterial fish pathogens | Recognizing that bacterial pathogens pose great threats to aquaculture and food production, this paper reviews the findings of over 300 studies that used a technique called Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) to identify fifty different bacterial pathogens associated with fish diseases. The author argues that if sample preparation processes become streamlined, then the integration of MALDI-TOF MS for disease detection will be user-friendly for aquaculture practitioners. | Çağatay, İ. T. (2024). Use of proteomic-based MALDI-TOF mass spectra for identification of bacterial pathogens in aquaculture: a review. Aquaculture International, 32(6), 7835-7871. | 14-May-24 | http://dx.doi.org/10.1007/s10499-024-01544-x | LASER-DESORPTION IONIZATION; TROUT ONCORHYNCHUS-MYKISS; MULTIPLEX PCR ASSAY; POLYMERASE-CHAIN-REACTION; RAINBOW-TROUT; LACTOCOCCUS-GARVIEAE; RAPID IDENTIFICATION; PISCIRICKETTSIA-SALMONIS; STREPTOCOCCUS-INIAE; CAUSATIVE AGENT; Fisheries | Opinion / Review | Theoretical | FW/SW | Global | |||
| Proteomics | endocrinology; histology; puberty; salmon | This is a data-based paper that collected coho salmon ovarian follicles at four different developmental stages to characterize the ovarian proteome. The authors discuss the advantages of using proteomics instead of transcriptomics, highlighting the clear role proteins play in physiological and molecular processes, which aligned with their goal to unravel the numerous pathways involved in oogenesis. Although the paper does not directly discuss the use of their methods/findings in aquaculture, the authors suggest that future work should build on these findings to improve hatchery reproductive success. | Timmins‐Schiffman, E., Telish, J., Field, C., Monson, C., Guzmán, J. M., Nunn, B. L., ... & Forsgren, K. (2025). An In‐Depth Coho Salmon (Oncorhynchus kisutch) Ovarian Follicle Proteome Reveals Coordinated Changes Across Diverse Cellular Processes during the Transition From Primary to Secondary Growth. Proteomics, 25(5-6), e202400311. | 8-Dec-24 | http://dx.doi.org/10.1002/pmic.202400311 | RAINBOW-TROUT; CARBOHYDRATE-METABOLISM; LIPOPROTEIN RECEPTORS; EXPRESSION; MATURATION; EGGS; VITELLOGENIN; INVESTMENT; OOCYTES; MYKISS; Biochemistry & Molecular Biology | Technical / Data | Applied | FW | North America | |||
| Proteomics | Shotgun proteomic; Ecotoxicology; Sparus aurata; Fish health; Lagoon; Cocktail effect | This data-based paper performed high throughput shotgun proteomics on juvenile gilthead seabreams to assess the physiological impacts of inorganic pollutant mixtures, and to identify biomarkers that can serve as long-term monitoring tools. Specifically, the authors charactrized the proteomes of two metabolically active organs, the liver and red muscle, in response to varying levels of inorganic contaminants (such as heavy metal pollutants). | Beauvieux, A., Fromentin, J. M., Romero, D., Couffin, N., Brown, A., Metral, L., ... & Schull, Q. (2024). Molecular fingerprint of gilthead seabream physiology in response to pollutant mixtures in the wild. Environmental Pollution, 340, 122789. | 1-Jan-24 | http://dx.doi.org/10.1016/j.envpol.2023.122789 | OXIDATIVE STRESS; SPARUS-AURATA; HEAVY-METALS; SEA BREAM; ALUMINUM TOXICITY; MARINE FISH; EXPOSURE; CONTAMINATION; INDICATORS; EVOLUTION; Environmental Sciences & Ecology | Technical / Data | Applied | SW | Europe | |||
| Metabolomics | salinity adaptation; teleost fish; osmoregulation; gut microbiota; metabolomics | This paper reviews the use of transcriptomics, gut microbiotia, and metabolomics to gain insight into the molecular and physiological processes that underlie adaptation to salinity changes. The authors argue that taking an integrated approach to understanding these mechanisms can serve to help assess fish health in aquaculture. | Mkulo, E. M., Iddrisu, L., Yohana, M. A., Zheng, A., Zhong, J., Jin, M., ... & Wang, Z. (2025). Exploring salinity adaptation in teleost fish, focusing on omics perspectives on osmoregulation and gut microbiota. Frontiers in Marine Science, 12, 1559871. | 19-May-25 | https://doi.org/10.3389/fmars.2025.1559871 | KILLIFISH FUNDULUS-HETEROCLITUS; FRESH-WATER; METABOLIC-RESPONSES; OXYGEN-CONSUMPTION; EURYHALINE TELEOST; HORMONAL-CONTROL; ATLANTIC SALMON; GENE-EXPRESSION; RECENT PROGRESS; TIGHT JUNCTION; Environmental Sciences & Ecology; Marine & Freshwater Biology | Opinion / Review | Applied | FW/SW | Global | |||
| Metabolomics | alkalinity stress; sturgeon; fishery breeding; ferroptosis; amino acid metabolism | Recognizing that alkaline water use in aquaculture can pose threats to fish health (immune function and antioxidant enzyme activity), this data-based paper examined the effects of alkalinity stress on liver function in hybrid sturgeon. Here, the researchers exposed hybrid sturgeon to different alkaline concentrations using sodium bicarbonate, and measured liver alterations through histopathology, apoptosis detection, antioxidant enzyme activity, stress- and immune-related gene transcription, and amino acid metabolism profiling. | Zhai, C., Liu, X., Li, Y., Wang, R., Lv, W., Ma, B., ... & Zhang, Y. (2024). Effects of alkalinity stress on amino acid metabolism profiles and oxidative-stress-mediated apoptosis/ferroptosis in hybrid sturgeon (Huso dauricus♀× Acipenser schrenckii♂) livers. International Journal of Molecular Sciences, 25(19), 10456. | 17-Sep-24 | http://dx.doi.org/10.3390/ijms251910456 | APOPTOSIS; GENES; Biochemistry & Molecular Biology; Chemistry | Technical / Data | Applied | FW | Asia | |||
| Metabolomics | NMR; Metabolomics; Chemometrics; Machine learning (ML); Fish origin; Fisheries survey | This is a data-based paper that assessed techniques to distinguish the origin of fish from closely related water bodies by combining NMR spectroscopy with statistical and machine learning methodologies. The authors demonstrated that one application of metabolomic profiling is to discriminate fish based on their environmental origin. The methods used in this paper can therefore be useful for traceability, ecological monitoring, and food authenticity accessment. | Kuhn, S., Reitel, K., Homapour, E., Kork, K., Vaino, V., Arula, T., ... & Reile, I. (2024). Discriminating the origin of fish from closely related water bodies by combining NMR spectroscopy with statistical analysis and machine learning. Ecological Informatics, 83, 102753. | 24-Nov | http://dx.doi.org/10.1016/j.ecoinf.2024.102753 | BREAM SPARUS-AURATA; GEOGRAPHICAL ORIGIN; PATTERN-RECOGNITION; OLIVE OILS; CLASSIFICATION; DIFFERENTIATION; SALMON; WILD; L.; Environmental Sciences & Ecology | Technical / Data | Applied | FW | Europe | |||
| Metabolomics | Temperature; Rainbow trout; Metabolomics; Amino acid metabolism; Lipid metabolism | This is a data-based paper that demonstrated the effect of different temperature treatments on the growth and performance of juvenile rainbow trout by using non-targeted metabolomics. The authors identified a temperature-dependent relationship in amino acid and lipid metabolism, providing insight into how thermal variations can shape physiological processes and better inform rearing practices. | Tian, Y., Wang, W., Jiang, W., Zhang, G., He, J., Dong, S., ... & Gao, Q. (2024). Non-targeted metabolomics provides insights into the distinct amino acid and lipid metabolism in liver tissues of rainbow trout (Oncorhynchus mykiss) cultured in seawater at different temperatures. Aquaculture, 579, 740188. | 30-Jan-24 | http://dx.doi.org/10.1016/j.aquaculture.2023.740188 | CARP CTENOPHARYNGODON-IDELLA; ATLANTIC SALMON; GROWTH-PERFORMANCE; FEED CONVERSION; PLASMA-MEMBRANE; FISH SIZE; SUPPLEMENTATION; SPHINGOLIPIDS; EXPRESSION; RESPONSES; Fisheries; Marine & Freshwater Biology | Technical / Data | Applied | FW | Asia |