Development of 27 new microsatellite markers for the shanny Lipophrys pholis.

BACKGROUND: The shanny Lipophrys pholis is an intertidal fish that is widely distributed throughout the Northeast Atlantic. Characterized by limited adult mobility and a long pelagic larval duration, the shanny stands as an ideal model to better understand larval dispersal and connectivity dynamics, which are critical parameters with implications for marine conservation and management. METHODS AND RESULTS: To this aim, we developed 27 highly polymorphic microsatellite markers and characterized a population of 42 individuals, presenting an average allelic diversity of 20.1 alleles per locus and heterozygosity ranging from 0.619 to 1. CONCLUSIONS: This set of newly developed microsatellite markers will be useful in providing critical insights into the processes which shape L. pholis gene flow and connectivity patterns and can be used to investigate local parentage lineages.

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition.

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.

Beware of oysters. Rapid advance of non-native species in tropical Pacific islands.

Non-indigenous species can become a problem for the ecosystem health, especially when their distribution grows to the detriment of native species. In this moment, they can become invasive species. In marine ecosystems, the maritime transport is the principal gate and corridor for the movement of alien species. The genetic identification, using barcoding tools, of different oyster species in ports of the remote French Polynesia islands and atolls, showed a significant increase of exotic versus native oyster species between 2011 and 2018. This supports the spread of exotic species with the maritime traffic as the main cause. Moreover, the 11% of inaccurate identification at species level obtained in this study shows the need to complete the genetic databases.

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection.

BACKGROUND: Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154T provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host-pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model. RESULTS: We showed that the infection of the host is characterised by an enhancement of functions associated with antibiotic and glucans catabolism functions but a reduction of sulfate assimilation process in T. maritimum. The fish host concurrently displays a large panel of immune effectors, notably involving innate response and triggering acute inflammatory response. In addition, our results suggest that fish activate an adaptive immune response visible through the stimulation of T-helper cells, Th17, with congruent reduction of Th2 and T-regulatory cells. Fish were, however, largely sensitive to infection, and less than 25% survived after 96 hpi. These surviving fish showed no evidence of stress (cortisol levels) or significant difference in microbiome diversity compared with controls at the same sampling time. The presence of T. maritimum in resistant fish skin and the total absence of any skin lesions suggest that these fish did not escape contact with the pathogen, but rather that some mechanisms prevented pathogens entry. In resistant individuals, we detected up-regulation of specific immune-related genes differentiating resistant individuals from controls at 96 hpi, which suggests a possible genomic basis of resistance, although no genetic variation in coding regions was found. CONCLUSION: Here we focus in detail on the interplay between common fish pathogens and host immune response during experimental infection. We further highlight key actors of defence response, pathogenicity and possible genomic bases of fish resistance to T. maritimum.

Millepora platyphylla (Cnidaria, Hydrozoa) range extended back to the Eastern Pacific, thanks to a new record from Clipperton Atoll.

The fire coral Millepora platyphylla Hemprich Ehrenberg, 1834 (Cnidaria, Hydrozoa) has a widespread Indo-Pacific distribution observed from the surface to 40 m (Razak Hoeksema 2003). However, its extirpation from the East Pacific (Gulf of Chiriqui, Panama) was documented after the 1982-1983 bleaching event (Glynn Weerdt 1991). Here, we report the discovery of 5 colonies of M. platyphylla from the eastern Pacific, specifically at Clipperton Atoll, during the TARA Pacific expedition (www.taraexpeditions.org).

Contrasting global, regional and local patterns of genetic structure in gray reef shark populations from the Indo-Pacific region.

Human activities have resulted in the loss of over 90% of sharks in most ocean basins and one in four species of elasmobranch are now listed at risk of extinction by the IUCN. How this collapse will affect the ability of populations to recover in the face of continued exploitation and global climate change remains unknown. Indeed, important ecological and biological information are lacking for most shark species, particularly estimates of genetic diversity and population structure over a range of spatial scales. Using 15 microsatellite markers, we investigated genetic diversity and population structure in gray reef sharks over their Indo-Pacific range (407 specimens from 9 localities). Clear genetic differentiation was observed between the Indian and the Pacific Ocean specimens (FST = 0.145***). Further differentiation within the Pacific included a West and East cleavage as well as North-Central and South-Central Pacific clusters. No genetic differentiation was detected within archipelagos. These results highlight the legacy of past climate changes and the effects of large ocean expanses and circulation patterns on contrasting levels of connectivity at global, regional and local scales. Our results indicate a need for regional conservation units for gray reef sharks and pinpoint the isolation and vulnerability of their French Polynesian population.

Rate of biological invasions is lower in coastal marine protected areas.

Marine biological invasions threaten biodiversity worldwide. Here we explore how Marine Protected areas, by reducing human use of the coast, confer resilience against the introduction of non-indigenous species (NIS), using two very different Pacific islands as case studies for developing and testing mathematical models. We quantified NIS vectors and promoters on Vancouver (Canada) and Moorea (French Polynesia) islands, sampled and barcoded NIS, and tested models at different spatial scales with different types of interaction among vectors and between marine protection and NIS frequency. In our results NIS were negatively correlated with the dimension of the protected areas and the intensity of the protection. Small to medium geographical scale protection seemed to be efficient against NIS introductions. The likely benefit of MPAs was by exclusion of aquaculture, principally in Canada. These results emphasize the importance of marine protected areas for biodiversity conservation, and suggest that small or medium protected zones would confer efficient protection against NIS introduction.

When endemic coral-reef fish species serve as models: endemic mimicry patterns in the Marquesas Islands.

This article documents several cases of widespread species, which usually mimic other widespread species throughout the Indo-Pacific, using endemic Marquesan species as a model and displaying endemic mimicry patterns. This discovery adds a new line of evidence to the uniqueness of the Marquesas Islands, which not only host a high number of endemic reef-fish species, but also endemic mimicry patterns.

Contemporary genetic structure and postglacial demographic history of the black scorpionfish, Scorpaena porcus, in the Mediterranean and the Black Seas.

Understanding the distribution of genetic diversity in the light of past demographic events linked with climatic shifts will help to forecast evolutionary trajectories of ecosystems within the current context of climate change. In this study, mitochondrial sequences and microsatellite loci were analysed using traditional population genetic approaches together with Bayesian dating and the more recent approximate Bayesian computation scenario testing. The genetic structure and demographic history of a commercial fish, the black scorpionfish, Scorpaena porcus, was investigated throughout the Mediterranean and Black Seas. The results suggest that the species recently underwent population expansions, in both seas, likely concomitant with the warming period following the Last Glacial Maximum, 20 000 years ago. A weak contemporaneous genetic differentiation was identified between the Black Sea and the Mediterranean Sea. However, the genetic diversity was similar for populations of the two seas, suggesting a high number of colonizers entered the Black Sea during the interglacial period and/or the presence of a refugial population in the Black Sea during the glacial period. Finally, within seas, an east/west genetic differentiation in the Adriatic seems to prevail, whereas the Black Sea does not show any structured spatial genetic pattern of its population. Overall, these results suggest that the Black Sea is not that isolated from the Mediterranean, and both seas revealed similar evolutionary patterns related to climate change and changes in sea level.

[Case report: Neuroleptic malignant syndrome and diagnostic difficulties]. / Syndrome malin des neuroleptiques et difficultés diagnostiques : à propos d'un cas.

BACKGROUND: Neuroleptic malignant syndrome (NMS) is an uncommon but potentially fatal adverse effect of neuroleptic drugs. It is commonly characterized by muscular rigidity, fever, altered mental status, and autonomic dysfunction. Emerging of NMS is possible with all neuroleptics, classic and atypical. NMS occurs most often during the first week of treatment or after increasing the dosage of the neuroleptic medication. The frequency of NMS ranges from 0.07 to 2.2%. Its pathophysiology is not clearly understood but the blockade of dopamine receptors appears to be the central mechanism. Issues of NMS are those of diagnosis, treatment and reintroduction of antipsychotic treatment or not. OBJECTIVE: We here present an interesting case because of its atypical clinical presentation and its slow resolution, illustrating the various problems linked to the NMS. CASE REPORT: A 55-year-old woman with a history of mental retardation and infantile psychosis is hospitalized for worsening of her psychiatric symptoms. She is treated by risperidone long-acting injection every 2weeks, escitalopram 20 mg/d and oxazepam 10 mg/d. Early December 2012, she had fever spikes treated with many antibiotics and neuroleptics were stopped, without improvement. Early January 2013, a pulmonary embolism was diagnosed, and a treatment with loxapine is introduced and her injection of risperidone is done because of the state of agitation of the patient. Two weeks later, a NMS is suspected to hyperthermia, tremor of the limbs, a slight stiffness, and neuroleptics are stopped. Dantrolene is then introduced, but after 7days of treatment the fever is still important. Other assumptions are then discussed: infection, serotonin syndrome, encephalopathy, catatonia, malignant hyperthermia. But diagnosis of NMS is finally retained because of the recurrence of symptoms after introduction of clozapine early February. DISCUSSION: In this patient, diagnosis was made more difficult by the use of long-acting neuroleptic. NMS was indeed partly rejected because of the lack of improvement despite 7 days of dantrolene treatment, but the release of risperidone lasts 7weeks after the injection. This NMS is also of atypical presentation with a minor muscular rigidity. And this case is particularly interesting because of the recurrence of NMS with clozapine, allowing to finally diagnose it. This atypical neuroleptic is not known to be a major provider of NMS but the very short period before reintroduction and possible persistence of risperidone in the body could explain the recurrence. CONCLUSION: NMS can be hard to diagnose. It is a diagnosis of exclusion, but we should keep in mind that there is great variability of its clinical presentation in order to not exclude too quickly this syndrome in a patient treated by neuroleptic.

Fringing reefs exposed to different levels of eutrophication and sedimentation can support similar benthic communities.

Benthic communities are sensitive to anthropogenic disturbances which can result in changes in species assemblages. A spatio-temporal survey of environmental parameters was conducted over an 18-month period on four different fringing reefs of Moorea, French Polynesia, with unusual vs. frequent human pressures. This survey included assessment of biological, chemical, and physical parameters. First, the results showed a surprising lack of a seasonal trend, which was likely obscured by short-term variability in lagoons. More frequent sampling periods would likely improve the evaluation of a seasonal effect on biological and ecological processes. Second, the three reef habitats studied that were dominated by corals were highly stable, despite displaying antagonistic environmental conditions through eutrophication and sedimentation gradients, whereas the reef dominated by macroalgae was relatively unstable. Altogether, our data challenge the paradigm of labelling environmental parameters such as turbidity, sedimentation, and nutrient-richness as stress indicators.

Population structure, spatial distribution and life-history traits of blacktip reef sharks Carcharhinus melanopterus.

During a survey of the population of blacktip reef shark Carcharhinus melanopterus in Moorea (French Polynesia) between 2007 and 2011, population structural characteristics were estimated from 268 individuals. Total length (LT ) ranged from 48 to 139 cm and 48 to 157 cm for males and females, respectively, demonstrating that the average LT of females was larger than that of males. The C. melanopterus population at Moorea showed an apparent spatial sexual segregation with females preferentially frequenting lagoons and males the fore-reefs. Mean growth rate was c. 6 cm year(-1) . Males reached sexual maturity at 111 cm LT . This study reports on the population characteristics of this widespread carcharhinid shark species and makes comparisons with other locations, confirming high geographic variability in the population structure of the species.

Larger female fish contribute disproportionately more to self-replenishment.

While chance events, oceanography and selective pressures inject stochasticity into the replenishment of marine populations with dispersing life stages, some determinism may arise as a result of characteristics of breeding individuals. It is well known that larger females have higher fecundity, and recent laboratory studies have shown that maternal traits such as age and size can be positively associated with offspring growth, size and survival. Whether such fecundity and maternal effects translate into higher recruitment in marine populations remains largely unanswered. We studied a population of Amphiprion chrysopterus (orange-fin anemonefish) in Moorea, French Polynesia, to test whether maternal size influenced the degree of self-recruitment on the island through body size-fecundity and/or additional size-related maternal effects of offspring. We non-lethally sampled 378 adult and young juveniles at Moorea, and, through parentage analysis, identified the mothers of 27 self-recruits (SRs) out of 101 recruits sampled. We also identified the sites occupied by each mother of an SR and, taking into account variation in maternal size among sites, we found that females that produced SRs were significantly larger than those that did not (approx. 7% greater total length, approx. 20% greater biomass). Our analyses further reveal that the contribution of larger females to self-recruitment was significantly greater than expected on the basis of the relationship between body size and fecundity, indicating that there were important maternal effects of female size on traits of their offspring. These results show, for the first time in a natural population, that larger female fish contribute more to local replenishment (self-recruitment) and, more importantly, that size-specific fecundity alone could not explain the disparity.

Marine reserves: fish life history and ecological traits matter.

Marine reserves are assumed to protect a wide range of species from deleterious effects stemming from exploitation. However, some species, due to their ecological characteristics, may not respond positively to protection. Very little is known about the effects of life history and ecological traits (e.g., mobility, growth, and habitat) on responses of fish species to marine reserves. Using 40 data sets from 12 European marine reserves, we show that there is significant variation in the response of different species of fish to protection and that this heterogeneity can be explained, in part, by differences in their traits. Densities of targeted size-classes of commercial species were greater in protected than unprotected areas. This effect of protection increased as the maximum body size of the targeted species increased, and it was greater for species that were not obligate schoolers. However, contrary to previous theoretical findings, even mobile species with wide home ranges benefited from protection: the effect of protection was at least as strong for mobile species as it was for sedentary ones. Noncommercial bycatch and unexploited species rarely responded to protection, and when they did (in the case of unexploited bentho-pelagic species), they exhibited the opposite response: their densities were lower inside reserves. The use of marine reserves for marine conservation and fisheries management implies that they should ensure protection for a wide range of species with different life-history and ecological traits. Our results suggest this is not the case, and instead that effects vary with economic value, body size, habitat, depth range, and schooling behavior.

Functional study of the pectoral spine stridulation mechanism in different mochokid catfishes.

Mochokidae are able to produce pectoral spine stridulation sounds. During sound production, high speed videos were used to study the pectoral fin movements to identify the mechanisms involved. A call consisted of a series of pulses and occurred during a spine sweep, which was in fact made up of a series of jerky movements. The morphology of the pectoral spines and associated muscles was also observed in different species. The contractions of adductor profundus and superficial adductor allows adduction and abduction movements (sweep) of the spine, respectively. Simultaneously, the contraction of the arrector ventralis or the arrector 3 of the pectoral spine allows the pulling and pressing the ridges of the dorsal process, against the rough lateral face of the spinal fossa. This results in the rubbing of the ridges of the dorsal process, producing sounds. In Synodontis the analogy for sound production would be a brake shoe pressing against a wheel.

Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios.

The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2-6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (F(ST )= 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.

Isolation and characterization of 16 microsatellite loci in the humbug damselfish, Dascyllus aruanus (family Pomacentridae).

Here we report on 16 microsatellite loci designed for the damselfish Dascyllus aruanus. All loci were tested on 98 individuals and were polymorphic (seven to 35 alleles). Expected heterozygosity ranged from 0.705 to 0.942. Six loci showed Hardy-Weinberg disequilibrium due to the occurrence of null alleles. Cross-species amplifications conducted within the genus Dascyllus (D. carneus, D. strasburgi, D. trimaculatus) lead to polymorphic fragments in 32 out of 48 tests. These 16 loci will enable future research into the behavioural ecology and population ecology of Dascyllus aruanus throughout the Indo-Pacific.

Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs.

Design and decision-making for marine protected areas (MPAs) on coral reefs require prediction of MPA effects with population models. Modeling of MPAs has shown how the persistence of metapopulations in systems of MPAs depends on the size and spacing of MPAs, and levels of fishing outside the MPAs. However, the pattern of demographic connectivity produced by larval dispersal is a key uncertainty in those modeling studies. The information required to assess population persistence is a dispersal matrix containing the fraction of larvae traveling to each location from each location, not just the current number of larvae exchanged among locations. Recent metapopulation modeling research with hypothetical dispersal matrices has shown how the spatial scale of dispersal, degree of advection versus diffusion, total larval output, and temporal and spatial variability in dispersal influence population persistence. Recent empirical studies using population genetics, parentage analysis, and geochemical and artificial marks in calcified structures have improved the understanding of dispersal. However, many such studies report current self-recruitment (locally produced settlement/settlement from elsewhere), which is not as directly useful as local retention (locally produced settlement/total locally released), which is a component of the dispersal matrix. Modeling of biophysical circulation with larval particle tracking can provide the required elements of dispersal matrices and assess their sensitivity to flows and larval behavior, but it requires more assumptions than direct empirical methods. To make rapid progress in understanding the scales and patterns of connectivity, greater communication between empiricists and population modelers will be needed. Empiricists need to focus more on identifying the characteristics of the dispersal matrix, while population modelers need to track and assimilate evolving empirical results.

DNA microarrays for identifying fishes.

In many cases marine organisms and especially their diverse developmental stages are difficult to identify by morphological characters. DNA-based identification methods offer an analytically powerful addition or even an alternative. In this study, a DNA microarray has been developed to be able to investigate its potential as a tool for the identification of fish species from European seas based on mitochondrial 16S rDNA sequences. Eleven commercially important fish species were selected for a first prototype. Oligonucleotide probes were designed based on the 16S rDNA sequences obtained from 230 individuals of 27 fish species. In addition, more than 1200 sequences of 380 species served as sequence background against which the specificity of the probes was tested in silico. Single target hybridisations with Cy5-labelled, PCR-amplified 16S rDNA fragments from each of the 11 species on microarrays containing the complete set of probes confirmed their suitability. True-positive, fluorescence signals obtained were at least one order of magnitude stronger than false-positive cross-hybridisations. Single nontarget hybridisations resulted in cross-hybridisation signals at approximately 27% of the cases tested, but all of them were at least one order of magnitude lower than true-positive signals. This study demonstrates that the 16S rDNA gene is suitable for designing oligonucleotide probes, which can be used to differentiate 11 fish species. These data are a solid basis for the second step to create a "Fish Chip" for approximately 50 fish species relevant in marine environmental and fisheries research, as well as control of fisheries products.

Inferring gene flow in coral reef fishes from different molecular markers: which loci to trust?

Contrasting results are usually reported in the literature regarding the factors influencing observed structuring of genetic variability. The goals of this study were, for five coral reef fishes in French Polynesia, (1) to infer the theoretical variance of single locus F(ST) estimates expected under neutrality in order to exclude outlier loci before inferring gene flow and (2) to test thereafter whether species laying pelagic eggs effectively disperse more than species laying benthic eggs in this system. For this purpose, a total of 952 individuals from five species belonging to two families (Chaetodontidae and Pomacentridae) were screened among populations sampled within a 60-600 km spatial range for intron length polymorphism at 11 loci in order to illuminate contrasting results previously published on allozymes and mitochondrial DNA (mtDNA) control region polymorphisms. Statistically speaking, among the five species, four loci (three allozymes and one intron) were identified as outliers and discarded before interpretation of genetic differentiation in terms of effective dispersal. Biologically speaking, our results suggest that the observed genetic structure is not significantly related to the reproductive strategy of coral reef fish in the island system we analysed and that observed random genetic differentiation accommodates Wright's island model in all five species surveyed. Overall, our study emphasizes how cautious one has to be when trying to interpret present-day genetic structure in terms of gene flow while using a limited number of loci and/or different sets of loci.