Novel tools for conservation genetics in marine fish: population structure and evolution of the European hake (Merluccius merluccius) inferred by SNP variation and applications to traceability

The research presented in my PhD thesis is part of a wider European project, FishPopTrace, focused on traceability of fish populations and products. My work was aimed at developing and analyzing novel genetic tools for a widely distributed marine fish species, the European hake (Merluccius merluccius), in order to investigate population genetic structure and explore potential applications to traceability scenarios. A total of 395 SNPs (Single Nucleotide Polymorphisms) were discovered from a massive collection of Expressed Sequence Tags, obtained by high-throughput sequencing, and validated on 19 geographic samples from Atlantic and Mediterranean. Genome-scan approaches were applied to identify polymorphisms on genes potentially under divergent selection (outlier SNPs), showing higher genetic differentiation among populations respect to the average observed across loci. Comparative analysis on population structure were carried out on putative neutral and outlier loci at wide (Atlantic and Mediterranean samples) and regional (samples within each basin) spatial scales, to disentangle the effects of demographic and adaptive evolutionary forces on European hake populations genetic structure. Results demonstrated the potential of outlier loci to unveil fine scale genetic structure, possibly identifying locally adapted populations, despite the weak signal showed from putative neutral SNPs. The application of outlier SNPs within the framework of fishery resources management was also explored. A minimum panel of SNP markers showing maximum discriminatory power was selected and applied to a traceability scenario aiming at identifying the basin (and hence the stock) of origin, Atlantic or Mediterranean, of individual fish. This case study illustrates how molecular analytical technologies have operational potential in real-world contexts, and more specifically, potential to support fisheries control and enforcement and fish and fish product traceability.

Demersal communities in the Mediterranean Sea: a case study of Triglidae (Osteichthyes, Scorpaeniformes) on the conservation and sustainable use of marine resources

An appropriate management of fisheries resources can only be achieved with the continuous supply of information on the structure and biology of populations, in order to predict the temporal fluctuations. This study supports the importance of investigating the bio-ecology of increasingly exploited and poorly known species, such as gurnards (Osteichthyes, Triglidae) from Adriatic Sea (Mediterranean), to quantify their ecological role into marine community. It also focuses on investigate inter and intra-specific structuring factor of Adriatic population. These objectives were achieved by: 1) investigating aspects of the population dynamics; 2) studying the feeding biology through the examination of stomach contents; 3) using sagittal otoliths as potential marker of species life cycle; 4) getting preliminary data on mDNA phylogeny. Gurnards showed a specie-specific “critical size” coinciding with the start of sexual maturity, the tendency to migrate to greater depths, a change of diet from crustaceans to fish and an increase of variety of food items eaten. Distribution of prey items, predator size range and depth distribution were the main dimensions that influence the breadth of trophic niche and the relative difference amongst Adriatic gurnards. Several feeding preferences were individuated and a possible impact among bigger-size gurnards and other commercial fishes (anchovy, gadoids) and Crustacea (such as mantis prawn and shrimps) were to be necessary considered. Otolith studies showed that gurnard species have a very fast growth despite other results in other areas; intra-specific differences and the increase in the variability of otolith shape, sulcus acusticus shape, S:O ratios, sulcus acusticus external crystals arrangement were shown between juveniles and adults and were linked to growth (individual genetic factors) and to environmental conditions (e.g. depth and trophic niche distribution). In order to facilitate correct biological interpretation of data, molecular data were obtained for comparing morphological distance to genetic ones.

Marine biodiversity survey in the Northern Red Sea: a large-scale monitoring carried out in collaboration with volunteer divers

Concerns over global change and its effect on coral reef survivorship have highlighted the need for long-term datasets and proxy records, to interpret environmental trends and inform policymakers. Citizen science programs have showed to be a valid method for collecting data, reducing financial and time costs for institutions. This study is based on the elaboration of data collected by recreational divers and its main purpose is to evaluate changes in the state of coral reef biodiversity in the Red Sea over a long term period and validate the volunteer-based monitoring method. Volunteers recreational divers completed a questionnaire after each dive, recording the presence of 72 animal taxa and negative reef conditions. Comparisons were made between records from volunteers and independent records from a marine biologist who performed the same dive at the same time. A total of 500 volunteers were tested in 78 validation trials. Relative values of accuracy, reliability and similarity seem to be comparable to those performed by volunteer divers on precise transects in other projects, or in community-based terrestrial monitoring. 9301 recreational divers participated in the monitoring program, completing 23,059 survey questionnaires in a 5-year period. The volunteer-sightings-based index showed significant differences between the geographical areas. The area of Hurghada is distinguished by a medium-low biodiversity index, heavily damaged by a not controlled anthropic exploitation. Coral reefs along the Ras Mohammed National Park at Sharm el Sheikh, conversely showed high biodiversity index. The detected pattern seems to be correlated with the conservation measures adopted. In our experience and that of other research institutes, citizen science can integrate conventional methods and significantly reduce costs and time. Involving recreational divers we were able to build a large data set, covering a wide geographic area. The main limitation remains the difficulty of obtaining an homogeneous spatial sampling distribution.