The Habitat and Birds Directives have set up the governance structure of bio- and landscape diversity at continental level in Europe, defining criteria and rules to build an impressively large European network of protected areas. Most studies addressing conservation in Nature 2000 sites from ecological perspectives have given priority attention on specific conservation issues, with respect to general pattern analysis of structural ecosystem properties, which determine the ecological context for ecosystem response to external pressures. Here, we focus on a pattern analysis of structural heterogeneity of Nature 2000 areas and on an evaluation of implications for the conservation of the most endangered species and habitat types in the cross-boundary Adriatic-Ionian region, including Puglia, Ionian Islands, Epirus and Western Greece. Original data on physiographic characteristics, habitat and species of Community Importance have been collected from the European Environment Agency and organised into a geo-database. Results show significant heterogeneity in the physiographic characteristics of protected sites among Regions. Overall Puglia Region has more but smaller sites than Greek trans-boundary Regions. The latter have more endemic species, some of which restricted to an extremely limited number of protected sites. Implications of physiographic heterogeneity on endemism conservation will be discussed.
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