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20 pages, 6 figures, 5 tables, supporting information https://dx.doi.org/10.1371/journal.pone.0160678.-- We have obtained the GenBank Accession numbers for all the sequences used in the work (GenBank from KX051564 to KX051577 and from KX002245 to KX002255) ; Gorgonian species show a high morphological variability in relation to the environment in which they live. In coastal areas, parameters such as temperature, light, currents, and food availability vary significantly with depth, potentially affecting morphology of the colonies and the structure of the populations, as well as their connectivity patterns. In tropical seas, the existence of connectivity between shallow and deep populations supported the hypothesis that the deep coral reefs could potentially act as (reproductive) refugia fostering re-colonization of shallow areas after mortality events. Moreover, this hypothesis is not so clear accepted in temperate seas. Eunicella singularis is one of the most common gorgonian species in Northwestern Mediterranean Sea, playing an important role as ecosystem engineer by providing biomass and complexity to the coralligenous habitats. It has a wide bathymetric distribution ranging from about 10m to 100 m. Two depth-related morphotypes have been identified, differing in colony morphology, sclerite size and shape, and occurrence of symbiotic algae, but not inmitochondrial DNA haplotypes. In the present study the genetic structure of E. singularis populations along a horizontal and bathymetric gradient was assessed using microsatellites and ITS1 sequences. Restricted gene flow was found at 30-40 m depth between the two Eunicella morphotypes. Conversely, no genetic structuring has been found among shallow water populations within a spatial scale of ten kilometers. The break in gene flow between shallow and deep populations contributes to explain the morphological variability observed at different depths.Moreover, the limited vertical connectivity hinted that the refugia hypothesis does not apply to E. singularis. Re-colonization of shallow water populations, occasionally affected by mass mortality events, should then be mainly fueled by larvae from other shallow water populations ; AG was funded by a I3P contract of the Consejo Superior de Investigaciones Cientificas (Ref. I3P-BPD2005). SR wants to thank the support of the Generalitat de Catalunya to MERS (2014 SGR-1356) and the Marie Curie International Outgoing Fellowship (ANIMAL FOREST HEALTH, project number 327845). The study was funded by a 2003-2004 INTERREG project between Catalonia-Languedoc Rouissillon ''Pirineus Mediterrànis: La muntanya que uneix'' of the CSIC and CNRS, of the 2009-2013 European project LIFE+ INDEMARES ''Inventario y designación de la red natura 2000 en áreas marinas del estado español'' (LIFE07/NAT/E/000732) of the European Union, and by a PRIN 2010-2011 project (prot. 2010Z8HJ5M) on 'Coastal bioconstructions: structure, function and management' Italian Ministry of Education, Univeristy and Research ; Peer Reviewed

15 páginas, 3 tablas, 2 figuras. ; Coastal areas play a crucial role in the economical, social and political development of most countries; they support diverse and productive coastal ecosystems that provide valuable goods and services. Globally flooding and coastal erosion represent serious threats along many coastlines, and will become more serious as a consequence of human-induced changes and accelerated sea-level rise. Over the past century, hard coastal defence structures have become ubiquitous features of coastal landscapes as a response to these threats. The proliferation of defence works can affect over half of the shoreline in some regions and results in dramatic changes to the coastal environment. Surprisingly little attention has been paid to the ecological consequences of coastal defence. Results from the DELOS (Environmental Design of Low Crested Coastal Defence Structures, EVK3-CT-2000-00041) project indicate that the construction of coastal defence structures will affect coastal ecosystems. The consequences can be seen on a local scale, as disruption of surrounding soft-bottom environments and introduction of new artificial hard-bottom habitats, with consequent changes to the native assemblages of the areas. Proliferation of coastal defence structures can also have critical impacts on regional species diversity, removing isolating barriers, favouring the spread of non-native species and increasing habitat heterogeneity. Knowledge of the environmental context in which coastal defence structures are placed is fundamental to an effective management of these structures as, while there are some general consequences of such construction, many effects are site specific. Advice is provided to meet specific management goals, which include mitigating specific impacts on the environment, such as minimising changes to surrounding sediments, spread of exotic species or growth of nuisance species, and/or enhancing specific natural resources, for example enhancing fish recruitment or promoting diverse assemblages for eco-tourism. The DELOS project points out that the downstream effects of defence structures on coastal processes and regional-scale impacts on biodiversity necessitate planning and management at a regional (large coastline) scale. To effectively understand and manage coastal defences, environmental management goals must be clearly stated and incorporated into the planning, construction, and monitoring stages. ; Work was supported by funds from the EU project DELOS (EVK3-CT-2000- 00041). Further funding from the project COFIN (ex 40%) to M. A. During the work, L. A. was supported by an bAssegno di RicercaQ of the University of Bologna. ; Peer reviewed