Publications by authors named "Planes Serge"

118 Publications

Investigating links between thermal tolerance and oxygen supply capacity in shark neonates from a hyperoxic tropical environment.

Sci Total Environ 2021 Apr 5;782:146854. Epub 2021 Apr 5.

Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland 4811, Australia.

Temperature and oxygen limit the distribution of marine ectotherms. Haematological traits underlying blood-oxygen carrying capacity are thought to be correlated with thermal tolerance in certain fishes, and this relationship is hypothesised to be explained by oxygen supply capacity. We tested this hypothesis using reef shark neonates as experimental models because they live near their upper thermal limits and are physiologically sensitive to low oxygen conditions. We first described in situ associations between temperature and oxygen at the study site (Moorea, French Polynesia) and found that the habitats for reef shark neonates (Carcharhinus melanopterus and Negaprion acutidens) were hyperoxic at the maximum recorded temperatures. Next, we tested for in situ associations between thermal habitat characteristics and haematological traits of neonates. Contrary to predictions, we only demonstrated a negative association between haemoglobin concentration and maximum habitat temperatures in C. melanopterus. Next, we tested for ex situ associations between critical thermal maximum (CT) and haematological traits, but only demonstrated a negative association between haematocrit and CT in C. melanopterus. Finally, we measured critical oxygen tension (p) ex situ and estimated its temperature sensitivity to predict oxygen-dependent values of CT. Estimated temperature sensitivity of p was similar to reported values for sharks and skates, and predicted values for CT equalled maximum habitat temperatures. These data demonstrate unique associations between haematological traits and thermal tolerance in a reef shark that are likely not explained by oxygen supply capacity. However, a relationship between oxygen supply capacity and thermal tolerance remains to be demonstrated empirically.
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http://dx.doi.org/10.1016/j.scitotenv.2021.146854DOI Listing
April 2021

Genetic homogeneity of the critically endangered fan mussel, Pinna nobilis, throughout lagoons of the Gulf of Lion (North-Western Mediterranean Sea).

Sci Rep 2021 Apr 8;11(1):7805. Epub 2021 Apr 8.

PSL Research University: EPHE - UPVD - CNRS, USR 3278 CRIOBE, 66860, Perpignan, France.

The fan mussel, Pinna nobilis, endemic to the Mediterranean Sea, is a critically endangered species facing mass mortality events in almost all of its populations, following the introduction of the parasite Haplosporidium pinnae. Such a unique pandemic in a marine organism, which spreads rapidly and with mortality rates reaching up to 100%, could lead to the potential extinction of the species. Only few regions, involving lagoon habitats, remain healthy throughout the entire Mediterranean Sea. This study describes the genetic structure of P. nobilis across the Gulf of Lion, including confined locations such as lagoons and ports. A total of 960 samples were collected among 16 sites distributed at 8 localities, and then genotyped using 22 microsatellite markers. Genetic diversity was high in all sites with mean allele numbers ranging between 10 and 14.6 and with observed heterozygosities (Ho) between 0.679 and 0.704. No genetic differentiation could be identified (F ranging from 0.0018 to 0.0159) and the percentages of related individuals were low and similar among locations (from 1.6 to 6.5%). Consequently, all fan mussels, over the entire coastline surveyed, including those in the most geographically isolated areas, belong to a large genetically homogeneous population across the Gulf of Lion. Considering the ongoing mass mortality context, this result demonstrates that almost all of the genetic diversity of P. nobilis populations is still preserved even in isolated lagoons, which might represent a refuge habitat for the future of the species.
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http://dx.doi.org/10.1038/s41598-021-87493-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8032772PMC
April 2021

Environmentally Driven Color Variation in the Pearl Oyster var. (Linnaeus, 1758) Is Associated With Differential Methylation of CpGs in Pigment- and Biomineralization-Related Genes.

Front Genet 2021 19;12:630290. Epub 2021 Mar 19.

IHPE, Université de Montpellier, CNRS, IFREMER, Université de Perpignan Via Domitia, Montpellier, France.

Today, it is common knowledge that environmental factors can change the color of many animals. Studies have shown that the molecular mechanisms underlying such modifications could involve epigenetic factors. Since 2013, the pearl oyster var. has become a biological model for questions on color expression and variation in Mollusca. A previous study reported color plasticity in response to water depth variation, specifically a general darkening of the nacre color at greater depth. However, the molecular mechanisms behind this plasticity are still unknown. In this paper, we investigate the possible implication of epigenetic factors controlling shell color variation through a depth variation experiment associated with a DNA methylation study performed at the whole genome level with a constant genetic background. Our results revealed six genes presenting differentially methylated CpGs in response to the environmental change, among which four are linked to pigmentation processes or regulations (, , , and ), especially those leading to darker phenotypes. Interestingly, the genes and , both involved in the biomineralization process (deposition of aragonite and calcite crystals), also showed differential methylation, suggesting that a possible difference in the physical/spatial organization of the crystals could cause darkening (iridescence or transparency modification of the biomineral). These findings are of great interest for the pearl production industry, since wholly black pearls and their opposite, the palest pearls, command a higher value on several markets. They also open the route of epigenetic improvement as a new means for pearl production improvement.
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http://dx.doi.org/10.3389/fgene.2021.630290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8018223PMC
March 2021

Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster var. (Linnaeus 1758).

Genes (Basel) 2021 Mar 15;12(3). Epub 2021 Mar 15.

IFREMER, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, BP 49, 98725 Tahiti, France.

The shell color of the Mollusca has attracted naturalists and collectors for hundreds of years, while the molecular pathways regulating pigment production and the pigments themselves remain poorly described. In this study, our aim was to identify the main pigments and their molecular pathways in the pearl oyster -the species displaying the broadest range of colors. Three inner shell colors were investigated-red, yellow, and green. To maximize phenotypic homogeneity, a controlled population approach combined with common garden conditioning was used. Comparative analysis of transcriptomes (RNA-seq) of with different shell colors revealed the central role of the heme pathway, which is involved in the production of red (uroporphyrin and derivates), yellow (bilirubin), and green (biliverdin and cobalamin forms) pigments. In addition, the Raper-Mason, and purine metabolism pathways were shown to produce yellow pigments (pheomelanin and xanthine) and the black pigment eumelanin. The presence of these pigments in pigmented shell was validated by Raman spectroscopy. This method also highlighted that all the identified pathways and pigments are expressed ubiquitously and that the dominant color of the shell is due to the preferential expression of one pathway compared with another. These pathways could likely be extrapolated to many other organisms presenting broad chromatic variation.
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http://dx.doi.org/10.3390/genes12030421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998362PMC
March 2021

Ship-driven biopollution: How aliens transform the local ecosystem diversity in Pacific islands.

Mar Pollut Bull 2021 Mar 11;166:112251. Epub 2021 Mar 11.

Department of Functional Biology, University of Oviedo, 33006 Oviedo, Spain.

Ships moving species across the oceans mix marine communities throughout latitudes. The introduction of new species may be changing the ecosystems even in remote islands. In tropical Pacific islands where maritime traffic is principally local, eDNA metabarcoding and barcoding revealed 75 introduced species, accounting in average for 28% of the community with a minimum of 13% in the very remote Rangiroa atoll. The majority of non-native species were primary producers -from diatoms to red algae, thus the ecosystem is being transformed from the bottom. Primary producers were more shared among sites than other exotics, confirming ship-mediated dispersal in Pacific marine ecosystems. Limited alien share and an apparent saturation of aliens (similar proportion in ports of very different size) suggests the occurrence of "alien drift" in port communities, or random retention of newly introduced aliens that reminds genetic drift of new mutations in a population.
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http://dx.doi.org/10.1016/j.marpolbul.2021.112251DOI Listing
March 2021

Natural hybridization between pen shell species: Pinna rudis and the critically endangered Pinna nobilis may explain parasite resistance in P. nobilis.

Mol Biol Rep 2021 Jan 4;48(1):997-1004. Epub 2021 Jan 4.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.

Recently, Pinna nobilis pen shells population in Mediterranean Sea has plummeted due to a Mass Mortality Event caused by an haplosporidian parasite. In consequence, this bivalve species has been included in the IUCN Red List as "Critically Endangered". In the current scenario, several works are in progress to protect P. nobilis from extinction, being identification of hybrids (P. nobilis x P. rudis) among survivors extremely important for the conservation of the species.Morphological characteristics and molecular analyses were used to identify putative hybrids. A total of 10 individuals of each species (P. nobilis and P. rudis) and 3 doubtful individuals were considered in this study. The putative hybrids showed shell morphology and mantle coloration intermingled exhibiting both P. nobilis and P. rudis traits. Moreover, the analyses of 1150 bp of the 28S gene showed 9 diagnostic sites between P. rudis and P. nobilis, whereas hybrids showed both parental diagnostic alleles at the diagnostic loci. Regarding the multilocus genotypes from the 8 microsatellite markers, the segregation of two Pinna species was clearly detected on the PCoA plot and the 3 hybrids showed intermediate positions.This is the first study evidencing the existence of hybrids P. nobilis x P. rudis, providing molecular methodology for a proper identification of new hybrids. Further studies testing systematically all parasite-resisting isolated P. nobilis should be undertaken to determine if the resistance is resulting from introgression of P. rudis into P. nobilis genome and identifying aspects related to resistance.
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http://dx.doi.org/10.1007/s11033-020-06063-5DOI Listing
January 2021

Chaotic genetic structure and past demographic expansion of the invasive gastropod Tritia neritea in its native range, the Mediterranean Sea.

Sci Rep 2020 12 10;10(1):21624. Epub 2020 Dec 10.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence « CORAIL », Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.

To better predict population evolution of invasive species in introduced areas it is critical to identify and understand the mechanisms driving genetic diversity and structure in their native range. Here, we combined analyses of the mitochondrial COI gene and 11 microsatellite markers to investigate both past demographic history and contemporaneous genetic structure in the native area of the gastropod Tritia neritea, using Bayesian skyline plots (BSP), multivariate analyses and Bayesian clustering. The BSP framework revealed population expansions, dated after the last glacial maximum. The haplotype network revealed a strong geographic clustering. Multivariate analyses and Bayesian clustering highlighted the strong genetic structure at all scales, between the Black Sea and the Adriatic Sea, but also within basins. Within basins, a random pattern of genetic patchiness was observed, suggesting a superimposition of processes involving natural biological effects (no larval phase and thus limited larval dispersal) and putative anthropogenic transport of specimens. Contrary to the introduced area, no isolation-by-distance patterns were recovered in the Mediterranean or the Black Seas, highlighting different mechanisms at play on both native and introduced areas, triggering unknown consequences for species' evolutionary trajectories. These results of Tritia neritea populations on its native range highlight a mixture of ancient and recent processes, with the effects of paleoclimates and life history traits likely tangled with the effects of human-mediated dispersal.
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http://dx.doi.org/10.1038/s41598-020-77742-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7730386PMC
December 2020

Correction: Reisser, C.M.O. et al. Population Connectivity and Genetic Assessment of Exploited and Natural Populations of Pearl Oysters within a French Polynesian Atoll Lagoon. 2020, , 426.

Genes (Basel) 2020 Nov 16;11(11). Epub 2020 Nov 16.

Institut de Recherche pour le Développement, UMR-9220 ENTROPIE, IRD, Université de la Réunion, IFREMER, CNRS, Université de la Nouvelle-Calédonie, Nouméa BPA5, New Caledonia.

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http://dx.doi.org/10.3390/genes11111358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7696931PMC
November 2020

The power struggle: assessing interacting global change stressors via experimental studies on sharks.

Sci Rep 2020 11 16;10(1):19887. Epub 2020 Nov 16.

Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia.

Ocean warming and acidification act concurrently on marine ectotherms with the potential for detrimental, synergistic effects; yet, effects of these stressors remain understudied in large predatory fishes, including sharks. We tested for behavioural and physiological responses of blacktip reef shark (Carcharhinus melanopterus) neonates to climate change relevant changes in temperature (28 and 31 °C) and carbon dioxide partial pressures (pCO; 650 and 1050 µatm) using a fully factorial design. Behavioural assays (lateralisation, activity level) were conducted upon 7-13 days of acclimation, and physiological assays (hypoxia tolerance, oxygen uptake rates, acid-base and haematological status) were conducted upon 14-17 days of acclimation. Haematocrit was higher in sharks acclimated to 31 °C than to 28 °C. Significant treatment effects were also detected for blood lactate and minimum oxygen uptake rate; although, these observations were not supported by adequate statistical power. Inter-individual variability was considerable for all measured traits, except for haematocrit. Moving forward, studies on similarly 'hard-to-study' species may account for large inter-individual variability by increasing replication, testing larger, yet ecologically relevant, differences in temperature and pCO, and reducing measurement error. Robust experimental studies on elasmobranchs are critical to meaningfully assess the threat of global change stressors in these data-deficient species.
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http://dx.doi.org/10.1038/s41598-020-76966-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7669887PMC
November 2020

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing.

Sci Rep 2020 09 28;10(1):15893. Epub 2020 Sep 28.

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processed in situ, during the Tara Pacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 h. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.
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http://dx.doi.org/10.1038/s41598-020-72589-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7522235PMC
September 2020

New microsatellite DNA markers to resolve population structure of the convict surgeonfish, Acanthurus triostegus, and cross-species amplifications on thirteen other Acanthuridae.

Mol Biol Rep 2020 Oct 8;47(10):8243-8250. Epub 2020 Sep 8.

UMR250 ENTROPIE, BPA5, Institut de Recherche pour le Développement (IRD), 101 Promenade Roger Laroque, 98848, Noumea cedex, New Caledonia.

Microsatellites are widely used to investigate connectivity and parentage in marine organisms. Despite surgeonfish (Acanthuridae) being dominant members of most reef fish assemblages and having an ecological key role in coral reef ecosystems, there is limited information describing the scale at which populations are connected and very few microsatellite markers have been screened. Here, we developed fourteen microsatellite markers for the convict surgeonfish Acanthurus triostegus with the aim to infer its genetic connectivity throughout its distribution range. Genetic diversity and variability was tested over 152 fishes sampled from four locations across the Indo-Pacific: Mayotte (Western Indian Ocean), Papua New Guinea and New Caledonia (Southwestern Pacific Ocean), and Moorea (French Polynesia). Over all locations, the number of alleles per locus varied from 5 to 24 per locus, and expected heterozygosities ranged from 0.468 to 0.941. Significant deviations from Hardy-Weinberg equilibrium were detected for two loci in two to three locations and were attributed to the presence of null alleles. These markers revealed for the first time a strong and significant distinctiveness between Indian Ocean and Pacific Ocean A. triostegus populations. We further conducted cross-species amplification tests in 13 Pacific congener species to investigate the possible use of these microsatellites in other Acanthuridae species. The phylogenetic placement of A. triostegus branching off from the clade containing nearly all Acanthurus + Ctenochaetus species likely explain the rather good transferability of these microsatellite markers towards other Acanthuridae species. This suggests that this fourteen new microsatellite loci will be helpful tools not only for inferring population structure of various surgeonfish but also to clarify systematic relationships among Acanthuridae.
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http://dx.doi.org/10.1007/s11033-020-05773-0DOI Listing
October 2020

Characterization of 25 new microsatellite markers for the fin whale (Balaenoptera physalus) and cross-species amplification in other cetaceans.

Mol Biol Rep 2020 Sep 6;47(9):6983-6996. Epub 2020 Sep 6.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, 66860, Perpignan, France.

Cetaceans are large mammals widely distributed on Earth. The fin whale, Balaenoptera physalus, is the second largest living animal. In the 20th century, commercial whaling reduced its global population by 70%, and in the Mediterranean Sea not only was their overall population depleted but the migration between the Mediterranean Sea and the Atlantic Ocean was reduced. Previous genetic studies identified isolation between these two regions, with a limited gene-flow between these adjacent populations based on nuclear and mitochondrial markers. However, only limited information exists for the Mediterranean population as genetic diversity and abundance trends are still unknown. In this study, 39 highly polymorphic microsatellite markers were tested, including 25 markers developed de novo together with 14 markers previously published. An average allelic diversity of 8.3 alleles per locus was reported, ranging from 3 to 15 alleles per locus, for B. physalus. Expected heterozygosity was variable among loci and ranged from 0.34 to 0.91. Only two markers in the new set were significantly deviant from the Hardy Weinberg equilibrium. Cross-species amplification was tested in four other cetacean species. A total of 27 markers were successfully amplified in the four species (Balaenoptera acutorostrata, Megaptera novaeangliae, Physeter macrocephalus and Globicephala melas). A multivariate analysis on the multilocus genotypes successfully discriminated the five species. This new set of microsatellite markers will not only provide a useful tool to identify and understand the genetic diversity and the evolution of the B. physalus population, but it will also be relevant for other cetacean species, and will allow further parentage analyses. Eventually, this new set of microsatellite markers will provide critical data that will shed light on important biological data within a conservation perspective.
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http://dx.doi.org/10.1007/s11033-020-05757-0DOI Listing
September 2020

Thermal tolerance and hypoxia tolerance are associated in blacktip reef shark () neonates.

J Exp Biol 2020 07 21;223(Pt 14). Epub 2020 Jul 21.

Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, 4811, Australia.

Thermal dependence of growth and metabolism can influence thermal preference and tolerance in marine ectotherms, including threatened and data-deficient species. Here, we quantified the thermal dependence of physiological performance in neonates of a tropical shark species (blacktip reef shark, ) from shallow, nearshore habitats. We measured minimum and maximum oxygen uptake rates ( ), calculated aerobic scope, excess post-exercise oxygen consumption and recovery from exercise, and measured critical thermal maxima (CT), thermal safety margins, hypoxia tolerance, specific growth rates, body condition and food conversion efficiencies at two ecologically relevant acclimation temperatures (28 and 31°C). Owing to high post-exercise mortality, a third acclimation temperature (33°C) was not investigated further. Acclimation temperature did not affect  or growth, but CT and hypoxia tolerance were greatest at 31°C and positively associated. We also quantified temperature (25, 30 and 35°C) and pH effects on haemoglobin-oxygen (Hb-O) affinity of wild-caught, non-acclimated sharks. As expected, Hb-O affinity decreased with increasing temperatures, but pH effects observed at 30°C were absent at 25 and 35°C. Finally, we logged body temperatures of free-ranging sharks and determined that neonates avoided 31°C We conclude that neonates demonstrate minimal thermal dependence of whole-organism physiological performance across a seasonal temperature range and may use behaviour to avoid unfavourable environmental temperatures. The association between thermal tolerance and hypoxia tolerance suggests a common mechanism warranting further investigation. Future research should explore the consequences of ocean warming, especially in nearshore, tropical species.
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http://dx.doi.org/10.1242/jeb.221937DOI Listing
July 2020

Genetic connectivity of lionfish () in marine protected areas of the Gulf of Mexico and Caribbean Sea.

Ecol Evol 2020 May 16;10(9):3844-3855. Epub 2020 Apr 16.

Laboratorio de Ecología de Ecosistemas de Arrecifes Coralinos Departamento de Recursos del Mar Centro de Investigación y de Estudios Avanzados del I.P.N.- Unidad Mérida Mérida México.

Lionfish () have rapidly invaded the tropical Atlantic and spread across the wider Caribbean in a relatively short period of time. Because of its high invasion capacity, we used it as a model to identify the connectivity among nine marine protected areas (MPAs) situated in four countries in the Gulf of Mexico and the Caribbean Sea. This study provides evidence of local genetic differentiation of in the Gulf of Mexico and the Caribbean Sea. A total of 475 lionfish samples were characterized with 12 microsatellites, with 6-20 alleles per locus. Departures from Hardy-Weinberg equilibrium (HWE) were found in 10 of the 12 loci, all caused by heterozygous excess. Moderate genetic differentiation was observed between Chiriviche, Venezuela and Xcalak, México localities ( = 0.012), and between the Los Roques and the Veracruz ( = 0.074) sites. STRUCTURE analysis found that four genetic entities best fit our data. A unique genetic group in the Gulf of Mexico may imply that the lionfish invasion unfolded both in a counterclockwise manner in the Gulf of Mexico. In spite of the notable dispersion of , our results show some genetic structure, as do other noninvasive Caribbean fish species, suggesting that the connectivity in some MPAs analyzed in the Caribbean is limited and caused by only a few source individuals with subsequent genetic drift leading to local genetic differentiation. This indicates that dispersion could be caused by mesoscale phenomena, which produce stochastic connectivity pulses. Due to the isolation of some MPAs from others, these findings may hold a promise for local short-term control of by means of intensive fishing, even in MPAs, and may have regional long-term effects.
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http://dx.doi.org/10.1002/ece3.5829DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244795PMC
May 2020

Population Connectivity and Genetic Assessment of Exploited and Natural Populations of Pearl Oysters within a French Polynesian Atoll Lagoon.

Genes (Basel) 2020 04 15;11(4). Epub 2020 Apr 15.

Institut de Recherche pour le Développement, UMR-9220 ENTROPIE, IRD, Université de la Réunion, IFREMER, CNRS, Université de la Nouvelle-Calédonie), Nouméa BPA5, New Caledonia.

In French Polynesia, the production and exportation of black pearls through the aquaculture of the black-lip pearl oyster provide the second largest economic income for the country after tourism. This industry entirely relies on the collection of natural spats from few highly recruiting lagoons. In recent years, pearl oyster producers have experienced variable success rates in spat collection, with significant spatial and temporal variability in spat supply, driving uncertainty in the future of pearl production. This study combines, for the first time in a farmed lagoon, genetic (SNPs), demographic (sex ratio, age), and biophysical data (larval dispersal modelling) to shed new light on population dynamics, connectivity, and spat recruitment in Ahe Atoll, a well-studied pearl farming site. Our results indicate that the geographical structuring of the natural populations and the contribution of both natural and exploited stocks to the production of spats result from the interaction of hydrodynamic features, life history traits and demographic parameters: the northeastern natural populations are older, not well connected to the southwestern natural populations and are not replenished by larvae produced by adjacent exploited populations. Moreover, we observe that the exploited populations did not contribute to larval production during our experiment, despite a sampling period set during the most productive season for spat collection. This is likely the result of a strong male bias in the exploited populations, coupled with a sweepstakes reproductive strategy of the species. Our results warrant further investigations over the future of the northeastern older natural populations and a reflection on the current perliculture techniques.
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http://dx.doi.org/10.3390/genes11040426DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7230779PMC
April 2020

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate.

Mol Ecol 2020 04 26;29(8):1508-1522. Epub 2020 Apr 26.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.
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http://dx.doi.org/10.1111/mec.15418DOI Listing
April 2020

Development of 26 highly polymorphic microsatellite markers for the highly endangered fan mussel Pinna nobilis and cross-species amplification.

Mol Biol Rep 2020 Apr 25;47(4):2551-2559. Epub 2020 Feb 25.

PSL Research University, EPHE - UPVD - CNRS, USR 3278 CRIOBE, 66860, Perpignan, France.

The fan mussel, Pinna nobilis is a highly endangered bivalve species endemic to the Mediterranean Sea. During the last few decades, populations have been greatly reduced due to anthropic impacts and they are now under strict protection in most Mediterranean countries. Today, the species is facing a major crisis following the introduction of an haplosporidan parasite which is driving mass mortality in almost all P. nobilis populations throughout the Mediterranean Sea. Gathering additional knowledge regarding dynamics and connectivity patterns of P. nobilis populations is now more than ever critical. Here, we describe the development of 26 highly polymorphic microsatellite markers. Average allelic diversity of 10.9 alleles per locus was reported and heterozygosity ranged from 0.0294 to 0.9737. We tested cross-species amplification in four Pinna species for the new markers together with 10 already published markers, and analysed its success according to the genetic distances among species. Cross-species transferability success ranged from 3 to 38% and had a negative relationship with the genetic distance between the target species and the tested species. The establishment of this new set of high-resolution markers provides a useful tool to understand processes driving gene flow and genetic diversity in P. nobilis populations and the closest congeneric species.
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http://dx.doi.org/10.1007/s11033-020-05338-1DOI Listing
April 2020

Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population.

Ecol Lett 2020 Feb 26;23(2):265-273. Epub 2019 Nov 26.

PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.

The relative contributions of environmental, maternal and additive genetic factors to the Lifetime reproductive success (LRS) determine whether species can adapt to rapid environmental change. Yet to date, studies quantifying LRS across multiple generations in marine species in the wild are non-existent. Here we used 10-year pedigrees resolved for a wild orange clownfish population from Kimbe Island (PNG) and a quantitative genetic linear mixed model approach to quantify the additive genetic, maternal and environmental contributions to variation in LRS for the self-recruiting portion of the population. We found that the habitat of the breeder, including the anemone species and geographic location, made the greatest contribution to LRS. There were low to negligible contributions of genetic and maternal factors equating with low heritability and evolvability. Our findings imply that our population will be susceptible to short-term, small-scale changes in habitat structure and may have limited capacity to adapt to these changes.
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http://dx.doi.org/10.1111/ele.13428DOI Listing
February 2020

The Tara Pacific expedition-A pan-ecosystemic approach of the "-omics" complexity of coral reef holobionts across the Pacific Ocean.

PLoS Biol 2019 09 23;17(9):e3000483. Epub 2019 Sep 23.

Centre Scientifique de Monaco, Monte Carlo, Principality of Monaco.

Coral reefs are the most diverse habitats in the marine realm. Their productivity, structural complexity, and biodiversity critically depend on ecosystem services provided by corals that are threatened because of climate change effects-in particular, ocean warming and acidification. The coral holobiont is composed of the coral animal host, endosymbiotic dinoflagellates, associated viruses, bacteria, and other microeukaryotes. In particular, the mandatory photosymbiosis with microalgae of the family Symbiodiniaceae and its consequences on the evolution, physiology, and stress resilience of the coral holobiont have yet to be fully elucidated. The functioning of the holobiont as a whole is largely unknown, although bacteria and viruses are presumed to play roles in metabolic interactions, immunity, and stress tolerance. In the context of climate change and anthropogenic threats on coral reef ecosystems, the Tara Pacific project aims to provide a baseline of the "-omics" complexity of the coral holobiont and its ecosystem across the Pacific Ocean and for various oceanographically distinct defined areas. Inspired by the previous Tara Oceans expeditions, the Tara Pacific expedition (2016-2018) has applied a pan-ecosystemic approach on coral reefs throughout the Pacific Ocean, drawing an east-west transect from Panama to Papua New Guinea and a south-north transect from Australia to Japan, sampling corals throughout 32 island systems with local replicates. Tara Pacific has developed and applied state-of-the-art technologies in very-high-throughput genetic sequencing and molecular analysis to reveal the entire microbial and chemical diversity as well as functional traits associated with coral holobionts, together with various measures on environmental forcing. This ambitious project aims at revealing a massive amount of novel biodiversity, shedding light on the complex links between genomes, transcriptomes, metabolomes, organisms, and ecosystem functions in coral reefs and providing a reference of the biological state of modern coral reefs in the Anthropocene.
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http://dx.doi.org/10.1371/journal.pbio.3000483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776362PMC
September 2019

Same species, different prerequisites: investigating body condition and foraging success in young reef sharks between an atoll and an island system.

Sci Rep 2019 09 17;9(1):13447. Epub 2019 Sep 17.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, 66860, Perpignan, France.

Acquiring and storing energy is vital to sharks of all age-classes. Viviparous shark embryos receive endogenous maternal energy reserves to sustain the first weeks after birth. Then, in order to maintain body condition, sharks must start foraging. Our goal was to understand whether maternal energy investments vary between blacktip reef sharks (Carcharhinus melanopterus) from two populations and to what extent body condition and the initiation of foraging might be affected by presumably variable maternal investments. A total of 546 young sharks were captured at St. Joseph atoll (Seychelles) and Moorea (French Polynesia) between 2014 and 2018, and indices of body condition and percentage of stomachs containing prey were measured. Maternal investment was found to be site-specific, with significantly larger, heavier, and better conditioned individuals in Moorea. Despite these advantages, as time progressed, Moorea sharks exhibited significant decreases in body condition and were slower to initiate foraging. We suggest that the young sharks' foraging success is independent of the quality of maternal energy resources, and that other factors, such as prey availability, prey quality, and/or anthropogenic stressors are likely responsible for the observed differences across sites. Insights into intraspecific variations in early life-stages may further support site-specific management strategies for young sharks from nearshore habitats.
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http://dx.doi.org/10.1038/s41598-019-49761-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748967PMC
September 2019

Tracking a mass mortality outbreak of pen shell Pinna nobilis populations: A collaborative effort of scientists and citizens.

Sci Rep 2019 09 16;9(1):13355. Epub 2019 Sep 16.

Oceanography and Global Change Department, Mediterranean Institute for Advanced Studies (CSIC-UIB), Esporles, Mallorca, Spain.

A mass mortality event is devastating the populations of the endemic bivalve Pinna nobilis in the Mediterranean Sea from early autumn 2016. A newly described Haplosporidian endoparasite (Haplosporidium pinnae) is the most probable cause of this ecological catastrophe placing one of the largest bivalves of the world on the brink of extinction. As a pivotal step towards Pinna nobilis conservation, this contribution combines scientists and citizens' data to address the fast- and vast-dispersion and prevalence outbreaks of the pathogen. Therefore, the potential role of currents on parasite expansion was addressed by means of drift simulations of virtual particles in a high-resolution regional currents model. A generalized additive model was implemented to test if environmental factors could modulate the infection of Pinna nobilis populations. The results strongly suggest that the parasite has probably dispersed regionally by surface currents, and that the disease expression seems to be closely related to temperatures above 13.5 °C and to a salinity range between 36.5-39.7 psu. The most likely spread of the disease along the Mediterranean basin associated with scattered survival spots and very few survivors (potentially resistant individuals), point to a challenging scenario for conservation of the emblematic Pinna nobilis, which will require fast and strategic management measures and should make use of the essential role citizen science projects can play.
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http://dx.doi.org/10.1038/s41598-019-49808-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6746856PMC
September 2019

Strong genetic isolation of the black-lipped pearl oyster (Pinctada margaritifera) in the Marquesas archipelago (French Polynesia).

Sci Rep 2019 08 6;9(1):11420. Epub 2019 Aug 6.

Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719 Taravao, Tahiti, French Polynesia.

The French Polynesian islands are internationally known for their black pearls, produced by culture of the black lipped pearl oyster Pinctada margaritifera. The ongoing development of hatcheries for P. margaritifera in French Polynesia poses new challenges for the industry, particularly regarding the maintenance of genetic diversity in the hatchery stocks. This emphasizes the necessity to characterize the genetic diversity and differentiation within natural and exploited populations, to carefully select putative parental populations. The present study aimed at validating the phylogenetic status and investigating genetic attributes of populations from the only two non-exploited archipelagos of French Polynesia, the Marquesas archipelago, and the Australes archipelago, never analysed before. We found that individuals from both archipelagos belonged to P. margaritifera species. However, while the Australes population was genetically similar to non-exploited populations of the Tuamotu, the Marquesas populations were highly differentiated from the rest of the populations. This differentiation cannot not be only attributed to geographic distance and aquaculture status, but likely to hydrodynamic barriers allowing vicariant events to take place. Our results add up to other studies describing the Marquesas archipelago as a hotspot for biodiversity and differentiation, with some of the highest levels of endemism and vicariance found among marine species worldwide and provide precious information on available genetic resources for the implementation of P. margaritifera selective breeding and its genetic conservation in French Polynesia.
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http://dx.doi.org/10.1038/s41598-019-47729-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684808PMC
August 2019

Microbiome of the Black-Lipped Pearl Oyster , a Multi-Tissue Description With Functional Profiling.

Front Microbiol 2019 5;10:1548. Epub 2019 Jul 5.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France.

Elucidating the role of prokaryotic symbionts in mediating host physiology has emerged as an important area of research. Since oysters are the world's most heavily cultivated bivalve molluscs, numerous studies have applied molecular techniques to understand the taxonomic and functional diversity of their associated bacteria. Here, we expand on this research by assessing the composition and putative functional profiles of prokaryotic communities from different organs/compartments of the black-lipped pearl oyster , a commercially important shellfish valued for cultured pearl production in the Pacific region. Seven tissues, in addition to mucous secretions, were targeted from individuals: the gill, gonad, byssus gland, haemolymph, mantle, adductor muscle, mucus, and gut. Richness of bacterial Operational Taxonomic Units (OTUs) and phylogenetic diversity differed between host tissues, with mucous layers displaying the highest richness and diversity. This multi-tissues approach permitted the identification of consistent microbial members, together constituting the core microbiome of , including - and , , and . We also found a high representation of symbionts, indicating that they may be of particular importance to oyster health, survival and homeostasis, as in many other coral reef animals. Our study demonstrates that the microbial communities and their associated predicted functional profiles are tissue specific. Inferred physiological functions were supported by current physiological data available for the associated bacterial taxa specific to each tissue. This work provides the first baseline of microbial community composition in , providing a solid foundation for future research into this commercially important species and emphasises the important effects of tissue differentiation in structuring the oyster microbiome.
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http://dx.doi.org/10.3389/fmicb.2019.01548DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6624473PMC
July 2019

A DNA barcode reference library of French Polynesian shore fishes.

Sci Data 2019 07 4;6(1):114. Epub 2019 Jul 4.

PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 58 Avenue Paul Alduy, 66860, Perpignan, France.

The emergence of DNA barcoding and metabarcoding opened new ways to study biological diversity, however, the completion of DNA barcode libraries is fundamental for such approaches to succeed. This dataset is a DNA barcode reference library (fragment of Cytochrome Oxydase I gene) for 2,190 specimens representing at least 540 species of shore fishes collected over 10 years at 154 sites across the four volcanic archipelagos of French Polynesia; the Austral, Gambier, Marquesas and Society Islands, a 5,000,000 km area. At present, 65% of the known shore fish species of these archipelagoes possess a DNA barcode associated with preserved, photographed, tissue sampled and cataloged specimens, and extensive collection locality data. This dataset represents one of the most comprehensive DNA barcoding efforts for a vertebrate fauna to date. Considering the challenges associated with the conservation of coral reef fishes and the difficulties of accurately identifying species using morphological characters, this publicly available library is expected to be helpful for both authorities and academics in various fields.
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http://dx.doi.org/10.1038/s41597-019-0123-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609690PMC
July 2019

Colour plasticity in the shells and pearls of animal graft model Pinctada margaritifera assessed by HSV colour quantification.

Sci Rep 2019 05 17;9(1):7520. Epub 2019 May 17.

IFREMER, UMR 241 Écosystèmes Insulaires Océaniens, Labex Corail, Centre Ifremer du Pacifique, BP 49, 98725, Tahiti, French Polynesia.

The bivalve Pinctada margaritifera has the capacity to produce the most varied and colourful pearls in the world. Colour expression in the inner shell is under combined genetic and environmental control and is correlated with the colour of pearls produced when the same individual is used as a graft donor. One major limitation when studying colour phenotypes is grader subjectivity, which leads to inconsistent colour qualification and quantification. Through the use of HSV (Hue Saturation Value) colour space, we created an R package named 'ImaginR' to characterise inner shell colour variations in P. margaritifera. Using a machine-learning protocol with a training dataset, ImaginR was able to reassign individual oysters and pearls to predefined human-based phenotype categories. We then tested the package on samples obtained in an experiment testing the effects of donor conditioning depth on the colour of the donor inner shell and colour of the pearls harvested from recipients following grafting and 20 months of culture in situ. These analyses successfully detected donor shell colour modifications due to depth-related plasticity and the maintenance of these modifications through to the harvested pearls. Besides its potential interest for standardization in the pearl industry, this new method is relevant to other research projects using biological models.
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http://dx.doi.org/10.1038/s41598-019-43777-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6525208PMC
May 2019

Relationship of the orange tissue morphotype with shell and pearl colouration in the mollusc Pinctada margaritifera.

Sci Rep 2019 03 26;9(1):5114. Epub 2019 Mar 26.

PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Labex Corail, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France.

Molluscs display a vast range of shell colours both between and within species. However, only a few species show colour variation in their soft tissues. In French Polynesia, the pearl oyster Pinctada margaritifera has three tissue morphotypes: the black wild-type and two rare mutations: white albino and orange mantle. Phenotypic transmission is known to occur from these phenotypes when they are used as graft donors for pearl production, leading to multicoloured and white pearls from black and albino mantle grafts, respectively. The present study furthers this knowledge by examining the phenotypic association between the orange mantle tissue morphotype and hard tissues: shells and cultured pearls. Based on a large experimental graft, shell colour quantification and pearl qualification showed that the orange morphotype is associated with light-coloured shells and pearls. Expression analysis of some candidate genes previously identified in the white mantle mutant, tested here on both graft and pearl sac tissues from orange mantle donors, confirmed the involvement of genes associated with shell matrix protein (shem4) and the melanin biosynthesis pathway (zinc). This study provides fundamental information on the mechanism behind mantle tissue colour in P. margaritifera and its association with biomineralisation and pigmentation processes that will be potentially valuable in future selection programs.
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http://dx.doi.org/10.1038/s41598-019-41581-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6435800PMC
March 2019

Within-generation consequences of postsettlement mortality for trait composition in wild populations: An experimental test.

Ecol Evol 2019 Mar 13;9(5):2550-2561. Epub 2019 Feb 13.

Laboratoire d'excellence "CORAIL" USR 3278 CNRS-EPHE-UPVD CRIOBE Perpignan France.

There is a critical need to understand patterns and causes of intraspecific variation in physiological performance in order to predict the distribution and dynamics of wild populations under natural and human-induced environmental change. However, the usual explanation for trait differences, local adaptation, fails to account for the small-scale phenotypic and genetic divergence observed in fishes and other species with dispersive early life stages. We tested the hypothesis that local-scale variation in the strength of selective mortality in early life mediates the trait composition in later life stages. Through in situ experiments, we manipulated exposure to predators in the coral reef damselfish and examined consequences for subsequent growth performance under common garden conditions. Groups of 20 recently settled were outplanted to experimental coral colonies in Moorea lagoon and either exposed to natural predation mortality (52% mortality in three days) or protected from predators with cages for three days. After postsettlement mortality, predator-exposed groups were shorter than predator-protected ones, while groups with lower survival were in better condition, suggesting that predators removed the longer, thinner individuals. Growth of both treatment groups was subsequently compared under common conditions. We did not detect consequences of predator exposure for subsequent growth performance: Growth over the following 37 days was not affected by the prior predator treatment or survival. Genotyping at 10 microsatellite loci did indicate, however, that predator exposure significantly influenced the genetic composition of groups. We conclude that postsettlement mortality did not have carryover effects on the subsequent growth performance of cohorts in this instance, despite evidence for directional selection during the initial mortality phase.
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http://dx.doi.org/10.1002/ece3.4911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6405511PMC
March 2019

Size frequency, dispersal distances and variable growth rates of young sharks in a multi-species aggregation.

J Fish Biol 2019 May 8;94(5):789-797. Epub 2019 Apr 8.

PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.

During a mark-recapture survey from November 2014 until April 2017, 333 neonatal and juvenile blacktip reef sharks Carcharhinus melanopterus and 302 neonatal and juvenile sicklefin lemon sharks Negaprion acutidens were tagged and measured at the uninhabited and isolated St. Joseph Atoll (Republic of Seychelles). Both species demonstrated seasonal reproductive synchronicity and relatively large sizes at birth. Despite the extended times at liberty > 2.5 years, the majority of recaptures were found in close proximity to the initial tagging location (< 500 m). Annual growth rates of C. melanopterus (n = 24) and N. acutidens (n = 62) ranged from 6.6 to 31.7 cm year (mean ± SE; 16.2 ± 1.2 cm year ) and 0.2 to 32.2 cm year (11.8 ± 1 cm year ), respectively and are to date the most variable ever recorded in wild juvenile sharks. High abundances of both species coupled with long-term and repeated recaptures are indicative of a habitat where juveniles can reside for their first years of life. However, large variability in annual growth rates in both species may suggest high intra and interspecific competition induced by a possibly resource limited, isolated habitat.
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http://dx.doi.org/10.1111/jfb.13968DOI Listing
May 2019

Exposure, vulnerability, and resiliency of French Polynesian coral reefs to environmental disturbances.

Sci Rep 2019 01 31;9(1):1027. Epub 2019 Jan 31.

École pratique des hautes études, PSL Research University, UPVD, CNRS, USR 3278 CRIOBE, BP 1013, 98729, Papetoai, Moorea, French Polynesia.

Preserving coral reef resilience is a major challenge in the Anthropocene, yet recent studies demonstrate failures of reef recovery from disturbance, globally. The wide and vigorous outer-reef system of French Polynesia presents a rare opportunity to assess ecosystem resilience to disturbances at a large-scale equivalent to the size of Europe. In this purpose, we analysed long-term data on coral community dynamics and combine the mixed-effects regression framework with a set of functional response models to evaluate coral recovery trajectories. Analyses of 14 years data across 17 reefs allowed estimating impacts of a cyclone, bleaching event and crown-of-thorns starfish outbreak, which generated divergence and asynchrony in coral community trajectory. We evaluated reef resilience by quantifying levels of exposure, degrees of vulnerability, and descriptors of recovery of coral communities in the face of disturbances. Our results show an outstanding rate of coral recovery, with a systematic return to the pre-disturbance state within only 5 to 10 years. Differences in the impacts of disturbances among reefs and in the levels of vulnerability of coral taxa to these events resulted in diverse recovery patterns. The consistent recovery of coral communities, and convergence toward pre-disturbance community structures, reveals that the processes that regulate ecosystem recovery still prevail in French Polynesia.
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http://dx.doi.org/10.1038/s41598-018-38228-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6355954PMC
January 2019