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.

Modellizzazione bioeconomica per la gestione dei piccoli pelagici nel Mar Adriatico

Stocks’ overexploitation and socio-economic sustainability are two major issues currently at stake in European fisheries. In this view the European Commission is considering the implementation of management plans as a means to move towards a longer-term perspective on fisheries management, to consider regional differences and to increase stakeholder involvement. Adriatic small pelagic species (anchovies and sardines) are some of the most studied species in the world from a biologic perspective; several economic analysis have also been realised on Italian pelagic fishery; despite that, no complete bioeconomic modelization has been carried out yet considering all biologic, technical and economic issues. Bioeconomic models cannot be considered foolproof tools but are important implements to help decision makers and can supply a fundamental scientific basis for management plans. This research gathers all available information (from biologic, technologic and economic perspectives) in order to carry out a bioeconomic model of the Adriatic pelagic fishery. Different approaches are analyzed and some of them developed to highlight potential divergences in results, characteristics and implications. Growth, production and demand functions are estimated. A formal analysis about interaction and competition between Italian and Croatian fleet is examined proposing different equilibriums for open access, duopoly and a form of cooperative solution. Anyway normative judgments are limited because of poor knowledge of population dynamics and data related to the Croatian fleet.

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.

The conundrum of human visceral leishmaniasis in Emilia-Romagna, Italy: are wild and peridomestic animals potential reservoirs?

Leishmaniasis is a complex parasitic disease caused by intracellular protozoans of the genus Leishmania mainly transmitted by the bite of sand flies. In Italy, leishmaniasis is caused by Leishmania infantum, responsible for the human visceral and canine leishmaniases (HVL and CanL, respectively). Within Emilia-Romagna region, Italy, recent molecular studies indicated that L. infantum strains circulating in dogs and humans are different. This suggests that an animal reservoir other than dog should be evaluated in the epidemiology of HVL in Emilia-Romagna. Therefore, the main aim of this PhD project was to investigate the role of wild and peridomestic mammals as potential animal reservoirs of L. infantum in the regional zones where HVL foci are still active, also evaluating the possible role of arthropod vectors other than phlebotomine sandflies as vectors of Leishmania spp. in the sylvatic cycle of the protozoa. Overall, 206 specimens of different animal species (roe deer, rats, mice, badgers, hares, polecats, foxes, beech martens, bank voles, hedgehogs, and shrews), collected in Emilia-Romagna were screened for Leishmania with a real-time PCR, revealing a prevalence of 33% for roe deer (first report in this species). Positivity was also found in brown rats (10.6%), black rats (13.1%), mice (10%), badgers (25%), hedgehogs (80%) and bank voles (11%). To distinguish the two strains of L. infantum circulating in Emilia-Romagna, a nested PCR protocol optimized for animal tissues was developed, demonstrating that over 90% of L. infantum infections in roe deer were due to the strain isolated from humans and suggesting their possible role as reservoirs in the study area. Furthermore, the presence of Leishmania kDNA was detected in unfed larvae, nymphs and males of questing Ixodes ricinus ticks collected in regional parks of Emilia-Romagna suggesting their possible role in the transmission of L. infantum in a sylvatic or rural cycle.

Moving toward stock units identification based on spatial population structure of marine species in the Mediterranean Sea and adjacent waters through multidisciplinary and holistic approaches for the sustainability of fisheries resources

Investigating stock identity of marine species in a multidisciplinary holistic approach can reveal patterns of complex spatial population structure and signatures of potential local adaptation. The population structure of common sole (Solea solea) in the Mediterranean Sea was delineated using genomic and otolith data, including single nucleotide polymorphisms (SNPs) markers and otolith data. SNPs were correlated with environmental and spatial variables to evaluate the impact of these features on the actual genetic population structure. Integrated holistic approach was applied to combine the tracers with different spatio-temporal scales. SNPs data was also used to illustrate the population structure of European hake (Merluccius merluccius) within the Alboran Sea, extending into the neighboring Mediterranean Sea and Atlantic Ocean. The aim was to identify patterns of neutral and potential adaptive genetic variation by applying seascape genomic framework. Results from both genetic and otolith data suggested significant divergence among putative populations of common sole, confirming a clear separation between Western, Adriatic Sea and Eastern Mediterranean Sea. Evidence of fine-scale population structure in the Western Mediterranean Sea was observed at outlier loci level and in the Adriatic. Our study not only indicates that separation among Mediterranean sole population is led primarily by neutral processes, but it also suggests the presence of local adaptation influenced by environmental and spatial factors. The holistic approach by considering the spatio-temporal scales of variation confirmed that the same pattern of separation between these geographical sites is currently occurring and has occurred for many generations. Results showed the occurrence of population structure in Merluccius merluccius by detecting westward–eastward differentiation among populations and distinct subgroups at a fine geographical scale using outlier SNPs. These results enhance the knowledge of the population structure of commercially relevant species to support the application of spatial stock assessment models, including a redefinition of fishery management units.

Bycatch and discard issues in the Adriatic demersal fisheries

Commercial fisheries exploiting the demersal resources of Western Adriatic Sea produce high bycatch and discard rates; the most important are bottom trawls, hydraulic dredges and passive nets. The five papers here published assess these fisheries’ impacts and investigate the potential of specific solutions to promote more sustainable exploitation. Papers I, II, III focused on bottom trawl fishery. Paper I compared the catch performance of the two legal codends by accounting for the entire species community in trawl catches. 50% of the catch in weight and 80% in count numbers consisted of discarded species, highlighting the severe impact of this fishery. Paper II estimated the selectivity of experimental codend having meshes turned 90° (T90) and of traditional diamond mesh codend with same mesh size. The T90 codend improved the size selection for all the target species. Paper III investigated the use of T90 meshes in the extension piece together with a reduction in mesh number at extension circumference. Results revealed that both these changes applied in the extension piece did not improve the selectivity of the main target species. Paper IV focused on hydraulic dredge fishery targeting the striped venus clam by assessing the clams’ size selection process operated by the dredge. 25% of the clams caught were not size selected due to clogging phenomenon in the dredge. The clam length with 50% retention probability was 18.9 mm, highlighting that the additional size selection process of sorting sieve is necessary to land only the legal clams >22 mm. Paper V compared the catch performance of innovative fish pots and of traditional trammel net. A similar catch efficiency between the two gears for the commercial portion was observed, while the trammel net produced significantly more discards in terms of species number and weight. All the results are discussed in fisheries management perspective.

Structural and stratigraphic control on hypogene dissolution in carbonate rocks: case studies of cave analogues and implications for karst reservoirs

The aim of this research is to improve the understanding of the factors that control the formation of karst porosity in hypogene settings and its associated patterns of void-conduit networks. Subsurface voids created by hypogene dissolution may span from few microns to decametric tubes providing interconnected conduit systems and forming highly anisotropic permeability domains in many reservoirs. Characterizing the spatial-morphological organization of hypogene karst is a challenging task that has dramatic implications for the applied industry, given that only partial data can be acquired from the subsurface by indirect techniques. Therefore, two outcropping cave analogues are examined: the Cavallone-Bove Cave in the Majella Massif (Italy), and the karst systems of the Salitre Formation (Brazil). In the latter, a peculiar example of hypogene speleogenesis associated with silicification has been studied, providing an analogue of many karstified reservoirs hosted in cherts or cherty-carbonates within mixed sedimentary sequences. The first part of the thesis is focused on the relationships between fracture patterns and flow pathways in deformed units in: 1) a fold-and-thrust setting (Majella Massif); 2) a cratonic block (Brazil). These settings represent potential playgrounds for the migration and accumulation of geofluids, where hypogene conduits may affect flow pathways, fluid storage, and reservoir properties. The results indicate that localized deformation producing cross-formational fracture zones associated with anticline hinges or fault damage zones is critical for hypogene fluid migration and karstification. The second part of the thesis deals with the multidisciplinary study of hydrothermal silicification and hypogene dissolution in Calixto Cave (Brazil). Petrophysical analyses and a geochemical characterization of silica deposits are used to unravel the spatial-morphological organization of the conduit system and its speleogenesis. The novel results obtained from this cave shed new light on the relationship between hydrothermal silicification, hypogene dissolution and the development of multistorey cave systems in layered carbonate-siliciclastic sequences.