2019 |
Heerah, K., et al. "Validation of Dive Foraging Indices Using Archived and Transmitted Acceleration Data: The Case of the Weddell Seal." Frontiers In Ecology And Evolution. 7 (2019).
Résumé: Dive data collected from archival and satellite tags can provide valuable information on foraging activity via the characterization of movement patterns (e.g., wiggles, hunting time). However, a lack of validation limits interpretation of what these metrics truly represent in terms of behavior and how predators interact with prey. Head-mounted accelerometers have proven to be effective for detecting prey catch attempt (PrCA) behaviors, and thus can provide a more direct measure of foraging activity. However, device retrieval is typically required to access the high-resolution data they record, restricting use to animals returning to predictable locations. In this study, we present and validate data obtained from newly developed satellite-relay data tags, capable of remotely transmitting summaries of tri-axial accelerometer measurements. We then use these summaries to assess foraging metrics generated from dive data only. Tags were deployed on four female Weddell seals in November 2014 at Dumont d'Urville, and successfully acquired data over similar to 2 months. Retrieved archival data for one individual, and transmitted data for four individuals were used to (1) compare and validate abstracted accelerometer transmissions against outputs from established processing procedures, and (2) assess the validity of previously developed dive foraging indices, calculated solely from time-depth measurements. We found transmitted estimates of PrCA behaviors were generally comparable to those obtained from archival processing, although a small but consistent over-estimation was noted. Following this, dive foraging segments were identified either from (1) sinuosity in the trajectories of high-resolution depth archives, or (2) vertical speeds between low resolution transmissions of key depth inflection points along a dive profile. In both cases, more than 93% of the estimated PrCA behaviors (from either abstracted transmissions or archival processing) fell into inferred dive foraging segments (i.e., “hunting” segments), suggesting the two methods provide a reliable indicator of foraging effort. The validation of transmitted acceleration data and foraging indices derived fromtime-depth recordings for Weddell seals offers new avenues for the study of foraging activity and dive energetics. This is especially pertinent for species from which tag retrieval is challenging, but also for the post-processing of the numerous low-resolution dive datasets already available.
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Le Fur, I., et al. "Re-oligotrophication trajectories of macrophyte assemblages in Mediterranean coastal lagoons based on 17-year time-series." Marine Ecology Progress Series. 608 (2019): 13–32.
Résumé: Since the mid-20th century, Mediterranean lagoons have been affected by eutrophication, leading to significant changes in primary producers. In the early 2000s, management actions have been implemented to reduce nutrient inputs with the aim to achieve a good ecological status as requested by the EU water framework directive. As a result of these actions, a sharp decline in nutrient loads has been recorded in several lagoons leading to an oligotrophication of the water column. The analyses of a long-term data set (1998-2015) of 21 polyhaline and euhaline lagoons with contrasting trophic status allowed us to infer a general scheme for the changes in macrophyte assemblages during the oligotrophication process. Placing hypertrophic and oligotrophic conditions end to end, we inferred that the general pattern for the re-oligotrophication trajectory in Mediterranean coastal lagoons is described by the following sequence, with regime shifts between each state: (1) bare non-vegetated sediments, phytoplankton-dominated state; (2) opportunistic macroalgae; (3) seagrass and perennial macroalgae dominated state. However, we did not observe the latter regime shift for the most eutrophicated lagoons, which, so far, remained stuck in the opportunistic macroalgae state. So far, the shift from dominance of opportunistic macroalgae to a system dominated by seagrasses was only observed in a single lagoon where seagrasses had never completely disappeared, which possibly relates to resilience. More generally, the conditions favoring regime shifts from opportunistic macroalgae to seagrasses are still poorly understood. In conclusion, we describe a generic pattern for re-oligotrophication of Mediterranean coastal lagoons, although a full recovery from highly eutrophied to oligotrophic conditions may require more than a decade and may include conditions that remain so far poorly recognized.
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2018 |
Batsleer, J., et al. "Exploring habitat credits to manage the benthic impact in a mixed fishery." Mar. Ecol.-Prog. Ser.. 586 (2018): 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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Baudrier, J., et al. "Optimising French fisheries surveys for marine strategy framework directive integrated ecosystem monitoring." Marine Policy. 94 (2018): 10–19.
Résumé: The French initial assessment of the Marine Strategy Framework Directive (MSFD) highlighted the lack of reliable data concerning offshore areas. During the planning of the monitoring programmes, the scientists therefore proposed to partially cover this gap by using existing fisheries research vessel surveys deployed for the purposes of the Common Fisheries Policy (CFP). This paper describes ways of improving the effectiveness of these surveys and making them better suited to delivering the information needed for the MSFD. The process took two years and became operational at the beginning of the year 2016. Testing phases from October 2013 to August 2015 had to be organized to fit within the ongoing fisheries tasks without significantly increasing the workload in terms of both time and human resources. Six fisheries research surveys henceforth collect new data, with or without additional sampling techniques. Specific examples are given with litter and hydrological data which will be used to assess the environmental status of French marine waters. The paper also identifies certain limitations regarding this approach. This French experiment enabled more efficient and effective use of current data collection efforts, while optimising vessel time and implementing an ecosystem approach in collecting data for fisheries management.
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Benedetti, F., et al. "Investigating uncertainties in zooplankton composition shifts under climate change scenarios in the Mediterranean Sea." Ecography. 41.2 (2018): 345–360.
Résumé: Ensemble niche modelling has become a common framework to predict changes in assemblages composition under climate change scenarios. The amount of uncertainty generated by the different components of this framework has rarely been assessed. In the marine realm forecasts have usually focused on taxa representing the top of the marine food-web, thus overlooking their basal component: the plankton. Calibrating environmental niche models at the global scale, we modelled the habitat suitability of 106 copepod species and estimated the dissimilarity between present and future zooplanktonic assemblages in the surface Mediterranean Sea. We identified the patterns (species replacement versus nestedness) driving the predicted dissimilarity, and quantified the relative contributions of different uncertainty sources: environmental niche models, greenhouse gas emission scenarios, circulation model configurations and species prevalence. Our results confirm that the choice of the niche modelling method is the greatest source of uncertainty in habitat suitability projections. Presence-only and presence-absence methods provided different visions of the niches, which subsequently lead to different future scenarios of biodiversity changes. Nestedness with decline in species richness is the pattern driving dissimilarity between present and future copepod assemblages. Our projections contrast with those reported for higher trophic levels, suggesting that different components of the pelagic food-web may respond discordantly to future climatic changes.
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Chiarello, M., et al. "Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet." Microbiome. 6 (2018): 147.
Résumé: Background: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.
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Dalongeville, A., et al. "Geographic isolation and larval dispersal shape seascape genetic patterns differently according to spatial scale." Evol. Appl.. 11.8 (2018): 1437–1447.
Résumé: Genetic variation, as a basis of evolutionary change, allows species to adapt and persist in different climates and environments. Yet, a comprehensive assessment of the drivers of genetic variation at different spatial scales is still missing in marine ecosystems. Here, we investigated the influence of environment, geographic isolation, and larval dispersal on the variation in allele frequencies, using an extensive spatial sampling (47 locations) of the striped red mullet (Mullus surmuletus) in the Mediterranean Sea. Univariate multiple regressions were used to test the influence of environment (salinity and temperature), geographic isolation, and larval dispersal on single nucleotide polymorphism (SNP) allele frequencies. We used Moran's eigenvector maps (db-MEMs) and asymmetric eigenvector maps (AEMs) to decompose geographic and dispersal distances in predictors representing different spatial scales. We found that salinity and temperature had only a weak effect on the variation in allele frequencies. Our results revealed the predominance of geographic isolation to explain variation in allele frequencies at large spatial scale (>1,000km), while larval dispersal was the major predictor at smaller spatial scale (<1,000km). Our findings stress the importance of including spatial scales to understand the drivers of spatial genetic variation. We suggest that larval dispersal allows to maintain gene flows at small to intermediate scale, while at broad scale, genetic variation may be mostly shaped by adult mobility, demographic history, or multigenerational stepping-stone dispersal. These findings bring out important spatial scale considerations to account for in the design of a protected area network that would efficiently enhance protection and persistence capacity of marine species.
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Ewald, M., et al. "LiDAR derived forest structure data improves predictions of canopy N and P concentrations from imaging spectroscopy." Remote Sensing of Environment. 211 (2018): 13–25.
Résumé: Imaging spectroscopy is a powerful tool for mapping chemical leaf traits at the canopy level. However, covariance with structural canopy properties is hampering the ability to predict leaf biochemical traits in structurally heterogeneous forests. Here, we used imaging spectroscopy data to map canopy level leaf nitrogen (Nmass) and phosphorus concentrations (Pmass) of a temperate mixed forest. By integrating predictor variables derived from airborne laser scanning (LiDAR), capturing the biophysical complexity of the canopy, we aimed at improving predictions of Nmass and Pmass. We used partial least squares regression (PLSR) models to link community weighted means of both leaf constituents with 245 hyperspectral bands (426–2425 nm) and 38 LiDAR-derived variables. LiDAR-derived variables improved the model's explained variances for Nmass (R2cv 0.31 vs. 0.41, % RSMEcv 3.3 vs. 3.0) and Pmass (R2cv 0.45 vs. 0.63, % RSMEcv 15.3 vs. 12.5). The predictive performances of Nmass models using hyperspectral bands only, decreased with increasing structural heterogeneity included in the calibration dataset. To test the independent contribution of canopy structure we additionally fit the models using only LiDAR-derived variables as predictors. Resulting R2cv values ranged from 0.26 for Nmass to 0.54 for Pmass indicating considerable covariation between biochemical traits and forest structural properties. Nmass was negatively related to the spatial heterogeneity of canopy density, whereas Pmass was negatively related to stand height and to the total cover of tree canopies. In the specific setting of this study, the importance of structural variables can be attributed to the presence of two tree species, featuring structural and biochemical properties different from co-occurring species. Still, existing functional linkages between structure and biochemistry at the leaf and canopy level suggest that canopy structure, used as proxy, can in general support the mapping of leaf biochemistry over broad spatial extents.
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Galand, P. E., et al. "A strong link between marine microbial community composition and function challenges the idea of functional redundancy." Isme J.. 12.10 (2018): 2470–2478.
Résumé: Marine microbes have tremendous diversity, but a fundamental question remains unanswered: why are there so many microbial species in the sea? The idea of functional redundancy for microbial communities has long been assumed, so that the high level of richness is often explained by the presence of different taxa that are able to conduct the exact same set of metabolic processes and that can readily replace each other. Here, we refute the hypothesis of functional redundancy for marine microbial communities by showing that a shift in the community composition altered the overall functional attributes of communities across different temporal and spatial scales. Our metagenomic monitoring of a coastal northwestern Mediterranean site also revealed that diverse microbial communities harbor a high diversity of potential proteins. Working with all information given by the metagenomes (all reads) rather than relying only on known genes (annotated orthologous genes) was essential for revealing the similarity between taxonomic and functional community compositions. Our finding does not exclude the possibility for a partial redundancy where organisms that share some specific function can coexist when they differ in other ecological requirements. It demonstrates, however, that marine microbial diversity reflects a tremendous diversity of microbial metabolism and highlights the genetic potential yet to be discovered in an ocean of microbes.
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Jacquemot, L., et al. "Therapeutic potential of a new jumbo phage that infects Vibrio coralliilyticus, a widespread coral pathogen." Front. Microbiol.. 9 (2018): 2501.
Résumé: Biological control using bacteriophages is a promising approach for mitigating the devastating effects of coral diseases. Several phages that infect Vibrio coralliilyticus, a widespread coral pathogen, have been isolated, suggesting that this bacterium is permissive to viral infection and is, therefore, a suitable candidate for treatment by phage therapy. In this study, we combined functional and genomic approaches to evaluate the therapeutic potential of BONAISHI, a novel V. coralliilyticus phage, which was isolated from the coral reef in Van Phong Bay (Vietnam). BONAISHI appears to be strictly lytic for several pathogenic strains of V. coralliilyticus and remains infectious over a broad range of environmental conditions. This candidate has an unusually large dsDNA genome (303 kb), with no genes that encode known toxins or implicated in lysogeny control. We identified several proteins involved in host lysis, which may offer an interesting alternative to the use of whole bacteriophages for controlling V. coralliilyticus. A preliminary therapy test showed that adding BONAISHI to an infected culture of Symbiodinium sp. cells reduced the impact of V. coralliilyticus on Symbiodinium sp. photosynthetic activity. This study showed that BONAISHI is able to mitigate V. coralliilyticus infections, making it a good candidate for phage therapy for coral disease.
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Pecoraro, C., et al. "The population genomics of yellowfin tuna (Thunnus albacares) at global geographic scale challenges current stock delineation." Sci Rep. 8 (2018): 13890.
Résumé: Yellowfin tuna, Thunnus albacares, is one of the most important seafood commodities in the world. Despite its great biological and economic importance, conflicting evidence arises from classical genetic and tagging studies concerning the yellowfin tuna population structure at local and global oceanic scales. Access to more powerful and cost effective genetic tools would represent the first step towards resolving the population structure of yellowfin tuna across its distribution range. Using a panel of 939 neutral Single Nucleotide Polymorphisms (SNPs), and the most comprehensive data set of yellowfin samples available so far, we found genetic differentiation among the Atlantic, Indian and Pacific oceans. The genetic stock structure analysis carried out with 33 outlier SNPs, putatively under selection, identified discrete populations within the Pacific Ocean and, for the first time, also within the Atlantic Ocean. Stock assessment approaches that consider genetic differences at neutral and adaptive genomic loci should be routinely implemented to check the status of the yellowfin tuna, prevent illegal trade, and develop more sustainable management measures.
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2017 |
Authier, M., C. Saraux, and C. Péron. "Variable selection and accurate predictions in habitat modelling: a shrinkage approach." Ecography. 40.4 (2017): 549–560.
Résumé: Habitat modelling is increasingly relevant in biodiversity and conservation studies. A typical application is to predict potential zones of specific conservation interest. With many environmental covariates, a large number of models can he investigated but multi-model inference may become impractical. Shrinkage regression overcomes this issue by dealing with the identification and accurate estimation of effect size for prediction. In a Bayesian framework we investigated the use of a shrinkage prior, the Horseshoe, for variable selection in spatial generalized linear models (GLM). As study cases, we considered 5 datasets on small pelagic fish abundance in the Gulf of Lion (Mediterranean Sea, France) and 9 environmental inputs. We compared the predictive performances of a simple kriging model, a full spatial GLM model with independent normal priors for regression coefficients, a full spatial GLM model with a Horseshoe prior for regression coefficients and 2 zero-inflated models (spatial and non-spatial) with a Horseshoe prior. Predictive performances were evaluated by cross validation on a hold-out subset of the data: models with a Horseshoe prior performed best, and the full model with independent normal priors worst. With an increasing number of inputs, extrapolation quickly became pervasive as we tried to predict from novel combinations of covariate values. By shrinking regression coefficients with a Horseshoe prior, only one model needed to be fitted to the data in order to obtain reasonable and accurate predictions, including extrapolations.
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Cowart, D. A., et al. "Investigation of bacterial communities within the digestive organs of the hydrothermal vent shrimp Rimicaris exoculata provide insights into holobiont geographic clustering." PLoS One. 12.3 (2017): e0172543.
Résumé: Prokaryotic communities forming symbiotic relationships with the vent shrimp, Rimicaris exoculata, are well studied components of hydrothermal ecosystems at the Mid-Atlantic Ridge (MAR). Despite the tight link between host and symbiont, the observed lack of spatial genetic structure seen in R. exoculata contrasts with the geographic differentiation detected in specific bacterial ectosymbionts. The geographic clustering of bacterial lineages within a seemingly panmictic host suggests either the presence of finer scale restriction to gene flow not yet detected in the host, horizontal transmission (environmental selection) of its endosymbionts as a consequence of unique vent geochemistry, or vertically transmitted endosymbionts that exhibit genetic differentiation. To identify which hypothesis best fits, we tested whether bacterial assemblages exhibit differentiation across sites or host populations by performing a 16S rRNA metabarcoding survey on R. exoculata digestive prokaryote samples (n = 31) taken from three geochemically distinct vents across MAR: Rainbow, Trans-Atlantic Geotraverse (TAG) and Logatchev. Analysis of communities across two organs (digestive tract, stomach), three molt colors (white, red, black) and three life stages (eggs, juveniles, adults) also provided insights into symbiont transmission mode. Examining both whole communities and operational taxonomic units (OTUs) confirmed the presence of three main epibionts: Epsilonproteobacteria, Mollicutes and Deferribacteres. With these findings, we identified a clear pattern of geographic segregation by vent in OTUs assigned to Epsilonproteobacteria. Additionally, we detected evidence for differentiation among all communities associated to vents and life stages. Overall, results suggest a combination of environmental selection and vertical inheritance of some of the symbiotic lineages.
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Maufroy, A., et al. "Massive increase in the use of drifting Fish Aggregating Devices (dFADs) by tropical tuna purse seine fisheries in the Atlantic and Indian oceans." ICES J. Mar. Sci.. 74.1 (2017): 215–225.
Résumé: Since the mid-1990s, drifting Fish Aggregating Devices (dFADs), artificial floating objects designed to aggregate fish, have become an important mean by which purse seine fleets catch tropical tunas. Mass deployment of dFADs, as well as the massive use of GPS buoys to track dFADs and natural floating objects, has raised serious concerns for the state of tropical tuna stocks and ecosystem functioning. Here, we combine tracks from a large proportion of the French GPS buoys from the Indian and Atlantic oceans with data from observers aboard French and Spanish purse seiners and French logbook data to estimate the total number of dFADs and GPS buoys used within the main fishing grounds of these two oceans over the period 2007-2013. In the Atlantic Ocean, the total number of dFADs increased from 1175 dFADs active in January 2007 to 8575 dFADs in August 2013. In the Indian Ocean, this number increased from 2250 dFADs in October 2007 to 10 300 dFADs in September 2013. In both oceans, at least a fourfold increase in the number of dFADs was observed over the 7-year study period. Though the relative proportion of natural to artificial floating objects varied over space, with some areas such as the Mozambique Channel and areas adjacent to the mouths of the Niger and Congo rivers being characterized by a relatively high percentage of natural objects, in no region do dFADs represent <50% of the floating objects and the proportion of natural objects has dropped over time as dFAD deployments have increased. Globally, this increased dFAD use represents a major change to the pelagic ecosystem that needs to be closely followed in order to assess its impacts and avoid negative ecosystem consequences.
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Oliveros-Ramos, R., et al. "A sequential approach to calibrate ecosystem models with multiple time series data." Progress in Oceanography. 151 (2017): 227–244.
Résumé: When models are aimed to support decision-making, their credibility is essential to consider. Model fitting to observed data is one major criterion to assess such credibility. However, due to the complexity of ecosystem models making their calibration more challenging, the scientific community has given more attention to the exploration of model behavior than to a rigorous comparison to observations. This work highlights some issues related to the comparison of complex ecosystem models to data and proposes a methodology for a sequential multi-phases calibration (or parameter estimation) of ecosystem models. We first propose two criteria to classify the parameters of a model: the model dependency and the time variability of the parameters. Then, these criteria and the availability of approximate initial estimates are used as decision rules to determine which parameters need to be estimated, and their precedence order in the sequential calibration process. The end-to-end (E2E) ecosystem model ROMS-PISCES-OSMOSE applied to the Northern Humboldt Current Ecosystem is used as an illustrative case study. The model is calibrated using an evolutionary algorithm and a likelihood approach to fit time series data of landings, abundance indices and catch at length distributions from 1992 to 2008. Testing different calibration schemes regarding the number of phases, the precedence of the parameters' estimation, and the consideration of time varying parameters, the results show that the multiple-phase calibration conducted under our criteria allowed to improve the model fit.
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Rey-Valette, H., et al. "To measure the impacts of geographic data infrastructures (GDI) and observatories – Application to IDG SIG-LR." Rev. Int. Geomat.. 27.3 (2017): 375–397.
Résumé: This paper analyses the economic effects generated by the SIG-LR Spatial Data Infrastructure (SDI) located in Languedoc-Roussillon region (France). From a literature review and the analysis of the functioning of SDI, a typology of SDI impacts was produced. A survey of 51 members of SIG-LR was used to measure the main effects in terms of employment, productivity gains and saving of inputs. In addition the survey also helped to characterize a beam of qualitative impacts in terms of diversification and quality of services, networking, transparency of information and impact on territorial governance. Knowing that the budget of SIG-LR is 0.9 million euros and that a total of 3.77 million euros of impacts has been measured, a ratio of one euro invested produces an economic impact of four euros within the SIG-LR community and the regional economy.
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2016 |
Capello, M., et al. "Population assessment of tropical tuna based on their associative behavior around floating objects." Sci Rep. 6 (2016): 36415.
Résumé: Estimating the abundance of pelagic fish species is a challenging task, due to their vast and remote habitat. Despite the development of satellite, archival and acoustic tagging techniques that allow the tracking of marine animals in their natural environments, these technologies have so far been underutilized in developing abundance estimations. We developed a new method for estimating the abundance of tropical tuna that employs these technologies and exploits the aggregative behavior of tuna around floating objects (FADs). We provided estimates of abundance indices based on a simulated set of tagged fish and studied the sensitivity of our method to different association dynamics, FAD numbers, population sizes and heterogeneities of the FAD-array. Taking the case study of yellowfin tuna (Thunnus albacares) acoustically-tagged in Hawaii, we implemented our approach on field data and derived for the first time the ratio between the associated and the total population. With more extensive and long-term monitoring of FAD-associated tunas and good estimates of the numbers of fish at FADs, our method could provide fisheries-independent estimates of populations of tropical tuna. The same approach can be applied to obtain population assessments for any marine and terrestrial species that display associative behavior and from which behavioral data have been acquired using acoustic, archival or satellite tags.
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Drouineau, H., et al. "The need for a protean fisheries science to address the degradation of exploited aquatic ecosystems." Aquat. Living Resour.. 29.2 (2016): Unsp-E201.
Résumé: In this introductory paper we highlight key questions that were discussed during the symposium on “Status, functioning and shifts in marine ecosystems” organized by the Association Francaise d'Halieutique (French Association for Fisheries Sciences, Montpellier, France, July 2015). This symposium illustrated that fisheries science is now working at multiple scales and on all dimensions of socio-ecosystems (ecological, political, sociological, and economic), with a great diversity of approaches and taking into account different levels of complexity while acknowledging diverse sources of uncertainty. We argue that we should go one step further and call for a protean fisheries science to address the deteriorated states of aquatic ecosystems caused by anthropogenic pressures. Protean science is constantly evolving to meet emerging issues, while improving its coherence and integration capacity in its complexity. This science must be nourished by multiple approaches and be capable of addressing all organizational scales, from individual fish or fishermen up to the entire ecosystem, include society, its economy and the services it derives from aquatic systems. Such a protean science is required to address the complexity of ecosystem functioning and of the impacts of anthropogenic pressures.
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Monsarrat, S., et al. "A spatially explicit estimate of the prewhaling abundance of the endangered North Atlantic right whale." Conserv. Biol.. 30.4 (2016): 783–791.
Résumé: The North Atlantic right whale (NARW) (Eubalaena glacialis) is one of the world's most threatened whales. It came close to extinction after nearly a millennium of exploitation and currently persists as a population of only approximately 500 individuals. Setting appropriate conservation targets for this species requires an understanding of its historical population size, as a baseline for measuring levels of depletion and progress toward recovery. This is made difficult by the scarcity of records over this species' long whaling history. We sought to estimate the preexploitation population size of the North Atlantic right whale and understand how this species was distributed across its range. We used a spatially explicit data set on historical catches of North Pacific right whales (NPRWs) (Eubalaena japonica) to model the relationship between right whale relative density and the environment during the summer feeding season. Assuming the 2 right whale species select similar environments, we projected this model to the North Atlantic to predict how the relative abundance of NARWs varied across their range. We calibrated these relative abundances with estimates of the NPRW total prewhaling population size to obtain high and low estimates for the overall NARW population size prior to exploitation. The model predicted 9,075-21,328 right whales in the North Atlantic. The current NARW population is thus <6% of the historical North Atlantic carrying capacity and has enormous potential for recovery. According to the model, in June-September NARWs concentrated in 2 main feeding areas: east of the Grand Banks of Newfoundland and in the Norwegian Sea. These 2 areas may become important in the future as feeding grounds and may already be used more regularly by this endangered species than is thought. Una Estimacion Espacialmente Explicita de la Abundancia Previa a la Caza de la Ballena Franca del Atlantico Norte en Peligro de Extincion La ballena franca del Atlantico Norte (BFAN) (Eubalaena glacialis) es una de las ballenas mas amenazadas del mundo. Su extincion estuvo proxima despues de casi un milenio de explotacion y actualmente persiste una poblacion de aproximadamente 500 individuos. El establecimiento de objetivos de conservacion apropiados para esta especie requiere del entendimiento del tamano historico de la poblacion como la linea base para la medida de los niveles de disminucion y el progreso hacia la recuperacion. Esto se dificulta por la escasez de registros sobre la larga historia de la caza de esta especie. Buscamos estimar el tamano poblacional previo a la explotacion de la ballena franca del Atlantico Norte y entender como se distribuia esta especie a lo largo de su extension. Usamos un conjunto de datos espacialmente explicitos sobre las capturas historicas de las ballenas francas del Pacifico Norte (BFPN) (Eubalaena japonica) para modelar la relacion entre la densidad relativa de ballenas francas y el ambiente durante la temporada de verano de alimentacion. Cuando asumimos que las dos especies de ballenas francas seleccionan ambientes similares, pudimos proyectar este modelo hacia el Atlantico Norte y asi poder predecir como la abundancia relativa de las BFAN vario a lo largo de su extension. Calibramos estas abundancias relativas con los estimados del tamano poblacional total previo a la caza de las BFPN y asi obtener estimados altos y bajos para el tamano poblacional general de las BFAN previo a la explotacion. El modelo predijo la existencia de 9, 075 – 21, 328 ballenas francas en el Atlantico Norte. La poblacion actual de BFAN es entonces <6 % a la capacidad de carga historica del Atlantico Norte, por lo que tiene un potencial enorme para la recuperacion. De acuerdo al modelo, entre junio y septiembre, las BFAN se concentraron en dos areas de alimentacion principales: al este de los Grandes Bancos de Terranova y en el Mar de Noruega. Estas dos areas pueden volverse importantes en el futuro como sitios de alimentacion y puede que ya sean usadas por esta especie de manera mas regular de lo que se cree. Resumen
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2015 |
Gaertner, D., and J. - P. Hallier. "Tag shedding by tropical tunas in the Indian Ocean and other factors affecting the shedding rate." Fisheries Research. 163.Si (2015): 98–105.
Résumé: A key objective of the Regional Tuna Tagging Project Indian Ocean was to estimate tag-shedding rates, Type-I (immediate tag shedding) and Type-II (long-term tag shedding). To assess this, a series of double-tagging experiments (26,899 double tags released with 4555 recoveries) were conducted as part of the broader tagging program. After omitting data from tags placed by less experienced taggers, the results of our analyses did not show any evidence that individual differences between taggers (i.e., a tagger effect) impacted estimates of tag-shedding rates. However, it was shown that the probability of retaining the second tag (inserted in the left side of the fish) was larger than retaining the first tag (inserted in the right side, i.e., the side typically tagged in single-tagging experiments). We used a Bayesian model averaging approach to account for model uncertainty in the estimates of the parameters a and L used to calculate the probability of tag retention Q(t)= alpha e-((L t)) for the right tag. The parameter estimates were alpha = 0.993 and L (per year) = 0.030 (skipjack); alpha = 0.972 and L (per year) = 0.040 (yellowfin); and alpha = 0.990 and L (per year) = 0.021 (bigeye). These results agree with estimates obtained by other large-scale tropical tuna tagging projects. We showed that tag loss has a moderate impact on the underestimation of the exploitation rate (bias = 2-6% depending on the tuna species). However, non-reporting leads to a bias of around 7% when using the high reporting rate estimate of purse seiners. Finally, tag shedding (specifically Type-II shedding) modified the individual weights of the samples of recaptures. Consequently, the total instantaneous mortality estimates (Z; calculated from mean times-at-large) were reduced by a range of 1-3%.
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Katsanevakis, S., et al. "Marine conservation challenges in an era of economic crisis and geopolitical instability: The case of the Mediterranean Sea." Marine Policy. 51 (2015): 31–39.
Résumé: In the Mediterranean Sea, socio-economic drivers may accelerate the process of exclusive economic zone (EEZ) declarations. Despite the challenges, the EEZ declarations may provide important opportunities for leveraging change to national policy towards the development of large-scale conservation of marine ecosystems and biodiversity in this zone. Using the Mediterranean Sea as a case study, we aim to highlight a set of best practices that will maximize the potential for the development of large-scale marine conservation initiatives. These include a range of approaches, such as using surrogates to fill the many biodiversity data gaps in the region, further the development of consistent and open access databases, and the utilization of technological developments to improve monitoring, research and surveillance of less accessible and under-explored marine areas. The integration of Mediterranean-wide and local conservation efforts, the facilitation of transboundary collaboration, and the establishment of regional funds for conservation will further enhance opportunities for marine conservation in this region.
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Ruiz, J., et al. "Electronic monitoring trials on in the tropical tuna purse-seine fishery." ICES J. Mar. Sci.. 72.4 (2015): 1201–1213.
Résumé: The difficulty of ensuring adequate statistical coverage of whole fleets is a challenge for the implementation of observer programmes and may reduce the usefulness of the data they obtain for management purposes. This makes it necessary to find cost-effective alternatives. Electronic monitoring (EM) systems are being used in some fisheries as an alternative or a complement to human observers. The objective of this study was to test the use and reliability of EM on the tropical tuna purse-seine fishery. To achieve this objective, seven trips of tuna purse seiners operating in the three Oceans were closely monitored to compare the information provided by EM and on-board observers to determine if EM can reliably document fishing effort, set type, tuna catch, and bycatch. Total tuna catch per set was not significantly different between EM and observer datasets; however, regarding species composition, only main species matched between EM and observers. Success on set-type identification using EM varied between 98.3 and 56.3%, depending on the camera placement. Overall, bycatch species were underestimated by EM, but large bodied species, such as billfishes, were well documented. The analyses in this study showed that EM can be used to determine the fishing effort (number of sets) and total tuna catch as reliably as observers can. Set-type identification also had very promising results, but indicated that refinement of the methods is still needed. To be fully comparable with observer data, improvements for accurately estimating the bycatch will need to be developed in the application and use of the EM system. Operational aspects that need to be improved for an EM programme to be implemented include standardizing installation and on-board catch handling methodology as well as improvements in video technology deployment.
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Young, J. W., et al. "Setting the stage for a global-scale trophic analysis of marine top predators: a multi-workshop review." Rev Fish Biol Fisheries. 25.1 (2015): 261–272.
Résumé: Global-scale studies of marine food webs are rare, despite their necessity for examining and understanding ecosystem level effects of climate variability. Here we review the progress of an international collaboration that compiled regional diet datasets of multiple top predator fishes from the Indian, Pacific and Atlantic Oceans and developed new statistical methods that can be used to obtain a comprehensive ocean-scale understanding of food webs and climate impacts on marine top predators. We loosely define top predators not as species at the apex of the food web, but rather a guild of large predators near the top of the food web. Specifically, we present a framework for world-wide compilation and analysis of global stomach-contents and stable-isotope data of tunas and other large pelagic predatory fishes. To illustrate the utility of the statistical methods, we show an example using yellowfin tuna in a “test” area in the Pacific Ocean. Stomach-contents data were analyzed using a modified (bagged) classification tree approach, which is being prepared as an R statistical software package. Bulk δ15N values of yellowfin tuna muscle tissue were examined using a Generalized Additive Model, after adjusting for spatial differences in the δ15N values of the baseline primary producers predicted by a global coupled ocean circulation-biogeochemical-isotope model. Both techniques in tandem demonstrated the capacity of this approach to elucidate spatial patterns of variations in both forage species and predator trophic positions and have the potential to predict responses to climate change. We believe this methodology could be extended to all marine top predators. Our results emphasize the necessity for quantitative investigations of global-scale datasets when evaluating changes to the food webs underpinning top ocean predators under long-term climatic variability.
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2014 |
Avadí, Á., I. Vázquez-Rowe, and P. Freon. "Eco-efficiency assessment of the Peruvian anchoveta steel and wooden fleets using the LCA+DEA framework." Journal of Cleaner Production. 70 (2014): 118–131.
Résumé: The Peruvian anchoveta fishery is currently targeted by a large fleet featuring a wide range of vessel sizes (segments), with highly variable capacities. In addition, the landings of the industrial fleet are used exclusively by the reduction industry, while those performed by small- and medium-scale vessels are destined mainly for direct human consumption. Despite these differences, the entire fleet is made up of purse seiners that perform similar operations when at sea. Therefore, the main aim of this study is to identify the differences in eco-efficiency between the different fleet segments in order to delve into the potential environmental improvements that could be attained through operational benchmarking. To this end, the combined use of Life Cycle Assessment (LCA) and Data Envelopment Analysis (DEA) was applied to the Peruvian anchoveta fleet. More specifically, a modified 5-step LCA + DEA method, whose particularities are broadly discussed throughout the study, was computed to obtain the desired operational benchmarks and, thereafter, estimate the target environmental gains. Results led to an average efficiency score of 86% throughout the segments, with a total of eight fleet segments out of 13 (62%) operating inefficiently. Nevertheless, no clear pattern was identified through the segments, although certain correlations with stock abundance, fuel use intensity, overcapacity and climatic conditions are discussed. Reduction in material inputs based on operational benchmarks translated into environmental gains that ranged from 26% to 53% for inefficient segments. Finally, it is expected that the findings in this study may aid stakeholders and policy makers when revising fuel use optimisation and overcapacity management strategies.
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Patino, J., et al. "Differences in species-area relationships among the major lineages of land plants: a macroecological perspective." Global Ecology and Biogeography. 23.11 (2014): 1275–1283.
Résumé: AimAlthough the increase in species richness with increasing area is considered one of the few laws in ecology, the role of environmental and taxon-specific features in shaping species-area relationships (SARs) remains controversial. Using 421 land-plant floras covering continents, continental islands and oceanic islands, we investigate whether variations in SAR parameters can be interpreted in terms of differences among lineages in speciation mode and dispersal capacities (TAXON), or of geological history and geographical isolation between continents and islands (GEO). LocationGlobal. MethodsLinear mixed-effects models describing variation in SARs, depending on the factors GEO and TAXON and controlling for differences between realms (REALM) and biomes (BIOME). ResultsThe best random-effect structure included both random slopes and random intercepts for GEO, TAXON, REALM and BIOME. This accounted for 77% of the total variation in species richness, substantially more than the 27% statistically explained by the model with fixed effects only (i.e. the simple SAR). The slopes of the SARs were higher for oceanic islands than for continental islands and continents, and higher in spermatophytes than in pteridophytes and bryophytes. The intercepts largely exhibited the reverse trend. TAXON was included in best-fit models restricted to oceanic and continental islands, but not continents. Analysing each plant lineage separately, the intercept of GEO was only included in the random structure of spermatophytes. Main conclusionsSAR parameters varied considerably depending on geological history and taxon-specific traits. Such differences in SARs among land plants challenge the neutral theory that the accumulation of species richness on islands is controlled exclusively by extrinsic factors. Taxon-specific differences in SARs were, however, confounded by interactions with geological history and geographical isolation. This highlights the importance of applying integrative frameworks that take both environmental context and taxonomic idiosyncrasies into account in SAR analyses.
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Saulquin, B., et al. "Multiscale Event-Based Mining in Geophysical Time Series: Characterization and Distribution of Significant Time-Scales in the Sea Surface Temperature Anomalies Relatively to ENSO Periods from 1985 to 2009." IEEE J. Sel. Top. Appl. Earth Observ. Remote Sens.. 7.8 (2014): 3543–3552.
Résumé: In this paper, one-dimensional (1-D) geophysical time series are regarded as series of significant time-scale events. We combine a wavelet-based analysis with a Gaussian mixture model to extract characteristic time-scales of 486 144 detected events in the Sea Surface Temperature Anomaly (SSTA) observed from satellite at global scale from 1985 to 2009. We retrieve four low-frequency characteristic time-scales of Nino Southern Oscillation (ENSO) in the 1.5- to 7-year range and show their spatial distribution. High-frequency (HF) SSTA event spatial distribution shows a dependency to the ENSO regimes, pointing out that the ENSO signal also involves specific signatures at these time-scales. These fine-scale signatures can hardly be retrieved from global EOF approaches, which tend to exhibit uppermost the low-frequency influence of ENSO onto the SSTA. In particular, we observe at global scale a major increase by 11% of the number of SSTA HF events during Nino periods, with a local maximum of 80% in Europe. The methodology is also used to highlight an ENSO-induced frequency shift during the major 1997-2000 ENSO event in the intertropical Pacific. We observe a clear shift from the high frequencies toward the 3.36-year scale with a maximum shift occurring 2 months before the ENSO maximum of energy at 3.36-year scale.
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Zilius, M., et al. "Feedback Mechanisms Between Cyanobacterial Blooms, Transient Hypoxia, and Benthic Phosphorus Regeneration in Shallow Coastal Environments." Estuaries and Coasts. 37.3 (2014): 680–694.
Résumé: We investigated the dissolved oxygen metabolism of the Curonian Lagoon (Baltic Sea) to assess the relative contributions of pelagic and benthic processes to the development of transient hypoxic conditions in shallow water habitats. Metabolism measurements along with the remote sensing-derived estimates of spatial variability in chlorophyll a were used to evaluate the risk of hypoxia at the whole lagoon level. Our data demonstrate that cyanobacterial blooms strongly inhibit light penetration, resulting in net heterotrophic conditions in which pelagic oxygen demand exceeds benthic oxygen demand by an order of magnitude. The combination of bloom conditions and reduced vertical mixing during calm periods resulted in oxygen depletion of bottom waters and greater sediment nutrient release. The peak of reactive P regeneration (nearly 30 mu mol m(-2) h(-1)) coincided with oxygen depletion in the water column, and resulted in a marked drop of the inorganic N:P ratio (from > 40 to < 5, as molar). Our results suggest a strong link between cyanobacterial blooms, pelagic respiration, hypoxia, and P regeneration, which acts as a feedback in sustaining algal blooms through internal nutrient cycling. Meteorological data and satellite-derived maps of chlorophyll a were used to show that nearly 70 % of the lagoon surface (approximately 1,000 km(2)) is prone to transient hypoxia development when blooms coincide with low wind speed conditions.
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2013 |
Boyer, S., M. Bouvy, and D. Bonnet. "What triggers Acartia species egg production in a Mediterranean lagoon?" Estuarine Coastal and Shelf Science. 117 (2013): 125–135.
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2012 |
Meynard, C. N., et al. "A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes." PLoS One. 7.5 (2012).
Résumé: The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically similar to 100-80 Mya, and most Perciformes families originated 80-50 Mya. Two important clade origin events were detected. The first at 100-80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.
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2011 |
Auguet, J. C., et al. "Seasonal changes of freshwater ammonia-oxidizing archaeal assemblages and nitrogen species in oligotrophic alpine lakes." Appl Environ Microbiol. 77.6 (2011): 1937–1945.
Résumé: The annual changes in the composition and abundance of ammonia-oxidizing archaea (AOA) were analyzed monthly in surface waters of three high mountain lakes within the Limnological Observatory of the Pyrenees (LOOP; northeast Spain) using both 16S rRNA and functional (ammonia monooxygenase gene, amoA) gene sequencing as well as quantitative PCR amplification. The set of biological data was related to changes in nitrogen species and to other relevant environmental variables. The whole archaeal assemblage was dominated by phylotypes closely related to the crenarchaeal 1.1a group (58% +/- 18% of total 16S rRNA gene sequences), and consistent structural changes were detected during the study. Water temperature was the environmental variable that better explained spring, summer, and winter (ice-covered lakes) archaeal assemblage structure. The amoA gene was detected year round, and seasonal changes in amoA gene composition were well correlated with changes in the archaeal 16S rRNA gene pool. In addition, copy numbers of both the specific 1.1a group 16 rRNA and archaeal amoA genes were well correlated, suggesting that most freshwater 1.1a Crenarchaeota had the potential to carry out ammonia oxidation. Seasonal changes in the diversity and abundance of AOA (i.e., amoA) were better explained by temporal changes in ammonium, the substrate for nitrification, and mostly nitrite, the product of ammonia oxidation. Lacustrine amoA gene sequences grouped in coherent freshwater phylogenetic clusters, suggesting that freshwater habitats harbor typical amoA-containing ecotypes, which is different from soils and seas. We observed within the freshwater amoA gene sequence pool a high genetic divergence (translating to up to 32% amino acid divergence) between the spring and the remaining AOA assemblages. This suggests that different AOA ecotypes are adapted to different temporal ecological niches in these lakes.
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Barberan, A., et al. "Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota." Mol Ecol. 20.9 (2011): 1988–1996.
Résumé: Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.
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DRUON, J. - N., et al. "Potential feeding and spawning habitats of Atlantic bluefin tuna in the Mediterranean Sea." Marine Ecology-progress Series. 439 (2011): 223–240.
Résumé: Atlantic bluefin tuna Thunnus thynnus (ABFT) is a fish of high market value which has recently become strongly overexploited, notably in the Mediterranean Sea. This area is an essential habitat for ABFT reproduction and growth. We present here an approach for deriving the daily mapping of potential ABFT feeding and spawning habitats based on satellite-derived sea surface temperature (SST) and chl a concentration. The feeding habitat was mainly derived from the simultaneous occurrence of oceanic fronts of temperature and chl a content while the spawning habitat was mostly inferred from the heating of surface waters. Generally, higher chl a contents were found to be preferred for the feeding habitat and a minimum SST value was found for the spawning habitat. Both habitats were defined by the presence of relevant oceanographic features and are therefore potential and functionally-linked habitats. This approach provides, for the first time, a synoptic view of the potential ABFT habitats in the Mediterranean Sea. The model performs well in areas where both satellite data and ABFT observations are available, as 80% of presence data are in the vicinity of potential habitats. The computed monthly, seasonal and annual maps of potential feeding and spawning habitat of ABFT from 2003 to 2009 are in good agreement with current knowledge on ABFT. Overall, the habitat size of ABFT is about 6% of the Mediterranean Sea surface. The results displayed a strong seasonality in habitat size and locations as well as high year-to-year variations (30 to 60%), particularly for the potential spawning habitat, which is key information for evaluating the utility of ABFT Marine Protected Areas in the Mediterranean Sea.
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2010 |
Jouffre, D., et al. "Estimating EAF indicators from scientific trawl surveys: theoretical and practical concerns." Ices Journal of Marine Science. 67.4 (2010): 796–806.
Résumé: Under the context of an ecosystem approach to fisheries (EAF), there is keen interest in providing insights into the evolution of exploited ecosystems using simple ecosystem indicators. Many nations have long-term scientific research surveys, originally driven by conventional approaches in fisheries assessment and management. The aim of this study is to address the practical concerns linked to current objectives of monitoring simple EAF indicators, using data from surveys that were not historically designed for the purpose. Based on the results of an expert survey designed to collect expert knowledge on research surveys from scientists working on different ecosystems worldwide, a list of challenges faced during indicator estimation is highlighted, along with associated concerns and constraints. The work provides additional information useful in the interpretation of the results obtained on the state and trends of ecosystems using EAF indicators by the IndiSeas WG. Further, the related discussion provides potential pathways that could be useful for future research and development aiming to improve the ecosystem indicator approach in the operational context of EAF. The question of the utility for EAF of using historical dataseries of scientific trawl series is also discussed. Such long-term series are concluded to be useful, that they are even inescapable (since the past cannot be resamplied), and that EAF therefore brings a supplementary reason for continuing such monitoring and to incorporate new insights in how research surveys may be conducted.
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Lliros, M., et al. "Vertical distribution of ammonia-oxidizing crenarchaeota and methanogens in the epipelagic waters of Lake Kivu (Rwanda-Democratic Republic of the Congo)." Appl Environ Microbiol. 76.20 (2010): 6853–6863.
Résumé: Four stratified basins in Lake Kivu (Rwanda-Democratic Republic of the Congo) were sampled in March 2007 to investigate the abundance, distribution, and potential biogeochemical role of planktonic archaea. We used fluorescence in situ hybridization with catalyzed-reported deposition microscopic counts (CARD-FISH), denaturing gradient gel electrophoresis (DGGE) fingerprinting, and quantitative PCR (qPCR) of signature genes for ammonia-oxidizing archaea (16S rRNA for marine Crenarchaeota group 1.1a [MCG1] and ammonia monooxygenase subunit A [amoA]). Abundance of archaea ranged from 1 to 4.5% of total DAPI (4',6-diamidino-2-phenylindole) counts with maximal concentrations at the oxic-anoxic transition zone ( approximately 50-m depth). Phylogenetic analysis of the archaeal planktonic community revealed a higher level of richness of crenarchaeal 16S rRNA gene sequences (21 of the 28 operational taxonomic units [OTUs] identified [75%]) over euryarchaeotal ones (7 OTUs). Sequences affiliated with the kingdom Euryarchaeota were mainly recovered from the anoxic water compartment and mostly grouped into methanogenic lineages (Methanosarcinales and Methanocellales). In turn, crenarchaeal phylotypes were recovered throughout the sampled epipelagic waters (0- to 100-m depth), with clear phylogenetic segregation along the transition from oxic to anoxic water masses. Thus, whereas in the anoxic hypolimnion crenarchaeotal OTUs were mainly assigned to the miscellaneous crenarchaeotic group, the OTUs from the oxic-anoxic transition and above belonged to Crenarchaeota groups 1.1a and 1.1b, two lineages containing most of the ammonia-oxidizing representatives known so far. The concomitant vertical distribution of both nitrite and nitrate maxima and the copy numbers of both MCG1 16S rRNA and amoA genes suggest the potential implication of Crenarchaeota in nitrification processes occurring in the epilimnetic waters of the lake.
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Walker, E., and N. Bez. "A pioneer validation of a state-space model of vessel trajectories (VMS) with observers' data." Ecological Modelling. 221 (2010): 2008–2017.
Résumé: In the context of the expansion of animal tracking and bio-logging, state-space models have been developed with the objective to characterise animals' trajectories and to understand the factors controlling their behaviour. In the fisheries community, the electronic tagging of vessels commonly designated by Vessel Monitoring Systems (VMS) is developing and provides a new insight for the understanding, the analysis and the modelling of the trajectories of vessels and their prospecting behaviour. VMS data are thus a clue for the proper definition of fishing effort which remains a fundamental parameter of tuna stock assessments. In this context, we used the VMS (recording of hourly positions) of the French tropical tuna purse-seiners operating in the Indian Ocean to characterise three types of movement (states) on the VMS trajectories (stillness, tracking, and cruising). Based on empirical evidences, and on the regular frequency of VMS acquisition, this was achieved by the development of a Bayesian Hidden Markov model for the speeds and turning angles derived from the hourly steps of the trajectories. In a second phase, states were related to activities disentangling stillness into fishing or stop at sea. Finally the quality of the model performances was rigorously quantified thanks to observers' data. Confronting model prediction and true activities allowed estimating that 10% of the hourly steps were misclassified. The assumptions and model' choices are discussed, highlighting the fact that VMS data and observers' data having different time resolutions, the effective use of validating data was troublesome. However, without validation, these analyses remain speculative. The validation part of this work represents an important step for the operational use of state-space models in ecology in the broad sense (predators' tracking data, e.g. birds or mammals trajectories).
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2008 |
Auguet, J. C., et al. "Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark." Environ Microbiol. 10.10 (2008): 2527–2536.
Résumé: We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.
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