Genetic survey of shallow populations of the Mediterranean red coral [ Corallium rubrum (Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation

International audienceCombined action from over-harvesting and recent mass mortality events potentially linked to ongoing climate changes has led to new concerns for the conservation of shallow populations (5-60 m) of Corallium rubrum, an octocorallian that is mainly found in the Mediterranean Sea. The present study was designed to analyse population structure and relationships at different spatial scales (from 10s of meters to 100s of kilometres) with a focus on dispersal pattern. We also performed the first analysis of the distribution of genetic diversity using a comparative approach between regional-clusters and samples. Forty populations dwelling in four distinct regions between 14 and 60 m in depth were genotyped using 10 microsatellites. Our main results indicate (i) a generalized pair-sample differentiation combined with a weak structure between regional-clusters; (ii) the occurrence of isolation by distance at the global scale, but also within two of the three analysed regional-clusters; (iii) a high level of genetic diversity over the surveyed area with a heterogeneous distribution from regional-cluster to sample levels. The evolutionary consequences of these results are discussed and their management implications are provided

Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes

The study of the interplay between speciation and hybridization is of primary importance in evolutionary biology. Octocorals are ecologically important species whose shallow phylogenetic relationships often remain to be studied. In the Mediterranean Sea, three congeneric octocorals can be observed in sympatry: Eunicella verrucosa, Eunicella cavolini and Eunicella singularis. They display morphological differences and E.singularis hosts photosynthetic Symbiodinium, contrary to the two other species. Two nuclear sequence markers were used to study speciation and gene flow between these species, through network analysis and Approximate Bayesian Computation (ABC). Shared sequences indicated the possibility of hybridization or incomplete lineage sorting. According to ABC, a scenario of gene flow through secondary contact was the best model to explain these results. At the intraspecific level, neither geographical nor ecological isolation corresponded to distinct genetic lineages in E.cavolini. These results are discussed in the light of the potential role of ecology and genetic incompatibilities in the persistence of species limits.French National Research Agency (ANR) program Adacni (ANR) [ANR-12-ADAP-0016]CNRSHubert Curien 'Tassili' program [12MDU853]CCMAR Strategic Plan from Fundacao para a Ciencia e a Tecnologia-FCT [PEst-C/MAR/LA0015/2011,FEDERinfo:eu-repo/semantics/publishedVersio

The Deep‐water corals of Cyprus: Environmental settings and ecological features (CYprus Cold‐corals Levantine SeA, Eastern MEditerraneaN: CYCLAMEN)

The recently started research project CYCLAMEN (CYprus Cold-corals Levantine SeA, Eastern MEditerraneaN), will conduct the first detailed study of cold-water coral communities in eastern Cypriot waters. Cold-water coral habitats have been found during exploratory surveys. The 2-yr long project will include the environmental characterization of the area, as well as the study of the spatial distribution of cold-water coral communities. In addition to the study of the biology of the coral species, genetic and eco-physiological studies will be included. This project is the first of its kind in Cyprus and will additionally have an associated scientific outreach programme in order to bring these ecosystems, still poorly known, to the general public. The project is led by the Spanish Institute of Oceanography (IEO), and relies on the participation of research Institutions in Cyprus: The Cyprus Institute (CyI) and the NGO Enalia Physis Environmental Research Centre (EPERC); France: Aix-Marseille University – Mediterranean Institute for Biodiversity & Ecology (AMU-IMBE); Greece: The Hellenic Centre for Marine Research (HCMR); Mónaco: Centre Scientifique de Monaco (CSM); United Kingdom: National Oceanography Centre (NOC), and Spain: Universitat de Barcelona (UB). Here we present the conceptual frame of the project, the background knowledge and the first obtained results in the oceanographic cruise carried out in summer 2015

Regional and local environmental conditions do not shape the response to warming of a marine habitat-forming species

The differential response of marine populations to climate change remains poorly understood. Here, we combine common garden thermotolerance experiments in aquaria and population genetics to disentangle the factors driving the population response to thermal stress in a temperate habitatforming species: the octocoral Paramuricea clavata. Using eight populations separated from tens of meters to hundreds of kilometers, which were differentially impacted by recent mortality events, we identify 25 degrees C as a critical thermal threshold. After one week of exposure at this temperature, seven of the eight populations were affected by tissue necrosis and after 30 days of exposure at this temperature, the mean % of affected colonies increased gradually from 3 to 97%. We then demonstrate the weak relation between the observed differential phenotypic responses and the local temperature regimes experienced by each population. A significant correlation was observed between these responses and the extent of genetic drift impacting each population. Local adaptation may thus be hindered by genetic drift, which seems to be the main driver of the differential response. Accordingly, conservation measures should promote connectivity and control density erosion in order to limit the impact of genetic drift on marine populations facing climate change

From In Situ to satellite observations of pelagic Sargassum distribution and aggregation in the Tropical North Atlantic Ocean

International audienceThe present study reports on observations carried out in the Tropical North Atlantic in summer and autumn 2017, documenting Sargassum aggregations using both ship-deck observations and satellite sensor observations at three resolutions (MSI-10 m, OLCI-300 m, VIIRS-750 m and MODIS-1 km). Both datasets reported that in summer, Sargassum aggre-gations were mainly observed off Brazil and near the Caribbean Islands, while they accumulated near the African coast in autumn. Based on in situ observations, we propose a five-class typology allowing standardisation of the description of in situ Sargassum raft shapes and sizes. The most commonly observed Sargassum raft type was windrows, but large rafts composed of a quasi-circular patch hundreds of meters wide were also observed. Satellite imagery showed that these rafts formed larger Sargassum aggregations over a wide range of scales, with smaller aggregations (of tens of m 2 area) nested within larger ones (of hundreds of km 2). Match-ups between different satellite sensors and in situ observations were limited for this dataset, mainly because of high cloud cover during the periods of observation. Nevertheless, comparisons between the two datasets showed that satellite sensors successfully detected Sargassum abundance and aggregation patterns consistent with in situ observations. MODIS and VIIRS sensors were better suited to describing the Sargas-sum aggregation distribution and dynamics at Atlantic scale, while the new sensors, OLCI and MSI, proved their ability to detect Sargassum aggregations and to describe their (sub-) mesoscale nested structure. The high variability in raft shape, size, thickness, depth and biomass density observed in situ means that caution is called for when using satellite maps of Sargassum distribution and biomass estimation. Improvements would require additional in situ and airborne observations or very high-resolution satellite imagery

An application of kernel methods to variety identification based on SSR markers genetic fingerprinting

<p>Abstract</p> <p>Background</p> <p>In crop production systems, genetic markers are increasingly used to distinguish individuals within a larger population based on their genetic make-up. Supervised approaches cannot be applied directly to genotyping data due to the specific nature of those data which are neither continuous, nor nominal, nor ordinal but only partially ordered. Therefore, a strategy is needed to encode the polymorphism between samples such that known supervised approaches can be applied. Moreover, finding a minimal set of molecular markers that have optimal ability to discriminate, for example, between given groups of varieties, is important as the genotyping process can be costly in terms of laboratory consumables, labor, and time. This feature selection problem also needs special care due to the specific nature of the data used.</p> <p>Results</p> <p>An approach encoding SSR polymorphisms in a positive definite kernel is presented, which then allows the usage of any kernel supervised method. The polymorphism between the samples is encoded through the Nei-Li genetic distance, which is shown to define a positive definite kernel between the genotyped samples. Additionally, a greedy feature selection algorithm for selecting SSR marker kits is presented to build economical and efficient prediction models for discrimination. The algorithm is a filter method and outperforms other filter methods adapted to this setting. When combined with kernel linear discriminant analysis or kernel principal component analysis followed by linear discriminant analysis, the approach leads to very satisfactory prediction models.</p> <p>Conclusions</p> <p>The main advantage of the approach is to benefit from a flexible way to encode polymorphisms in a kernel and when combined with a feature selection algorithm resulting in a few specific markers, it leads to accurate and economical identification models based on SSR genotyping.</p

A well-kept treasure at depth: precious red coral rediscovered in Atlantic deep coral gardens (SW Portugal) after 300 years

The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years.info:eu-repo/semantics/publishedVersio

Genetic diversity and local connectivity in the mediterranean red gorgonian coral after mass mortality events

Estimating the patterns of connectivity in marine taxa with planktonic dispersive stages is a challenging but crucial task because of its conservation implications. The red gorgonian Paramuricea clavata is a habitat forming species, characterized by short larval dispersal and high reproductive output, but low recruitment. In the recent past, the species was impacted by mass mortality events caused by increased water temperatures in summer. In the present study, we used 9 microsatellites to investigate the genetic structure and connectivity in the highly threatened populations from the Ligurian Sea (NW Mediterranean). No evidence for a recent bottleneck neither decreased genetic diversity in sites impacted by mass mortality events were found. Significant IBD pattern and high global F-ST confirmed low larval dispersal capability in the red gorgonian. The maximum dispersal distance was estimated at 20-60 km. Larval exchange between sites separated by hundreds of meters and between different depths was detected at each site, supporting the hypothesis that deeper subpopulations unaffected by surface warming peaks may provide larvae for shallower ones, enabling recovery after climatically induced mortality events

Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals

This is the final version of the article. Available from Springer Nature via the DOI in this record.Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of thirteen and eight microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland, and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Unsurprisingly, historical patterns of gene flow appeared more complex, though again southwest Britain appeared an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as ‘Vulnerable’, and for the designation and management of European MPAs.We thank Natural England (project No. RP0286, contract No. SAE 03-02-146), the NERC (grant No. NE/L002434/1) and the University of Exeter for funding this research. Additional funding for sample collection, travel and microsatellite development was provided by the EU Framework 7 ASSEMBLE programme, agreement no. 227799, and NERC grant No. NBAF-362

Atlantic-Mediterranean and within-Mediterranean molecular variation in Coris julis (L. 1758) (Teleostei, Labridae)

Sequence variation in the mitochondrial control region was studied in the Mediterranean rainbow wrasse (Coris julis), a species with pronounced pelagic larval phase inhabiting the Mediterranean Sea and the adjacent coastal eastern Atlantic Ocean. A total of 309 specimens from 19 sampling sites were analysed with the aim of elucidating patterns of molecular variation between the Atlantic and the Mediterranean as well as within the Mediterranean Sea. Phylogeographic analyses revealed a pronounced structuring into a Mediterranean and an Atlantic group. Samples from a site at the Moroccan Mediterranean coast in the Alboran Sea showed intermediate frequencies of “Mediterranean” and “Atlantic” haplotypes. We recognised a departure from molecular neutrality and a star-like genealogy for samples from the Mediterranean Sea, which we propose to have happened due to a recent demographic expansion. The results are discussed in the light of previous studies on molecular variation in fish species between the Atlantic and the Mediterranean and within the Mediterranean