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Auteur Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S.
Titre RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r Type Article scientifique
Année 2016 Publication Revue Abrégée Methods Ecol. Evol.
Volume 7 Numéro 8 Pages 966-970
Mots-Clés clonal diversity; clonality; clonal population; diversity; genotype; markers; multilocus genotypes; multilocus lineages; organisms; population-genetics; program; software; spatial autocorrelation
Résumé Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one-shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next-generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).
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ISSN 2041-210x ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1637
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Auteur Boavida, J.; Becheler, R.; Choquet, M.; Frank, N.; Taviani, M.; Bourillet, J.-F.; Meistertzheim, A.-L.; Grehan, A.; Savini, A.; Arnaud-Haond, S.
Titre Out of the Mediterranean? Post-glacial colonization pathways varied among cold-water coral species Type Article scientifique
Année 2019 Publication Revue Abrégée J. Biogeogr.
Volume 46 Numéro 5 Pages 915-931
Mots-Clés biodiversity; cold-water corals; computer-program; deep-sea; deep-sea corals; genetic-structure; glacial marine refugia; glacial refugia; growth; in-situ; Last Glacial Maximum; Lophelia pertusa; lophelia-pertusa; Madrepora oculata; marine phylogeography; north-atlantic ocean; software
Résumé Aim: To infer cold-water corals' (CWC) post-glacial phylogeography and assess the role of Mediterranean Sea glacial refugia as origins for the recolonization of the northeastern Atlantic Ocean. Location: Northeastern Atlantic Ocean and Mediterranean Sea. Taxon: Lophelia pertusa, Madrepora oculata. Methods: We sampled CWC using remotely operated vehicles and one sediment core for coral and sediment dating. We characterized spatial genetic patterns (microsatellites and a nuclear gene fragment) using networks, clustering and measures of genetic differentiation. Results: Inferences from microsatellite and sequence data were congruent, and showed a contrast between the two CWC species. Populations of L. pertusa present a dominant pioneer haplotype, local haplotype radiations and a majority of endemic variation in lower latitudes. Madrepora oculata populations are differentiated across the northeastern Atlantic and genetic lineages are poorly admixed even among neighbouring sites. Conclusions: Our study shows contrasting post-glacial colonization pathways for two key habitat-forming species in the deep sea. The CWC L. pertusa has likely undertaken a long-range (post-glacial) recolonization of the northeastern Atlantic directly from refugia located along southern Europe (Mediterranean Sea or Gulf of Cadiz). In contrast, the stronger genetic differentiation of M. oculata populations mirrors the effects of long-term isolation in multiple refugia. We suggest that the distinct and genetically divergent, refugial populations initiated the post-glacial recolonization of the northeastern Atlantic margins, leading to a secondary contact in the northern range and reaching higher latitudes much later, in the late Holocene. This study highlights the need to disentangle the influences of present-day dispersal and evolutionary processes on the distribution of genetic polymorphisms, to unravel the influence of past and future environmental changes on the connectivity of cosmopolitan deep-sea ecosystems associated with CWC.
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Langue English Langue du Résumé Titre Original
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Volume de collection Numéro de collection Edition
ISSN 0305-0270 ISBN Médium
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Notes WOS:000471344900007 Approuvé pas de
Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2602
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Auteur Coll, M.; Steenbeek, J.
Titre Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models Type Article scientifique
Année 2017 Publication Revue Abrégée Environ. Modell. Softw.
Volume 89 Numéro Pages 120-130
Mots-Clés biodiversity; Conservation; Ecological standardized indicators; Ecopath with Ecosim; ecospace; Ecosystem indicators; Environmental status; Fisheries management; Food web models; impacts; index; marine ecosystems; Mediterranean Sea; network analysis; ocean; Software plug-in
Résumé Ecological indicators are useful tools to analyse and communicate historical changes in ecosystems and plausible future scenarios while evaluating environmental status. Here we introduce a new plug-in to the Ecopath with Ecosim (EwE) food web modelling approach, which is widely used to quantitatively describe aquatic ecosystems. The plug-in (ECOIND) calculates standardized ecological indicators. We describe the primary functionality of ECOIND and provide an example of its application in both static and temporal-spatial dynamic modelling, while we highlight several related features including a new taxonomy input database (species traits) and the ability to analyse input uncertainty on output results. ECOIND adds new capabilities to the widely used EwE food web modelling approach and enables broadening its applications into biodiversity and conservation-based frameworks to contribute to integrated ecosystem analyses. (C) 2016 Elsevier Ltd. All rights reserved.
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Volume de collection Numéro de collection Edition
ISSN 1364-8152 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2088
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Auteur Pirog, A.; Jaquemet, S.; Blaison, A.; Soria, M.; Magalon, H.
Titre Isolation and characterization of eight microsatellite loci from Galeocerdo cuvier (tiger shark) and cross-amplification in Carcharhinus leucas, Carcharhinus brevipinna, Carcharhinus plumbeus and Sphyrna lewini Type Article scientifique
Année 2016 Publication Revue Abrégée PeerJ
Volume 4 Numéro Pages e2041
Mots-Clés age; bull; Carcharhiniform; Control region; growth; hawaiian waters; markers; microsatellites; movements; patterns; Population Genetics; software; western north-atlantic
Résumé The tiger shark Galeocerdo cuvier (Carcharhinidae) is a large elasmobranch suspected to have, as other apex predators, a keystone function in marine ecosystems and is currently considered Near Threatened (Red list IUCN). Knowledge on its ecology, which is crucial to design proper conservation and management plans, is very scarce. Here we describe the isolation of eight polymorphic microsatellite loci using 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries. Their characteristics were tested on a population of tiger shark (n = 101) from Reunion Island (South-Western Indian Ocean). All loci were polymorphic with a number of alleles ranging from two to eight. No null alleles were detected and no linkage disequilibrium was detected after Bonferroni correction. Observed and expected heterozygosities ranged from 0.03 to 0.76 and from 0.03 to 0.77, respectively. No locus deviated from Hardy-Weinberg equilibrium and the global F-IS of the population was of 0.04(NS). Some of the eight loci developed here successfully cross-amplified in the bull shark Carcharhinus leucas (one locus), the spinner shark Carcharhinus brevi pi n n a (four loci), the sandbar shark Carcharhinus plumbeus (five loci) and the scalloped hammerhead shark Sphyrna lewini (two loci). We also designed primers to amplify and sequence a mitochondrial marker, the control region. We sequenced 862 bp and found a low genetic diversity, with four polymorphic sites, a haplotype diversity of 0.15 and a nucleotide diversity of 2 x 10(-4).
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ISSN 2167-8359 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1651
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