The species of coralline red algae recorded at each site will be identified and characterized from a phylogenetic point of view using molecular tools (sequences of selected nuclear and plastid markers). The molecular work will be supported by morphological investigations based on Scanning Electron Microscopy (SEM).

Target species of coralline algae and invertebrate species will be selected for analyses of intraspecific levels of variability and genetic structuring across a range of spatial scales, and to compare different typologies of MBHs. Patterns of structuring and connectivity will be analysed to identify major barriers and dispersal corridors contributing to the establishment of effective discontinuity zone. Genetic variability of molecular markers with different levels of polymorphism (mitochondrial and nuclear DNA for invertebrates, mitochondrial and plastid DNA for algae) will be analysed. Based on the level of intraspecific genetic structuring we will estimate gene flow among populations and, indirectly, the effective scales of larval and propagule dispersal. This approach will allow formulating hypotheses on environmental variables and ecological processes that could affect differences in species composition among habitats and evaluate common patterns of recovery potential of the assemblages towards disturbances. Selected target species from different phyla (e.g. cnidarian, mollusc, chordate) and one key bioconstructor species of coralline alga will be analysed using highly variable, polymorphic and selectively neutral molecular markers (e.g. microsatellites; Estoup and Angers 1998). Microsatellites have been shown to be extremely sensitive in detecting species genetic structuring at different spatial scales. Molecular data will be processed using the software packages RAxML (Stamatakis 2006), MEGA (Tamura et al. 2013), GENETIX (Belkhir et al. 1996-2004), GENEPOP (Raymond and Rousset 1995) and ARLEQUIN (Excoffier and Lischer 2010). This information will be summarised into a database describing the relationship between the genetic structuring and the bio-ecological features of the species, pointing out the connectivity patterns and the biogeographic discontinuities.

Belkhir, K., Borsa, P., Chikhi, L., Raufaste, N., Bonhomme, F., 1996-2004. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5000, Université de Montpellier II, Montpellier (France).

Estoup, A., Angers, B., 1998. Microsatellites and minisatellites for molecular ecology: Theoretical and empirical considerations. NATO Adv. Sci. I A-Lif. 306, 55-86.

Excoffier, L., Lischer, H.E.L., 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564-567. http://dx.doi.org/10.1111/j.1755-0998.2010.02847.x

Raymond, M., Rousset, F., 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248-249.

Stamatakis, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688-2690. http://dx.doi.org/10.1093/bioinformatics/btl446

Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S., 2013. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 30, 2725-2729. http://dx.doi.org/10.1093/molbev/mst197