The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into the melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1, 840 contigs with an N50 of 1, 203, 211 bp. These contigs were successfully anchored into 24 chromosomes of 843, 582, 782 bp and annotated with 25, 050 protein-coding genes encompassing 97.0% of conserved actinopterygian genes, making the quality and completeness of this genome the highest among all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanocyte development) in A. clarkii compared with other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkii's many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines

Role of habitat definition on Aichi Target 11: Examples from New Caledonian coral reefs

The Aichi 2020 Biodiversity Targets are the backbone of many conservation projects. As the 2020 deadline is approaching, countries assess their progress. Target 11 (ABT11) calls for the protection of at least 10% of coastal and marine areas, while encouraging to focus on areas with particularly important habitats, notably for coral reefs. This target indirectly poses the question of the definition of habitats and their level of representation in Marine Protected Areas (MPAs). We hypothesized that success or failure in achieving the targets could depend on how habitats are defined and considered. To address this issue, the current level of protection with respect to ABT11 is quantified for a hierarchical inventory of coral reef habitats in New Caledonia, a country with complex governance and diverse coral reefs. At the country scale, ABT11 is met with respect to broadly-defined coral reefs due to the presence of large MPAs. However, reserves are too spatially limited to comply with ABT11 at the provincial scale. The results appear dependent upon the hierarchical level of precision used to define habitats. While reefs as a whole meet Target 11, specific habitats, defined at a more detailed description levels, have varying levels of protection; and some do not meet ABT11. The results highlight that assessments of the achievement of the 11th Aichi target strongly depend upon spatial scales and habitat classification, at least for coral reefs. The findings suggest that Aichi compliance assessments worldwide need to take into account variability and biases linked to habitat description

Validation of a novel immersive virtual reality set-up with responses of wild-caught freely moving coral reef fish

International audienceVirtual reality (VR) enables standardized stimuli to provoke behavioural responses in animals; however, in fish studies VR has been limited to either basic virtual simulation projected below the bowl for freely swimming individuals or a simple virtual arena rendered over a large field of view for head-restrained individuals. We developed a novel immersive VR set-up with real-time rendering of animated 3D scenarios, validated in a proof-of-concept study on the behaviour of coral reef postlarval fish. Fish use a variety of cues to select a habitat during the recruitment stage, and to recognize conspecifics and predators, but which visual cues are used remains unknown. We measured behavioural responses of groups of five convict postlarval surgeonfish, Acanthurus triostegus, to simulations of habitats, static or moving shoals of conspecifics, predators and nonaggressive heterospecifics. Postlarval fish were consistently attracted to virtual corals and conspecifics presented statically, but repulsed by their predators (bluefin jacks, Caranx melampygus). When simulated shoals repeatedly passed nearby, they were again attracted by conspecifics, showing a tendency to follow the shoal, whereas they moved repeatedly to the back of the passing predator shoal. They also discriminated between species of similar sizes: they were attracted more to conspecifics than butterflyfish, Forcipiger longirostris, and repulsed more by predators than parrotfish, Scarus psittacus. The quality of visual simulations was high enough to identify visual cues (size, body shape, colour pattern) used by postlarval fish in species recognition. Despite a tracking technology limited to fish 2D positions in the aquarium, preventing the real-time updating of the rendered viewpoint, we could show that VR and modern tracking technologies offer new possibilities to investigate fish behaviour through the quantitative analysis of their physical reactions to highly controlled scenarios

The environment: A vector of phenotypic disparity during the settlement phase of coral reef fishes

peer reviewedIn coral reef fish, the transition from pelagic larvae to reef-associated juveniles is a complete metamorphosis in which coordinated physiological, morphological, and behavioural changes occur, enabling the fish to settle and grow in coastal habitats and then recruit into the adult population. Environmental factors can modulate different aspects of metamorphosis such as the timing of its initiation, its duration, and the coordination of the morphological changes. Here, we raised the coral-reef-dwelling convict surgeonfish, Acanthurus triostegus, in different types of habitats during the post-settlement period. The selected habitats, whether natural (beach rock, mangrove, and sand beach habitats where A. triostegus settle naturally), or experimental (pelagic ocean and oxygen depleted ‘dead’ zone) were characterized by their substrate type, fish community composition, and physico-chemical profile. By using landmark-based geometric morphometric methods, we compared growth, body shape changes, and quantified phenotypic disparity levels among and within the different habitats. The results showed that fish raised in mangrove grew faster than in the other habitats and, most importantly that different habitats lead to variations in the rate and the nature of shape transformation. The ontogenetic tra- jectories defined in the shape space differed across habitats in terms of length and direction. A peak of shape disparity was observed for the natural habitats at three days post settlement when compared to fish reared in dead zone or oceanic environment. Overall, these results suggest that environmental diversity could generate developmental plasticity, ultimately producing phenotypic disparity that may allow the acclimation of fish to their local environment

Validation of a novel immersive Virtual Reality setup with responses of wild-caught freely-moving coral reef fish

International audienceVirtual Reality (VR) enables standardised stimuli to invoke behavioural responses in animals, however, in fish studies VR has been limited to either basic 2D visual stimuli for freely-moving individuals or simple 3D stimuli for head-restrained individuals. We developed a novel fully immersive VR setup with 3D scenarios, validated in a proof of concept study on the behaviour of coral reef post-larvae. Larval fish use a variety of cues to select a habitat during recruitment, and to recognize conspecifics and predators, but which visual cues are used remains unknown. We measured behavioural responses of groups of five convict surgeonfish ( Acanthurus triostegus ) to simulations of habitats, static or moving shoals of conspecifics, predators, and non-aggressive heterospecifics. Post-larvae were consistently attracted to virtual corals and conspecifics, but repulsed by their predators. Post-larvae also discriminated between species of similar sizes: they were attracted more to conspecifics than butterflyfish, and repulsed more by predators than parrotfish. The quality of visual simulations was high enough to identify between visual cues – size, body shape, colour pattern – used by post-larval fish in species recognition. Our VR and tracking technologies offer new possibilities to investigate fish behaviour through the quantitative analysis of their physical reactions to highly-controlled scenarios

Multi-decadal coastal evolution of remote Pacific islands: armouring of Taha’a, Raiatea, Maupiti, and Rangiroa (French Polynesia)

International audienc

‘Habitat-associated soundscape’ hypothesis tested on several coral reefs within a lagoon (Bora-Bora Island, French Polynesia)

Coral reefs encompass different habitats that have their own living communities. The present study aimed to test the hypothesis that these different kinds of habitats were characterized by specific soundscapes. Within the lagoon of Bora-Bora, acoustic recordings and visual surveys of substrate type and fish communities were conducted on four reef sites belonging to the three main geomorphological habitats (fringing reef, channel reef, barrier reef) from February to April 2021. Two acoustic parameters were measured for each site and month, during the day and at night: the peak frequency (Fpeak, in Hz) and the corresponding power spectral density (PSDpeak, in dB re 1 µPa2 Hz−1). Our results showed that each geomorphological unit could be characterized by these two parameters and therefore had a specific acoustic signature. Moreover, our study showed that a higher living coral cover was significantly positively correlated with Fpeak in the low-frequency band (50–2000 Hz) during day-time. Although biodiversity indices based on visual surveys did not differ significantly, fish communities and soundscapes were significantly different between sites. Overall, our study underlines the importance of passive acoustics in coral reef monitoring as soundscapes are habitat specific

Spatiotemporal Trends of Bora Bora’s Shoreline Classification and Movement Using High-Resolution Imagery from 1955 to 2019

International audienceCoastal urbanisation is a widespread phenomenon throughout the world and is often linked to increased erosion. Small Pacific islands are not spared from this issue, which is of great importance in the context of climate change. The French Polynesian island of Bora Bora was used as a case study to investigate the historical evolution of its coastline classification and position from 1955 to 2019. A time series of very high-resolution aerial imagery was processed to highlight the changes of the island’s coastline. The overall length of natural shores, including beaches, decreased by 46% from 1955 to 2019 while human-made shores such as seawalls increased by 476%, and as of 2019 represented 61% of the coastline. This evolution alters sedimentary processes: the time series of aerial images highlights increased erosion in the vicinity of seawalls and embankments, leading to the incremental need to construct additional walls. In addition, the gradual removal of natural shoreline types modifies landscapes and may negatively impact marine biodiversity. Through documenting coastal changes to Bora Bora over time, this study highlights the impacts of human-made structures on erosional processes and underscores the need for sustainable coastal management plans in French Polynesia

Coral reef fish communities of natural habitats and man-made coastal structures in Bora-Bora (French Polynesia)

Coastal habitats have long been recognised to be nurseries and growing grounds for many marine organisms. Worldwide, coastal hardening and urbanisation are leading to the removal of natural ecosystems. The tropical island of Bora-Bora in the South Pacific has undergone extensive coastal changes, with the construction of seawalls along more than half of its coastline since the 1950s. The daytime and night-time juvenile and adult fish communities were surveyed with multiple temporal replicates on a range of lagoon and coastal habitats on Bora-Bora. Over 47% of all fish on coastal habitats were juveniles. Mangroves, traditionally viewed as nurseries, had a high daytime and night-time abundance of juveniles, but less than 1% of the coastline of Bora-Bora consists of mangroves. The manmade seawalls, which are the most common type of coastal habitat on the island, were associated with lower juvenile densities during the day and promoted the presence of predators. The comparison of coastal and lagoon sites also highlighted contrasting life history strategies depending on coral reef fish species: although many favour coastal habitats as juveniles, others do not undergo ontogenetic shifts and thus other habitats must be considered when designing management plans to protect juvenile fish. Overall, our surveys show the importance of natural coastal zones in the lifecycle of numerous coral reef fish species in the lagoon of Bora-Bora and highlight the potential long-term impacts of coastal hardening on fish communities

Characterization of the different sound sources within the soundscape of coastline reef habitats (Bora Bora, French Polynesia)

peer reviewe