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Thambithurai D, Kuparinen A. Environmental forcing alters fisheries selection. Trends Ecol Evol 2024; 39:131-140. [PMID: 37743188 PMCID: PMC10850982 DOI: 10.1016/j.tree.2023.08.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023]
Abstract
Fishing-induced evolution (FIE) threatens the ecology, resilience, and economic value of fish populations. Traits under selection, and mechanisms of selection, can be influenced by abiotic and biotic perturbations, yet this has been overlooked. Here, we present the fishery selection continuum, where selection ranges from rigid fisheries selection to flexible fisheries selection. We provide examples on how FIE may function along this continuum, and identify selective processes that should be considered less or more flexible. We also introduce fishery reaction norms, which serve to conceptualise how selection from fishing may function in a dynamic context. Ultimately, we suggest an integrative approach to studying FIE that considers the environmental conditions in which it functions.
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Affiliation(s)
- Davide Thambithurai
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, Sète, France; School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | - Anna Kuparinen
- Department of Biological and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland.
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2
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Beukeboom R, Phillips JS, Ólafsdóttir GÁ, Benhaïm D. Personality in juvenile Atlantic cod ecotypes and implications for fisheries management. Ecol Evol 2023; 13:e9952. [PMID: 37091554 PMCID: PMC10116030 DOI: 10.1002/ece3.9952] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/10/2023] [Accepted: 03/14/2023] [Indexed: 04/25/2023] Open
Abstract
Animals show among-individual variation in behaviors, including migration behaviors, which are often repeatable across time periods and contexts, commonly termed "personality." These behaviors can be correlated, forming a behavioral syndrome. In this study, we assessed the repeatability and correlation of different behavioral traits, i.e., boldness, exploration, and sociality, and the link to feeding migration patterns in Atlantic cod juveniles. To do so, we collected repeated measurements within two short-term (3 days) and two long-term (2 months) intervals of these personality traits and genotypes of the Pan I locus, which is correlated with feeding migration patterns in this species. We found high repeatabilities for exploration behavior in the short- and long-term intervals, and a trend for the relationship between exploration and the Pan I locus. Boldness and sociality were only repeatable in the second short-term interval indicating a possible development of stability over time and did not show a relation with the Pan I locus. We found no indication of behavioral syndromes among the studied traits. We were unable to identify the existence of a migration syndrome for the frontal genotype, which is the reason that the link between personality and migration remains inconclusive, but we demonstrated a possible link between exploration and the Pan I genotype. This supports the need for further research that should focus on the effect of exploration tendency and other personality traits on cod movement, including the migratory (frontal) ecotype to develop management strategies based on behavioral units, rather than treating the population as a single homogeneous stock.
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Affiliation(s)
- Rosanne Beukeboom
- Research Centre of the WestfjordsUniversity of IcelandBolungarvikIceland
- Department of Aquaculture and Fish BiologyHólar UniversitySaudárkrókurIceland
| | - Joseph S. Phillips
- Department of Aquaculture and Fish BiologyHólar UniversitySaudárkrókurIceland
- Department of BiologyCreighton UniversityOmahaNebraskaUSA
| | | | - David Benhaïm
- Department of Aquaculture and Fish BiologyHólar UniversitySaudárkrókurIceland
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3
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Thambithurai D, Lanthier I, Contant E, Killen SS, Binning SA. Fish vulnerability to capture by trapping is modulated by individual parasite density. Proc Biol Sci 2022; 289:20221956. [PMID: 36515121 PMCID: PMC9748777 DOI: 10.1098/rspb.2022.1956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/17/2022] [Indexed: 12/15/2022] Open
Abstract
Commercial fishery harvest is a powerful evolutionary agent, but we know little about whether environmental stressors affect harvest-associated selection. We test how parasite infection relates to trapping vulnerability through selective processes underlying capture. We used fish naturally infected with parasites, including trematodes causing black spots under fish skin. We first assessed how individual parasite density related to standard metabolic rate (SMR), maximum metabolic rate (MMR) and absolute aerobic scope (AAS)-then used laboratory fishing simulations to test how capture vulnerability was related to parasite density. We further explored group-trapping dynamics using experimental shoals containing varying proportions of infected fish (groups of six with either 0, 2, 4 or 6 infected individuals). At the individual level, we found a positive relationship between parasite presence and SMR, but not MMR or AAS. While we saw no relationship between individual metabolic capacity and vulnerability to trapping, we found the length of time fish spent in traps increased with increasing parasite density, a predictor of trapping-related capture probability. At the group level, the number of infected individuals in a shoal did not affect overall group trapping vulnerability. Our results suggest that parasite infection has some capacity to shift individual vulnerability patterns in fisheries, and potentially influence the evolutionary outcomes of fisheries-induced evolution.
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Affiliation(s)
- Davide Thambithurai
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- MARBEC, University of Montpellier, Ifremer, Sète 32400, France
| | - Isabel Lanthier
- Département de sciences biologiques, l'Université de Montréal, Montréal, Québec, Canada
| | - Eloi Contant
- École Pratique des Hautes Études, Université Paris Sciences et Lettres, 4-14 rue Ferrus, Paris 75014, France
| | - Shaun S. Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Sandra A. Binning
- Département de sciences biologiques, l'Université de Montréal, Montréal, Québec, Canada
- Ressources Aquatiques Québec (RAQ), Institut des sciences de la mer (ISMER), Université de Québec à Rimouski, 310 avenue des Ursulines, Rimouski, Québec, Canada G5L 2Z9
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4
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Beukeboom R, Morel A, Phillips JS, Ólafsdóttir GÁ, Benhaïm D. Activity vs exploration: Locomotion in a known and unknown environment differs in Atlantic cod juveniles (Gadus morhua). Behav Processes 2022; 202:104736. [PMID: 36028060 DOI: 10.1016/j.beproc.2022.104736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 11/02/2022]
Abstract
Individuals within a population often behave differently and these differences can be consistent over time and/or context, also termed "animal personality". Animal personality has been commonly classified into five axes with studies aiming to validate these axes. One subject that has surprisingly not received full attention yet is the difference between the two personality axes "activity" and "exploration-avoidance", i.e. behaviour in a known vs an unknown environment. Despite this clear difference in definition, many studies measure activity in an unknown environment and term it activity, while underlying motivations between the two environments are different. This study aimed to detect the two personality traits "activity" and "exploration" in Atlantic cod juveniles, and to investigate whether they support the distinctive definitions proposed by previous authors. This study showed significant consistency in locomotion variation in both environments, i.e. personality. In addition, the two environments clearly elicited different behaviours; Atlantic cod juvenile behaviour was more repeatable and they moved more in the known vs the unknown environment, and no correlation of the proportional locomotion between the two was found. This demonstrates that locomotion in both environments, i.e. the personality axes "activity" and "exploration", should not be confused nor treated as if they reflect the same personality trait.
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Affiliation(s)
- Rosanne Beukeboom
- University of Iceland, Research Centre of the Westfjords, Bolungarvik, Iceland; Department of Aquaculture and Fish Biology, Hólar University, Saudárkrókur, Iceland.
| | - Antoine Morel
- University of Iceland, Research Centre of the Westfjords, Bolungarvik, Iceland
| | - Joseph S Phillips
- Department of Aquaculture and Fish Biology, Hólar University, Saudárkrókur, Iceland
| | | | - David Benhaïm
- Department of Aquaculture and Fish Biology, Hólar University, Saudárkrókur, Iceland
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5
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Thambithurai D, Rácz A, Lindström J, Parsons KJ, Killen SS. Simulated trapping and trawling exert similar selection on fish morphology. Ecol Evol 2022; 12:e8596. [PMID: 35169454 PMCID: PMC8840878 DOI: 10.1002/ece3.8596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
Commercial fishery harvest can influence the evolution of wild fish populations. Our knowledge of selection on morphology is however limited, with most previous studies focusing on body size, age, and maturation. Within species, variation in morphology can influence locomotor ability, possibly making some individuals more vulnerable to capture by fishing gears. Additionally, selection on morphology has the potential to influence other foraging, behavioral, and life‐history related traits. Here we carried out simulated fishing using two types of gears: a trawl (an active gear) and a trap (a passive gear), to assess morphological trait‐based selection in relation to capture vulnerability. Using geometric morphometrics, we assessed differences in shape between high and low vulnerability fish, showing that high vulnerability individuals display shallower body shapes regardless of gear type. For trawling, low vulnerability fish displayed morphological characteristics that may be associated with higher burst‐swimming, including a larger caudal region and narrower head, similar to evolutionary responses seen in fish populations responding to natural predation. Taken together, these results suggest that divergent selection can lead to phenotypic differences in harvested fish populations.
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Affiliation(s)
- Davide Thambithurai
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Anita Rácz
- Department of Genetics ELTE Eötvös Loránd University Budapest Hungary
| | - Jan Lindström
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Kevin J. Parsons
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Shaun S. Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
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6
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Jónsson EP, Campana SE, Sólmundsson J, Jakobsdóttir KB, Bárðarson H. The effect of growth rate on otolith-based discrimination of cod (Gadus morhua) ecotypes. PLoS One 2021; 16:e0247630. [PMID: 34587180 PMCID: PMC8480848 DOI: 10.1371/journal.pone.0247630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/09/2021] [Indexed: 01/10/2023] Open
Abstract
Otolith shape has previously been used to identify ecotypes within the Icelandic cod (Gadus morhua) stock, using DST profiles to validate the results. Fish otolith shape variation has repeatedly been found to be largely determined by growth rate. To examine the effect of growth rate on the relationship between otolith shape and cod ecotypes (using the Pan I genotype as a proxy for ecotype), 826 archived sagittal otoliths collected over a 58 year sampling period were retrieved, the individual growth rate calculated, and otolith shape described using both Normalized Elliptic Fourier transform and Discrete Wavelet transform. Discriminant functions of otolith shape successfully classified ecotype, whether using Fourier or Wavelet descriptors, but only when excluding a heterozygous genotype from the analysis. The otolith shape variability of this genotype lowered the classification success, while otolith shape, in turn, was significantly affected by growth rate and cohort. Growth rate differences previously reported for the ecotypes were present, but were less marked than expected and indeed, growth rate variance attributable to ecotype identity was dwarfed by cohort- and location-related variance in growth. Such a strong effect of growth rate suggests that cod ecotype discrimination based on otolith shape is sensitive to both temporal and spatial variations in growth, which can mask the effect of ecotype-related growth rate differences on otolith shape.
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Affiliation(s)
- Einar Pétur Jónsson
- School of Engineering and Natural Sciences, University of Iceland, Askja, Reykjavík, Iceland
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
- * E-mail:
| | - Steven E. Campana
- School of Engineering and Natural Sciences, University of Iceland, Askja, Reykjavík, Iceland
| | - Jón Sólmundsson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
| | | | - Hlynur Bárðarson
- Marine and Freshwater Research Institute, Hafnarfjörður, Iceland
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Maes SM, Christiansen H, Mark FC, Lucassen M, Van de Putte A, Volckaert FAM, Flores H. High gene flow in polar cod (Boreogadus saida) from West-Svalbard and the Eurasian Basin. JOURNAL OF FISH BIOLOGY 2021; 99:49-60. [PMID: 33559136 DOI: 10.1111/jfb.14697] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/24/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
The current and projected environmental change of the Arctic Ocean contrasts sharply with the limited knowledge of its genetic biodiversity. Polar cod Boreogadus saida (Lepechin, 1774) is an abundant circumpolar marine fish and ecological key species. The central role of polar cod in the Arctic marine food web warrants a better understanding of its population structure and connectivity. In this study, the genetic population structure of 171 juveniles, collected from several fjords off West-Svalbard (Billefjorden, Hornsund and Kongsfjorden), the northern Sophia Basin and the Eurasian Basin of the Arctic Ocean, was analysed using nine DNA microsatellite loci. Genetic analyses indicated moderate to high genetic diversity, but absence of spatial population structure and isolation-by-distance, suggesting ongoing gene flow between the studied sampling regions. High levels of connectivity may be key for polar cod to maintain populations across wide spatial scales. The adaptive capacity of the species will be increasingly important to face challenges such as habitat fragmentation, ocean warming and changes in prey composition. In view of a limited understanding of the population dynamics and evolution of polar cod, a valuable next step to predict future developments should be an integrated biological evaluation, including population genomics, a life-history approach, and habitat and biophysical dispersal modelling.
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Affiliation(s)
- Sarah M Maes
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Henrik Christiansen
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Felix C Mark
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Magnus Lucassen
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Anton Van de Putte
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Filip A M Volckaert
- Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Hauke Flores
- Alfred-Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
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8
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Puncher GN, Rowe S, Rose GA, Parent GJ, Wang Y, Pavey SA. Life-stage-dependent supergene haplotype frequencies and metapopulation neutral genetic patterns of Atlantic cod, Gadus morhua, from Canada's Northern cod stock region and adjacent areas. JOURNAL OF FISH BIOLOGY 2021; 98:817-828. [PMID: 33244791 DOI: 10.1111/jfb.14632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 06/11/2023]
Abstract
Among highly migratory fish species, nursery areas occupied by juveniles often differ from adult habitats. To better understand the spatial dynamics of Canada's Northern cod stock, juveniles caught off the east coast of Newfoundland and Labrador were compared to adults from the same region as well as individuals from other areas in Atlantic Canada using double-digest restriction site-associated DNA sequencing-derived single nucleotide polymorphisms. A reduced proportion of homozygotes with a chromosomal inversion located in linkage group 1 (LG1) was detected between juvenile and adult samples in the Northern cod stock region, potentially indicating age-dependent habitat use or ontogenetic selection for attributes associated with the many genes located in LG1. No selectively neutral genetic differences were found between samples from the Northern cod stock; nevertheless, significant differences were found between some of these samples and cod collected from St. Pierre Bank, Bay of Fundy, Browns Bank and the southern Scotian Shelf. Clustering analysis of variants at neutral loci provided evidence for three major genetic units: (a) the Newfoundland Atlantic Coast, (b) eastern and southern Gulf of St. Lawrence and Burgeo Bank and (c) the Bay of Fundy, Browns Bank and southern Scotian Shelf. Both adaptive and neutral population structure within the Northern cod stock should be considered by managers to promote demographic rebuilding of the stock.
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Affiliation(s)
- Gregory Neils Puncher
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, Canada
- Genomics Laboratory, Maurice-Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Canada
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, Canada
| | - Sherrylynn Rowe
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute, Memorial University of Newfoundland, St. John's, Canada
| | - George A Rose
- Institute for the Oceans and Fisheries, University of British Columbia, Vancouver, Canada
| | - Geneviève J Parent
- Genomics Laboratory, Maurice-Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Canada
| | - Yanjun Wang
- Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, Canada
| | - Scott A Pavey
- Department of Biological Sciences, Canadian Rivers Institute, University of New Brunswick, Saint John, Canada
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9
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Otterå H, Johansen T, Folkvord A, Dahle G, Solvang Bingh MK, Westgaard JI, Glover KA. The pantophysin gene and its relationship with survival in early life stages of Atlantic cod. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191983. [PMID: 33204437 PMCID: PMC7657904 DOI: 10.1098/rsos.191983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 09/21/2020] [Indexed: 06/11/2023]
Abstract
Genetic markers are widely used in fisheries management around the world. While the genetic structure and markers selected are usually based on samples from the wild, very few controlled experiments have been carried out to investigate possible differences in influence on traits between markers. Here we examine the bi-allelic gene pantophysin (Pan I), widely used in the management of Atlantic cod, in a series of in vitro crosses under a range of temperatures. It has been proposed that this gene, or another tightly linked gene, may be under strong divergent selection. Resolving this issue is essential in order to interpret results when using this gene marker for stock management. We found no evidence of departure from the expected 1 : 2 : 1 Mendelian ratio for any of the three genotypes during the egg stage, while both the 6 and 12°C temperature regimes in tank experiments favoured the survival of the Pan IAA genotype. No difference in genotype survival was, however, found in a more natural mesocosm environment. Collectively, these results suggest that for the early life stages of Atlantic cod, and under the current experimental conditions, there is no strong consistent influence of Pan I genotype on survival. The results also emphasize the importance of varied experimental studies to verify the importance of environmental factors influencing genotype selection.
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Affiliation(s)
- Håkon Otterå
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | - Torild Johansen
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Arild Folkvord
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
| | - Geir Dahle
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
| | | | - Jon-Ivar Westgaard
- Institute of Marine Research, Tromsø Division, Framsenteret 9296 Tromsø, Norway
| | - Kevin A. Glover
- Institute of Marine Research, POB 1870, 5817 Bergen, Norway
- Department of Biological Sciences, University of Bergen, Thormøhlensgt. 53, 5020Bergen
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10
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Abstract
We performed over 19,000 lure-assisted, underwater visual fish census transects at over 140 shallow coastal sampling locations in the mid- eastern Adriatic sea of the Croatian mainland and islands, recording all fish taxa observed, their predatory behavior in response to the lure, and the cover of benthic habitats with which they were associated. We hypothesized that prey habitat preference was a learned or selected response to aggressive behavior by piscivorous mesopredators, and predicted that mobile prey would be spatially segregated from aggressive predators into different benthic habitats within local sampling sites. We found that aggressive piscivores were primarily wait-chase or cruise-chase mesopredators that preferentially foraged along heterogeneous habitat edges within juxtapositions of rock, unconsolidated sediment, macroalgae (Cystoseira spp.) and seagrass (usually Posidonia oceanica). Prey species and less aggressive piscivores avoided these heterogeneous habitats and preferred more homogeneous habitats that the aggressive predators in turn avoided. We found strong and consistent spatial segregation between aggressive predators on the one hand, and less aggressive predators and prey on the other hand. These results are consistent with the hypothesis that aggressive behavior by piscivorous species is the primary organizing force shaping assembly of fish communities at our study sites, driving preference and occupancy of heterogeneous and homogeneous benthic habitats. Management of shallow benthic resources should recognize the value of complementarity in habitats allowing coexistence of predators and prey through contrasting habitat preferences.
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Thambithurai D, Crespel A, Norin T, Rácz A, Lindström J, Parsons KJ, Killen SS. Hypoxia alters vulnerability to capture and the potential for trait-based selection in a scaled-down trawl fishery. CONSERVATION PHYSIOLOGY 2019; 7:coz082. [PMID: 31803472 PMCID: PMC6880855 DOI: 10.1093/conphys/coz082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 08/29/2019] [Accepted: 09/18/2019] [Indexed: 06/10/2023]
Abstract
Lay summary Selective harvest of wild organisms by humans can influence the evolution of plants and animals, and fishing is recognized as a particularly strong driver of this process. Importantly, these effects occur alongside environmental change. Here we show that aquatic hypoxia can alter which individuals within a fish population are vulnerable to capture by trawling, potentially altering the selection and evolutionary effects stemming from commercial fisheries.
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Affiliation(s)
- Davide Thambithurai
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Amelie Crespel
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Tommy Norin
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
- DTU Aqua: National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet, Building 202, 2800 Kgs. Lyngby, Denmark
| | - Anita Rácz
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
- Department of Genetics, Eötvös Loránd University, Pázmány P.s. 1C, H-1117 Budapest, Hungary
| | - Jan Lindström
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Kevin J Parsons
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
| | - Shaun S Killen
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Graham Kerr Building, Glasgow G12 8QQ, UK
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12
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Árnason E, Halldórsdóttir K. Codweb: Whole-genome sequencing uncovers extensive reticulations fueling adaptation among Atlantic, Arctic, and Pacific gadids. SCIENCE ADVANCES 2019; 5:eaat8788. [PMID: 30906856 PMCID: PMC6426462 DOI: 10.1126/sciadv.aat8788] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 02/04/2019] [Indexed: 05/11/2023]
Abstract
Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.
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Affiliation(s)
- Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
- Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland, Sturlugata 7, 101 Reykjavík, Iceland
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13
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Bernatchez L, Wellenreuther M, Araneda C, Ashton DT, Barth JMI, Beacham TD, Maes GE, Martinsohn JT, Miller KM, Naish KA, Ovenden JR, Primmer CR, Young Suk H, Therkildsen NO, Withler RE. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends Ecol Evol 2017; 32:665-680. [PMID: 28818341 DOI: 10.1016/j.tree.2017.06.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 11/15/2022]
Abstract
Best use of scientific knowledge is required to maintain the fundamental role of seafood in human nutrition. While it is acknowledged that genomic-based methods allow the collection of powerful data, their value to inform fisheries management, aquaculture, and biosecurity applications remains underestimated. We review genomic applications of relevance to the sustainable management of seafood resources, illustrate the benefits of, and identify barriers to their integration. We conclude that the value of genomic information towards securing the future of seafood does not need to be further demonstrated. Instead, we need immediate efforts to remove structural roadblocks and focus on ways that support integration of genomic-informed methods into management and production practices. We propose solutions to pave the way forward.
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Affiliation(s)
- Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada.
| | - Maren Wellenreuther
- The New Zealand Institute for Plant & Food Research Limited, Port Nelson, Nelson 7043, New Zealand; Department of Biology, Lund University, Lund, Sweden
| | - Cristián Araneda
- Universidad de Chile, Facultad de Ciencias Agronómicas Departamento de Producción Animal, Avda. Santa Rosa 11315, La Pintana 8820808, Santiago, Chile
| | - David T Ashton
- The New Zealand Institute for Plant & Food Research Limited, Port Nelson, Nelson 7043, New Zealand
| | - Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Terry D Beacham
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Gregory E Maes
- Centre for Sustainable Tropical Fisheries and Aquaculture, Comparative Genomics Centre, College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia; Laboratory of Biodiversity and Evolutionary Genomics, University of Leuven (KU Leuven), B-3000 Leuven, Belgium; Genomics Core, UZ Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jann T Martinsohn
- European Commission, Joint Research Centre (JRC), Directorate D - Sustainable Resources, Unit D2 - Water and Marine Resources, Via Enrico Fermi 2749, 21027 Ispra, Italy
| | - Kristina M Miller
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
| | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98105, USA
| | - Jennifer R Ovenden
- Molecular Fisheries Laboratory, School of Biomedical Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Craig R Primmer
- Department of Biosciences, Institute of Biotechnology, 00014, University of Helsinki, Finland
| | - Ho Young Suk
- Department of Life Sciences, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongsangbuk-do 38541, South Korea
| | | | - Ruth E Withler
- Fisheries and Oceans Canada, Pacific Biological Station, 3190 Hammond Bay Road, Nanaimo, BC V9T 6N7, Canada
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14
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Teterina AA, Zhivotovsky LA. DNА markers for identification of stationary and migratory ecotypes of Atlantic cod Gadus morhua. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417070122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Leclerc M, Zedrosser A, Pelletier F. Harvesting as a potential selective pressure on behavioural traits. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12893] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Martin Leclerc
- Canada Research Chair in Evolutionary Demography and Conservation & Centre for Northern Studies; Département de biologie; Université de Sherbrooke; Sherbrooke QC J1K2R1 Canada
| | - Andreas Zedrosser
- Faculty of Technology, Natural Sciences and Maritime Sciences; Department of Natural Sciences and Environmental Health; University College of Southeast Norway; N-3800 Bø i Telemark Norway
- Department of Integrative Biology; Institute of Wildlife Biology and Game Management; University of Natural Resources and Applied Life Sciences, Vienna; Gregor Mendel Str. 33 A - 1180 Vienna Austria
| | - Fanie Pelletier
- Canada Research Chair in Evolutionary Demography and Conservation & Centre for Northern Studies; Département de biologie; Université de Sherbrooke; Sherbrooke QC J1K2R1 Canada
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16
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Diaz Pauli B, Sih A. Behavioural responses to human-induced change: Why fishing should not be ignored. Evol Appl 2017; 10:231-240. [PMID: 28250808 PMCID: PMC5322409 DOI: 10.1111/eva.12456] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/29/2016] [Indexed: 01/20/2023] Open
Abstract
Change in behaviour is usually the first response to human‐induced environmental change and key for determining whether a species adapts to environmental change or becomes maladapted. Thus, understanding the behavioural response to human‐induced changes is crucial in the interplay between ecology, evolution, conservation and management. Yet the behavioural response to fishing activities has been largely ignored. We review studies contrasting how fish behaviour affects catch by passive (e.g., long lines, angling) versus active gears (e.g., trawls, seines). We show that fishing not only targets certain behaviours, but it leads to a multitrait response including behavioural, physiological and life‐history traits with population, community and ecosystem consequences. Fisheries‐driven change (plastic or evolutionary) of fish behaviour and its correlated traits could impact fish populations well beyond their survival per se, affecting predation risk, foraging behaviour, dispersal, parental care, etc., and hence numerous ecological issues including population dynamics and trophic cascades. In particular, we discuss implications of behavioural responses to fishing for fisheries management and population resilience. More research on these topics, however, is needed to draw general conclusions, and we suggest fruitful directions for future studies.
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Affiliation(s)
- Beatriz Diaz Pauli
- Department of Biology University of Bergen Bergen Norway; Department of Biosciences Centre for Ecological and Evolutionary Syntheses (CEES) University of Oslo Oslo Norway; Inst. d'Ecologie et des Sciences de l'Environnement - Paris (iEES-Paris) Sorbonne Universités/UPMC Univ Paris 06/CNRS/INRA/IRD/Paris Diderot Univ Paris 07/UPEC/Paris France
| | - Andrew Sih
- Department of Environmental Science and Policy University of California Davis CA USA
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17
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Ross ST. Fish Out of Water: Evolutionary and Ecological Issues in the Conservation of Fishes in Water-Altered Environments: Introduction to the Symposium: Eco-Evolutionary Change and the Conundrum of Darwinian Debt. COPEIA 2015. [DOI: 10.1643/ot-14-189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Árnason E, Halldórsdóttir K. Nucleotide variation and balancing selection at the Ckma gene in Atlantic cod: analysis with multiple merger coalescent models. PeerJ 2015; 3:e786. [PMID: 25755922 PMCID: PMC4349156 DOI: 10.7717/peerj.786] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 01/11/2023] Open
Abstract
High-fecundity organisms, such as Atlantic cod, can withstand substantial natural selection and the entailing genetic load of replacing alleles at a number of loci due to their excess reproductive capacity. High-fecundity organisms may reproduce by sweepstakes leading to highly skewed heavy-tailed offspring distribution. Under such reproduction the Kingman coalescent of binary mergers breaks down and models of multiple merger coalescent are more appropriate. Here we study nucleotide variation at the Ckma (Creatine Kinase Muscle type A) gene in Atlantic cod. The gene shows extreme differentiation between the North (Canada, Greenland, Iceland, Norway, Barents Sea) and the South (Faroe Islands, North-, Baltic-, Celtic-, and Irish Seas) with FST > 0.8 between regions whereas neutral loci show no differentiation. This is evidence of natural selection. The protein sequence is conserved by purifying selection whereas silent and non-coding sites show extreme differentiation. The unfolded site-frequency spectrum has three modes, a mode at singleton sites and two high frequency modes at opposite frequencies representing divergent branches of the gene genealogy that is evidence for balancing selection. Analysis with multiple-merger coalescent models can account for the high frequency of singleton sites and indicate reproductive sweepstakes. Coalescent time scales vary with population size and with the inverse of variance in offspring number. Parameter estimates using multiple-merger coalescent models show that times scales are faster than under the Kingman coalescent.
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Affiliation(s)
- Einar Árnason
- Institute of Life and Environmental Sciences, University of Iceland , Reykjavík , Iceland
| | - Katrín Halldórsdóttir
- Institute of Life and Environmental Sciences, University of Iceland , Reykjavík , Iceland
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19
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Abstract
There is increasing evidence that fishing may cause rapid contemporary evolution in freshwater and marine fish populations. This has led to growing concern about the possible consequences such evolutionary change might have for aquatic ecosystems and the utility of those ecosystems to society. This special issue contains contributions from a symposium on fisheries-induced evolution held at the American Fisheries Society Annual Meeting in August 2008. Contributions include primary studies and reviews of field-based and experimental evidence, and several theoretical modeling studies advancing life-history theory and investigating potential management options. In this introduction we review the state of research in the field, discuss current controversies, and identify contributions made by the papers in this issue to the knowledge of fisheries-induced evolution. We end by suggesting directions for future research.
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Affiliation(s)
- Erin S Dunlop
- Aquatic Research and Development Section, Ontario Ministry of Natural Resources Peterborough, ON, Canada ; Department of Biology, University of Bergen Bergen, Norway ; Institute of Marine Research Nordnes, Bergen, Norway
| | - Katja Enberg
- Department of Biology, University of Bergen Bergen, Norway
| | | | - Mikko Heino
- Department of Biology, University of Bergen Bergen, Norway ; Institute of Marine Research Nordnes, Bergen, Norway ; International Institute for Applied Systems Analysis Laxenburg, Austria
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20
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Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
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21
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Ólafsdóttir GÁ, Westfall KM, Edvardsson R, Pálsson S. Historical DNA reveals the demographic history of Atlantic cod (Gadus morhua) in medieval and early modern Iceland. Proc Biol Sci 2014; 281:20132976. [PMID: 24403343 DOI: 10.1098/rspb.2013.2976] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Atlantic cod (Gadus morhua) vertebrae from archaeological sites were used to study the history of the Icelandic Atlantic cod population in the time period of 1500-1990. Specifically, we used coalescence modelling to estimate population size and fluctuations from the sequence diversity at the cytochrome b (cytb) and Pantophysin I (PanI) loci. The models are consistent with an expanding population during the warm medieval period, large historical effective population size (NE), a marked bottleneck event at 1400-1500 and a decrease in NE in early modern times. The model results are corroborated by the reduction of haplotype and nucleotide variation over time and pairwise population distance as a significant portion of nucleotide variation partitioned across the 1550 time mark. The mean age of the historical fished stock is high in medieval times with a truncation in age in early modern times. The population size crash coincides with a period of known cooling in the North Atlantic, and we conclude that the collapse may be related to climate or climate-induced ecosystem change.
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Affiliation(s)
- Guðbjörg Ásta Ólafsdóttir
- Research Centre of the Westfjords, University of Iceland, , Adalstraeti 21, IS415 Bolungarvik, Iceland, VÖR Marine Research Centre, , Nordurtangi, IS355 Snæfellsbær, Iceland, Department of Environmental and Life Science, University of Iceland, , Sturlugata 7, IS101 Reykjavík, Iceland
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22
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Therkildsen NO, Hemmer-Hansen J, Als TD, Swain DP, Morgan MJ, Trippel EA, Palumbi SR, Meldrup D, Nielsen EE. Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod. Mol Ecol 2013; 22:2424-40. [PMID: 23551301 DOI: 10.1111/mec.12260] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 12/29/2012] [Accepted: 01/09/2013] [Indexed: 01/09/2023]
Abstract
Little is known about how quickly natural populations adapt to changes in their environment and how temporal and spatial variation in selection pressures interact to shape patterns of genetic diversity. We here address these issues with a series of genome scans in four overfished populations of Atlantic cod (Gadus morhua) studied over an 80-year period. Screening of >1000 gene-associated single-nucleotide polymorphisms (SNPs) identified 77 loci that showed highly elevated levels of differentiation, likely as an effect of directional selection, in either time, space or both. Exploratory analysis suggested that temporal allele frequency shifts at certain loci may correlate with local temperature variation and with life history changes suggested to be fisheries induced. Interestingly, however, largely nonoverlapping sets of loci were temporal outliers in the different populations and outliers from the 1928 to 1960 period showed almost complete stability during later decades. The contrasting microevolutionary trajectories among populations resulted in sequential shifts in spatial outliers, with no locus maintaining elevated spatial differentiation throughout the study period. Simulations of migration coupled with observations of temporally stable spatial structure at neutral loci suggest that population replacement or gene flow alone could not explain all the observed allele frequency variation. Thus, the genetic changes are likely to at least partly be driven by highly dynamic temporally and spatially varying selection. These findings have important implications for our understanding of local adaptation and evolutionary potential in high gene flow organisms and underscore the need to carefully consider all dimensions of biocomplexity for evolutionarily sustainable management.
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Affiliation(s)
- Nina O Therkildsen
- Section for Population Ecology and Genetics, National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark.
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23
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Pukk L, Kuparinen A, Järv L, Gross R, Vasemägi A. Genetic and life-history changes associated with fisheries-induced population collapse. Evol Appl 2013; 6:749-760. [PMID: 29387163 PMCID: PMC5779128 DOI: 10.1111/eva.12060] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/21/2013] [Accepted: 01/29/2013] [Indexed: 11/30/2022] Open
Abstract
Over the recent years, growing number of studies suggests that intensive size-selective fishing can cause evolutionary changes in life-history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. We detected marked changes in size- and age-distributions and increase in juvenile growth rate. We also observed reduction of age at sexual maturity in males that has frequently been considered to support the hypothesis of fisheries-induced evolution. However, combined individual-based life-history and genetic analyses indicated increased immigration of foreign individuals with different life-history patterns as an alternative mechanism behind the observed phenotypic change. This study demonstrates the value of combining genetic and phenotypic analyses and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.
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Affiliation(s)
- Lilian Pukk
- Department of Aquaculture Estonian University of Life Sciences Estonia
| | - Anna Kuparinen
- Department of Environmental Sciences University of Helsinki Finland.,Ecological Genetics Research Unit Department of Biosciences University of Helsinki Finland
| | - Leili Järv
- Estonian Marine Institute University of Tartu Estonia
| | - Riho Gross
- Department of Aquaculture Estonian University of Life Sciences Estonia
| | - Anti Vasemägi
- Department of Aquaculture Estonian University of Life Sciences Estonia.,Department of Biology University of Turku Finland
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24
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Alós J, Palmer M, Arlinghaus R. Consistent selection towards low activity phenotypes when catchability depends on encounters among human predators and fish. PLoS One 2012; 7:e48030. [PMID: 23110164 PMCID: PMC3480476 DOI: 10.1371/journal.pone.0048030] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 09/26/2012] [Indexed: 11/18/2022] Open
Abstract
Together with life-history and underlying physiology, the behavioural variability among fish is one of the three main trait axes that determines the vulnerability to fishing. However, there are only a few studies that have systematically investigated the strength and direction of selection acting on behavioural traits. Using in situ fish behaviour revealed by telemetry techniques as input, we developed an individual-based model (IBM) that simulated the Lagrangian trajectory of prey (fish) moving within a confined home range (HR). Fishers exhibiting various prototypical fishing styles targeted these fish in the model. We initially hypothesised that more active and more explorative individuals would be systematically removed under all fished conditions, in turn creating negative selection differentials on low activity phenotypes and maybe on small HR. Our results partly supported these general predictions. Standardised selection differentials were, on average, more negative on HR than on activity. However, in many simulation runs, positive selection pressures on HR were also identified, which resulted from the stochastic properties of the fishes' movement and its interaction with the human predator. In contrast, there was a consistent negative selection on activity under all types of fishing styles. Therefore, in situations where catchability depends on spatial encounters between human predators and fish, we would predict a consistent selection towards low activity phenotypes and have less faith in the direction of the selection on HR size. Our study is the first theoretical investigation on the direction of fishery-induced selection of behaviour using passive fishing gears. The few empirical studies where catchability of fish was measured in relation to passive fishing techniques, such as gill-nets, traps or recreational fishing, support our predictions that fish in highly exploited situations are, on average, characterised by low swimming activity, stemming, in part, from negative selection on swimming activity.
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Affiliation(s)
- Josep Alós
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA-CSIC-UIB, Esporles, Illes Balears, Spain.
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25
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McAdam BJ, Grabowski TB, Marteinsdóttir G. Identification of stock components using morphological markers. JOURNAL OF FISH BIOLOGY 2012; 81:1447-1462. [PMID: 23020555 DOI: 10.1111/j.1095-8649.2012.03384.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This study investigated the development of a quantitative method for distinguishing stock components of Icelandic cod Gadus morhua based on visual examination of morphology. The stock is known to be structured into genetically distinct geographic components (north and south of Iceland) and behavioural types that spawn sympatrically. Differences in morphology were tested between locations, genotypes (a proxy for behaviour) and sexes. Results show morphological markers on the head, fins and body of G. morhua that are correlated with the sex, genotype of the fish at the pantophysin (pan-I) locus and the location at which the fish were caught. Females were found to have relatively deep bodies, and the pan-I(BB) genotype (associated with deep-water feeding behaviour) have greater gaps between their fins. Overall, morphology is more useful for distinguishing sympatric genotypes but less powerful at identifying genetically distinct geographic sub-populations, perhaps because counter-gradient evolution reduces phenotypic differences even with an underlying genetic cause.
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Affiliation(s)
- B J McAdam
- Institute of Biology, University of Iceland, Sturlugata 7, Reykjavik 101, Iceland
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26
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Olsen EM, Heupel MR, Simpfendorfer CA, Moland E. Harvest selection on Atlantic cod behavioral traits: implications for spatial management. Ecol Evol 2012; 2:1549-62. [PMID: 22957161 PMCID: PMC3434912 DOI: 10.1002/ece3.244] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 12/16/2022] Open
Abstract
Harvesting wild populations may contrast or reinforce natural agents of selection and potentially cause evolutionary changes in life-history traits such as growth and maturation. Harvest selection may also act on behavioral traits, although this field of research has so far received less attention. We used acoustic tags and a network of receivers to monitor the behavior and fate of individual Atlantic cod (Gadus morhua, N = 60) in their natural habitat on the Norwegian Skagerrak coast. Fish with a strong diel vertical migration, alternating between shallow- and deep-water habitats, had a higher risk of being captured in the fishery (traps, gillnet, hand line) as compared to fish that stayed in deeper water. There was also a significant negative correlation between fish size (30–66 cm) and the magnitude of diel vertical migration. Natural selection on behavior was less clear, but tended to favor fish with a large activity space. On a monthly time scale we found significant repeatabilities for cod behavior, meaning that individual characteristics tended to persist and therefore may be termed personality traits. We argue that an evolutionary approach to fisheries management should consider fish behavior. This would be of particular relevance for spatial management actions such as marine reserve design.
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Affiliation(s)
- Esben Moland Olsen
- Institute of Marine Research FlødevigenN-4817 His, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of OsloP.O. Box 1066 Blindern, N-0316 Oslo, Norway
| | - Michelle R Heupel
- Australian Institute of Marine ScienceTownsville, Queensland 4811, Australia
- Fishing and Fisheries Research Centre, School of Earth and Environmental Sciences, James Cook UniversityTownsville, Queensland 4811, Australia
| | - Colin A Simpfendorfer
- Fishing and Fisheries Research Centre, School of Earth and Environmental Sciences, James Cook UniversityTownsville, Queensland 4811, Australia
| | - Even Moland
- Institute of Marine Research FlødevigenN-4817 His, Norway
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27
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Alós J, Palmer M, Arlinghaus R. Consistent selection towards low activity phenotypes when catchability depends on encounters among human predators and fish. PLoS One 2012. [PMID: 23110164 DOI: 10.1371/journal.pone.00480300.1186/s12864-018-5108-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023] Open
Abstract
Together with life-history and underlying physiology, the behavioural variability among fish is one of the three main trait axes that determines the vulnerability to fishing. However, there are only a few studies that have systematically investigated the strength and direction of selection acting on behavioural traits. Using in situ fish behaviour revealed by telemetry techniques as input, we developed an individual-based model (IBM) that simulated the Lagrangian trajectory of prey (fish) moving within a confined home range (HR). Fishers exhibiting various prototypical fishing styles targeted these fish in the model. We initially hypothesised that more active and more explorative individuals would be systematically removed under all fished conditions, in turn creating negative selection differentials on low activity phenotypes and maybe on small HR. Our results partly supported these general predictions. Standardised selection differentials were, on average, more negative on HR than on activity. However, in many simulation runs, positive selection pressures on HR were also identified, which resulted from the stochastic properties of the fishes' movement and its interaction with the human predator. In contrast, there was a consistent negative selection on activity under all types of fishing styles. Therefore, in situations where catchability depends on spatial encounters between human predators and fish, we would predict a consistent selection towards low activity phenotypes and have less faith in the direction of the selection on HR size. Our study is the first theoretical investigation on the direction of fishery-induced selection of behaviour using passive fishing gears. The few empirical studies where catchability of fish was measured in relation to passive fishing techniques, such as gill-nets, traps or recreational fishing, support our predictions that fish in highly exploited situations are, on average, characterised by low swimming activity, stemming, in part, from negative selection on swimming activity.
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Affiliation(s)
- Josep Alós
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA-CSIC-UIB, Esporles, Illes Balears, Spain.
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28
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Stocking of captive-bred fish can cause long-term population decline and gene pool replacement: predictions from a population dynamics model incorporating density-dependent mortality. THEOR ECOL-NETH 2011. [DOI: 10.1007/s12080-011-0128-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Evidence of segregated spawning in a single marine fish stock: sympatric divergence of ecotypes in Icelandic cod? PLoS One 2011; 6:e17528. [PMID: 21408180 PMCID: PMC3049785 DOI: 10.1371/journal.pone.0017528] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 02/03/2011] [Indexed: 11/19/2022] Open
Abstract
There is increasing recognition of intraspecific diversity and population structure within marine fish species, yet there is little direct evidence of the isolating mechanisms that maintain it or documentation of its ecological extent. We analyzed depth and temperature histories collected by electronic data storage tags retrieved from 104 Atlantic cod at liberty ≥1 year to evaluate a possible isolating mechanisms maintaining population structure within the Icelandic cod stock. This stock consists of two distinct behavioral types, resident coastal cod and migratory frontal cod, each occurring within two geographically distinct populations. Despite being captured together on the same spawning grounds, we show the behavioral types seem reproductively isolated by fine-scale differences in spawning habitat selection, primarily depth. Additionally, the different groups occupied distinct seasonal thermal and bathymetric niches that generally demonstrated low levels of overlap throughout the year. Our results indicate that isolating mechanisms, such as differential habitat selection during spawning, might contribute to maintaining diversity and fine-scale population structure in broadcast-spawning marine fishes.
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30
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André C, Larsson LC, Laikre L, Bekkevold D, Brigham J, Carvalho GR, Dahlgren TG, Hutchinson WF, Mariani S, Mudde K, Ruzzante DE, Ryman N. Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci. Heredity (Edinb) 2011; 106:270-80. [PMID: 20551979 PMCID: PMC3183876 DOI: 10.1038/hdy.2010.71] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Revised: 04/14/2010] [Accepted: 05/05/2010] [Indexed: 11/09/2022] Open
Abstract
In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species.
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Affiliation(s)
- C André
- Department of Marine Ecology-Tjärnö, University of Gothenburg, Strömstad, Sweden.
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Jakobsdóttir KB, Pardoe H, Magnússon Á, Björnsson H, Pampoulie C, Ruzzante DE, Marteinsdóttir G. Historical changes in genotypic frequencies at the Pantophysin locus in Atlantic cod (Gadus morhua) in Icelandic waters: evidence of fisheries-induced selection? Evol Appl 2011; 4:562-73. [PMID: 25568005 PMCID: PMC3352422 DOI: 10.1111/j.1752-4571.2010.00176.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2010] [Accepted: 11/18/2010] [Indexed: 01/28/2023] Open
Abstract
The intense fishing mortality imposed on Atlantic cod in Icelandic waters during recent decades has resulted in marked changes in stock abundance, as well as in age and size composition. Using a molecular marker known to be under selection (Pan I) along with a suite of six neutral microsatellite loci, we analysed an archived data set and revealed evidence of distinct temporal changes in the frequencies of genotypes at the Pan I locus among spawning Icelandic cod, collected between 1948 and 2002, a period characterized by high fishing pressure. Concurrently, temporal stability in the composition of the microsatellite loci was established within the same data set. The frequency of the Pan IBB genotype decreased over a period of six decades, concomitant with considerable spatial and technical changes in fishing effort that resulted in the disappearance of older individuals from the fishable stock. Consequently, these changes have likely led to a change in the genotype frequencies at this locus in the spawning stock of Icelandic cod. The study highlights the value of molecular genetic approaches that combine functional and neutral markers examined in the same set of individuals for investigations of the selective effects of harvesting and reiterates the need for an evolutionary dimension to fisheries management.
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Affiliation(s)
- Klara B Jakobsdóttir
- Marine Research Institute Reykjavik, Iceland ; Institute of Biology, University of Iceland Reykjavik, Iceland
| | - Heidi Pardoe
- Institute of Biology, University of Iceland Reykjavik, Iceland
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Nielsen EE, Hemmer-Hansen J, Poulsen NA, Loeschcke V, Moen T, Johansen T, Mittelholzer C, Taranger GL, Ogden R, Carvalho GR. Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua). BMC Evol Biol 2009; 9:276. [PMID: 19948077 PMCID: PMC2790465 DOI: 10.1186/1471-2148-9-276] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 12/01/2009] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Marine fishes have been shown to display low levels of genetic structuring and associated high levels of gene flow, suggesting shallow evolutionary trajectories and, possibly, limited or lacking adaptive divergence among local populations. We investigated variation in 98 gene-associated single nucleotide polymorphisms (SNPs) for evidence of selection in local populations of Atlantic cod (Gadus morhua L.) across the species distribution. RESULTS Our global genome scan analysis identified eight outlier gene loci with very high statistical support, likely to be subject to directional selection in local demes, or closely linked to loci under selection. Likewise, on a regional south/north transect of central and eastern Atlantic populations, seven loci displayed strongly elevated levels of genetic differentiation. Selection patterns among populations appeared to be relatively widespread and complex, i.e. outlier loci were generally not only associated with one of a few divergent local populations. Even on a limited geographical scale between the proximate North Sea and Baltic Sea populations four loci displayed evidence of adaptive evolution. Temporal genome scan analysis applied to DNA from archived otoliths from a Faeroese population demonstrated stability of the intra-population variation over 24 years. An exploratory landscape genetic analysis was used to elucidate potential effects of the most likely environmental factors responsible for the signatures of local adaptation. We found that genetic variation at several of the outlier loci was better correlated with temperature and/or salinity conditions at spawning grounds at spawning time than with geographic distance per se. CONCLUSION These findings illustrate that adaptive population divergence may indeed be prevalent despite seemingly high levels of gene flow, as found in most marine fishes. Thus, results have important implications for our understanding of the interplay of evolutionary forces in general, and for the conservation of marine biodiversity under rapidly increasing evolutionary pressure from climate and fisheries induced changes in local environments.
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Affiliation(s)
- Einar E Nielsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Jakob Hemmer-Hansen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
| | - Nina A Poulsen
- National Institute of Aquatic Resources, Technical University of Denmark, Vejlsøvej 39, DK-8600 Silkeborg, Denmark
- Department of Biological Sciences, Genetics and Ecology, University of Aarhus, Building 1540, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | - Volker Loeschcke
- Department of Biological Sciences, Genetics and Ecology, University of Aarhus, Building 1540, Ny Munkegade, DK-8000 Aarhus C, Denmark
| | | | - Torild Johansen
- Institute of Marine Research Tromsø, PO Box 6404, N-9294 Tromsø, Norway
| | - Christian Mittelholzer
- Institute of Marine Research, PO Box 1870, Nordnes N-5817 Bergen, Norway
- Current address: University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | | | - Rob Ogden
- Tepnel Research Products and Services, Appleton Place, Livingston, EH54 7EZ, UK
| | - Gary R Carvalho
- Molecular Ecology & Fisheries Genetics Laboratory, School of Biological Sciences, Environment Centre Wales, Bangor University, Bangor, Gwynedd LL57 2UW, UK
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