The Mediterranean Sea is a marine biodiversity hot spot. Here we combined an extensive literature analysis with expert opinions to update publicly available estimates of major taxa in this marine ecosystem and to revise and update several species lists. We also assessed overall spatial and temporal patterns of species diversity and identified major changes and threats. Our results listed approximately 17,000 marine species occurring in the Mediterranean Sea. However, our estimates of marine diversity are still incomplete as yet—undescribed species will be added in the future. Diversity for microbes is substantially underestimated, and the deep-sea areas and portions of the southern and eastern region are still poorly known. In addition, the invasion of alien species is a crucial factor that will continue to change the biodiversity of the Mediterranean, mainly in its eastern basin that can spread rapidly northwards and westwards due to the warming of the Mediterranean Sea. Spatial patterns showed a general decrease in biodiversity from northwestern to southeastern regions following a gradient of production, with some exceptions and caution due to gaps in our knowledge of the biota along the southern and eastern rims. Biodiversity was also generally higher in coastal areas and continental shelves, and decreases with depth. Temporal trends indicated that overexploitation and habitat loss have been the main human drivers of historical changes in biodiversity. At present, habitat loss and degradation, followed by fishing impacts, pollution, climate change, eutrophication, and the establishment of alien species are the most important threats and affect the greatest number of taxonomic groups. All these impacts are expected to grow in importance in the future, especially climate change and habitat degradation. The spatial identification of hot spots highlighted the ecological importance of most of the western Mediterranean shelves (and in particular, the Strait of Gibraltar and the adjacent Alboran Sea), western African coast, the Adriatic, and the Aegean Sea, which show high concentrations of endangered, threatened, or vulnerable species. The Levantine Basin, severely impacted by the invasion of species, is endangered as well.This abstract has been translated to other languages (File S1).

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In the late summer of 1999, an extensive mortality of gorgonians and other epi‐benthic organisms was observed in the Ligurian Sea (Mediterranean Sea) from the Tuscan Archipelago to Marseille. Quantitative data from Tino Island and Portofino Promontory indicated that the proportion of affected gorgonians ranged from 60% to 100% in populations having a density of 9–27.8 colonies m−2, suggesting that millions of sea fans died along the coast of Liguria. This mass mortality episode coincided with a sudden increase of sea water temperature down to more than 50 m depth. Laboratory analyses showed that the colonies stressed by high temperature also underwent extensive attack by microrganisms (protozoans and fungi), which are interpreted as opportunistic pathogens.

Present-day Mediterranean marine biodiversity is undergoing rapid alteration.

Present-day Mediterranean marine biodiversity is undergoing rapid alteration. Because of the increased occurrence of warmwater biota, it has been said that the Mediterranean is under a process of 'tropicalization'. This paper analyses the main patterns of the Mediterranean Sea tropicalization and considers briefly its extent and consequences. As happened during previous interglacial phases of the Quaternary, Atlantic water, entering via the Straits of Gibraltar, carries into the Mediterranean species that are prevalently of (sub)tropical affinity. On the other side of the basin, Red Sea species penetrate through the Suez Canal, a phenomenon called lessepsian migration from the name of F. de Lesseps, the French engineer who promoted the cutting of the Canal. Also the many exotic species introduced by humans voluntarily or involuntarily are nearly always typical of warm waters. Climate change combines with Atlantic influx, lessepsian migration and the introduction of exotic species by humans to the establishment of tropical marine biota in the Mediterranean Sea. Present-day warming ultimately favours the spread of warmwater species through direct and indirect effects, and especially by changing water circulation. It is impossible at present to foresee to what extent the exuberance of warm-water species will affect the trophic web and the functioning of marine ecosystems in the Mediterranean Sea of tomorrow. While Mediterranean Sea communities are modifying their pattern of species composition, they do not seem to be acquiring a more marked tropical physiognomy: Mediterranean coastal marine ecosystems are still dominated by frondose algae (even if the species that are gaining ascendancy are of tropical origin) and not by corals as is normal in tropical seas.

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A rapid visual assessment (RVA) approach for the characterization and assessment of the integrity of coralligenous reefs was applied in 21 stations subjected to different levels of anthropogenic pressure, along the French Mediterranean coasts. The reefs were characterized from both the geomorphologic and bionomic (biotic cover, conspicuous species richness, canopy-forming species, etc.) points of view, and their health status was estimated through the COARSE (COralligenous Assessment by ReefScape Estimate) index. The sensitivity of the COARSE index and the robustness of the RVA approach to observer biases were analyzed. Results showed that most coralligenous reefs were characterized by (sub) vertical cliffs or platforms with variable slope, usually dominated by biotic facies with Paramuricea clavata and/or Eunicella cavolini in healthy stations, or by algal associations or facies of impoverishment in the most impacted situations. The overall quality scores of the COARSE index generally reflected the putative level of stress of the sampling stations; differences due to observer biases resulted negligible. Coupling the RVA approach with the COARSE index proved an effective protocol for both the characterization and the evaluation of coralligenous reefs: the former is achieved by the analysis of the whole complexity of this habitat, the latter provides for the first time an indication of sea-floor integrity, differently from previous indices that aim at estimating water quality.

Understanding the effects of environmental change on ecosystems requires the identification of baselines that may act as reference conditions. However, the continuous change of these references challenges our ability to define the true natural status of ecosystems. The so-called sliding baseline syndrome can be overcome through the analysis of quantitative time series, which are, however, extremely rare. Here we show how combining historical quantitative data with descriptive ‘naturalistic’ information arranged in a chronological chain allows highlighting long-term trends and can be used to inform present conservation schemes. We analysed the long-term change of a coralligenous reef, a marine habitat endemic to the Mediterranean Sea. The coralligenous assemblages of Mesco Reef (Ligurian Sea, NW Mediterranean) have been studied, although discontinuously, since 1937 thus making available both detailed descriptive information and scanty quantitative data: while the former was useful to understand the natural history of the ecosystem, the analysis of the latter was of paramount importance to provide a formal measure of change over time. Epibenthic assemblages remained comparatively stable until the 1990s, when species replacement, invasion by alien algae, and biotic homogenisation occurred within few years, leading to a new and completely different ecosystem state. The shift experienced by the coralligenous assemblages of Mesco Reef was probably induced by a combination of seawater warming and local human pressures, the latter mainly resulting in increased water turbidity; in turn, cumulative stress may have favoured the establishment of alien species. This study showed that the combined analysis of quantitative and descriptive historical data represent a precious knowledge to understand ecosystem trends over time and provide help to identify baselines for ecological management.