Molecular forensics in the precious Mediterranean red coral, Corallium rubrum: testing DNA extraction and microsatellite genotyping using dried colonies

6 pages, 1 figure, 1 tableCorallium rubrum is an overharvested precious coral submitted to strong environmental pressures. The development of new management tools such as assignment tests is crucial to assess the origin of traded colonies and to reinforce existing regulations in order to ultimately reduce poaching. As a starting point, we test the feasibility of DNA extractions and PCR amplifications of ten microsatellites using dried tissues such as those that can be obtained from traded or seized colonies. We genotype the same ten colonies conserved in alcohol and after five drying periods (from 7 days to 8 months) as well as ten dried colonies coming from a seizure conducted in 2009. Estimating the rate of negative PCRs through time, PCR repeatability and frequencies of null alleles, we demonstrate that dried colonies can be successfully genotyped. This study opens new avenues for the conservation of C. rubrum and other precious coralsThis study was funded by the ‘‘Provence–Alpes– Côte d’Azur’’ region (J.-B. Ledoux Doctoral Fellowship) and by the IFB Foundation (Institut Français de la Biodiversite´), the environmental department of TOTAL-FINA-ELF group, an ‘Action Concertée Initiative’ (ACI) program ‘Jeunes chercheurs 2003’ (number JC5360) from the French research Ministry and the MEDCHANGE project funded by the Agence Nationale pour la Recherche (ANR). We thank the associate editor Dr. Michael Kruetzen and one anonymous reviewer for useful comments. During writing process, J-B. Ledoux was supported by a post-doctoral grant SFRH/BPD/74400/2010 from Fundação para a Ciência e Tecnologia (FCT). Genotyping was conducted at the Plateforme Génome Transcriptome de Pierroton in Bordeaux (France; http://www4.bordeaux-aquitaine.inra.fr/pgtb)Peer reviewe

Phylogeography of the red coral (Corallium rubrum): inferences on the evolutionary history of a temperate gorgonian

15 pages, 4 figures, 4 tablesThe red coral Corallium rubrum (Cnidaria, Octocorallia) is an exploited, long-lived sessile species from the Mediterranean Sea and the adjacent coastline in the Atlantic Ocean. Surveys of genetic variation using microsatellites have shown that populations of C. rubrum are characterized by strong differentiation at the local scale but a study of the phylogeography of this species was still lacking. Here, we used seven polymorphic microsatellite loci, together with sequence data from an intron of the elongation factor 1 (EF1) gene, to investigate the genetic structure of C. rubrum across its geographical range in the western Mediterranean Sea and in the Adriatic Sea. The EF1 sequences were also used to analyse the consequences of demographic fluctuations linked with past environmental change. Clustering analysis with microsatellite loci highlighted three to seven genetic groups with the distinction of North African and Adriatic populations; this distinction appeared significant with AMOVA and differentiation tests. Microsatellite and EF1 data extended the isolation by distance pattern previously observed for this species at the western Mediterranean scale. EF1 sequences confirmed the genetic differentiation observed between most samples with microsatellites. A statistical parsimony network of EF1 haplotypes provided no evidence of high sequence divergence among regions, suggesting no long-term isolation. Selective neutrality tests on microsatellites and EF1 were not significant but should be interpreted with caution in the case of EF1 because of the low sample sizes for this locus. Our results suggest that recent Quaternary environmental fluctuations had a limited impact on the genetic structure of C. rubrumThis work was funded by the French ANR (National Research Agency) in the Medchange program (www.medchange.org). This was also part of the EPIC project in the European Union Network of Excellence Marine Genomics. Some samples were obtained through the GBIRM project in the European Union Network of Excellence MARBEF. J.-B.L’s PhD was funded by the Région Provence Alpes Côte d’AzurPeer reviewe

Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum

13 pages, 3 figures, 3 tablesIdentifying microevolutionary processes acting in populations of marine species with larval dispersal is a challenging but crucial task because of its conservation implications. In this context, recent improvements in the study of spatial genetic structure (SGS) are particularly promising because they allow accurate insights into the demographic and evolutionary processes at stake. Using an exhaustive sampling and a combination of image processing and population genetics, we highlighted significant SGS between colonies of Corallium rubrum over an area of half a square metre, which sheds light on a number of aspects of its population biology. Based on this SGS, we found the mean dispersal range within sites to be between 22.6 and 32.1 cm, suggesting that the surveyed area approximately corresponded to a breeding unit. We then conducted a kinship analysis, which revealed a complex half-sib family structure and allowed us to quantify the level of self-recruitment and to characterize aspects of the mating system of this species. Furthermore, significant temporal variations in allele frequencies were observed, suggesting low genetic drift. These results have important conservation implications for the red coral and further our understanding of the microevolutionary processes acting within populations of sessile marine species with a larval phaseThis study was funded by the ‘‘Provence–Alpes–Coˆ te d’Azur’’ region (J-B. Ledoux Doctoral Fellowship) and by the IFB Foundation (Institut Franc¸ais de la Biodiversite´), the environmental department of TOTAL-FINA-ELF group, an ‘Action Concerte´e Initiative’ (ACI) program ‘Jeunes chercheurs 2003¢ (number JC5360) from the French Research Ministry and the MEDCHANGE project funded by the Agence Nationale pour la Recherche (ANR)Peer Reviewe

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

16 pages, 3 figures, 4 tables, supporting Iinformation http://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2009.04516.x/suppinfoCombined 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 providedThis study was funded by the ‘Provence–Alpes– Côte d’Azur’ region (J-B Ledoux Doctoral Fellowship) and by the IFB Foundation (Institut Français de la Biodiversité), the environmental department of TOTAL-FINA-ELF group, an ‘Action Concertée Initiative’ (ACI) program ‘Jeunes chercheurs 2003’ (number JC5360) from the French Research Ministry and the MEDCHANGE project funded by the Agence Nationale pour la Recherche (ANR). It is also a contribution to the responsive mode project GBIRM (European Network of Excellence MARBEF)Peer Reviewe

From global to local genetic structuring in the red gorgonian Paramuricea clavata: the interplay between oceanographic conditions and limited larval dispersal

15 pages, 3 figures, 4 tablesDefining the scale of connectivity among marine populations and identifying the barriers to gene flow are tasks of fundamental importance for understanding the genetic structure of populations and for the design of marine reserves. Here, we investigated the population genetic structure at three spatial scales of the red gorgonian Paramuricea clavata (Cnidaria, Octocorallia), a key species dwelling in the coralligenous assemblages of the Mediterranean Sea. Colonies of P. clavata were collected from 39 locations across the Mediterranean Sea from Morocco to Turkey and analysed using microsatellite loci. Within three regions (Medes, Marseille and North Corsica), sampling was obtained from multiple locations and at different depths. Three different approaches (measures of genetic differentiation, Bayesian clustering and spatially explicit maximum-difference algorithm) were used to determine the pattern of genetic structure. We identified genetic breaks in the spatial distribution of genetic diversity, which were concordant with oceanographic conditions in the Mediterranean Sea. We revealed a high level of genetic differentiation among populations and a pattern of isolation by distance across the studied area and within the three regions, underlining short effective larval dispersal in this species. We observed genetic differentiation among populations in the same locality dwelling at different depths, which may be explained by local oceanographic conditions and which may allow a process of local adaptation of the populations to their environment. We discuss the implications of our results for the conservation of the species, which is exposed to various threatsK.M.J.’s PhD was funded by the French Ministe`re de l’Enseignement Supe´rieur et de la Recherche. This research was partly supported by the MEDCHANGE project funded by the Agence Nationale pour la Recherche and research grants CGL2007-66757-C02-01 from the MECPeer reviewe

Fine-scale spatial genetic structure in the brooding sea urchin Abatus cordatus suggests vulnerability of the Southern Ocean marine invertebrates facing global change

13 pages, 2 figures, 3 tablesThe Southern Ocean benthic communities are characterized by their levels of endemism and their diversity of invertebrate brooding species. Overall, biological processes acting within these species remain poorly understood despite their importance to understand impacts of ongoing global change. We take part in filling this gap by studying the genetic structure over different spatial scales (from centimeters to tens of kilometers) in Abatus cordatus, an endemic and brooding sea urchin from the Kerguelen Islands. We developed three microsatellites and two exon-primed intron crossing markers and conducted a two-scale sampling scheme (from individuals to patches) within two dense localities of Abatus cordatus. Between patches, all pairwise comparisons, covering distances from few meters (between patches within locality) to 25 km (between localities), revealed significant genetic differentiation, a higher proportion of the molecular variance being explained by the comparisons between localities than within localities, in agreement with an isolation by distance model. Within patches, we found no significant correlation between individual pairwise spatial and genetic distances, except for the most polymorphic locus in the patch where the largest range of geographical distances had been analyzed. This study provides an estimation of the dispersal capacities of Abatus cordatus and highlights its low recolonization ability. Similar low recolonization capacities are thus expected in other Antarctic and Subantarctic brooding invertebrate species and suggest a high vulnerability of these species facing global changeDevelopment of EPIC markers, corresponding salaries, and genotyping was possible owing to two European networks of excellence, NoE MARBEF (GOCE-CT-2003-505446) and NoE Marine Genomics Europe (GOCE-CT-2004-505403) and a French ANR Antflock. Logistic and collection of Abatus cordatus were supported by the program Macrobenthos no 195 of the French Polar Institute (IPEV), and thanks to Thomas Abiven for help in samples collection and management in fieldworkPeer reviewe

Describing the Bay of Biscay's continental shelf food-web using an OSPAR common indicator: the Mean Trophic Level indicator.

The current development of biodiversity indicators adopted as common in the North East Atlantic (Under OSPAR Regional Sea Convention) is missing some elements necessary for their application as food-web indicators. The Mean Trophic Level (MTL) indicator is based on species biomass and their trophic level (TL). These metrics are commonly used in the food-web holistic approach of interactions in an ecosystem. Species TL, giving the position of an organism in the food web, is influenced by spatiotemporal variability and ontogeny of species. MTL is also shaped by the species biomasses and their data source (i.e. landings or survey data). The aim of the present study was to propose a methodology (1) considering a better regionalisation of the indicator (i.e. using local TL estimations and ecosystem survey data), (2) looking at the MTL sensitivity regarding ecosystem species and compartments and (3) discussing the food web approach of the indicator. Different scenarios were thus tested on MTL indicator with EVHOE survey data (i) using various data sources of TL and (ii) applying several cut-offs to focus on different compartments in the ecosystem. Species influence on each scenario was also investigated. Two species were found to be highly influencing the MTL indicator trend. Capros aper, a low TL species catching the bottom up effect in the food-web, was strongly acting on MTL when considering all species in the ecosystem. Meanwhile, Merluccius merluccius was driving the indicator when low trophic level species were cut-off. This high predator reflected more the top down effect on the ecosystem. This work concluded the need to assess the MTL indicator using three TL cut-offs (TL= 2, 3.25 and 4) to capture a holistic view of changes in the ecosystem. Furthermore, scientific surveys and local estimations of TL are crucial in order to reduce uncertainty around the MTL estimation

Food web indicators under the Marine Strategy Framework Directive: From complexity to simplicity?

International audienceThe Marine Strategy Framework Directive (MSFD) requires that European Union Member States achieve "Good Environmental Status" (GES) in respect of 11 Descriptors of the marine environment by 2020. Of those, Descriptor 4, which focuses on marine food webs, is perhaps the most challenging to implement since the identification of simple indicators able to assess the health of highly dynamic and complex interactions is difficult. Here, we present the proposed food web criteria/indicators and analyse their theoretical background and applicability in order to highlight both the current knowledge gaps and the difficulties associated with the assessment of GES. We conclude that the existing suite of indicators gives variable focus to the three important food web properties: structure, functioning and dynamics, and more emphasis should be given to the latter two and the general principles that relate these three properties. The development of food web indicators should be directed towards more integrative and process-based indicators with an emphasis on their responsiveness to multiple anthropogenic pressures. © 2013 Elsevier Ltd