AquaMaps model represents a modified version of the relative environmental suitability model (RES) developed by Kaschner et al. . It is an environmental envelope model that generates standardized range maps and the relative probability of occurrence within that range for marine species based on the environmental conditions in each 0.5 degree latitude by 0.5 degree longitude cell of global grid. The model was developed specifically to deal with the sampling biases, such as heterogeneous sampling effort and species misidentifications, affecting most of the large-scale data sets that are currently available for species distribution modelling in the marine realm [2,3]. The model currently includes more than 9,000 fishes, marine mammals, reptiles and invertebrate species. Predictions are generated based on species-specific environmental tolerances computed using available point occurrences, which are obtained from online databases such as OBIS, or the Global Biodiversity Information Facility , but which are then supplemented with other types of habitat usage information obtained directly from online species databases such as FishBase and SeaLifeBase [2,3]. Moreover, an expert-review function in the AquaMaps algorithm explicitly allows for the incorporation of expert knowledge about species occurrence to counteract or compensate known sampling biases. AquaMaps outputs have been successfully validated using independent, effort-corrected survey data and, in the face of the existing sub-optimal input data sets, AquaMaps model performance compares well with that of other presence-only habitat prediction models, such as GARP, Maxent or GAMs .
Species richness maps for the Mediterranean Sea were generated by superimposing generated range maps of all individual species and then counting the number of species predicted to be present in each half degree cell.
A summary of the number of species, by different taxa, which are known to occur in and/or are endemic to the Mediterranean Sea based on the data provided by online species databases such as FishBase and SeaLifeBase can be found in Table S3 and Table S4. The appendix also shows the proportion of species currently covered by AquaMaps. Based on the comparison with FishBase and SeaLifeBase data, AquaMaps coverage of higher vertebrate and fish taxa is either complete or relatively comprehensive (Table S5-S6). In contrast, most invertebrate groups are much less well represented and other groups, such as plants, fungi, bacteria, but also seabirds, have not yet been incorporated at all. Of those species covered by AquaMaps and included in this analysis, more than half are ray-finned fishes (Actinopterygii), and roughly a third are invertebrates, and only a very small percentage are higher vertebrates such as cetaceans, pinnipeds or marine turtles. Based on the information available from FishBase and SeaLifeBase, only a relatively small proportion of all species that are native in the Mediterranean Sea are also endemic. At the moment, most AquaMaps available for the Mediterranean species represent the computer-generated default maps, which have not been checked explicitly for consistency with published range maps or fully reviewed by experts. In general, though, a relative high proportion of species in taxa that are often the focus of conservation efforts, such as marine mammals, marine turtles and elasmobranch, have already been reviewed. On average, approximately 16% of all species included in this analysis are listed by the IUCN as endangered, vulnerable or threatened, thus requiring special protection and conservation measures. However, while less than one percent of the ray-finned fishes is considered endangered, 30% and more of the Mediterranean marine mammal species and elasmobranches, and all marine turtles and Holocephali species occurring in this ocean basin are threatened or endangered.
The World Register of Marine Species (WoRMS) lists 8,470 species records for the Mediterranean Sea  which is surpassed by an even higher estimate of up to 17,000 marine Mediterranean species based on the information provided in the main part of this paper. Thus, the approximately 700 Mediterranean species currently covered by AquaMaps, which formed the basis for our biodiversity maps, represent only a fraction of all species known to occur in this ocean basin. However, the species list provided by WoRMS also includes all non-Animalia species that are, at the moment, mostly not represented by any of the existing online species databases and for which there are mostly few if any occurrence records available . In terms of predicted patterns of species richness, AquaMaps outputs are probably relatively representative for fishes and marine mammals, although increasing the number of expert-reviews for Mediterranean Actinopterygii species would increase confidence in biodiversity maps for this taxonomic group. Similarly, while the selected presence threshold and the resulting species richness predictions for marine mammals have successfully been validated , this type of analysis still remains to be carried out for other taxa. For most taxa, the maps showing biodiversity patterns of endangered species in the Mediterranean Sea, however, can be regarded as reliable and representative, since more than 70% of all underlying species maps have been reviewed by experts.
Table S3. Mediterranean native and endemic marine species reported by FishBase/SeaLifeBase by different taxa and current extent of coverage of AquaMaps
Native and Endemic Species Reported from the Mediterranean Sea