This thesis addresses species richness estimation for benthic data by describing the clustering of individuals within a species using a Neyman Type A distribution, and incorporating this into species richness estimates. A review of current species richness estimation methods is included . The maximumlikelihood approach to species richness estimation is extended to incorporate the Neyman Type A model, with a gamma mixing distribution on the mean abundance of individuals within a species. Species richness estimates of this model are compared •1 to those of the simpler negative binomial and Poisson models. The use of a penalisedlikelihood is applied to avoid sp uriously large estimates of species richness that can be associated with the 'boundary problem'. The Bayesian approach to species richness is considered, using uninformative and informative priors. Informative priors are elicited using expert opinion obtained from a number of benthic ecologists at the Centre for Environment, Fisheries and Aquaculture Science. These are iDcorporated into species richness estimation in the form of priors, and also converted into penalties for use in the frequentist approach. Several benthic data sets aTe anaJysed throughout, along with a Lepidoptera data set, and a data set from a common bird census carried out in the USA. In addition, several simulation studies are undertaken to illustrate the performance of the estimators. The research culminates in the application of species richness estimators to estimate species mortality due to dredging carried out off the Norfolk coast. Several estimators can be considered to gain a picture of the effect of dredging, and I recommend that species richness estimators should reflect the underlying distribution of t he data. I also recommend that a precautionary approach should be taken when using these estimators in practical applications.

Macrobenthic assemblages and sedimentary conditions of five areas were described and compared; the role of abiotic factors in shaping benthic distributions was also examined. Two of the study sites were actively dredged at the time of sample collection and the effects of this aggregate extraction were investigated. It was concluded that trailer dredging (at the level intensity employed at these sites) was not associated with any significant disruption to benthic community structure, despite the differences in abiotic and biotic characteristics of the two dredged areas. A meta-analysis of findings from published dredging impact studies revealed a differential response to dredging that was related to habitat type. Full recovery of the benthos following the cessation of dredging was not observed in any of the habitat types suggesting that dredging is associated with a long-term alteration of macrobenthic resources.

With the advent of an ecosystem approach to marine management, the importance of developing methods to investigate ecological functioning is receiving increasing attention. This thesis develops a novel approach for describing ecological functioning in marine benthic systems. Biological traits analysis (BTA) uses a suite of life history, morphology and behaviour characteristics of species to describe aspects of their functioning. Comparison of BTA with two other approaches proposed for describing functioning in marine ecosystems established that BTA identified a range of biological attributes important for differentiating benthic communities and was better able to describe spatial patterns in assemblage composition than the other measures. Appraisal of the analytical tools proposed for use in BTA revealed they provided similar views of assemblage functioning, with the nonparametric tool being appropriate for providing a general picture of functioning, while the more complex parametric tools had greater power to detect anthropogenic impacts. Evaluation of the type and number of traits included in BTA showed it was sensitive to the number of traits selected for analysis, with optimal results being gained by maximising trait number. Examination of the relationship between functioning and environmental variability revealed that trait composition was related to changes in a number of environmental factors, although this relationship was complex and the nature of associations between traits and specific environmental factors varied depending on the location of assemblages. Further analyses focussed on the impacts of anthropogenic activities on benthic assemblage functioning. These revealed that assemblage functioning was impacted by fishing disturbance in both subtidal and intertidal assemblages. A number of traits were impacted by fishing, including some associated with vulnerability to physical stress and others related to resistance to disturbance, while other aspects of functioning remained unaffected. The thesis has increased our understanding of biological traits analysis as a tool for describing functioning in marine benthic systems. It has also contributed to some interesting ecological and management issues, such as the relationship between species and functioning and the importance of, information required for, and strategies available for conservation of ecological functioning in marine ecosystems.

Little is known about the fauna that inhabits non-chemosynthetic environments associated with mid-ocean ridges. This thesis investigates a ridge and fracture zone system to assess its influence as a barrier to faunal dispersal, and as a unique bathyal habitat. It also describes the ecology of megabenthic communities inhabiting a ridge. Sites were chosen on the Mid-Atlantic Ridge in the vicinity of the Charlie-Gibbs Fracture Zone, at a target depth of 2,500 m. Four superstations were chosen north and south of the Fracture Zone, on either side of the ridge. Different productivity levels and hydrographic features were characteristic for the northern and southern sites. In order to characterise the benthic megafauna 50 ha were trawled and 32,000 m2 of seafloor were sampled with HD video footage, targeting both flat and 10 ◦ sloped habitats. Holothurians were the most abundant megafauna. In order to assess their evolutionary relationship 43 holothurian specimens were genetically studied by modelling five of their genes (16S, 18S, 28S, COI, H3) in a phylogenetic analysis. All four sites exhibited noticeably different faunal characteristics. The biomass was highest at the SE, and lowest at the NW site. Body sizes differed between sites for most taxa, that were sufficient in numbers to be compared between sites, most likely as a result of different adaptations to food supply. Differences in species richness were observed between the sampling methods, with the highest richness at the SE site in trawl samples, and highest at the NW and SW sites in the video survey. Species densities were highest at the northern sites with both methods. Differences in diversity were also observed, with trawl samples providing a higher taxonomic resolution than the video survey and showing highest diversity at the SE site and lowest at the NE site. Community composition was significantly different between sites. Variations in the composition of megabenthic assemblages were observed between flat and 10 ◦ sloped habitats, although the effect of slope appears to be site dependent. The genetic analyses revealed a close relationship between individuals from different families. The extent to which the Ridge acts as a faunal barrier was unclear as the southern sites lacked an obvious difference in community composition. Faunal differences to the north and south of the Fracture Zone, however, suggest that this feature is a barrier to dispersal. The contrasting megafaunal assemblages of the sites probably reflect a combination of environmental drivers including sediment type, phytodetrital quality, hydrography, and habitat complexity.

Les symbioses ont un role majeur dans le fonctionnement et l'equilibre des ecosystemes. Dans les oceans, qui couvrent pres de 70 % de la surface de la planete, vivent une multitude d'organismes incapables de lutter contre les courants et la plupart sont microscopiques, il s'agit du plancton. Les organismes du plancton, comme ceux d'autres ecosystemes, entretiennent des symbioses, mais la nature et l'ampleur de ces interactions sont encore mal connues dans le plancton du fait la petite taille de ces organismes et de la difficulte d'echantillonnage des ecosystemes planctoniques, surtout dans les zones les plus eloignees des cotes. Les principaux objectifs de cette these sont de donner un apercu global de la place occupee par ces symbioses dans le plancton et de proposer des methodes originales permettant leur detection. Les travaux presentes dans ce manuscrit s'appuient sur l'analyse des donnees generees lors de l'expedition Tara Oceans (2009-2013) pendant laquelle 210 stations oceaniques ont ete echantillonnees a travers le monde. Ils concernent plus precisement le jeu de donnees environnemental obtenu grace au sequencage a haut debit (Illumina) de la region hypervariable V9 (130 nucleotides) de la sousunite 18S de l'ADN ribosomique des organismes eucaryotes (metabarcoding). Dans un premier temps, un etat des lieux de la diversite et de la structure des communautes du pico-nano-micro-mesoplancton (0,8-2000 μm) eucaryote de la zone photique des oceans temperes a tropicaux est realise. Il met en evidence la place importante occupee par les symbiotes au sein de ces communautes. Ensuite, l'etude de deux cas de symbiose (Blastodinium- Copepodes et Symbiodinium-Tiarina) montre les difficultes inherentes a la detection de couples symbiotiques a partir d’un jeu de donnees issue d'etudes par metabarcoding du plancton (flexibilite de la specificite des symbioses dans le plancton), mais aussi la possibilite de distinguer les differentes phases de vie des symbiotes (libres et symbiotiques) lorsque les echantillons etudies ont ete fractionnes. Enfin, un ensemble de methodes est propose afin d'ameliorer l'efficacite de la detection de symbioses dans le cadre d'etudes par reseau de cooccurrences des communautes planctoniques. L'analyse de la distribution des metabarcodes le long des fractions de taille (piconano- (0.8-5 μm), nano- (5-20 μm), micro- (20-180 μm), et meso-plancton (180-2000 μm)) permet de differencier ceux provenant d'organismes symbiotiques de ceux d'organismes libres, sans a priori. De plus la comparaison de l'abondance de groupes genetiques definis a differents niveaux de resolution permet de detecter des associations symbiotiques peu specifiques et d'apprecier leur niveau de specificite. / The oceans, which cover nearly 70 % of the earth's surface, is host to a myriad of mostly microscopic organisms that drift with the currents and are collectively called plankton. As in other ecosystems, symbioses play a major role in the functioning and equilibrium of the plankton. But the exact nature and strength of those symbiotic interactions are still poorly known, not only due to the small size of most planktonic organisms, but also because of the inherent difficulty of sampling planktonic ecosystems, especially in the high-seas. The main goals of this thesis are to give a global view of the importance of planktonic symbioses and to propose novel methods for their detection. The work presented in this manuscript is based on analyses of data generated during the Tara Oceans expedition (2009-2013), during which sea water was collected and size fractionated by filtration at 210 sampling locations distributed across the world's oceans. The data analyses presented herein mostly focus on an environmental metabarcoding dataset obtained from next-generation sequencing (Illumina) of the V9 hypervariable region (~130 nucleotides long) of the 18S small ribosomal subunit of eukaryotic organisms. We begin by assessing the diversity and structure of pico-, nano-, micro and meso-planktonic eukaryotic communities (0.8-2000 μm) in the photic zone of tropical to temperate sea regions. Then, we present two cases of symbioses (Blastodinium-Copepods and Symbiodinium-Tiarina) to illustrate both the difficulties encountered when trying to detect symbiotic relationships using metabarcoding data due to varying specificities of symbiotic relationships, but also the potential solutions offered by size-fractionated sampling to distinguish between the different stages of the life cycle of symbiotic organisms (free living and symbiotic stages). Finally, we propose a set of methods to improve the detection of symbioses by studying the co-occurrence of organisms in planktonic communities: we use the distribution of metabarcodes along size fractions ((piconano- (0.8-5 μm), nano- (5-20 μm), micro- (20-180 μm), and meso-plancton (180-2000 μm)) to distinguish likely free living organisms from those that have a symbiotic life style, and we compare the abundance of genetic groups constructed by clustering metabarcodes at different resolution levels, which allows us to detect interactions occurring above the species level and to evaluate their level of specificity.

L'apparition de nouvelles structures telles que la crête neurale, les placodes et le mésoderme crânien a été essentielle pour l'émergence de la tête des vertébrées. Fait intéressant, le mésoderme de la tête des vertébrés n'est pas segmenté alors qu'il est supposé que le mésoderme de l'ancêtre de tous les chordés était totalement segmenté. De même le corps du le céphalochordé amphioxus est entièrement segmenté. Des travaux menés par l'équipe ont montré le rôle central du signal FGF dans la formation des somites les plus antérieures chez l'amphioxus. Afin de mieux comprendre le rôle de ce signal pour la formation de ces somites, nous avons réalisé une étude transcriptomique comparative par RNA-seq. Cette analyse a mis en évidence plusieurs gènes que sont impliqués dans la somitogenèse et la myogenèse et sous le contrôle du signal FGF. Nous avons pu montrer grâce à des analyses fonctionnelles que ER81/Erm/PEA3 et Six1/2 ont un rôle majeur dans la formation des somites les plus antérieures chez l'amphioxus. Inversement, Pax3/7 est impliqué dans la formation des somites postérieures. Cette cascade de régulation est semblable à celle observée lors de la somitogenèse pour les muscles du tronc chez les vertébrés, mais diverge de la cascade de gènes contrôlant la formation des muscles de la tête chez les vertébrés. Tous ces résultats supportent l'hypothèse selon laquelle le changement de fonction du signal FGF durant le développement précoce a été une étape clé pour la perte des somites antérieures, libérant ainsi les contraintes dans la partie antérieure de l'embryon et permettant dans un second temps l'acquisition des muscles de la tête chez l'ancêtre commun des vertébrés. / A central question in Evo-Devo is to understand the origin of the vertebrates’ head. The appearance of new structures such as the neural crest, placodes and a cranial mesoderm were essential for the appearance of the head in the vertebrates. Interestingly, it is supposed that the ancestor of all chordates was completely segmented. Remarkably, the cephalochordate amphioxus is completely segmented in the full length of its body as the hypothetical ancestor of all chordates. Moreover, it has been showed that the FGF signal plays a central role in the formation of the anterior-most somites of amphioxus. Thus, in order to understand the downstream signaling pathway under the control of the FGF signal for the formation of the anterior-most somites in amphioxus, we performed a comparative RNA-seq analysis. This analysis revealed several vertebrates orthologues genes playing roles in somitogenesis or myogenesis and under the control of the FGF signal. Furthermore, functional analysis revealed that ER81/Erm/PEA3 and Six1/2 plays majors roles in the formation of the anterior-most somites in amphioxus. Conversely, Pax3/7 is involved in the formation of the posterior somites. This regulatory cascade resembles that for the control of trunk somitogenesis in vertebrates and diverges from the gene cascades controlling the formation of the vertebrate head muscles. Altogether, our results strengthen the hypothesis that changes in the FGF function during early development were instrumental for the loss of anterior somites, releasing developmental constraints in the anterior part of the embryo and allowing a secondary acquisition of head muscles in the ancestor of vertebrates.

L'importance des symbioses dans l'évolution du vivant est désormais admise et les associations symbiotiques sont observées dans une grande diversité d'habitats. Notre étude porte sur une symbiose au sein d'un écosystème réduit, les sources hydrothermales de l'océan profond. Bathymodiolus azoricus est un bivalve hydrothermal vivant le long de la ride Médio-Atlantique, qui héberge dans des cellules branchiales spécialisées, deux types de γ-protéobactéries différentes : des méthanotrophes (MOX) et des sulfo-oxydantes (SOX). Ces dernières sont capables d'oxyder les composés réduits présents dans le fluide hydrothermal fournissant ainsi énergie et/ou source de carbone à leur hôte. Cette double endosymbiose est plastique ainsi, l'abondance relative du type de symbionte hébergé (SOX vs. MOX) varie en fonction des concentrations en composés réduits présent dans le milieu (H2S, CH4). L'objectif de ce travail de thèse est d'identifier les acteurs moléculaires impliqués dans l'acquisition, le maintien et la régulation des bactéries symbiotiques. Pour ce faire, une analyse OMICs globale (protéomique -nano LC-MS/MS- et transcriptomique -micro-array-) a été mise en ¿uvre sur des individus symbiotiques issus de population naturelle (site hydrothermal Lucky Strike, -1700m) et sur des individus ayant expérimentalement perdu ou maintenu leurs symbiotes. Suite à cette approche globale et exploratoire, une approche plus spécifique a été menée sur des familles de protéines impliquées dans des processus immunitaire et/ou d'interactions hôte/symbiotes. Cette thèse apporte un éclaircissement sur les mécanismes régissant les relations et la communication hôte/symbiote. / Hydrothermal vents are located on the mid-ocean ridges, and are characterized by challenging physico-chemical conditions. Despite these conditions dense hydrothermal communities develop down around hydrothermal fluid emissions. The presence of marine invertebrates relies on their capacity to cope with these challenging factors, and, for those forming most of the biomass, on their ability to live in symbiosis with chemoautotrophic bacteria. Bathymodiolus azoricus is one of these symbiotic species that harbors two types of γ-proteobacteria, a sulfide-oxidizing bacterium (SOX) (using the oxidation of H2S as the source of energy and CO2 as source of carbon) and a methane-oxidizing bacterium (MOX) (that uses the oxidation of CH4 as both a source of energy and carbon). These bacteria are located in specific epithelial cells in the gill tissue of the mussel. The proportion and number of these symbiont types (SOX vs. MOX) in B.azoricus can change in response to environmental conditions, and especially on the relative concentration of reduced compounds. The aim of our study is to understand the molecular mechanisms of acquisition, regulation and maintenance of the symbiotic charge in B .azoricus gills. We therefore, performed a global OMICs analysis (proteomics –nano LC-MS/MS and transcriptomics- micro-array) on mussels from natural population (Lucky Strike, -1700m) and on mussels that experimentally loose or maintain their symbiotic rate. This exploratory approach was followed by a more specific approach on family of proteins involved in immunity process and/or in host/symbiont interactions. This PhD provides hypotheses on the mechanisms governing the relationship and communication between host and symbionts.

Les activités humaines sont à l’origine de profondes modifications de la distribution naturelle des espèces. Les introductions d’espèces sont en particulier à l’origine de contacts secondaires entre espèces non isolées reproductivement et ayant divergé en allopatrie. Cette situation est un cas d’étude particulièrement intéressant pour étudier des processus éco-évolutifs, tels que la coexistence d’espèces occupant de même niches écologiques ou les flux de gènes contemporains (i.e. hybridation et introgression) entre espèces indigènes et non-indigènes. Cette thèse s’est ainsi intéressée aux interactions écologiques et génomiques entre deux ascidies congénériques et interfertiles, Ciona robusta et Ciona intestinalis. Ces deux ascidies, abondantes dans les habitats portuaires, sont en sympatrie en Manche Occidentale suite à l’introduction récente de C. robusta (supposée originaire du Pacifique Nord-Ouest) dans l’aire de distribution naturelle de C. intestinalis. Par une étude de la distribution spatiale et temporelle (inter-saisonnière et inter- annuelle) des adultes des deux espèces et de la sédentarisation de leurs juvéniles, nous avons montré que les deux espèces coexistent de façon durable, au sein de communautés similaires, à l’échelle régionale. Elles vivent en syntopie dans la majorité des habitats portuaires étudiés, bien qu’il existe une importante dynamique saisonnière de leur abondance relative : C. robusta est surtout présente en fin d’été et en automne, et toujours en moindre abondance par rapport à sa congénère indigène. Cette syntopie, l’interfertilité des deux espèces et le synchronisme de leur maturité sexuelle indiquent un potentiel d’hybridation important entre les deux espèces. L’hybridation réalisée est pourtant faible, comme montré avec quatre marqueurs moléculaires diagnostiques des deux espèces, analysés sur plus de 3000 individus : seulement 4% des individus présentent des génotypes compatibles avec de l’hybridation ou de l’introgression. Ces résultats ont été complétés par une étude de génomique des populations (310 marqueurs SNPs et 450 individus collectés dans différents océans) : ils confirment que les flux de gènes interspécifiques sont très rares. Par ailleurs, les rares locus présentant du polymorphisme partagé montrent un taux d’introgression hétérogène, et l’introgression est également observée dans des localités où seule l’une des espèces existe (ex. côtes américaines et chiliennes). L’ensemble des résultats génétiques et génomiques indiquent que le flux de gènes interspécifique observé résulte d’introgressions anciennes (probablement au Pléistocène) et non contemporaines. Une dernière étude menée à l’échelle mondiale avec des marqueurs mitochondriaux a par ailleurs permis de montrer que les processus d’introduction de C. robusta diffèrent selon les régions d’introduction et pose la question du statut réellement non-indigène des deux espèces dans certaines régions. Ainsi, cette thèse a montré la (quasi)-absence d’hybridation actuelle entre C. robusta et C. intestinalis, en situation de syntopie. Elle ouvre des perspectives quant à l’étude des mécanismes d’isolement reproductif entre ces deux espèces. La question du devenir à long terme des deux espèces, qui par leur coexistence étroite sont en compétition, est posée. Cette compétition pourrait être modulée par leurs préférences environnementales et les changements climatiques en cours dans l’Atlantique Nord. Enfin, cette thèse illustre comment des processus contemporains et anciens interagissent pour façonner la distribution et l’évolution des espèces, la structure génétique de leurs populations et l’architecture de leur génome. / Human activities severely alter species ranges that have been built on evolutionary time scales, and biological introductions promote secondary contacts between non-reproductively isolated species that were in allopatry. Such a situation is a very interesting case-study to examine eco-evolutionary processes, for instance coexistence between species sharing the same ecological niche or inter-specific gene flow (i.e. hybridization and introgression) between native and non-native species. This PhD thesis studied ecological and genomic interactions between two biologically similar, interfertile and congeneric tunicates, namely Ciona robusta and Ciona intestinalis. They are both abundant in harbours and marinas. They are sympatric in the Western English Channel because of the recent introduction of C. robusta (putatively native to Asia) in the natural range of C. intestinalis. Based on spatial and temporal (seasons and years) adult abundance data and examination of recruitment patterns of the two species, we showed that the two species are sustainably coexisting at a regional scale in Brittany, within similar communities. They live in syntopy in most of the study marinas. However, there are significant changes in their relative abundance through time: C. robusta is mostly present at the end of the summer and in the autumn, although always being less abundant than its native congener. Syntopy, interfertility between the two species and synchronous sexual maturity all indicated a high likelihood of hybridization between the two species. The realized hybridization is however very low, as shown by 4 species-diagnostic molecular markers genotyped over more than 3000 individuals: only 4% of the individuals displayed a genotype compatible with hybridization or introgression. This result has been confirmed with a population genomics study (310 SNPs; 450 individuals collected worldwide): inter-specific gene flow is very low. In addition, the few loci showing shared polymorphism displayed variable introgression rates and introgression was observed even in allopatric localities (where only one of the two species exists nowadays). Overall, the genetic and genomic results indicate that interspecific gene flow is most likely due to past introgression events (that may have occurred during the Pleistocene). Finally, a study carried out at a worldwide scale with two mitochondrial loci, showed that the introduction processes of C. robusta are different among the introduced regions. This study also questions the non-native status of the two Ciona species in some regions. This work showed the near absence of contemporary hybridization between C. robusta and C. intestinalis, even in syntopy, opening new research perspectives about the mechanisms preventing their reproduction in the wild. It also questions the fate of these two competing species; this competition may depend on the interaction between their specific environmental preferences and on on-going climatic changes in the North Atlantic. Altogether, this work illustrates the interplay between contemporary and past processes on species distribution and evolution, population genetic structure and genomic architecture.

La fixation de N2, ou diazotrophie, est un processus biogéochimique majeur en raison de son apport en azote nouveau dans la couche de surface de l’océan. Cependant ses facteurs de contrôle restent mal connus. Le fer, dont les concentrations de surface sont faibles, est un élément potentiellement limitant de la fixation de N2 du fait du contenu en fer important de la nitrogénase. En raison de leur découverte récente, peu d’études ont été menées sur les cyanobactéries diazotrophes unicellulaires (UCYN) pouvant être responsables de ~50% de la fixation de N2 à l’échelle globale. Des expériences en culture ont permis de caractériser et quantifier pour la première fois la réponse d’une UCYN, Crocosphaera watsonii, face à la limitation en fer. En condition de limitation en fer, il a été observé une réduction de la croissance et des taux de fixation de N2 ainsi qu’une stratégie d’adaptation des cellules avec une diminution de leur volume. La stimulation de la croissance et de l’activité de C. watsonii cultivées en condition de limitation en fer suite à l’ajout d’une pluie saharienne artificielle a permis de mettre en évidence qu’une partie au moins du fer issu de poussières désertiques est biodisponible. En Atlantique subtropical Nord, où nous avons déterminé une forte contribution de la fixation de N2 à la production nouvelle, nous avons observé une limitation de la fixation de N2 et de la production primaire principalement par les phosphates et mis en évidence le rôle des métaux traces dans le contrôle de la fixation de N2. Un ajout de pluie saharienne a permis de stimuler systématiquement la fixation de N2 et la production primaire. / Despite the biogeochemical importance of N2 fixation, which represents the largest source of newly-Fixed nitrogen to the open ocean, some uncertainties remain about its controlling factors. Iron (Fe) is widely suspected as a key controlling factor due to the high Fe content of the nitrogenase complex and to its low concentration in oceanic surface seawaters. N2 fixation rates associated with unicellular N2 fixing cyanobacteria (UCYN) were estimated to be ~50% of the total N2 fixation at global scale, but as they have been recently discovered few studies have been conducted on these organisms. We performed culture experiments in order to quantify for the first time the response of an UCYN, Crocosphaera watsonii, to Fe limitation. Reduction of ambient Fe concentration led to significant decreases in growth rate and N2 fixation rates per cell and we observed an adaptive strategy to Fe limitation with a cell volume reduction. Then, the enhancement of growth and activity of C. watsonii under Fe limitation condition after artificial Saharan rain addition highlighted that at least a part of the Fe released by the dust is bioavailable. In subtropical North Atlantic, an important contribution of N2 fixation to new production was observed and we showed that primary production and N2 fixation were globally P-Limited. We revealed that trace metals play a key role in controlling N2 fixation in this area. Saharan rain addition stimulated N2 fixation, presumably by supplying these nutrients. All these results contribute to our knowledge of the control of oceanic N2 fixation and provide new insight about interactions between Fe, nitrogen and carbon biogeochemical cycles.