International initiatives aimed at generating genomic resources, and particularly reference genomes, have flourished in recent years. Some focus on specific taxa, such as the Vertebrate Genomes Project, Bird Genome 10K Project, Bat1K Project, Global Invertebrate Genomics Alliance, 10 000 Plant Genomes Project, and 1000 Fungal Genomes project. Others focus on geographic regions, such as the California Conservation Genomics Project, Darwin Tree of Life for Britain and Ireland, Catalan Initiative for the Earth BioGenome Project in the Catalan territories, Endemixit in Italy, Norwegian Earth Biogenome Project, and SciLifeLab in Sweden, on applications such as the LOEWE Translational Biodiversity Genomics in Germany, or on ecological systems such as the Aquatic Symbiosis Genomics project. Collectively part of the Earth BioGenome Project (EBP), in Europe these initiatives are organized under the umbrella of the European Reference Genome Atlas (ERGA). A genome atlas of European biodiversityERGA is a pan-European scientific response to the current threats to biodiversity. Approximately one fifth of the ~200 000 eukaryotic species present in Europe can be inferred to be at risk of extinction according to the International Union for Conservation of Nature (IUCN) Red List classification (this estimate only considers the assessed species; https://www.iucn.org/regions/europe/our-work/biodiversity-conservation/european-red-list-threatened-species).ERGA aims to generate reference genomes of European eukaryotic species across the tree of life, including threatened, endemic, and keystone species, as well as pests and species important to agriculture, fisheries, and ecosystem function and stability. ERGA builds upon current genomic consortia in EU member states, EU Associated Countries, representatives of other countries within the European bioregion, and international collaborators. These reference genomes will address fundamental and applied questions in conservation, biology, and health. ERGA seeks to alert the EU about the potential of conservation genomics, and particularly the role of reference genomes, in biodiversity assessment, conservation strategies, and restoration efforts.

Cetacean stranding reports in the North Aegean Sea were recorded since 1998 from Strimonikos Gulf in Chalkidiki up to Alexandroupoli on the Turkish border and in a few northern Aegean islands. On site, the specimens were examined to identify species, gender, approximate age and, when possible, cause for stranding. A total of 26 filled stomachs of five cetacean species collected since 2002 were analysed: bottlenose dolphinsTursiops truncatus(N = 8), common dolphinsDelphinus delphis(N = 8), harbour porpoisesPhocoena phocoena(N = 5), striped dolphinsStenella coeruleoalba(N = 4) and Risso's dolphinsGrampus griseus(N = 1). From the analysed stomachs it was found that the bottlenose dolphins fed mainly on snake blennyOphidion barbatum(34%), bogueBoops boops(22%) and round sardinellaSardinella aurita(13%); common dolphins on round sardinella (17%), picarelsSpicaraspp. (10%) and Cocco's lantern fishLobianchia gemellaris(9%); harbour porpoises on Gobidae (four-spotted gobyDeltentosteus quadrimaculatus41% and black gobyGobius niger37%) and round sardinella (7%); striped dolphins on Myctophydae (Madeira lantern fishCeratoscopelus maderensis51%), and on Pfeffer's enople squidAbraliopsis morisii(10%) and bogue (8%); and Risso's dolphin exclusively on Teuthidae (31%), the umbrella squidHistioteuthis bonellii(30%) and the reverse jewel squidH. reversa(14%). The present work represents the first attempt to investigate the diet up to species level for several cetaceans in Greek waters and for harbour porpoises stranded in the Mediterranean Sea.

Heterogeneous data collection in the marine environment has led to large gaps in our knowledge of marine species distributions. To fill these gaps, models calibrated on existing data may be used to predict species distributions in unsampled areas, given that available data are sufficiently representative. Our objective was to evaluate the feasibility of mapping cetacean densities across the entire Mediterranean Sea using models calibrated on available survey data and various environmental covariates. We aggregated 302,481 km of line transect survey effort conducted in the Mediterranean Sea within the past 20 years by many organisations. Survey coverage was highly heterogeneous geographically and seasonally: large data gaps were present in the eastern and southern Mediterranean and in non-summer months. We mapped the extent of interpolation versus extrapolation and the proportion of data nearby in environmental space when models calibrated on existing survey data were used for prediction across the entire Mediterranean Sea. Using model predictions to map cetacean densities in the eastern and southern Mediterranean, characterised by warmer, less productive waters, and more intense eddy activity, would lead to potentially unreliable extrapolations. We stress the need for systematic surveys of cetaceans in these environmentally unique Mediterranean waters, particularly in non-summer months.

Greek fisheries (purse seine, trawling and small‐scale coastal, by order of importance) mostly operate in the Thracian Sea, which despite its relatively small size relative to the Aegean Sea (≈4.4%) is the most productive region in Greek waters due to its elevated nutrient concentration. The Thracian Sea is also vital to several species of cetaceans, mainly bottlenose dolphin, Tursiops truncatus (Montagu), and common dolphin, Delphinus delphis L. The area has been proposed as a potential cetacean conservation hotspot. For this reason, the interactions between fishing activities and local cetacean populations have been investigated through reports of stranded dolphins, interviews with fishers, surveys and detailed dolphin stomach content analysis. Reports of stranded cetaceans and interviews with fishers revealed cases of cetacean entanglement in fishing nets, as well as frequent dolphin damage to fishing nets. Necropsy stomach analysis of stranded dolphins revealed a preference for fish and cephalopods of low commercial value, indicating a low trophic overlap between cetaceans and commercial fisheries. Recommendations for the management of fisheries–cetacean interactions in the Thracian Sea are provided.

1. Preservation of endangered species is now recognized as a relevant component of regional and global conservation actions achieved through the maintenance of the remaining populations in a favourable conservation status. The Mediterranean common dolphin (Delphinus delphis) is listed as an Endangered subpopulation in the International Union for Conservation of Nature Red List, with declining numbers in some of the areas where it has been studied for numerous years. Prey depletion, fisheries bycatch, pollution, health risks, and climate change are among the recognized threats that the species is facing in the region.2. The existing national, regional, and international legislation pertinent to Mediterranean countries should aid greater science-policy-management integration and support innovative research and monitoring towards effective conservation. The challenges inherent in studying the pelagic D. delphis should not preclude the use of long-term, year-round, multiplatform surveys, side by side with the latest molecular tools, which aid our understanding of its populations' genetic diversity, resistance to diseases, and resilience in a semi-enclosed fast-changing sea.3. Addressing the multiplicity of problems confronting the species requires collaborative effort at all levels to share and merge resources, data, and expertise more efficiently. In this review, we provide an overview of the current knowledge on the Mediterranean common dolphin, the main threats, and knowledge gaps that are priorities for addressing its conservation, while providing clear recommendations for effectively safeguarding the species and its habitat at both local and regional levels.

No abstract

1. The abundance, distribution and diet of the short-beaked common dolphin were investigated as part of the first detailed study on cetacean populations in the North Aegean Sea. Since 2004, the area has been proposed by national and international entities as a marine protected area for common dolphins and other cetacean species owing to its high biodiversity.2. Abundance and distribution were investigated between 2005 and 2013 through dedicated scientific marine transect surveys, covering 14,701 km, in sea conditions of Beaufort sea state 3 and below. The line-transect sampling method was used to estimate relative abundance, using Distance 6.0 software. Encounter rate for this species in the study area was estimated to be 0.24 groups/100 km (1.5 dolphins/100 km), with a mean group size of 6.88 (SE = 1.90).3. Common dolphin sightings were analysed for correlations with eight environmental variables (distance from the coast, depth, slope, median salinity, gradient of salinity, median temperature, gradient of temperature and mean current) using generalized additive modelling. Common dolphin sightings were significantly correlated to depth, temperature and salinity. 4. Stomach-content analyses were performed on eight suitable samples from common dolphins stranded in the study area. The trophic level of the species was calculated, indicating that this species is a top predator.5. This research provides the first estimates for abundance and distribution and the first diet analysis for this Mediterranean Endangered dolphin species in the study area based on a year-round long-term study.

The objective of this study is to describe the genetic population structure and demographic history of the endangered marine fish, Epinephelus marginatus, within Malta’s Fisheries Management Zone for the purpose of localised conservation planning. Epinephelus marginatus is a long-lived, sedentary, reef-associated protogynous hermaphrodite with high commercial and recreational value that is at risk of extinction throughout its global distribution. Based on global trends, population substructuring and gaps in local knowledge this has led to an increased interest in evaluation of local stock. Assessment of Maltese demography was based on historical and contemporary catch landings data whilst genetic population structure and regional connectivity patterns were evaluated by examining 175 individuals collected within the central Mediterranean region between 2002 and 2009 using 14 nuclear microsatellite loci. Demographic stock assessment of Maltese E. marginatus’ revealed a 99% decline in catch landings between 1947 and 2009 within the Fisheries Management Zone. A contemporary modest mean size was observed, 3 ± 3 kg, where approximately 17% of the population was juvenile, 68% female/sex-changing and 15% were male with a male-to-female sex ratio of 1:5. Genetic analysis describes the overall population of E. marginatus’ within the Fisheries Management Zone as decreasing in size (ƟH = 2.2), which has gone through a significant size reduction in the past (M = 0.41) and consequently shows signs of moderate inbreeding (FIS = 0.10, p < 0.001) with an estimated effective population size of 130 individuals. Results of spatially explicit Bayesian genetic cluster analysis detected two geographically distinct subpopulations within Malta’s Fisheries Management Zone and that they are connected to a larger network of E. marginatus’ within the Sicily Channel. Results suggest conservation management should be designed to reflect E. marginatus’ within Malta’s Fisheries Management Zone as two management units.