Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Deep-sea bivalves found at hydrothermal vents, cold seeps and organic falls are sustained by chemosynthetic bacteria which ensure part or all of their carbon nutrition. These symbioses are of prime importance for the functioning of the ecosystems. Similar symbioses occur in other bivalve species living in shallow and coastal reduced habitats worldwide. In recent years, several deep-sea species have been investigated from continental margins around Europe, West Africa, East America, the Gulf of Mexico, and from hydrothermal vents on the Mid-Atlantic Ridge. In parallel, numerous more easily accessible shallow marine species were studied. We here provide a summary of the current knowledge available on chemosymbiotic bivalves in the area ranging west-to-east from the Gulf of Mexico to Marmara Sea, and north-to-south from the Arctic to the Gulf of Guinea. Characteristics of symbioses in 51 species from the area are summarized for each of the five bivalve families documented to harbor chemosynthetic symbionts (Mytilidae, Vesicomyidae, Solemyidae, Thyasiridae and Lucinidae), and compared among families with special emphasis on ecology, life cycle, and connectivity. Chemosynthetic symbioses are a major adaptation to ecosystems and habitats exposed to reducing conditions, yet relatively little is known regarding their diversity and functioning apart from a few "model species" on which effort has focused over the last 30 yr. In the context of increasing concern about biodiversity and ecosystems, and increasing anthropogenic pressure on Oceans, we advocate for a better assessment of bivalve symbioses diversity in order to evaluate the capacities of these remarkable ecological and evolutionary units to withstand environmental change
Biogeosciences (1726-4170) (Copernicus Gesellschaft Mbh), 2013 , Vol. 10 , N. 5 , P. 3241-3267

Droits : Author(s) 2012. CC Attribution 3.0 License.
http://archimer.ifremer.fr/doc/00133/24417/22431.pdf
DOI:10.5194/bg-10-3241-2013
http://archimer.ifremer.fr/doc/00133/24417/

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) : Wiley-blackwell
Résumé : Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.
Fish And Fisheries (1467-2960) (Wiley-blackwell), 2014-03 , Vol. 15 , N. 1 , P. 65-96

Droits : 2012 John Wiley & Sons Ltd
http://archimer.ifremer.fr/doc/00124/23522/21409.pdf
DOI:10.1111/faf.12007
http://archimer.ifremer.fr/doc/00124/23522/

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
AimThe global biodiversity crisis requires the identification of regions with high evolutionary potential, i.e. evolutionary hotspots (evospots). We created an analytical framework based on comparative phylogeography and coalescent methods to assess the dynamics of diversification and population persistence in the reef ecosystem of a little-studied region: the Southwestern Indian Ocean (SWIO).LocationCoral reefs of the SWIO, with comparative data from the Pacific Ocean.MethodsWe generated sequences of mitochondrial DNA (COI and 16S) for 10 widespread brittle-stars (345 specimens) from 21 localities (8 in the SWIO). We analysed them by combining comparative phylogeography approaches, coalescent-based methods, molecular clocks and the concept of evolutionarily significant units (ESUs) to draw conclusions about the drivers of biodiversity in the region.ResultsCryptic diversity was prevalent, increasing lineage diversity within the 10 nominal species by 70% within the SWIO and by 200% across the Indo-West Pacific. All seven new SWIO lineages meet the criteria for ESUs and at least six are biological species. We detected likely intraregional diversifications dating to the Plio-Pleistocene, supporting the SWIO as a generator of biodiversity. Geographical restriction of ESUs, long coalescent times (> 80 ka) and old in situ diversification (> 1 Ma) point to the persistence of populations over multiple glacio-eustatic cycles. We provide data suggesting demographic expansion during sea-level high stands. Regional connectivity was lower, and cryptic differentiation higher in lecithotrophs than in planktotrophs.Main conclusionsThe analytical framework based on a biodiversity survey makes it possible to identify evospots by assessing the potential of a region to maintain and generate biodiversity and by evaluating the evolutionary processes and potential drivers at play.
ISSN: 0305-0270

hal-01369697
http://hal.univ-reunion.fr/hal-01369697
DOI : 10.1111/jbi.12155

Résumé : Les mutualismes, interactions interspécifiques où chaque partenaire retire un bénéfice net de leur association, sont centraux dans l’origine et l’organisation de la biodiversité. Bien que globalement bénéfiques pour chacun des partenaires, ces interactions n’enlèvent rien à l’égoïsme inhérent de chaque espèce pour sa survie et sa reproduction, générant des conflits d’intérêts entre les espèces. Ainsi, comprendre les processus écologiques et évolutifs qui maintiennent le caractère mutualiste d’interactions entre plusieurs espèces est primordial dans la compréhension du maintien de la biodiversité. Néanmoins, le corpus scientifique s’est jusqu'à présent surtout concentré sur des paires d’espèces en interaction. Or, ces avancées scientifiques restent partielles car la plupart de ces interactions s’englobent dans un contexte communautaire. C’est dans ce cadre conceptuel que se place mon travail de thèse. Alors que la diversité structurelle des mutualismes de protection entre plantes et fourmis en ont fait un modèle d’étude clé dans la compréhension des mutualismes, j’ai concentré mes recherches sur l’intégration d’un troisième partenaire fongique pour comprendre ses conséquences sur les résultantes écologiques et évolutives de ces mutualismes tripartites. Je me suis tout d’abord intéressé à définir la relation qui lie de façon mutualiste le champignon aux deux autres partenaires et à établir les conflits d’intérêts émanant de ces différentes interactions pour comprendre quels facteurs permettaient de les réguler. Ainsi, la relation qui lie le champignon aux fourmis peut être qualifiée d’agriculture. Les fourmis protègent, nourrissent et disséminent le champignon et celui-ci, via ses propriétés structurales, permet l’élaboration de galeries servant de piège pour capturer des proies. Ce phénomène crée cependant un conflit d’allocation de la force ouvrière des fourmis et nuit directement aux bénéfices de la plante par une diminution de l’intensité des patrouilles sur ses feuilles, diminuant consécutivement sa protection et sa fitness. Néanmoins, le rôle du champignon dans les transferts de nutriments entre les fourmis et la plante, ainsi que certaines réponses évolutives de la plante permettent de réguler ces conflits, stabilisant les bénéfices nets de chaque partenaire dans ce mutualisme tripartite. Puis, je me suis concentré à comprendre comment certains facteurs évolutifs pouvaient moduler cette résultante écologique. La prise en compte du caractère multipartite d’un mutualisme change radicalement la vision de l’évolution des mutualismes jusqu’alors étudiée entre paires d’espèces. Alors que le corpus scientifique s’accorde à dire que la spécialisation entre espèce par coévolution renforce la stabilité et les bénéfices perçus par chaque partenaire, le contexte multipartite semble altérer ces prédictions. Au contraire la spécialisation multipartite peut être dans certains cas un moteur d’instabilité et de baisse des bénéfices. Enfin cette thèse permet de faire le lien entre deux concepts qui s’opposent : la coévolution diffuse et la coévolution par paire. Je montre ainsi que la coévolution peut intervenir sur plus de deux espèces à la fois, mais qu’elle peut quand même entrainer une spécialisation multispécifique. Finalement, au contraire des prédictions de la coévolution diffuse, cette thèse montre que plusieurs pressions de sélection contrastées émanant de différentes espèces envers un seul trait d’une troisième espèce peuvent promouvoir la spécialisation multi-spécifique.
Mutualisms, defined as interspecific interactions where each partner receives net benefices from their interactions, are central to the organization of earth biodiversity. Although globally beneficial for each partner, such interactions do not modify the inherent selfishness of species for their survival and reproduction, generating conflicts of interests between species. Thus understanding the ecological and the evolutionary processes maintaining positive outcomes in mutualisms is fundamental to understand how mutualisms shape earth biodiversity. However, scientific research on mutualisms has most of the time focused on interaction between pairs of species. Such knowledge is thus partial as mutualisms are embraced in a community context. My doctoral thesis takes place in this conceptual framework. I focused my research on the integration of a third fungal partner in protective interactions between ants and plants to evaluate its consequences on the ecological and evolutionary outcomes of such mutualisms, taken as multispecies interactions. I first focused my researches in defining the mutualistic interaction linking the fungal partner with its two other associates and in revealing any conflict of interests and their regulation that may emerge from such tripartite interactions. The interactions between the ants and the fungi can be qualified as a case of non-food fungiculture. The ants protect, provide food and disseminate the fungus, and the latter, thanks to its structural properties, allows the elaboration of galleries used that are then used as trap to capture preys. This phenomenon creates a conflict of interest in the allocation of the worker force, altering host plant benefits through a decrease of worker patrolling activity and consequently leaves protection and thus fitness. However, the role of the fungus in the nutrient transfers between ants and plants added to evolutionary responses from the plant allows regulating this conflict, stabilizing the net benefits towards the plant. Then I have concentrated my researches in understanding how evolutionary factors would modulate the ecological outcomes of such interactions. Taking into account the multispecific character of mutualisms changes radically the vision on the evolution of mutualisms when pair of species are considered. While it is widely accepted that specialization of mutualist species through coevolution reinforce the stability of the interaction and the net benefit of each partner, the multispecific context seems to deviate these predictions. Conversely, I show that specialization between three mutualistic partners can drive instability and decrease of benefits. Finally, the results of this thesis join the gap between two previously opposed concepts: diffuse coevolution and pairwise coevolution. I show that coevolution can happen between more than two species simultaneously and that it can drive mutlispecific specialization. Opposed to the diffuse coevolution, I show that contrasting selective pressures on a same trait from different partner can promote specialization of species.

http://www.theses.fr/2013AGUY0622/document

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : Devil's gardens are one of the most remarkable mutualistic associations between ants and plants. Myrmelachista ants eliminate all vegetation from around their host plants, resulting in wide forest clearings which have intrigued scientists from the start. Despite their noticeability, here we report the discovery of devil's gardens in remote highland cloud forests of the Eastern Amazon, more than 2000 km away from their nearest known analogues in Western Amazonia. We describe the ecological characteristics of these gardens and consider what factors could have produced the geographic isolation of Eastern Amazonian devil's gardens. Three hypotheses are investigated: (1) the host plant distribution restricts the distribution of the mutualism, (2) the ecological tolerances of Myrmelachista explain the isolation, and (3) the devil's gardens of the Eastern Amazon constitute relicts from ancient forest refugia. The distribution of the possible associated myrmecophytes and previously described ecological ranges of devil's gardens cannot explain their ecological restriction to cloud forests in Eastern Amazonia, but our discovery is consistent with the biogeographic refuge hypothesis (i.e. highlands along the Amazon Basin constitute refugia for humid forests that spread during the Cenozoic). Our finding opens exciting perspectives for comparative studies of the origin, ecology and evolutionary history of this ant-plant mutualism.
ISSN: 0266-4674

hal-01532640
https://hal.archives-ouvertes.fr/hal-01532640
DOI : 10.1017/S0266467416000195
PRODINRA : 384619

Éditeur(s) : HAL CCSD WILEY-BLACKWELL Wiley
Résumé : International audience
Connectivity among populations determines the dynamics and evolution of populations, and its assessment is essential in ecology in general and in conservation biology in particular. The robust basis of any ecological study is the accurate delimitation of evolutionary units, such as populations, metapopulations and species. Yet a disconnect still persists between the work of taxonomists describing species as working hypotheses and the use of species delimitation by molecular ecologists interested in describing patterns of gene flow. This problem is particularly acute in the marine environment where the inventory of biodiversity is relatively delayed, while for the past two decades, molecular studies have shown a high prevalence of cryptic species. In this study, we illustrate, based on marine case studies, how the failure to recognize boundaries of evolutionary-relevant unit leads to heavily biased estimates of connectivity. We review the conceptual framework within which species delimitation can be formalized as falsifiable hypotheses and show how connectivity studies can feed integrative taxonomic work and vice versa. Finally, we suggest strategies for spatial, temporal and phylogenetic sampling to reduce the probability of inadequately delimiting evolutionary units when engaging in connectivity studies.
ISSN: 0962-1083

hal-01218810
https://hal.archives-ouvertes.fr/hal-01218810
DOI : 10.1111/mec.13048

Éditeur(s) : HAL CCSD Ecological Society of America
Résumé : Herbivory is viewed as a major driver of plant evolution and the mostimportant energy pathway from plants to higher trophic levels. Therefore, understandingpatterns of herbivory on plants remains a key focus in evolution and ecology. Theevolutionary impacts of leaf herbivory include altering plant fitness, local adaptation, theevolution of defenses, and the diversification of plants as well as natural enemies. Leafherbivory also impacts ecological processes such as plant productivity, communitycomposition, and ecosystem nutrient cycling. Understanding the impact of herbivory onthese ecological and evolutionary processes requires species-specific, as opposed tocommunity-level, measures of herbivory. In addition, species-specific data enables the use ofmodern comparative methods to account for phylogenetic non-independence. Althoughhundreds of studies have measured natural rates of leaf consumption, we are unaware of anyaccessible compilation of these data. We created such a data set to provide the raw dataneeded to test general hypotheses relating to plant–herbivore interactions and to test theinfluence of biotic and abiotic factors on herbivory rates across large spatial scales. A largerepository will make this endeavor more efficient and robust. In total, we compiled 2641population-level measures for either annual or daily rates of leaf herbivory across 1145 speciesof vascular plants collected from 189 studies. All damage measures represent naturaloccurrences of herbivory that span numerous angiosperm, gymnosperm, and fern species. Toenable researchers to explore the causes of variation in herbivory and how these mightinteract, we added information about the study sites including: geolocation, climateclassification, habitat descriptions (e.g., seashore, grassland, forest, agricultural fields), andplant trait information concerning growth form and duration (e.g., annual vs. perennial). Wealso included extensive details of the methodology used to measure leaf damage, includingseasons and months of sampling, age of leaves, and the method used to estimate percentagearea missing. We anticipate that these data will make it possible to test important hypothesesin the plant–herbivore literature, including the plant apparency hypothesis, the latitudinalherbivorydefense hypothesis, the resource availability hypothesis, and the macroevolutionaryescalation of defense hypothesis.
ISSN: 0012-9658

hal-01601627
https://hal.archives-ouvertes.fr/hal-01601627
DOI : 10.1890/13-1741.1
PRODINRA : 397136
PUBMED : 24870043

Éditeur(s) : HAL CCSD Elsevier
Résumé : Recent evolutionary studies clearly indicate that evolution is mainly driven by changes in the complex mechanisms of gene regulation and not solely by polymorphism in protein-encoding genes themselves. After a short description of the cis-regulatory mechanism, we intend in this review to argue that by applying newly available technologies and by merging research areas such as evolutionary and developmental biology, population genetics, ecology and molecular cell biology it is now possible to study evolution in an integrative way. We contend that, by analysing the effects of promoter sequence variation on phenotypic diversity in natural populations, we will soon be able to break the barrier between the study of extant genetic variability and the study of major developmental changes. This will lead to an integrative view of evolution at different scales. Because of their sessile nature and their continuous development, plants must permanently regulate their gene expression to react to their environment, and can, therefore, be considered as a remarkable model for these types of studies. (C) 2010 Elsevier Ireland Ltd. All rights reserved.
ISSN: 0168-9452

hal-01032399
https://hal.archives-ouvertes.fr/hal-01032399
DOI : 10.1016/j.plantsci.2010.09.009

Éditeur(s) : HAL CCSD Publisher : Baltimore : Williams & Wilkins, c1950-. Latest Publisher : Bethesda, MD : American Association of Immunologists
Résumé : International audience
Hepatic periportal fibrosis, which affects 5–10% of subjects infected by Schistosoma mansoni, is caused by the T cell-dependent granuloma that develop around schistosome eggs. Experimental models of infection have shown that granuloma and fibrosis are tightly regulated by cytokines. However, it is unknown why advanced periportal fibrosis occurs only in certain subjects. The goal of the present study was to evaluate the cytokine response of S. mansoni-infected subjects with advanced liver disease in an attempt to relate susceptibility to periportal fibrosis with an abnormal production of cytokines that regulate granuloma and fibrosis. Fibrosis was evaluated by ultrasound on 795 inhabitants of a Sudanese village in which S. mansoni is endemic: advanced periportal fibrosis was observed in 12% of the population; 35% of the affected subjects exhibited signs of portal hypertension. Age (odds ratio (OR), 11.5), gender (OR, 4.2), and infection levels (OR, 2.2) were significantly (p < 0.01) associated with hepatic fibrosis. Cytokines produced by egg-stimulated blood mononuclear cells from 99 subjects were measured (75 with no or mild fibrosis; 24 subjects with advanced fibrosis). Multivariate analysis of cytokine levels showed that high IFN-γ levels were associated with a marked reduction of the risk of fibrosis (p = ‫OR, 0.1); in contrast, high TNF-α levels were associated with an increased risk (p = 0.05; OR, 4.6) of periportal fibrosis. Moreover, infection levels were negatively associated with IFN-γ production. These results with observations in experimental models strongly suggest that IFN-γ plays a key role in the protection of S. mansoni-infected patients against periportal fibrosis, whereas TNF-α may aggravate the disease.
ISSN: 0022-1767

Droits : http://creativecommons.org/licenses/by-nc-nd/
hal-01211587
https://hal.archives-ouvertes.fr/hal-01211587
https://hal.archives-ouvertes.fr/hal-01211587/document
https://hal.archives-ouvertes.fr/hal-01211587/file/929.full.pdf
DOI : 10.4049/jimmunol.169.2.929

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Conflict between mates, as well as conflict between parents and offspring are due to divergent evolutionary interests of the interacting individuals. Hormone systems provide genetically based proximate mechanisms for mediating phenotypic adaptation and maladaptation characteristic of evolutionary conflict between individuals. Testosterone (T) is among the most commonly studied hormones in evolutionary biology, and as such, its role in shaping sexually dimorphic behaviors and physiology is relatively well understood, but its role in evolutionary conflict is not as clear. In this review, we outline the genomic conflicts arising within the family unit, and incorporate multiple lines of evidence from the bank vole (Myodes glareolus) system to outline how T impacts traits associated with reproduction and survival, resulting in a sexually antagonistic genetic trade-off in fitness. A major prediction arising from this work is that lower T is favored in females, whereas the optimal T level in males fluctuates in relation to social and ecological factors. We additionally discuss future directions to further integrate endocrinology into the study of sexual and parent–offspring conflicts.
ISSN: 1540-7063

hal-01357902
https://hal-univ-perp.archives-ouvertes.fr/hal-01357902
DOI : 10.1093/icb/icw053

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : International audience
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
ISSN: 1664-302X

hal-01546980
http://hal.upmc.fr/hal-01546980
DOI : 10.3389/fmicb.2013.00414

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
ISSN: 2072-4292

hal-01429052
https://hal.archives-ouvertes.fr/hal-01429052
DOI : 10.3390/rs4103244

Éditeur(s) : HAL CCSD Royal Society, The
Résumé : International audience
Bathymodiolin mussels occur at hydrothermal vents and cold seeps, where they thrive thanks to symbiotic associations with chemotrophic bacteria. Closely related genera Idas and Adipicola are associated with organic falls, ecosystems that have been suggested as potential evolutionary 'stepping stones' in the colonization of deeper and more sulphide-rich environments. Such a scenario should result from specializations to given environments from species with larger ecological niches. This study provides molecular-based evidence for the existence of two mussel species found both on sunken wood and bones. Each species specifically harbours one bacterial phylotype corresponding to thioautotrophic bacteria related to other bathymodiolin symbionts. Phylogenetic patterns between hosts and symbionts are partially congruent. However, active endocytosis and occurrences of minor symbiont lineages within species which are not their usual host suggest an environmental or horizontal rather than strictly vertical transmission of symbionts. Although the bacteria are close relatives, their localization is intracellular in one mussel species and extracellular in the other, suggesting that habitat choice is independent of the symbiont localization. The variation of bacterial densities in host tissues is related to the substrate on which specimens were sampled and could explain the abilities of host species to adapt to various substrates.
ISSN: 0950-1193

hal-00755293
https://hal.univ-antilles.fr/hal-00755293
DOI : 10.1098/rspb.2008.1101

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) : 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) : HAL CCSD Wiley
Résumé : International audience
Studies focusing on the effect of invasive species on the genetic diversity of native marine invertebrates remain scant. Here we report diversity among French populations of the intertidal gastropod Ocenebra erinacea (Linnaeus, 1758) sampled in the presence and absence of the invasive Ocenebra inornata (Recluz, 1851). Between 1999 and 2004, a total of 352 individuals of O. erinacea was collected from 15 sites, five of which had the invasive present, and genotyped at the mitochondrial locus cox1. No statistical difference was observed between polymorphism levels recorded within native populations exposed to the invasive, compared with populations sampled in the absence of O. inornata. No sign of native population decline was detected in response to the invader. While significant shifts in native O. erinacea population sizes have previously been reported in the literature, genetic effects may take longer to accumulate, or may be undetectable without a larger panel of genetic markers. By contrast, large genetic distances and significant population differentiation were recorded between Atlantic and Mediterranean O. erinacea samples, suggesting that these populations have distinct evolutionary histories. Comparison of genetic divergence within the closely related genus Nucella suggests that the Atlantic populations of O. erinacea and those from Thau Lagoon in the Mediterranean may belong to different species or subspecies.
ISSN: 0173-9565

hal-01064464
https://hal.archives-ouvertes.fr/hal-01064464
https://hal.archives-ouvertes.fr/hal-01064464/document
https://hal.archives-ouvertes.fr/hal-01064464/file/Ocenebra_revision_submission_to_MarEcol.pdf
DOI : 10.1111/maec.12208

Éditeur(s) : Wiley-blackwell
Résumé : The reef fauna connectivity of the West Indian Ocean (WIO) is one of the least studied globally. Here we use genetic analyses of the grouper Epinephelus merra (Bloch 1793) to determine patterns of connectivity and to identify barriers to dispersal in this WIO marine area. Phylogeographic and population-level analyses were conducted on cytochrome b sequences and microsatellites (13 loci) from 557 individuals sampled in 15 localities distributed across the West Indian Ocean. Additional samples from the Pacific Ocean were used to benchmark the WIO population structure. The high level of divergence revealed between Indian and Pacific localities (of about 4.5% in sequences) might be the signature of the major tectonic and climatic changes operating at the Plio-Pleistocene transition, congruently with numerous examples of Indo-Pacific speciation. In comparison, the E. merra sequences from the Indian Ocean constitute a monophyletic clade with a low average genetic distance (d < 0.5%). However both genetic markers indicated some structure within this ocean. The main structure revealed was the isolation of the Maldives from the WIO localities (a different group signature identified by clustering analysis, great values of differentiation). Both marker types reveal further significant structure within the WIO, mainly the isolation of the Mascarene Islands (significant AMOVA and isolation-by-distance patterns) and some patchy structure between the northernmost localities and within the Mozambique Channel. The WIO genetic structure of E. merra appeared congruent with main biogeographic boundaries and oceanographic currents.
Marine Ecology-an Evolutionary Perspective (0173-9565) (Wiley-blackwell), 2015-09 , Vol. 36 , N. 3 , P. 447-461

Droits : 2014 Blackwell Verlag GmbH
http://archimer.ifremer.fr/doc/00189/30046/28566.pdf
DOI:10.1111/maec.12153
http://archimer.ifremer.fr/doc/00189/30046/

Éditeur(s) : HAL CCSD Wiley-Blackwell
Résumé : International audience
Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.
ISSN: 1471-8278

hal-01330323
https://hal-univ-perp.archives-ouvertes.fr/hal-01330323
DOI : 10.1111/mec.13616

Éditeur(s) : HAL CCSD
Résumé : International audience
https://hal.archives-ouvertes.fr/hal-01436542

hal-01436542
https://hal.archives-ouvertes.fr/hal-01436542
DOI : 10.1109/IGARSS.2011.6049595