Assessment of the population structure and temporal changes in spatial dynamics and genetic characteristics of the Atlantic bluefin tuna under a fishery independent framework.

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.

Molecular mechanisms controlling physiological plasticity in marine mussels under the influence of natural and anthropogenic stress factors

Marine mussels are exceptionally well-adapted to live in transitional habitats where they are exposed to fluctuating environmental parameters and elevated levels of natural and anthropogenic stressors throughout their lifecycle. However, there is a dearth of information about the molecular mechanisms that assist in dealing with environmental changes. This project aims to investigate the molecular mechanisms governing acclimatory and stress responses of the Mediterranean mussel (Mytilus galloprovincialis) by addressing relevant life stages and environmental stressors of emerging concern. The experimental approach consisted of two phases to explore (i) the physiological processes at early life history and the consequences of plastic pollution and (ii) the adult physiology processes under natural habitats. As the first phase, I employed a plastic leachate (styrene monomer), and polystyrene microplastics to understand the modulation of cytoprotective mechanisms during the early embryo stages. Results revealed the onset of transcriptional impairments of genes involved in MXR-related transporters and other physiological processes induced by styrene and PS-MPs. In the second phase, as a preliminary analysis, microbiota profile of adult mussels at the tissue scale and its surrounding water was explored to understand microbiota structures that may reflect peculiar adaptations to the respective tissue functions. The broader experiment has been implemented to understand the variability of transcriptional profiles in the mussel digestive glands in the natural setting. All the genes employed in this study have shown possibilities to use as molecular biomarker responses throughout the year for monitoring the physiology of mussels living in a particular environment and, in turn, more properly detecting changes in the environment. As a whole, my studies provide insights into the interactions between environmental parameters, and intrinsic characters, and physiology of marine bivalves, and it could help to interpretation of responses correctly under stress conditions and climate change scenarios.

The Social Life of Pots. The reconstruction of ceramic production and distribution patterns of pottery assemblages in the Northern Levant during the Iron Age

The aim of the project is the creation of a new model for the analysis of the political and social structures of the Northern Levant during the Iron Age, through the study of the production and circulation of ceramics in urban and rural centers. The project includes an innovative approach compared to a traditional contextual and analytical study of ceramic material. The geographical area under consideration represents an ideal context for understanding these dynamics, as a place of interaction between culturally different but constantly communicating areas (Eastern Mediterranean, Syria, Upper Mesopotamia). They corresponds to present-day southeastern Turkey and northern Syria, with the Mediterranean coast and the Euphrates River as limits to the west and east, respectively. The chronological interval taken into consideration by the study extends from the twelfth century BC. to the seventh century BC, corresponding to a phase of political fragmentation of the region into small-medium state entities and their subsequent conquest by the Neo-Assyrian empire starting from the end of the ninth century BC.

Physiological and biochemical adaptation to salinity in wild halophytes suitable for Mediterranean agriculture

Due to the accelerating processes of soil salinization and shortage of fresh water, the practice of saline agriculture is gaining momentum in many areas of the world. However, there are some concerns that using saline water for irrigation may be non-environmentally sustainable, with potential to cause irreversible soil degradation. In addition, there is a lack of information on the morphological, physiological, and biochemical changes that can occur in plants when irrigated with saline water. In light of the above, the major aim of this work was to investigate the effects of a range of water salinity levels and irrigation regimes on the performances of salt tolerant species promising as future crop plants for saline agriculture. The following objectives were addressed: To determine the effects of different water regimes (leaching irrigation vs. no leaching irrigation) with water at increasing salinity concentrations on the growth, ion accumulation and water relations of Sorghum bicolor plants grown under saline soil conditions. To describe the germination response of Salicornia europaea seeds across a wide range of water salinity levels through six reliable indices for screening salinity tolerance at the seed germination stage. To explore the different physiological responses of six wild halophytes commonly found in the Mediterranean area (Artemisia absinthium, Artemisia vulgaris, Atriplex halimus, Chenopodium album, Salsola komarovii, and Sanguisorba minor), and rank their tolerance after exposure to growing levels of water salinity. To identify the main adaptation mechanisms that distinguish C3 from C4 halophytes when exposed to increasing salinity in the growth media, through a comparative study between the C3 species Atriplex hortensis and the C4 species Atriplex halimus. To identify the main adaptation mechanisms that distinguish annual from perennial halophytes when exposed to severe conditions of salinity and drought, through a comparative analysis between two annual Salicornia spp. and the perennial Sarcocornia fruticosa.

Towards a broader understanding of the effects of tidal forcing on the global ocean circulation

The study of tides and their interactions with the complex dynamics of the global ocean represents a crucial challenge in ocean modelling. This thesis aims to deepen this study from a dynamical point of view, analysing what are the tidal effects on the general circulation of the ocean. We perform different experiments of a mesoscale-permitting global ocean model forced by both atmospheric fields and astronomical tidal potential, and we implement two parametrizations to include in the model tidal phenomena that are currently unresolved, with particular emphasis to the topographic wave drag for locally dissipating internal waves. An additional experiment using a mesoscale-resolving configuration is used to compare the simulated tides at different resolutions with observed data. We find that the accuracy of modelled tides strongly depends on the region and harmonic component of interest, even though the increased resolution allows to improve the modelled topography and resolve more intense internal waves. We then focus on the impact of tides in the Atlantic Ocean and find that tides weaken the overturning circulation during the analysed period from 1981 to 2007, even though the interannual differences strongly change in both amplitude and phase. The zonally integrated momentum balance shows that tide changes the water stratification at the zonal boundaries, modifying the pressure and therefore the geostrophic balance over the entire basin. Finally, we describe the overturning circulation in the Mediterranean Sea computing the meridional and zonal streamfunctions both in the Eulerian and residual frameworks. The circulation is characterised by different cells, and their forcing processes are described with particular emphasis to the role of mesoscale and a transient climatic event. We complete the description of the overturning circulation giving evidence for the first time to the connection between meridional and zonal cells.

Spatial based approach to fisheries management. An application to bottom trawling in the strait of Sicily

At the beginning of my thesis project, considering that some stocks are in overfishing status due to both high fishing effort and high level of juveniles in the catch, my main purpose was to understand how to contribute to improving the state of the fishery resources of the Mediterranean Sea. To mitigate the overfishing, the General Fisheries Commission for the Mediterranean (GFCM) adopted several Fishery Restricted Areas, which are geographically defined areas where some specific fishing activities are temporarily or permanently banned or restricted in order to reduce the exploitation patterns and conservation of specific stocks as well as of habitats and deep-sea ecosystems, including the Essential Fish Habitats (EFH) and the Vulnerable Marine Ecosystems (VME). Considering that GFCM established 3 Fisheries Restricted Areas (FRAs) in the Strait of Sicily (SoS) in 2016 aimed at protecting the nursery areas of the deep-water rose shrimp (DPS, Parapenaeus longirostris – Lucas, 1846) and the European hake (HKE, Merluccius merluccius – Linnaeus, 1758) to reduce the exploitation pattern of undersized species, in my thesis project I devoted myself to evaluate the effect of the FRAs on the status stock and the fishery performance using a spatial bio-economic model.

Monitoring of Mediterranean marine benthic biodiversity through novel, standardized, and integrated approaches

Marine healthy ecosystems support life on Earth and human well-being thanks to their biodiversity, which is proven to decline mainly due to anthropogenic stressors. Monitoring how marine biodiversity changes trough space and time is needed to properly define and enroll effective actions towards habitat conservation and preservation. This is particularly needed in those areas that are very rich in species compared to their low surface extension and are characterized by strong anthropic pressures, such as the Mediterranean Sea. Subtidal rocky benthic Mediterranean habitats have a complex structural architecture, hosting a panoply of tiny organisms (cryptofauna) that inhabit crevices and caves, but that are still unknown. Different artificial standardized sampling structures (SSS) and methods have been developed and employed to characterize the cryptofauna, allowing for data replicability and comparability across regions. Organisms growing on these artificial structures can be identified coupling morphological taxonomy and DNA barcoding and metabarcoding. The metabarcoding allows for the identification of organisms in a bulk sample without morphological analysis, and it is based on comparing the genetic similarities of the assessed organisms with barcoding sequences present in online barcoding repositories. Nevertheless, barcoded species nowadays represent only a small portion of known species, and barcoding reference databases are not always curated and updated on a regular basis. In this Thesis I used an integrative approach to characterize benthic marine biodiversity, specifically coupling morphological and molecular techniques with the employment of SSS. Moreover, I upgraded the actual status of COI (cytochrome c oxidase subunit I) barcoding of marine metazoans, and I built a customized COI barcoding reference database for metabarcoding studies on temperate biogenic reefs. This work implemented the knowledge about diversity of Mediterranean marine communities, laying the groundworks for monitoring marine and environmental changes that will occur in the next future as consequences of anthropic and climate threats.

Evaluation and management of demersal stocks in the Adriatic: the case of common sole (Solea solea, L.) in the northern and central Adriatic Sea

This PhD thesis aimed to assess the status of common sole, one of the main commercial stocks in the Adriatic Sea, using a mix of conventional and innovative techniques to provide more reliable estimates of stock status compared to past advice. First, a meta-analysis was carried out using data-poor assessment model to analyze the whole catch assemblage of rapido fishery. The outcomes were used to estimate rebuilding time and forecast catches under different harvest control rule scenarios, with a reduction of 20% of fishing effort being suggested as a way to allow most of the species to recover to sustainable levels. Secondly, an ensemble of data-rich assessment models was developed to better incorporate uncertainty by using alternative hypotheses of main parameters. This was the first time an ensemble of models has been used in the Mediterranean to provide management advice. Consistent with data-poor analysis results, the ensemble outcomes indicated that the common sole stock was showing a recovering trend probably due to the effective management actions underway in the area rather than the moderate effort reduction according to the actual management plan. Moreover, back-calculation measurements were used to fit and compare monophasic and biphasic growth curves through the use of non-linear mixed effects models. The analyses revealed that the fitting of the biphasic curve was superior, confirming the theory that growth in size would decrease as a consequence of reproductive effort. A stock assessment simulation showed how the use of the monophasic pattern would result in a critical overestimation of biomass that could lead to a greater risk of overfishing. As a final step, a simulation-testing procedure was applied to determine the best performing reference points using stock-specific characteristic. The procedure could be routinely adopted to increase transparency in reference points calculation enhancing the credibility of scientific advice.

A coupled ocean-atmosphere system for short term forecasting in the southern european seas

This coupled model combines two state-of-the-art numerical models, NEMO for the oceanic component and WRF for the atmospheric component and implements them at an appropriate resolution. The oceanic model has been implemented starting from the Mediterranean Forecasting System with a resolution of 1/24° and the domain was extended to exactly match the grid of a newly implemented atmospheric model for the same area. The uncoupled ocean model has been validated against SST observed data, both in the simulation of an extreme event and in the short-term forecast of two seasonal periods. A new setup of the model was successfully tested in which the downward radiative fluxes were prescribed from atmospheric forecasts. Various physical schemes, domain, boundary, and initial conditions were tested with the atmospheric model to obtain the best representation of medicane Ianos. The heat fluxes calculated by the uncoupled models were compared to determine which setup gave the best energy balance between the components of the coupled model. The coupling strategy used is the traditional one, where the ocean is driven by the surface stress, heat fluxes, and radiative fluxes computed in the atmospheric component, which in turn receives the SST and surface currents. As expected, the overall skills of the coupled model are slightly degraded compared to the uncoupled models, even though the positioning and timing of the cyclone at the time of the landfall is enhanced. The mean heat fluxes do not change compared to the uncoupled model, whereas the pattern of the shortwave radiation and latent heat is changed. Moreover, the two energy fluxes are larger in absolute values than those calculated with the MFS formulas. The fact that they have opposite signs give raise to a compensation error that limits the overall degradation of the coupled simulation.

Acoustic backscatter of small pelagic fish species in the Adriatic Sea

The aim of the present study is to apply a broad range of techniques to increase the knowledge of acoustic properties of Sprattus sprattus, Scomber colias and Trachurus mediterraneus in the Adriatic Sea. A novel study using tethered live fish but not involving hooks and anesthetic was tested on T. mediterraneus and S. colias through several ex situ experiments using a split-beam scientific echosounder operating at 38, 120, and 200 kHz. The mean TS was estimated for 29 live specimens, resulting in a conversion factor b20 value of -71.4 dB re 1 m2 and -71.6 dB re 1 m2 respectively which is ~3 dB lower than the current one in use in the Mediterranean Sea. Successively, two monospecific trawl hauls were analyzed through the application of in situ approach for the computation of TS values of S. sprattus which led to six b20 values for sprat (range, -68.8 dB re 1 m2 to -65.6 dB re 1 m2), all higher than the current known value of -71.7 dB re 1 m2. The high difference up to 4.2 dB compared to the current value translates in a significant decrease of absolute sprat biomass along the time series un to 20%. Finally, 149 specimens of the three species were collected for backscattering model application(i.e. Kirchhoff-ray mode model (KRM) and Finite Element Method (FEM)) from digital images of the fish body and swimbladder obtained from Computer Tomography (CT) and X-Ray scans. The values resulting from the application of KRM and FEM are in agreement with empirical results. In general terms the present work proposes the acoustic backscatter characterization of S. colias, S. sprattus and T. mediterraneus in the Mediterranean Sea.

Methylmercury and polycyclic aromatic hydrocarbons in Mediterranean seafood: a molecular anthropological perspective

Seafood carries several contaminants, among which mercury and polycyclic aromatic hydrocarbons are those that cause major concern. Evidence exists that human populations are exposed to these environmental chemicals since ancient times, which may have driven the positive selection of specific genetic polymorphisms related to chemicals toxicokinetic. Both mercury and polycyclic aromatic hydrocarbons are able to cause DNA methylation changes in humans. Some Mediterranean populations may be particularly exposed to these contaminants, being the Mediterranean Sea at a high-risk for contamination by toxic compounds, and because of their traditionally high consumption of locally caught seafood. Starting from these premises the present thesis aims to contribute to the understanding of the molecular impact of seafood consumption on the biology of the Mediterranean population. To this end the work has been divided into four main parts: (1) the development and meta-analysis of a georeferenced database on polycyclic aromatic hydrocarbons in Mediterranean seafood aimed at identifying geographical patterns of contamination and trends that could be related to the biology of the marine organisms, to the physico-chemical properties of each hydrocarbon and to the oceanographic characteristic of the Mediterranean; (2) the development and validation of a food frequency questionnaire to estimate the intake of mercury through seafood consumption among a population living in a geographic area that is usually considered a contamination hotspot; (3) the creation of a biobank made of biological samples from members of several Italian communities together with information on their dietary habits, lifestyle and general health; (4) a review of the literature on the genetic component of individual susceptibility to methylmercury and polycyclic aromatic hydrocarbons exposure in humans, to the effects that these pollutants have on human DNA methylation, and to the evidence that Mediterranean coastal communities represent an informative case study to investigate the potential molecular impact of these chemicals.

The genetic prehistory of Northern Calabria. Archeogenomic investigation of the human remains from Grotta di Pietra Sant’Angelo and Grotta della Monaca.

Given its strategic position at the center of the Mediterranean Basin, and its unique history of contacts and migrations, Calabria is an ideal region to decipher the genetic traces of at least some of the numerous demographic prehistoric events in Southern Italy. This thesis focuses on the genetic and social changes of ancient inhabitants of Calabria, covering a timeline of approximately 7000 to 3300 years ago, ranging from the Middle Neolithic to the Middle Bronze Age. We generated the first genome-wide data from Calabria, by focusing on the single inhumation of “Grotta di Pietra Sant’Angelo” (San Lorenzo Bellizzi, Cosenza) and on the vast community found buried in “Grotta della Monaca” (Sant’Agata di Esaro, Cosenza). Supported by archaeological evidence, the primary objective of this research was to employ paleogenomic evidence to decipher funerary customs, social organization, family ties, and demographic shifts in Southern Italy over a period extending beyond three millennia. The possibility of gender-related burial practices and kinship ties among the deceased was also explored. Subsequently, the biogeographical origin and ancestry of prehistoric people of Calabria was contextualized within the broad landscape of existing data on Mediterranean populations. By generating the first genomic evidence from prehistoric Calabria, unresolved questions were addressed, related to the appearance and persistence of distinct genomic components, such as the Iran-related and the Steppe-related ancestry, whose impact on ancient Southern Italian genomes remains uncharted.