Two new Cocconeis taxa (Bacillariophyceae) from coral sands off the Mascarenes (Western Indian Ocean) and some related unidentified taxa

Coral sands off Réunion Island and Rodrigues (Mascarene archipelago, Western Indian Ocean) support diverse diatom communities, particularly rich in Monoraphidineae. Recent surveys of reef environments (June 2005 and June 2007) permitted the recognition of several taxa belonging to the diatom genus Cocconeis, among which are two new, relatively small taxa, epipsammic on coral sand. Cocconeis coronata Riaux-Gobin et Romero sp. nov. is similar to C. scutellum but has its own distinctive features. In external view, the concave raphe valve possesses uniseriate striae and a subsident hyaline marginal rim, while the strongly convex sternum valve has a submarginal, generally continuous crest, a hexagonal pattern of areolation, short, rounded spines that are often regularly arranged around valve face areolae, a complex areola hymen and small marginal chambers. Some morphometric differences were noted between the populations of C. coronata at Réunion and Rodrigues. Cocconeis margaritata Riaux-Gobin et Al-Handal, sp. nov. is smaller, possesses a sternum valve like that of C. placentula and C. neothumensis, but has denser striation and small pearl-like concretions around the areola aperture on the sternum valve. Several other taxa that resemble, or may be varieties of, C. margaritata require further study before being formally described. Cocconeis margaritata and C. coronata are small and relatively rare, so their study requires scanning electron microscopy.     

Degradation of chemical alarm cues and assessment of risk throughout the day

The use of chemical information in assessment of predation risk is pervasive across animal taxa. However, by its very nature, chemical information can be temporally unreliable. Chemical cues persist for some period of time after they are released into the environment. Yet, we know surprisingly little about the rate of degradation of chemical cues under natural conditions and hence little about how they function in temporal risk assessment under natural conditions. Here, we conducted an experiment to identify a concentration of fresh alarm cues that evoke a strong antipredator response in coral reef damselfish, Pomacentrus ambonensis. We then tested the rate at which these alarm cues degraded under natural conditions in ocean water, paying attention to whether the rate of degradation varied throughout the day and whether the temporal pattern correlated with physicochemical factors that could influence the rate of degradation. Fresh alarm cues released into ocean water evoke strong avoidance responses in juvenile fish, while those aged for 30 min no longer evoke antipredator responses. Fish exposed to cues aged for 10 or 20 min show intermediate avoidance responses. We found a marked temporal pattern of response throughout the day, with much faster degradation in early to mid‐afternoon, the time of day when solar radiation, temperature, dissolved oxygen, and pH are nearing their peak. Ecologists have spent considerable effort elucidating the role of chemical information in mediating predator–prey interactions, yet we know almost nothing about the temporal dynamics of risk assessment using chemical information. We are in dire need of additional comparative field experiments on the rate of breakdown of chemical cues, particularly given that global change in UV radiation, temperature, and water chemistry could be altering the rates of degradation and the potential use of this information in risk assessment.     

Limited contemporary gene flow and high self‐replenishment drives peripheral isolation in an endemic coral reef fish

Extensive ongoing degradation of coral reef habitats worldwide has lead to declines in abundance of coral reef fishes and local extinction of some species. Those most vulnerable are ecological specialists and endemic species. Determining connectivity between locations is vital to understanding recovery and long‐term persistence of these species following local extinction. This study explored population connectivity in the ecologically‐specialized endemic three‐striped butterflyfish (Chaetodon tricinctus) using mt and msatDNA (nuclear microsatellites) to distinguish evolutionary versus contemporary gene flow, estimate self‐replenishment and measure genetic diversity among locations at the remote Australian offshore coral reefs of Middleton Reef (MR), Elizabeth Reef (ER), Lord Howe Island (LHI), and Norfolk Island (NI). Mt and msatDNA suggested genetic differentiation of the most peripheral location (NI) from the remaining three locations (MR, ER, LHI). Despite high levels of mtDNA gene flow, there is limited msatDNA gene flow with evidence of high levels of self‐replenishment (≥76%) at all four locations. Taken together, this suggests prolonged population recovery times following population declines. The peripheral population (NI) is most vulnerable to local extinction due to its relative isolation, extreme levels of self‐replenishment (95%), and low contemporary abundance.     

The distribution of the thermally tolerant symbiont lineage (Symbiodinium clade D) in corals from Hawaii: correlations with host and the history of ocean thermal stress

Spatially intimate symbioses, such as those between scleractinian corals and unicellular algae belonging to the genus Symbiodinium, can potentially adapt to changes in the environment by altering the taxonomic composition of their endosymbiont communities. We quantified the spatial relationship between the cumulative frequency of thermal stress anomalies (TSAs) and the taxonomic composition of Symbiodinium in the corals Montipora capitata, Porites lobata, and Porites compressa across the Hawaiian archipelago. Specifically, we investigated whether thermally tolerant clade D Symbiodinium was in greater abundance in corals from sites with high frequencies of TSAs. We recovered 2305 Symbiodinium ITS2 sequences from 242 coral colonies in lagoonal reef habitats at Pearl and Hermes Atoll, French Frigate Shoals, and Kaneohe Bay, Oahu in 2007. Sequences were grouped into 26 operational taxonomic units (OTUs) with 12 OTUs associated with Montipora and 21 with Porites. Both coral genera associated with Symbiodinium in clade C, and these co‐occurred with clade D in M. capitata and clade G in P. lobata. The latter represents the first report of clade G Symbiodinium in P. lobata. In M. capitata (but not Porites spp.), there was a significant correlation between the presence of Symbiodinium in clade D and a thermal history characterized by high cumulative frequency of TSAs. The endogenous community composition of Symbiodinium and an association with clade D symbionts after long‐term thermal disturbance appear strongly dependent on the taxa of the coral host.     

A novel algorithm with differential evolution and coral reef optimization for extreme learning machine training

Extreme learning machine (ELM) is a novel and fast learning method to train single layer feed-forward networks. However due to the demand for larger number of hidden neurons, the prediction speed of ELM is not fast enough. An evolutionary based ELM with differential evolution (DE) has been proposed to reduce the prediction time of original ELM. But it may still get stuck at local optima. In this paper, a novel algorithm hybridizing DE and metaheuristic coral reef optimization (CRO), which is called differential evolution coral reef optimization (DECRO), is proposed to balance the explorative power and exploitive power to reach better performance. The thought and the implement of DECRO algorithm are discussed in this article with detail. DE, CRO and DECRO are applied to ELM training respectively. Experimental results show that DECRO-ELM can reduce the prediction time of original ELM, and obtain better performance for training ELM than both DE and CRO.     

Differential antioxidant response between two Symbiodinium species from contrasting environments

High sea surface temperature accompanied by high levels of solar irradiance is responsible for the disruption of the symbiosis between cnidarians and their symbiotic dinoflagellates from the genus Symbiodinium. This phenomenon, known as coral bleaching, is one of the major threats affecting coral reefs around the world. Because an important molecular trigger to bleaching appears related to the production of reactive oxygen species (ROS), it is critical to understand the function of the antioxidant network of Symbiodinium species. In this study we investigated the response of two Symbiodinium species, from contrasting environments, to a chemically induced oxidative stress. ROS produced during this oxidative burst reduced photosynthesis by 30 to 50% and significantly decreased the activity of superoxide dismutase. Lipid peroxidation levels and carotenoid concentrations, especially diatoxanthin, confirm that these molecules act as antioxidants and contribute to the stabilization of membrane lipids. The comparative analysis between the two Symbiodinium species allowed us to highlight that Symbiodinium sp. clade A temperate was more tolerant to oxidative stress than the tropical S. kawagutii clade F. These differences are very likely a consequence of adaptation to their natural environment, with the temperate species experiencing conditions of temperature and irradiance much more variable and extreme.     

How accessible are coral reefs to people? A global assessment based on travel time

The depletion of natural resources has become a major issue in many parts of the world, with the most accessible resources being most at risk. In the terrestrial realm, resource depletion has classically been related to accessibility through road networks. In contrast, in the marine realm, the impact on living resources is often framed into the Malthusian theory of human density around ecosystems. Here, we develop a new framework to estimate the accessibility of global coral reefs using potential travel time from the nearest human settlement or market. We show that 58% of coral reefs are located < 30 min from the nearest human settlement. We use a case study from New Caledonia to demonstrate that travel time from the market is a strong predictor of fish biomass on coral reefs. We also highlight a relative deficit of protection on coral reef areas near people, with disproportional protection on reefs far from people. This suggests that conservation efforts are targeting low‐conflict reefs or places that may already be receiving de facto protection due to their isolation. Our global assessment of accessibility in the marine realm is a critical step to better understand the interplay between humans and resources.     

Finding Nemo’s Genes: A chromosome‐scale reference assembly of the genome of the orange clownfish Amphiprion percula

The iconic orange clownfish, Amphiprion percula, is a model organism for studying the ecology and evolution of reef fishes, including patterns of population connectivity, sex change, social organization, habitat selection and adaptation to climate change. Notably, the orange clownfish is the only reef fish for which a complete larval dispersal kernel has been established and was the first fish species for which it was demonstrated that antipredator responses of reef fishes could be impaired by ocean acidification. Despite its importance, molecular resources for this species remain scarce and until now it lacked a reference genome assembly. Here, we present a de novo chromosome‐scale assembly of the genome of the orange clownfish Amphiprion percula. We utilized single‐molecule real‐time sequencing technology from Pacific Biosciences to produce an initial polished assembly comprised of 1,414 contigs, with a contig N50 length of 1.86 Mb. Using Hi‐C‐based chromatin contact maps, 98% of the genome assembly were placed into 24 chromosomes, resulting in a final assembly of 908.8 Mb in length with contig and scaffold N50s of 3.12 and 38.4 Mb, respectively. This makes it one of the most contiguous and complete fish genome assemblies currently available. The genome was annotated with 26,597 protein‐coding genes and contains 96% of the core set of conserved actinopterygian orthologs. The availability of this reference genome assembly as a community resource will further strengthen the role of the orange clownfish as a model species for research on the ecology and evolution of reef fishes.