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Auteur (up) Arnaud-Haond, S.; Moalic, Y.; Barnabé, C.; Ayala, F.J.; Tibayrenc, M. url  doi
openurl 
  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 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 (up) ARNAUD-HAOND, S.; MOALIC, Y.; HERNANDEZ-GARCIA, E.; EGUILUZ, V.M.; ALBERTO, F.; SERRAO, E.A.; DUARTE, C.M. url  openurl
  Titre Disentangling the Influence of Mutation and Migration in Clonal Seagrasses Using the Genetic Diversity Spectrum for Microsatellites Type Article scientifique
  Année 2014 Publication Revue Abrégée Journal Of Heredity  
  Volume 105 Numéro 4 Pages 532-541  
  Mots-Clés clonality; genetic divergence; Genetic Diversity Spectrum; microsatellites; Seagrass; stepwise mutation  
  Résumé The recurrent lack of isolation by distance reported at regional scale in seagrass species was recently suggested to stem from stochastic events of large-scale dispersal. We explored the usefulness of phylogenetic information contained in microsatellite loci to test this hypothesis by using the Genetic Diversity Spectrum (GDS) on databases containing, respectively, 7 and 9 microsatellites genotypes for 1541 sampling units of Posidonia oceanica and 1647 of Cymodocea nodosa. The simultaneous increase of microsatellite and geographic distances that emerges reveals a coherent pattern of isolation by distance in contrast to the chaotic pattern previously described using allele frequencies, in particular, for the long-lived P. oceanica. These results suggest that the lack of isolation by distance, rather than the resulting from rare events of large-scale dispersal, reflects at least for some species a stronger influence of mutation over migration at the scale of the distribution range. The global distribution of genetic polymorphism may, therefore, result predominantly from ancient events of step-by-step (re)colonization followed by local recruitment and clonal growth, rather than contemporary gene flow. The analysis of GDS appears useful to unravel the evolutionary forces influencing the dynamics and evolution at distinct temporal and spatial scales by accounting for phylogenetic information borne by microsatellites, under an appropriate mutation model. This finding adds nuance to the generalization of the influence of large-scale dispersal on the dynamics of seagrasses.  
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  ISSN 0022-1503 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1138  
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Auteur (up) Ashiq Ur Rahman, M.; Ajmal Khan, S.; Lyla, P.S.; Durand, J.-D. url  doi
openurl 
  Titre First record of Osteomugil perusii (Teleostei: Mugilidae) in Indian waters Type Article scientifique
  Année 2014 Publication Revue Abrégée Marine Biodiversity Records  
  Volume 7 Numéro Pages null-null  
  Mots-Clés India; Indo-West Pacific; Kochi; Mugilidae; Parangipettai; long-finned mullet; record  
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  ISSN 1755-2672 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 594  
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Auteur (up) Avadi, A.; Freon, P.; Quispe, I. url  doi
openurl 
  Titre Environmental assessment of Peruvian anchoveta food products : is less refined better ? Type Article scientifique
  Année 2014 Publication Revue Abrégée International Journal of Life Cycle Assessment  
  Volume 19 Numéro 6 Pages 1276-1293  
  Mots-Clés Cold chain; Engraulis ringens; Frozen, canned and cured fish; Life cycle assessment; Peru  
  Résumé Life cycle assessments (LCAs) of various anchovy (anchoveta) direct human consumption products processed in Peru were carried out, to evaluate their relative environmental performance as alternative products to enhance nutrition of communities with low access to fish products in the country. LCA was carried out for fresh, frozen, canned, salted and cured anchoveta products, both at plant gate and featuring local and national distribution over non-refrigerated, chilled and fully refrigerated distribution chain. The functional unit used was 1 kg of fish in the final product. Results demonstrate that, in environmental terms, more-refined products (cured and canned anchoveta products) represent a much higher burden than less- refined products (fresh, frozen and salted). Although this is a likely result, the magnitude of this difference (4 to 27 times when expressed as an environmental single score) is higher than expected and had not been quantified before for salted and cured products, as far as we know. This difference is mainly due to differences in energy consumption between types of products. Furthermore, cured and salted products feature larger biotic resource use, when calculated based on the whole fish equivalent, due to higher processing losses/discards. The relevance of taking into account the different transportation and storage needs is highlighted. For those products requiring refrigerated transportation and storage, over a national distribution chain, those activities increase the overall environmental impacts of the products by 55 % (fresh chilled) to 67 % (frozen). However, such an increase does not worsen the environmental performance of fresh and frozen products in comparison to the energy-intensive canned and cured products. It is concluded that a more sustainability-oriented analysis, including the social and economic pillars of sustainability, is required towards decision-making involving promotion of either product for addressing nutritional deficiencies in Peru.  
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  ISSN 0948-3349 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1144  
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Auteur (up) Avadi, A.; Freon, P.; Tam, J. url  doi
openurl 
  Titre Coupled ecosystem/supply chain modelling of fish products from sea to shelf : the Peruvian anchoveta case Type Article scientifique
  Année 2014 Publication Revue Abrégée Plos One  
  Volume 9 Numéro 7 Pages  
  Mots-Clés  
  Résumé Sustainability assessment of food supply chains is relevant for global sustainable development. A framework is proposed for analysing fishfood (fish products for direct human consumption) supply chains with local or international scopes. It combines a material flow model (including an ecosystem dimension) of the supply chains, calculation of sustainability indicators (environmental, socio-economic, nutritional), and finally multi-criteria comparison of alternative supply chains (e.g. fates of landed fish) and future exploitation scenarios. The Peruvian anchoveta fishery is the starting point for various local and global supply chains, especially via reduction of anchoveta into fishmeal and oil, used worldwide as a key input in livestock and fish feeds. The Peruvian anchoveta supply chains are described, and the proposed methodology is used to model them. Three scenarios were explored: status quo of fish exploitation (Scenario 1), increase in anchoveta landings for food (Scenario 2), and radical decrease in total anchoveta landings to allow other fish stocks to prosper (Scenario 3). It was found that Scenario 2 provided the best balance of sustainability improvements among the three scenarios, but further refinement of the assessment is recommended. In the long term, the best opportunities for improving the environmental and socio-economic performance of Peruvian fisheries are related to sustainability-improving management and policy changes affecting the reduction industry. Our approach provides the tools and quantitative results to identify these best improvement opportunities.  
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  ISSN 1932-6203 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1145  
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