Evaluation of Silver European EEL (anguilla anguilla) for the implementation of an Effective EEL Management plan in Mediterranean Coastal Lagoons

This thesis presents SEELF (Sustainable EEL fishery) Index, a methodology for evaluation of European eel (Anguilla anguilla) for the implementation of an effective Eel Management Plan, as defined by EU Regulation No.1100/2007. SEELF uses internal and external indices, age and blood parameters, and selects suitable specimen for restocking; it is also a reliable tool for eel stock management. In fact, SEELF Index, was developed in two versions: SEELF A, to be used in field operations (catch&release, eel status monitoring) and SEELF B to be used for quality control (food production) and research (eel status monitoring). Health status was evaluated also by biomarker analysis (ChE), and data were compared with age of eel. Age determination was performed with otolith reading and fish scale reading and a calibration between the two methods was possible. The study area was the Comacchio lagoon, a brackish coastal lagoon in Italy, well known as an example of suitable environment for eel fishery, where the capability to use the local natural resources has long been a key factor for a successful fishery management. Comacchio lagoon is proposed as an area where an effective EMP can be performed, in agreement with the main features (management of basins, reduction of mortality due to predators,etc.) highlighted for designation of European Restocking Area (ERA). The ERA is a new concept, proposed as a pillar of a new strategy on eel management and conservation. Furthermore, the features of ERAs can be useful in the framework of European Scale Eel Management Plan (ESEMP), proposed as a European scale implementation of EMP, providing a more effectiveness of conservation measures for eel management.

Identificazione di possibili unita' di stock di Anguilla anguilla mediante analisi microchimica e morfometrica degli otoliti

L’anguilla europea, è una specie eurialina catadroma con un complesso ciclo biologico: l’area di riproduzione, unica, si trova molto distante da quella di distribuzione. La specie necessita di una gestione dello stock a fini conservazionistici. Il problema è europeo: lo stock è unico, distribuito in Europa e nell’Africa settentrionale, si riproduce in Atlantico ed è panmittico. C’è preoccupazione per il declino del reclutamento e delle catture di adulti. Lo scopo del progetto è di individuare possibili unità di stock nella penisola italiana. La ricerca è basata sullo studio degli otoliti mediante analisi morfometrica e microchimica. I contorni degli otoliti sono sottoposti ad analisi ellittica di Fourier per individuare eventuali gruppi. Gli otoliti sono stati levigati per effettuare: letture d’età, indagini microstrutturali al SEM delle fasi larvali, analisi microchimiche LA-ICP-MS del nucleo, studiarne l’origine e valutare l’ambiente di sviluppo. Le indagini morfometriche mostrano evidenti pattern ontogenetici, ma non legati ocorrelati alla località, sesso o anno di nascita. Le indagini microstrutturali hanno evidenziano l’alto contenuto organico nucleare, un pattern comune di crescita ed eventi chiave delle fasi larvali, con una media di 212 anelli giornalieri. La microchimica rivela che le larve si sviluppano in acque salate fino alla metamorfosi, poi migrano verso acque meno salate. Le analisi su campioni nati nello stesso anno, evidenziano due gruppi: individui di rimonta naturale e individui di ripopolamento. I profili nucleo bordo evidenziano la permanenza a salinità intermedie degli adulti. L’attività di ricerca si è dimostrata proficua dal punto di vista tecnico con la messa a punto di protocolli innovativi e con forti ricadute sulla riduzione dei tempi e costi d’analisi. Il debole segnale di possibili unità di stock andrà verificato in futuro mediante analisi più dettagliate discriminando meglio la storia di ogni singolo individuo.

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.

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.

Asset management of wastewater networks

Asset Management (AM) is a set of procedures operable at the strategic-tacticaloperational level, for the management of the physical asset’s performance, associated risks and costs within its whole life-cycle. AM combines the engineering, managerial and informatics points of view. In addition to internal drivers, AM is driven by the demands of customers (social pull) and regulators (environmental mandates and economic considerations). AM can follow either a top-down or a bottom-up approach. Considering rehabilitation planning at the bottom-up level, the main issue would be to rehabilitate the right pipe at the right time with the right technique. Finding the right pipe may be possible and practicable, but determining the timeliness of the rehabilitation and the choice of the techniques adopted to rehabilitate is a bit abstruse. It is a truism that rehabilitating an asset too early is unwise, just as doing it late may have entailed extra expenses en route, in addition to the cost of the exercise of rehabilitation per se. One is confronted with a typical ‘Hamlet-isque dilemma’ – ‘to repair or not to repair’; or put in another way, ‘to replace or not to replace’. The decision in this case is governed by three factors, not necessarily interrelated – quality of customer service, costs and budget in the life cycle of the asset in question. The goal of replacement planning is to find the juncture in the asset’s life cycle where the cost of replacement is balanced by the rising maintenance costs and the declining level of service. System maintenance aims at improving performance and maintaining the asset in good working condition for as long as possible. Effective planning is used to target maintenance activities to meet these goals and minimize costly exigencies. The main objective of this dissertation is to develop a process-model for asset replacement planning. The aim of the model is to determine the optimal pipe replacement year by comparing, temporally, the annual operating and maintenance costs of the existing asset and the annuity of the investment in a new equivalent pipe, at the best market price. It is proposed that risk cost provide an appropriate framework to decide the balance between investment for replacing or operational expenditures for maintaining an asset. The model describes a practical approach to estimate when an asset should be replaced. A comprehensive list of criteria to be considered is outlined, the main criteria being a visà- vis between maintenance and replacement expenditures. The costs to maintain the assets should be described by a cost function related to the asset type, the risks to the safety of people and property owing to declining condition of asset, and the predicted frequency of failures. The cost functions reflect the condition of the existing asset at the time the decision to maintain or replace is taken: age, level of deterioration, risk of failure. The process model is applied in the wastewater network of Oslo, the capital city of Norway, and uses available real-world information to forecast life-cycle costs of maintenance and rehabilitation strategies and support infrastructure management decisions. The case study provides an insight into the various definitions of ‘asset lifetime’ – service life, economic life and physical life. The results recommend that one common value for lifetime should not be applied to the all the pipelines in the stock for investment planning in the long-term period; rather it would be wiser to define different values for different cohorts of pipelines to reduce the uncertainties associated with generalisations for simplification. It is envisaged that more criteria the municipality is able to include, to estimate maintenance costs for the existing assets, the more precise will the estimation of the expected service life be. The ability to include social costs enables to compute the asset life, not only based on its physical characterisation, but also on the sensitivity of network areas to social impact of failures. The type of economic analysis is very sensitive to model parameters that are difficult to determine accurately. The main value of this approach is the effort to demonstrate that it is possible to include, in decision-making, factors as the cost of the risk associated with a decline in level of performance, the level of this deterioration and the asset’s depreciation rate, without looking at age as the sole criterion for making decisions regarding replacements.

Assessing the state of Nephrops norvegicus and management measures in the Central Adriatic Sea

Nephrops norvegicus is a sedentary bottom-dwelling crustacean that represents one of the main commercial species exploited in the Adriatic Sea (Central Mediterranean). An evaluation of the status of this important resource is thus extremely important in order to manage it in a sustainable way. The evaluation of N. norvegicus is complicated by several issues, mainly: (i) the complex biology and behaviour of the species itself, (ii) the presence of subpopulations with different biological traits within the same stock unit. Relevant concentration of N.norvegicus occurs within the Pomo/Jabuka Pits area which is characterised by peculiar oceanographic and geophysical conditions. This area represented for a long time an important fishing ground shared by Italian and Croatian fleets and recently a Fishery Restricted Area (FRA) was established there. The aim of the present study is to perform for the first time an evaluation of the status of the N.norvegicus subpopulation inhabiting the Pomo/Jabuka Pits also accounting for the possible effects on it of the management measures. To achieve this, the principal fisheryindependent and fishery-dependent dataset available for the study area were firstly analysed and then treated. Data collected by the CNR-IRBIM of Ancona through both indirect (“UWTV”) and direct (trawling) methods were refined by means of a revision of the time series and related biases, and a modelling approach accounting for environmental and fishery effects, respectively. Commercial data for both Italy and Croatia were treated in order to obtain landings and length distributions for the Pomo area only; an historical reconstruction of data starting from 1970 was carried out for both countries. The obtained information was used as input for a Bayesian length-based stock assessment model developed through the CASAL software; the flexibility of this model is recommended for N.norvegicus and similar species allowing to deal with sex- and fleet-based integrated assessment method

The environmental DNA in the risk assessment and decision making processes for the invasive species management in agri-food sector, hydraulic security and biodiversity conservation

The use of environmental DNA (eDNA) analysis as a monitoring tool is becoming more and more widespread. The eDNA metabarcoding methods allow rapid community assessments of different target taxa. This work is focused on the validation of the environmental DNA metabarcoding protocol for biodiversity assessment of freshwater habitats. Scolo Dosolo was chosen as study area and three sampling points were defined for traditional and eDNA analyses. The gutter is a 205 m long anthropic canal located in Sala Bolognese (Bologna, Italy). Fish community and freshwater invertebrate metazoans were the target groups for the analysis. After a preliminary study in summer 2019, 2020 was devoted to the sampling campaign with winter (January), spring (May), summer (July) and autumn (October) surveys. Alongside with the water samplings for the eDNA study, also traditional fish surveys using the electrofishing technique were performed to assess fish community composition; census on invertebrates was performed using an entomological net and a surber sampler. After in silico analysis, the MiFish primer set amplifying a fragment of the 12s rRNA gene was selected for bony fishes. For invertebrates the FWHF2 + FWHR2N primer combination, that amplifies a region of the mitochondrial coi gene, was chosen. Raw reads were analyzed through a bioinformatic pipeline based on OBITools metabarcoding programs package and QIIME2. The OBITools pipeline retrieved seven fish taxa and 54 invertebrate taxa belonging to six different phyla, while QIIME2 recovered eight fish taxa and 45 invertebrate taxa belonging to the same six phyla as the OBITools pipeline. The metabarcoding results were then compared with the traditional surveys data and bibliographic records. Overall, the validated protocol provides a reliable picture of the biodiversity of the study area and an efficient support to the traditional methods.

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.

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.

Catchability and survival of the resources during fishing operation

The present Ph.D. thesis aims to test and evaluate by-catch reduction devices (BRDs) that minimize the retention of undersized fish and do not penalize revenues of the fishing industry. Considering that a fraction of fish that escape from fishing gear or that are rejected at the sea probably does not survive (unaccounted mortality), it is a major concern for sustainable fisheries management, as unaccounted mortality may lead to biased stock assessment since they will tend to underestimate fishing mortality and overestimate stock size. In this context, in the present Ph.D. thesis, the escape survival (i.e. survival of the fish escaped through the trawl net codend) of the Mullus barbatus Linnaeus 1758 and the discard survival (survival of fish rejected at the sea after being hauled on deck) of Trachurus trachurus were evaluated for the first time in the central Mediterranean Sea. In conclusion, the use of underwater lights in Mediterranean trawl fisheries should be carefully regulated through ad hoc measures that are currently lacking, to minimize the potential impacts of artificial light on some already overexploited stocks. Even if further works should be carried out in the future to test BRDs performances in different areas and seasons, the T90 50 mm codend and the Grid-T45 40 mm seem promising tools to reduce the catch of undersized individuals and contribute to mitigating the current overfishing of Parapenaeus longirostris and Merluccius merluccius. The escape survival of M. barbatus was high and thanks to an improved methodology the bias in the sampling was minimized. However, for improved stock assessment of M. barbatus, the experiment should be repeated to provide accurate escape mortality estimates. While the discard survival of T. trachurus was very low and according to the landing obligation (Reg. EU 1380/2013) all the juveniles of the species should be landed.