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  • 1
    Online Resource
    Online Resource
    Disentangling the components of coastal fish biodiversity in southern Brittany by applying an environmental DNA approach
    Wiley ; 2022
    In:  Environmental DNA Vol. 4, No. 4 ( 2022-07), p. 920-939
    Details
    In: Environmental DNA, Wiley, Vol. 4, No. 4 ( 2022-07), p. 920-939
    Abstract: The global biodiversity crisis from anthropogenic activities significantly weakens the functioning of marine ecosystems and jeopardizes their ecosystem services. Increasing monitoring of marine ecosystems is crucial to understand the breadth of the changes in biodiversity, ecosystem functioning and propose more effective conservation strategies. Such strategies should not only focus on maximizing the number of species (i.e., taxonomic diversity) but also the diversity of phylogenetic histories and ecological functions within communities. To support future conservation decisions, multicomponent biodiversity monitoring can be combined with high‐throughput species assemblage detection methods such as environmental DNA (eDNA) metabarcoding. Here, we used eDNA to assess fish biodiversity along the coast of southern Brittany (France, Iroise Sea). We filtered surface marine water from 17 sampling stations and applied an eDNA metabarcoding approach targeting Actinopterygii and Elasmobranchii taxa. We documented three complementary biodiversity components—taxonomic, phylogenetic, and functional diversity—and three diversity facets—richness, divergence and regularity. We identified a north/south contrast with higher diversity for the three facets of the biodiversity components in the northern part of the study area. The northern communities showed higher species richness, stronger phylogenetic overdispersion and lower functional clustering compared to the ones in the southern part, due to the higher diversity of habitats (reefs, rocky shores) and restricted access for fishing. Moreover, we also detected a higher level of taxonomic, phylogenetic, and functional uniqueness in many offshore stations compared to more coastal ones, with the presence of species typically living at greater depths ( 〉  300 m), which suggests an influence of hydrodynamic structures and currents on eDNA dispersion and hence sample composition. eDNA metabarcoding can, therefore, be used as an efficient sampling method to reveal fine‐scale community compositions and in combination with functional and phylogenetic information to document multicomponent biodiversity gradients in coastal marine systems.
    Type of Medium: Online Resource
    ISSN: 2637-4943 , 2637-4943
    URL: Issue
    URL: Article
    DOI: 10.1002/edn3.v4.4
    DOI: 10.1002/edn3.305
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 3001165-6
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  • 2
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    Temporal synchrony among juvenile marine fishes and potential climate and environmental drivers in the Bay of Biscay
    Elsevier BV ; 2023
    In:  Progress in Oceanography Vol. 211 ( 2023-02), p. 102969-
    Details
    In: Progress in Oceanography, Elsevier BV, Vol. 211 ( 2023-02), p. 102969-
    Type of Medium: Online Resource
    ISSN: 0079-6611
    URL: Article
    DOI: 10.1016/j.pocean.2023.102969
    RVK:
    RB 10402
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1497436-8
    detail.hit.zdb_id: 4062-9
    SSG: 21,3
    SSG: 14
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  • 3
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    Considerations for management strategy evaluation for small pelagic fishes
    Wiley ; 2021
    In:  Fish and Fisheries Vol. 22, No. 6 ( 2021-11), p. 1167-1186
    Details
    In: Fish and Fisheries, Wiley, Vol. 22, No. 6 ( 2021-11), p. 1167-1186
    Abstract: Management strategy evaluation (MSE) is the state‐of‐the‐art approach for testing and comparing management strategies in a way that accounts for multiple sources of uncertainty (e.g. monitoring, estimation, and implementation). Management strategy evaluation can help identify management strategies that are robust to uncertainty about the life history of the target species and its relationship to other species in the food web. Small pelagic fish (e.g. anchovy, herring and sardine) fulfil an important ecological role in marine food webs and present challenges to the use of MSE and other simulation‐based evaluation approaches. This is due to considerable stochastic variation in their ecology and life history, which leads to substantial observation and process uncertainty. Here, we summarize the current state of MSE for small pelagic fishes worldwide. We leverage expert input from ecologists and modellers to draw attention to sources of process and observation uncertainty for small pelagic species, providing examples from geographical regions where these species are ecologically, economically and culturally important. Temporal variation in recruitment and other life‐history rates, spatial structure and movement, and species interactions are key considerations for small pelagic fishes. We discuss tools for building these into the MSE process, with examples from existing fisheries. We argue that model complexity should be informed by management priorities and whether ecosystem information will be used to generate dynamics or to inform reference points. We recommend that our list of considerations be used in the initial phases of the MSE process for small pelagic fishes or to build complexity on existing single‐species models.
    Type of Medium: Online Resource
    ISSN: 1467-2960 , 1467-2979
    URL: Issue
    URL: Article
    DOI: 10.1111/faf.v22.6
    DOI: 10.1111/faf.12579
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2024569-5
    SSG: 21,3
    SSG: 12
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  • 4
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    Physiological biomarkers and fisheries management
    Springer Science and Business Media LLC ; 2021
    In:  Reviews in Fish Biology and Fisheries Vol. 31, No. 4 ( 2021-12), p. 797-819
    Details
    In: Reviews in Fish Biology and Fisheries, Springer Science and Business Media LLC, Vol. 31, No. 4 ( 2021-12), p. 797-819
    Abstract: The benefits of physiological biomarkers, knowledge and concepts are well-established in fish and wildlife management as they confer the ability to understand mechanistic processes, identify cause-and-effect relationships, and develop predictive models. Although this approach is gaining momentum in the context of species conservation, the use of physiological biomarkers in exploited marine fish stock management and recovery plans remains relatively rare. Here, we present five essential issues to consider to implement physiological biomarkers in fisheries management: (i) choice of relevant biomarkers that have a well-known mechanistic basis, (ii) identification of species-specific biomarkers reflecting a meaningful timespan for management, (iii) selection of biomarkers compatible with data collection during routine scientific fisheries surveys, (iv) use of biomarkers as early-warning signals and complementary indicators of population-level changes in life history traits and (v) how physiological biomarkers may help to refine long-term population dynamic projections under climate change and management scenarios. Overall, if based on well-established mechanisms linked to individuals’ fitness, a focus on physiological biomarkers should help to better understand the mechanisms behind stock declines, changes in stock characteristics, and thus more efficiently manage marine fisheries and conserve populations. As this approach is transferable among species, locations, and times, the integration of physiological biomarkers in fisheries science has the potential to more broadly enhance assessments and management of fish stocks.
    Type of Medium: Online Resource
    ISSN: 0960-3166 , 1573-5184
    URL: Article
    DOI: 10.1007/s11160-021-09677-5
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 30768-3
    detail.hit.zdb_id: 1498719-3
    SSG: 21,3
    SSG: 12
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  • 5
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    Comparison of approaches for incorporating depredation on fisheries catches into Ecopath
    Oxford University Press (OUP) ; 2020
    In:  ICES Journal of Marine Science Vol. 77, No. 7-8 ( 2020-12-01), p. 3153-3167
    Details
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 77, No. 7-8 ( 2020-12-01), p. 3153-3167
    Abstract: Ecosystem-based approaches are increasingly used in fisheries management to account for the direct trophic impacts of fish population harvesting. However, fisheries can also indirectly alter ecosystem structure and functioning, for instance via the provision of new feeding opportunities to marine predators. For instance, marine depredation, where predators feed on fishery catches on fishing gear, is a behaviour developed by many marine species globally. This behaviour can modify both the ecological role of predators and fisheries performance. Yet, these ecosystem-wide effects of depredation are rarely considered holistically. In this study, we explored different ways of incorporating depredation into an Ecopath trophic model. We assessed, through a subantarctic case study, how three alternative model structures can account for depredation effects on fishery catches, predator and non-commercial prey populations, as well as target fish stocks. While none adequately addresses all facets of depredation, the alternative models can to some extent capture how depredation can lead to increased fishing pressure on stocks. As structural specificities of Ecopath prevented us from representing other depredation effects such as provisioning effects for predator populations, we conclude this study with a set of guidance to effectively capture the complex effects of depredation in marine ecosystems and fisheries models.
    Type of Medium: Online Resource
    ISSN: 1095-9289
    URL: Article
    DOI: 10.1093/icesjms/fsaa219
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2463178-4
    detail.hit.zdb_id: 1468003-8
    detail.hit.zdb_id: 29056-7
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  • 6
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    Close-kin mark–recapture abundance estimation: practical insights and lessons learned
    Oxford University Press (OUP) ; 2022
    In:  ICES Journal of Marine Science Vol. 79, No. 2 ( 2022-03-10), p. 413-422
    Details
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 79, No. 2 ( 2022-03-10), p. 413-422
    Abstract: We present practical lessons learned from applying the recent close-kin mark–recapture (CKMR) abundance estimation method to thornback ray (Raja clavata). For CKMR, related individuals are identified from their genotypes and their number and pattern is used for abundance estimation. We genotyped over 7000 individuals collected in the Bay of Biscay using Single Nucleotide Polymorphism (SNP) markers finding 99 parent–offspring pairs. The estimated number of adult thornback rays in the central Bay of Biscay was around 135000 (CV 0.19) in 2013. In total, four lessons were drawn: (i) CKMR helps identifying metapopulation structure, which if ignored might affect abundance estimates and/or time trends. There was strong evidence for two distinct local populations of thornback ray with no demographic connectivity. (ii) Demographic sample composition can affect precision and needs to include a range of birth years, which turned out to be difficult for thornback ray. (iii) Reasonable age information for potential offspring is essential. (iv) The sex of potential parents is needed and might be identified from sex-related SNPs. Reliable abundance estimation by CKMR appears feasible for a wide range of species provided that: sampling adequately covers potential local population structure, has appropriate demographic composition, and the age of potential offspring is reasonably well-known.
    Type of Medium: Online Resource
    ISSN: 1054-3139 , 1095-9289
    URL: Article
    DOI: 10.1093/icesjms/fsac002
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 2463178-4
    detail.hit.zdb_id: 1468003-8
    detail.hit.zdb_id: 29056-7
    SSG: 12
    SSG: 21,3
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  • 7
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    Estimating effective population size using RADseq: Effects of SNP selection and sample size
    Wiley ; 2020
    In:  Ecology and Evolution Vol. 10, No. 4 ( 2020-02), p. 1929-1937
    Details
    In: Ecology and Evolution, Wiley, Vol. 10, No. 4 ( 2020-02), p. 1929-1937
    Abstract: Effective population size ( N e ) is a key parameter of population genetics. However, N e remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on N e estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient F IS was positively correlated with the amount of missing data, implying data were missing nonrandomly. The precision of N e estimates decreased with the number of SNPs. Mean N e estimates (averaged across 50 random data sets with2000 SNPs) ranged between 237 and 1784. Increasing the percentage of missing data from 25% to 50% increased N e estimates between 82% and 120%, while increasing the minor allele frequency (MAF) threshold from 0.01 to 0.1 decreased estimates between 71% and 75%. Considering these effects is important when interpreting RADseq data‐derived estimates of effective population size in empirical studies.
    Type of Medium: Online Resource
    ISSN: 2045-7758 , 2045-7758
    URL: Issue
    URL: Article
    DOI: 10.1002/ece3.v10.4
    DOI: 10.1002/ece3.6016
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2635675-2
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  • 8
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    Robust identification of potential habitats of a rare demersal species (blackspot seabream) in the Northeast Atlantic
    Elsevier BV ; 2023
    In:  Ecological Modelling Vol. 477 ( 2023-03), p. 110255-
    Details
    In: Ecological Modelling, Elsevier BV, Vol. 477 ( 2023-03), p. 110255-
    Type of Medium: Online Resource
    ISSN: 0304-3800
    URL: Article
    DOI: 10.1016/j.ecolmodel.2022.110255
    RVK:
    AR 10100
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 191971-4
    detail.hit.zdb_id: 2000879-X
    SSG: 12
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  • 9
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    Methods for identifying and interpreting sex‐linked SNP markers and carrying out sex assignment: application to thornback ray ( Raja clavata )
    Wiley ; 2020
    In:  Molecular Ecology Resources Vol. 20, No. 6 ( 2020-11), p. 1610-1619
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 20, No. 6 ( 2020-11), p. 1610-1619
    Abstract: Sex‐determining modes remain unknown in numerous species, notably in fishes, in which a variety of modalities have been reported. Additionally, noninvasive individual sexing is problematic for species without external sex attributes or for early life stages, requiring cytogenetic or molecular analyses when sex chromosomes or sex‐linked markers have been characterized. Genomics now provide a means to achieve this. Here, we review common sex‐determination systems and corresponding statistical methods for identifying sex‐linked genetic markers and their use for sex assignment, focusing on single nucleotide polymorphism (SNP) markers derived from reduced representation sequencing methods. We demonstrate the dependence of expected sex assignment error on the number of sex‐linked SNPs and minor allele frequency. The application of three methods was made here: (a) identification of heterozygote excess in one sex, (b) F ST outlier analysis between the two sexes and (c) neuronal net modelling. These methods were applied to a large SNP data set (4604 SNPs) for 1680 thornback rays ( Raja clavata ). Using method (a), nineteen putative sex‐linked SNPs were identified. Comparison with the reference genome of a related species ( Amblyraja radiata ) indicated that all 19 SNPs are probably located on the same chromosome. These results suggest that thornback ray has a XX/XY sex‐determination system. Method (b) identified eight SNPs probably located on different chromosomes. Method (a) led to the lowest sex assignment error among the three methods (4.2% error for females and 3.7% for males).
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.v20.6
    DOI: 10.1111/1755-0998.13225
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 10
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    Interpretation of interannual variability in long-term aquatic ecological surveys
    Canadian Science Publishing ; 2020
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 77, No. 5 ( 2020-05), p. 894-903
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 77, No. 5 ( 2020-05), p. 894-903
    Abstract: Long-term ecological surveys (LTES) often exhibit strong variability among sampling dates. The use and interpretation of such interannual variability is challenging due to the combination of multiple processes involved and sampling uncertainty. Here, we analysed the interannual variability in ∼30 years of 150 species density (fish and invertebrate) and environmental observation time series in four aquatic systems (stream, river, estuary, and marine continental shelf) with different sampling efforts to identify the information provided by this variability. We tested, using two empirical methods, whether we could observe simultaneous fluctuation between detrended time series corresponding to widely acknowledged assumptions about aquatic population dynamics: spatial effects, cohort effects, and environmental effects. We found a low number of significant results (36%, 9%, and 0% for spatial, cohort, and environmental effects, respectively), suggesting that sampling uncertainty overrode the effects of biological processes. Our study does not question the relevance of LTES for detecting important trends, but clearly indicates that the statistical power to interpret interannual variations in aquatic species densities is low, especially in large systems where the degree of sampling effort is always limited.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/cjfas-2019-0146
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2020
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
    SSG: 21,3
    SSG: 12
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