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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) Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S. doi  openurl
  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 (up) BECHELER, R.; BENKARA, E.; MOALIC, Y.; HILY, C.; ARNAUD-HAOND, S. url  openurl
  Titre Scaling of processes shaping the clonal dynamics and genetic mosaic of seagrasses through temporal genetic monitoring Type Article scientifique
  Année 2014 Publication Revue Abrégée Heredity  
  Volume 112 Numéro 2 Pages 114-121  
  Mots-Clés clonality; Seagrass; spatio-temporal genetic structure; Zostera marina  
  Résumé Theoretically, the dynamics of clonal and genetic diversities of clonal plant populations are strongly influenced by the competition among clones and rate of seedling recruitment, but little empirical assessment has been made of such dynamics through temporal genetic surveys. We aimed to quantify 3 years of evolution in the clonal and genetic composition of Zostera marina meadows, comparing parameters describing clonal architecture and genetic diversity at nine microsatellite markers. Variations in clonal structure revealed a decrease in the evenness of ramet distribution among genets. This illustrates the increasing dominance of some clonal lineages (multilocus lineages, MLLs) in populations. Despite the persistence of these MLLs over time, genetic differentiation was much stronger in time than in space, at the local scale. Contrastingly with the short-term evolution of clonal architecture, the patterns of genetic structure and genetic diversity sensu stricto (that is, heterozygosity and allelic richness) were stable in time. These results suggest the coexistence of (i) a fine grained (at the scale of a 20 x 30 m quadrat) stable core of persistent genets originating from an initial seedling recruitment and developing spatial dominance through clonal elongation; and (ii) a local (at the scale of the meadow) pool of transient genets subjected to annual turnover. This simultaneous occurrence of initial and repeated recruitment strategies highlights the different spatial scales at which distinct evolutionary drivers and mating systems (clonal competition, clonal growth, propagule dispersal and so on) operate to shape the dynamics of populations and the evolution of polymorphism in space and time.  
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  ISSN 0018-067x ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1139  
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Auteur (up) Becheler, R.; Cassone, A.-L.; Noel, P.; Mouchel, O.; Morrison, C.L.; Arnaud-Haond, S. doi  openurl
  Titre Low incidence of clonality in cold water corals revealed through the novel use of a standardized protocol adapted to deep sea sampling Type Article scientifique
  Année 2017 Publication Revue Abrégée Deep-Sea Res. Part II-Top. Stud. Oceanogr.  
  Volume 145 Numéro Pages 120-130  
  Mots-Clés diversity; dispersal; disturbance; Lophelia pertusa; Madrepora oculata; organisms; population-structure; asexual reproduction; Clonality; Cold-water coral; Fine-grained spatial genetic structure; gorgonian coral; lophelia-pertusa; pertusa linnaeus 1758; spatial genetic-structure; Standardized sampling  
  Résumé Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6-7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.  
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  Langue English Langue du Résumé Titre Original  
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  ISSN 0967-0645 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2257  
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