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As a large and long-lived species with high economic value, restricted spawning areas and short spawning periods, the Atlantic bluefin tuna (BFT; Thunnus thynnus) is particularly susceptible to over-exploitation. Although BFT have been targeted by fisheries in the Mediterranean Sea for thousands of years, it has only been in these last decades that the exploitation rate has reached far beyond sustainable levels. An understanding of the population structure, spatial dynamics, exploitation rates and the environmental variables that affect BFT is crucial for the conservation of the species. The aims of this PhD project were 1) to assess the accuracy of larval identification methods, 2) determine the genetic structure of modern BFT populations, 3) assess the self-recruitment rate in the Gulf of Mexico and Mediterranean spawning areas, 4) estimate the immigration rate of BFT to feeding aggregations from the various spawning areas, and 5) develop tools capable of investigating the temporal stability of population structuring in the Mediterranean Sea. Several weaknesses in modern morphology-based taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance of the taxonomic community to embrace advances in digital communications and a general scarcity of modern user-friendly materials are reviewed. Barcoding of scombrid larvae revealed important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology-based methods. Using a Genotyping-by-Sequencing a panel of 95 SNPs was developed and used to characterize the population structuring of BFT and composition of adult feeding aggregations. Using novel molecular techniques, DNA was extracted from bluefin tuna vertebrae excavated from late iron age, ancient roman settlements Byzantine-era Constantinople and a 20th century collection. A second panel of 96 SNPs was developed to genotype historical and modern samples in order to elucidate changes in population structuring and allele frequencies of loci associated with selective traits.

The international effort to prevent the collapse of Atlantic bluefin tuna (BFT, Thunnus thynnus, Scombridae) stocks exemplifies the challenges associated with modern marine resource conservation. Rampant mismanagement, under-reporting and IUU fishing led to decades of over-exploitation in the BFT fishery. Surveys of larval abundance in both the Gulf of Mexico and the Mediterranean Sea have been used as a proxy for both spawning biomass and recruitment by researchers attempting to improve estimates of stock abundance. Herein we used both mitochondrial and nuclear genes (CO1 and ITS1, respectively) to barcode larvae (n=188) collected from three spawning areas in the Mediterranean Sea. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following traditional methods. This disparity suggests that the efficacy of the taxonomic techniques employed during the identification of fish larvae is highly dependent on the expertise of the researchers or technicians involved. Misidentification of larvae can lead to uncertainty about the spatial distribution of a species, confusion over life history traits and population dynamics, and potentially disguise the collapse/recovery of localized spawning sites. In an effort to identify the source of these errors, we uncover several weaknesses in modern morphological taxonomy including demographic decline of expert taxonomists, flawed identification keys, reluctance to embrace technological advances and paucity of available user-friendly and modern materials. We advocate a more constructive integration of taxonomy and barcoding in order to strengthen fisheries management and safeguard against stock collapse.

The relationship between Mediterranean civilizations and Atlantic bluefin tuna (Thunnus thynnus) is the stuff of legends, having survived the rise and fall of several empires, endured dramatic climate shifts and witnessed the passing of millennia. While this relationship was documented by ancient philosophers and poets and is presently studied by scientists and the fishing industry, mysteries surrounding the species endure. Today traditional fishing techniques are fading into the past and industrial fisheries threaten the survival of the species. Herein, we have used novel molecular techniques to analyze DNA extracted from tuna bones excavated from late iron age and ancient roman settlements in coastal Iberia (4th-2nd century BC), tuna remains buried beneath the sands of Constantinople’s Byzantine-era harbour (4th-15th century AD), vertebrae closeted away in Europe’s oldest university (1911-1925) and flesh harvested from present day giant tunas. Several techniques were used to scan the entire genome for single nucleotide polymorphisms and the migration of non-coding genetic elements (NGS) as well as target changes occurring in genes subject to selective pressures (PCR and Sanger sequencing). By focusing on genes associated with metabolism, growth and immune response and changing allele frequencies indicative of population structuring, we are attempting to reconstruct the species’ adaptive response to fisheries pressure and a changing sea. Perhaps by understanding the evolutionary path taken by a species with which we have a shared past, we can discover a way to preserve a species and our relationship with the eternal sea, our past and future.

The origin of a population of great white sharks (GWS), Carcharodon carcharias, L.1758, residing in the Mediterranean Sea has remained a mystery despite repeated scientific endeavours to retrace their history. Here we analyze 18 historical specimens (30-180 years old) collected from several museums, research institutes and private collections in Italy, creating the largest dataset of Mediterranean GWS mitochondrial DNA gene sequences (i.e. D-loop and COI). Comparative phylogenetic analyses of the Mediterranean GWS with populations from global range suggested a closer evolutionary relationship with sharks in Australia- New Zealand, Japan and the Pacific US rather than to the South-African population. Estimates of the most recent common ancestor carried out using internal calibration with fossil and paleo-geographical data revealed that Mediterranean GWS population originated in the early Pliocene at the end of the Messinian Salinity Crisis (ca. 5.3 MYA). This dating supports a GWS historical long-dispersal and paleo-colonization of the Mediterranean via a route of migration through Central America, before the formation of the Isthmus of Panama in contrast with a ad hoc previous hypothesis which suggested a colonization via South Africa due to navigational errors during past climatic oscillations.