In the marine realm, two of the main stressors causing significant changes are ocean warming and acidification. Of particular concern are organisms reliant on the generation of calcium carbonate, such as corals. Reproduction and population structure are strongly related to environmental parameters and may be indicators for stability or decline of coral populations. Part of my research focused on the reproductive cycle of the Mediterranean non-zooxanthellate coral Caryophyllia inornata in relation to seasonal variations of seawater temperature and photoperiod. Moreover, an unusual embryogenesis was found in females, males and inactive individuals during the entire year, indicating a possible agamic origin of embryos. This was a pilot study for a broader investigation along a wide latitudinal gradient of temperature and solar radiation. Reproductive traits of this coral do not vary along the gradient as observed for another non-zooxanthellate species, Leptopsammia pruvoti, indicating that these species could be quite tolerant to environmental changes, probably due to the lack of symbiosis with the zooxanthellae. A study on the spermatogenesis of the zooxanthellate coral Balanophyllia europaea living along a natural pCO2 gradient showed no significant variations with low pH. We hypothesized that high CO2 levels probably enhance zooxanthellae photosynthesis, leading to an increase of the available energy for gonadal development. The ability to reproduce in particular conditions is related to population structure, providing information on coral responses to the environment. I investigated the population structure of the tropical coral Montastraea cavernosa along a depth gradient in Bermuda. Deeper populations were characterized by smaller but more numerous colonies compared to shallow ones, with no variation in the percent cover among depths. Thus, mesophotic populations of M. cavernosa in Bermuda seem quite stable, indicating that these reefs may serve as a source of propagules to maintain shallower reefs and help guide future management and conservation strategies.

Gli elementi trasponibili (TEs) sono componenti universali dei genomi di tutti gli esseri viventi. L'attività ed il movimento degli TEs hanno importanti effetti sul genoma ospite e per questo sono considerati dei fattori importanti nell'evoluzione del genoma. Le relazioni che intercorrono tra TEs e il loro genoma ospite sono ancora ampiamente dibattute. Hickey già nel 1982 suggerì che queste relazioni potevano essere influenzate dalla modalità di riproduzione del genoma ospite. Organismi bisessuali, attraverso i meccanismi propri della meiosi, riuscirebbero a contrastare la proliferazione degli TEs, al contrario negli organismi unisessuali, proprio a causa della mancanza di questi meccanismi, gli TEs tendono a proliferare ed accumulare all'interno del genoma. Al fine di valutare queste ipotesi, ho isolato e caratterizzato gli TEs in organismi con strategie riproduttive non canoniche. Ho condotto le mie analisi in due organismi: gli insetti stecco del genere Bacillus e nel fossile vivente Triops cancriformis. Entrambi presentano strategie riproduttive che vanno dal gonocorismo alla partenogenesi, rendendoli un eccellente modello per lo studio e la caratterizzazione degli TEs. Nel genere Bacillus mi sono focalizzata sullo studio del retrotransposone non-LTR R2. Ho isolato e caratterizzato sette elementi R2 completi; sia in specie gonocoriche che partenogenetiche. Ho trovato un elemento R2 degenerato presente nel genoma di B. rossius da almeno 5 milioni di anni. In oltre, le mie analisi suggeriscono per la prima volta che anche gli elementi R2 possono trasferirsi attraverso eventi di trasferimento orizzontale. I miei dati mostrano una panoramica della composizione di TEs nel genoma di una popolazione partenogenetica di Triops cancriformis. Dalle mie analisi si evince che il 20% della library di triops è composta da TEs. / Transposable elements (TEs) are universal components of all living organisms. TEs activity and movement have profound effects on host genome and today many researchers agree to consider them as important actors in genome evolution. The relationships between TEs and their host genomes are still under debate. Different hypotheses were proposed to explain TEs dynamics in host genome; one of these propose that host reproductive strategies can influence TEs evolutionary dynamics (Hickey, 1982). In fact, bisexual organisms, through homologous chromosomes recombination and reassortment during meiosis and amphimixis, can control the spread and proliferation of mobile elements, while unisexual organisms would experience an increase of these elements density due to the inability to eliminate them through exclusive mechanisms of sexual reproduction. In order to evaluate these hypothesis, I isolated and characterized TEs in organisms with non-canonical reproductive strategies. I performed my analyses in two organisms: the stick insects of the Bacillus genus and in the tadpole shrimps T. cancriformis. In both instances reproductive strategies range from bisexual gonochoric reproduction, to unisexual parthenogenesis, making them an excellent model for the study and characterization of TEs. In the Bacillus genus I focused on the R2 non-LTR retrotranposon. I isolated and sequenced by primer walking seven R2 complete elements; both gonochoric and parthenogenetic Bacillus species. I found a R2 degenerate element present in the B. rossius genome since 5 Myr ago. In addition, my analyses for the first time suggest that also R2 retrotransposons can use horizontal transfer as a strategy to colonize a new genome. My data showed a TEs overview in a T. cancriformis parthenogenetic population. In contrast with the theoretical, my analyses highlighted that the 20% of the library is composed by TEs, in which both TEs classes are widely represented (class I, 11.4% and class II, 8.9%).

Yellowfin tuna (Thunnus albacares; YFT) represents one of the most important seafood commodities in the world. The rationale of this Ph.D. project was identified by prioritizing key issues as objectives for contributing to the conservation of YFT and helping to develop a more realistic stock assessment and sustainable management of this species. Specifically, in this work the current mismatch between the biology and/or ecology and the realized management strategies was highlighted, putting particular emphasis on YFT population structure, which is currently characterized by a high degree of uncertainty at both local and global scale. This general pattern was confirmed by the results obtained using a panel of microsatellite loci, which cannot reject the null hypothesis of the existence of only one panmictic population at the global scale. On the contrary, the access to more powerful and cost effective genetic tools would represent the first step for resolving YFT population structure at both global and local scale. After having evaluated the efficiency and usefulness of 2b-RAD genotyping technique for investigating population genetic structure in highly migratory fish species, a panel of 972 SNPs (Single Nucleotide Polymorphisms) was generated. Using this panel, three distinct populations were identified in the Atlantic, Indian and Pacific Oceans. Additionally, it was possible to define a subset of 33 outlier loci putatively under selection to delineate and separate sub-populations within both the Atlantic and the Pacific Oceans (following an east-west division). Finally, it was emphasized for the first time that in the Atlantic Ocean larger YFT females allocate a greater fraction of surplus energy to egg production than smaller ones, improving noticeably the spawning quality. This result sheds light on the important contribution that larger and most experienced spawners have for the YFT productivity.

Al voltant d‘unes 1.400 espècies del gènere Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) s’han descrit a nivell mundial, algunes de les quals són conegudes com a transmissores de protozous, filàries i virus que poden afectar tant a humans com a animals domèstics i/o salvatges. El virus de la Llengua Blava i el recent descobert virus Schmallenberg són responsables de malalties infeccioses no contagioses, detectades en remugants domèstics i salvatges, transmeses per espècies del gènere Culicoides. Al llarg d’aquesta tesi doctoral podem diferenciar dos eixos de recerca que ens permeten millorar en el coneixement de la epidemiologia de les malalties de la Llengua Blava (LB) i Schmallenberg (SB). El primer eix de recerca proporciona una millora en el coneixement de la diversitat, morfologia i distribució de les espècies de Culicoides a la Península Ibèrica. Les dades obtingudes a través de la morfologia i la seqüenciació del ADN ens han permès detectar la presència de 26 espècies no identificades prèviament a l’àrea d’estudi. En aquesta àrea dues zones ecològiques s’han pogut diferenciar, la zona del nord amb espècies amb distribució típica del nord paleàritc europeu, i la zona del sud amb espècies amb una distribució típica del sud paleàrtic. Un anàlisi concís de les característiques morfològiques i les seqüències d’ADN es va realitzar als individus pertanyents als grups Pulicaris i Punctatus. Els resultats obtinguts revelen la presència de dues noves espècies dins el subgènere Culicoides: C. cryptipulicaris i C. quasipulicaris, ambues espècies es troben estretament relacionades filogenèticament a altres espècies de Culicoides que actuen com a vectors de malalties a Europa. El segon eix de recerca està dirigit a caracteritzar les comunitats de Culcioides presents a diverses àrees naturals habitades per diferents espècies de remugants salvatges localitzades al llarg de la Península Ibèrica. Els resultats mostren que a escala local, la presència de les principals espècies vectores dels virus de la LB i SB en les àrees de remugants salvatges coincideix amb la de les granges sentinella properes. Les dades suggereixen que aquestes espècies podrien tenir un paper destacat com a vectors pont de diferents patògens entre remugants domèstics i salvatges. Els resultats donarien suport a la hipòtesi de que els remugants salvatges podrien actuar com a reservori de la LB i SB, i posteriorment estar involucrats en la reintroducció d’aquestes malalties a les granges de remugants domèstics. En aquest context, és essencial el coneixement precís dels hàbits alimentaris de les comunitats de Culicoides en contacte amb remugants salvatges. / Around 1,400 species of biting midges of the genus Culicoides Latreille, 1809 (Diptera: Ceratopogonidae), have been described in the world, some of these are well known transmitters of protozoa, filarial worms and viruses that affect humans and domestic and/or wild animals. The Bluetongue virus (BTV) and the recently emerged Schmallenberg virus (SBV) are responsible of important infectious, non-contagious, insect-borne viral diseases found in domestic and wild ruminants and transmitted by Culicoides spp. Two research axes are distinguished in the doctoral thesis to improve our comprehension on the epidemiology of Bluetongue (BT) and Schmallenberg (SB) diseases. The first research axe provides an improvement on the knowledge of the diversity, morphology and distribution of Culicoides species in the Iberian Peninsula. Data derived from morphology and sequencing allowed to detect the presence of 26 species not recorded previously in the surveillance area. Two eco-zones were detected in the region; the northern had species with typical northern Palaearctic European distribution whereas the southern one had species with typical southern Palaearctic distribution. A concise analysis of morphological traits and DNA sequencing was performed on specimens of the Pulicaris and Punctatus groups. Results revealed the presence of two new species in the subgenus Culicoides: C. cryptipulicaris and C. quasipulicaris, both species phylogenetically closely related to other Culicoides acting as diseases-vectors in Europe. The second research axe aimed at characterizing Culicoides midge communities in natural ecosystems inhabited by different wild ruminants along the Iberian Peninsula. The results showed that at a local scale, the presence of major BTV and SBV vector species in areas with wild ruminants was coincident with that of the nearest sentinel farms. Data suggested certain species could play a prominent role as bridge vectors for different pathogens between wild and domestic ruminants. Results support the hypothesis that wild ruminants act as reservoir for BT and SB, and could eventually be involved in the reintroduction of such diseases into livestock farms. In this context, it is essential to define precisely the bloodfeeding behaviour of Culicoides communities in contact with wild ruminants.

Los Phoridae constituyen una familia muy diversa del orden Diptera, de la que se conocen más de 3.400 especies distribuidas en 240 géneros. Es una de las familias de Diptera con mayor diversidad de formas de vida larvaria, con especies saprófagas, depredadoras, fungívoras, parásitas o parasitoides. Los adultos de algunas especies pueden ser utilizados para el control biológico de plagas (hormigas), constituyen plagas de cultivos de hongos o pueden utilizarse en entomología forense. Este trabajo tiene tres objetivos básicos. Primero ampliar el conocimiento faunístico y taxonómico de los Phoridae en nuestro país. Segundo, llevar a cabo un estudio ecológico de esta familia analizando la estructura de la comunidad y su dinámica estacional, estratificación vertical en la vegetación y ritmos nictemerales. Tercero, evaluar la efectividad de distintos métodos de muestreo. El área muestreada de estudio es el Parque Natural del Montseny (Barcelona y Girona), declarado por la UNESCO como reserva de la biosfera. Se seleccionaron hábitats a diferentes altitudes que se diferencian por las condiciones ambientales y composición y estructura de la vegetación: el hayedo, con tres parcelas que se diferenciaban en el grado de humedad, y las landas culminales. El muestreo se realizó durante un año utilizando métodos de captura indirectos (interceptores de vuelo, trampas de agua, trampas de caída, trampas de emergencia y trampas de luz) y directos (biocenómetro, batidos y mangueos). Se capturaron un total de 14.032 Phoridae, identificando 165 especies pertenecientes a 15 géneros. Diez especies son nuevas para la ciencia, 42 son nuevas citas para la Península Ibérica y 71 para España peninsular. Los resultados ecológicos indican que la familia Phoridae es una de las más abundantes dentro de los Diptera. El hayedo está dominado por unas pocas especies, en su mayoría saprófagas, destacando Megaselia pectoralis, M. subpleuralis y M. pectorella, mientras que en las landas, las especies dominantes pertenecen a distintos grupos tróficos, destacando Megaselia pusilla, M. pumila, M. diversa y M. superciliata. Los saprófagos dominan en todas las estaciones, aunque en primavera disminuyen por el aumento de los polífagos y zoófagos. El rendimiento del esfuerzo de muestreo ha sido superior en el hayedo seco, aunque en ninguna zona el muestreo ha sido completo. La mayoría de las especies capturadas son de distribución europea o paleártica. Los dos hábitats (hayedo y landa) difirieron en la composición de la comunidad de Phoridae, tanto en el espacio como en el tiempo. La densidad y riqueza de Phoridae fue superior en el hayedo que en la landa, mientras que la uniformidad fue mayor en las landas que en el hayedo. El periodo de máxima actividad de la familia se produjo en verano, La temperatura fue la variable climática que mejor explicó la dinámica de la familia a lo largo del año, mientras que la precipitación contribuyó poco. La mayor parte de las especies del hayedo presentaron un ciclo bivoltino, con un pico primaveral y otro estival, mientras que en las landas son univoltinas, con un pico estival. En invierno se registró la presencia de especies psicrófilas del género Triphleba. El periodo de máxima actividad diario se produjo en las horas centrales del día, aunque encontramos especies con hábitos nocturnos o crepusculares como Megaselia diversa. La abundancia y riqueza de Phoridae en el hayedo es superior en los estratos herbáceo y arbustivo que en el arbóreo. Las trampas de agua fueron el método más efectivo para la captura de Phoridae. Concluimos, que la elevada abundancia y riqueza de esta familia, junto con su diversidad de formas de vida, hacen de ella una candidata excepcional para futuros estudios evaluativos conservacionistas de espacios naturales. / The Phoridae are a highly diverse family of the Diptera, with more than 3.400 known species in 240 genera. It has one of the highest diversity of larval life forms among Diptera, with saprophagous, predators, fungivorous, and parasites or parasitoids species. Several species can be used for biological control of ant pests, in some cases they are pests in mushroom farms, or can be used in forensic enthomology. This Thesis has three main objectives. First increase the fauna and taxonomic knowledge of the Phoridae in our country. Second, analyze the ecology of this family, mainly the community structure and temporal dinamic, vertical stratification across vegetation, and the nictemeral rhythms. Third, assess the effectivity of different sampling methods. The study area was the Montseny Natural Park, located between Barcelona and Girona (Catalonia, Spain), which is an UNESCO biosphere reserve. Several habitats that differed in environmental conditions and in the composition and structure of vegetation have been selected: Beech (Fagus sylvatica L.) forest, with three stands differing in water availability, and a highland heathland, located in the summit of the mountain range. Sampling was carried out for one year using both indirect (flight interception, water, pitfall, emergence and light traps) and direct (biocenometer, beating tray and sweep-net capture) sampling methods. We captured 14.032 phorids, identifying 165 species belonging to 15 genera. Ten species are new to Science, 42 species are new citations to the Iberian Peninsula, while 71 species are new to continental Spain. Our ecological results point out that the Phoridae is one of the most abundance families amongst the Diptera. Beech stands are dominated by a few species, most of which are saprophagous, with Megaselia pectoralis, M. subpleuralis and M. pectorella being the most important species. In the heathland, dominant species belong to different trophic groups with Megaselia pusilla, M. pumila, M. diversa and M. superciliata being the most important species. Saprophagous forms dominate in all habitats but their relative abundance decreases in spring due to the appearance of polyphagous and zoophagous. Sampling effort yield was greater in the driest beech stand than in the remainder sites, though sampling was not complete in any study site. Most studied species have a European or Palearctic distribution. Both habitats (beech forest and heathland) differed in composition of the Phoridae community, both in space and through season. Density and specific richness was higher but uniformity was lower in the beech forest than in the heathland. Overall, the highest activity of the family occurred in summer. Temperature was the climatic variable that best explained the dinamic of this family through the year, while rainfall had a low influence. Most species in the beech forest had a bivoltine cycle, with two maximums in spring and in summer, while heathland species have and univoltine cycle with their maximum activity concentrated in summer. In winter, we found psycrophilic species of the genus Triphleba. The daily maximum activity was at midday, although several species, such as M. diversa, had a nocturnal or crepuscular activity. In the beech forest, abundance and species richness was higher in the herb and shrub layer than in the tree canopy. Water traps was comparatively the most effective sampling method for the Phoridae. We conclude that the high abundance and richness of the phorids together with its high life forms diversity, makes it a suitable candidate for evaluative conservation studies of natural sites.

La búsqueda de fuentes naturales podría ser una alternativa viable para prevenir o tratar infecciones bacterianas, así mejorando la salud de los animales y obteniendo productos de origen animal más seguros. Esta Tesis se elaboró con el objetivo de evaluar la capacidad de reducir la adhesión bacteriana, en concreto de Escherichia coli enterotoxigénica (ETEC) K88 por parte de diferentes fuentes naturales, para prevenir colibacilosis en lechones. Las fuentes naturales seleccionadas consistieron en productos de origen vegetal (salvado de trigo, cascarilla de soja, pulpa de remolacha, algarroba (vaina+semilla, semilla), goma guar, arándanos, inulina, fructooligosacáridos y champiñones), de origen lácteo (casein glicomacropéptido) y subproductos de origen microbiano (mananoligosacáridos, el extracto de la fermentación de Aspergillus oryzae y exopolisacáridos), los cuales podrían ser considerados como candidatos para ser incluidos en las dietas de los lechones. La hipótesis sobre el papel anti-adhesivo del salvado de trigo (WB) en contra de enteropatógenos derivó de resultados previos de nuestro grupo y ha sido confirmado en los primeros dos ensayos de la presente Tesis. Por esta razón, consideramos que el WB merecía un fraccionamiento adicional para elucidar las moléculas anti-adhesivas involucradas en el reconocimiento de ETEC K88. Además, esta Tesis pretendió explorar la actividad anti-biofilm del WB en un modelo in vitro bien conocido de Staphylococcus aureus, pero también en su posible interferencia con los sistemas de comunicación bacteriana o, también conocidos como sistemas quorum sensing (QS). Con el fin de alcanzar estos objetivos principales, una serie de cuatro ensayos fueron diseñados. Los resultados expuestos en esta Tesis indican que los extractos solubles de casein glicomacropeptido, exopolisacáridos, algarroba (vaina+semilla) y WB podrían considerarse como posibles fuentes naturales para el desarrollo de nuevos aditivos para ser incorporados en las dietas de los lechones al destete y prevenir la colibacilosis post-destete. El interés particular fijado en las propiedades anti-adhesivas del WB llevó al fraccionamiento para comprender mejor el reconocimiento molecular (MW) del proceso de bloqueo que tiene lugar. El fraccionamiento del WB por peso molecular y cromatografía de exclusión molecular reveló que la actividad de bloqueo se mantiene en la fracción >300 kDa. La identificación por espectrometría de masas de algunas de las bandas más relevantes de bajo MW en esta fracción, reveló la presencia de varios inhibidores de proteasa que podrían estar implicados en los efectos de bloqueo presentados en contra de ETEC K88. Finalmente, se encontró que el extracto soluble de WB y la fracción >300 kDa fueron capaces de inhibir la formación de biofilm y también de destruir el biofilm previamente formado por parte de S. aureus. En ese mismo ensayo se demostró que el WB así como la fracciones >300 kDa y <300 kDa contienen cierta actividad lactanasa capaz de reducir la concentración de AHL en el medio. Toda la información recogida puede considerarse para el desarrollo de nuevos agentes anti-adhesion, anti-biofilm y quorum quenching a partir del salvado de trigo para prevenir infecciones bacterianas. / Looking for natural sources may be a feasible alternative to prevent or treat bacterial infections, thus enhancing animal health and obtaining safer animal products. This Thesis was devised with the aim of screening among natural sources their ability to reduce bacterial adhesion, in particular against enterotoxigenic Eschericha coli (ETEC) K88, to prevent colibacillosis in young pigs. The selected natural sources consisted of products of vegetable origin (wheat bran, soybean hulls, sugar beep pulp, locust bean and gum, guar gum. cranberry, inulin, fructooligosaccharides and mushrooms), dairy (casein glycomacropeptide) and microbial by-products (mannan-oligosaccharides, the fermented extract of Aspergillus oryzae and exopolysaccharides), which could be considered as candidates to be included in a piglet’s diet. The hypothesis on the anti-adhesive role of wheat bran (WB) against enteropathogens derived from previous results from our group and was subsequently confirmed in the first two trials of the current Thesis. For this reason we considered that WB deserved further fractionation to elucidate the putative anti-adhesive molecules involved in the ETEC K88 recognition. Moreover, this Thesis professed into exploring the anti-biofilm activity of WB in an in vitro well-known biofilm model of Staphylococcus aureus, but also in its possible interference with bacterial quorum-sensing (QS) systems. In order to achieve these main objectives a set of four trials were designed. Results exposed in this Thesis indicate that soluble extract of casein glycomacropeptide, exopolysaccharides, locust bean and WB should be considered as possible natural sources for the development of new additives to be included in weaned piglet’s diets and prevent post-weaning collibacillosis. The particular interest set on WB anti-adhesive properties led to the fractionation to gain understanding of the molecular recognition of the blocking process that takes place. The fractionation of WB by molecular weight (MW) and size-exclusion chromatography revealed that blocking activity is retained in the >300-kDa fraction. The identification of some relevant bands of low MW in this fraction by mass spectrometry revealed the presence of various protease inhibitors that could be implicated in the reported blocking effects against ETEC K88. Finally, it was found that the soluble extract of WB and the >300-kDa fraction were able to inhibit the biofilm formation and also the destruction the biofilm previously formed by S. aureus. In the same trials was demonstrated that WB as well as the >300 kDa and the <300 kDa contain certain lactanase activity able to reduce AHL concentration in the medium. All the gathered information can eventually pave the way for the development of novel anti-adhesion, anti-biofilm and quorum quenching therapeutic agents from wheat bran to prevent bacterial pathogenesis.

La presente tesis doctoral tiene como objetivos principales valorar el efecto del tipo de carbohidratos en el alimento sobre el engrasamiento de la canal, en dos razas porcinas: el cerdo ibérico y el landrace. En una primera fase experimental se utilizaron 48 cerdos (88,4 kg PV), 24 Ibéricos y 24 Landrace, a los que se administraron dos raciones que diferían en las principales fuentes de carbohidratos: maíz (Dieta MZ), altamente digestible, o maíz-sorgo y bellota (Dieta SB), más resistente a la digestión enzimática y con mayor tendencia a ser fermentada. Cuando los animales alcanzaron un peso vivo medio de 110 kg, se sacrificó a la mitad. La segunda fase se llevó a cabo con los 24 animales restantes, 12 ibéricos y 12 landrace (108 kg PV). Se mantuvieron los tratamientos dietéticos, incrementando el aporte de bellota en la dieta SB en detrimento del maíz. El sacrificio se realizó a un peso vivo medio de 135 kg.Durante el periodo experimental, los cerdos ibéricos manifestaron una superior ingestión voluntaria (entre un 25 y 35%: P < 0.01), que les impuso los peores índices de transformación. Entre dietas experimentales no se observaron diferencias en los rendimientos productivos, salvo en la segunda fase experimental donde el incremento del aporte de bellota provocó un descenso de la ingestión voluntaria (P = 0,08). La digestibilidad ileal de la materia orgánica fue superior en los cerdos landrace que en los ibéricos (P < 0,05) y con la dieta MZ que con la SB (P < 0.01). La fermentación en el tracto digestivo posterior de los animales permitió compensar en parte estas diferencias, salvo en el caso del cerdo ibérico alimentado con SB, que continuó presentando los menores coeficientes de digestibilidad para el tracto digestivo total. Esta incapacidad por parte del cerdo ibérico para fermentar todo el substrato alcanzaba su intestino grueso vino determinada, principalmente, por la superior velocidad de tránsito de la digesta en su compartimento digestivo, calculada con el marcador inerte. Todas estas diferencias entre razas y entre dietas afectaron a la extensión y tipo de fermentación en el intestino grueso. En concreto, se observaron diferencias en la concentración y el perfil de ácidos grasos volátiles. También en la concentración de bases púricas, como medida cuantitativa de la flora microbiana presente, y en la actividad enzimática de esta flora microbiana frente a diferentes substratos de carbohidratos. En general, los cerdos landrace tuvieron una mayor presencia microbiana en el ciego (P < 0,05), y menor en el colon (P < 0.05) que los cerdos ibéricos. Sin embargo, la flora microbiana presente en el ciego de los cerdos ibéricos presentó una mayor actividad in vitro frente a todos los substratos de carbohidratos analizados.Con referencia al engrasamiento, los cerdos ibéricos presentaron una mayor actividad enzimática lipogénica que los cerdos landrace, tanto en el depósito subcutáneo como en el intramuscular. Estos resultados se correspondieron con un superior (P < 0,001) espesor de la grasa dorsal y contenido de grasa intramuscular. Además, la grasa del cerdo ibérico se caracterizó por tener un menor contenido de AG poliinsaturados y superior de monoinsaturados. Entre dietas, no hubo diferencias importantes salvo una tendencia (P = 0,07) en el espesor de la grasa subcutánea dorsal, superior para la ración MZ que para la SB. Como conclusión, es evidente la participación genética en muchas de las diferencias que definen al cerdo ibérico y al landrace. Sin embargo, el tipo de carbohidratos de la ración puede promover en cada raza diferentes estrategias digestivas para su aprovechamiento. Como resultado, también podrían tener cierta influencia en el metabolismo lipídico, aunque de forma diferente para cada raza. / This current thesis has as main objectives to assess the effect of the source of dietary carbohydrates on the carcasse fatness in two different swine breeds: the Iberian and the Landrace pigs. In one first experimental phase 48 pigs were used (88.4 kg LW), 24 Iberian and 24 Landrace, which were fed with two experimental diets differing in the main sources of carbohydrates: maize (Diet MZ), highly digestible, or maize-sorghum and acorn (Diet SB), more resistant to the enzymatic digestion and with a higher tendency to be fermented. When animals reached an average body weight of 110 kg, the half of them were slaughtered. The second experimental phase were developed with the rest of pigs, 12 iberian and 12 landrace (108 kg LW). Dietary treatments were maintained, increasing the proportion of acorn in the diet SB in spite of maize. Pigs were slaughtered at an average body weight of 135 kg.Along the experimental period, Iberian pigs showed a higher voluntary feed intake (about 30%: P < 0.01), promoting worse feed:gain ratios. Between experimental diets were not observed differences in productive performances, except for a lower feed intake in pigs fed diet SB in the second experimental phase (P = 0,08), when acorn proportion was increased. Ileal digestibility of the organic matter was higher in landrace than in iberian pigs (P < 0,05) and in diet MZ than in SB (P < 0.01). Fermentation in hindgut allowed to compensate these differences in part, except for Iberian pigs fed diet SB, which showed the lowest digestibility coefficients in the whole of the digestive tract. The lower ability to ferment the whole of the substrate that reached the hindgut by Iberian pig was mainly associated to the lower transit time of digesta throughout its digestive compartment, calculated based on an indigestible flow marker.All these differences between breeds and diets affected to the extent and type of fermentation in the hindgut. In particular, differences were observed in the volatile fatty acids concentration and profile. Differences were also observed in purine bases concentration, as a quantitative value of the microflora, and in enzymatic activity of this microflora against different carbohydrate substrates. Landrace pigs showed a higher microflora concentration in caecum (P < 0,05), and lower in colon (P < 0.05) than Iberian pigs. However, microflora in caecum of Iberian pigs showed a higher in vitro activity against all carbohydrate substrates analysed. In reference to the fatness, Iberian pigs showed a higher lipogenic enzymatic activity than Landrace ones in both, subcutaneous and intramuscular depots. These results were associated with a higher (P < 0.001) backfat thickness and intramuscular fat content. Moreover, the Iberian pig fat had a lower polyunsaturated and higher monounsaturated FA contents. Between diets, there were not differences except for a tendency (P = 0,07) in backfat thickness, higher for diet MZ than for diet SB. In conclusion, it is evident a genetic contribution in many differences between Iberian and Landrace pigs. However, the type of dietary carbohydrates can promote in each breed different digestive strategies to their digestion. As a result, carbohydrates also could influence in lipid metabolism, although in different way depending on breed.

Global climate changes, driven by increasing temperature and pCO2, negatively affect marine ecosystem and mainly calcifying organisms. The reproduction of the zooxanthellate coral, Balanophyllia europaea, varied significantly along a latitudinal gradient of temperature and solar radiation. The warmer populations showed a lower reproductive efficiency due to the inhibition of the zooxanthellae photosynthesis, leading less available energy for reproduction. On the contrary, the B. europaea population, naturally living along a pCO2 gradient, did not show differences in oocytes development, production and morphology, probably by reallocating additional energy due to increasing of photosynthetic efficiency of zooxanthellae under pCO2 conditions. Increasing pCO2 negatively influenced spermaries production and development in L. pruvoti, causing a delayed in fertilization process, probably due to the lack of zooxanthellae involving in a lack of additional energy available for coral. The effects of high temperature, pCO2 and their interaction were tested on two symbiotic tropical corals, Fungia granulosa (solitary) and Pocillopora verrucosa (colonial). F. granulosa showed negative effects only in interaction treatment, while P. verrucosa showed decreased photosynthetic efficiency, increased bleaching tissue and mortality in all treatments. The more sensitivity of P. verrucosa could be explained by lower tissue thickness, making it more exposed and vulnerable to external environmental conditions. To investigate the role of intra-skeletal organic matrix in coral biomineralization, four Mediterranean species with different trophic strategy and growth form were selected. B. europaea organic matrix presented stronger control and higher independence from the crystallization environment than the other corals. Shell features of clam Chamelea gallina varied along a latitudinal gradient of temperature and solar radiation. Shells from the warmest and the most irradiated population were ~30% lighter due to thinner and more porous shells. No variation was observed in shell polymorphism at the nanoscale level, indicating no effects of environmental parameters on its composition and crystallography.

Aquaculture is a growing agricultural sector that due to the actual market saturation by sea bass and gilthead sea bream, needs for new fish species diversification. Sparid fishes are important candidates for species diversification in the Mediterranean aquaculture. Under culture conditions, parasites may cause serious problems. This thesis aims to improve our knowledge of myxozoan and aporocotylid parasites in sparids which are new candidates or existing Mediterranean aquaculture species. The present study seeks to identify, describe and clarify the taxonomic position of the parasite taxa by morphological and molecular approaches, and by defining their phylogenetical position and relationship with previously described species. Development, habitat selection in the host and pathology are analysed in order to evaluate the pathogenic potential of the parasites described. Also this thesis focuses on the study of parasite life cycles, seasonality, transmission and routes of infection in the fish host, with the final aim to provide information allowing for the development of management strategies for aquaculture systems. The study led to the following findings and conclusions: -A new genus and species of blood fluke, Skoulekia meningialis n. gen., n. sp. was described from the common two-banded seabream Diplodus vulgaris in a non common location, the ectomeningeal veins surrounding the optic lobes of the brain. The adults of S. meningialis were found to cause mild, chronic, localised meningitis. Its special location surrounding a vital organ should be kept in mind when establishing D. vulgaris in aquaculture systems. -Large cysts of myxosporean spores of the species Unicapsula pflugfelderi were detected in the fillets of sand steenbras Lithognathus mormyrus. Myoliquefaction process was not found to occur in U. pflugfelderi. However, the massive presence of macroscopic plasmodia in the fillets of L. mormyrus could produce marketing problems, affecting to the potential of the sand steenbras as an aquaculture candidate. -A new myxozoan parasite Ceratomyxa puntazzi n. sp. was found to cause histopathological changes in the liver and in the gall bladder of the sharpsnout seabream Diplodus puntazzo and has to be considered as an opportunistic parasite in immunocompromised hosts. The genus Ceratomyxa seems to be very host-specific in sparids and high species diversity can be expected in Mediterranean sparids. The phylogenetical analyses revealed that all ceratomyxid species of sparids from the Mediterranean rise from a common ancestor. -This thesis provides unique insights into the development and cellular organisation of the myxozoan C. puntazzi. This study is the first use of confocal laser scanning microscopy with specific stains on developmental stages of a myxozoan. C. puntazzi seems to follow a sequence of development with two pathways in the bile: pre-sporogonic proliferative development where stages show high degree of motility, cellular divisions and budding by plasmotomy, and sporogonic development, characterized by the formation and maturation of spores. For the first time in myxozoans, motility and the distribution of potential effectors of motility were analysed. F-actin rich cytoskeletal elements were found to concentrate at one end of the parasite, which produces localised filopodia, thus facilitating parasite motility. The mechanism of budding was identified, for the first time, as an active F-actin dependent separation process. -Natural exposures of sharpsnout seabream to a C. puntazzi enzootic habitat are the first attempt of conducting a seasonality study in marine myxozoans and provide important insights into the seasonal patterns of myxozoan abundance in a temperate marine environment. C. puntazzi infection in the bile shows a marked temperature-related seasonality, with visual detection of parasites exclusively between April - November. However, PCR detection in the bile is possible all year round. Blood stages were detected all year round by PCR. This indicates that actinospores are present in the sea water and the blood of exposed fish is invaded throughout the whole year. Implications for D. puntazzo culture are discussed. / La acuicultura mediterránea necesita diversificación de especies de peces para el cultivo debido a la saturación del mercado con dorada y lubina. En condiciones de cultivo, los peces pueden verse afectados por diversos patógenos, entre ellos los parásitos. Entre los parásitos mas problemáticos en la acuicultura mediterránea, figuran los mixozoos y los aporocotílidos. En esta tesis doctoral se presentan nuevas y se aportan nuevos datos de especies ya descritas de estos dos grupos parásitos, se estudia la relación parasito-hospedador y se incluyen nuevos datos del desarrollo, rutas de infección, ciclo de vida y estacionalidad en especies de peces candidatas para el cultivo. Un nuevo género y especie de aporocotílido Skoulekia meningialis n. gen. n. sp. se halló en un hábitat poco común, las venas ectomeningeales del cerebro de la mojarra Diplodus vulgaris, donde los adultos provocan una meningitis moderada pero crónica. Plasmodios alargados con esporas del mixozoo Unicapsula pflugfelderi se hallaron en la musculatura de la herrera Lithognathus mormyrus y aunque no se observó mioliquefaccion, la presencia masiva de estas estructuras en los filetes puede afectar al potencial de la herrera como especie para la acuicultura. Ceratomyxa puntazzi n. sp. es una nueva especie de mixozoo descrita de la vesícula biliar del sargo picudo Diplodus puntazzo. C. puntazzi provoca cambios histopatológicos en el hígado y la vesícula biliar del sargo picudo y debe considerarse como un patógeno oportunista. C. puntazzi forma parte del complejo de especies del género Ceratomyxa hallado en espáridos del Mediterráneo los cuales provienen de un ancestro común. Dentro del estudio de C. puntazzi, se describen los componentes celulares, y los mecanismos que intervienen en la motilidad de los mixozoos y como estos elementos están implicados en los procesos de gemación y citocinesis en los mixozoos. Experimentos de transmisión con jaulas en el mar a un medio natural enzoótico para C. puntazzi reveló una estacionalidad marcada, con presencia de esporas en la bilis de Abril a Noviembre, pero con detección por PCR durante todo el año tanto en la bilis como en la sangre. Estos resultados tienen implicaciones para el manejo del cultivo del sargo picudo.

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.