DNA+eDNA: integration of traditional and emerging tools for monitoring marine ecosystems

This thesis highlights the critical role of accurate species identification for evaluating marine biodiversity, ecological roles, and conservation needs. Traditional taxonomy often struggles with the identification of cryptic species, leading to the reliance on molecular methods such as DNA analysis. These techniques have improved species identification, revealed cryptic speciation, and informed fisheries management by delineating stock boundaries, tracking movements, and assessing reproductive strategies like multiple paternity. Moreover, genetic tools can help assess population vulnerabilities, providing vital data for conservation efforts. Environmental DNA (eDNA) has revolutionized biodiversity studies, offering high-throughput, non-invasive methods for assessing community composition and species distribution. Indeed, part of the present thesis focuses on optimizing eDNA methodologies and applying them to assess the effects of microplastic exposure on meiofaunal diversity. Preliminary findings suggest that eDNA’s potential is hindered by incomplete public reference libraries. On the other hand, the method needs improving the protocols for sampling and laboratory processes. For this reason, good-practices strategies were evaluated and proposed, aiming to enhance the reliability and comparability of eDNA studies. The thesis also investigates taxonomic uncertainties in cartilaginous fish, including sharks, rays, and chimaeras. By building curated reference libraries for species inhabiting five FAO regions, we identified gaps in public datasets and highlights the need for a systematic review of a few taxonomic groups. The genetic diversity and connectivity of Mediterranean torpedoes, as soon as the uncovering cryptic species, emphasized the necessity of a comprehensive revision of the Torpediniformes order. Similarly, using molecular markers we reported the first record of a rare stingray species in Sardinia. Additionally, we exposed taxonomic ambiguities in Mediterranean stingrays, advocating for further research and conservation actions. Further chapters present case studies on the first record, genetic structure and population connectivity of rare and endangered skates along the Sardinian coast. Applying integrated approaches, we improved our knowledge about these elusive species and their ecological roles. Data from these studies contribute to baseline knowledge, critical for fisheries management and conservation planning. Lastly, the final chapters focus on the population genetic structure and variability of two commercially important elasmobranch species using nuclear DNA markers. These studies provide foundational data for monitoring population dynamics and assessing the effectiveness of fisheries management. In conclusion, this thesis integrates traditional and innovative molecular methods to enhance marine biodiversity assessment and conservation, with a particular focus on sharks, rays, skates, and chimaeras. By addressing critical gaps in knowledge and methodology, it offers a pathway toward more effective management and protection of marine ecosystems and of these vulnerable ecologically vital species.