| 1. |
- Andersson, Leif, et al.
(författare)
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How Fish Population Genomics Can Promote Sustainable Fisheries : A Road Map
- 2024
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Ingår i: Annual Review of Animal Biosciences. - : ANNUAL REVIEWS. - 2165-8102 .- 2165-8110. ; 12, s. 1-20
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Forskningsöversikt (refereegranskat)abstract
- Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.
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| 2. |
- Bekkevold, Dorte, et al.
(författare)
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Genetic monitoring uncovers long-distance marine feeding coupled with strong spatial segregation in sea trout (Salmo trutta L.) consistent at annual and decadal time scales
- 2024
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Ingår i: ICES JOURNAL OF MARINE SCIENCE. - 1054-3139 .- 1095-9289.
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Tidskriftsartikel (refereegranskat)abstract
- Genetic data have greatly increased means to understand fish marine migration behaviours at large spatial scale within a quantitative framework. The anadromous sea trout is a prized target of recreational fishery and an important ecosystem component in freshwater and marine coastal habitats in large parts of temperate northern Europe. Nonetheless, little is known about population distributions while feeding at sea. To reconcile notions about feeding migrations being predominantly locally restricted or not, we used SNP data for 3465 trout representing >100 rivers to identify population origins of 903 coastally feeding fish captured throughout the North Sea-Baltic Sea transition area. Across areas, coastal collections generally showed marked stock-mixing and overall 70:30% native:non-native fish with seasonal variation corresponding with spawning run timing. Data revealed strong spatial feeding segregation between trout from the Scandinavian Peninsula and the European continent. This is surprising given the short distances between areas, but is in alignment with strong genetic differentiation between populations in these areas. Estimation of stock complexity of coastal feeding aggregations showed no spatial trend through the North Sea-Baltic Sea transition area otherwise characterized by strong environmental clines. Analyses of scale samples collected in the 1950s indicate that stock-mixing was consistent over almost 70 years.
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| 3. |
- Bekkevold, Dorte, et al.
(författare)
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Mixed-stock analysis of Atlantic herring (Clupea harengus) : a tool for identifying management units and complex migration dynamics
- 2023
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Ingår i: ICES Journal of Marine Science. - : Oxford University Press. - 1054-3139 .- 1095-9289. ; 80:1, s. 173-184
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Tidskriftsartikel (refereegranskat)abstract
- We developed and validated a mixed-stock analysis (MSA) method with 59 single-nucleotide polymorphisms selected from genome-wide data to assign individuals to populations in mixed-stock samples of Atlantic herring from the North and Baltic seas. We analysed 3734 herring from spawning locations and scientific catches of mixed feeding stocks to demonstrate a "one-fits-all" tool with unprecedented accuracy for monitoring spatio-temporal dynamics throughout a large geographical range with complex stock mixing. We re-analysed time-series data (2002-2021) and compared inferences about stock composition with estimates from morphological data. We show that contributions from the western Baltic spring-spawning stock complex, which is under management concern, have likely been overestimated. We also show that a genetically distinctive population of western Baltic autumn spawners, ascribed low fisheries importance, contributes non-negligible and potentially temporally increasing proportions to mixed-stock aggregations, calling for a re-evaluation of stock definitions. MSA data can be implemented in stock assessment and in a variety of applications, including marine ecosystem description, impact assessment of specific fleets, and stock-rebuilding plans.
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| 4. |
- Farrell, Edward D. D., et al.
(författare)
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A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c
- 2022
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Ingår i: Royal Society Open Science. - : The Royal Society. - 2054-5703. ; 9:9
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Tidskriftsartikel (refereegranskat)abstract
- Atlantic herring in International Council for Exploration of the Sea (ICES) Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographical delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 single-nucleotide polymorphisms, derived from whole-genome sequencing, were used to genotype 3480 baseline spawning samples (2014-2021). A temporally stable baseline comprising 2316 herring from populations known to inhabit Division 6.a was used to develop a genetic assignment method, with a self-assignment accuracy greater than 90%. The long-term temporal stability of the assignment model was validated by assigning archive (2003-2004) baseline samples (270 individuals) with a high level of accuracy. Assignment of non-baseline samples (1514 individuals) from Divisions 6.a, 7.b-c indicated previously unrecognized levels of mixing of populations outside of the spawning season. The genetic markers and assignment models presented constitute a 'toolbox' that can be used for the assignment of herring caught in mixed survey and commercial catches in Division 6.a into their population of origin with a high level of accuracy.
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| 5. |
- Han, Fan, et al.
(författare)
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Ecological adaptation in Atlantic herring is associated with large shifts in allele frequencies at hundreds of loci
- 2020
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Ingår i: eLIFE. - : ELIFE SCIENCES PUBLICATIONS LTD. - 2050-084X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Atlantic herring is widespread in North Atlantic and adjacent waters and is one of the most abundant vertebrates on earth. This species is well suited to explore genetic adaptation due to minute genetic differentiation at selectively neutral loci. Here, we report hundreds of loci underlying ecological adaptation to different geographic areas and spawning conditions. Four of these represent megabase inversions confirmed by long read sequencing. The genetic architecture underlying ecological adaptation in herring deviates from expectation under a classical infinitesimal model for complex traits because of large shifts in allele frequencies at hundreds of loci under selection.
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| 6. |
- Hill, Jason, et al.
(författare)
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Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin
- 2019
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 116:37, s. 18473-18478
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Tidskriftsartikel (refereegranskat)abstract
- The evolutionary process that occurs when a species colonizes a new environment provides an opportunity to explore the mechanisms underlying genetic adaptation, which is essential knowledge for understanding evolution and the maintenance of biodiversity. Atlantic herring has an estimated total breeding stock of about 1 trillion (10(12)) and has colonized the brackish Baltic Sea within the last 10,000 y. Minute genetic differentiation between Atlantic and Baltic herring populations at selectively neutral loci combined with this rapid adaptation to a new environment facilitated the identification of hundreds of loci underlying ecological adaptation. A major question in the field of evolutionary biology is to what extent such an adaptive process involves selection of novel mutations with large effects or genetic changes at many loci, each with a small effect on phenotype (i.e., selection on standing genetic variation). Here we show that a missense mutation in rhodopsin (Phe261Tyr) is an adaptation to the red-shifted Baltic Sea light environment. The transition from phenylalanine to tyrosine differs only by the presence of a hydroxyl moiety in the latter, but this results in an up to 10-nm red-shifted light absorbance of the receptor. Remarkably, an examination of the rhodopsin sequences from 2,056 species of fish revealed that the same missense mutation has occurred independently and been selected for during at least 20 transitions between light environments across all fish. Our results provide a spectacular example of convergent evolution and how a single amino acid change can have a major effect on ecological adaptation.
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| 7. |
- Pettersson, Mats, et al.
(författare)
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Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring
- 2024
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Ingår i: Genome Biology and Evolution. - : Oxford University Press. - 1759-6653. ; 16:7
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Tidskriftsartikel (refereegranskat)abstract
- The European sprat is a small plankton-feeding clupeid present in the northeastern Atlantic Ocean, in the Mediterranean Sea, and in the brackish Baltic Sea and Black Sea. This species is the target of a major fishery and, therefore, an accurate characterization of its genetic population structure is crucial to delineate proper stock assessments that aid ensuring the fishery's sustainability. Here, we present (i) a draft genome assembly, (ii) pooled whole genome sequencing of 19 population samples covering most of the species' distribution range, and (iii) the design and test of a single nucleotide polymorphism (SNP)-chip resource and use this to validate the population structure inferred from pooled sequencing. These approaches revealed, using the populations sampled here, three major groups of European sprat: Oceanic, Coastal, and Brackish with limited differentiation within groups even over wide geographical stretches. Genetic structure is largely driven by six large putative inversions that differentiate Oceanic and Brackish sprats, while Coastal populations display intermediate frequencies of haplotypes at each locus. Interestingly, populations from the Baltic and the Black Seas share similar frequencies of haplotypes at these putative inversions despite their distant geographic location. The closely related clupeids European sprat and Atlantic herring both show genetic adaptation to the brackish Baltic Sea, providing an opportunity to explore the extent of genetic parallelism. This analysis revealed limited parallelism because out of 125 independent loci detected in the Atlantic herring, three showed sharp signals of selection that overlapped between the two species and contained single genes such as PRLRA, which encodes the receptor for prolactin, a freshwater-adapting hormone in euryhaline species, and THRB, a receptor for thyroid hormones, important both for metabolic regulation and the development of red cone photoreceptors.
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| 8. |
- Sunde, Johanna, et al.
(författare)
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Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments
- 2022
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Ingår i: Molecular Ecology. - : John Wiley & Sons. - 0962-1083 .- 1365-294X. ; 31:4, s. 1093-1110
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6 degrees N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.
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