The genetic signature of Neolithic in Greece

The Neolithic is characterized by the transition from a subsistence economy, based on hunting and gathering, to one based on food producing. This important change was paralleled by one of the most significant demographic increase in the recent history of European populations. The earliest Neolithic sites in Europe are located in Greece. However, the debate regarding the colonization route followed by the Middle-eastern farmers is still open. Based on archaeological, archaeobotanical, craniometric and genetic data, two main hypotheses have been proposed. The first implies the maritime colonization of North-eastern Peloponnesus from Crete, whereas the second points to an island hopping route that finally brought migrants to Central Greece. To test these hypotheses using a genetic approach, 206 samples were collected from the two Greek regions proposed as the arrival point of the two routes (Korinthian district and Euboea). Expectations for each hypothesis were compared with empirical observations based on the analysis of 60 SNPs and 26 microsatellite loci of Y-chromosome and mitochondrial DNA hypervariable region I. The analysis of Y-chromosome haplogroups revealed a strong genetic affinity of Euboea with Anatolian and Middle-eastern populations. The inferences of the time since population expansion suggests an earlier usage of agriculture in Euboea. Moreover, the haplogroup J2a-M410, supposed to be associated with the Neolithic transition, was observed at higher frequency and variance in Euboea showing, for both these parameters, a decreasing gradient moving from this area. The time since expansion estimates for J2a-M410 was found to be compatible with the Neolithic and slightly older in Euboea. The analysis of mtDNA resulted less informative. However, a higher genetic affinity of Euboea with Anatolian and Middle-eastern populations was confirmed. These results taken as a whole suggests that the most probable route followed by Neolithic farmers during the colonization of Greece was the island hopping route.

A molecular phylogeny of bivalve mollusks: ancient radiations and divergences as revealed by mitochondrial genes

The main scope of my PhD is the reconstruction of the large-scale bivalve phylogeny on the basis of four mitochondrial genes, with samples taken from all major groups of the class. To my knowledge, it is the first attempt of such a breadth in Bivalvia. I decided to focus on both ribosomal and protein coding DNA sequences (two ribosomal encoding genes -12s and 16s -, and two protein coding ones - cytochrome c oxidase I and cytochrome b), since either bibliography and my preliminary results confirmed the importance of combined gene signals in improving evolutionary pathways of the group. Moreover, I wanted to propose a methodological pipeline that proved to be useful to obtain robust results in bivalves phylogeny. Actually, best-performing taxon sampling and alignment strategies were tested, and several data partitioning and molecular evolution models were analyzed, thus demonstrating the importance of molding and implementing non-trivial evolutionary models. In the line of a more rigorous approach to data analysis, I also proposed a new method to assess taxon sampling, by developing Clarke and Warwick statistics: taxon sampling is a major concern in phylogenetic studies, and incomplete, biased, or improper taxon assemblies can lead to misleading results in reconstructing evolutionary trees. Theoretical methods are already available to optimize taxon choice in phylogenetic analyses, but most involve some knowledge about genetic relationships of the group of interest, or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications. The method I proposed measures the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, it also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses.

Open source intelligence applicata all'analisi criminologica del terrorismo

A partire dagli anni '70, si è assistito ad un progressivo riassetto geopolitico a livello mondiale Grazie anche all’evoluzione tecnologica ed alla sua diffusione di massa, il tempo e lo spazio si contraggono nel processo di globalizzazione che ha caratterizzato le società contemporanee ove l'informazione e la comunicazione assumono ormai un ruolo centrale nelle dinamiche di conoscenza. Il presente studio, intende far luce in primis sulla disciplina dell'intelligence, così come enunciata in ambito militare e "civile", in particolare nel contesto USA, NATO ed ONU, al fine quindi di evidenziare le peculiarità di una nuova disciplina di intelligence, cosiddetta Open Source Intelligence, che ha come elemento di innovazione l'utilizio delle informazioni non classificate. Dopo aver affrontato il problema della concettualizzazione ed evoluzione del fenomeno terroristico, sarà posto il focus sull’espressione criminale ad oggi maggiormente preoccupante, il terrorismo internazionale di matrice islamica, in prospettiva multidimensionale, grazie all’adozione di concetti criminologici interdisciplinari. Sotto il profilo della sperimentazione, si è, quindi, deciso di proporre, progettare e sviluppare l’architettura della piattaforma Open Source Intellicence Analysis Platform,un tool operativo di supporto per l’analista Open Source Intelligence, che si pone quale risorsa del’analisi criminologica, in grado di fornire un valido contributo, grazie al merge tra practice e research, nell’applicazione di tale approccio informativo al fenomeno terroristico.

Diet of bluefin tuna (Thunnus thynnus) and swordfish (Xhipias gladius) in the Adriatic Sea

The present issue analyses bluefin tuna (Thynnus thunnus) and swordfish (Xiphias glaudis) diet, caught by professional long-line fishing in the middle Adriatic Sea (Pomo pit). These species represent apex predators in pelagic environment that may play key roles in determining food web structure and ecosystem dynamics. The studies about their feedings habits, based upon stomach contents analysis, are important for the comprehension of biological and ecological interaction. Over the years, many studies have been performed on the diet of tuna and swordfish in the Mediterranean Sea. This research is based on a fairly wide number of analyzed stomach contents, in comparison with the previous ones. In this work, the analysis of 340 stomach contents of bluefin tuna caught by long-line in the central Adriatic sea confirms in general the opportunistic behaviour of this species. Finding support the hypothesis that Adriatic tuna and swordfish chase their food over a wide bathymetric zone and probably near the surface at night. No indication of food preference respect to size of predator or sample season are found. It seems that the two species are able to cohabit because their trophic niche are not overlapped, changing during the time and the vertical and horizontal space.

Distribution and state of fishery resources in the Northern and Central Adriatic Sea using trawl surveys data

The Ecosystem Approach to Fisheries represents the most recent research line in the international context, showing interest both towards the whole community and toward the identification and protection of all the “critical habitats” in which marine resources complete their life cycles. Using data coming from trawl surveys performed in the Northern and Central Adriatic from 1996 to 2010, this study provides the first attempt to appraise the status of the whole demersal community. It took into account not only fishery target species but also by-catch and discharge species by the use of a suite of biological indicators both at population and multi-specific level, allowing to have a global picture of the status of the demersal system. This study underlined the decline of extremely important species for the Adriatic fishery in recent years; adverse impact on catches is expected for these species in the coming years, since also minimum values of recruits recently were recorded. Both the excessive exploitation and environmental factors affected availability of resources. Moreover both distribution and nursery areas of the most important resources were pinpointed by means of geostatistical methods. The geospatial analysis also confirmed the presence of relevant recruitment areas in the North and Central Adriatic for several commercial species, as reported in the literature. The morphological and oceanographic features, the relevant rivers inflow together with the mosaic pattern of biocenoses with different food availability affected the location of the observed relevant nursery areas.

Genetic characterization, population history and evolutionary medicine perspective in two native south american populations: Yanesha and Wichi

Two Amerindian populations from the Peruvian Amazon (Yanesha) and from rural lowlands of the Argentinean Gran Chaco (Wichi) were analyzed. They represent two case study of the South American genetic variability. The Yanesha represent a model of population isolated for long-time in the Amazon rainforest, characterized by environmental and altitudinal stratifications. The Wichi represent a model of population living in an area recently colonized by European populations (the Criollos are the population of the admixed descendents), whose aim is to depict the native ancestral gene pool and the degree of admixture, in relation to the very high prevalence of Chagas disease. The methods used for the genotyping are common, concerning the Y chromosome markers (male lineage) and the mitochondrial markers (maternal lineage). The determination of the phylogeographic diagnostic polymorphisms was carried out by the classical techniques of PCR, restriction enzymes, sequencing and specific mini-sequencing. New method for the detection of the protozoa Trypanosoma cruzi was developed by means of the nested PCR. The main results show patterns of genetic stratification in Yanesha forest communities, referable to different migrations at different times, estimated by Bayesian analyses. In particular Yanesha were considered as a population of transition between the Amazon basin and the Andean Cordillera, evaluating the potential migration routes and the separation of clusters of community in relation to different genetic bio-ancestry. As the Wichi, the gene pool analyzed appears clearly differentiated by the admixed sympatric Criollos, due to strict social practices (deeply analyzed with the support of cultural anthropological tools) that have preserved the native identity at a diachronic level. A pattern of distribution of the seropositivity in relation to the different phylogenetic lineages (the adaptation in evolutionary terms) does not appear, neither Amerindian nor European, but in relation to environmental and living conditions of the two distinct subpopulations.

Study of variability and genetic structure of European populations of Myotis emarginatus and Myotis capaccinii (Chiroptera, Vespertilionidae)

The Geoffroy’s bat Myotis emarginatus is mainly present in southern, south-eastern and central Europe (Červerný, 1999) and is often recorded from northern Spain (Quetglas, 2002; Flaquer et al., 2004). It has demonstrated the species’ preference for forest. Myotis capaccinii, confined to the Mediterranean (Guille´n, 1999), is classified as ‘vulnerable’ on a global scale (Hutson, Mickleburgh & Racey, 2001). In general, the species preferred calm waters bordered by well-developed riparian vegetation and large (> 5 m) inter-bank distances (Biscardi et al. 2007). In this study we present the first results about population genetic structure of these two species of genus Myotis. We used two methods of sampling: invasive and non-invasive techniques. A total of 323 invasive samples and a total of 107 non-invasive samples were collected and analyzed. For Myotis emarginatus we have individuated for the first time a set of 7 microsatellites, which can work on this species, started from a set developed on Myotis myotis (Castella et al. 2000). We developed also a method for analysis of non-invasive samples, that given a good percentage of positive analyzed samples. The results have highlighted for the species Myotis emarginatus the presence on the European territory of two big groups, discovered by using the microsatellites tracers. On this species, 33 haplotypes of Dloop have been identified, some of them are presented only in some colonies. We identified respectively 33 haplotypes of Dloop and 10 of cytB for Myotis emarginatus and 25 of dloop and 15 of cytB for Myotis capaccinii. Myotis emarginatus’ results, both microsatellites and mtDNA, show that there is a strong genetic flow between different colonies across Europe. The results achieved on Myotis capaccinii are very interesting, in this case either for the microsatellites or the mitochondrial DNA sequences, and it has been highlighted a big difference between different colonies.

Ecological genetics and conservation genomics of wolf (Canis lupus)

In the present work, we apply both traditional and Next Generation Sequencing (NGS) tools to investigate some of the most important adaptive traits of wolves (Canis lupus). In the first part, we analyze the variability of three Major Histocompatibility Complex (MHC) class II genes in the Italian wolf population, also studying their possible role in mating choice and their influence on fitness traits. In the second section, as part of a larger canid genome project, we will exploit NGS data to investigate the transcript-level differences between the wolf and the dog genome that can be correlated to domestication.

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.

Taxonomy, phylogeny and reproductive ecology of Gentiana lutea L.

This research focuses on taxonomy, phylogeny and reproductive ecology of Gentiana lutea. L.. Taxonomic analysis is a critical step in botanical studies, as it is necessary to recognize taxonomical unit. Herbarium specimens were observed to assess the reliability of several subspecies-diagnostic characters. The analysis of G. lutea genetic variability and the comparison with that of the other species of sect. Gentiana were performed to elucidate phylogenetic relationships among G. lutea subspecies and to propose a phylogenetic hypothesis for the evolution and the colonization dynamics of the section. Appropriate scientific information is critical for the assessment of species conservation status and for effective management plans. I carried out field work on five natural populations and performed laboratory analyses on specific critical aspects, with special regard to G. lutea breeding system and type and efficiency of plant-pollinator system. Bracts length is a reliable character to identify subsp. vardjanii, however it is not exclusive, hence to clearly identify subsp. vardjanii, other traits have to be considered. The phylogenetic hypotheses obtained from nuclear and chloroplast data are not congruent. Nuclear markers show a monophyly of sect. Gentiana, a strongly species identity of G. lutea and clear genetic identity of subsp. vardjanii. The little information emerging from plastid markers indicate a weak signal of hybridization and incomplete sorting of ancestral lineages. G. lutea shows a striking variation in intra-floral dichogamy probably evolved to reduce pollen-stigma interference. Although the species is partially self-compatible, pollen vectors are necessary for a successful reproduction, and moreover it shows a strong inbreeding depression. G. lutea is a generalist species: within its spectrum of visitors is possible to recognize "nectar thieves" and pollinators with sedentary or dynamic behaviour. Pollen limitation is frequent and it could be mainly explained by poor pollen quality.

Mitochondrial inheritance and germ line determination in a bivalve species with Doubly Uniparental Inheritance (DUI)

Mitochondria are inherited maternally in most metazoans. However, in some bivalves, two mitochondrial lineages are present: one transmitted through eggs (F), the other through sperm (M). This is called Doubly Uniparental Inheritance (DUI). During male embryo development, spermatozoon mitochondria aggregate and end up in the primordial germ cells, while they are dispersed in female embryos. The molecular mechanisms of segregation patterns are still unknown. In the DUI species Ruditapes philippinarum, I examined sperm mitochondria distribution by MitoTracker, microtubule staining and TEM, and I localized germ line determinants with immunocytochemical analysis. I also analyzed the gonad transcriptome, searching for genes involved in reproduction and sex determination. Moreover, I analyzed an M-type specific open reading frame that could be responsible for maintenance/degradation of M mitochondria during embryo development. These transcripts were also localized in tissues using in situ hybridization. As in Mytilus, two distribution patterns of M mitochondria were detected in R. philippinarum, supporting that they are related to DUI. Moreover, the first division midbody concurs in positioning aggregated M mitochondria on the animal-vegetal axis of the male embryo: in organisms with spiral segmentation this zone is not involved in further cleavages, so aggregation is maintained. Moreover, sperm mitochondria reach the same embryonic area where germ plasm is transferred, suggesting their contribution in male germ line formation. The finding of reproduction and ubiquitination transcripts led to formulate a model in which ubiquitination genes stored in female oocytes during gametogenesis would activate sex-gene expression in the early embryonic developmental stages (preformation). Only gametogenetic cells were labeled by in situ hybridization, proving their specific transcription in developing gametes. Other than having a role in sex determination, some ubiquination factors could also be involved in mitochondrial inheritance, and their differential expression could be responsible for the different fate of sperm mitochondria in the two sexes.

Ultrasuoni focalizzati guidati da imaging di risonanza magnetica: studio delle potenziali applicazioni in campo scheletrico, esempio n.1 - osteoma osteoide

La chirurgia con ultrasuoni focalizzati guidati da MRI (MR-g-FUS) è un trattamento di minima invasività, guidato dal più sofisticato strumento di imaging a disposizione, che utilizza a scopo diagnostico e terapeutico forme di energia non ionizzante. Le sue caratteristiche portano a pensare un suo possibile e promettente utilizzo in numerose aree della patologia umana, in particolare scheletrica. L'osteoma osteoide affligge frequentemente pazienti di giovane età, è una patologia benigna, con origine ed evoluzione non chiare, e trova nella termoablazione con radiofrequenza continua sotto guida CT (CT-g-RFA) il suo trattamento di elezione. Questo lavoro ha valutato l’efficacia, gli effetti e la sicurezza del trattamento dell’osteoma osteoide con MR-g-FUS. Sono stati presi in considerazione pazienti arruolati per MR-g-FUS e, come gruppo di controllo, pazienti sottoposti a CT-g-RFA, che hanno raggiunto un follow-up minimo di 18 mesi (rispettivamente 6 e 24 pazienti). Due pazienti erano stati esclusi dal trattamento MR-g-FUS per claustrofobia (2/8). Tutti i trattamenti sono stati portati a termine con successo tecnico e clinico. Non sono state registrate complicanze o eventi avversi correlati all’anestesia o alle procedure di trattamento, e tutti i pazienti sono stati dimessi regolarmente dopo 12-24 ore. La durata media dei trattamenti di MR-g-FUS è stata di 40±21 min. Da valori di score VAS pre-trattamento oscillanti tra 6 e 10 (su scala 0-10), i trattamenti hanno condotto tutti i pazienti a VAS 0 (senza integrazioni farmacologiche). Nessun paziente ha manifestato segni di persistenza di malattia o di recidiva al follow-up. Nonostante la neurolisi e la risoluzione dei sintomi, la perfusione del nidus è stata ritrovata ancora presente in oltre il 70% dei casi sottoposti a MR-g-FUS (4/6 pazienti). I risultati derivati da un'analisi estesa a pazienti più recentemente arruolati confermano questi dati. Il trattamento con MR-g-FUS sembra essere efficace e sicuro nel risolvere la sintomatologia dell'osteoma osteoide.

Environment of radio sources in the vla-cosmos survey

Sebbene studiati a fondo, i processi che hanno portato alla formazione ed alla evoluzione delle galassie così come sono osservate nell'Universo attuale non sono ancora del tutto compresi. La visione attuale della storia di formazione delle strutture prevede che il collasso gravitazionale, a partire dalle fluttuazioni di densità primordiali, porti all'innesco della formazione stellare; quindi che un qualche processo intervenga e la interrompa. Diversi studi vedono il principale responsabile di questa brusca interruzione della formazione stellare nei fenomeni di attività nucleare al centro delle galassie (Active Galactic Nuclei, AGN), capaci di fornire l'energia necessaria a impedire il collasso gravitazionale del gas e la formazione di nuove stelle. Uno dei segni della presenza di un tale fenomeno all'interno di una galassia e l'emissione radio dovuta ai fenomeni di accrescimento di gas su buco nero. In questo lavoro di tesi si è studiato l'ambiente delle radio sorgenti nel campo della survey VLA-COSMOS. Partendo da un campione di 1806 radio sorgenti e 1482993 galassie che non presentassero emissione radio, con redshift fotometrici e fotometria provenienti dalla survey COSMOS e dalla sua parte radio (VLA-COSMOS), si è stimata la ricchezza dell'ambiente attorno a ciascuna radio sorgente, contando il numero di galassie senza emissione radio presenti all'interno di un cilindro di raggio di base 1 Mpc e di altezza proporzionale all'errore sul redshift fotometrico di ciascuna radio sorgente, centrato su di essa. Al fine di stimare la significatività dei risultati si è creato un campione di controllo costituito da 1806 galassie che non presentassero emissione radio e si è stimato l'ambiente attorno a ciascuna di esse con lo stesso metodo usato per le radio sorgenti. I risultati mostrano che gli ammassi di galassie aventi al proprio centro una radio sorgente sono significativamente più ricchi di quelli con al proprio centro una galassia senza emissione radio. Tale differenza in ricchezza permane indipendentemente da selezioni basate sul redshift, la massa stellare e il tasso di formazione stellare specifica delle galassie del campione e mostra che gli ammassi di galassie con al proprio centro una radio sorgente dovuta a fenomeni di AGN sono significativamente più ricchi di ammassi con al proprio centro una galassia senza emissione radio. Questo effetto e più marcato per AGN di tipo FR I rispetto ad oggetti di tipo FR II, indicando una correlazione fra potenza dell'AGN e formazione delle strutture. Tali risultati gettano nuova luce sui meccanismi di formazione ed evoluzione delle galassie che prevedono una stretta correlazione tra fenomeni di AGN, formazione stellare ed interruzione della stessa.

Analysis and development of ecologically based approaches to coastal defense

Climate-change related impacts, notably coastal erosion, inundation and flooding from sea level rise and storms, will increase in the coming decades enhancing the risks for coastal populations. Further recourse to coastal armoring and other engineered defenses to address risk reduction will exacerbate threats to coastal ecosystems. Alternatively, protection services provided by healthy ecosystems is emerging as a key element in climate adaptation and disaster risk management. I examined two distinct approaches to coastal defense on the base of their ecological and ecosystem conservation values. First, I analyzed the role of coastal ecosystems in providing services for hazard risk reduction. The value in wave attenuation of coral reefs was quantitatively demonstrated using a meta-analysis approach. Results indicate that coral reefs can provide wave attenuation comparable to hard engineering artificial defenses and at lower costs. Conservation and restoration of existing coral reefs are cost-effective management options for disaster risk reduction. Second, I evaluated the possibility to enhance the ecological value of artificial coastal defense structures (CDS) as habitats for marine communities. I documented the suitability of CDS to support native, ecologically relevant, habitat-forming canopy algae exploring the feasibility of enhancing CDS ecological value by promoting the growth of desired species. Juveniles of Cystoseira barbata can be successfully transplanted at both natural and artificial habitats and not affected by lack of surrounding adult algal individuals nor by substratum orientation. Transplantation success was limited by biotic disturbance from macrograzers on CDS compared to natural habitats. Future work should explore the reasons behind the different ecological functioning of artificial and natural habitats unraveling the factors and mechanisms that cause it. The comprehension of the functioning of systems associated with artificial habitats is the key to allow environmental managers to identify proper mitigation options and to forecast the impact of alternative coastal development plans.

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.