AIMS:

Coralligenous habitats are emblematic biogenic constructions of the Mediterranean Sea built-up in dim light conditions by organisms from various phylogenetic groups such as calcareous coralline algae (CCA), bryozoans, polychaetes, cnidarians, mollusks, sponges, crustaceans and foraminiferans (Ballesteros 2006). The resulting framework harbors micro-habitats sheltering at least 1600 species making coralligenous habitats biodiversity hot-spots which provide various ecosystems services. The main builders are CCA, in particular Lithophyllum stictaeforme (Areschoug) Hauck and L. cabiochae (Boudouresque & Verlaque) Athanasiadis below 20 meters' depth. Molecular (and morphological) data revealed cryptic species (CS) within this species complex, i.e. reproductively isolated entities sharing the same species name. Recent studies showed that L. stictaeforme survival and reproduction were affected by irradiance and temperature, that L. cabiochae photosynthesis was reduced under elevated pCO2 and that cryptic species within this complex have slightly differentiated irradiance requirements.  More than 500 individuals were collected in 10 sites displaying contrasting environmental conditions within sites (eg. depth, topography, exposition and dominant species of the surrounding community). Connectivity in the study zone (around Marseille) is well understood owing to physical oceanography and comparative population genetics. We sequenced transcriptomes of the red alga to identify target coding sequences, then thousands of SNPs were characterized by capture sequencing to investigate the distribution of adaptive variation. At these sites, we also characterized coralligenous species composition by metabarcoding.  This design allows separating connectivity from local effects, and testing whether the same factors shape diversity at the intraspecific and at the community levels. Identifying populations adapted to specific environmental conditions is useful to the design of protection area for these emblematic habitats of the Mediterranean Sea. Such information is crucial for the protection of both the bioengineer species and the coralligenous habitats.