Rediscovering our relationship with the sea: Unlocking the evolutionary history of the mighty bluefin tuna using novel paleogenetic techniques and ancient tuna remains

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\u2019s Byzantine-era harbour (4th-15th century AD), vertebrae closeted away in Europe\u2019s 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\u2019 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

Misidentification of fish larvae: A call for caution and taxonomic reform

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

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n= 326) and from these 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p=0.034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts. This article is protected by copyright. All rights reserved.status: accepte