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).

Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to 'barrens' when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs.

A pronounced, widespread and persistent regime shift among marine ecosystems is observable on temperate rocky reefs as a result of sea urchin overgrazing. Here, we empirically define regime-shift dynamics for this grazing system which transitions between productive macroalgal beds and impoverished urchin barrens. Catastrophic in nature, urchin overgrazing in a well-studied Australian system demonstrates a discontinuous regime shift, which is of particular management concern as recovery of desirable macroalgal beds requires reducing grazers to well below the initial threshold of overgrazing. Generality of this regime-shift dynamic is explored across 13 rocky reef systems (spanning 11 different regions from both hemispheres) by compiling available survey data (totalling 10 901 quadrats surveyed in situ ) plus experimental regime-shift responses (observed during a total of 57 in situ manipulations). The emergent and globally coherent pattern shows urchin grazing to cause a discontinuous ‘catastrophic’ regime shift, with hysteresis effect of approximately one order of magnitude in urchin biomass between critical thresholds of overgrazing and recovery. Different life-history traits appear to create asymmetry in the pace of overgrazing versus recovery. Once shifted, strong feedback mechanisms provide resilience for each alternative state thus defining the catastrophic nature of this regime shift. Importantly, human-derived stressors can act to erode resilience of desirable macroalgal beds while strengthening resilience of urchin barrens, thus exacerbating the risk, spatial extent and irreversibility of an unwanted regime shift for marine ecosystems.

The state-of-art on alien species in the Mediterranean Sea is presented, making distinctions among the four subregions defined in the EU Marine Strategy Framework Directive: (i) the Western Mediterranean Sea (WMED); (ii) the Central Mediterranean Sea (CMED); (iii) the Adriatic Sea (ADRIA); and (iv) the Eastern Mediterranean Sea (EMED). The updated checklist (December 2010) of marine alien species within each subregion, along with their acclimatization status and origin, is provided. A total of 955 alien species is known in the Mediterranean, the vast majority of them having being introduced in the EMED (718), less in the WMED (328) and CMED (267) and least in the Adriatic (171). Of these, 535 species (56%) are established in at least one area.Despite the collective effort of experts who attempted in this work, the number of introduced species remains probably underestimated. Excluding microalgae, for which knowledge is still insufficient, aliens have increased the total species richness of the Mediterranean Sea by 5.9%. This figure should not be directly read as an indication of higher biodiversity, as spreading of so many aliens within the basin is possibly causing biotic homogenization. Thermophilic species, i.e. Indo-Pacific, Indian Ocean, Red Sea, Tropical Atlantic, Tropical Pacific, and circum(sub)tropical, account for 88.4% of the introduced species in the EMED, 72.8% in the CMED, 59.3% in the WMED and 56.1% in the Adriatic. Cold water species, i.e. circumboreal, N Atlantic, and N Pacific, make up a small percentage of the introduced species, ranging between 4.2% and 21.6% and being more numerous in the Adriatic and less so in the EMED.Species that are classified as invasive or potentially invasive are 134 in the whole of the Mediterranean: 108 are present in the EMED, 76 in the CMED, 53 in the Adriatic and 64 in the WMED. The WMED hosts most invasive macrophytes, whereas the EMED has the lion’s share in polychaetes, crustaceans, molluscs and fish.

More than 60 marine non-indigenous species (NIS) have been removed from previous lists and 84 species have been added, bringing the total to 986 alien species in the Mediterranean [775 in the eastern Mediterranean (EMED), 249 in the central Mediterranean (CMED), 190 in the Adriatic Sea (ADRIA) and 308 in the western Mediterranean (WMED)]. There were 48 new entries since 2011 which can be interpreted as approximately one new entry every two weeks. The number of alien species continues to increase, by 2-3 species per year for macrophytes, molluscs and polychaetes, 3-4 species per year for crustaceans, and 6 species per year for fish. The dominant group among alien species is molluscs (with 215 species), followed by crustaceans (159) and polychaetes (132). Macrophytes are the leading group of NIS in the ADRIA and the WMED, reaching 26-30% of all aliens, whereas in the EMED they barely constitute 10% of the introductions. In the EMED, molluscs are the most species-rich group, followed by crustaceans, fish and polychaetes. More than half (54%) of the marine alien species in the Mediterranean were probably introduced by corridors (mainly Suez). Shipping is blamed directly for the introduction of only 12 species, whereas it is assumed to be the most likely pathway of introduction (via ballasts or fouling) of another 300 species. For approximately 100 species shipping is a probable pathway along with the Suez Canal and/or aquaculture. Approximately 20 species have been introduced with certainty via aquaculture, while >50 species (mostly macroalgae), occurring in the vicinity of oyster farms, are assumed to be introduced accidentally as contaminants of imported species. A total of 18 species are assumed to have been introduced by the aquarium trade. Lessepsian species decline westwards, while the reverse pattern is evident for ship-mediated species and for those introduced with aquaculture. There is an increasing trend in new introductions via the Suez Canal and via shipping.