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Batsleer, J., Marchal, P., Vaz, S., Vermard, V., Rijnsdorp, A. D., & Poos, J. J. (2018). Exploring habitat credits to manage the benthic impact in a mixed fishery. Mar. Ecol.-Prog. Ser., 586, 167–179.
Résumé: The performance of a combined catch quota and habitat credit system was explored to manage the sustainable exploitation of a mix of demersal fish species and reduce the benthic impacts of bottom trawl fisheries using a dynamic state variable model approach. The model was parameterised for the Eastern English Channel demersal mixed fishery using otter trawls or dredges. Target species differed in their association with habitat types. Restricting catch quota for plaice and cod had a limited effect on benthic impact, except when reduced to very low values, forcing the vessels to stay in port. Quota management had a minimal influence on fishing behaviour and hence resulted in a minimal reduction of benthic impact. Habitat credits may reduce the benthic impacts of the trawl fisheries at a minimal loss of landings and revenue, as vessels are still able to reallocate their effort to less vulnerable fishing grounds, while allowing the fishery to catch their catch quota and maintain their revenue. Only if they are reduced to extremely low levels can habitat credits potentially constrain fishing activities to levels that prevent the fisheries from using up the catch quota for the target species.
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Borsa, P., Durand, J. D., Shen, K. N., Arlyza, I. S., Solihin, D. D., & Berrebi, P. (2013). Himantura tutul sp nov (Myliobatoidei: Dasyatidae), a new ocellated whipray from the tropical Indo-West Pacific, described from its cytochrome-oxidase I gene sequence. Comptes Rendus Biologies, 336(2), 82–92.
Résumé: It has been previously established that the Leopard Whipray, Himantura leoparda, consists of two genetically isolated, cryptic species, provisionally designated as 'Cluster 1' and 'Cluster 4' (Arlyza et al., Mol. Phylogenet. Evol. 65 (2013) [11). Here, we show that the two cryptic species differ by the spotting patterns on the dorsal surface of adults: Cluster-4 individuals tend to have larger-ocellated spots, which also more often have a continuous contour than Cluster-1 individuals. We show that H. leopard a's holotype has the typical larger-ocellated spot pattern, designating Cluster 4 as the actual H. leoparda. The other species (Cluster 1) is described as Himantura tutul sp. nov. on the basis of the nucleotide sequence of a 655-base pair fragment of its cytochrome-oxidase I gene (GENBANK accession No. JX263335). Nucleotide synapomorphies at this locus clearly distinguish H. tutul sp. nov. from all three other valid species in the H. uarnak species complex, namely H. leoparda, H. uarnak, and H. undulata. H. tutul sp. nov. has a wide distribution in the Indo-West Pacific, from the shores of eastern Africa to the Indo-Malay archipelago. H. leoparda under its new definition has a similarly wide Indo-West Pacific distribution. (C) 2013 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.
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Brandt, M., Trouche, B., Henry, N., Liautard-Haag, C., Maignien, L., de Vargas, C., et al. (2020). An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities. Front. Mar. Sci., 7, 234.
Résumé: The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.
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Brehmer, P., Sarre, A., Guennegan, Y., & Guillard, J. (2019). Vessel Avoidance Response: A Complex Tradeoff Between Fish Multisensory Integration and Environmental Variables. Rev. Fish. Sci. Aquac.., 27(3), 380–391.
Résumé: The avoidance reaction by fish in front of an approaching vessel is a major source of bias in direct biomass assessment and ecological studies based on fisheries acoustics data. An experiment was carried out to compare echosounder data obtained using a small speedboat and a research fisheries vessel generating significant higher noise above conventional reduced-noise standard. The results show that there was no significant difference between the individual fish target strength distributions, and the numbers of schools recorded by both boats, these schools having similar areas and perimeters. However, the schools detected by the noisier vessel were significantly deeper, and unexpectedly had a significantly higher energy level. These findings suggest that noise-reduced vessels trigger a different vessel avoidance reaction. The noise-reduction standard is not sufficient to reduce avoidance behavior. It is also to take into consideration the ambient noise, which could impair perception of the platform by the fish, and the probability that the acoustic stimuli could be less important than visual perception under some local conditions. The paper introduces the concept of partial avoidance and presents a conceptual diagram of the strength of the avoidance reaction. Last, it is not recommended, because of noise reasons, that vessels routinely used for pelagic stock assessment surveys be changed. Indeed standardized time series, which could be disrupted when switching to a new vessel, are more important than the hypothetical gain from change to quieter vessels. Obviously, all long-term surveys must change vessels; best practice will be to estimate the vessel effect before any change to avoid disrupting the time series and/or perform vessel intercalibration surveys.
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Capietto, A., Escalle, L., Chavance, P., Dubroca, L., Delgado de Molina, A., Murua, H., et al. (2014). Mortality of marine megafauna induced by fisheries: Insights from the whale shark, the world’s largest fish. Biological Conservation, 174, 147–151.
Résumé: The expansion of human activities is endangering megafauna in both terrestrial and marine ecosystems. While large marine vertebrates are often vulnerable and emblematic species, many are considered to be declining, primarily due to fisheries activities. In the open ocean, certain fisheries improve their efficiency of detecting tuna schools by locating and fishing close to some macro-organisms, such as whale sharks or marine mammals. However, collecting accurate data on the accidental capture and mortality of these organisms is a complex process. We analyzed a large database of logbooks from 65 industrial vessels with and without scientific observers on board (487,272 and 16,096 fishing sets since 1980 and 1995 respectively) in both the Atlantic and Indian Oceans. Distribution maps of Sightings Per Unit of Effort highlights major hotspots of interactions between the fishery and whale sharks in the coastal area from Gabon to Angola in the Atlantic from April to September, and in the Mozambique Channel in the Indian Ocean between April and May. The incidence of apparent whale shark mortality due to fishery interaction is extremely low (two of the 145 whale sharks encircled by the net died, i.e. 1.38%). However, these two hotspots presented a relatively high rate of incidental whale shark capture. Thus, we underline the importance of estimating long-term post-release mortality rates by tracking individuals and/or by photographic identification to define precise conservation management measures.
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