Andrello, M., Guilhaumon, F., Albouy, C., Parravicini, V., Scholtens, J., Verley, P., et al. (2017). Global mismatch between fishing dependency and larval supply from marine reserves. Nat. Commun., 8, 16039.
Résumé: Marine reserves are viewed as flagship tools to protect exploited species and to contribute to the effective management of coastal fisheries. Yet, the extent to which marine reserves are globally interconnected and able to effectively seed areas, where fisheries are most critical for food and livelihood security is largely unknown. Using a hydrodynamic model of larval dispersal, we predict that most marine reserves are not interconnected by currents and that their potential benefits to fishing areas are presently limited, since countries with high dependency on coastal fisheries receive very little larval supply from marine reserves. This global mismatch could be reversed, however, by placing new marine reserves in areas sufficiently remote to minimize social and economic costs but sufficiently connected through sea currents to seed the most exploited fisheries and endangered ecosystems.
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Auguet, J. C., Montanie, H., Hartmann, H. J., Lebaron, P., Casamayor, E. O., Catala, P., et al. (2009). Potential effect of freshwater virus on the structure and activity of bacterial communities in the Marennes-Oleron Bay (France). Microb Ecol, 57(2), 295–306.
Résumé: Batch culture experiments using viral enrichment were conducted to test the response of a coastal bacterial community to autochthonous (i.e., co-existing) or allochthonous riverine viruses. The effects of viral infections on bacterial dynamics and activity were assessed by epifluorescence microscopy and thymidine incorporation, respectively, whereas the effect of viral infection on bacterial community composition was examined by polymerase chain reaction-single strand conformation polymorphism 16S ribosomal RNA fingerprinting. The percentages of high nucleic acid-containing cells, evaluated by flow cytometry, were significantly correlated (r2=0.91, n=12, p<0.0001) to bacterial production, making this value a good predictor of active cell dynamics along the study. While confinement and temperature were the two principal experimental factors affecting bacterial community composition and dynamics, respectively, additions of freshwater viruses had significant effects on coastal bacterial communities. Thus, foreign viruses significantly reduced net bacterial population increase as compared to the enrichment treated with inactivated virus. Moreover, freshwater viruses recurrently and specifically affected bacterial community composition, as compared to addition of autochthonous viruses. In most cases, the combined treatment viruses and freshwater dissolved organic matter helped to maintain or even enhance species richness in coastal bacterial communities in agreement to the 'killing the winner' hypothesis. Thus, riverine virus input could potentially influence bacterial community composition of the coastal bay albeit with modest modification of bulk bacterial growth.
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Ba, K., Thiaw, M., Fall, M., Thiam, N., Meissa, B., Jouffre, D., et al. (2018). Long-term fishing impact on the Senegalese coastal demersal resources: diagnosing from stock assessment models. Aquat. Living Resour., 31, 8.
Résumé: For the first time in Senegal, assessments based on both stochastic and deterministic production models were used to draw a global diagnosis of the fishing impact on coastal demersal stocks. Based one national fisheries databases and scientific trawl surveys data: (i) trends in landings since 1971 were examined, (ii) abundance indices of 10 stocks were estimated using linear models fitted to surveys data and commercial catch per unit efforts, and (iii) stock assessments were carried out using pseudo-equilibrium Fox and Pella-Tomlinson models and a Biomass dynamic production model fitted in a Bayesian framework to abundance indices. Most stocks have seen their abundance sharply declining over time. All stocks combined, results of stock assessments suggest a 63% reduction compared to virgin state. Three fifth of demersal stocks are overexploited and excess in fishing effort was estimated until 75% for the worst case. We conclude by suggesting that the fishing of such species must be regulated and an ecosystem approach to fisheries management should be implemented in order to monitor the whole ecosystem.
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Bailleul, D., Stoeckel, S., & Arnaud-Haond, S. (2016). RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r. Methods Ecol. Evol., 7(8), 966–970.
Résumé: Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one-shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next-generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).
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Bakker, J., Wangensteen, O. S., Chapman, D. D., Boussarie, G., Buddo, D., Guttridge, T. L., et al. (2017). Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact. Sci Rep, 7, 16886.
Résumé: Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.
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