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Auteur KIVELA, M.; ARNAUD-HAOND, S.; SARAMAKI, J.
Titre EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics Type Article scientifique
Année 2015 Publication Revue Abrégée Molecular Ecology Resources
Volume (down) 15 Numéro 1 Pages 117-122
Mots-Clés Biogeography; biological communities; graph theory; microbial ecology; network analysis; population genetics
Résumé The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.
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ISSN 1755-098x ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1119
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Auteur Evans, S.M.; McKenna, C.; Simpson, S.D.; Tournois, J.; Genner, M.J.
Titre Patterns of species range evolution in Indo-Pacific reef assemblages reveal the Coral Triangle as a net source of transoceanic diversity Type Article scientifique
Année 2016 Publication Revue Abrégée Biol. Lett.
Volume (down) 12 Numéro 6 Pages 20160090
Mots-Clés Bayesian skyline plot; biogeography; climate change; coral reef; fishes global patterns; marine biodiversity; ocean; phylogeography; refugia; species distributions
Résumé The Coral Triangle in the Indo-Pacific is a region renowned for exceptional marine biodiversity. The area could have acted as a 'centre of origin' where speciation has been prolific or a 'centre of survival' by providing refuge during major environmental shifts such as sea-level changes. The region could also have acted as a 'centre of accumulation' for species with origins outside of the Coral Triangle, owing to it being at a central position between the Indian and Pacific oceans. Here, we investigated support for these hypotheses using population-level DNA sequence-based reconstructions of the range evolution of 45 species (314 populations) of Indo-Pacific reef-associated organisms. Our results show that populations undergoing the most ancient establishment were significantly more likely to be closer to the centre of the Coral Triangle than to peripheral locations. The data are consistent with the Coral Triangle being a net source of coral-reef biodiversity for the Indo-Pacific region, suggesting that the region has acted primarily as a centre of survival, a centre of origin or both. These results provide evidence of how a key location can influence the large-scale distributions of biodiversity over evolutionary timescales.
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Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 1744-9561 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1694
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Auteur Kadarusman; Sugeha, H.Y.; Pouyaud, L.; Hocdé, R.; Hismayasari, I.B.; Gunaisah, E.; Widiarto, S.B.; Arafat, G.; Widyasari, F.; Mouillot, D.; Paradis, E.
Titre A thirteen-million-year divergence between two lineages of Indonesian coelacanths Type Article scientifique
Année 2020 Publication Revue Abrégée Sci Rep
Volume (down) 10 Numéro 1 Pages 192
Mots-Clés biogeography; halmahera; latimeria-chalumnae; living fossils; mindanao; multiple sequence alignment; phylogenies; population; speciation; tectonic evolution
Résumé Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these 'living fossils' using new molecular data, including the possibility of 'cryptic' species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.
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Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 2045-2322 ISBN Médium
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Notes WOS:000511157800002 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2737
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Auteur Escalas, A.; Hale, L.; Voordeckers, J.W.; Yang, Y.; Firestone, M.K.; Alvarez-Cohen, L.; Zhou, J.
Titre Microbial functional diversity: From concepts to applications Type Article scientifique
Année 2019 Publication Revue Abrégée Ecol. Evol.
Volume (down) 9 Numéro 20 Pages 12000-12016
Mots-Clés bacterial communities; biodiversity; biogeography; differentiation; functional diversity; functional traits; genes; microbial communities; niche space; redundancy; soil; taxonomy; theoretical frameworks of diversity; trait-based ecology; traits
Résumé Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.
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Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 2045-7758 ISBN Médium
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Notes WOS:000488395500001 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2649
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Auteur Pommier, T.; Douzery, E.J.P.; Mouillot, D.
Titre Environment drives high phylogenetic turnover among oceanic bacterial communities Type Article scientifique
Année 2012 Publication Revue Abrégée Biol. Lett.
Volume (down) 8 Numéro 4 Pages 562-566
Mots-Clés Biogeography; connectivity; diversity; dynamics; patterns; phylogenetic turnover
Résumé Although environmental filtering has been observed to influence the biodiversity patterns of marine bacterial communities, it was restricted to the regional scale and to the species level, leaving the main drivers unknown at large biogeographic scales and higher taxonomic levels. Bacterial communities with different species compositions may nevertheless share phylogenetic lineages, and phylogenetic turnover (PT) among those communities may be surprisingly low along any biogeographic or environmental gradient. Here, we investigated the relative influence of environmental filtering and geographical distance on the PT between marine bacterial communities living more than 8000 km apart in contrasted abiotic conditions. PT was high between communities and was more structured by local environmental factors than by geographical distance, suggesting the predominance of a lineage filtering process. Strong phenotype-environment mismatches observed in the ocean may surpass high connectivity between marine microbial communities.
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Editeur Lieu de Publication Éditeur
Langue English Langue du Résumé Titre Original
Éditeur de collection Titre de collection Titre de collection Abrégé
Volume de collection Numéro de collection Edition
ISSN 1744-9561 ISBN Médium
Région Expédition Conférence
Notes Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 567
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