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As a region renowned for high biodiversity, endemism and extreme temperature and salinity levels, the Red Sea is of high ecological interest. Despite this, there is relatively little literature on basic broad scale characteristics of the biodiversity or overall reef fish communities and how they change across latitude. We conducted visual transects recording the abundance of over 200 species of fish from 45 reefs spanning over 1000 km of Saudi Arabian coastline and used hierarchical cluster analysis to find that for combined depths from 0m-10m across this geographical range, the reef fish communities are relatively similar. However we find some interesting patterns both at the community level across depth and latitude as well as in endemic community distributions. We find that the communities, much like the environmental factors, shift gradually along latitude but do not show distinct clusters within the range we surveyed (from Al-Wajh in the north to the Farasan Banks in the south). Numbers of endemic species tend to be higher in the Thuwal region and further south. This type of baseline data on reef fish distribution and possible factors that may influence their ranges in the Red Sea are critical for future scientific studies as well as effective monitoring and in the face of the persistent anthropogenic influences such as coastal development, overfishing and climate change.

The field of marine population connectivity is receiving growing attention from ecologists worldwide. The degree to which metapopulations are connected via larval dispersal has vital ramifications for demographic and evolutionary dynamics and largely determines the way we manage threatened coastal ecosystems. Here we addressed different questions relating to connectivity by integrating direct and indirect genetic approaches over different spatial and ecological scales in a coral reef fish in the Red Sea. We developed 35 novel microsatellite loci for our study organism the two-band anemonefish Amphiprion bicinctus (Rüppel 1830), which served as the basis of the following approaches. First, we collected nearly one thousand samples of A. bicinctus from 19 locations across 1500 km along the Saudi Arabian coast to infer population genetic structure. Genetic variability along the northern and central coast was weak, but showed a significant break at approximately 20°N. Implementing a model of isolation by environment with chlorophyll-a concentrations and geographic distance as predictors we were able to explain over 90% of the genetic variability in the data (R2 = 0.92). For the second approach we sampled 311 (c. 99%) putative parents and 172 juveniles at an isolated reef, Quita al Girsh (QG), to estimate self-recruitment using genetic parentage analysis. Additionally we collected 176 juveniles at surrounding locations to estimate larval dispersal from QG and ran a biophysical dispersal model of the system with real5 time climatological forcing. In concordance with model predictions, we found a complete lack (c. 0.5%) of self-recruitment over two sampling periods within our study system, thus presenting the first empirical evidence for a largely open reef fish population. Lastly, to conceptualize different hypotheses regarding the underlying processes and mechanisms of self-recruitment versus long-distance dispersal in marine organisms with pelagic larval stages, I introduce and discuss the concept of “origin effects”, providing the theoretical background to some of the questions that have arisen during this research. Overall, this thesis has generated significant new insights into the patterns of coral reef fish connectivity, specifically for the Red Sea, where such information has previously been scarce.

L’étude de la diversité des espèces de poissons habitant les récifs coralliens fascine les chercheurs du monde entier depuis plus de 200ans. Comment ces organismes qui n’occupent que 1% de la surface des océans du globe ont-ils pu former un des groupes les plus riches des vertébrés existants ? La complexité de cette question ne réside pas seulement dans l’exceptionnelle diversité de formes, de couleurs et de comportements de ces espèces mais aussi dans l’inégale répartition de cette richesse. Des explorations du lagon de Mayotte, des côtes Cubaines ou de la grande barrière de corail donneront des perspectives très différentes de la diversité des poissons coralliens. Ces différences très importantes sont le résultat de processus ayant modelé, pendant des millions d’années, la répartition des espèces coralliennes, leur morphologie et leur comportement. Pendant ces millions d’années d’évolution, les poissons coralliens, ainsi que les espèces de coraux qui les abritent, ont été confrontés à des changements drastiques des conditions climatiques et à la dérive des continents. C’est l’influence de ces facteurs sur la répartition et la diversité des poissons coralliens, que j’ai étudié pendant ma thèse. Comprendre comment les espèces et les écosystèmes ont réagi aux changements environnementaux passés peut nous apporter des clés essentielles pour anticiper les changements à venir des écosystèmes que nous connaissons, sous l’influence des changements globaux. Les récifs coralliens étant sous une menace de plus en plus présente, je me suis particulièrement intéressé à l’influence de la disponibilité de l’habitat corallien sur les processus d’extinction, de dispersion et de spéciation (formation de nouvelles espèces par divergence génétique) des poissons coralliens.Afin de répondre à ces objectifs, plusieurs méthodes ont été employées. Dans un premier temps, une approche descriptive basée sur la répartition de la co-occurrence entre espèces sœurs et une comparaison entre une reconstruction globale de la dynamique des habitats coralliens allant du Crétacé (≈ -140 millions d’années) et les taux de diversification de plusieurs grands groupes de poissons récifaux, ont permis de montrer que les taux de diversification de plusieurs familles de poissons récifaux étaient dépendant de la fragmentation des habitats coralliens, et d’observer la concordance entre des évènements climatiques et tectoniques majeurs et l’évolution de la biodiversité des poissons coralliens.Après avoir identifié un lien entre fragmentation de l’habitat corallien et la diversification des poissons, une grande question demeure : Comment cette dynamique de l’habitat influence-t-elle dans l’espace et le temps la diversité des poissons récifaux ? Pour répondre à cette question, une approche unique permettant de modéliser la dispersion, la spéciation et l’extinction des espèces dans un espace formé de grilles d’habitat dynamique a été développée et appliquée à plusieurs clades d’organismes marins côtiers (coraux, palétuviers et poissons). Cette approche a permis de démontrer comment la dérive des continents a contraint la dynamique de l’habitat corallien et a façonné les gradients de diversité de plusieurs groupes d’organismes marins côtiers. Enfin, l’extension de cette approche aux récifs tempérés, a permis de montrer l’interaction entre l’influence de la dérive des continents et des processus écologiques sur la colonisation et le maintien d’espèces de poissons récifaux dans les milieux tempérés, expliquant en partie la formation du gradient latitudinal de diversité des poissons récifaux.Ces travaux ouvrent la voie vers l’utilisation d’une nouvelle génération de modèles spatialisés de diversification et la prise en compte de la dynamique des habitats passés dans l’étude des processus de diversification. / The exceptional diversity of fishes that inhabit coral reefs fascinates researched from all over the world since over 200years. How can those organisms, that only occupy 1% of the surface of the oceans, form one of the richest group of extant vertebrates? The complexity of this question does not only lie in the extraordinary diversity of morphologies, colors and behaviors, but also roots in the heterogeneous repartition of that richness. Explorations of Mayotte’s lagoon, Cuban coasts or the great barrier reef will show different perspectives of coral-reef fish’ diversity. Those pervasive differences are the result of processes that shaped, during millions of years the repartition of coral-reef species, their morphology and their behavior. During those millions of years of evolution, coral-reef fishes along with species that shelter them, faced massive climatic and tectonic changes. During my PhD, I studied the influence of those factors on the repartition and the diversity of coral-reef fishes. Understanding how species and ecosystems responded to important environmental changes can provide essential insights to anticipate future changes of ecosystem composition and functioning under global changes’ pressure. As coral-reefs are under more and more threatening pressures, I particularly focused on the influence of coral habitat availability on extinction, dispersion and speciation processes of coral-reef fishes.To achieve this goal, several methods have been employed. First, a descriptive approach based on sister-species co-occurrence patterns and the comparison between a global reconstruction of coral-reef habitat dynamics from the Cretaceous (≈ -140 million years) to present and the evolution of several speciose groups of coral-reef fishes permitted to identify a link between diversification rates of several groups of coral-reef fishes and coral habitat fragmentation and to observe the concordance between major earth-history events and biodiversity dynamics of coral-reef fishes.After the identification of a link between habitat fragmentation and coral-reef fishes’ diversification, an important question remains: What are the mechanisms underlying the influence of habitat dynamics on temporal and spatial variations of reef-fish biodiversity? To answer this question a unique approach allowing modeling of species dispersal, extinction and speciation in a gridded space varying in function of habitat dynamics, has been developed and applied to several groups of coastal marine organisms (corals, mangroves, fishes). This approach provided mechanistic insights about how plate movements drove coral reef habitat dynamics and shaped biodiversity gradients of several groups of coastal marine organisms. Finally, the extension of this approach to temperate reefs (rocky reefs), provided mechanistic insights about the interplay between the influence of tectonic events and ecological processes in the formation of present-day latitudinal gradient of biodiversity of reef-fishes.This thesis paves the way towards the use of a new generation of spatialized mechanistic models of macroevolution and the consideration of the influence of past-habitat dynamics in the study of diversification processes.

Parental care is a critical component of many breeding systems that enhances both parent and offspring fitness. It is widely recognized that parental care varies in quality and quantity in response to variation in offspring need, parental condition, and ecological context. One context that has been underexplored, however, is the difference in parental care between day and night, with many parental care studies focused on diurnal care. To fully understand the evolution of parental care, the costs and benefits and the negotiations between parents, both diurnal and nocturnal care must be accounted for. Here, we show that nocturnal parental care exists in the clownfish Amphiprion percula, with males and females actively caring for offspring at night throughout embryo development and during hatching in a laboratory setting. At night, as during the day, males are the dominant caregivers and both parents increase care as embryos mature. At night, in contrast to the day, females provide substantially more care. This increase in energy expended by parents on care may be a mechanism to increase dissolved oxygen in the water at night, improving embryo survival. We also document the existence of three new nocturnal parental care behaviors, not previously seen during the day: vigorous fanning, vigorous mouthing, and anemone biting. These behaviors are particularly frequent during hatching, and although they are not necessary for hatching to occur, they may serve to enhance the embryos’ successful transition from the benthos to the water column. This study contributes to our understanding of parental care, demonstrating the importance of considering nocturnal care if we are to gain a complete understanding of the evolution of parental care. / 2023-03-16T00:00:00Z

Coral reef fish are known to have a bipartite life cycle: a dispersive pelagic larval phase (DPL), where larvae ‘travel’ away from their parents to occupy new habitats, and a sedentary reef phase characterized by juveniles and adults. Study of the DPL is an essential prerequisite to understand how persistence, connectivity, and gene flow operate between populations. Clownfish have been the subject of considerably varied fields of research in recent decades, not only due to their economic value, but also because of their ease of maintenance in laboratory settings, regular spawning, and short DPL. Their life cycle is also defined as bipartite, with a DPL lasting around 15 days until settlement, and the fish exhibit a symbiotic relationship with sea anemones. The transitions between phases are associated with a series of morphological, behavioural, genetic, cellular and molecular changes. However, these changes are poorly characterized in some species of clownfish. Therefore, the Red Sea clownfish, Amphiprion bicinctus, was reared to fill the gap in the literature by investigating their i) morphology, ii) swimming abilities, and iii) differential gene expression (DGE) throughout ontogeny. The DPL was characterized in the preflexion, flexion and postflexion stages, according to flexion of the notochord, on 0, 2 and 10 days post hatch (dph), respectively. Metamorphosis was defined by a morphological transition between the DPL and juvenile phases, associated with the appearance of white stripes, on day 10 and until the end of the experiment, on day 14. Additionally, metamorphosis is followed by a behavioural change at 14 dph, called settlement, where larvae transition from free swimming in the water column to associating with the substrate. We also demonstrate that the larvae present active swimming from the moment they hatch, and the swimming speed increases throughout DPL. Overall, the development of A. bicinctus is similar to other clownfish species. This work provides a strong baseline on the development of A. bicinctus, which may open the door to a deeper understanding of the role of dispersal behaviours and enhance our ability to design effective marine reserve networks in the Red Sea.

Halichoeres socialis Randall & Lobel, 2003, is the only wrasse species (Teleostei: Labridae) with a restricted distribution within the Caribbean Meso-American Barrier Reef (MABR), Central America. This study examined the early life history of H. socialis to gain insight into its natural history and to assess if any pattern in otolith microstructure could be linked to its endemism. The sagittal otoliths from 67 individuals (ranging 9.8–43.4mm SL) were analyzed to determine the daily age and increment profile. Results indicate that (1) H. socialis displays a typical “settlement mark”; (2) the pelagic larval duration (PLD) ranged from 22 to 32 (mean=27, n=59) days, which was similar to its congeners; and (3) the juvenile growth rate is 0.7mm/d, which was faster than most congeners. The endemism of H. socialis is not explained by its PLD. Alternatively, it is possible that larval behaviors (vertical migration and/or schooling) play a key factor in how H. socialis larvae are retained within the MABR region. / 2026-03-19T00:00:00Z

No description available.

People are active participants in coral reef ecosystems. This ethnobiology study considers and contrasts folkbiological knowledge of people living in two groups of artisanal fishing villages in Kadavu Province, Fiji. The high level of biological diversity on the Astrolabe Reef provides insights into folk categorization and classification methods that include colour, shape, size, physical features, and habits of certain reef fish and marine animals. Surveying large numbers of experts and novices on defined groups of creatures yields more depth and range of responses allowing higher confidence levels in response accuracy. A comparison of the data with Berlins (1992) proposed principles yields mixed results. Sea cucumbers have high ecological salience and their identification requires attention to the affect of two centuries of trade on Fijian society. Effective ethnobiological research provides productive options to contribute to coral reef sustainability programs with long term benefits for local people and marine life. Key words: Kadavu, naming and classification of fish, coral reef ethnobiology.

L’estimation de la diversité et de l’abondance des espèces de poisson est fondamentale pour comprendre la structure des communautés et la dynamique des récifs coralliens. Les observations sont généralement obtenues par des recensements visuels en scaphandre autonome (UVC). Ces informations peuvent également être obtenues de manière originale grâce aux observations issues des techniques vidéo sous-marines modernes sans plongeur qui permettent des couvertures spatiales et temporelles accrues.La première phase de ce travail de thèse synthétise l’ensemble des travaux ayant été effectués avec des techniques vidéo entre 1952 et 2012. La seconde phase, présente deux systèmes vidéo rotatifs complémentaires, utilisés pour étudier la diversité de l’ichtyofaune et des habitats marins dans le lagon de Nouvelle-Calédonie : le STAVIRO (pour « STAtion VIdéo ROtative ») et le MICADO (pour « Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine »). La troisième phase de ce travail consiste à comparer ces systèmes vidéo aux UVC puis à examiner l’effet « observateur » inhérent aux techniques vidéo rotatives. Il résulte de cette étude que : (i) les observations des communautés de poissons par UVC et STAVIRO différaient significativement, (ii) la richesse spécifique etla densité des espèces de grande taille n'étaient pas significativement différentes entre les techniques, (iii) la diversité et la densité des espèces de petite taille étaient plus élevés avec les UVC; (iv) la densité des espèces pêchées était plus élevée avec les STAVIRO et (v) seuls les UVC ont détecté des différences de structure des assemblages en fonction du type de récif. L’étude de l’effet « observateur » a montré que sur une liste d’espèces définie, les dénombrements et les identifications des individus peuvent être considérées comme similaires entre observateurs ayant une expérience suffisante (> 6 mois). La dernière phase de ce travail a permis d’appliquer la technique MICADO à l’étude des variations temporelles del’ichtyofaune d’un site corallien à l’échelle de la journée. Elle a permis de mettre en évidence des variations cycliques journalières en fonction de l’heure et de la marée et des « profils type » de variations ont pu être identifiés pour certains groupes d’espèces. Ce travail de thèse permet ainsi de participer au développement de nouvelles techniques d’observations complémentaires des techniques traditionnelles afin d’enrichir les connaissances du fonctionnement et de la dynamique des écosystèmes coralliens. / Estimating diversity and abundance of fish is fundamental for the understanding of community structure and dynamics of coral reefs. Observations are generally gathered using Underwater VisualCensus (UVC). These informations can also be collected by underwater video techniques involving no diver and allowing a high spatial and temporal coverage. The first part of this PhD thesis is a review ofpublications using underwater video techniques between 1952 and 2012. The second part present two rotating video systems used to study the diversity of ichthyofauna and habitats in the lagoon of NewCaledonia: the STAVIRO (for "STAtion VIdeo ROtative") and the MICADO (for "Module d’Imagerie Côtier, Autonome pour le Développement de l’Observation sous-marine"). The third part of this work is acomparison of these techniques with UVCs and an analysis of the “observer effect” for the rotating video techniques. The comparison between rotating video systems and UVC showed that: (i) fish communitydata collected by UVC and by STAVIRO differed significantly; (ii) species richness and density of large species were not significantly different between techniques; (iii) species richness and density of smallspecies were higher for UVC; (iv) density of fished species was higher for STAVIRO; and (v) only UVC detected significant differences in fish assemblages structure across reef type. The comparison of fishcounts obtained from the same videos by different observers showed that for a defined list of species, estimates of species richness and total abundance can be considered as similar between observers withsufficient experiences (> 6 months). The last part of this PhD is an application of rotating video techniques to the study of daily temporal variations of the ichthyofauna. Daily variations were observed depending onthe time of day and the tidal state and typical patterns of variations have been described for some species groups. The outcomes of this work bring original insights of new techniques complementary to traditionaltechniques in order to enhance our understanding of the functioning and dynamic of coral reef.