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Auteur Cardiec, F.; Bertrand, S.; Witt, M.J.; Metcalfe, K.; Godley, B.J.; McClellan, C.; Vilela, R.; Parnell, R.J.; Loc’h, F. le url  doi
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  Titre “Too Big To Ignore”: A feasibility analysis of detecting fishing events in Gabonese small-scale fisheries Type Article scientifique
  Année 2020 Publication Revue Abrégée Plos One  
  Volume 15 Numéro 6 Pages (down) e0234091  
  Mots-Clés Animal behavior; Animal tagging; Boats; Engines; Fish; Fisheries; Gabon; Hidden Markov models  
  Résumé In many developing countries, small-scale fisheries provide employment and important food security for local populations. To support resource management, the description of the spatiotemporal extent of fisheries is necessary, but often poorly understood due to the diffuse nature of effort, operated from numerous small wooden vessels. Here, in Gabon, Central Africa, we applied Hidden Markov Models to detect fishing patterns in seven different fisheries (with different gears) from GPS data. Models were compared to information collected by on-board observers (7 trips) and, at a larger scale, to a visual interpretation method (99 trips). Models utilizing different sampling resolutions of GPS acquisition were also tested. Model prediction accuracy was high with GPS data sampling rates up to three minutes apart. The minor loss of accuracy linked to model classification is largely compensated by the savings in time required for analysis, especially in a context of nations or organizations with limited resources. This method could be applied to larger datasets at a national or international scale to identify and more adequately manage fishing effort.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2815  
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Auteur Trombetta, T.; Vidussi, F.; Mas, S.; Parin, D.; Simier, M.; Mostajir, B. url  doi
openurl 
  Titre Water temperature drives phytoplankton blooms in coastal waters Type Article scientifique
  Année 2019 Publication Revue Abrégée Plos One  
  Volume 14 Numéro 4 Pages (down) e0214933  
  Mots-Clés Artificial light; Biomass; Food web structure; Phytoplankton; Salinity; Spring; Surface water; Wind  
  Résumé Phytoplankton blooms are an important, widespread phenomenon in open oceans, coastal waters and freshwaters, supporting food webs and essential ecosystem services. Blooms are even more important in exploited coastal waters for maintaining high resource production. However, the environmental factors driving blooms in shallow productive coastal waters are still unclear, making it difficult to assess how environmental fluctuations influence bloom phenology and productivity. To gain insights into bloom phenology, Chl a fluorescence and meteorological and hydrological parameters were monitored at high-frequency (15 min) and nutrient concentrations and phytoplankton abundance and diversity, were monitored weekly in a typical Mediterranean shallow coastal system (Thau Lagoon). This study was carried out from winter to late spring in two successive years with different climatic conditions: 2014/2015 was typical, but the winter of 2015/2016 was the warmest on record. Rising water temperature was the main driver of phytoplankton blooms. However, blooms were sometimes correlated with winds and sometimes correlated with salinity, suggesting nutrients were supplied by water transport via winds, saltier seawater intake, rain and water flow events. This finding indicates the joint role of these factors in determining the success of phytoplankton blooms. Furthermore, interannual variability showed that winter water temperature was higher in 2016 than in 2015, resulting in lower phytoplankton biomass accumulation in the following spring. Moreover, the phytoplankton abundances and diversity also changed: cyanobacteria (< 1 μm), picoeukaryotes (< 1 μm) and nanoeukaryotes (3–6 μm) increased to the detriment of larger phytoplankton such as diatoms. Water temperature is a key factor affecting phytoplankton bloom dynamics in shallow productive coastal waters and could become crucial with future global warming by modifying bloom phenology and changing phytoplankton community structure, in turn affecting the entire food web and ecosystem services.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2565  
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Auteur Henckel, L.; Meynard, C.N.; Devictor, V.; Mouquet, N.; Bretagnolle, V. doi  openurl
  Titre On the relative importance of space and environment in farmland bird community assembly Type Article scientifique
  Année 2019 Publication Revue Abrégée PLoS One  
  Volume 14 Numéro 3 Pages (down) e0213360  
  Mots-Clés beta diversity; dispersal; ecology; habitat; landscape; metacommunity structure; model; patterns; scale; skylarks alauda arvensis  
  Résumé The relative contribution of ecological processes in shaping metacommunity dynamics in heavily managed landscapes is still unclear. Here we used two complementary approaches to disentangle the role of environment and spatial effect in farmland bird community assembly in an intensive agro-ecosystem. We hypothesized that the interaction between habitat patches and dispersal should play a major role in such unstable and unpredictable environments. First, we used a metacommunity patterns analysis to characterize species co-occurrences and identify the main drivers of community assembly; secondly, variation partitioning was used to disentangle environmental and geographical factors (such as dispersal limitation) on community structure and composition. We used high spatial resolution data on bird community structure and composition distributed among 260 plots in an agricultural landscape. Species were partitioned into functional classes, and point count stations were classified according to landscape characteristics before applying metacommunity and partitioning analyses within each. Overall we could explain around 20% of the variance in species composition in our system, revealing that stochasticity remains very important at this scale. However, this proportion varies depending on the scale of analysis, and reveals potentially important contributions of environmental filtering and dispersal. These conclusions are further reinforced when the analysis was deconstructed by bird functional classes or by landscape habitat classes, underlining trait-related filters, thus reinforcing the idea that wooded areas in these agroecosystems may represent important sources for a specific group of bird species. Our analysis shows that deconstructing the species assemblages into separate functional groups and types of landscapes, along with a combination of analysis strategies, can help in understanding the mechanisms driving community assembly.  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2548  
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Auteur Rabearisoa, N.; Sabarros, P. S.; Romanov, E. V.; Lucas, V.; Bach, P. url  doi
openurl 
  Titre Toothed whale and shark depredation indicators: A case study from the Reunion Island and Seychelles pelagic longline fisheries Type Article scientifique
  Année 2018 Publication Revue Abrégée PLOS ONE  
  Volume 13 Numéro 8 Pages (down) e0202037  
  Mots-Clés Indian Ocean; Seychelles; Sharks; Tuna; Fisheries; Economics; Killer whales; Whales  
  Résumé Depredation in marine ecosystems is defined as the damage or removal of fish or bait from fishing gear by predators. Depredation raises concerns about the conservation of species involved, fisheries yield and profitability, and reference points based on stock assessment of depredated species. Therefore, the development of accurate indicators to assess the impact of depredation is needed. Both the Reunion Island and the Seychelles archipelago pelagic longline fisheries targeting swordfish (Xiphias gladius) and tuna (Thunnus spp.) are affected by depredation from toothed whales and pelagic sharks. In this study, we used fishery data collected between 2004 and 2015 to propose depredation indicators and to assess depredation levels in both fisheries. For both fisheries, the interaction rate (depredation occurrence) was significantly higher for shark compared to toothed whale depredation. However, when depredation occurred, toothed whale depredation impact was significantly higher than shark depredation impact, with higher depredation per unit effort (number of fish depredated per 1000 hooks) and damage rate (proportion of fish depredated per depredated set). The gross depredation rate in the Seychelles was 18.3%. A slight increase of the gross depredation rate was observed for the Reunion Island longline fleet from 2011 (4.1% in 2007–2010 and 4.4% in 2011–2015). Economic losses due to depredation were estimated by using these indicators and published official statistics. A loss of 0.09 EUR/hook due to depredation was estimated for the Reunion Island longline fleet, and 0.86 EUR/hook for the Seychelles. These results suggest a southward decreasing toothed whale and shark depredation gradient in the southwest Indian Ocean. Seychelles depredation levels are among the highest observed in the world revealing this area as a “hotspot” of interaction between pelagic longline fisheries and toothed whales. This study also highlights the need for a set of depredation indicators to allow for a global comparison of depredation rates among various fishing grounds worldwide.  
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Auteur Debieu, M.; Sine, B.; Passot, S.; Grondin, A.; Akata, E.; Gangashetty, P.; Vadez, V.; Gantet, P.; Fonceka, D.; Cournac, L.; Hash, C.T.; Kane, N.A.; Vigouroux, Y.; Laplaze, L. doi  openurl
  Titre Response to early drought stress and identification of QTLs controlling biomass production under drought in pearl millet Type Article scientifique
  Année 2018 Publication Revue Abrégée PLoS One  
  Volume 13 Numéro 10 Pages (down) e0201635  
  Mots-Clés arabidopsis; association; burrows-wheeler transform; l. r. br.; nitrite reductase; read alignment; roots; siroheme; trait; yield  
  Résumé Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress.  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2442  
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