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Chapter 1 - General Introduction. Part I reviews the structure and function of fish muscle, including fibre orientation, the properties of different muscle fibre types and the recruitment of muscle fibres during swimming. Part II concerns the effects of acute temperature changes on fish muscle and describes a variety of mechanisms underlying temperature adaptation, with particular emphasis on the mechanical performance of fish muscle. Chapter 2 - Temperature and the mechanical properties of live muscle fibres from the teleost Myoxocephalus scorpius. Small bundles of fast fibres were isolated from the myotomal muscle of the teleost Myoxocephalus scorpius. The temperature dependence of isometric contractile properties and the force-velocity (P-V) relation were studied. Fibres were found to deteriorate above 18°, and the force plateau during tetanic stimulation was not maintained above 15°. Twitch and tetanic tension (Po) showed optima at around 8°. Force-velocity curves were fitted using either Hill's hyperbolic equation or a hyperbolic-linear (hyp-lin) equation. The best fit to the data was provided by the hyp-1in equation, which gave consistently higher values for unloaded contraction velocity (Vmax): 4.3, 8.1 and 9.5 muscle lengths s-1 at °, 8°, and 12° respectively. Both isometric and isotonic data from live fibres was compared with skinned fibres and live fibres from other vertebrates. The P-V relation was found to become progressively more curved at higher temperatures. Muscle power output calculated from the hyp-lin equation was 124 Wkg-1 at ° and 256 Wkg-1 at 8°. Curves normalised for Po and Vmax at each temperature show that the change in curvature is sufficient to increase the relative power output of the muscle by around 15% on decreasing the temperature from 8° to °. Chapter 3 - The myology of the pectoral fin of the common carp Cyprinus carpio L. and variation in fibre composition with temperature acclimation. Common carp (Cyprinus carpio L.) were acclimated to either 8° or 20° for 8 weeks (12h light:12h dark). The myology and skeletal structure of the pectoral assemblage of the carp was studied. Cross-sections of the entire assemblage were taken for histochemistry in order to determine the distribution of fibre types within the musculature. Examination of the fibre diameter range data reveals a larger number of smaller slow fibres in the muscle of 8° C-acclimated fish, commensurate with a hypothesis that the slow fibre mass is proliferating during cold-acclimation by producing new slow fibres. Chapter 4 - Temperature acclimation in the common carp: force-velocity characteristics and myosin subunit composition of slow muscle fibres. Common carp were acclimated to either 8° or 20° for 6-12 weeks (12h light:12h dark). Bundles of 20-50 fibres were isolated from the superficial region of the pectoral fin abductor superficialis muscle. Histochemical studies showed preparations to contain 93-100% slow muscle fibres. The maximum tetanic tension (Po) produced by fibre bundles was similar when measured at the acclimation temperature of each group. Chapter 5 - General Discussion The results detailed in this thesis are discussed in relation to the effects of temperature on fish swimming. Recent developments in technique are described and some suggestions for further work using these techniques are outlined.

The structure of the autonomic innervation of the gastro-intestinal tract and heart of a number of teleosts was examined using light and electron microscopy and fluorescence histochemistiy. In the scorpion fish, the structure of the coeliac ganglion and the distribution of aminergic neurones in the brain was also investigated. The distribution of monoamine-containing nerves in the gut of scorpion fish, plaice, herring and ice fish was described using fluorescence histochemistry. Castecholaminergic fibres are found in the myenteric plexus and in the submucosa where they frequently run with blood vessels. They also supply the longitudinal muscle of the rectum and are often prominent in the circular muscle of the pyloric and anal sphincters. Serotonergic nerves pass through the submucosa to the subepithelial plexus and 5HT can be isolated chromatographically from gut wall homogenates. Serotonergic enterochromaffin cells are present in the stomach and distal rectum and in the herring a catecholamine-containing form was observed in the pyloric stomach. Ultrastructurally two types of axonal profiles are seen in the gut. The first contains small agranular vesicles typical of cholinergic nerves and these synapse with the perikarya of myenteric neurones, while the second contains a mixture of large and small granular vesicles and though often found adjacent to ganglion and muscle cells is not involved in conventional synapses. Both types are present in the subepithelial plexus. Histochemical and drug depletion studies suggest that some of the granular vesicles contain biogenic amines. The hearts of plaice, dab and angler fish do not contain adrenergic nerves Taut these were found in all other species examined. In the lingcod, aminergic perikarya are also present in the cardiac ganglion. With the electron microscope, the densest innervation of cardiac muscle was found close to the cardiac ganglion but though fluorescent nerves are abundant, nerve profiles contain predominantly agranular vesicles. The coeliac ganglion of scorpion fish is similar in structure to sympathetic ganglia in other vertebrates. It contains two types of principal cell as well as a population of small intensely fluorescent (SIP) cells. The SIP cells appear to become more numerous in early summer when vesicles in the equivalent cells observed ultrastructurally develop electron dense granules. The catecholaminergic and serotonergic structures in the brain of scorpion fish were described and compared to those of other teleosts and higher vertebrates.

Les duplications de gènes et de génome sont considérées comme des moteurs de l’évolution des génomes eucaryotes. Trois duplications de génome complet (ou polyploïdisations) sont survenues au cours de l’évolution des vertébrés, dont deux à la base des vertébrés, et une troisième chez l’ancêtre commun des poissons téléostéens. La diversité morphologique, anatomique et écologique des espèces qui partagent un ancêtre commun polyploïde chez les chordés suggère un rôle des duplications de génome dans la diversification des espèces. En particulier, les duplications de génome semblent avoir facilité l’émergence du plan d’organisation des vertébrés, et être à l’origine de la radiation évolutive survenue chez les poissons téléostéens. Cependant, la portée évolutive des duplications de génome, et notamment les deux hypothèses majeures formulées ci-Avant, restent des questions ouvertes et en grande partie non résolues. Le groupe des téléostéens, qui compte plus de la moitié des espèces vertébrés existantes et partage un ancêtre commun polyploïde, constitue un modèle pertinent pour évaluer la contribution des duplications de génome dans l’expansion des familles multigéniques chez les vertébrés, pour comprendre les mécanismes évolutifs qui façonnent l’évolution des familles de gènes, et finalement tester les hypothèses moléculaires qui peuvent relier duplication de génome et biodiversité. Ainsi, nous avons étudié l’impact de la duplication de génome survenue à la base des téléostéens sur l’évolution de la famille multigénique sox, essentielle pour le développement et l’homéostasie des vertébrés. Notre analyse du contenu et de l’organisation des gènes sox dans 15 génomes de vertébrés, dont 10 téléostéens, révèle une importante expansion de l’ensemble de la famille des gènes sox dans ce vaste groupe de vertébrés, et démontre que cette expansion est essentiellement due à la duplication de génome survenue à la base des téléostéens. Les gènes sox dupliqués par duplication de génome semblent avoir été perdus par non-Fonctionnalisation dans certaines lignées, et préservés en deux copies par sous-Fonctionnalisation et/ou néo-Fonctionnalisation dans certaines autres lignées. Notre étude indique en effet une divergence lignée-Spécifique des patrons d’expression entre les gènes sox dupliqués chez différentes espèces de téléostéens. Ainsi, l’expansion du répertoire des gènes sox à la base des téléostéens semble avoir été suivi d’une évolution lignée-Spécifique du contenu et des fonctions de la famille des gènes sox chez les poissons téléostéens. Cette étude supporte l’hypothèse d’un rôle des duplications de génome dans l’enrichissement et la diversification subséquente des répertoires de gènes du développement tels que les gènes sox, et son rôle potentiel dans la diversification des espèces vertébrés. / Gene and genome duplications are major engines of eukaryotic genome evolution. Three rounds of whole genome duplication (WGD) have occurred during vertebrate evolution, two rounds at the base of the vertebrate lineage, and a third round in the common ancestor of the teleostean fish (the so-Called teleost-Specific WGD). In chordates, species that share a polyploid ancestor are characterized by a huge morphological, anatomical and ecological diversity suggesting a role of WGDs in species diversification. For instance, it is considered that these drastic genomic events provided the raw material for the emergence of the vertebrate body plan, and facilitated speciation processes during the teleost radiation. However, how WGD is related to phenotypic diversification or to major evolutionary transitions are fundamental questions that remain largely unsolved. Teleostean fish constitute more than half of all extant vertebrates and share a polyploid ancestor. Thus, they provide a relevant model to study the importance of WGDs in gene families expansion, to understand evolutionary mechanisms that drive the evolution of these families and, finally, to test molecular hypotheses that might relate WGD and biodiversity. In this project, we studied the impact of the teleost-Specific WGD on the evolution of the sox gene family which are involved in development and homeostasis in vertebrates. Our analysis of the content and the genomic organization of the sox genes in 15 vertebrate genomes, including 10 teleosts, reveals an important expansion of this family in the teleost lineage, and demonstrates that this expansion is mainly due to the teleost-Specific WGD. The duplicated sox genes seem to have been lost by non-Functionalization in certain lineages, and preserved in two copies in others by neo-Functionalization and/or sub-Functionalization. Indeed, this study indicates lineage-Specific divergence in expression patterns between duplicated sox genes in different teleostean species. Hence, the sox family expansion that occurred in the last common ancestor of teleostean fish seems to have been followed by a lineage-Specific evolution of the content and functions of the sox family in this group. Our study supports the hypothesis for a role of WGDs in the enrichment and diversification of developmental genes repertories and its potential role in species diversification in vertebrates.

La perte d'habitat engendrée par l'artificialisation des côtes a de graves conséquences sur la biodiversité marine. Aussi, dans une optique de maintien de la biodiversité et des stocks de poissons, il peut s’avérer intéressant de restaurer certaines fonctions écologiques dans les zones anthropisées. Cette thèse avait pour objectif d’estimer le rôle potentiel des ports en tant qu’habitat pour les juvéniles de poissons côtiers et d’évaluer dans quelle mesure ce rôle peut être amélioré par le biais d’actions de restauration. Des expérimentations en aquarium ont permis d’estimer que le taux de survie des juvéniles sur des habitats artificiels utilisés à des fins de restauration était comparable à celui observé sur des roches. Une étude de la distribution spatiale des juvéniles à l’échelle d’un paysage sous-marin a ensuite montré que les ports pouvaient abriter des densités en juvéniles représentant de 50 à 90 % de celles retrouvées en milieu naturel. Les densités à l'intérieur des ports étaient cependant tributaires du type d’habitat considéré; les quais sans complexité structurale abritant les densités les plus faibles. Enfin, l'étude de cas concrets, a montré que la réhabilitation des ports pouvait significativement augmenter les densités de juvéniles à l’échelle de l’habitat, celles-ci pouvant atteindre des niveaux comparables au milieu naturel. Toutefois, ces bénéfices restaient faibles à l’échelle d’un port dans sa globalité. Ces travaux suggèrent un réel potentiel des infrastructures portuaires en tant qu’habitat juvénile alternatif, en particulier si des actions de restauration y sont entreprises. Cependant, pour plus d’efficacité, les projets de restauration devraient être menés à large échelle et utiliser une diversité d’habitats artificiels. La restauration écologique des ports peut ainsi être employée comme un outil complémentaire aux mesures de protection dans le cadre d’une gestion intégrée des zones côtières à l’échelle du paysage. / Habitat loss caused by urban sprawl has harmful consequences on marine biodiversity. With a view to maintaining biodiversity and fish stocks, it may be worthwhile to restore some ecological features in anthropized areas. The aim of this thesis was to estimate the potential role of ports as habitat for juvenile coastal fish and to evaluate how this role can be improvedthrough restoration actions. Tank experiments revealed that juvenile survival rate on artificial habitats used for restoration purpose could be equivalent to that observed on natural habitat. The assessment of the spatial distribution of juvenile at the scale of a seascape permitted to estimate that harbors could host densities of juvenile that were between 50 to 90% of thoseobserved in natural sites. Within harbors densities were highly dependent on the type of habitat, featureless dock hosting the lowest densities. Subsequently, based on case studies, this work demonstrated that harbors rehabilitation could significantly enhance juvenile densities at the habitat scale. Densities on restored habitat might reach those observed in natural habitats.However, at the scale of the whole harbor benefits were low. This work suggests that harbors have a real potential as an alternative juvenile habitat, especially if restoration actions are undergone. However, for more efficiency, restoration projects should be led at the scale of the whole site and include a diversity of artificial habitats. Thereby, restoration approaches shouldbe considered as a complementary tool to protection measures in a seascape integrated management approach of coastal areas