Dynamique des populations de coraux scléractiniaires en milieu insulaire fragmenté (Polynésie française) : importance des traits d’histoire de vie, susceptibilité aux perturbations naturelles, et implications pour la trajectoire des populations et la résilience des récifs coralliens

Coral reefs are experiencing increased frequency, intensity, and diversity of disturbances that threaten not only the corals themselves, but many associated species as well. The reefs located in the Society archipelago, French Polynesia, recently underwent two major disturbances: an outbreak of the corallivorous sea star Acanthaster planci and a cyclone. This investigation focuses on the dynamics of coral populations and of the major associated communities of the outer reef slopes of the islands Moorea and Raiatea in the context of these two disturbances.Coral population dynamics, as well as reef community dynamics, are governed by a combination of intrinsic factors specific to species (e.g., recruitment, growth, and mortality rates, and susceptibilities to various regulations) and extrinsic factors characteristic of their environment (e.g., quality of habitats, levels of biotic and abiotic stress, frequency andintensity of disturbances). In French Polynesia, these dynamics are strongly influenced by natural disturbances that affect the size, the structure, and the composition of communities.The first section of this PhD estimates the impact of two successive disturbances, the aforementioned Acanthaster outbreak and cyclone, on the dynamics of reef communities, and evaluates their consequences for species diversity and abundance by detailing the progression of these disturbances and quantifying their effects, including their spatial and temporal scales. For the sea star outbreak, on both studied islands Acanthaster densities were first observed in relatively restricted locations situated at the bottom of the outer reef slopes, where these predators greatly depleted coral populations before moving successively to adjacent sites, progressively spreading the outbreak to the whole insular reef system. Aside from this mode of progression, Acanthaster displayed strong feeding preferences among coral taxa, with the genera Acropora, Montipora, other scleractinians, and Pocillopora hierarchically preyed upon before these predators significantly impacted the genus Porites. While the cyclone did not display a significant impact on the coral cover of these reefs, which had already been highly impacted by Acanthaster; however, the cyclone did strongly damage the physical structure of the reef habitats upon which many species rely. Overall, the decline of corals resulted in an increase in the cover of turf algae, enabled by the relaxed competition for space, and it indirectly affected the trophic chain leading to a collapse of corallivorous fish assemblages (family Chaetodontidae) and a relative increase of herbivore fish assemblages (family Scaridae). This response of the ecosystem, with respect to consumer pressures which favor algae regulation and coral recovery, seems to characterize an ecosystem with high resilience potential; however, the exceptional severity of recent disturbances and the progressive drift in the structure of coral communities facing recurrent perturbations are of concern for the maintenance of the ecological services and the diversity of reefs in French Polynesia.The second section of this thesis investigates the spatial and temporal variability of coral population dynamics and their link with species life history traits and environmental conditions. This second part qualifies the size structure and quantifies the recruitment, growth, and mortality rates of the dominant coral species in French Polynesia, and identifies the life strategies of these taxa. Pocillopora displays an opportunistic strategy, with high production and dispersion of larvae, and small, relatively short-lived colonies. In contrast, Porites engages in a strategy based on the persistence of colonies on the reef, with a low rate of habitat colonization counterbalanced by elevated longevity and high resistance todisturbances. Acropora engages in a different strategy from both Pocillopora and Porites, which is based on competition and which displays an intermediate recruitment rate and relatively fast growth, but also high susceptibility to disturbances. Considering their respective life strategies, these coral taxa must rely on different environmental scenarios for their maintenance and for dominating reef habitats. The third section of this doctoral investigation focuses on the elaboration of a mathematical model that allows predicting the trajectory of coral assemblages under various environmental scenarios. This third part simulates the population dynamics of the major scleractinian taxa in French Polynesia both (1) during the colonization of the reef habitat, and (2) in the face of a hypothetical increase in the frequency of Acanthaster outbreaks. In accordance with the life strategies identified in the second section of this thesis, Pocillopora appears as the best colonizer of reef habitats, Acropora dominates the assemblages in a relatively stable environment, and Porites is the less impacted by repeated disturbances. The recurrence of disturbances affects the structure and the perennity of coral assemblages.Thanks to the relatively low and spatially restricted anthropic pressures in French Polynesia, coral reefs in this region are among the most resilient on our planet. As on many reefs, however, long term monitoring programs show an increase in the frequency and intensity of disturbances that threaten the maintenance of corals, as well as their associated communities. Today, coral reefs are in decline globally, and they seem to be heralds of a dynamic shared by many natural ecosystems. In the present era of anthropic disturbances and global climate change, the investigation of community regulation and resilience processes appears crucial for the durable management of these valuable ecosystems.Les récifs coralliens sont soumis à une augmentation de la fréquence, de l’intensité et de la diversité des perturbations qui menacent la persistance des populations de coraux, ainsi que celle des espèces qui y sont associées. Les récifs de l’archipel de la Société en Polynésie française ont récemment connu deux perturbations majeures, une explosion démographique de l’étoile de mer corallivore Acanthaster planci et un cyclone. Dans ce contexte, ce programme de recherche a porté sur l’étude de la dynamique des populations de coraux et des principales communautés qui y sont associées sur la pente externe des îles de Moorea et de Raiatea.Les dynamiques des populations coralliennes et des communautés récifales sont gouvernées par une combinaison de facteurs intrinsèques propres aux espèces (e.g., taux de recrutement, vitesse de croissance, taux de mortalité, et susceptibilité aux facteurs de régulation) et de facteurs extrinsèques caractéristiques de leur environnement (e.g., qualité de l’habitat, degré de stress biotique et abiotique, fréquence et intensité des perturbations). En Polynésie française, ces dynamiques sont fortement orientées par les perturbations naturelles de grandes ampleurs qui influencent fortement la taille, la structure et la composition des communautés.Le premier volet de ce doctorat évalue l’impact de deux perturbations successives, l’explosion démographique d’Acanthaster et le cyclone, sur la dynamique des communautés récifales, et les conséquences sur la diversité et l’abondance des espèces. Cette première partie permet notamment de qualifier les modalités d’action de ces perturbations, ainsi que de quantifier leurs effets à différentes échelles spatiales et temporelles. Sur chacune des îles étudiées, les densités d’Acanthaster ont d’abord été observées sur une localité relativement restreinte à la base du récif de la pente externe, où les prédateurs ont fortement extirpé les populations coralliennes avant de se propager successivement aux sites et profondeurs adjacents, propageant ainsi progressivement la prolifération à l’ensemble du système récifal insulaire. De même, les Acanthaster ont montré des préférences alimentaires marquées selon les taxa coralliens, avec les genres Acropora, Montipora, autres genres scléractiniaires et Pocillopora ont été préférentiellement dévorés avant que ces prédateurs n’impactent significativement le genre Porites. Le passage du cyclone a montré relativement peu d’impact sur le recouvrement corallien sur des récifs déjà fortement affectés par les Acanthaster, mais a cependant fortement dégradé la structure physique des habitats récifaux auxquels sont inféodées de nombreuses espèces. Dans l’ensemble, le déclin corallien a résulté en une augmentation de la couverture en turf algal suite à une libération de la pression de compétition sur le substrat, et s’est répercuté dans le réseau trophique avec un effondrement des assemblages de poissons corallivores (famille Chaetodontidae) et, à l’inverse, un certain essor des assemblages de poissons herbivores (famille Scaridae). Cette réponse de l’écosystème, en termes de remaniement des assemblages de consommateurs en faveur de la régulation algale et la récupération corallienne, semble caractériser un écosystème à fort potentiel de résilience. Cependant, l’ampleur exceptionnelle des deux récentes perturbations, et la dérive progressive de la structure des communautés coralliennes face à la récurrence des perturbations, s’avèrent préoccupantes quant au maintien des services écologiques et de la diversité des récifs de la Polynésie française.Le second volet de ce manuscrit examine plus spécifiquement la dynamique des populations de coraux, sa variabilité spatiale et temporelle, et son lien avec les traits d’histoire de vie des espèces et avec les conditions environnementales. Cette seconde partie permet notamment de qualifier la structure de taille et de quantifier les taux de recrutement, de croissance et de mortalité des espèces dominantes du paysage corallien en Polynésie française, et d’identifier les stratégies de vie de ces taxa. Pocillopora montre une stratégie de type opportuniste, avec un fort investissement dans la production et la dispersion larvaire, et une taille et une durée de vie relativement limitée des colonies. A l’inverse, Porites montre une stratégie basée sur la persistance des colonies sur le récif, avec un faible taux de colonisation des habitats, mais en contrepartie une longévité importante et une forte résistance face aux perturbations. Acropora montre une stratégie encore distincte et basée sur la compétition, avec un taux de recrutement intermédiaire et une forte vitesse de croissance, mais cependant une susceptibilité importante aux perturbations. Avec leurs traits d’histoire de vie respectifs, ces différents taxa coralliens montrent des habilités variées à se maintenir et à dominer l’habitat récifal selon différents scénarios environnementaux.Le troisième volet de ce programme de recherche doctoral se concentre sur l’élaboration d’un modèle mathématique qui permet de prédire la trajectoire des assemblages coralliens sous divers scénarios environnementaux. Cette troisième partie permet notamment de simuler la dynamique des populations des principaux taxa scléractiniaires de Polynésie française, (1) lors d’une phase de colonisation de l’habitat récifal, et (2) face à une augmentation hypothétique de la fréquence des proliférations du prédateur Acanthaster. En concordance avec les stratégies de vie des espèces telles qu’identifiées au second volet de cemanuscrit, Pocillopora s’avère être le meilleur colonisateur des habitats, Acropora domine les assemblages sous un environnement relativement stable, et Porites est le moins affecté par les perturbations répétitives. La récurrence des perturbations affecte la structure et la pérennité des assemblages coralliens.Grâce à une pression anthropique relativement faible et restreinte à quelques sites particuliers, les récifs coralliens de la Polynésie française figurent parmi les plus résilients de notre planète. Cependant, à l’image d’autres récifs, les suivis à long terme montrent une augmentation de la fréquence et de l’intensité des perturbations qui en viennent à menacer le maintien des coraux, ainsi que des communautés récifales qui y sont associées. Aujourd’hui, les récifs coralliens sont globalement en déclin, et semblent être les précurseurs d’une dynamique partagée par de nombreux écosystèmes naturels. Dans l’ère actuelle des perturbations anthropiques et des changements climatiques globaux, l’investigation des processus de régulation des communautés et des capacités de résilience s’avère primordiale pour une gestion durable de ces écosystèmes si précieux

Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans

Defining and quantifying the resilience of responses to disturbance: a conceptual and modelling approach from soil science

There are several conceptual definitions of resilience pertaining to environmental systems and, even if resilience is clearly defined in a particular context, it is challenging to quantify. We identify four characteristics of the response of a system function to disturbance that relate to “resilience”: (1) degree of return of the function to a reference level; (2) time taken to reach a new quasi-stable state; (3) rate (i.e. gradient) at which the function reaches the new state; (4) cumulative magnitude of the function (i.e. area under the curve) before a new state is reached. We develop metrics to quantify these characteristics based on an analogy with a mechanical spring and damper system. Using the example of the response of a soil function (respiration) to disturbance, we demonstrate that these metrics effectively discriminate key features of the dynamic response. Although any one of these characteristics could define resilience, each may lead to different insights and conclusions. The salient properties of a resilient response must thus be identified for different contexts. Because the temporal resolution of data affects the accurate determination of these metrics, we recommend that at least twelve measurements are made over the temporal range for which the response is expected

Transformative choices towards a sustainable academic publishing system

Communicating new scientific discoveries is key to human progress. Yet, this endeavor has been increasingly hindered by monetary restrictions that restrain scientists from publishing their findings and accessing other scientists’ reports. This process is further exacerbated by a large portion of publishing media owned by private companies that, in contrast with journals from scientific societies, do not reinject academic publishing benefits into the scientific community. As the academic world is not exempt from economic crises and funding restrictions, new alternatives are necessary to support a fair and economically sustainable publishing system for scientists and society as a whole. After summarizing major shortcomings of academic publishing today, we present several solutions that span the levels of the individual scientist, the scientific community, and the publisher to initiate a transformative change towards more sustainable scientific publishing. By providing a voice to the many scientists who are fundamental protagonists, yet often powerless witnesses, of the academic publishing system, as well as a roadmap for implementing solutions, we hope this initiative will go beyond sparking increased awareness and promote a shift towards more sustainable scientific publishing practices

The war of corals: patterns, drivers and implications of changing coral competitive performances across reef environments

Amidst global environmental changes, predicting species' responses to future environments is a critical challenge for preserving biodiversity and associated human benefits. We explored the original idea that coral competitive performances, the ability of corals to preempt ecological space on the reef through territorial warfare, serve as indicators of species’ ecological niches and environmental windows, and therefore, responses to future environments. Our surveys indicated that coral performances varied with taxonomic identity, size and position along environmental gradients, highlighting complex interplays between life-history, warfare-strategy and niche segregation. Our results forewarn that growing alterations of coastal environments may trigger shifts in coral dominance, with the decline of major reef-building taxa like acroporids, and emphasize the importance of limiting human impacts for coastal resilience. Our empirical approach untangles the complexity of species' battle-like interactions and can help identify winners and losers in various communities caught in the interplay between ecological niches, environmental windows and global changes

Humanity and the 21 st century’s resource gauntlet: a commentary on Ripple et al.’s article “World scientists’ warning to humanity: a second notice”

International audienceA year ago, Ripple et al.'s "Warning to Humanity" was published (Ripple et al. 2017), reigniting debate on the importance of addressing the environmental crisis that humanity will increasingly face in the 21 st century. While we fully endorse the pertinence of this initiative, we identify critical gaps which impede the capacity of this call to action in fostering the positive change that humanity needs. With our present manuscript, we provide a complementary assessment to Ripple et al.'s article for addressing the current environmental crisis, as well as some alternative paths forward. We emphasize the importance of considering historical patterns and underlying drivers of the current global socio-ecosystem, particularly in relation to social inequalities , human demography, and food production systems. Without such considerations, several of the steps proposed in the warning might be interpreted as prescriptions from a western-biased vision of our global socio-ecosystem, undermining the fundamental message of this unique initiative for achieving sustainability

Multi-species consumer jams and the fall of guarded corals to crown-of-thorns seastar outbreaks [version 2; referees: 2 approved]

Outbreaks of predatory crown-of-thorns seastars (COTS) can devastate coral reef ecosystems, yet some corals possess mutualistic guardian crabs that defend against COTS attacks. However, guarded corals do not always survive COTS outbreaks, with the ecological mechanisms sealing the fate of these corals during COTS infestations remaining unknown. In August 2008 in Moorea (17.539° S, 149.830° W), French Polynesia, an unusually dense multi-species aggregation of predators was observed feeding upon guarded corals following widespread coral decline due to COTS predation. Concurrent assaults from these amplified, mixed-species predator guilds likely overwhelm mutualistic crab defense, ultimately leading to the fall of guarded corals. Our observations indicate that guarded corals can sustain devastating COTS attacks for an extended duration, but eventually concede to intensifying assaults from diverse predators that aggregate in high numbers as alternative prey decays. The fall of guarded corals is therefore suggested to be ultimately driven by an indirect trophic cascade that leads to amplified attacks from diverse starving predators following prey decline, rather than COTS assaults alone

Bias associated with the detectability of the coral-eating pest crown-of-thorns seastar and implications for reef management

International audienceOutbreaks of the predator crown-of-thorns seastar (COTS) Acanthaster planci cause widespread coral mortality across the Indo-Pacific. Like many marine invertebrates, COTS is a nocturnal species whose cryptic behaviour during the day can affect its detectability, particularly in structurally complex reef habitats that provide many refuges for benthic creatures. We performed extensive day and night surveys of COTS populations in coral reef habitats showing differing levels of structural complexity and COTS abundance. We tested whether estimations of COTS density varied between day and night observations, and if the differences were related to changes in COTS abundance, reef structural complexity and the spatial scale of observation. Estimations of COTS density were on average 27% higher at night than during the day. Differences in COTS detection varied with changing seastar abundance but not reef structural complexity or scale of observation. Underestimation of COTS abundance in daytime was significant for a broad seastar density range, thus potentially affecting most outbreak events. Our study suggests that portions of COTS populations can be undetected during conventional surveys and control campaigns, which are exclusively conducted by day, and significantly affect the trajectory of coral reefs. Accounting for bias in COTS detection can strengthen coral reef management broadly

Video Transect-Based Coral Demographic Investigation

Demographic studies that quantify species’ performances for survival, growth, and reproduction are powerful means to characterize sources of demographic bottlenecks and predict community dynamics. However, they require fine-scale surveys of populations in the field, and are often too effort-intensive to be replicable at a large scale and in the long term. We developed a standardized digital approach for extracting demographic data on species’ abundances, sizes, and positions within video transects, enabling back-from-the-field data acquisition and therefore optimizing time spent in the field. The approach is based on manual species identification, size measurements, and mapping in video transects, mimicking what is traditionally performed in the field, though it can be automated in the future with the deployment of artificial intelligence. We illustrate our approach using video surveys of a reef-building coral community in New Caledonia. The results characterize the composition of the coral community and demographic performances as key ecological indicators of coral reef health, shed light on species’ life strategies and constraints to their demographics, and open paths for further quantitative investigations. Key findings include the diversity of life strategies with contrasting levels of investment in survival, growth, and reproduction found among the six taxa dominating the coral community (Acropora, Montipora, Porites, Galaxea, Favia, Millepora), indicating the diversity of demographic paths to ecological success. Our results also indicate that several species have adapted mechanisms to prevail under limiting hydrodynamic environments through the propagation of coral fragments. Our approach facilitates image-based demographic investigations, supporting endeavors in ecology and ecosystem management