Phylogénie, phylogéographie, mode de reproduction et structure démographique dans le complexe d'espèces de l'ophiure hermaphrodite incubante Amphipholis squamata

La découverte de nouvelles espèces cryptiques est un enjeu considérable pour l étude de la biodiversité. Les complexes d espèces représentent d excellentes opportunités pour comprendre et étudier les processus de spéciation. A. squamata est une ophiure (phylum des échinodermes) qui forme un complexe d espèces composé de lignées très divergentes. L organisme a une distribution cosmopolite, ce qui représente un paradoxe car il ne possède pas de phase larvaire dispersive : il incube en effet sa progéniture jusqu au stade juvénile. Une approche multidisciplinaire a été nécessaire afin d appréhender le fonctionnement général du complexe d espèces A. squamata. Tout d abord l étude phylogénétique a permis de révéler la monophylie du complexe d espèces, ainsi que son ancienneté (estimation : > 20 Ma). Une étude morphologique a révélé une absence de différenciation entre les lignées du complexe. Les causes possibles de cette stase morphologique sont discutées. Ensuite, l approche phylogéographique a permis d identifier l existence de certaines lignées à large distribution tropicale (E) ou antitropicale (A et B) et d autres lignées restreintes à une échelle locale ou régionale (AIV, AV, AMaine). L étude des flux de gènes sur l ensemble de l aire de répartition a montré que ces flux sont rares entre les bassins océanographiques (monophylie réciproque) et qu à des échelles plus régionales ils sont fortement contraints par la courantologie. Toutefois, certains haplotypes sont retrouvés dans des localités distantes de plusieurs milliers de km. Une autre approche basée sur l étude conjointe de marqueurs mitochondriaux et de marqueurs nucléaires a révélé une absence de croisement entre les lignées présentes en Méditerranée nord occidentale, ce qui suggère qu elles peuvent être considérées comme des espèces au sens biologique du terme. Ensuite, l étude de la reproduction de ces espèces à partir de l analyse du taux d autofécondation (FIS) et l analyse parent/progéniture a révélé que l autofécondation était le mode de reproduction principal. Le suivi démographique temporel sur deux ans dans un site proche de Marseille (Les Goudes) n a pas permis de révéler de différences dans les traits d histoire de vie de ces espèces (taille, mortalité, fécondité, saison de reproduction). Enfin, toutes ces caractéristiques sont confrontées afin de proposer un fonctionnement global du complexe d espèces tant d un point de vue évolutif que démographique sur l ensemble de son aire de répartitionThe discovery of cryptic species is a challenge for the assessment of biodiversity. The species complexes are a great opportunity to study and understand the process of speciation. A. squamata is a small brittle star (Echinodermata) forming a species complex made of very divergent lineages. This organism is found worldwide which is paradoxal since it lacks a dispersive larval phase: it broods it offspring until a crawl away stage. A multidisciplinary approach has been necessary to better understand the general functioning of the species complex A. squamata. Firstly, the phylogenetic study revealed the monophyly of the complex and its antiquity. The morphological study revealed a lack of differentiation even between the most divergent lineages. The possible causes of the morphological stasis are discussed. The phylogeographic approach revealed both the existence of worldwide tropical (E) and antitropical (A and B) lineages and other locally or regionally restricted lineages (AVI, AV, AMaine). This study of the gene flow across the entire distribution area revealed that the flow are scarce between the oceanographical basins and that, at a regional scale, they are constrained by the currents. Some haplotypes are shared across thousands of km. The study of both mitochondrial and nuclear markers revealed a lack of crossing between lineages of the North western Mediterranean Sea, which makes of them valid biological species following Mayr s concept. The study of their reproduction showed that selfing is the main mode of reproduction. A temporal survey revealed that the different species do not display conspicuous differences in their life history traits. Finally, considering all these characteristics, we propose a global functioning of the species complex across its entire distribution area.AIX-MARSEILLE2-BU Sci.Luminy (130552106) / SudocSudocFranceF

CIGESMED: Coralligenous based indicators to evaluate and monitor the "good environmental statut" of the Mediterranean coastal waters, a SeasEra project

International audienceCoralligenous is one the main shallow Mediterranean milieu generating structural complexity and biodiversity. It produces goods and services for several sectors. Pollution, anchors and trawling may cause its degradation, whilst traditional fishing as well as angling mainly affect target species. Diver frequentation is another cause of degradation. Coralligenous may also be susceptible to invasive alien species. These habitats, which are of great ecological, socioeconomic and patrimonial importance, are also under the pressures caused by the global warming. CIGESMED's (2013-2016) goal is to understand the links and consequences of natural and anthropogenic pressures to the functioning of these habitats and to define and maintain their Good Environmental Status (GES) in the Mediterranean Sea. Indexes, specific to coralligenous habitat, will be co-constructed and collectively tested by scientists, marine natural parks and reserves, through the implementation of a " citizen science " network. Among other methods, trees of knowledge will be experimented as tools to sort, organize and illustrate very large heterogeneous sets of data. CIGESMED outcome will be an integrative assessment of the GES within the Marine Strategy Framework Directive. CIGESMED gathers scientists from France, Greece and Turkey, making it possible to access to sites and to work on the same issues in both the northwestern Mediterranean basin and the Aegean-Levantine one. Ten trained (scientific diving and ROV) laboratories of marine ecology are involved. A Committee of External Advisors (scientists, stakeholders and policy-makers), meeting at an annual basis, and aiming at providing advice on all aspects of the execution of the project is helping the scientific steering committee and is ensuring CIGESMED to meet its objectives

CIGESMED’s protocol and network (Coralligenous based Indicators to evaluate and monitor the “Good Environmental Status” of Mediterranean coastal waters)

International audienceCoralligenous habitats are part of the most important Mediterranean marine ecosystems in terms of complexity and biodiversity. They provide protection, feeding and reproduction areas for more than 1600 species. This biodiversity is essential for economic activities such as fishing and scuba diving. The European program CIGESMED (ERA-NET funding), involving France, Greece and Turkey, investigates the “Good Environmental Status” of these habitats in the framework of the MFSD (Marine Strategy Framework Directive). One major objective of CIGESMED is to propose an operational, long-term, large-scale protocol to monitor coralligenous habitats in the Mediterranean Sea.This protocol is currently tested in French sites: the effects of (sampling) methods, materials and operators are studied in order to evaluate the influence of protocol implementation, and to find the easiest and most reliable procedure that could be implemented by and for a large public, also consisting of non-scientists, and would provide workable data for longterm monitoring. This protocol is based on photo-quadrats observations. The analyses are done on occurrences, relative abundances, species associations and species’ favourite environmental profile. In parallel, complementary protocols are implemented: one concerns the cartography of coralligenous habitats, and two are about population genetics of significant habitat-forming species Myriapora truncata (Pallas, 1766) and Lithophyllum cabiochiae ((Areschoug) Hauck, 1877)). All the data and results are organized as a non-centralized information system, with configurable plugins that can be installed free by all new partner

CIGESMED. Protocols: how to implement a multidisciplinary approach on a large scale for coralligenous habitats surveys

International audienceThe European program CIGESMED addresses the Good Environmental Status of the coralligenous habitats. Its implementation on the field is firstly attempted by 4 protocols to be applied in France, Greece and Turkey. They have been tested in Marseille's region, since early 2014. These protocols are the following: (i) cartography of chosen coralligenous sites, (ii) spatial variability analysis by means of photo-quadrats and image processing, (iii) population genetics study of two common biobuilding species that may be cryptic (the bryozoan Myriapora truncata, and the rhodophyta Lithophyllum cabiochiae), and (iv) metagenomic approach of benthic species. The ultimate aim of these protocols is to link the results from the population genetics analysis and the spatial variability analysis to the sites' features thanks to the cartography. First results suggest that different clades exist for both complex of the previous species. Cartography forshadows models of repartition for species assemblages; they will then be compared between regions in the second part of the project

CIGESMED habitat's characterization: a simple ans reusable typology at the Mediterranean scale

International audienceThe so-called coralligenous makes Mediterranean marine habitats that are of the most important in terms of complexity and biodiversity. Coralligenous is formed by the development of several types of communities where bio-constructor, bio-erodor engeneer and " habitat " species interact to build complex structures. The European program CIGESMED studies the Good Environmental Status (G.E.S.) of these habitats. Several protocols are implemented, in particular the cartography of abiotic context, and species observation by means of photo-quadrats. The cartography inventories the profiles types of the coralligenous sites with as robust as possible categories: depth, orientation, slope, roughness, and main coralligenous stands. The objective is to establish a link between the species occurrence features, and the profiles features in order to understand the " natural " spatial variability of coralligenous habitats

CIGESMED habitat's characterization: a simple ans reusable typology at the Mediterranean scale

International audienceThe so-called coralligenous makes Mediterranean marine habitats that are of the most important in terms of complexity and biodiversity. Coralligenous is formed by the development of several types of communities where bio-constructor, bio-erodor engeneer and " habitat " species interact to build complex structures. The European program CIGESMED studies the Good Environmental Status (G.E.S.) of these habitats. Several protocols are implemented, in particular the cartography of abiotic context, and species observation by means of photo-quadrats. The cartography inventories the profiles types of the coralligenous sites with as robust as possible categories: depth, orientation, slope, roughness, and main coralligenous stands. The objective is to establish a link between the species occurrence features, and the profiles features in order to understand the " natural " spatial variability of coralligenous habitats

AN INTEGRATED APPROACH TO EVALUATE AND MONITOR THE CONSERVATION STATE OF CORALLIGENOUS BOTTOMS: THE INDEX-COR METHOD

International audienceCoralligenous outcrops represent a "hotspot" of Mediterranean marine biodiversity. Algae and sessile invertebrate taxa (mainly sponges, cnidarians, bryozoans and tunicates) structure the associated benthic assemblages and constitute remarkable seascapes. Nevertheless, this fragile habitat is submitted to a wide array of human impacts such as sewage outfalls, eutrophication, physical impacts linked to fishing and diving activities, as well as global warming effects. The current European legislative context (EU WFD, EU Habitat Directive, EU MSFD) imposes to reach or maintain a good environmental status for marine ecosystems. In this context, the MPA stakeholders need to have robust and accessible tools allowing the evaluation of the conservation state of the habitats. Concerning coralligenous bottoms, we propose a new method based on an integrated approach taking into account (i) the ratio between sensitive and tolerant species according to human impacts, (ii) the richness of macrotaxonomic descriptors assessed from direct observation (in situ or from images) and (iii) their structural complexity (basal, intermediate and upper layers present in coralligenous bottoms). These three metrics are combined into a global index called INDEX-COR. Datasets were acquired along the French coasts. In each site, 2 transects 15m long were installed on the bottom. Along each transect, 15 photo quadrats (40 cm x 60 cm) and 1 video were recorded and notes were taken by a SCUBA diver-Observer. This method was applied between 15 and 50 meters depth and can be also performed by a ROV (Remotely Operating Vehicule) or an AUV (Autonomous Underwater Vehicle). INDEX-COR is intended to be applied to other Mediterranean areas using metrics and species lists adapted to the different regional contexts

IndexMEED cases studies using "Omics" data with graph theory

International audienceData produced within marine and terrestrial biodiversity research projects that evaluate and monitor Good Environmental Status, have a high potential for use by stakeholders involved in environmental management. However, environmental data, especially in ecology, are not readily accessible to various users. The specific scientific goals and the logics of project organization and information gathering lead to a decentralized data distribution. In such a heterogeneous system across different organizations and data formats, it is difficult to efficiently harmonize the outputs. Few tools are available to assist. For instance standards and specific protocols can be applied to interconnect databases. Such semantic approaches greatly increase data interoperability.This communication present the recent results and the consortium IndexMEED (Indexing for Mining Ecological and Environmental Data) activity that aims to build new approaches to investigate complex research questions, and support the emergence of new scientific hypotheses based on graph theory Auber et al. 2014). Current developments in data mining based on graphs, as well as the potential for relevant contributions to environmental research, particularly about strategic decision-making, and new ways of organizing data will be presented (David et al. 2015). In particular, the consortium makes decisions on how i) to analyze heterogeneous distributed data spread throughout different databases combining molecular and habitat characteristics data [3], ii) to create matches and incorporate some approximations, iii) to identify statistical relationships between observed data and the emergence of contextual patterns using a calculation library and distributed calculation center at the European level, iv) to encourage openness and sharing data while complying with the general principles of FAIR (Findable, Accessible, Interoperable, Re-usable and citable) in order to enhance data value and their utilization. IndexMEED participants are now exploring the ability of two scientific communities (ecology sensu lato and computer sciences) to work together, using several studies cases. The ECOSCOPE project aims to meet the need to access structured and complementary omics-datasets to better understand biodiversity state and its dynamics. Indeed, the ECOSCOPE case study targets to visualize, through the graph approach, links between datasets and databases from genetics to ecosystems. Another case study, displaying anthropology fossils and omics on the same graph, will also be presented. DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) and CIGESMED (Coralligenous based Indicators to evaluate and monitor the "Good Environmental Status" of the MEDiterranean coastal water) European projects, conducted by IMBE, are focused on photo quadrats, cartography and omics data of the marine hard bottom in order to discover context patterns helpful to build decision support system building. Study case “65 Millions d’observateurs” French project is testing AskOmics to provide a graph-based querying interface using RDF (Resource Description Framework) and SPARQL technologies.Scientific questions can be resolved by the new data mining approaches that offer new ways to investigate heterogeneous environmental data with graph mining (Muñoz et al. 2017). The uses of data from biodiversity research demonstrate the prototype functionalities (David et al. 2016) and introduce new perspectives to analyze environmental and societal responses including decision-making at large scale, both at the information system level and the observing system level than at the observed system level