Il lavoro svolto durante il dottorato di ricerca ha permesso lo sviluppo e la verifica della attendibilità di marcatori molecolari neutrali (loci microsatelliti) specifici per Aristeus antennatus. Tali marcatori sono stati poi utilizzati per studiare la struttura genetica di popolazione della specie del Mediterraneo occidentale e i risultati ottenuti sono stati confrontati con quelli di un progetto di ricerca parallelo su Aristeaomorpha foliacea, analizzando differenze ed analogie fra le due specie. I risultati delle analisi su Aristeus antennatus hanno evidenziato una completa assenza di struttura di popolazione e come i due sessi contribuiscano in modo diverso al flusso genico. La specie infatti presenta un sex-ratio a favore dei maschi oltre gli 800m, mentre tale rappoorto è a favore delle femmine in strati più superficiali, dove sono probabilmente soggette a condizioni oceanografiche più dispersive. Tramite test genetici appropriati è stato possibile valutare indirettamente il grado di dospersione dei sessi dimostrando che nell'area analizzati i maschi erano rappresentati maggiormente da individui stanziali, mentre gli individui di sesso femminile erano migranti. Le femmine appaiono pertanto giocare un ruolo preminente rispetto ai maschi nel determinare l'entità del flusso genico. Il confronto dei risultati ottenuti in Aristeus antennatus con quelli di Aristaeomorpha foliacea ha evidenziato la relazione fra alta capacità dispersiva, sia allo stato larvale che adulto, e completo rimescolamento genetico nei gamberi aristeidi nel Mediterraneo occidentale anche se in quest'ultima specie non ci sono evidenze di dispersione genetica mediata dal sesso. E' pertanto di forte interesse (dato anche il valore economico di questi organismi) come una struttura di popolazione qualitativamente e quantitavamente comporabile venga raggiunta con dinamiche di popolazione molto diverse.

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.

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.

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.

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.

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.

My PhD project was focused on Atlantic bluefin tuna, Thunnus thynnus, a fishery resource overexploited in the last decades. For a better management of stocks, it was necessary to improve scientific knowledge of this species and to develop novel tools to avoid collapse of this important commercial resource. To do this, we used new high throughput sequencing technologies, as Next Generation Sequencing (NGS), and markers linked to expressed genes, as SNPs (Single Nucleotide Polymorphisms). In this work we applied a combined approach: transcriptomic resources were used to build cDNA libreries from mRNA isolated by muscle, and genomic resources allowed to create a reference backbone for this species lacking of reference genome. All cDNA reads, obtained from mRNA, were mapped against this genome and, employing several bioinformatics tools and different restricted parameters, we achieved a set of contigs to detect SNPs. Once a final panel of 384 SNPs was developed, following the selection criteria, it was genotyped in 960 individuals of Atlantic bluefin tuna, including all size/age classes, from larvae to adults, collected from the entire range of the species. The analysis of obtained data was aimed to evaluate the genetic diversity and the population structure of Thunnus thynnus. We detect a low but significant signal of genetic differentiation among spawning samples, that can suggest the presence of three genetically separate reproduction areas. The adult samples resulted instead genetically undifferentiated between them and from the spawning populations, indicating a presence of panmictic population of adult bluefin tuna in the Mediterranean Sea, without different meta populations.

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.

Un experimento in vitro y dos in vivo se han llevado a cabo para explorar diferentes alternativas a los antibióticos promotores del crecimiento y reducir la incidencia de trastornos digestivos. En el primer experimento se usaron 8 fermentadores de doble flujo continuo, en un diseño factorial 2 x 2 durante dos periodos de 9 días (6 para adaptación y 3 para muestreo), para determinar el efecto de las levaduras vivas y el tipo de cereal sobre la fermentación microbiana ruminal y la digestibilidad de nutrientes. Los factores principales fueron las levaduras vivas (Levucell®SC): sin adición (NY) vs 2x107 UFC de levaduras/g de dieta (LY); y el tipo de cereal predominante en la dieta: concentrado de maíz (CO) vs concentrado de cebada (BA). Los resultados obtenidos sugieren beneficios potenciales de LY en la estabilización de la fermentación de dietas ricas en cebada. En el segundo experimento, se evaluaron los efectos de un cambio brusco de dieta para inducir trastornos digestivos y la suplementación con cultivo de levaduras sobre la fermentación microbiana ruminal, usando 12 terneros Holstein con cánula ruminal, en un diseño crossover de dos periodos de 5 semanas. En cada periodo, tras 3 semanas de adaptación a una dieta 100% forrajera, se aumentó la proporción de concentrado en 2,5 kg/d (en materia fresca) durante 4 días, hasta alcanzar una dieta 10:90 de forraje:concentrado, y entonces se mantuvo durante 10 días más. Los tratamientos empezaron el primer día de cada periodo, y fueron un a dieta control (CL) o la misma dieta con la adición de cultivo de levaduras (YC, Diamond V XPCLSTM). El diseño propuesto resultó efectivo causando trastornos digestivos, pero la adición de YC no tuvo un impacto significativo sobre la fermentación ruminal. En el último experimento, 80 terneros de engorde fueron usados durante 52 días con un diseño de bloques al azar generalizados, para evaluar si la selección individual de ingredientes modula el pH ruminal y mejora la función ruminal. Los tratamientos fueron: una ración totalmente mezclada (TMR) (85% concentrado de cebada (BG), 10% ensilado de maíz (CS), 5% suplemento); o dietas a libre elección (FC) entre concentrado de cebada y ensilado de maíz (BGCS); granos de destilería de trigo (DG) y concentrado de cebada (BGDG); o ensilado de maíz y granos de destilería de trigo (CSDG). Los resultados sugieren que terneros de engorde alimentados con dietas FC que contengan BG autorregulan la ingesta y mantienen un perfil fermentativo ruminal similar que aquellos alimentados con dietas TMR. Del trabajo realizado en esta tesis doctoral se puede concluir que la adición de levaduras, bajo las circunstancias de nuestros estudios, muestra efectos moderados a la hora de prevenir la aparición de trastornos digestivos. Estrategias a nivel de manejo de la alimentación, sin embargo, pueden resultar tanto o más determinantes en el control del pH ruminal. / One in vitro and two in vivo experiments were conducted to evaluate the alternatives to antibiotic growth promoters in order to reduce the incidence of digestive upsets. In the first experiment, 8 dual flow continuous culture fermenters were used in a 2 x 2 factorial design in two replicated periods of 9 days (6 for adaptation and 3 for sampling) to determine the effect of live yeast and type of cereal on rumen microbial fermentation and nutrient digestibility. Main factors were live yeast (Levucell®SC): no yeast (NY) vs 2x107 CFU of yeast/g of diet (LY); and type of predominant cereal in the diet: corn concentrate (CO) vs barley concentrate (BA). The results obtained in this study suggest potential benefits of LY in stabilizing the fermentation of barley-based diets. In the second experiment, we evaluated the effects of a dietary challenge to induce digestive upsets and supplementation with yeast culture on rumen microbial fermentation, by using 12 Holstein heifers fitted with ruminal cannula, in a crossover design with 2 periods of 5 wk. In each period, after 3 wk of adaptation to a 100% forage diet, the dietary challenge consisted of increasing the amount of grain at a rate of 2.5 kg/d (as-fed basis) over a period of 4 d, until a 10:90 forage:concentrate diet was reached, and then it was maintained for 10 d. Treatments started the first day of each period, and they were a control diet (CL) or the same diet with addition of yeast culture (YC, Diamond V XPCLS). The proposed dietary challenge model was successful in causing a digestive upset, as indicated by reduced feed intake, but the YC addition had no significant impact on rumen fermentation. In the last experiment, 80 crossbred beef heifers, were used in a 52-d experiment with a generalized randomized block design, to assess if self-selection of dietary ingredients modulates ruminal pH and improves rumen function of feedlot finishing cattle. Treatments were: total mixed ration (TMR) (85% barley-grain (BG), 10% corn silage (CS), 5% supplement); or free-choice (i.e., self-selection) (FC) diets of barley-grain and corn silage (BGCS); wheat distillers’ grain (DG) and barley grain (BGDG); or corn silage and wheat distillers’ grain (CSDG). Results suggests that finishing feedlot cattle fed FC diets containing BG self-regulate intake of diets that have a similar composition, intake level and ruminal fermentation profile to those fed a TMR. With the work realised in this thesis doctoral we can conclude that the addition of yeasts, under the circumstances of our studies, shows moderate effects on the prevention of digestive disorders. However, strategies related with the feeding management can be more effectives in the control of ruminal pH.

Esta tesis doctoral se planteó debido a la necesidad de evaluar la capacidad de los aceites esenciales y de sus compuestos como aditivos ruminales. En el primer estudio se utilizaron 8 fermentadores (1320 ml) de doble flujo continuo en dos períodos (8 d) para estudiar el efecto de una mezcla de compuestos de aceites esenciales (BEO, CRINA? RUMINANTS) sobre la fermentación microbiana y el flujo de nutrientes. Los tratamientos se distribuyeron en un diseño factorial 2 x 2, donde el tipo de ración (alta en concentrado: 90% concentrado y 10% paja; vs alta en forraje: 60% heno de alfalfa y 40% concentrado) y la adición de BEO (0 mg/l vs 1.5 mg/l) fueron los efectos principales. La adición de BEO no afectó a la digestibilidad de MS, MO, FND, FAD y PB, pero incrementó la concentración de AGV totales (122.8 vs 116.2 mM) sin modificar significativamente las proporciones individuales de AGV o el metabolismo nitrogenado. El segundo estudio consistió en varias pruebas experimentales diseñadas para estudiar el efecto de la dosis y del periodo de adaptación a la adición de BEO sobre el metabolismo nitrogenado de los microorganismos ruminales. En la primera, se utilizaron de nuevo 8 fermentadores de doble flujo continuo (1320 ml) en dos períodos (6 d de adaptación y 3 de muestreo) para estudiar el efecto de la dosis de BEO sobre la fermentación microbiana ruminal. Los tratamientos fueron: CTR (sin adición de BEO), D5 (5 mg/l de BEO), D50 (50 mg/l de BEO) y D500 (500 mg/l de BEO). En la segunda prueba experimental se utilizaron 8 ovejas (peso medio de 57 kg) para estudiar el efecto de una adaptación larga del líquido ruminal a la adición de BEO sobre la fermentación ruminal. El tratamiento CTR (sin adición de BEO) se asignó al azar a 4 ovejas, y las otras 4 ovejas se adaptaron a BEO (110 mg/d de BEO) durante 4 semanas (ADBEO). La adición de 5 mg BEO/l de líquido ruminal en cultivo continuo incrementó la concentración de AGV totales y la relación acetato:propionato después de 6 d de fermentación, pero los cambios sobre el metabolismo N sólo aparecieron en el líquido ruminal de ovejas alimentados con BEO durante 28 d.En el tercer estudio se evaluaron los efectos de cinco compuestos de aceites esenciales sobre la fermentación microbiana ruminal. En la primera prueba experimental, los efectos de 4 dosis crecientes (5, 50, 500, y 5000 mg/l) de 5 compuestos de aceites esenciales se evaluaron en incubaciones in vitro de líquido ruminal durante 24 h con dos dietas diferentes: una dieta 60:40 forraje:concentrado (18% PB; 30% FND) y la otra 10:90 forraje:concentrado (16% PB; 25% FND). Los tratamientos fueron: control (CTR), eugenol (EUG), guaiacol, limoneno, timol (TIM), y vanillin. En la segunda prueba experimental se utilizaron 8 fermentadores de doble flujo continuo (1320 ml) en 3 periodos (6 d de adaptación y 3 d de muestreo) para estudiar el efecto del TIM y del EUG sobre la fermentación microbiana ruminal y el flujo de nutrientes. Los tratamientos fueron: CTR (control negativo), MON (control positivo, 10 mg/l de monensina), T5 (5 mg/l de TIM), T50 (50 mg/l de TIM), T500 (500 mg/l de TIM), E5, E50 y E500, y se asignaron aleatoriamente a los fermentadores dentro de cada periodo. La mayoría de estos compuestos de aceites esenciales a dosis elevadas demostraron poseer actividad antimicrobiana disminuyendo la concentración total de VFA. Sin embargo, EUG en incubaciones de 24 h y T5 en cultivo continuo modificaron el perfil de AGV sin inhibir la concentración total de AGV, y EUG disminuyó la concentración de N amoniacal. Una selección cuidadosa de estos compuestos permitiría la manipulación de la fermentación microbiana ruminal. / This doctoral thesis was planned to test the potential of essential oils and their compounds as ruminal additives. In the first study, eight dual flow continuous culture fermenters (1320 ml) were used in two replicated periods (8 d each) to study the effects of a specific blend of essential oil compounds (BEO, CRINA? RUMINANTS) on rumen microbial fermentation and nutrient flow. Treatments were arranged in a 2 x 2 factorial design. Main factors were type of diet (10 to 90 vs 60 to 40 forage to concentrate ratios) and the addition of BEO (0 vs 1.5 mg/l of BEO). There were no effects of BEO on DM, OM, NDF, ADF and CP digestion. The use of BEO increased the concentration of total VFA (122.8 vs 116.2 mM) without affecting individual VFA proportions or N metabolism. The second experiment was designed to study the effect of dose of BEO and adaptation time to the addition of BEO on N metabolism of rumen microorganisms. The second study consisted in several tests. In the first, eight dual flow continuous culture fermenters (1320 ml) were used in two periods (6 d of adaptation and 3 d of sampling) to study the effects of increasing doses of a specific blend of essential oils (BEO, CRINA? RUMINANTS) on rumen microbial fermentation. Fermenters were fed with the same high forage ration of the first study and the sampling protocol and processing were identical. Treatments were: CTR (no BEO), D5 (5 mg/l of BEO), D50 (50 mg/l of BEO) and D500 (500 mg/l of BEO). In the second experiment, eight sheep (average body weight of 57 kg) were used to study the effects of long term adaptation of rumen fluid to BEO on ruminal fermentation. Four sheep were assigned at random to the CTR treatment (no BEO) and four sheep were adapted to BEO (110 mg/d of BEO) for four weeks (ADBEO). The addition of 5 mg BEO/l of rumen fluid in continuous culture increased total VFA concentration and acetate to propionate ratio after 6 d of fermentation, but changes in N metabolism were only apparent when using rumen fluid from sheep fed BEO for 28 d.In the third study, several essential oil compounds were evaluated on rumen microbial fermentation. In the first experiment, the effects of 4 different doses (5, 50, 500, and 5000 mg/l) of five essential oil compounds were evaluated in in vitro 24 h batch culture of rumen fluid with two different diets: a 60 to 40 forage to concentrate diet (18% CP; 30% NDF) and a 10 to 90 forage to concentrate diet (16% CP; 25% NDF). Treatments were: control (CTR), eugenol (EUG), guaiacol, limonene, thymol (THY), and vanillin. In the second experiment, eight dual flow continuous culture fermenters (1320 ml) were used in three periods (6 d of adaptation and 3 d of sampling) to study the effects of THY and EUG on rumen microbial fermentation and nutrient flow. Treatments were: CTR (negative control), MON (positive control, 10 mg/l of monensin), T5 (5 mg/l of THY), T50 (50 mg/l of THY), T500 (500 mg/l of THY), E5, E50 and E500, and were randomly assigned to fermenters within periods. Most of these essential oil compounds demonstrated their antimicrobial activity decreasing total VFA concentration at high doses. However, EUG in batch fermentation and T5 in continuous culture modified VFA profile without decreasing total VFA concentration, and EUG decreased ammonia N concentration. Careful selection of these essential oils compounds may allow manipulation of rumen microbial fermentation.