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Auteur Arnaud-Haond, S.; Moalic, Y.; Barnabé, C.; Ayala, F.J.; Tibayrenc, M.
Titre Discriminating Micropathogen Lineages and Their Reticulate Evolution through Graph Theory-Based Network Analysis: The Case of Trypanosoma cruzi, the Agent of Chagas Disease Type Article scientifique
Année (down) 2014 Publication Revue Abrégée PLoS ONE
Volume 9 Numéro 8 Pages
Mots-Clés
Résumé Micropathogens (viruses, bacteria, fungi, parasitic protozoa) share a common trait, which is partial clonality, with wide variance in the respective influence of clonality and sexual recombination on the dynamics and evolution of taxa. The discrimination of distinct lineages and the reconstruction of their phylogenetic history are key information to infer their biomedical properties. However, the phylogenetic picture is often clouded by occasional events of recombination across divergent lineages, limiting the relevance of classical phylogenetic analysis and dichotomic trees. We have applied a network analysis based on graph theory to illustrate the relationships among genotypes of Trypanosoma cruzi, the parasitic protozoan responsible for Chagas disease, to identify major lineages and to unravel their past history of divergence and possible recombination events. At the scale of T. cruzi subspecific diversity, graph theory-based networks applied to 22 isoenzyme loci (262 distinct Multi-Locus-Enzyme-Electrophoresis -MLEE) and 19 microsatellite loci (66 Multi-Locus-Genotypes -MLG) fully confirms the high clustering of genotypes into major lineages or “near-clades”. The release of the dichotomic constraint associated with phylogenetic reconstruction usually applied to Multilocus data allows identifying putative hybrids and their parental lineages. Reticulate topology suggests a slightly different history for some of the main “near-clades”, and a possibly more complex origin for the putative hybrids than hitherto proposed. Finally the sub-network of the near-clade T. cruzi I (28 MLG) shows a clustering subdivision into three differentiated lesser near-clades (“Russian doll pattern”), which confirms the hypothesis recently proposed by other investigators. The present study broadens and clarifies the hypotheses previously obtained from classical markers on the same sets of data, which demonstrates the added value of this approach. This underlines the potential of graph theory-based network analysis for describing the nature and relationships of major pathogens, thereby opening stimulating prospects to unravel the organization, dynamics and history of major micropathogen lineages.
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Numéro d'Appel LL @ pixluser @ collection 390
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Auteur Darnaude, A.M.; Sturrock, A.; Trueman, C.N.; Mouillot, D.; Eimf; Campana, S.E.; Hunter, E.
Titre Listening In on the Past: What Can Otolith δ18O Values Really Tell Us about the Environmental History of Fishes? Type Article scientifique
Année (down) 2014 Publication Revue Abrégée PLoS ONE
Volume 9 Numéro 10 Pages
Mots-Clés
Résumé Oxygen isotope ratios from fish otoliths are used to discriminate marine stocks and reconstruct past climate, assuming that variations in otolith δ18O values closely reflect differences in temperature history of fish when accounting for salinity induced variability in water δ18O. To investigate this, we exploited the environmental and migratory data gathered from a decade using archival tags to study the behaviour of adult plaice (Pleuronectes platessa L.) in the North Sea. Based on the tag-derived monthly distributions of the fish and corresponding temperature and salinity estimates modelled across three consecutive years, we first predicted annual otolith δ18O values for three geographically discrete offshore sub-stocks, using three alternative plausible scenarios for otolith growth. Comparison of predicted vs. measured annual δ18O values demonstrated >96% correct prediction of sub-stock membership, irrespective of the otolith growth scenario. Pronounced inter-stock differences in δ18O values, notably in summer, provide a robust marker for reconstructing broad-scale plaice distribution in the North Sea. However, although largely congruent, measured and predicted annual δ18O values of did not fully match. Small, but consistent, offsets were also observed between individual high-resolution otolith δ18O values measured during tag recording time and corresponding δ18O predictions using concomitant tag-recorded temperatures and location-specific salinity estimates. The nature of the shifts differed among sub-stocks, suggesting specific vital effects linked to variation in physiological response to temperature. Therefore, although otolith δ18O in free-ranging fish largely reflects environmental temperature and salinity, we counsel prudence when interpreting otolith δ18O data for stock discrimination or temperature reconstruction until the mechanisms underpinning otolith δ18O signature acquisition, and associated variation, are clarified.
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Numéro d'Appel MARBEC @ alain.herve @ collection 1195
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Auteur Rishworth, G.M.; Tremblay, Y.; Green, D.B.; Connan, M.; Pistorius, P.A.
Titre Drivers of Time-Activity Budget Variability during Breeding in a Pelagic Seabird Type Article scientifique
Année (down) 2014 Publication Revue Abrégée PLoS ONE
Volume 9 Numéro 12 Pages
Mots-Clés
Résumé During breeding, animal behaviour is particularly sensitive to environmental and food resource availability. Additionally, factors such as sex, body condition, and offspring developmental stage can influence behaviour. Amongst seabirds, behaviour is generally predictably affected by local foraging conditions and has therefore been suggested as a potentially useful proxy to indicate prey state. However, besides prey availability and distribution, a range of other variables also influence seabird behavior, and these need to be accounted for to increase the signal-to-noise ratio when assessing specific characteristics of the environment based on behavioural attributes. The aim of this study was to use continuous, fine-scale time-activity budget data from a pelagic seabird (Cape gannet, Morus capensis) to determine the influence of intrinsic (sex and body condition) and extrinsic (offspring and time) variables on parent behaviour during breeding. Foraging trip duration and chick provisioning rates were clearly sex-specific and associated with chick developmental stage. Females made fewer, longer foraging trips and spent less time at the nest during chick provisioning. These sex-specific differences became increasingly apparent with chick development. Additionally, parents in better body condition spent longer periods at their nests and those which returned later in the day had longer overall nest attendance bouts. Using recent technological advances, this study provides new insights into the foraging behaviour of breeding seabirds, particularly during the post-guarding phase. The biparental strategy of chick provisioning revealed in this study appears to be an example where the costs of egg development to the female are balanced by paternal-dominated chick provisioning particularly as the chick nears fledging.
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1202
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Auteur Rossi, F.; Gribsholt, B.; Gazeau, F.; Di Santo, V.; Middelburg, J.J.
Titre Complex Effects of Ecosystem Engineer Loss on Benthic Ecosystem Response to Detrital Macroalgae Type Article scientifique
Année (down) 2013 Publication Revue Abrégée PLoS One
Volume 8 Numéro 6 Pages
Mots-Clés Community structure; assemblages; biodiversity; carbon flow; diversity; experiment; field; impact; marine-sediments; species richness; stability
Résumé Ecosystem engineers change abiotic conditions, community assembly and ecosystem functioning. Consequently, their loss may modify thresholds of ecosystem response to disturbance and undermine ecosystem stability. This study investigates how loss of the bioturbating lugworm Arenicola marina modifies the response to macroalgal detrital enrichment of sediment biogeochemical properties, microphytobenthos and macrofauna assemblages. A field manipulative experiment was done on an intertidal sandflat (Oosterschelde estuary, The Netherlands). Lugworms were deliberately excluded from 1x m sediment plots and different amounts of detrital Ulva (0, 200 or 600 g Wet Weight) were added twice. Sediment biogeochemistry changes were evaluated through benthic respiration, sediment organic carbon content and porewater inorganic carbon as well as detrital macroalgae remaining in the sediment one month after enrichment. Microalgal biomass and macrofauna composition were measured at the same time. Macroalgal carbon mineralization and transfer to the benthic consumers were also investigated during decomposition at low enrichment level (200 g WW). The interaction between lugworm exclusion and detrital enrichment did not modify sediment organic carbon or benthic respiration. Weak but significant changes were instead found for porewater inorganic carbon and microalgal biomass. Lugworm exclusion caused an increase of porewater carbon and a decrease of microalgal biomass, while detrital enrichment drove these values back to values typical of lugworm-dominated sediments. Lugworm exclusion also decreased the amount of macroalgae remaining into the sediment and accelerated detrital carbon mineralization and CO2 release to the water column. Eventually, the interaction between lugworm exclusion and detrital enrichment affected macrofauna abundance and diversity, which collapsed at high level of enrichment only when the lugworms were present. This study reveals that in nature the role of this ecosystem engineer may be variable and sometimes have no or even negative effects on stability, conversely to what it should be expected based on current research knowledge.
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Langue English Langue du Résumé Titre Original
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ISSN 1932-6203 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 513
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Auteur Joo, R.; Bertrand, S.; Tam, J.; Fablet, R.
Titre Hidden Markov Models: The Best Models for Forager Movements? Type Article scientifique
Année (down) 2013 Publication Revue Abrégée PLoS ONE
Volume 8 Numéro 8 Pages
Mots-Clés
Résumé One major challenge in the emerging field of movement ecology is the inference of behavioural modes from movement patterns. This has been mainly addressed through Hidden Markov models (HMMs). We propose here to evaluate two sets of alternative and state-of-the-art modelling approaches. First, we consider hidden semi-Markov models (HSMMs). They may better represent the behavioural dynamics of foragers since they explicitly model the duration of the behavioural modes. Second, we consider discriminative models which state the inference of behavioural modes as a classification issue, and may take better advantage of multivariate and non linear combinations of movement pattern descriptors. For this work, we use a dataset of \textgreater200 trips from human foragers, Peruvian fishermen targeting anchovy. Their movements were recorded through a Vessel Monitoring System (∼1 record per hour), while their behavioural modes (fishing, searching and cruising) were reported by on-board observers. We compare the efficiency of hidden Markov, hidden semi-Markov, and three discriminative models (random forests, artificial neural networks and support vector machines) for inferring the fishermen behavioural modes, using a cross-validation procedure. HSMMs show the highest accuracy (80%), significantly outperforming HMMs and discriminative models. Simulations show that data with higher temporal resolution, HSMMs reach nearly 100% of accuracy. Our results demonstrate to what extent the sequential nature of movement is critical for accurately inferring behavioural modes from a trajectory and we strongly recommend the use of HSMMs for such purpose. In addition, this work opens perspectives on the use of hybrid HSMM-discriminative models, where a discriminative setting for the observation process of HSMMs could greatly improve inference performance.
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Numéro d'Appel LL @ pixluser @ collection 260
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