The fish order Pleuronectiformes (flatfishes) include over 800 fish species, and are generally considered to be monophyletic. Phylogenetic relationships within the order remain largely unresolved, particularly for the Paralichthyidae, a very poorly defined family. In addition to the lack of consensus on intrarelationships within this order, flatfish diversification patterns are still poorly understood. Here we want to test the hypothesis that (i) a densely sampled phylogenetic tree will help to unravel the phylogenetic relationships within flatfish, and (ii) that the formation of the Isthmus of Panama has played a role in the diversification of flatfish, following their distribution in both oceans, Atlantic and Pacific. Maximum likelihood and Bayesian analyzes were performed on a dataset consisting of nine mitochondrial and nuclear loci on a set of 309 flatfish species. The heterogeneity of substitution rates, known to cause phylogenetic errors in large multigene alignments, can be corrected by data partitioning, or by using heterogeneous site models. Very few studies have compared the effects of using these approaches. We present a robust phylogenetic tree with different heterogeneous and well-supported models, and the intraordinal relationships of flatfish are discussed in light of these results. We present evidence for three new suborders within the flatfishes. The monophyletic status of most families is corroborated. The family Paralichthyidae and the family Poecilopsettidae were found to be polyphyletic. Heterogeneous models have not been able to solve the deeper relationships between flatfish. We also show that flatfish diversification occurred in a few families in at least two stages, related to distinct geological events.

Demographic characteristics of juvenile Dover sole (Microstomus pacificus) were examined in relation to physical and biotic factors to develop a hypothesis explaining annual variations in recruitment. Surveys were conducted along the Oregon continental shelf at depths between 50-400 m bimonthly during 1989 and annually (in March) between 1990 and 1993. To determine settlement timing, growth, and mortality, daily growth increments were validated, as was position of the first post-settlement annulus. A method of estimating precision of otolith elemental composition with the electron microprobe was developed; otolith microstructure and microchemistry were used to identify a landmark associated with settlement. Mean density of 0-group settlers varied annually, with 1989 and 1990 high, 1991 and 1992 low, and 1993 intermediate. 0-group abundance was correlated with fall offshore divergence one year before settlement and with southward geostrophic velocity during the summer before settlement. These conditions may be related to production of prey available to pelagic larvae. Density of 0-group Dover sole was highest between 100-119 m, but deeper areas were also utilized in years of highest abundance. Density was not correlated with spawning stock biomass or density of older juveniles. It was correlated with rex sole (Glyptocephalus [Errex] zachirus) density. Growth rate was positively correlated with mean April-October upwelling and was not related to density or mortality of Dover sole. First-year mortality was positively correlated with early settlement of 0-group larvae, possibly due to an advantage of settling and migrating to the primary nursery area well in advance of the spring transition. A multiple regression model predicting density of 1-group Dover sole from three physical environmental factors was applied to an independent time series of Dover sole "age-5" recruitment estimates (Turnock and Methot 1992). The model was a poor predictor of annual recruitment to fisheries but a good predictor of trends based on five-year running averages. Results suggest that multi-year trends in Dover sole recruitment to fisheries can be explained by a small set of density-independent physical factors. / Graduation date: 1995

Fish are not abundant at hydrothermal vents due to the toxicity of venting fluids. Those that are present usually roam the periphery of the vent field or visit occasionally to feed on the abundance of life supported by chemosynthesis. In the past decade, dense aggregations of a newly described flatfish, Symphurus n.sp, have been observed in association with hydrothermal vents in the western Pacific hydrothermal vent biogeographic province. In this thesis I provide evidence that Symphurus n.sp is a vent obligate and consider the ramifications that this association with hydrothermal vents may have for its distribution, population characteristics, behaviour and diet. Symphurus n.sp has a widespread but disjunct distribution throughout the western Pacific hydrothermal vent biogeographic province. Symphurus n.sp appears to be restricted to hydrothermally active, shallow, sulphur rich seamounts. Symphurus n.sp occurs on unconsolidated volcanoclastic ash and solid sulphur crusts and in close association with molten elemental sulphur. The obvious affinity that this species has for native sulphur is unusual and remains unexplained. Unlike most vent-associated fish, Symphurus n.sp occurs in close contact with point source venting and its distribution extends to the periphery of vent fields but not beyond. The density of flatfish on these seamounts surpasses density estimates of flatfish nursery grounds on the continental shelf. On Daikoku Seamount (Mariana Volcanic Arc), mean flatfish abundances were 100 and 66 individuals m-2 in 2005 and 2006 respectively. The prey items that support such high densities of flatfish vary over spatial scales. Differing prey, in turn, results in differing foraging modes. On Nikko Seamount (Mariana Volcanic Arc), Symphurus n.sp is a “sit and wait” predator that feeds exclusively on a vent endemic shrimp, Opaepele loihi. On other seamounts, Symphurus n.sp is an opportunistic forager that preys mostly on polychaetes and small crustaceans. By counting annuli on otoliths I constructed growth curves and determined that growth rates differ between seamounts. This difference in growth rates is likely due to differences in their diet and foraging strategies. Symphurus n.sp may be allocating more energy to growth when less energy is required to forage. Furthermore, size distributions also differ between populations, likely due to variability in growth rates as well as differences in strong recruitment years.

Thesis (M.S.)--University of North Carolina Wilmington, 2006. / Includes bibliographical references (leaves: 77-79)

Les zones intertidales jouent un rôle essentiel dans le renouvellement des ressources halieutiques. De nombreuses espèces marines, poissons comme macro-crustacés ont un cycle de vie qui leur impose de passer au cours de leur période juvénile par ces écosystèmes. De par sa position à l'interface terre-mer, la zone intertidale est soumise à d'importantes fluctuations des facteurs environnementaux. Cependant, la façon dont cet écosystème répond aux forçages environnementaux, notamment en ce qui concerne la composition et la structure des peuplements, leurs dynamiques et persistances saisonnières et interannuelles sont encore mal connues. En Manche Orientale, l'estran sableux représente plus de 70 % du littoral et constitue d'importantes zones de nourriceries pour les juvéniles de poissons. Dans ce contexte scientifique et régional, l'objectif global de cette thèse a été de décrire les assemblages des peuplements de poissons et de macro-crustacés de la zone intertidale et d'analyser l'influence de l'environnement sur les assemblages et la dynamique des espèces. Une telle étude a pour but de mieux comprendre le fonctionnement de cet écosystème et de préciser son importance dans le cycle biologique des espèces marines, notamment des espèces d'intérêt halieutique. Une première partie de ce travail a permis de déterminer la composition et la variabilité des assemblages de poissons et de macro-crustacés en relation avec les fluctuations environnementales et climatiques. A partir d'un suivi à long terme (11 années) mais aussi saisonnier, nous avons mis en évidence une stabilité des assemblages des peuplements de la macrofaune (poissons et crustacés). A l'inverse les abondances présentent des fluctuations interannuelles et saisonnières en relation avec des facteurs comme la NAO, la température, la salinité ou encore la turbidité. Dans la deuxième partie de la thèse, nous avons analysé si les variations des conditions environnementales de la zone intertidale pendant la période printanière sont d'ordre à affecter les performances physiologiques et la survie des juvéniles qui colonisent cet écosystème. Nous avons focalisé notre étude sur l'espèce de poisson dominante et la zone intertidale, la plie "Pleuronectes platessa". Différents indices qui reflètent les performances physiologiques des juvéniles (croissance et indices de conditions) ont été mesurés sur les juvéniles de plie tout au long de la période de colonisation. Les résultats montrent que la croissance récente, la condition K et l'état nutritionnel (ARN/ADN) des juvéniles de poissons sont élevés tout au long de la période de colonisation des juvéniles et présentent peu de variations intra- et interannuelles, indiquant que l'estran offre des conditions favorables au développement et à la survie des juvéniles de poisson et par conséquent à leur recrutement. Malgré l'importance du bloom de "Phaeocystis globosa" dans la région et de ses fortes variations interannuelles, nous n'avons pas constaté d'effets de ce bloom sur les assemblages, les abondances ou encore les performances physiologiques des poissons. / Intertidal areas provide an essential habitat to fish and macrocrustaceans. These systems are particularly used by juveniles of many fish and macrocrustacean species as nurseries because of the potential advantages they provide for the growth and survival of young fish, namely high prey availability, refuge from predators and good environmental conditions. These habitats are in permanence subject to strong environmental and human fluctuations.Therefore, the comprehension of the functioning and the conservation of the sandy beaches are necessary to maintain the biodiversity and to guarantee the renewal of the fisheries. It is in this framework that our study oriented us to determine the importance of the environmental factors on one hand on the dynamic of the ichtyofauna and on the other hand on physiological performances of the juveniles of fish on the intertidal zones of the English Channel. First, this work allowed us to determine the composition and variability of the fish and macrocrustaceans assemblages in relationship with the environmental and climatic fluctuations. According to our results, the importance of the role of the intertidal habitats of the English Channel in the renewal of the fisheries was proved. Standard qualitative community ecology metrics (species composition, richness, diversity, evenness and similarity) indicated notable inter-annual stability over the study period. Afterward, a 2nd part of this study was consecrated to the seasonal study of the assemblages and the impact of the environmental changes. Our results allowed us to demonstrate that abiotic and climatic factors (mainly temperature, salinity, suspended matter and the winter NAO) have a great influence on the structure of fish and macrocrustacean assemblages but also the impact of Phaeocystis globosa blooms on the population structure. To better understand the nursery functions, the study of physiological performances of juvenile common plaice Pleuronectes platessa during the spring period on the intertidal zone was discussed in order to understand if changes in the environment have an impact on their healthy development. For this, we analyzed various indices that reflect the physiological performance of juvenile common plaice (growth and condition indeces). The results show that the recent growth, the Fulton's K and nutritional ratio RNA/DNA juvenile fish are high throughout the juvenile period of colonization, indicating that nurseries are favorable to the development and survival of fish and therefore their recruitment. Finally, all the work presented shows that the environment of the intertidal areas of the Eastern English Channel is favorable to good life cycle course of marine fish fauna.

Les plages de sable sont des écosystèmes dynamiques couvrant 70% des côtes mondiales. Ces systèmes abritent un cortège spécifique unique et assurent des fonctions essentielles de nourricerie, de nurserie et d’épuration des eaux. Or à proximité des côtes, la population humaine est en développement constant ce qui accroît les multiples pressions d’origine anthropique sur les écosystèmes côtiers. L’apport en excès de nutriments constitue une menace majeure qui peut se traduire par le développement d’importantes biomasses de macroalgues opportunistes (eutrophisation). La fréquence et l’intensité de ces blooms, communément formés de chlorophycées à court cycle de vie (ulves) et appelés marées vertes (MV), s'amplifient sur les côtes françaises et dans le Monde menaçant le fonctionnement de systèmes prépondérants et uniques.La plupart des études visant à déterminer les effets des MV sur la structure et le fonctionnement d’écosystèmes sédimentaires ont été conduites dans des environnements abrités, micro- ou atidaux. Cette problématique est restée presqu’inexplorée dans des écosystèmes plus dynamiques (systèmes ouverts et macrotidaux) en raison des difficultés de mise en place d’échantillonnage et de détection des effets de stress d’origine anthropique, inhérentes à la variabilité de ces systèmes. Cette thèse a donc eu pour objectif principal de combler ce manque et produire des connaissances en étudiant les réponses in situ des communautés benthiques de plages de sable fin macrotidales en présence ou non de MV. Quatre études ont été menées à différentes échelles spatio-temporelles et en considérant différents compartiments biologiques pour répondre à cette question générale.Ce travail de thèse montre qu’à l’échelle de la région Bretagne (variabilité intégrée sur 2700km de côtes et 7 ans) les communautés benthiques d’écosystèmes dynamiques sont modifiées significativement et de manière conservative par la présence de MV. Ce travail démontre aussi que les marées vertes impactent différemment la faune benthique en fonction du type d’habitat (plages semi-exposées vs. exposées), de la profondeur (mediolittoral vs. infralittoral), et du compartiment biologique (macrofaune benthique vs. juvéniles de poissons plats). Ces comparaisons ont permis d’identifier la faune benthique de médiolittoral inférieur des plages exposées comme étant le système le plus affecté par les MV. L’étude des variations à fine échelle spatio-temporelle de ce dernier montre que les caractéristiques faunistiques (uni- et multi-variées) sont modifiées le long d’un gradient de couverture d’algues vertes. Par exemple, la β-diversité décroît significativement le long de ce gradient. Afin d’explorer les processus pouvant expliquer ces modifications, et déterminer si ces changements ont des répercussions sur le fonctionnement de l’écosystème « plage de sable », les effets de l’accumulation d’ulves sur le réseau trophique à différent(e)s niveaux/échelles ont été mesurés. Les résultats de cette étude montrent qu’une importante biomasse d’ulves induit un changement de la structure entière du réseau trophique et une modification importante du fonctionnement trophique des plages. Les expérimentations menées au cours de cette thèse montrent que les changements observés sont induits par des effets directs (consommation de débris d’ulves) et indirects (modifications d’autres sources de nourriture) de la présence des MV.Cette thèse propose un cadre de travail visant à mieux détecter les effets de stress anthropiques sur la structure et le fonctionnement d’écosystèmes dynamiques. Dans un contexte de changement global forçant les écosystèmes à faire face à de multiples stress, cette approche pourrait se révéler particulièrement utile pour démêler, comprendre et prédire les effets de perturbations induites par les activités humaines sur le fonctionnement des écosystèmes et constituer une aide à la gestion de ces environnements particuliers. / Highly dynamic systems, often considered as resilient systems, are characterised by abiotic and biotic processes under continuous and strong changes in space and time. Because of this variability, the detection of overlapping anthropogenic stress is challenging. Coastal areas harbour dynamic ecosystems in the for of open sandy beaches, which cover the vast majority of the world’s ice-free coastline. These ecosystems are currently threatened by increasing human-induced pressure, among which mass-development of opportunistic macroalgae (mainly composed of Chlorophyta, so called green tides), resulting from the eutrophication of coastal waters. The ecological impact of opportunistic macroalgal blooms (green tides, and blooms formed by other opportunistic taxa), has long been evaluated within sheltered and non-tidal ecosystems. Little is known, however, on how more dynamic ecosystems, such as open macrotidal sandy beaches, respond to such stress. This thesis assesses the effects of anthropogenic stress on the structure and the functioning of highly dynamic ecosystems using sandy beaches impacted by green tides as a study case. The thesis is based on four field studies, which analyse natural sandy sediment benthic community dynamics over several temporal (from month to multi-year) and spatial (from local to regional) scales. In this thesis, I report long-lasting responses of sandy beach benthic invertebrate communities to green tides, across thousands of kilometres and over seven years; and highlight more pronounced responses of zoobenthos living in exposed sandy beaches compared to semi-exposed sands. Within exposed sandy sediments, and across a vertical scale (from inshore to nearshore sandy habitats), I also demonstrate that the effects of the presence of algal mats on intertidal benthic invertebrate communities is more pronounced than that on subtidal benthic invertebrate assemblages, but also than on flatfish communities. Focussing on small-scale variations in the most affected faunal group (i.e. benthic invertebrates living at low shore), this thesis reveals a decrease in overall beta-diversity along a eutrophication-gradient manifested in the form of green tides, as well as the increasing importance of biological variables in explaining ecological variability of sandy beach macrobenthic assemblages along the same gradient. To illustrate the processes associated with the structural shifts observed where green tides occurred, I investigated the effects of high biomasses of opportunistic macroalgae (Ulva spp.) on the trophic structure and functioning of sandy beaches. This work reveals a progressive simplification of sandy beach food web structure and a modification of energy pathways over time, through direct and indirect effects of Ulva mats on several trophic levels. Through this thesis I demonstrate that highly dynamic systems respond differently (e.g. shift in δ13C, not in δ15N) and more subtly (e.g. no mass-mortality in benthos was found) to anthropogenic stress compared to what has been previously shown within more sheltered and non-tidal systems. Obtaining these results would not have been possible without the approach used through this work; I thus present a framework coupling field investigations with analytical approaches to describe shifts in highly variable ecosystems under human-induced stress.