SummaryIllegal killing/taking of birds is a growing concern across the Mediterranean. However, there are few quantitative data on the species and countries involved. We assessed numbers of individual birds of each species killed/taken illegally in each Mediterranean country per year, using a diverse range of data sources and incorporating expert knowledge. We estimated that 11-36 million individuals per year may be killed/taken illegally in the region, many of them on migration. In each of Cyprus, Egypt, Italy, Lebanon and Syria, more than two million birds may be killed/taken on average each year. For species such as Blackcap Sylvia atricapilla , Common Quail Coturnix coturnix , Eurasian Chaffinch Fringilla coelebs , House Sparrow Passer domesticus and Song Thrush Turdus philomelos , more than one million individuals of each species are estimated to be killed/ taken illegally on average every year. Several species of global conservation concern are also reported to be killed/taken illegally in substantial numbers: Eurasian Curlew Numenius arquata , Ferruginous Duck Aythya nyroca and Rock Partridge Alectoris graeca . Birds in the Mediterranean are illegally killed/taken primarily for food, sport and for use as cage-birds or decoys. At the 20 worst locations with the highest reported numbers, 7.9 million individuals may be illegally killed/ taken per year, representing 34% of the mean estimated annual regional total number of birds illegally killed/taken for all species combined. Our study highlighted the paucity of data on illegal killing/taking of birds. Monitoring schemes which use systematic sampling protocols are needed A-L. Brochet et al. 2 to generate increasingly robust data on trends in illegal killing/taking over time and help stakeholders prioritise conservation actions to address this international conservation problem. Large numbers of birds are also hunted legally in the region, but specific totals are generally unavailable. Such data, in combination with improved estimates for illegal killing/taking, are needed for robustly assessing the sustainability of exploitation of birds.

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species’ boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a ‘functional metagenomics’ platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.