Understanding ecological functioning of coralligenous habitats, and building new indicators based on genetic tools to assess their GES (good environmental status)

The coralligenous is a typical Mediterranean marine habitat and hosts the highest concentration of biodiversity of this sea. Paradoxically, unlike Posidonia meadows, it is poorly studied. Like the famous tropical coral reefs, it is a complex biogenic habitat, based on encrusting red algae (numerous metazoan phyla also participate to bio-construction). The PhD will significantly improve our understandingof its functioning and resilience capacity, and establish biodiversity and connectivity patterns among localities and ecological profiles, providing information for rationalizing the design of Marine Protected Area networks and monitoring methods. To reach this goal, he will use thesynergy of interdisciplinarity, combining population genetics, community ecology, microbial ecology and physical oceanography. The scientific originality relies on testing hypotheses related to the niche and neutral biodiversity theories that include both inter- and intra-specific levels of biodiversity. The societal interest relies on the setup of innovative, cost-effective and accurate methods forbiodiversity characterization and monitoring, based on genetic tools rigorously inter-calibrated with traditional taxonomy and photo-quadrate approaches. This requests four taskspartly using the same data, but different analysis methods:

1- Establishment of the taxonomic composition of the engineer corallinale algae. Several cryptic species in red algae were revealed by genetic markers (cf. B-4). Molecular tools (IMBE) and classical taxonomy (Dr Marc Verlaque, MIO) will be used. Algal composition will be related to ecological profiles (depth, orientation, light exposition, rugosity, etc.) which are being thoroughly mapped and sampled in CIGESMED, a European ERANET project.

2- Establishment of the species composition for numerous small quadrates of coralligenous using meta-barcoding in different ecological profiles x sites (same as for 2-). Statistical analysis of the possible role of ecological factors.

3- Population structure and phylogeography of two selected taxa: a red alga Lithophyllum spp. and a bryozoan Myriapora truncata, on the CIGESMED sampling network, contextualized by ecological factors (cf above). Available data from other species will be included in the comparisons. Connectivity patterns will be established, from the local to the whole Mediterranean scale, and related to explanatory factors such as the present ecological context, paleo-environments, and physical connectivity (depending on the region and comparison scale).

4- Synthesis and Comparisons: 
- Compare intra-specific diversity among species (determine site-effects vs species-effects). 
- Compare species assemblages assessed by meta-barcoding/ traditional taxonomy/quadrate photography methods. Deduce some rules of inter-calibration among methods. 
- Compare intra- and inter-specific diversity (including microbial), trying to distinguish the part due to connectivity from that of local demography (perturbation regime), and ecological factors using genetic and demographic models and hydrological models. 
- Compare how these coralligenous data support niche vs neutral biodiversity theories. 
- Propose new GES (good environmental status) indicators for the coralligenous and biodiversity management rules.