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  • 1
    Online Resource
    Online Resource
    Modeling and mapping fish abundance across wadeable streams of Illinois, USA, based on landscape-level environmental variables
    Canadian Science Publishing ; 2016
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 73, No. 7 ( 2016-07), p. 1031-1046
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 73, No. 7 ( 2016-07), p. 1031-1046
    Abstract: To effectively conserve and restore stream ecosystems, we need to better understand the distribution and abundance of individual fish species in relation to natural environments and anthropological stressors. In this study, we modeled the abundance of 97 fish species in small wadeable streams of Illinois, USA, based on random forests regression and landscape-level environmental variables. Model R 2 values for intermediately common species were higher than for common species, but highly variable among rare ones. Models for 50 species reached R 2 of 0.2–0.70 and were tested with a separate set of samples and applied to unsampled wadeable reaches to show the population hotspots of each species across the state. Furthermore, we evaluated the importance of individual environmental variables to a given fish species as well as the directional responses of each species to top 10 key predictors. Climate and land use were the best predictors for most species, followed by topography, geology, and soil permeability. Spatial connection of a stream also was associated with a large number of species. These findings improved our understanding of the relationships between fish species and landscape environments. The distribution maps could guide resource management, restoration, and monitoring of stream fish assemblages.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/cjfas-2015-0343
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2016
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  • 2
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    Supplemental Information 3: R Package rBiscayCodeData: Code and Data for Bay of Biscay Ecosystem
    PeerJ ; 2019
    In:  PeerJ Vol. 7 ( 2019-08-09), p. e7422-
    Details
    In: PeerJ, PeerJ, Vol. 7 ( 2019-08-09), p. e7422-
    Abstract: The transitory and long-term elasticities of the Bay of Biscay ecosystem to density-independent and density-dependent influences were estimated within a state space model that accounted for both process and observation uncertainties. A functional group based model for the Bay of Biscay fish ecosystem was fit to time series obtained from scientific survey and commercial catch and effort data. The observation model parameters correspond to the unknown catchabilities and observation error variances that vary across the commercial fisheries and fishery-independent scientific surveys. The process model used a Gompertz form of density dependence, which is commonly used for the analysis of multivariate ecological time series, with unknown time-varying fishing mortalities. Elasticity analysis showed that the process model parameters are directly interpretable in terms of one-year look-ahead prediction elasticities, which measure the proportional response of a functional group in the next year given a proportional change to a variable or parameter in the current year. The density dependent parameters were also shown to define the elasticities of the long term means or quantiles of the functional groups to changes in fishing pressure. Evidence for the importance of indirect effects, mediated by density dependence, in determining the ecosystem response of the Bay of Biscay to changes in fishing pressure is presented. The state space model performed favourably in an assessment of model adequacy that compared observations of catch per unit effort against cross-validation predictive densities blocked by year.
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
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    DOI: 10.7717/peerj.7422
    DOI: 10.7717/peerj.7422/fig-1
    DOI: 10.7717/peerj.7422/fig-2
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    DOI: 10.7717/peerj.7422/table-1
    DOI: 10.7717/peerj.7422/table-2
    DOI: 10.7717/peerj.7422/supp-1
    DOI: 10.7717/peerj.7422/supp-2
    DOI: 10.7717/peerj.7422/supp-3
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    DOI: 10.7717/peerj.7422/supp-6
    DOI: 10.7717/peerj.7422/supp-7
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    DOI: 10.7717/peerj.7422/supp-9
    DOI: 10.7717/peerj.7422/supp-10
    DOI: 10.7717/peerj.7422/supp-11
    Language: English
    Publisher: PeerJ
    Publication Date: 2019
    detail.hit.zdb_id: 2703241-3
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  • 3
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    A Bayesian state-space model to estimate population biomass with catch and limited survey data: application to the thornback ray ( Raja clavata ) in the Bay of Biscay
    EDP Sciences ; 2016
    In:  Aquatic Living Resources Vol. 29, No. 2 ( 2016-4), p. 209-
    Details
    In: Aquatic Living Resources, EDP Sciences, Vol. 29, No. 2 ( 2016-4), p. 209-
    Type of Medium: Online Resource
    ISSN: 0990-7440 , 1765-2952
    URL: Article
    DOI: 10.1051/alr/2016020
    Language: English
    Publisher: EDP Sciences
    Publication Date: 2016
    detail.hit.zdb_id: 2019083-9
    detail.hit.zdb_id: 291280-6
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  • 4
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    Effects of shoreline armouring and overwater structures on coastal and estuarine fish: opportunities for habitat improvement
    Wiley ; 2017
    In:  Journal of Applied Ecology Vol. 54, No. 5 ( 2017-10), p. 1373-1384
    Details
    In: Journal of Applied Ecology, Wiley, Vol. 54, No. 5 ( 2017-10), p. 1373-1384
    Abstract: Shoreline armouring and overwater structures often compromise fish habitats. These threats to nearshore fish habitats will become more severe as growing coastal populations and rising sea levels increase demands for shoreline infrastructure. Our ability to assess and rehabilitate nearshore fish habitats along modified shorelines will be enhanced by: focusing research attention on metrics that directly indicate fish habitat quality; implementing and evaluating shoreline features that repair compromised habitat functions within human‐use constraints; collating natural history knowledge of nearshore ecosystems; and embracing the socio‐ecological nature of habitat improvements by educating the public about conservation efforts and fostering appreciation of local nearshore ecosystems. Actions to reduce impacts of shoreline modifications on fish are particularly feasible when they align with societal goals, such as improving flood protection and providing spaces that facilitate recreation, education, and connections between people and nature.
    Type of Medium: Online Resource
    ISSN: 0021-8901 , 1365-2664
    URL: Issue
    URL: Article
    DOI: 10.1111/jpe.2017.54.issue-5
    DOI: 10.1111/1365-2664.12906
    Language: English
    Publisher: Wiley
    Publication Date: 2017
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  • 5
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    Estimating effective population size of large marine populations, is it feasible?
    Wiley ; 2019
    In:  Fish and Fisheries Vol. 20, No. 1 ( 2019-01), p. 189-198
    Details
    In: Fish and Fisheries, Wiley, Vol. 20, No. 1 ( 2019-01), p. 189-198
    Abstract: Sustainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size ( N e ), a concept founded in population genetics. We reviewed recent empirical studies on N e and carried out a simulation study to evaluate the feasibility of estimating N e in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical N e values were very similar despite differences in species and total population sizes ( N ). Genetic simulations for an age‐structured fish population were carried out for a range of population and samples sizes, and N e was estimated using the Linkage Disequilibrium method. The results showed that already for medium‐sized populations (1 million individuals) and common sample sizes (50 individuals), negative estimates were likely to occur which for real applications is commonly interpreted as indicating very large (infinite) N e . Moreover, on average, N e estimates were negatively biased. The simulations further indicated that around 1% of the total number of individuals might have to be sampled to ensure sufficiently precise estimates of N e . For large marine populations, this implies rather large samples (several thousands to millions of individuals). If however such large samples were to be collected, many more population parameters than only N e could be estimated.
    Type of Medium: Online Resource
    ISSN: 1467-2960 , 1467-2979
    URL: Issue
    URL: Article
    DOI: 10.1111/faf.2019.20.issue-1
    DOI: 10.1111/faf.12338
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2024569-5
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  • 6
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    How to provide scientific advice for ecosystem‐based management now
    Wiley ; 2018
    In:  Fish and Fisheries Vol. 19, No. 2 ( 2018-03), p. 390-398
    Details
    In: Fish and Fisheries, Wiley, Vol. 19, No. 2 ( 2018-03), p. 390-398
    Abstract: In this paper, I argue that we have at hand what is needed to provide scientific advice for ecosystem‐based management of small pelagics and other species groups now. The ingredients for this advice are (i) large marine ecosystems as spatial management units; (ii) maintaining ecosystem productivity and exploiting at multispecies maximum yield as overarching management objectives; (iii) assessment of ecosystems by evaluating changes in primary productivity; (iv) an operational management procedure in which single‐species catch proposals are adjusted to ecosystem productivity using a set of control rules. Inspection of historic landings for small pelagics and other small species in the Northeast Atlantic ( ICES area) reveals that most likely fisheries exploitation does not, and never did, exceed system productivity in most LME s and is therefore overall sustainable, although not necessarily for individual stocks.
    Type of Medium: Online Resource
    ISSN: 1467-2960 , 1467-2979
    URL: Issue
    URL: Article
    DOI: 10.1111/faf.2018.19.issue-2
    DOI: 10.1111/faf.12263
    Language: English
    Publisher: Wiley
    Publication Date: 2018
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  • 7
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    Determining long‐term changes in a skate assemblage with aggregated landings and limited species data
    Wiley ; 2019
    In:  Fisheries Management and Ecology Vol. 26, No. 4 ( 2019-08), p. 365-373
    Details
    In: Fisheries Management and Ecology, Wiley, Vol. 26, No. 4 ( 2019-08), p. 365-373
    Abstract: Sustainable fisheries management requires assessment of exploited populations and communities. Traditional fisheries stock assessment methods need species‐specific input data, which for skates have only recently become available in Europe. To overcome this limitation, a Bayesian multispecies biomass production model was developed. In addition to aggregated landings, input data are short time series with species‐specific information (landings and biomass indices). Applying the approach to four main skate species and a group of two skate species, all managed together in the Bay of Biscay (Northeast Atlantic), long‐term changes in the skate assemblage composition were identified. Since the 1990s, Leucoraja naevus became increasingly dominant, while the contributions of the other three species ( Raja brachyura , Raja clavata and Raja montagui ) declined. The abundance of the grouped Leucoraja fullonica and L. circularis has also strongly decreased, suggesting long‐term overexploitation. All species except this species group are expected to increase over the next decade under current harvest rates. Currently, the species considered here are managed under a single fishing quota making it unlikely that the group of the two most depleted species will recover soon. The multispecies modelling approach bears promise for other harvested assemblages for which only grouped harvest information is available for certain periods.
    Type of Medium: Online Resource
    ISSN: 0969-997X , 1365-2400
    URL: Issue
    URL: Article
    DOI: 10.1111/fme.2019.26.issue-4
    DOI: 10.1111/fme.12367
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 1193882-1
    detail.hit.zdb_id: 2020299-4
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  • 8
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    Observing the ocean interior in support of integrated management
    Oxford University Press (OUP) ; 2016
    In:  ICES Journal of Marine Science Vol. 73, No. 8 ( 2016-09-01), p. 1947-1954
    Details
    In: ICES Journal of Marine Science, Oxford University Press (OUP), Vol. 73, No. 8 ( 2016-09-01), p. 1947-1954
    Abstract: Active- and passive-acoustic methods are widely used tools for observing, monitoring, and understanding marine ecosystems. From 25 to 28 May 2015, 214 scientists from 31 nations gathered for an ICES symposium on Marine Ecosystem Acoustics (SoME Acoustics) to discuss three major themes related to acoustic observations of marine ecosystems: (i) recent developments in acoustic and platform technologies; (ii) acoustic characterisation of aquatic organisms, ecosystem structure, and ecosystem processes; and (iii) contribution of acoustics to integrated ecosystem assessments and management. The development of, and access to new instruments, such as broad bandwidth systems, enables insightful ecological studies and innovative management approaches. Unresolved ecological questions and the increasing move towards ecosystem based management pose further challenges to scientists and instrument developers. Considering the SoME Acoustics presentations in the context of three previous ICES symposia on fisheries acoustics, topics increasingly emphasize ecosystem studies and management. The continued expansion of work and progress in marine ecosystem acoustics is due to the cross-disciplinary work of fisheries acousticians, engineers, ecologists, modellers, and others. An analysis of the symposium co-authorship network reveals a highly connected acoustic science community collaborating around the globe.
    Type of Medium: Online Resource
    ISSN: 1095-9289 , 1054-3139
    URL: Article
    DOI: 10.1093/icesjms/fsw132
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2016
    detail.hit.zdb_id: 2463178-4
    detail.hit.zdb_id: 1468003-8
    detail.hit.zdb_id: 29056-7
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  • 9
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    Catch estimation in the federal trawl fisheries off Alaska: a simulation approach to compare the statistical properties of three trip-specific catch estimators
    Canadian Science Publishing ; 2015
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 72, No. 7 ( 2015-07), p. 1024-1036
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 72, No. 7 ( 2015-07), p. 1024-1036
    Abstract: Quantifying catch has been recognized worldwide as a critical component in fisheries management. Assessment of discard is challenging because of the requirement for at-sea observation, which is both logistically difficult and costly to fishery agencies. Statistical estimators using robust sampling methods may yield accurate and imprecise estimates given the variability associated with many at-sea discard species and inability for agencies to obtain high sampling fractions. However, biased estimates occur if an inappropriate estimator is used. Using Alaska trawl fisheries as an example, we investigated the statistical properties and implementation issues for three commonly used estimators: the ratio estimator; a simple mean estimator; and a deterministic imputation method currently in use in federal fisheries off Alaska. We used a simulation approach to evaluate the performance of these estimators to estimate trip-specific catch. Several statistical properties were evaluated: bias of the estimators, variability of the estimators, and accuracy of the variance estimators. The simple mean estimator had the best performance for vessels landing catch at shoreside processors. The choice of estimator was less clear for vessels processing catch, owing to sensitivity associated with species composition and implementation issues for the simple mean and ratio estimators.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/cjfas-2014-0347
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2015
    detail.hit.zdb_id: 7966-2
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  • 10
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    Efficient statistical estimators and sampling strategies for estimating the age composition of fish
    Canadian Science Publishing ; 2015
    In:  Canadian Journal of Fisheries and Aquatic Sciences Vol. 72, No. 6 ( 2015-06), p. 938-953
    Details
    In: Canadian Journal of Fisheries and Aquatic Sciences, Canadian Science Publishing, Vol. 72, No. 6 ( 2015-06), p. 938-953
    Abstract: Estimates of age compositions of fish populations or catches that are fundamental inputs to analytical stock assessment models are generally obtained from sample surveys, and multistage cluster sampling of fish is the norm. We use simulations and extensive empirical survey data for Northeast Arctic cod (Gadus morhua) to compare the efficiency of estimators that use age–length keys (ALKs) with design-based estimators for estimating age compositions of fish. The design-based weighted ratio estimator produces the most accurate estimates for cluster-correlated data, and an alternative estimator based on a weighted ALK is equivalent under certain constraints. Using simulations to evaluate subsampling strategies, we show that otolith collections from a length-stratified subsample of one fish per 5 cm length bin (∼10 fish total) per haul or trip is sufficient and nearly as efficient as a random subsample of 20 fish. Our study also indicates that the common practice of applying fixed ALKs to length composition data can severely underestimate the variance in estimates of age compositions and that “borrowing” of ALKs developed for other gears, areas, or time periods can cause serious bias.
    Type of Medium: Online Resource
    ISSN: 0706-652X , 1205-7533
    URL: Article
    DOI: 10.1139/cjfas-2014-0408
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2015
    detail.hit.zdb_id: 7966-2
    detail.hit.zdb_id: 1473089-3
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