Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This work deals with the problem of finding for a given industrial target the molecule conformation leading to the most efficient crystal polymorph and/or designing unknown crystal packing of new molecules. The originality of the method relies first on constraining the domain of the most probable crystals, before converging towards the predicted packing by a double genetic-refining optimization algorithm. Validation of this approach is discussed on the case study of 46 energetic crystal compounds, using the semi Ab Initio and Molecular Mechanics code GenMol™. This validation shows that all observed structures are retrieved in any circumstances with a relatively high number of good rankings.
ISSN: 0022-0248

hal-00857875
https://hal.archives-ouvertes.fr/hal-00857875
DOI : 10.1016/j.jcrysgro.2009.04.002

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The distribution of the lagoon cockle Cerastoderma glaucum is strongly fragmented and usually restricted to isolated, shallow and nontidal lagoons. A high level of genetic structuring was found among the European populations of this species based on mtDNA (COI) sequences, as well as allozymic and microsatellite markers. However, the strengths and geographic locations of the major divisions differed among markers. In the present study we characterized the diversity of a new, potentially universal exon-primed intron-crossing marker, i34, for 17 C. glaucum populations. Allele frequency data at the i34 locus were informative and relevant with respect to geography. Multivariate analyses of new data together with previously published microsatellites confirmed the divergent character of the Ionian Sea and the Aegean-Ponto-Caspian populations, but also revealed the existence of a genetic cline from the Bay of Biscay to the Baltic Sea. Some noncongruent patterns among loci were detected, which may reflect either differential introgression along the genome at the hypothetical contact zone, or selective sweeps. This strong genetic differentiation, and the occurrence of private alleles, may hint at the presence of cryptic species within C. glaucum.
ISSN: 0260-1230

hal-01444646
https://hal.archives-ouvertes.fr/hal-01444646
DOI : 10.1093/mollus/eyw019

Éditeur(s) : HAL CCSD SAGE Publications (UK and US)
Résumé : International audience
Molecular evolutionary analysis is an efficient method to predict and/or validate amino acid substitutions that could lead to a genetic disease and to highlight residues and motifs that could play an important role in the protein structure and/or function. We have applied such analysis to amelotin (AMTN), a recently identified enamel protein in the rat, mouse, and humans. An in silico search for AMTN provided 42 new mammalian sequences that were added to the 3 published sequences with which we performed the analysis using a dataset representative of all lineages (circa 220 million years of evolution), including 2 enamel-less species, sloth and armadillo. During evolution, of the 209 residues of human AMTN, 17 were unchanged and 34 had conserved their chemical properties. Substituting these important residues could lead to amelogenesis imperfecta (AI). Also, AMTN possesses a well-conserved signal peptide, 2 conserved motifs whose function is certainly important but unknown, and a putative phosphorylation site (SXE). In addition, the sequences of the 2 enamel-less species display mutations revealing that AMTN underwent pseudogenization, which suggests that AMTN is an enamel-specific protein.
ISSN: 0022-0345

hal-01545488
https://hal.archives-ouvertes.fr/hal-01545488
DOI : 10.1177/0022034512460551

Éditeur(s) : HAL CCSD
Résumé : International audience
Symbiosis is a widespread phenomenon in the biosphere. In marine benthic environments breakdown of symbiosis is responsible for coral bleaching and dramatically affects coral reef ecosystems functioning [1]. In the water column, planktonic organisms are key component of pelagic ecosystems and a number of species form mutualistic association with microalgae forming a photosymbiosis [2]. Here we intended to investigate the genetic basis of photosymbiosis, through a transcriptomic approach on marine plankton organisms. We focused more specifically on associations occurring between radiolarian host (protist, zooplankton) and dinoflagellates symbiont (protist, phytoplankton) living inside the host cell. It has recently been highlighted that these holobionts are widespread in oligotrophic open oceans and there are also evidences of their fundamental implication in biogeochemical carbon, silica and strontium cycles [3, 4, 5, 6]. RNA-seq technologies allow obtaining an unprecedented amount of data for unicellular organisms isolated from the environment [7]. The study of such non-model holobionts datasets requires de novo assembly, which implies considerable computational resources and the potential production of chimeric sequences [8, 9].We therefore developed an original strategy aiming at accelerating and improving de novo assembly for holobiont datasets. We chose SIMKA [10] a fast kmer-based method initially developed to estimate the similarity between numerous metagenomic datasets, and which has been recently adapted to extract their common sequences. As our symbionts are identified, we used SIMKA to compare our holobionts transcriptomes to publicly available dinoflagellates transcriptomes [11] generating two datasets, one composed of reads from the symbionts and another with reads from the host (for which no reference data are currently available). Independent assemblies were then performed in parallel, accelerating the study process, and minimizing the proportion of resulting chimeric sequences. Our strategy produced a unique and comprehensive genomic dataset for Radiolaria [12, 13], and offers a pragmatic, large scale, comparison strategy to assemble and study holobionts [9]. Our new sequences obtained from holobionts study will be used for phylogenomics investigation, as reference for environmental metagenomic studies and ultimately to understand and characterize the molecular basis of symbiotic relationships in the plankton.Bibliografic references :[1] Simon K. Davy, Denis Allemand, and Virginia M. Weis. “Cell Biology of Cnidarian-Dinoflagellate Symbiosis”. In: Microbiology and Molecular Biology Reviews 76.2 (June 1, 2012), pp. 229–261. issn: 1092-2172, 1098- 5557. doi: 10.1128/MMBR.05014-11.[2] Janouškovec, J. et al. “Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics”. in: PNAS 201614842 (2016). doi:10.1073/pnas.1614842114[3] Tristan Biard et al. “In situ imaging reveals the biomass of giant protists in the global ocean”. In: Nature advance online publication (Apr. 20, 2016). issn: 0028-0836. doi: 10.1038/nature17652.[4] Lionel Guidi et al. “Plankton networks driving carbon export in the olig- otrophic ocean”. In: Nature 532.7600 (Apr. 28, 2016), pp. 465–470. issn: 0028-0836. doi: 10.1038/nature16942.[5] Diane K. Stoecker et al. “Acquired phototrophy in aquatic protists”. In: Aquatic Microbial Ecology 57.3 (Nov. 24, 2009), pp. 279–310. doi: 10.3354/ame01340.[6] Johan Decelle et al. “An original mode of symbiosis in open ocean plankton”. In: Proceedings of the National Academy of Sciences 109.44 (Oct. 30, 2012), pp. 18000–18005. issn: 0027-8424, 1091-6490. doi: 10. 1073/pnas.1212303109.[7] Sergio Balzano et al. “Transcriptome analyses to investigate symbiotic relationships between marine protists”. In: Frontiers in Microbiology 6 (Mar. 17, 2015). issn: 1664-302X. doi: 10.3389/fmicb.2015.00098.[8] Li, B. et al. “Evaluation of de novo transcriptome assemblies from RNA-Seq data”. In: Genome Biology 15, 553 (2014).[9] Sangwan, N., Xia, F. & Gilbert, J. A. “Recovering complete and draft population genomes from metagenome datasets”. In: Microbiome 4, 8 (2016).[10] Gaëtan Benoit et al. “Multiple comparative metagenomics using mul- tiset k -mer counting”. In: PeerJ Computer Science 2 (Nov. 14, 2016). doi: 10.7717/peerj-cs.94.[11] Patrick J. Keeling et al. “The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing”. In: PLOS Biol 12.6 (June 2014), e1001889. issn: 1545-7885. doi: 10.1371/journal.pbio.1001889.[12] Burki, F. et al. “Evolution of Rhizaria: new insights from phylogenomic analysis of uncultured protists”. In BMC Evolutionary Biology 10, 377 (2010).
International Conference on Holobionts
Paris, France

hal-01575069
https://hal.inria.fr/hal-01575069

Éditeur(s) : Natl Marine Fisheries Service Scientific Publ Office
Résumé : Twenty homologous microsatellite markers, or simple sequence repeats (SSRs), were developed for blackfin tuna (Thunnus atlanticus) through the use of a direct Seq-to-SSR approach. The number of alleles per locus ranged between 5 and 26, and the expected heterozygosity ranged between 0.640 and 0.969. Three loci displayed significant departure from Hardy-Weinberg equilibrium expectations, likely reflecting occurrence of null alleles. Another locus showed consecutive alleles that differed by one base pair only. Consequently, this locus may be prone to elevated rates of scoring errors. The remaining 16 loci will be valuable for studies in conservation genetics of blackfin tuna.
Fishery Bulletin (0090-0656) (Natl Marine Fisheries Service Scientific Publ Office), 2014-10 , Vol. 112 , N. 4 , P. 322-325

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00239/34999/33529.pdf
DOI:10.7755/FB.112.4.8
http://archimer.ifremer.fr/doc/00239/34999/

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Cell proliferation is a hallmark of cancer and depends on complex signaling networks that are chiefly supported by protein kinase activities. Therapeutic strategies have been used to target specific kinases but new methods are required to identify combined targets and improve treatment. Here, we propose a small interfering RNA genetic screen and an integrative approach to identify kinase networks involved in the proliferation of cancer cells. The functional siRNA screen of 714 kinases in HeLa cells identified 91 kinases implicated in the regulation of cell growth, most of them never being reported in previous whole-genome siRNA screens. Based on gene ontology annotations, we have further discriminated between two classes of kinases that, when suppressed, result in alterations of the mitotic index and provoke cell-cycle arrest. Extinguished kinases that lead to a low mitotic index mostly include kinases implicated in cytosolic signaling. In contrast, extinguished kinases that result in a high mitotic index mostly include kinases implicated in cell division. By mapping hit kinases in the PhosphPOINT phosphoprotein database, we generated scale-free networks consisting of 449 and 661 protein-protein interactions for kinases from low MI and high MI groups, respectively. Further analyses of the kinase interactomes revealed specific modules such as FER- and CRKL-containing modules that connect three members of the epidermal growth factor receptor (EGFR) family, suggesting a tight control of the mitogenic EGF-dependent pathway. Based on experimental studies, we confirm the involvement of these two kinases in the regulation of tumor cell growth. Based on a combined approach of large kinome-wide siRNA screens and ontology annotations, our study identifies for the first time two kinase groups differentially implicated in the control of cell proliferation. We further demonstrate that integrative analysis of the kinase interactome provides key information which can be used to facilitate or optimize target design for new therapeutic strategies. The complete list of protein-protein interactions from the two functional kinase groups will provide a useful database for future investigations.
ISSN: 1471-2164

hal-01118475
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118475
DOI : 10.1186/1471-2164-15-1169
PUBMED : 25540073

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
A hallmark of living systems is the management and the storage of information through genetic and epigenetic mechanisms. Although the notion of epigenetics was originally given to any regulation beyond DNA sequence, it has often been restricted to chromatin modifications, supposed to behave as cis-markers, specifying the sets of genes to be expressed or repressed. This definition does not take into account the initial view of epigenetics, based on nonlinear interaction networks whose "attractors" can remain stable without need for any chromatin mark. In addition, most chromatin modifications are the steady state resultants of highly dynamic modification and de-modification activities and, as such, seem poorly appropriate to work as long-term memory keepers. Instead, the basic support of epigenetic memory could remain the attractors, to which chromatin modifications belong as do many other components. The influence of chromatin modifications in memory is highly questionable when envisioned as static structural marks, but can be recovered under the dynamic circuitry perspective, thanks to their self-templating properties. Beside their standard repressive or permissive functions, chromatin modifications can also influence transcription in multiple ways such as: (1) by randomizing or inversely stabilizing gene expression, (2) by mediating cooperativity between pioneer and secondary transcription factors, and (3) in the hysteresis and the ultrasensitivity of gene expression switches, allowing the cells to take unambiguous transcriptional decisions.
ISSN: 1420-682X

hal-01063617
https://hal.archives-ouvertes.fr/hal-01063617
DOI : 10.1007/s00018-012-0923-7
PUBMED : 22331281

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: Ameloblastin (AMBN) is a phosphorylated, proline/glutamine-rich protein secreted during enamel formation. Previous studies have revealed that this enamel matrix protein was present early in vertebrate evolution and certainly plays important roles during enamel formation although its precise functions remain unclear. We performed evolutionary analyses of AMBN in order to (i) identify residues and motifs important for the protein function, (ii) predict mutations responsible for genetic diseases, and (iii) understand its molecular evolution in mammals. Results: In silico searches retrieved 56 complete sequences in public databases that were aligned and analyzed computationally. We showed that AMBN is globally evolving under moderate purifying selection in mammals and contains a strong phylogenetic signal. In addition, our analyses revealed codons evolving under significant positive selection. Evidence for positive selection acting on AMBN was observed in catarrhine primates and the aye-aye. We also found that (i) an additional translation initiation site was recruited in the ancestral placental AMBN, (ii) a short exon was duplicated several times in various species including catarrhine primates, and (iii) several polyadenylation sites are present. Conclusions: AMBN possesses many positions, which have been subjected to strong selective pressure for 200 million years. These positions correspond to several cleavage sites and hydroxylated, O-glycosylated, and phosphorylated residues. We predict that these conserved positions would be potentially responsible for enamel disorder if substituted. Some motifs that were previously identified as potentially important functionally were confirmed, and we found two, highly conserved, new motifs, the function of which should be tested in the near future. This study illustrates the power of evolutionary analyses for characterizing the functional constraints acting on proteins with yet uncharacterized structure.
ISSN: 1471-2148

Droits : http://creativecommons.org/licenses/by/
hal-01212816
http://hal.upmc.fr/hal-01212816
http://hal.upmc.fr/hal-01212816/document
http://hal.upmc.fr/hal-01212816/file/s12862-015-0431-0.pdf
DOI : 10.1186/s12862-015-0431-0

Résumé : Les variétés modernes de canne à sucre sont d'origine bispécifique et possèdent une structure génétique complexe, aneuploïde et hautement polyploïde rendant difficile les études de résistance génétique. La feuille jaune de la canne a sucre est une maladie dont l'agent causal est le sugarcane yellow leaf virus (scylv). Ce virus a une large diversité. Seuls trois génotypes viraux, différenciables par rtpcr, ont été trouves en Guadeloupe. Les objectifs de l'étude sont d'évaluer: l/la possibilité de marquer la résistance de la plante au scylv grâce a une étude d'association pan-génomique 2/l'impact de la diversité de l'agent pathogène sur la résistance de la canne a sucre au scylv. Les études d'association ont été menées avec plus de 4000 marqueurs aflp et d'art sur quatre types de données phénotypiques (intensité et densité virale dans les feuilles et les tiges). Les phénotypes ont été mesures sur 189 variétés de cannes à sucre dans deux essais successifs dans un dispositif en trois blocs randomises. De ces variétés, 40 ont été sélectionnées et ont permis d'obtenir 10 croisements biparentaux. Les descendances obtenues ont été suivies sur deux essais. L'incidence et la diversité du scylv ont été évaluées pour les 40 variétés et les descendances. L'héritabilité au sens strict de la résistance aux scylv a été déterminée. Six marqueurs de résistance au scylv ont été identifies ainsi que deux gènes ayant potentiellement un rôle dans la résistance au virus. L'étude montre également que la résistance de la plante est variable en fonction du génotype du scylv et que cette résistance est en partie transmise aux descendances. Créer des variétés résistantes au scylv est donc possible.
Modern varieties of sugarcane have a bispecific origin and a complex genetic structure, aneuploid and highly polyploid, maklng genetic resistance study uneasy to perform. Yellow leaf of sugarcane is a viral disease whose causal agent is the sugarcane yellow leaf virus (scylv). This virus has a wide range of diversity. Only three viral genotypes, distinguishable by rt-pcr, were found in guadeloupe. The objectives of this srudy are to assess: l/the possibility to find markers associated with plant resistance to scylv through a genome wide association study 2 1 the impact of the pathogen diversity on the resistance of sugarcane to scylv. Association studies have been conducted with more than 4000 aflp and dart markers on four types of phenotypic data (virus intensity and density in leaves and canes). Phenotypes were measured on 189 varieties of sugarcane in two successive trials in a three randomized complete block design. From these varieties, 40 were selected and allowed to obtain 10 biparental crosses. The offspring were followed during two trials. The incidence and the diversity of scylv were evaluated in the 40 varieties and the offspring. The narrow sense heritability of the resistance to the scylvs was determined. Six markers of the resistance to the scylv and two genes, with potential contribution in virus resistance, have been identified. The study also shows that the resistance of the plant is variable depending on the scylv genotype and that this resistance is partly transmitted to the offspring. Breeding for scylv resistance is practicable.

http://www.theses.fr/2012AGUY0554/document

Éditeur(s) : HAL CCSD Inter-Research
Résumé : International audience
Many large groupers form spawning aggregations, returning to the same spawning sites in consecutive spawning seasons. Connectivity between spawning aggregations is thus assured by larval dispersal. This study looks into the genetic structure and gene flow among spawning aggregations of a large grouper, the gulf coney Hyporthodus acanthistius, in the northern Gulf of California. First, using the mitochondrial control region and 11 microsatellites, we calculated FST metrics and conducted a Bayesian clustering analysis to determine structure among 5 spawning aggregations. Shallow genetic structure was found, separating the southernmost spawning aggregate from the remainder. Second, we used the results from the structure analysis and local water circulation patterns to delineate 3 distinct models of gene flow. The best-supported model, in which the southernmost spawning aggregate formed one group and all other spawning aggregates were nested into a second group, was the one that was consistent with water circulation during the species’ spawning season. Larval retention within a seasonal anticyclonic gyre that formed during the gulf coney’s spawning season may be responsible for the patterns found. This study highlights the importance of local oceanographic conditions in dictating the structure among spawning aggregations even at small geographic scales and contributes to informed management plans for this overexploited grouper.
Marine Ecology Progress Series

hal-01301199
https://hal-univ-perp.archives-ouvertes.fr/hal-01301199
DOI : 10.3354/meps10637

Éditeur(s) : HAL CCSD SpringerLink
Résumé : The development of microsatellite markers can be a time-consuming process, especially in species such as conifers where many microsatellites have been shown to be associated with the repetitive fraction of the genome and to produce complex banding patterns following electrophoresis. Therefore, procedures to eliminate this fraction from further processing are sought. In this paper, we report on the development of 53 dinucleotide SSR markers in Norway spruce, 35 of which (66%) produce simple, polymorphic patterns. This high efficiency is obtained by introducing a dot-blot selection against high copy number sequences, performed on the microsatellite-containing clones. The resulting markers turned out to be polymorphic and useful for population genetic studies and for linkage mapping. Seven additional markers that were not subject to the dot-blot selection are also presented.
Theoretical and Applied Genetics

hal-01031865
https://hal.archives-ouvertes.fr/hal-01031865
DOI : 10.1007/s00122-001-0843-7

Éditeur(s) : HAL CCSD
Résumé : International audience
Estrogen receptor alpha (ERα) has been recognized now for several decades as playing a key role in reproduction and exerting functions in numerous nonreproductive tissues. In this review, we attempt to summarize the in vitro studies that are the basis of our current understanding of the mechanisms of action of ERα as a nuclear receptor and the key roles played by its two activation functions (AFs) in its transcriptional activities. We then depict the consequences of the selective inactivation of these AFs in mouse models, focusing on the prominent roles played by ERα in the reproductive tract and in the vascular system. Evidence has accumulated over the two last decades that ERα is also associated with the plasma membrane and activates non-nuclear signaling from this site. These rapid/nongenomic/membrane-initiated steroid signals (MISS) have been characterized in a variety of cell lines, and in particular in endothelial cells. The development of selective pharmacological tools that specifically activate MISS and the generation of mice expressing an ERα protein impeded for membrane localization have begun to unravel the physiological role of MISS in vivo. Finally, we discuss novel perspectives for the design of tissue-selective ER modulators based on the integration of the physiological and pathophysiological roles of MISS actions of estrogens.
Physiological Reviews

hal-01533249
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01533249
DOI : 10.1152/physrev.00024.2016
PUBMED : 28539435

Éditeur(s) : HAL CCSD BMJ Publishing Group
Résumé : International audience
BACKGROUND: Mutations in the leucine-rich-repeat kinase 2 (LRRK2) gene have been identified in families with autosomal dominant Parkinson's disease (ADPD), the most common of which is the p.G2019S substitution that has been found at varying frequencies worldwide. Because of the size of the LRRK2 gene, few studies have analysed the entire gene in large series of ADPD families. METHODS: We performed extensive mutation analyses of all 51 coding exons of the LRRK2 gene in index cases from 226 Parkinson's disease families compatible with autosomal dominant inheritance, mostly from France (n = 182) and North Africa (n = 14). RESULTS: We found 79 sequence variants, 29 of which were novel. Eight potentially or proven pathogenic mutations were found in 22 probands (9.7%). There were four novel amino acid substitutions that are potentially pathogenic (p.S52F, p.N363S, p.I810V, p.R1325Q) and two novel variants, p.H1216R and p.T1410M, that are probably not causative. The common p.G2019S mutation was identified in 13 probands (5.8%) including six from North Africa (43%). The known heterozygous p.R1441H and p.I1371V mutations were found in two probands each, and the p.E334K variant was identified in one single patient. Most potentially or proven pathogenic mutations were located in the functional domains of the Lrrk2 protein. CONCLUSION: This study leads us to conclude that LRRK2 mutations are a common cause of autosomal dominant Parkinson's disease in Europe and North Africa.
ISSN: 0022-2593

inserm-00529272
http://www.hal.inserm.fr/inserm-00529272
DOI : 10.1136/jmg.2008.062612
PUBMED : 19357115

Éditeur(s) : HAL CCSD National Academy of Sciences
Résumé : International audience
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
ISSN: 0027-8424

hal-01417471
https://hal-univ-perp.archives-ouvertes.fr/hal-01417471
DOI : 10.1073/pnas.1611797113

Éditeur(s) : HAL CCSD Wiley
Résumé : The extent of gene dispersal is a fundamental factor of the population and evolutionary dynamics of tropical tree species, but directly monitoring seed and pollen movement is a difficult task. However, indirect estimates of historical gene dispersal can be obtained from the fine-scale spatial genetic structure of populations at drift-dispersal equilibrium. Using an approach that is based on the slope of the regression of pairwise kinship coefficients on spatial distance and estimates of the effective population density, we compare indirect gene dispersal estimates of sympatric populations of 10 tropical tree species. We re-analysed 26 data sets consisting of mapped allozyme, SSR (simple sequence repeat), RAPD (random amplified polymorphic DNA) or AFLP (amplified fragment length polymorphism) genotypes from two rainforest sites in French Guiana. Gene dispersal estimates were obtained for at least one marker in each species, although the estimation procedure failed under insufficient marker polymorphism, limited sample size, or inappropriate sampling area. Estimates generally suffered low precision and were affected by assumptions regarding the effective population density. Averaging estimates over data sets, the extent of gene dispersal ranged from 150 m to 1200 m according to species. Smaller gene dispersal estimates were obtained in species with heavy diaspores, which are presumably not well dispersed, and in populations with high local adult density. We suggest that limited seed dispersal could indirectly limit effective pollen dispersal by creating higher local tree densities, thereby increasing the positive correlation between pollen and seed dispersal distances. We discuss the potential and limitations of our indirect estimation procedure and suggest guidelines for future studies
ISSN: 0962-1083

hal-01031603
https://hal.archives-ouvertes.fr/hal-01031603
DOI : 10.1111/j.1365-294X.2005.02785.x

Éditeur(s) : HAL CCSD
Résumé : The recent accumulation of genomic sequence data has shown that gene evolution is not strictly tree-Like. Many evolutionary processes, like exon shuffling, gene fusion or nonhomologous recombination remodel genes by creating composite structures that are made from parts with different evolutionary histories. The development of sequence similarity networks provides an analytical framework to study the impact of these processes on molecular evolution, by structuring the resemblance relationships between sequences and by formalizing, in terms of graph theory, the detection of composite genes (intransitive triplets) and gene families (clique minimal separators). The size of current data sets, typically several million sequences, has also required the development of new tools and methods: sequence comparison parallelization, large networks visualization with Louvain communities and large cycles identification. When applied to eukaryotic and viral genome data sets, these methods have shown that composite genes are found throughout cellular organisms and mobile genetic elements. Proportionally, composite genes are more numerous in eukaryotic genomes; in absolute number, they are more numerous in viruses. In the latter, composite genes functional distribution is biased (enrichment of genes families that are essential for the perpetuation of the viral cycle), and the various parts of composite genes sometimes even originate from the genetic material of different viral classes. More generally, the extent of combinatorial processes, by unravelling other evolutionary bonds than homology bonds in the strictest sense, legitimates a pluralistic study of similarity relationships between sequences.
L’accumulation récente de données de séquences génomiques a montré que l’évolution des gènes n’est pas strictement arborescente. De nombreux processus évolutifs, comme l’exon shuffling, la fusion de gènes ou la recombinaison illégitime remodèlent les gènes, créant des structures composites, formées de parties dont les histoires évolutives sont différentes. Le développement de réseaux de similarité de séquences fournit un cadre analytique permettant d’étudier l’impact de ces processus sur l’évolution moléculaire, en structurant les relations de ressemblance entre séquences et en formalisant en termes de graphes la détection de gènes (triplets intransitifs) et de familles de gènes (cliques minimales séparatrices) composites. La taille des jeux de données actuels, de l’ordre de plusieurs millions de séquences, a également requis le développement de nouveaux outils et méthodes : parallélisation des comparaisons de séquences, visualisation de très grands réseaux par simplification en communautés de Louvain et identification de grands cycles. Appliquées à des jeux de données de génomes eucaryotes et viraux, ces méthodes ont démontré la présence de gènes composites dans tout le vivant et les éléments génétiques mobiles. En proportion, les gènes composites sont plus nombreux dans les génomes eucaryotes ; en nombre absolu, ils sont plus nombreux à être portés par des virus. Chez ces derniers, la distribution fonctionnelle des gènes composites est biaisée (enrichissement dans les familles essentielles pour la perpétuation du cycle viral), et les éléments des gènes composites trouvent même parfois leurs origines dans le matériel génétique de classes virales différentes. Plus généralement, l’étendue des processus combinatoires, en révélant des liens évolutionnaires autres que les liens d’homologie au sens fort, justifie une étude pluraliste des relations de similarité entre séquences.
https://tel.archives-ouvertes.fr/tel-01127379

NNT : 2014PA066358
tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379
https://tel.archives-ouvertes.fr/tel-01127379/document
https://tel.archives-ouvertes.fr/tel-01127379/file/2014PA066358.pdf

Éditeur(s) : HAL CCSD HUMANA PRESS INC
Résumé : International audience
Ever since Darwin, the familiar genealogical pattern known as the Tree of Life (TOL) has been prominent in evolutionary thinking and has dominated not only systematics, but also the analysis of the units of evolution. However, recent findings indicate that the evolution of DNA, especially in prokaryotes and such DNA vehicles as viruses and plasmids, does not follow a unique tree-like pattern. Because evolutionary patterns track a greater range of processes than those captured in genealogies, genealogical patterns are in fact only a subset of a broader set of evolutionary patterns. This fact suggests that evolutionists who focus exclusively on genealogical patterns are blocked from providing a significant range of genuine evolutionary explanations. Consequently, we highlight challenges to tree-based approaches, and point the way toward more appropriate methods to study evolution (although we do not present them in technical detail). We argue that there is significant benefit in adopting wider range of models, evolutionary representations, and evolutionary explanations, based on an analysis of the full range of evolutionary processes. We introduce an ecosystem orientation into evolutionary thinking that highlights the importance of ``type 1 coalitions'' (functionally related units with genetic exchanges, aka ``friends with genetic benefits''), ``type 2 coalitions'' (functionally related units without genetic exchanges), ``communal interactions,'' and ``emergent evolutionary properties.'' On this basis, we seek to promote the study of (especially prokaryotic) evolution with dynamic evolutionary networks, which are less constrained than the TOL, and to provide new ways to analyze an expanded range of evolutionary units (genetic modules, recombined genes, plasmids, phages and prokaryotic genomes, pangenomes, microbial communities) and evolutionary processes. Finally, we discuss some of the conceptual and practical questions raised by such network-based representation.
EVOLUTIONARY GENOMICS: STATISTICAL AND COMPUTATIONAL METHODS, VOL 2

ISBN : 978-1-61779-584-8
hal-01544801
https://hal.archives-ouvertes.fr/hal-01544801
DOI : 10.1007/978-1-61779-585-5_4

Éditeur(s) : HAL CCSD Thai Society of Higher Education Institutes on Environment
Résumé : International audience
Due to the high level of endemic species that they support and the high threats they are facing, such as unsustainable limestone quarrying, hunting and urbanization, limestone karsts are recognized as biodiversity hotspots needing urgent protection. The first aim of our study was to investigate the mammal rodent diversity of Thai limestone karsts. Our second aim was to examine the diversity at a finer scale than the species level (intraspecific biodiversity) using phylogeographic approaches. Therefore, we studied the phylogeographic structure of a threatened rodent, endemic to limestone karsts of Thailand, the Murinae Leopoldamys neilli. We sampled 76 limestone karsts in whole Thailand and live-trapped 444 rodents including 115 Leopoldamys neilli. Our study revealed an important rodent diversity in Thai limestone karsts. Besides endemic rodent species, karsts also host typical forest species to which they provide forest refugia in deforested regions. At the intraspecific level, our study revealed an unexpected high level of genetic differentiation within the rodent species L. neilli. As each limestone area of Thailand is characterized by a particular genetic lineage of L. neilli, the destruction of these karsts would lead to the disappearance of unique intraspecific strains not found elsewhere. Our results highlight the importance of protecting limestone habitats to preserve not only their interspecific but also intraspecific rodent diversity that is highly threatened as more than 20% of limestone karsts in Thailand have already been quarried. Management plans of limestone, a non-renewable resource, should urgently take into account this high biological importance of karsts.
The 1st EnvironmentAsia International Conference on "Environmental Supporting in Food and Energy Security: Crisis and Opportunity"
Bangkok, Thailand

ird-00714455
http://hal.ird.fr/ird-00714455
http://hal.ird.fr/ird-00714455/document
IRD : fdi:010056152

Résumé : Les deux principaux objectifs de ce travail sont de proposer des outils pour la selection d'animaux résistants aux strongles gastro-intestinaux, parasites du tube digestif, et de faire progresser la compréhension des mécanismes de résistance chez la chèvre créole. La variabilité génétique du caractère de résistance au parasitisme digestif a été étudiée afin de vérifier quels critères décrivant le mieux la résistance, peuvent être utilisés pour la sélection. L'ensemble des résultats obtenus suggèrent que le critère d'excrétion d'oeufs et le critère d'éosinophilie sont les plus adaptés pour un schéma de sélection puisqu'ils possèdent une héritabillté moyenne et représentent le mieux la résistance. De plus, ils ne semblent pas en opposition avec le poids, principal critère de production. Le déterminisme génétique de la résistance aux strongles gastro-intestinaux a été étudié et a permis de mettre en évidence l'existence d'un gène majeur pour la résistance chez la population de chèvre créole. De plus, la primo-détection de qtl a permis d'identifier 13 régions du génome ayant un effet sur les critères de résistance. Les mécanismes responsables de la résistance aux strongles gastro-intestinaux ont également été à l'étude. L'ensemble des résultats met en évidence le rôle des éosinophiles dans la mise en place de la résistance aux strongles gastro-intestinaux. L'activité des immunogobulines e semblent dirigés vers les larves l3 d'haemonchus contortus et suggère la mise en place d'une réaction protectrice. Chez la chèvre créole. Ces deux mécanismes semblent donc jouer un rôle important dans la mise en place de la résistance aux strongles gastro-intestinaux
The two main objectives of this work are to propose tools for the selection of resistant animals to gastrointestinal nematodes and advance knowledge on mechanisms of resistance of creole goats. this work has analysed the genetic variability of resistance to digestive parasitism in order to determine which criteria best describes the resistance and can be use for selection. the overall results suggest that the egg excretion and the eosinophilia are the criteria most suitable for a breeding scheme because they have moderate heritability estimates and best represent the resistance. moreover, they do not seem in conflict with the weight, the main criterion of production. the genetic determinism of resistance to gastrointestinal parasites has been studied and has highlighted the existence of a major gene for resistance in creole goats. in addition, the primodetection of qtl identified 13 genomic regions that affect the resistance. the mechanisms behind the resistance to gastrointestinal parasites were also studied and first hypothesis regarding the involvment of the immune response in resistance have been made in goats. the overall results highlighted the role of eosinophils in the development of resistance to gastrointestinal nematodes. the activity of immunoglobulin e seems directed toward l3 larvae of haemonchus contortus and may be imply in the establishment of a protective response agasint nematode parasites. in creole goats, these two mechanisms seem to play an important role in the development of resistance to gastrointestinal nematode infections

http://www.theses.fr/2011AGUY0407/document

Éditeur(s) : HAL CCSD PeerJ
Résumé : International audience
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 (SouthWestern 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 brevipinna (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 × 10 −4 .
ISSN: 2167-8359

hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961
https://hal.archives-ouvertes.fr/hal-01317961/document
https://hal.archives-ouvertes.fr/hal-01317961/file/Pirog_2016PeerJ_microsat_tiger_shark.pdf
DOI : 10.7717/peerj.2041