Éditeur(s) : HAL CCSD
Résumé : Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.
Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.
https://tel.archives-ouvertes.fr/tel-01405400

NNT : 2015YANE0005
tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400
https://tel.archives-ouvertes.fr/tel-01405400/document
https://tel.archives-ouvertes.fr/tel-01405400/file/these_-_tinaut.pdf

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé :  
In this paper, we report a study of the mating system and gene flow of Symphonia globulifera, a hermaphroditic, mainly bird-pollinated tree species with a large geographic distribution in the tropical Americas and Africa.Using three microsatellites, we analysed 534 seeds of 28 open pollinated families and 164 adults at the experimental site 'Paracou' in French Guiana. We observed, compared to other tropical tree species, relatively high values for the effective number of alleles. Significant spatial genetic structure was detected, with trees at distances up to 150 m more genetically similar than expected at random. We estimated parameters of the mating system and gene flow by using the mixed mating model and the TwoGener approach. The estimated multilocus outcrossing rate, tm, was 0.920. A significant level of biparental inbreeding and a high proportion of full-sibs were estimated for the 28 seed arrays. We estimated mean pollen dispersal distances between 27 and 53 m according to the dispersal models used. Although the adult population density of S. globulifera in Paracou was relatively high, the joint estimation of pollen dispersal and density of reproductive trees gave effective density estimates of 1.6 and 1.3trees/ha. The parameters of the mating system and gene flow are discussed in the context of spatial genetic and demographic structures, flowering phenology and pollinator composition and behaviour.
ISSN: 0018-067X

hal-01032178
https://hal.archives-ouvertes.fr/hal-01032178
DOI : 10.1038/sj.hdy.6800560

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699
Spontaneous gene flow between wild and cultivated chicory, Cichorium intybus L., may have implications for the genetic structure and evolution of populations and varieties. One aspect of this crop-wild gene flow is the dispersal of transgenes from genetically modified varieties, e.g. gene flow from GM chicory to natural chicory could have unwanted consequences. With the purpose to identify and quantify crop-wild gene flow in chicory, we analysed introgression in 19 wild chicory populations and 16 accessions of chicory varieties and landraces distributed across Northern, Central and Mediterranean Europe. The analysis used 281 AFLP markers and 75 SSAP markers giving a total of 356 polymorphic markers. Results from model based assignments with the program STRUCTURE indicated many incidents of recent gene flow. Gene flow was observed both between cultivars and wild populations, between landraces and wild populations, between different wild populations as well as between cultivars. Population structure visualized by distance-based clustering showed a North-South geographical structuring of the wild populations, and a general grouping of the cultivars corresponding to known origin. The results indicated, however, that the structuring between the two groups of wild and cultivated types was weak. As crop and wild recipients are genetically close and genes are transferred between the two types rather frequently, focus on mitigating crop-wild gene flow should be increased, before transgenic varieties are cultivated openly.
ISSN: 0925-9864

hal-01032184
https://hal.archives-ouvertes.fr/hal-01032184
DOI : 10.1007/s10722-008-9375-1

Éditeur(s) : HAL CCSD
Résumé : il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : ACTIVITY_REPORT
Understanding genomic evolution in wild populations is of particular importance because evolution is a central process in our understanding of populations’ history and their future response to global changes. In addition to fundamental knowledge, the study of populations’ evolution has wide applications such as conservation/restoration genetics or epidemiology. Indeed, genetic diversity is the ‘fuel’ for populations’ evolution and adaptation to new conditions, and estimating the extent and the geographic structure of genetic diversity, as well as identifying the evolutionary forces behind (demography, gene flow, and adaptation) are thus major challenges in the current context of global changes. [br/]A particular attention is currently devoted to the process of genetic divergence in wild populations, with emphases on gene flow, local adaptation, and their interactions. Indeed, adaptation in wild populations is supported in many species by many kinds of experiments based on both quantitative phenotypic traits and molecular data. However, the processes governing populations’ evolution are poorly understood in the tropical rainforest of Amazonia, and the relative influence of neutral and adaptive processes are continuously discussed. [br/]I am a young scientist interested in the process of genomic divergence in wild (tree) populations. I aimed at understanding how evolution structures the genetic diversity and governs molecular divergence in wild populations, with particular emphases on gene flow and local adaptation. During five years as a young scientist, I worked on answering the following questions, focusing on two tree species occupying vulnerable areas: mainly [i]Eperua falcata[/i] in Amazonia and, to a lesser extent, [i]Abies alba[/i] in the Mediterranean area.[br/][u]Scientific questions:[/u][br/]- Which evolutionary drivers are responsible of the structure of genetic diversity in wild populations occupying wide areas? This question was addressed at different geographical scales: from large (regional) to very local (microgeographic) scales. [br/]- What is the relative influence of neutral (gene flow, inbreeding) and adaptive drivers in the process of genetic divergence?[br/]- Is microgeographic adaptation possible in spite of extensive gene flow between populations occupying the extreme boundaries of an ecological gradient? [br/]- What is the extent of natural selection in the (whole) genome of wild populations? [br/][br/]My research work is at the interface between three promising disciplines: Evolutionary genomics (i.e. the study of populations evolution and the evolutionary drivers behind), Bioinformatics (i.e. the treatment of next-generation data), and Bayesian modelling (i.e. the empirical calibration of complex mechanistic model). I intend to take advantage of the recent advances in sequencing and informatic technologies to bring up to date the field of ecological genetics and evolutionary biology, by developing modern research strategies to study the process of genomic divergence in wild populations.
https://hal.archives-ouvertes.fr/hal-01204218

hal-01204218
https://hal.archives-ouvertes.fr/hal-01204218
PRODINRA : 286326

Éditeur(s) : Public Library Science
Résumé : Background: Reconstructing the history of divergence and gene flow between closely-related organisms has long been a difficult task of evolutionary genetics. Recently, new approaches based on the coalescence theory have been developed to test the existence of gene flow during the process of divergence. The deep sea is a motivating place to apply these new approaches. Differentiation by adaptation can be driven by the heterogeneity of the hydrothermal environment while populations should not have been strongly perturbed by climatic oscillations, the main cause of geographic isolation at the surface. Methodology/Principal Finding: Samples of DNA sequences were obtained for seven nuclear loci and a mitochondrial locus in order to conduct a multi-locus analysis of divergence and gene flow between two closely related and hybridizing species of hydrothermal vent mussels, Bathymodiolus azoricus and B. puteoserpentis. The analysis revealed that (i) the two species have started to diverge approximately 0.760 million years ago, (ii) the B. azoricus population size was 2 to 5 time greater than the B. puteoserpentis and the ancestral population and (iii) gene flow between the two species occurred over the complete species range and was mainly asymmetric, at least for the chromosomal regions studied. Conclusions/Significance: A long history of gene flow has been detected between the two Bathymodiolus species. However, it proved very difficult to conclusively distinguish secondary introgression from ongoing parapatric differentiation. As powerful as coalescence approaches could be, we are left by the fact that natural populations often deviates from standard assumptions of the underlying model. A more direct observation of the history of recombination at one of the seven loci studied suggests an initial period of allopatric differentiation during which recombination was blocked between lineages. Even in the deep sea, geographic isolation may well be a crucial promoter of speciation.
Plos One (1932-6203) (Public Library Science), 2009-08 , Vol. 4 , N. 8 , P. 1-15

Droits : 2009 Faure et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
http://archimer.ifremer.fr/doc/00129/24012/21972.pdf
DOI:10.1371/journal.pone.0006485
http://archimer.ifremer.fr/doc/00129/24012/

Éditeur(s) : HAL CCSD Wiley
Résumé : Unveiling the genetic basis of local adaptation to environmental variation is a major goal in molecular ecology. In rugged landscapes characterized by environmental mosaics, living populations and communities can experience steep ecological gradients over very short geographical distances. In lowland tropical forests, interspecific divergence in edaphic specialization (for seasonally flooded bottomlands and seasonally dry terra firme soils) has been proven by ecological studies on adaptive traits. Some species are nevertheless capable of covering the entire span of the gradient; intraspecific variation for adaptation to contrasting conditions may explain the distribution of such ecological generalists. We investigated whether local divergence happens at small spatial scales in two stands of Eperua falcata (Fabaceae), a widespread tree species of the Guiana Shield. We investigated Single Nucleotide Polymorphisms (SNP) and sequence divergence as well as spatial genetic structure (SGS) at four genes putatively involved in stress response and three genes with unknown function. Significant genetic differentiation was observed among sub-populations within stands, and eight SNP loci showed patterns compatible with disruptive selection. SGS analysis showed genetic turnover along the gradients at three loci, and at least one haplotype was found to be in repulsion with one habitat. Taken together, these results suggest genetic differentiation at small spatial scale in spite of gene flow. We hypothesize that heterogeneous environments may cause molecular divergence, possibly associated to local adaptation in E. falcata.
ISSN: 1010-061X

hal-01032412
https://hal.archives-ouvertes.fr/hal-01032412
DOI : 10.1111/jeb.12069

Éditeur(s) : HAL CCSD
Résumé :  Diffusion du document : INRA Antilles-Guyane, UMR ECOFOG, F97387 Kourou, Guyane (France)Diplôme : Master Recherche
il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : DISSERTATION
Origin and maintenance of species diversity is one of the main questions in evolutive biology. Species complexes, ie sister species still exchanging genes, are common in tropical forests and contribute to this diversity. This poster describes the organization of the genetic diversity in two closely related tree species, Carapa guianensis and C. procera, which are in sympatry in French Guiana. By using a clustering method based on nuclear markers (Pritchard et al. 2000), 506 trees sampled in French Guiana have been assigned to a species. Interestingly, many individuals harbored intermediate genome and we assigned to an hybrid group. The geographic distribution of these individuals revealed the presence of a contact zone between the two carapa species in the Eastern part of French Guiana. We then analysed genetic diversity at cholroplast genome and revealed a symmetrical gene flow between the two sister species. In addition, hybridization between hybrids and parental species ar likely possible but still need validations thanks to control crosses. Within species, we finally revealed the presence of a departure from the neutral equilibrium in thedirection of a population expansion likely related to Holocene perturbations. This expansion may have contributed to the hybrid zone formation in French Guiana.
L'origine et le maintien de la diversité spécifique des forêts tropicales humides est une question clé en biologie évolutive. Ce travail contribue à améliorer la compréhension de ces mécanismes à travers l'étude de la distribution de la diversité génétique de deux espèces sœurs interfertiles, le Carapa procera et C. guianensis en Guyane. L'assignation botanique des arbres échantillonnés (506) a été effectuée en adoptant une approche moléculaire qui repose sur l'analyse de la répartition des fréquences alléliques de six microsatellites nucléaires (Pritchard et al. 2000). Chaque locus présente des allèles dont les différences de fréquences entre espèces sont importantes, permettant ainsi d'envisager des outils simples de reconnaissances pour ces espèces difficilement identifiables sur la seule base de leurs caractères phénotypiques. Une zone de contact des deux espèces où les phénomènes d'hybridations sont fréquents a par ailleurs été localisée. En associant une analyse de la diversité au niveau du génome chloroplastique sur un sous ensemble d'individus (244), j'ai pu montrer que l'introgression est bidirectionnelle et que les backcross sont possibles. Les flux de gènes entre les deux espèces sont fréquents, et à l'intérieur des espèces, les populations sont peu structurées bien que la différenciation soit significative entre les sites les plus éloignés. Enfin, ce travail met en évidence que les populations de chacune des deux espèces présentent un signal d'expansion de population, avec un signal plus fort pour le C. procera, qui laisse présager une expansion récente, vraisemblablement à l'origine de la zone de contact. L'impact des évènements climatiques et/ou des activités amérindiennes des 10 000 dernières années pourrait expliquer la restriction puis l'expansion de ce genre post pionnier.
https://hal.archives-ouvertes.fr/hal-01189488

hal-01189488
https://hal.archives-ouvertes.fr/hal-01189488
PRODINRA : 42333

Éditeur(s) : Université de La Rochelle, Ecole doctorale Gay Lussac
Résumé : The thesis work is part of the very current issue on mass mortality outbreaks affecting Pacific oyster, C. gigas, spat and juveniles and questions about the involvement of pesticides in this phenomenon. The first part of this thesis was devoted to study the effects of pesticides on hemocyte parameters in the Pacific oyster (in vitro and in vivo). The immunomodulator effect of selected pesticides (alone or in mixture) has been explored principally through flow cytometry. The second part concerned the study of the effects of a pesticides mixture on OsHV-1 itself. No direct effects have been reported on the viral particles in presence of the pollutants. Moreover, pesticide effects on Pacific oysters were also explored through experimental pathology assays after treatment of animals with a polluant mixture. Results showed that pesticide treated oysters appeared more susceptible to the viral infection in experimental conditions. The third part concerned the study of autophagy in the Pacific oyster, C. gigas. The publication of the complete genome in 2012 has opened up new possibilities for the study of innate immunity in this species. The study of autophagy for the first time in oysters consisted in a first step in the in silico search for genes involved in this pathway and the corresponding proteins by Western blotting. Then, the role of this important process in innate immunity has been explored through reproduction infections tests with or without modulators of autophagy. Results showed that autophagy appeared as involved in defence mechanisms against viral and bacterial infection in Pacific oysters.
Le travail de thèse s’inscrit dans la problématique très actuelle des mortalités massives de naissain et de juvéniles d’huîtres creuses, C. gigas, et des questionnements autour de l’implication des pesticides dans ce phénomène. La première partie de la thèse a été consacrée à l’étude des effets de pesticides sur les capacités hémocytaires de l’huître creuse (in vitro et in vivo). L’effet immunomodulateur des xénobiotiques sélectionnés (seul ou en mélange) a été exploré principalement au travers de la cytométrie en flux. La deuxième partie de la thèse a concerné l’étude des effets d’un mélange de pesticides sélectionnés sur le virus OsHV-1 et l’infection qu’il induit chez l’huître creuse. Les effets des pesticides sur le virus lui-même ont été évalués. Les expériences réalisées non pas permis de mettre en évidence dans les conditions testées, de dégradation des particules virales en présence des polluants. D’autre part, leurs effets sur les huîtres elles-mêmes ont été explorés après traitement des animaux avec un mélange de pesticides lors d’essais de pathologie expérimentale. Il a ainsi pu être montré que des huîtres préalablement comtaminées par un mélange de pesticides à des concentrations retrouvées dans l’environnement semblaient être plus sensibles à l’infection virale. La troisième partie de la thèse a concerné l’étude de l’autophagie chez l’huître creuse, C. gigas. La publication du génome complet de cette espèce en 2012 a ouvert de nouvelles possibilités pour étudier l'immunité innée. L’étude de l’autophagie réalisée pour la première fois chez l’huître creuse a consisté lors d’une première étape en la recherche in silico de gènes impliqués dans cette voie et des protéines correspondantes par western blotting. Puis, le rôle de ce processus important dans l’immunité innée a été exploré au travers d’essais de reproduction d’infections en présence ou non de modulateurs de l’autophagie. Les résultats obtenus semblent montrer que l’autophagie soit un processus important pouvant être impliqué dans les capacités de défense de l’huître creuse vis-à-vis d’infections virales et bactériennes.

Droits : 2014 Université de La Rochelle
http://archimer.ifremer.fr/doc/00226/33740/32149.pdf
http://archimer.ifremer.fr/doc/00226/33740/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
The development of inflammatory granulomas around infected Kupffer cells is necessary for hepatic parasite clearance during visceral leishmaniasis. Invariant NKT (iNKT) cells are predominant T cells in the mouse liver and can synthesize large quantities of IL-4 and IFN-γ, two cytokines involved in granuloma formation. This study analyzed the role of iNKT cells in the hepatic immune response during Leishmania donovani infection, using a murine model of wild-type (WT) and iNKT cell-deficient (Jα18⁻/⁻) C57BL/6 mice sacrificed 15, 30 or 60 days post-infection. We recorded hepatic parasite loads, cytokine expression, and analyzed granulomatous response by immunohistochemistry and hepatic immune cell infiltration by flow cytometry. Whereas WT animals rapidly controlled the infection and developed an inflammatory response associated with a massive influx of iNKT cells observed by flow cytometry, Jα18⁻/⁻ mice had significantly higher parasitic loads on all time points. This lack of control of parasite burden was associated with a delay in granuloma maturation (28.1% of large granulomas at day 60 versus 50.7% in WT). Cytokine transcriptome analysis showed that mRNA of 90/101 genes encoding chemokines, cytokines and their receptors, was underexpressed in Jα18⁻/⁻ mice. Detection of IL-4 and TNF-α by ELISA in liver extracts was also significantly lower in Jα18⁻/⁻ mice. Consistent with flow cytometry analysis, cytokinome profile in WT mice showed a bias of expression towards T cell-chemoattractant chemokines on D15, and displayed a switch towards expression of granulocytes and/or monocytes -chemoattractant chemokines on D60. In Jα18⁻/⁻ mice, the significantly lower expression of CXCL5, MIP-2 and CCL2 mRNA was correlated with a defect in myeloperoxidase positive-cell attraction observed by immunohistochemistry and with a lower granulocyte and monocyte infiltration in the liver, as shown by flow cytometry. These data indicate that iNKT cells play a role in early and sustained pro-inflammatory cytokine response warranting efficient organization of hepatic granulomas and parasite clearance.
ISSN: 1932-6203

hal-00696897
https://hal.archives-ouvertes.fr/hal-00696897
https://hal.archives-ouvertes.fr/hal-00696897/document
https://hal.archives-ouvertes.fr/hal-00696897/file/Invariant_NKT_Cells_Drive-accepted.pdf
DOI : 10.1371/journal.pone.0033413

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : Understanding the genetic mechanisms of speciation and basis of species differences is among the most important challenges in evolutionary biology. Two questions of particular interest are what roles divergent selection and chromosomal differentiation play in these processes. A number of recently proposed theories argue that chromosomal rearrangements can facilitate the development and maintenance of reproductive isolation and species differences by suppressing recombination within rearranged regions. Reduced recombination permits the accumulation of alleles contributing to isolation and adaptive differentiation and protects existing differences from the homogenizing effects of introgression between incipient species. Here, we examine patterns of genetic diversity and divergence in rearranged versus collinear regions in two widespread, extensively hybridizing sunflower species, Helianthus annuus and Helianthus petiolaris, using sequence data from 77 loci distributed throughout the genomes of the two species. We find weak evidence for increased genetic divergence near chromosomal break points but not within rearranged regions overall. We find no evidence for increased rates of adaptive divergence on rearranged chromosomes; in fact, collinear chromosomes show a far greater excess of fixed amino acid differences between the two species. A comparison with a third sunflower species indicates that much of the nonsynonymous divergence between H. annuus and H. petiolaris probably occurred during or soon after their formation. Our results suggest a limited role for chromosomal rearrangements in genetic divergence, but they do document substantial adaptive divergence and provide further evidence of how species integrity and genetic identity can be maintained at many loci in the face of extensive hybridization and gene flow.
ISSN: 0737-4038

hal-01032153
https://hal.archives-ouvertes.fr/hal-01032153
DOI : 10.1093/molbev/msp043

Éditeur(s) : HAL CCSD Wiley
Résumé : The evolutionary potential of long-lived species, such as forest trees, is fundamental for their local persistence under climate change (CC). Genome–environment association (GEA) analyses reveal if species in heterogeneous environments at the regional scale are under differential selection resulting in populations with potential preadaptation to CC within this area. In 79 natural [i]Fagus sylvatica[/i] populations, neutral genetic patterns were characterized using 12 simple sequence repeat (SSR) markers, and genomic variation (144 single nucleotide polymorphisms (SNPs) out of 52 candidate genes) was related to 87 environmental predictors in the latent factor mixed model, logistic regressions and isolation by distance/environmental (IBD/IBE) tests. SSR diversity revealed relatedness at up to 150m intertree distance but an absence of large-scale spatial genetic structure and IBE. In the GEA analyses, 16 SNPs in 10 genes responded to one or several environmental predictors and IBE, corrected for IBD, was confirmed. The GEA often reflected the proposed gene functions, including indications for adaptation to water availability and temperature. Genomic divergence and the lack of large-scale neutral genetic patterns suggest that gene flow allows the spread of advantageous alleles in adaptive genes. Thereby, adaptation processes are likely to take place in species occurring in heterogeneous environments, which might reduce their regional extinction risk under CC
ISSN: 0028-646X

hal-01309135
https://hal.archives-ouvertes.fr/hal-01309135
PRODINRA : 343710
DOI : 10.1111/nph.13809

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : Isozyme markers were used to characterize levels of diversity, genotypic structure and spatial genetic structure for the low-density tree species, Carapa procera (five adults per ha), within 300 ha of a continuous tropical rain forest stand. Both seed and adult stages were investigated, a high level of genetic diversity being found in both. Fixation indices showed excess homozygosity in seeds, and excess heterozygosity in adults, which might be caused by selection in favour of heterozygotes. Autocorrelation analysis of the spatial distribution of genotypes revealed no significant pattern in adults or in seeds before dispersal, and there was a high variability in correlogram shapes among alleles. This suggests that gene flow is extensive in C. procera, probably mainly through long-distance pollen dispersal, as seed dispersal is expected to be rather limited in this species (maximum distances of about 50 m). No clear-cut spatial pattern was observed in pollen allele frequencies, which supports the hypothesis of extensive pollen flow. This overall lack of structure is consistent with the data already available on the mating system of this predominantly outcroissing species.
ISSN: 0018-067X

hal-01032057
https://hal.archives-ouvertes.fr/hal-01032057
DOI : 10.1038/hdy.1997.124

Éditeur(s) : HAL CCSD
Résumé : In the tropical rainforest of Amazonia, the factors driving the evolution of tree species remain poorly understood, and the relative influence of neutral and adaptive processes is continuously debated. In particular, local habitat patchiness draws much attention, as profound changes in the structure and composition of forest communities occur among micro-habitats. Thus, micro-environmental variations related to topography have frequently been invoked as drivers of adaptive radiation leading to sympatric speciation in Neotropical trees. On one hand, the hypothesis of local adaptation has never been investigated at the intra-specific level, i.e. within species currently undergoing population differentiation; on the other hand, many tree species are genetically structured over local scales due to neutral processes, mainly limited gene flow (caused by restricted pollen and seed dispersal). In this study, I used populations of a common tree species of the Guiana Shield - Eperua falcata (Fabaceae) - to study how neutral and adaptive processes shape the distribution of genetic diversity across forest landscapes characterized by local micro-habitat patchiness. I asked three main questions by combining both phenotypic (quantitative genetics) and molecular (population genetics) approaches: 1) How is the genetic diversity structured in forest landscapes of French Guiana? 2) Which evolutionary drivers are relevant to explain the structure of genetic diversity at local scale? 3) Does local adaptation contribute to structure genetic diversity within continuous populations?
En forêt tropicale humide Amazonienne, les facteurs gouvernant l'évolution des espèces d'arbres restent peu connus et continuellement débattus. En particulier, les micro-variations environnementales attirent beaucoup d'attention car elles induisent de profondes modifications de structure et composition des communautés. Les variations micro-environnementales associées à la topographie ont couramment été évoquées comme facteur de radiations adaptatives chez les espèces d'arbres. Cependant, l'hypothèse de l'adaptation locale n'a jamais été testée au niveau intra-spécifique chez les arbres de forêt amazonienne alors que l'on sait que la diversité génétique des arbres tropicaux est couramment structurée à faibles échelles spatiales par des processus neutres (en particulier du fait de restrictions de flux de gènes). Dans cette étude, j'ai étudié le processus de différentiation génétique d'une espèce d'arbre (Eperua falcata, Fabaceae) dans les paysages forestiers de Guyane française grâce à la combinaison d'une approche phénotypique (génétique quantitative) et d'une approche moléculaire (génétique des populations). Je me suis attachée à répondre à trois questions principales : 1) Comment se distribue la diversité génétique dans les paysages forestiers de Guyane française ? 2) Quelles forces évolutives sont impliquées dans le processus de différentiation génétique à faible échelle spatiale ? 3) Est-ce que le processus d'adaptation locale contribue à structurer la diversité génétique à faible échelle spatiale ?
https://tel.archives-ouvertes.fr/tel-00967318

NNT : 2013LORR0188
tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318
https://tel.archives-ouvertes.fr/tel-00967318/document
https://tel.archives-ouvertes.fr/tel-00967318/file/THESE_Louise_Brousseau.pdf

Éditeur(s) : Université de la Réunion
Résumé : The green turtle (Chelonia mydas) is an emblematic species of marine life. However, nowadays it is subject to many threats (poaching, by-catch). Even if there is deep growing measures for its protection, the green turtle still is an endangered species and it is listed in Appendix I of Washington Convention (CITES). In order to elaborate efficient conservation and management plans, perfect knowledge of green turtle biology, but also of its population structure and their characteristics, are needed. In this thesis, we have assessed genetic structure of green turtle populations in the South-Western Indian Ocean by using genetic tools. In all, 1551 tissue samples have been collected from our study zone and from our control site French Polynesia (37 samples). All kinds if individuals were sampled (except males in reproductive phase) from 15 sampling sites including nesting, foraging, and immature development site. We used both control region of mitochondrial DNA and 6 microsatellite loci to better infer maternal and paternal lineages. We identified 29 haplotypes in the South-Western Indian Ocean. They are distributed in 3 independent and highly divergent clades, including one composed with haplotypes from Atlantic Ocean. For 7 of these haplotypes, it was the first time they were detected in the study zone. Fifteen haplotypes were previously undescribed, distributed in all the 3 clades. These new haplotypes seem to be specific to the South-Western Indian Ocean, which is then an original zone. Besides, we found a high allelic richness. These results show the South-western Indian Ocean is rich and very diversified. This region plays an important role in the global diversity of the species. The South-Western Indian Ocean is one of the two contact zones presently known between the two metapopulations of green turtles (Atlantic-Mediterranean and Indo-Pacific). This contact induces a genetic cline based on CM8 (Atlantic) and C3 (Indo-Pacific) haplotype frequencies. Analysis of the microsatellite differentiation between individuals provides evidence of genetic exchanges between the two metapopulations in the region. The South-Western Indian Ocean participates to green turtle global genetic mixing. Studying the influence of several intrinsic and extrinsic factors on population structuring provides useful information for management plan elaboration. We found no significant difference between genetic structures of foraging females and males, contrary to immature turtles which seem to be organised in 'regional pools'. This organisation could be due to both immature natal homing and influence of oceanic currents. High mitochondrial differentiation of nesting females and low global microsatellite differentiation of our samples indicate male-mediated gene flow among populations of the study zone. The genetic composition of a sampling site presents no significant variation along the year, even if we could notice some trends. Nevertheless, it can be significantly different from a year to an other one. This may result from alternation of distinct populations on the same site. We noticed different evolution in 10 or 20 years of the genetic composition depending on the sampling site. Geographic distance seems not to have significant influence on population structuring concerning microsatellite markers. Nesting females of Saziley Beach (Mayotte Island, Comoros Archipelago) present genetic divergence from females nesting in the two other sampled beaches of this island. The observed population structure shows no contradiction with the organisation of oceanic currents in the South-Western Indian Ocean. Comparing the results from the two genetic markers used, we identified 8 genetic differentiated clusters of turtles in the study zone and at least 6 distinct populations. These clusters constitute 8 potential management units (MUs) which could serve as basis in the elaboration of conservation and management plans.
La tortue verte (Chelonia mydas) constitue l'un des espèces emblématiques de la vie marine, pourtant de nombreuses menaces pèsent de nos jours encore sur sa survie (braconnage, captures accidentelles). Ainsi, malgré l'essor de mesures de protection menées à travers pour sa sauvegarde, la tortue verte constitue une espèce 'en danger d'extinction' et figure dans l'Annexe I de la Convention de Washington (CITES). Afin d'élaborer des plans de gestion et de conservation qui soient efficaces, il est important d'avoir une parfaite connaissance de la biologie de la tortue verte, mais aussi de la structure de ses populations et de leurs caractéristiques. C'est dans ce cadre que s'inscrit la présente étude. L'objectif de cette étude était d'acquérir des connaissances sur la structure des populations de tortues vertes dans le sud-ouest de l'océan Indien grâce à l'utilisation de l'outil génétique. Au total, 1551 échantillons de tissu ont été collectés dans la zone d'étude et dans notre site témoin la Polynésie française (37 échantillons). Toutes les catégories d'individus ont été échantillonnées (excepté les mâles en phase de reproduction) et les 15 sites d'échantillonnage comprennent à la fois des sites de ponte, d'alimentation et de développement pour les immatures. Deux types de marqueurs ont été utilisés : la région contrôle de l'ADN mitochondrial et 6 loci microsatellites, afin d'appréhender au mieux l'apport des lignées maternelles et paternelles. Nous avons pu mettre en évidence la présence dans le sud-ouest de l'océan Indien de 29 haplotypes distincts, appartenant à trois clades fortement divergents dont l'un constitué d'haplotypes originaires de l'océan Atlantique. Parmi ces haplotypes, 7 ont été détectés pour la première fois dans la zone d'étude, et 15 autres n'ont jamais été précédemment décrits chez cette espèce. Ils sont présents dans chacun des 3 clades d'haplotypes. Ces nouveaux haplotypes semblent spécifiques à la région, et en font une zone originale. On observe par ailleurs une grande richesse allélique dans les effectifs analysés. Ces résultats montrent que le sud-ouest de l'océan Indien est une zone riche et très diversifiée. Cette région joue un rôle important dans la diversité génétique globale de l'espèce. Le sud-ouest de l'océan Indien constitue l'une des deux seules zones connues à l'heure actuelle de contact entre les deux métapopulations de tortues vertes (Atlantique-Méditerranée et Indo-Pacifique). Ce contact a entraîné la formation d'un cline génétique portant principalement sur les fréquences relatives des haplotypes CM8 (Atlantique) et C3 (Indo-Pacifique). Les résultats obtenus lors de l'analyse microsatellite de la différenciation entre les individus originaires des deux métapopulations montrent que le sud-ouest de l'océan Indien constitue une zone d'échanges génétiques entre les deux métapopulations, participant au brasage génétique de l'espèce. L'étude de facteurs, intrinsèques et extrinsèques, pouvant influencer la structuration des populations apportent de nombreuses informations qui pourraient s'avérer utiles lors de l'élaboration de plans de gestion. La structure des femelles et des mâles en alimentation ne diffère pas, contrairement à celle des immatures qui semble s'organiser en 'pools régionaux' qui seraient le fruit de l'interaction d'un comportement de philopatrie et d'une influence des courants océaniques. La forte différenciation mitochondriale des femelles en ponte et la très faible différenciation microsatellite observée à l'échelle de la région, indiquent l'existence de flux de gènes via les mâles. La composition génétique d'un site ne varie pas de manière significative au cours de l'année. Par contre, elle peut varier d'une année à l'autre, signifiant l'alternance dans certains sites de ponte de plusieurs populations distinctes. L'évolution de la composition génétique d'un groupe, au cours de 10 ou 20 ans, diffère selon le site considéré. La distance ne semble pas influencer de manière significative la structuration des populations au niveau microsatellite. Les femelles en ponte sur la plage de Saziley (Mayotte) diffèrent génétiquement de celles pondant sur les deux autres plages de l'île. La structure observée des populations est en accord avec l'organisation des courants océanique dans la région. La confrontation des résultats obtenus à partir des deux marqueurs génétiques utilisés, permet la détermination de 8 ensembles génétiquement différenciés dans la zone d'étude et l'identification d'au moins 6 populations distinctes. Ces ensembles constituent autant d'unités de gestion (MUs) potentielles qui pourront servir de base à l'élaboration de plans de gestion et de conservation.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2007/these-3532.pdf
http://archimer.ifremer.fr/doc/00000/3532/

Éditeur(s) : Natl Acad Sciences
Résumé : The marine realm represents 70% of the surface of the biosphere and contains a rich variety of organisms, including more than 34 of the 36 living phyla, some of which are only found in the oceans. The number of marine species used by humans is growing at unprecedented rates, including the rapid domestication of marine species for aquaculture and the discovery of natural products and genes of medical and biotechnological interest in marine biota. The rapid growth in the human appropriation of marine genetic resources (MGRs), with over 18,000 natural products and 4,900 patents associated with genes of marine organisms, with the latter growing at 12% per year, demonstrates that the use of MGRs is no longer a vision but a growing source of biotechnological and business opportunities. The diversification of the use of marine living resources by humans calls for an urgent revision of the goals and policies of marine protected areas, to include the protection of MGRs and address emerging issues like biopiracy or benefit sharing. Specific challenges are the protection of these valuable resources in international waters, where no universally accepted legal framework exists to protect and regulate the exploitation of MGRs, and the unresolved issues on patenting components of marine life. Implementing steps toward the protection of MGRs is essential to ensure their sustainable use and to support the flow of future findings of medical and biotechnological interest.
Proceedings Of The National Academy Of Sciences Of The United States Of America (0027-8424) (Natl Acad Sciences), 2010-10 , Vol. 107 , N. 43 , P. 18318-18324

Droits : 2010 by the National Academy of Sciences
http://archimer.ifremer.fr/doc/00018/12897/9935.pdf
DOI:10.1073/pnas.0911897107
http://archimer.ifremer.fr/doc/00018/12897/

Éditeur(s) : Blackwell science
Résumé : Patterns of mitochondrial DNA (mtDNA) variation were used to analyse the population genetic structure of southwestern Indian Ocean green turtle (Chelonia mydas) populations. Analysis of sequence variation over 396 bp of the mtDNA control region revealed seven haplotypes among 288 individuals from 10 nesting sites in the Southwest Indian Ocean. This is the first time that Atlantic Ocean haplotypes have been recorded among any Indo-Pacific nesting populations. Previous studies indicated that the Cape of Good Hope was a major biogeographical barrier between the Atlantic and Indian Oceans because evidence for gene flow in the last 1.5 million years has yet to emerge. This study, by sampling localities adjacent to this barrier, demonstrates that recent gene flow has occurred from the Atlantic Ocean into the Indian Ocean via the Cape of Good Hope. We also found compelling genetic evidence that green turtles nesting at the rookeries of the South Mozambique Channel (SMC) and those nesting in the North Mozambique Channel (NMC) belong to separate genetic stocks. Furthermore, the SMC could be subdivided in two different genetic stocks, one in Europa and the other one in Juan de Nova. We suggest that this particular genetic pattern along the Mozambique Channel is attributable to a recent colonization from the Atlantic Ocean and is maintained by oceanic conditions in the northern and southern Mozambique Channel that influence early stages in the green turtle life cycle.
Molecular Ecology (0962-1083) (Blackwell science), 2007 , Vol. 16 , N. 1 , P. 175-186

Droits : 2007 Blackwell
http://archimer.ifremer.fr/doc/2007/publication-2185.pdf
DOI:10.1111/j.1365-294X.2006.03122.x
http://archimer.ifremer.fr/doc/00000/2185/

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
Patterns of connectivity and self-recruitment are recognized as key factors shaping the dynamics of marine populations. Connectivity is also essential for maintaining and restoring natural ecological processes with genetic diversity contributing to the adaptation and persistence of any species in the face of global disturbances. Estimates of connectivity are crucial to inform the design of both marine protected areas (MPAs) and MPA networks. Among several approaches, genetic structure is frequently used as a proxy for patterns of connectivity. Using 8 microsatellite loci, we investigated genetic structure of the two-banded sea bream Diplodus vulgaris, a coastal fish that is both commercially and ecologically important. Adults were sampled in 7 locations (stretches of coastline approximately 8 km long) and juveniles in 14 sites (~100 to 200 m of coastline) along 200 km of the Apulian Adriatic coast (SW Adri-atic Sea), within and outside an MPA (Torre Guaceto MPA, Italy). Our study found similar genetic diversity indices for both the MPA and the surrounding fished areas. An overall lack of genetic structure among samples suggests high gene flow (i.e. connectivity) across a scale of at least 200 km. However, some local genetic divergences found in two locations demonstrate some heterogeneity in processes renewing the population along the Apulian Adriatic coast. Furthermore, two sites appeared genetically divergent, reinforcing our observations within the genetic makeup of adults and confirming heterogeneity in early stage genetics that can come from either different supply populations or from chaotic genetic patchiness occurring under temporal variation in recruitment and in the reproductive success. While the specific role of the MPA is not entirely known in this case, these results confirm the presence of regional processes and the key role of connectivity in maintaining the local population supply.
ISSN: 1932-6203

hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/document
https://hal-univ-perp.archives-ouvertes.fr/hal-01442055/file/journal.pone.0167441.pdf
DOI : 10.1371/journal.pone.0167441.s009

Éditeur(s) : Soc Geol France
Résumé : The Lesser Antilles subduction zone has produced no recent strong thrust earthquakes, making it difficult to quantify the seismic hazard from such events. The Lesser Antilles arc has a low subduction rate and an accretionary wedge that is very wide at its southern end. To investigate the effect of the wedge on seismogenesis, numerical models of forearc thermal structure were constructed along six transects perpendicular to the arc in order to determine the thermally predicted width of the seismogenic zone. The geometry of each section is constrained by published seismic profiles and crustal models derived from gravity and seismic data and by earthquake hypocenters at depth. A major constraint on the deep part of the model is that mantle temperature beneath the volcanic arc should achieve a temperature of 1,100 degrees C to generate partial melts. Predicted surface heat flow is compared to the available heat flow observations. Thermal modeling results indicate a systematic southward increase in the width of the seismogenic zone, more than doubling in width from north to south and corresponding to a dramatic southward increase in forearc width (distance from the arc to the deformation front of the accretionary wedge). The minimum width of the seismogenic zone (distance between the intersections of the subduction interface with the 150 degrees C and 350 degrees C isotherms) increases from about 80 km, north of 16 degrees N, to 230 km, at 13 degrees N. The maximum width (between the 100 degrees C and 450 degrees C isotherms) ranges from about 150 km in the north to up to 320 km in the south. This large variation in the width of the seismogenic zone is a consequence of the increasing width of the accretionary wedge to the south, caused by the increased thickness of sediment on the subducting plate. There is good agreement between the thermally predicted seismogenic limits and the sparse distribution of recorded thrust earthquakes, which are observed only in the northern portion of the arc. Possible scenarios for mega-thrust earthquakes are discussed. Depending on the segment length (along-strike) of the rupture plane, the occurrence of an event of magnitude 8-9 cannot be excluded.
L’absence de grands séismes récents à mécanismes chevauchants dans la zone de subduction des Petites Antilles rend difficile l’évaluation de l’aléa sismique lié à de tels événements. L’arc des Petites Antilles est caractérisé par une faible vitesse de subduction et par la présence d’un prisme d’accrétion très développé à son extrémité méridionale. Afin d’évaluer les effets de la largeur de ce prisme sur la genèse des séismes, nous avons étudié six sections perpendiculaires à l’arc, du nord au sud de celui-ci, pour déterminer la largeur de la zone sismogène prédite par les modèles thermiques appliqués à chacune de ces coupes. La géométrie de ces dernières est contrainte par les profils sismiques publiés, par les modèles de structure crustale déduits des données gravitaires et sismiques, et enfin par la distribution des hypocentres des séismes. Un contrôle important permettant de tester la validité des modèles thermiques en profondeur est qu’une température minimale de 1 100oC, compatible avec la fusion partielle du manteau hydraté, doit être atteinte sous l’arc volcanique actif. Par ailleurs, le flux thermique en surface prédit par ces modèles doit être compatible avec les mesures de flux de chaleur. Les modèles thermiques retenus d’après ces critères montrent une augmentation du simple au double vers le sud de la largeur de la zone sismogène, qui correspond à un élargissement considérable de la taille du domaine avant-arc. En effet, la largeur minimale de la zone sismogène (définie comme la distance entre les intersections de l’interface des plaques avec les isothermes 150o et 350oC) augmente d’environ 80 km au nord de 16oN jusqu’à 230 km à 13oN. La largeur maximale de cette zone (définie par les intersections de l’interface avec les isothermes 100o et 450oC) augmente, quant à elle, d’environ 150 km au nord jusqu’à 320 km au sud de l’arc. Cette variation considérable est la conséquence de l’augmentation de la largeur du prisme d’accrétion, elle-même causée par l’accumulation croissante des sédiments déposés sur la plaque plongeante. Les largeurs de la zone sismogène prédites à l’aide des modèles thermiques sont en bon accord avec les rares données disponibles sur les séismes à mécanismes chevauchants dans la partie nord de l’arc. Les scénarios possibles relatifs à des méga-séismes de ce type n’excluent pas de futurs événements atteignant des magnitudes de 8 à 9.
Bulletin De La Societe Geologique De France (0037-9409) (Soc Geol France), 2013 , Vol. 184 , N. 1-2 , P. 47-59

Droits : 2013 Societe Geologique de France
http://archimer.ifremer.fr/doc/00140/25140/29432.pdf
DOI:10.2113/gssgfbull.184.1-2.47
http://archimer.ifremer.fr/doc/00140/25140/

Éditeur(s) : HAL CCSD Royal Society of Chemistry
Résumé : International audience
Abstract View references (60)Here we show the long term performance at high temperatures of a multi-tube module containing 8 membranes in 4 parallel lines with a total of 545 cm 2 area. The membranes were prepared via thin film dip coating of cobalt oxide silica (CoO xSi) sol-gel on tubular alumina supports. A preliminary study found that the sol-gel containing 20 mol% cobalt oxide formed the best microporous structure with the highest surface area and pore volume. All resulting membranes delivered permeances of ∼1 × 10 -7 mol m -2 s -1 Pa -1 at 500 °C, indicating a high repeatability for the membrane fabrication process. The permselectivities of helium (He) and hydrogen (H 2) over carbon dioxide (CO 2) and nitrogen (N 2) increased from 10-20 at 100 °C to values close to 1000 at 500 °C. Additionally, the apparent energies of activation (E act) for the smaller kinetic diameter gases He and H 2 at 12.2 and 19.5 kJ mol -1 were high and contrary to the negative values for larger gases N 2 and CO 2 at -1.8 and -7.4 kJ mol -1. These remarkable results were attributed to the molecular sieving mechanism of the microporous silica which was enhanced by the embedding of cobalt oxide into the matrix, delivering structural control with an average pore size of 3 Å. The E act for H 2 permeance was higher than that of He, indicating that the cobalt oxide played an important role in H 2 transport. Two membrane lines performed exceptionally well for binary gas mixture processing with H 2 purity reaching values close to 100% in the permeate stream for argon (Ar) concentrations of up to 80% in the retentate stream. A major finding here is that the binary gas selectivity was independent of temperature, contrary to the permselectivity observed for single gas permeance. Further, the H 2 flow rate was greatly affected by the concentration of Ar in the mixture, while the temperature dependency played only a marginal role. In particular, competitive adsorption in the percolative pathways containing pore constrictions or bottlenecks of the anisotropic CoO xSi matrix allowed Ar to impede H 2 diffusion. Finally, the CoO xSi membranes proved thermally stable and robust for 2000 h of testing for various thermal cycles up to 500 °C. © The Royal Society of Chemistry 2012.
Energy & Environmental Science

hal-01683199
https://hal.univ-antilles.fr/hal-01683199
DOI : 10.1039/c2ee03247c

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Background. In wild plant populations, genetic divergence within continuous stands is common, sometimes at very short geographical scales. While restrictions to gene flow combined with local inbreeding and genetic drift may cause neutral differentiation among subpopulations, microgeographical variations in environmental conditions can drive adaptive divergence through natural selection at some targeted loci. Such phenomena have recurrently been observed in plant populations occurring across sharp environmental boundaries, but the interplay between selective processes and neutral genetic divergence has seldom been studied.[br/]Methods. We assessed the extent of within-stand neutral and environmentally-driven divergence in the Neotropical tree [i]Eperua falcate Aubl[/i]. (Fabaceae) through a genome-scan approach. Populations of this species grow in dense stands that cross the boundaries between starkly contrasting habitats. Within-stand phenotypic and candidate-gene divergence have already been proven, making this species a suitable model for the study of genome-wide microgeographic divergence. Thirty trees from each of two habitats (seasonally flooded swamps and well-drained plateaus) in two separate populations were genotyped using thousands of AFLPs markers. To avoid genotyping errors and increase marker reliability, each sample was genotyped twice and submitted to a rigorous procedure for data cleaning, which resulted in 1196 reliable and reproducible markers.[br/]Results. Despite the short spatial distances, we detected within-populations genetic divergence, probably caused by neutral processes, such as restrictions in gene flow. Moreover, habitat-structured subpopulations belonging to otherwise continuous stands also diverge in relation to environmental variability and habitat patchiness: we detected convincing evidence of divergent selection at the genome-wide level and for a fraction of the analyzed loci (comprised between 0.25% and 1.6%). Simulations showed that the levels of differentiation for these outliers are compatible with scenarios of strong divergent selection
ISSN: 1932-6203

hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220
https://hal.archives-ouvertes.fr/hal-01204220/document
https://hal.archives-ouvertes.fr/hal-01204220/file/journal.pone.0121394.PDF
PRODINRA : 287494