Ocean acidification (OA) together with other anthropogenic perturbations is projected to dramatically alter marine environments over the coming centuries. The vast majority of marine species reproduce by freely spawning sperm directly into the water column, where fertilisation can then either be external or a female can draw sperm into a burrow, brooding chamber or onto her external surface. Hence, sperm are now being released into rapidly changing seawater conditions. In this thesis, I firstly assess what is currently known on the potential for OA and other anthropogenic stressors to influence freely spawned sperm in marine invertebrate taxa. I then present a series of experimental chapters investigating the influence of OA, as a single stressor or in conjunction with a second stressor, copper, on sperm function, physiology and competitive fertilisation performance in a range of invertebrate taxa. My research demonstrates that sperm are vulnerable to the projected changes in seawater carbonate chemistry under OA, with responses observed at all biological levels from sperm physiology, swimming performance, fertilisation ecology and sperm competitiveness. In a multi-stressor experiment on polychaete gametes and larvae, I provide empirical evidence that changes to seawater pH under OA can alter the susceptibility of early life stages including sperm, to the common coastal pollutant copper. Sperm DNA damage increased by 150 % and larval survivorship was reduced by 44 % in combined exposures, than when exposed to copper alone. As a single stressor OA also acted to significantly reduce Arenicola marina sperm swimming speeds and fertilisation success. This work was followed up with a mechanistic investigation of A. marina sperm swimming performance under OA conditions. I found that the length of time between spawning and fertilisation can strongly influence the impact of OA on sperm performance. Key fitness-related aspects of sperm functioning declined after several hours under OA conditions, and these declines could not be explained by changes in sperm ATP content, oxygen consumption or viability. In a final set of experiments, I ran a set of paired competitive fertilisation trials in the sea urchin, Paracentrotus lividus. In addition to reducing fundamental sperm performance parameters, OA conditions affected competitive interactions between males during fertilisation, with potential implications for the proportion of offspring contributed by each male under the new conditions. This work suggests that the ‘best’ males currently may not be the most competitive under OA. Overall this body of work reveals a series of significant changes to sperm performance under OA that might act to perturb sperm functioning in future oceans.

Benthic foraminifera inhabiting the mudflats of the Eden Estuary, NE Scotland, exhibited a single annual peak in abundance at both high (270 individuals 10 cm⁻²) and low shore (210 individuals 10 cm⁻²) intertidal sampling stations during June 2000. The increased total abundance coincided with reproduction in the two dominant foraminiferal species Elphidium williamsoni (May) and Haynesina germanica (June) at both sites. Benthic diatom biomass, measured as chlorophyll c, peaked at the high intertidal site during March and April 2001 (36 and 37 mg m cm⁻², respectively) and at the low intertidal site in June2000 (45 mg m cm⁻²). The high intertidal foraminiferal populations appeared to display a lagged response to increases in chlorophyll c. Multivariate statistics suggest that abiotic factors control the abundance of foraminifera at the high intertidal site. At the low intertidal site, total foraminiferal abundance demonstrated an almost immediate response to increased chlorophyll c and multivariate statistics suggested biotic factors are more important in controlling foraminiferal species abundance here. Ingestion rates of ¹³C-Iabelled benthic diatoms over a five-day experimental period were high (e.g. enrichment values for Elphidium were recorded as 687 ± 121 % after 1 day) in intertidal benthic foraminifera. Laboratory observations of E. williamsoni demonstrated rapid asexual reproduction (within 3 days) and growth rates of up to 14 µm day⁻¹ were estimated. Three benthic foraminiferal species E. williamsoni, H germanica and E. oceanensis ingest motile benthic diatoms as a food resource on the intertidal mudflats of the Eden Estuary. Novel application of natural abundance stable isotope (δ¹³C and δ¹⁵N) techniques demonstrated the trophic position of intertidal benthic foraminifera, confirming that they largely ingest and assimilate organic matter derived from benthic diatoms. Foraminifera have largely been overlooked in meiofaunal studies, but play a significant role in the rapid transfer of autotrophic carbon to higher trophic levels within benthic marine food webs.

Elucidating patterns of connectivity for species of conservation concern is crucial in the design of networks of ecologically coherent marine protected areas, and therefore is considered in the design of such a network recently proposed to the UK Government. However, data concerning connectivity are deficient for most invertebrate sessile taxa. Therefore, this study used microsatellite panels developed de novo to assess the population genetic structure and genetic connectivity of two temperate octocorals in the North East Atlantic. Microsatellite panels for both species show evidence of cross-species transferability, and therefore in future may prove to be useful monitoring tools for the target species but also for congenerics further afield in Europe. Eunicella verrucosa (O. Alcyonacea: S.O.Holaxonia: F. Gorgoniidae), a threatened and IUCN red-listed sea fan, was sampled in the northerly extremes of its eastern Atlantic range in southern Portugal, Brittany, the South West UK and western Ireland. In this vicinity, connectivity appears to be defined at regional scales and localised cases of inbreeding and differentiation suggest that the population structure of this species is best described as a metapopulation. Alcyonium digitatum (O. Alcyonacea: S.O. Alcyoniina: F. Alcyoniidae), a soft coral, was sampled in the central portion of its range in Brittany, western Ireland, south west UK and the North Sea. This species exhibited very little population structure and apparent panmixia across the sampled range. However, high levels of heterozygote deficiencies and inbreeding in the majority of populations implies that the genetic structure of some populations of this species may be defined by self-seeding and rarer dispersal events that occur sufficiently often to offset divergence via genetic drift. Coalescent analyses indicate that in both species, migration between regions occurs asymmetrically. The presence of few duplicate genotypes in both datasets implies that sexual reproduction predominates in both species in the sampled area. Eunicella verrucosa is a charismatic species that is often used to promote marine conservation efforts in the UK and A. digitatum is a ubiquitous animal around western European coasts; the two species often occur together and both may suffer the damaging effects of mobile fishing gears. This research represents the first population genetic assessment of both species and the first time microsatellites have been used to assess population structure of octocorals in the North East Atlantic.

Dans le contexte d'un environnement soumis à des pressions humaines de plus en plus importantes, l'évaluation de la qualité écologique des milieux naturels est devenue un enjeu scientifique, politique et sociétal majeur. Au début des années 2000, les méthodes de bio-évaluation existantes se sont révélées insuffisantes au regard des exigences affichées par la Directive Européenne Cadre sur l'Eau de maintenir ou recouvrer le bon état écologique pour les masses d'eau continentales. En parallèle de cette prise de conscience politique de la nécessité d'une amélioration des méthodes de bio-évaluation, un certain nombre d'auteurs ont plaidé pour une prise en compte explicite des caractéristiques biologiques et écologiques des espèces (i.e. leurs « traits ») de façon à mieux comprendre les processus de mise-en-place et d'organisation des communautés en relation avec les caractéristiques de leur habitat. Le but principal de ce travail de thèse a été d'étudier comment les approches « traits », à plusieurs échelles d'organisation biologique, peuvent permettre d'améliorer la bio-évaluation des cours d'eau Français. Pour cela, nous avons étudié dans un premier temps l'application sur les communautés benthiques de l'approche « traits bio-écologiques potentiels » pour l'évaluation (i) de la qualité écologique, (ii) des risques d'altération et (iii) du degré d'homogénéisation fonctionnelle des cours d'eaux. Ensuite, nous avons exploré le potentiel de nouveaux traits (i.e. isotopiques, stoechiométriques et protéomiques) pour la caractérisation des réponses biologiques des invertébrés benthiques soumis à des pressions anthropiques 'simples' (i.e. acidification et contamination organique). Nos résultats ont démontré que les traits bio-écologiques potentiels permettaient d'améliorer de manière significative l'évaluation du statut écologique des cours d'eaux et des pressions anthropiques qu'ils subissent, à large échelle spatiale (e.g. sur les réseaux nationaux de suivi de la qualité de l'eau). Les analyses isotopique et stoechiométrique ont permis également, sur des problématiques plus locales, de relier des informations sur des traits biologiques (régime alimentaire et développement) aux transferts de nutriments et de matière organique réalisés par les communautés benthiques au sein des systèmes lotiques. Enfin, l'analyse protéomique réalisée le long d'un gradient d'acidification ouvre des perspectives intéressantes pour la mise en place d'un « système expert » précoce des effets d'une détérioration de la qualité de l'eau sur les invertébrés benthiques / In a global change context, ecosystems are subjected to more and more severe human pressures. In this context, optimizing the biomonitoring of natural ecosystems has become a major scientific, political and societal issue. In the early 2000th, most of the freshwater bioassessment methods did not succeed in fulfilling the requirements of the European Water Framework Directive, for efficiently evaluating the ecological status of rivers with the main objective to maintain or to reach the good ecological status for all the water bodies. In the same time, a major advance in community ecology was the explicit consideration of the biological and ecological attributes of species (i.e. their ?traits?) to better explain the role of habitat characteristics in community assembly. The main goal of this PhD work was to establish how trait-based approaches, at different biological scales, could enhance the bioassessment of French streams. We have first focused on the utilization of potential bio-ecological traits of macrobenthic communities for (i) evaluating the ecological quality of rivers, (ii) assessing the risk of significant alteration of benthic assemblages by specific pressure categories and (iii) appraising the human pressure-drived functional homogenization process in benthic communities. We examined the potential of new traits (derived from stable isotopy, stoichiometry and proteomics) for depicting the benthic invertebrate responses to 'simple' anthropogenic pressures (i.e. acidification and organic contamination). We have demonstrated that using potential bio-ecological traits efficiently enhances the ecological monitoring of wadeable rivers, at large spatial scale (e.g. on National survey networks). The stable isotope and stoichiometry analyses, when applied at reach scale, have allowed to link biological traits (i.e. diet and development) to ecological functions provided by macrobenthic communities, such as nutriment and organic matter flows in rivers. Finally, the proteomic analysis, performed along an acidification gradient, has brought out very interesting perspectives for the development of an integrative ?expert system? that early detects the biological effects of water quality alteration on benthic invertebrate assemblages

Les dinoflagellés forment un groupe complexe de protistes avec une grande diversité de morphologies, physiologies, et cycles de vies qui leur confèrent une forte capacité d'adaptation à l'ensemble des milieux (marins et dulçaquicoles) et habitats (pélagiques et benthiques) aquatiques rendant difficile l¿étude de leur diversité et de leur écologie. L'objectif de cette thèse a été la recherche de patrons globaux de biodiversité et de structuration des communautés de dinoflagellés pélagiques marins à l'échelle planétaire. Un protocole d'échantillonnage morphogénétique, couvrant la totalité de leur spectre de taille et une partie importante de leurs variabilités spatio-temporelles, a été développé (Tara-Oceans). Divers outils d'acquisition automatique à haut débit des données ont été testés. La diversité, l'abondance relative et la distribution géographique des espèces du genre Neoceratium ont été évaluées en mer Méditerranée par FlowCAM. Une étude de la structuration de la biodiversité a été réalisée par metabarcoding de l¿ADNr 18S (fragment V9). La construction d'une base de séquences ADNr de référence (DinR2) a permis l¿assignation taxonomique des metabarcodes environnementaux. L¿approche par metabarcode révèle une diversité remarquable et insoupçonnée des pico-dinoflagellés (<5µm) et que, indépendamment de l'écosystème étudié et de la période d'échantillonnage, l¿abondance des différents ordres dépend essentiellement de la taille (pico-, nano-, micro-, et meso-plancton). La structuration des communautés de dinoflagellés de différentes fractions de tailles de la zone photique a été confrontée à certains facteurs environnementaux ouvrant des pistes de recherche prometteuses / Dinoflagellates form a complex group of protists with a variety of morphologies, physiologies, and life cycles that give them a strong adaptation to all aquatic environments (marine and freshwater) and habitats (pelagic and benthic) making difficult to study their diversity and ecology. The objective of this thesis was the search for global biodiversity patterns and community structure of marine pelagic dinoflagellates across the world?s oceans. A morphogenetic sampling protocol, covering the entire spectrum of their size and an important part of their spatio-temporal variability, was developed (Tara-Oceans). Various tools for an automatic acquisition broadband data were tested. Diversity, relative abundance and geographical distribution of the genus Neoceratium were evaluated by FlowCAM in Mediterranean Sea. A study of the structure of biodiversity was conducted by metabarcoding with 18S rDNA (V9 fragment). Building a base of rDNA reference sequences (DinR2) allowed the taxonomic assignment of environmental metabarcodes. The metabarcode approach reveals a remarkable and unexpected diversity of pico-dinoflagellates (<5?m) and, regardless of the studied ecosystem and the sampling period, that abundance of different levels mainly depends to the size fractions (pico-, nano-, micro- and meso- plankton). Structuring of dinoflagellates communities in different size fractions of the photic zone was facing to some environmental factors and opens promising avenues for research

Les espèces protistes ont été traditionnellement classifiées comme des plantes ou des animaux en raison de l’absence ou présence des chloroplastes. L’état actuel de la connaissance indique qu’un grand nombre d’espèces protistes portent des chloroplastes mais que physiologiquement elles sont capables d’utiliser l’autotrophie (photosynthèse) ou l’hétérotrophie pour se nourrir. La combinaison de ces deux modes trophiques par une même cellule est nommée mixotrophie. Chez les protistes l’hétérotrophie peut s’effectuer soit par la consommation des particules par phagocytose, e.g. des proies bactériennes, ou bien par l’absorption des composants organiques dissouts, i.e. osmotrophie. La mixotrophie est de plus en plus décrit chez les protistes dans tous les habitats aquatiques. Les écologistes du plancton constatent la récurrence de la mixotrophie chez les formes traditionnelles « phyto»plancton et micro »zoo »plancton. Cependant, identifier et quantifier la mixotrophie reste toujours un défi méthodologique. Dans cette étude nous nous sommes intéressés à la mixotrophie chez les espèces phytoplanctoniques marines, en particulier à leur nutrition phagotrophique de proies bactériennes. Nous avons testé des techniques modernes afin d’identifier la mixotrophie dans des cellules phytoplanctoniques. La technique cytogénétique d’hybridation in situ Card-FISH en utilisant de sondes d’ARN ribosomique 16S a été effectuée suivant des protocoles existant pour des bactéries et des protistes. Cette technique s’est avérée être un outil précieux pour visualiser des groupes phylogénétiques bactériens en association avec le phytoplancton à l’aide de la microscopie à épifluorescence, sans avoir besoin d'un isolement préalable des cellules ou des interférences avec l'association microbienne. Cependant, la méthode a échoué pour visualiser mixotrophie chez le phytoplancton car la sonde eubactérienne générale(EUB338) combine une large gamme d'espèces phytoplanctoniques, ce qui rend impossible de discriminer les signaux fluorescents provenant de tissus bactérienne ou phytoplanctonique. Le contexte de ces études est le phytoplancton et les bactéries hétérotrophes lesquels constituent des principaux concurrents pour les nutriments inorganiques dissouts. Dans le cas où la croissance bactérienne est limitée par le carbone, l'augmentation de la concentration de carbone organique dissous(DOC) renforce la croissance bactérienne et la consommation de nutriments dissous et ainsi affecte négativement la croissance du phytoplancton autotrophe. Cependant, les consommateurs de bactéries, i.e.phytoflagellés mixotrophes, peuvent être favorisés dans de telles situations car la hausse de DOC donne lieu à l'abondance plus élevé des proies bactériennes.En outre, nos résultats indiquent un potentiel effet positif de la température sur le mode de nutrition hétérotrophe de l’espèce, ainsi qu’une croissante contribution des espèces mixotrophes au sein des communautés de phytoplancton dans des conditions des hautes températures des eaux de surface de la mer. / Protist species were traditionally classified morphologically as either „plants“ or „animals“, based on the absence or presence of chloroplasts. State of science is that a high number of protist species carrychloroplasts but are nutritionally able to employ both autotrophy (photosynthesis) and heterotrophywithin a single cell. This combination of autotrophic and heterotrophic mode of nutrition within a single species is named mixotrophy. In protists, heterotrophy can be realized either by the uptake of food particles (e.g. bacterial prey) through phagocytosis or by the uptake of dissolved organic compounds (i.e.osmotrophy). Mixotrophy is globally and increasingly described in protists from all types of aquatic habitats. Plankton ecologists nowadays assess mixotrophy among the traditionally typified “phyto”plankton and mikro”zoo”plankton species as regularity. Nevertheless, detection and quantification of mixotrophy is still a methodological challenge. In this study, we focused on mixotrophy in marine phytoplankton species and put emphasis on its phagotrophic nutrition from heterotrophic bacterial prey. State of the art methodology was tested to visualize mixotrophy in single phytoplankton cells. Catalyzedreported deposition-fluorescence in situ hybridization (Card-FISH), using 16S ribosomal RNA probes,was employed based on existing protocols for bacteria and protists. The method proved to be a valuable tool to visualise bacterial phylogenetic groups in association with phytoplankton by epifluorescence microscopy without need for prior isolation of cells or interference with the microbial association.However, the method failed to visualize mixotrophy in phytoplankton since the general eubacterial probe(EUB338) hybridised a broad range of phytoplankton species making it impossible to discriminate fluorescent signals originating from bacterial or phytoplankton tissue. Background of these studies is phytoplankton and heterotrophic bacteria being major competitors for dissolved inorganic nutrients. In case that bacterial growth is carbon limited, increasing concentrations of degradable dissolved organic carbon (DOC) enhance bacterial growth and consumption of dissolved nutrients and there by negatively affect autotrophic phytoplankton growth. Bacteria consuming mixotrophic phytoflagellates, however, may gain in importance in such situations since DOC provokes higher bacterial prey supply.In addition, our results indicate a potential positive effect of temperature on O. minima´s heterotrophic nutrition mode, and indicate a potential increasing contribution of mixotrophic species to phytoplankton communities under increasing sea surface water temperatures.

Η εργασία αυτή φιλοδοξεί να εκτιμήσει την περιβαλλοντική κατάσταση στο στενό Ψυττάλειας -Κερατσινίου,όπου ο κεντρικός αποχετευτικός αγωγός απέριπτε αστικά λύματα και βιομηχανικά απόβλητα του νομού Αττικής. Προσδιορίσθηκαν οι συγκεντρώσεις των βαρέων μετάλλων του οργανικού άνθρακα, των φυσικών ραδιονουκλιδίων και του Cs-137. Έξι δειγματοληπτικές πυρηνοληψίες που εκτελέσθηκαν σε επιλεγμένα σημεία οδήγησαν στον καθορισμό του στρώματος της οργανικής λάσπης, ενώ διαπιστώθηκαν οι υψηλές συγκεντρώσεις των βαρέων μετάλλων που περιέχονται σε αυτή. Οι τιμές της ειδικής ραδιενέργειας των φυσικών ραδιονουκλιδίων είναι αντίστοιχες με αυτές των φυσικών ιζημάτων ενώ αυτές του Cs-137 ήταν σχετικά υψηλές παρουσιάζοντας σαφείς κατανομές με το βάθος. / The present research estimates the environmental situation in the Psittalia – Keratsini strait, where the outfall sewer of Athens discharged untreated sewage to the sea. The concentrations of heavy metals, organic carbon, natural radionuclides and Cs-137 were determined. Six sample cores were collected. The geochemical analysis determined high concentrations of heavy metals and Corg in the layer of organic mud. The concentrations of natural radionuclides were similar of those in natural sediments while those of Cs-137 were relatively high presenting explicit distributions with depth.

With growing human pressures on the oceans and seas, the resulting decline of ecosystem health and biodiversity is increasingly limiting the ability of marine ecosystems to provide essential functions and resources for human wellbeing. To prevent further marine degradation, an ecosystem based approach to marine management is needed. An integral part of this is constructive stakeholder engagement. However, in a marine context, engagement is often difficult due to traditionally sectoral management and the complexity of marine issues. This thesis presents an interdisciplinary study that evaluates the potential of the ecosystem services approach to support and improve marine stakeholder engagement. First, opportunities and challenges of using the approach in participatory marine management processes were explored through interviews with 39 stakeholders who participated in the application of ecosystem service assessment to marine management in six French and UK case studies. The interviews revealed that the ecosystem services approach can facilitate participatory engagement by improving understanding of complex ecological-socioeconomic systems and fostering constructive dialogue. Second, the potential of the approach for communicating marine management decisions to marine users was tested with a scenario based survey. Responses to three versions of the survey, two with and one without ecosystem services content, were compared, showing that the ecosystem services information did not increase agreement with the management measures proposed in the scenario. An evaluation of the results in the context of environmental behaviour research suggests that the novelty and complexity of the ecosystem services approach might limit its usefulness for top down communication. In contrast, if the approach is integrated in participatory processes, it was concluded that this could have multiple benefits for ecosystem based marine management. From these findings, a conceptual model was developed that provides a normative framework for the effective use of the ecosystem services approach to support constructive participatory engagement in marine governance.

La lignée verte (i.e. les plantes) est représentée dans l'océan par les algues appartenant aux Chlorophyta. Celles-ci contribuent en moyenne à 25% des séquences photosynthétiques (Dinoflagellés exclus) retrouvées dans les inventaires moléculaires pan-océanique. Bien que les Chlorophyta jouent un rôle important dans l'écologie de l'océan et nous permettent de comprendre l'histoire évolutive des plantes terrestres, leur diversité et leur distribution dans les eaux marines du globe est peu documentée. Après avoir optimisé une base de données de séquences de références ARNr 18S, j'ai procédé à l'analyse de données de métabarcodes produits par Ocean Sampling Day (OSD), qui a fourni des données utilisant 2 régions hypervariables du gène du 18S appelées V4 et le V9. La comparaison des images de diversité produites par le V4 et le V9 a illustré l'influence de la base de référence sur la diversité. Ensuite, l'analyse de l'ensemble des V4 a permis d'étudier la distribution des Chlorophyta dans l'océan mondial. De plus, la vérification de l'assignation automatique des OTUs par reconstruction phylogénétique grâce à la base de référence produite en début de thèse, a permis de confirmer l'existence de nouvelles lignées de prasinophytes et de confirmer que la classe des Mamiellophyceae dominait les eaux côtières, alors que les clades VII et IX des prasinophytes dominaient les eaux océaniques oligotrophiques. Ces analyses ont aussi permis de montrer l'écart entre la diversité environnementale et celle dans la base de référence, en particulier pour les genres Ostreococcus et Micromonas (Mamiellophyceae). / The green lineage that dominates on land is represented by Chlorophyta which account in average for 25% of photosynthetic sequences (Dinoflagellates excluded) in global marine molecular inventories. Although Chlorophyta are major keys for ecological understanding of the ocean, as well as the evolutionary story understanding of land plants, their diversity and distribution in marine waters has been understudied. This thesis aims at investigating the environmental diversity of marine Chlorophyta and describing their distributions based on available large scale metabarcoding datasets. First, a reference database of publicly available 18S rRNA sequences of Chlorophyta was assembled and critically curated. Next, the Ocean Sampling Day (OSD) 18S metabarcode datasets were analysed. Chlorophyta diversity was compared for a limited sample set based on two regions of the 18S rRNA: the V4 and V9 regions. Then, Chlorophyta distribution was studied using the full OSD V4 dataset. Careful taxonomic investigations using both automatic and hand checked assignation of OTUs using alignments and phylogenies allowed to confirm the existence of new environmental prasinophytes clades and to confirme, that the Mamiellophyceae were the major group in coastal waters, while prasinophytes Clade VII and IX were dominating the oceanic oligotrophic stations. Comparing V4 and V9 regions illustrated the influence of the reference database on diversity. Moreover, the taxonomic investigation highlighted the diversity gaps between reference databases and environmental datasets. This work emphasizes the neglected importance of Chlorophyta in marine waters and provides some suggestions for future research.

Dans l’étude de la spéciation, l'existence de zones dans lesquelles deux espèces en sympatrie montrent différents niveaux de différenciation génétique constitue une bonne opportunité pour comprendre la nature et l'évolution des barrières à la reproduction entre espèces. Jaera (albifrons) albifrons et Jaera (albifrons) praehirsuta sont deux espèces d’isopodes marins qui coexistent en sympatrie le long des côtes nord-européennes. Des barrières écologiques, comportementales, et génétiques cloisonnent efficacement ces deux espèces, à l'exception d'une région unique (Normandie, France) dans laquelle des morphotypes intermédiaires avaient été décrits dans les années 60.Au cours de cette thèse, l'utilisation de microsatellites et de SNPs obtenus par séquençage RAD ont permis de démontrer que le niveau d'isolement interspécifique varie fortement entre sites, de l'hybridation introgressive à l'isolement quasi-complet. Une analyse comparative de ces sites combinant échantillonnage en populations naturelles, croisements expérimentaux et analyses génomiques a ensuite permis de : i) mettre en avant le rôle prépondérant de l'isolement sexuel (qui reste fort dans les populations introgressées) accompagné d'une barrière post-zygotique relativement faible, ii) découvrir la présence de bactéries Wolbachia au sein des deux espèces, iii) démontrer que la coexistence des deux espèces résulte d'une spéciation allopatrique suivie de contacts secondaires avec reprise de flux de gènes d'intensité variable, et iv) montrer que ces flux de gènes varient également fortement au sein du génome, les chromosomes sexuels et des chromosomes réarrangés semblant limiter fortement l'introgression. / Within the field of speciation, sympatric areas with different levels of interspecific genetic differentiation offer a good opportunity to understand the nature and evolution of reproductive barriers between species. Jaera (albifrons) albifrons and Jaera (albifrons) praehirsuta are two species of marine isopods that coexist in sympatry along the northern European coasts. Ecological, behavioral and genetic barriers efficiently isolate these two species, except in a unique region (Normandy, France) where morphological phenotypes were described in the 60's.In this thesis, microsatellites and SNPs obtained from RAD-sequencing allowed me to demonstrate that the level of interspecific isolation varies widely between sites, from introgressive hybridization to quasi-complete isolation. A comparative analysis of these sites combining sampling from natural populations, experimental crosses, and genomic analyses then allowed me to: i) demonstrate the predominant role of sexual isolation (which remains strong in introgressed populations), together with a relatively weaker post-zygotic barrier, ii) discover the presence of Wolbachia bacteria within the two species, iii) demonstrate that the coexistence of these species originate from an allopatric speciation followed by secondary contacts with varying levels of heterospecific gene flow renewal, and iv) show that gene flow varies also strongly along the genome, with an effect of sex chromosomes and rearranged chromosomes apparently limiting introgression.