The Diversity of Coral Reefs: What Are We Missing?

Tropical reefs shelter one quarter to one third of all marine species but one third of the coral species that construct reefs are now at risk of extinction. Because traditional methods for assessing reef diversity are extremely time consuming, taxonomic expertise for many groups is lacking, and marine organisms are thought to be less vulnerable to extinction, most discussions of reef conservation focus on maintenance of ecosystem services rather than biodiversity loss. In this study involving the three major oceans with reef growth, we provide new biodiversity estimates based on quantitative sampling and DNA barcoding. We focus on crustaceans, which are the second most diverse group of marine metazoans. We show exceptionally high numbers of crustacean species associated with coral reefs relative to sampling effort (525 species from a combined, globally distributed sample area of 6.3 m2). The high prevalence of rare species (38% encountered only once), the low level of spatial overlap (81% found in only one locality) and the biogeographic patterns of diversity detected (Indo-West Pacific>Central Pacific>Caribbean) are consistent with results from traditional survey methods, making this approach a reliable and efficient method for assessing and monitoring biodiversity. The finding of such large numbers of species in a small total area suggests that coral reef diversity is seriously under-detected using traditional survey methods, and by implication, underestimated

Neutralising Antibodies against Ricin Toxin

The Centers for Disease Control and Prevention have listed the potential bioweapon ricin as a Category B Agent. Ricin is a so-called A/B toxin produced by plants and is one of the deadliest molecules known. It is easy to prepare and no curative treatment is available. An immunotherapeutic approach could be of interest to attenuate or neutralise the effects of the toxin. We sought to characterise neutralising monoclonal antibodies against ricin and to develop an effective therapy. For this purpose, mouse monoclonal antibodies (mAbs) were produced against the two chains of ricin toxin (RTA and RTB). Seven mAbs were selected for their capacity to neutralise the cytotoxic effects of ricin in vitro. Three of these, two anti-RTB (RB34 and RB37) and one anti-RTA (RA36), when used in combination improved neutralising capacity in vitro with an IC50 of 31 ng/ml. Passive administration of association of these three mixed mAbs (4.7 µg) protected mice from intranasal challenges with ricin (5 LD50). Among those three antibodies, anti-RTB antibodies protected mice more efficiently than the anti-RTA antibody. The combination of the three antibodies protected mice up to 7.5 hours after ricin challenge. The strong in vivo neutralising capacity of this three mAbs combination makes it potentially useful for immunotherapeutic purposes in the case of ricin poisoning or possibly for prevention

Are well-studied marine biodiversity hotspots still blackspots for animal barcoding?

Marine biodiversity underpins ecosystem health and societal well-being. Preservation of biodiversity hotspots is a global challenge. Molecular tools, like DNA barcoding and metabarcoding, hold great potential for biodiversity monitoring, possibly outperforming more traditional taxonomic methods. However, metabarcoding-based biodiversity assessments are limited by the availability of sequences in barcoding reference databases; a lack thereof results in high percentages of unassigned sequences. In this study we (i) present the current status of known vs. barcoded marine species at a global scale based on online taxonomic and genetic databases; and (ii) compare the current status with data from ten years ago. Then we analyzed occurrence data of marine animal species from five Large Marine Ecosystems (LMEs) classified as biodiversity hotspots, to identify any consistent disparities in COI barcoding coverage between geographic regions and at phylum level. Barcoding coverage varied among LMEs (from 36.8% to 62.4% COI-barcoded species) and phyla (from 4.8% to 74.7% COI-barcoded species), with Porifera, Bryozoa and Platyhelminthes being highly underrepresented, compared to Chordata, Arthropoda and Mollusca. We demonstrate that although barcoded marine species increased from 9.5% to 14.2% since the last assessment in 2011, about 15,000 (corresponding to 7.8% increase) new species were described from 2011 to 2021. The next ten years will thus be crucial to enroll concrete collaborative measures and long term initiatives (e.g., Horizon 2030, Ocean Decade) to populate barcoding libraries for the marine realm.the Department of Biological, Geological and Environmental Sciences (BiGeA) of the University of Bologna (UniBo). The CoMBoMed initiative was supported by the European Marine Research Network (EUROMARINE Network), the Inter-Departmental Research Centre for Environmental Sciences (CIRSA – UniBo), the Cultural Heritage Department (DBC - UniBo, https://beniculturali.unibo.it/it), the Fondazione Flaminia and the ERANet Mar-Tera Project SEAMoBB (Solutions for sEmi-Automated Monitoring of Benthic Biodiversity).Peer reviewe

Diversité des parasites en milieu marin fragmenté (Taxonomie, phylogénie et biogéographie des monogènes de poissons-papillons de l'Océan Indo-Pacifique)

LA DIVERSITE DES MONOGENES DE POISSONS-PAPILLONS DANS SIX ILES DE L'OCEAN INDO-PACIFIQUE A ETE ETUDIEE AVEC TROIS APPROCHES DIFFERENTES. L'ETUDE TAXONOMIQUE A PERMIS D'IDENTIFIER ONZE ESPECES APPARTENANT AUX ANCYROCEPHALINAE (DACTYLOGYRIDAE) DONT 5 NOUVELLES. SUR LA BASE DE CARACTERES MORPHOLOGIQUES , LES ONZE ESPECES ONT ETE PLACEES DANS 3 GENRES: HALIOTREMA JOHNSTON ET TIEGS, 1922, EURYHALIOTREMATOIDES GEN. N. ET ALIATREMA GEN. N. DANS 4 ETUDES DE PHYLOGENIE MOLECULAIRE , NOUS AVONS MIS EN EVIDENCE : QUE ANCYROCEPHALINAE EST UN TAXON POLYPHYLETIQUE (ETUDE 1); QUE LES PARASITES DE POISSONS-PAPILLONS NE FORMENT PAS UN TAXON MONOPHYLETIQUE ET APPARTIENNENT A 2 CLADES SEPARES SUGGERANT DEUX ORIGINES INDEPENDANTES DU GROUPE DES MONOGENES SUR LES POISSONS (ETUDE 2); QUE LES GENRES DETERMINES SUR UNE BASE MORPHOLOGIQUE SONT MONOPHYLETIQUES ET QUE ALIATREMA ET EURYHALIOTREMATOIDES FORMENT UN CLADE (ETUDE 3); LA PRESENCE POSSIBLE DE PLUSIEURS ESPECES CRYPTIQUES PAR UNE PHYLOGENIE INTER ET INTRASPECIFIQUE (ETUDE 4). LA PHYLOGEOGRAPHIE DE DEUX ESPECES, EURYHALIOTREMATOIDES GRANDIS ET HALIOTREMA AURIGAE, A ETE ETUDIEE PAR L'ANALYSE INTRASPECIFIQUE DU COI. L'ESPECE H. AURIGAE NE MONTRE PAS DE STRUCTURATION GENETIQUE ALORS QUE E. GRANDIS MONTRE UNE TRES FORTE STRUCTURATION POPULATIONNELLE LIEE A LA LOCALITE ET MOOREA SERAIT LE CENTRE D'ORIGINE DE CETTE DERNIERE. CETTE HYPOTHESE EST CONFORTEE PAR LA PRESENCE DE LA SEULE ESPECE ENDEMIQUE E. BERENGUELAE DANS CETTE LOCALITE. LES MONOGENES DE POISSONS-PAPILLONS AURAIENT UN FAIBLE GRADIENT DE DIVERSITE ALLANT DE L'OUEST VERS L'EST, NE SUIVANT PAS LE GRADIENT EST-OUEST DE LEURS HOTES TYPIQUE DES ORGANISMES DE L'OCEAN INDO-PACIFIQUE OUEST.THE DIVERSITY OF MONOGENEANS OF BUTTERFLYFISHES WAS STUDIED FROM 6 INDO-WEST PACIFIC ISLANDS USING 3 DIFFERENT APPROACHES. IN THE TAXONOMIC STUDY, WE IDENTIFIED 11 SPECIES BELONGING TO THE ANCYROCEPHALINAE (DACTYLOGYRIDAE) INCLUDING 5 SPECIES NEW TO SCIENCE. ON THE BASIS OF MORPHOLOGICAL CHARACTERS, THE 11 SPECIES REPRESENTED 3 GENREA: HALIOTREMA JOHNSTON ET TIEGS, 1922, EURYHALIOTREMATOIDES N. GEN. AND ALIATREMA N. GEN. IN 4 SEPARATE MOLECULAR PHYLOGENETIC STUDIES, WE SHOWED THAT 1) THE ANCYROCEPHALIANE IS A POLYPHYLETIC TAXON, 2) BUTTERFLYFISHES MONOGENEAN PARASITES DO NOT FORM A MONOPHYLETIC GROUP, BUT INSTEAD BELONG TO 2 SEPARATED CLADES SUGGESTING INDEPENDANT COLONIZATION EVENTS, 3) THE GENERA DEFINED ON A MORPHOLOGICAL BASIS ARE EACH MONOPHYLETIC AND ALIATREMA AND EURYHALIOTREMATOIDES ARE SISTER TAXA, 4) RESULTS OF INTER- AND INTRASPECIFIC PHYLOGENETIC STUDY SUGGESTS THE PRESENCE OF CRYPTIC SPECIES. IN ADDITION, THE PHYLOGEOGRAPHY OF EURYHALIOTREMATOIDES GRANDIS AND HALIOTREMA AURIGAE WAS STUDIED BASED ON SEQUENCES OF COI. THE POPULATION STRUCTURE OF H. AURIGAE WAS NOT FOUND TO BE CORRELATED WITH LOCATION WHEREAS THOSE OF E. GRANDIS FORMED HIGLY STRUCTURED POPULATIONS LINKED WITH THEIR LOCALITIES, INDICATING MORREA AS THE CENTER OF ORIGIN. THIS HYPOTHESIS IS SUPPORTED BY THE PRESENCE OF THE ONLY ENDEMIC SPECIES E. BERENGUELAE IN THIS LOCALITY. BUTTERFLYFISHES MONOGENEANS SHOW A WEAK DIVERSITY GRADIENT FROM WEST TO EAST, WHEREAS THEIR HOST SHOW A EAST TO WEST GRADIENT TYPICAL OF INDO-WEST PACIFIC MARINE ORGANISMS.PERPIGNAN-BU Sciences (661362101) / SudocSudocFranceF

GenBank accession links of the invertebrates collected from Autonomous Reef Monitoring Structures (ARMS) from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea in 2014

Dataset: Invertebrate Barcodes from Papua New GuineaThis dataset contains GenBank accession links of the invertebrates collected in April and November of 2014 from Autonomous Reef Monitoring Structures (ARMS) on the acidification gradient from shallow fringing reefs near Dobu and Upa Upasina, Milne Bay Province, Papua New Guinea. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/874478NSF Division of Ocean Sciences (NSF OCE) OCE-155886

Colonization of Pacific islands by parasites of low dispersal ability: phylogeography of two monogenean species parasitizing butterflyfishes in the South Pacific Ocean

International audienceAim To investigate the phylogeographical patterns of two poorly dispersing but widely distributed monogenean species, Haliotrema aurigae and Euryhaliotrematoides grandis, gill parasites of coral reef fishes from the family Chaetodontidae. Location South Pacific Ocean (SPO). Methods Sequence data from the mitochondrial cytochrome oxidase subunit I (COI) gene were obtained from samples from five localities of the SPO (Heron Island, Lizard Island, Moorea, Palau and Wallis) for the two parasite species. Phylogenetic and genetic diversity analyses were used to reconstruct phylogeographical patterns, and dates of cladogenetic events were estimated. Results Overall, 50 individuals of 17 Haliotrema aurigae and 33 of Euryhaliotrematoides grandis were sequenced from five localities of the SPO for COI mtDNA (798 bp). Our results revealed a deep phylogeographical structure in the species Euryhaliotrematoides grandis. The molecular divergence between individuals from Moorea and individuals from the remaining localities (7.7%) may be related to Pleistocene sea-level fluctuations. In contrast, Haliotrema aurigae shows no phylogeographical patterns with the presence of most of the mitochondrial haplotypes in every locality sampled. Main conclusions Our study shows contrasting phylogeographical patterns of the two monogenean parasite species studied, despite many shared characteristics. Both parasites are found on the same host family, share the same geographical range and ecology, and are phylogenetically close. We propose two hypotheses that may help explain the diparity: the hypotheses involve differences in the evolutionary age of the parasite species and their dispersal capabilities. Additionally, the lack of phylogeographical structure in Haliotrema aurigae contrasts with its apparently restricted dispersion, which is likely to occur during the egg stage of the life cycle, inducing a passive dispersal mechanism in butterflyfish monogeneans

Using DNA Barcoding and Standardized Sampling to Compare Geographic and Habitat Differentiation of Crustaceans: A Hawaiian Islands Example

Recently, the Census of Marine Life has explored methods to assess coral reef diversity by combining standardized sampling (to permit comparison across sites) with molecular techniques (to make rapid counts of species possible). To date, this approach has been applied across geographically broad scales (seven sites spanning the Indian, Pacific and Atlantic Oceans), focusing on similar habitats at all sites (10–12 m forereef). Here we examine crustacean spatial diversity patterns for a single atoll, comparing results for four sites (comprising forereef, backreef, and lagoon habitats) at French Frigate Shoals (FFS), Northwestern Hawaiian Islands, Hawaii, USA, within the Papahanaumokuakea Marine National Monument. The Bray-Curtis index of similarity across these habitats at FFS was the same or greater than the similarity between similar habitats on Heron Island and Lizard Island in the Great Barrier Reef and much greater than similarity between more widely separated localities in the Indo-Pacific Ocean (e.g., Ningaloo, Moorea, French Polynesia or the Line Islands). These results imply that, at least for shallow reefs, sampling multiple locations versus sampling multiple habitats within a site maximizes the rate at which we can converge on the best global estimate of coral reef biodiversity

Sampling details and diversity results for each site and sites combined.

<p>Presented are numbers of sampling units [dead coral heads or settlement devices (ARMS, see Methods)]; estimated total planar area sampled for each locality; the numbers of DNA sequences analyzed; the numbers of taxa (OTUs) for all crustaceans, all decapods, and brachyuran crabs; the numbers of crustacean singletons (see text) (percentages in parenthesis); and for crustaceans the ACE (Abundance-based Coverage Estimator) and Chao1 estimated diversity values [based both on all samples and just six samples per site (in parentheses, to eliminate biases caused by unequal sample numbers)]. The “IWP” and “CP” columns show the results for the localities of the Indo-West Pacific combined (Ningaloo, Lizard Island and Heron Island) and the Central Pacific combined [Moorea, Northern Line Islands and French Frigate Shoals (FFS), Hawaii] respectively.</p

Bray-Curtis similarity indices for all pairwise comparisons between localities.

<p>FFS corresponds to French Frigate Shoals, Hawaii. The values were obtained by pooling all samples at each site and calculating the between site Bray-Curtis Index value, yielding one value for each pairwise by site comparison.</p

Mapping tropical forest trees across large areas with lightweight cost-effective terrestrial laser scanning

Key message We used lightweight terrestrial laser scanning (TLS) to detect over 3000 stems per hectare across a 12-ha permanent forest plot in French Guiana, 81% of them = 10 cm DBH previously censused in the plot, 85% were identified by TLS. Automatic DBH estimation from TLS data had an RMSE of 6 cm. RMSE was improved to 3 cm by a manual verification of the shape and quality of the stem points. The initial census map had substantial bias in tree geolocation with a maximum value around 6 m. Conclusion Lightweight TLS technology is a promising tool for the estimation of stem tapering and volume. Here, we show that it also facilitates the establishment of large tropical forest inventories, by improving the positioning of trees, thus increasing the accuracy of forest inventories and their cost-effectiveness