Il genere Rhododendron L.: diversità genetica e fenomeni di ibridazione.

La terra, nel corso della sua storia, ha subito molteplici cambiamenti con la comparsa e scomparsa di numerose specie animali e vegetali. Attualmente, l’estinzioni delle specie, la riduzione degli areali e il depauperamento degli ecosistemi è da ricollegare alle attività dell’uomo. Per tali motivi, in questi ultimi decenni si è iniziato a dare importanza alla conservazione della biodiversità, alla creazione di zone protette e a sviluppare interventi di reintroduzione e rafforzamento di specie rare e a rischio di estinzione. Questo lavoro di tesi si propone di analizzare la variabilità genetica delle popolazioni di Rhododendron ferrugineum L. lungo il suo areale, con particolare attenzione alle aree marginali dell’Appennino, dove la specie rappresenta un caso di pseudo rarità, al fine di valutare lo stato di salute della specie al limite del suo areale e valutare appropriati interventi di conservazione o reintroduzione. Per effettuare le analisi sono stati messi a punto dei marcatori molecolari discontinui, i microsatelliti, che, essendo dei marcatori co-dominati, permettono di valutare differenti parametri legati alla diversità genetica delle popolazioni inclusi i livelli di eterozigotà ed il flusso genico tra popolazioni limitrofe. I campionamenti sono stati effettuati nelle uniche 3 stazioni presenti sugli Appennini. Al fine di confrontare la struttura genetica di queste popolazioni sono state considerate anche popolazioni delle Alpi Marittime, delle Alpi centro-orientali e dei Pirenei. L’analisi della diversità genetica effettuata su questo pool di popolazioni analizzate con 7 marcatori microsatelliti, ha messo in evidenza che le popolazioni relitte dell’Appennino Tosco-Emiliano presentano un ridotto livello di eterozigosità che suggerisce quindi un elevato livello di inbreeding. Si ritiene che ciò sia dovuto alla loro dislocazione sul territorio, che le rende isolate sia tra di loro che dalle popolazioni delle vicine Alpi Marittime. La stima delle relazioni genetiche tra le popolazioni appenniniche e le vicine piante alpine evidenzia come non vi sia scambio genetico tra le popolazioni. Le analisi dei cluster suggeriscono che due delle popolazioni Appenniniche siano più simili alle popolazioni della Alpi Marittime, mentre la terza ha più affinità con le popolazioni delle Alpi centro-orientali. Le popolazioni dei Pirenei risultano essere geneticamente più simili alle popolazioni delle Alpi Marittime, in particolare alle tre popolazioni del versante francese. In questo lavoro abbiamo affrontato anche il problema delle specie ibride. Rhododendron x intermedium Tausch è un ibrido frutto dell’incrocio tra Rhododendron ferrugineum L. e Rhododendron hirsutum L., in grado di incrociarsi sia con altri ibridi, sia con i parentali (fenomeno dell’introgressione). L’origine di questo ibrido risiede nella simpatria delle due specie parentali, che tuttavia, presentano esigenze ecologiche differenti. Ad oggi la presenza di Rhododendron x intermedium è stata accertata in almeno tre stazioni sulle Alpi Italiane, ma la letteratura documenta la sua presenza anche in altre zone dell’Arco Alpino. L’obiettivo di questa ricerca è stato quello di verificare la reale natura ibrida di Rhododendron x intermedium in queste stazioni utilizzando un approccio integrato ossia sia attraverso un’analisi di tipo morfologico sia attraverso un analisi di tipo molecolare. In particolare l’approccio molecolare ha previsto prima un’analisi filogenetica attraverso l’utilizzo di marcatori molecolari filogenetici nucleari e plastidiali (ITS, At103, psbA-trnH e matK) e quindi un’analisi della struttura delle popolazioni della specie ibrida attraverso l’utilizzo di marcatori molecolari microsatelliti. Da un’analisi morfologica, risulta che gli esemplari ibridi possono essere molto differenti tra loro e ciò supporta la formazione di sciami ibridi. Al fine di verificare la natura di questa specie e la struttura delle popolazioni ibride e dei rispettivi parentali, sono state campionate differenti popolazioni in tutta l’area di interesse. I campioni ottenuti sono stati quindi analizzati geneticamente mediante marcatori molecolari del DNA. I risultati ottenuti hanno permesso innanzitutto di confermare l’origine ibrida degli individui di prima generazione della specie Rhododendron x intermedium e quindi di distinguere i parentali dagli ibridi ed evidenziare la struttura genetica delle popolazioni ibride.

L’allevamento della sogliola comune (Solea solea L.): riproduzione controllata e nuovi sviluppi di nutrizione e alimentazione in fase larvale e giovanile

In questa tesi sono illustrate alcune sperimentazioni finalizzate alla standardizzazione del ciclo produttivo della sogliola comune (Solea solea) in cattività. E’ stato creato un parco di riproduttori selvatici ed è stata standardizzata la riproduzione ad un livello compatibile con la realtà produttiva del settore. Indagini genetiche di assegnazione parentale hanno evidenziato come alcuni esemplari siano stati predominanti negli accoppiamenti e nel conseguente contributo alla generazione della prole. Ciò ha determinato una diminuzione della variabilità genetica dei discendenti. La composizione quali-quantitativa degli acidi grassi delle uova è stata correlata con la sopravvivenza larvale nel corso di un’intera stagione riproduttiva. Tale composizione non ha subito importanti variazioni su scala temporale e sembra essere stata influenzata dall’alimentazione somministrata ai riproduttori nel periodo precedente alla riproduzione. Le analisi di interazione tra momento riproduttivo e qualità delle uova hanno confermato che è stato possibile ottenere uova di buona qualità in termini di sopravvivenza larvale nel corso di tutta la stagione riproduttiva. Larve di sogliola sono state svezzate precocemente 13 giorni dopo la schiusa riducendo l’impiego di cibo vivo a favore di micro diete commerciali. Tale svezzamento ha ridotto le performance di accrescimento, ma non la sopravvivenza e lo sviluppo della metamorfosi quando comparati ad un trattamento standard. La riduzione del cibo vivo ha ottimizzato i costi di produzione e migliorato l’igiene in vasca. L’ontogenesi di precursori di enzimi digestivi è stata determinata tramite PCR quantitativa. I risultati di espressione di tripsinogeno, chimotripsinogeno e amilasi hanno mostrato come tali enzimi rivestano un ruolo chiave nei processi digestivi delle prime fasi larvali. Esemplari giovanili hanno ottenuto un significativo maggiore indice di accrescimento e migliore indice di conversione quando alimentati con diete sperimentali contenenti un elevato tenore proteico. Un aumento dell’incidenza di vacuoli lipidici a livello epatico è stato osservato all’aumentare del tenore proteico della dieta.

Design and implementation of a novel multi-constellation FPGA-based dual frequency GNSS receiver for space applications

The PhD activity described in the document is part of the Microsatellite and Microsystem Laboratory of the II Faculty of Engineering, University of Bologna. The main objective is the design and development of a GNSS receiver for the orbit determination of microsatellites in low earth orbit. The development starts from the electronic design and goes up to the implementation of the navigation algorithms, covering all the aspects that are involved in this type of applications. The use of GPS receivers for orbit determination is a consolidated application used in many space missions, but the development of the new GNSS system within few years, such as the European Galileo, the Chinese COMPASS and the Russian modernized GLONASS, proposes new challenges and offers new opportunities to increase the orbit determination performances. The evaluation of improvements coming from the new systems together with the implementation of a receiver that is compatible with at least one of the new systems, are the main activities of the PhD. The activities can be divided in three section: receiver requirements definition and prototype implementation, design and analysis of the GNSS signal tracking algorithms, and design and analysis of the navigation algorithms. The receiver prototype is based on a Virtex FPGA by Xilinx, and includes a PowerPC processor. The architecture follows the software defined radio paradigm, so most of signal processing is performed in software while only what is strictly necessary is done in hardware. The tracking algorithms are implemented as a combination of Phase Locked Loop and Frequency Locked Loop for the carrier, and Delay Locked Loop with variable bandwidth for the code. The navigation algorithm is based on the extended Kalman filter and includes an accurate LEO orbit model.

Genetic variability and differentiation in the Mediterranean endemic starry ray Raja asterias (Delaroche, 1809)

The present study deal with the population structure and connectivity of the Mediterranean endemic starry ray Raja asterias (Delaroche, 1809) in the Western and Eastern Mediterranean basin. A panel of eight microsatellite loci which cross-amplify in Rajidae (El Nagar, 2010) was used to assess population connectivity and structure. Those aims were investigated by analyzing the genetic variation of 9 population sample for a total of 185 individuals collected during past scientific surveys (MEDITS, GRUND), commercial trawling and also directly at fish markets. The purpose of this thesis is to estimate the genetic divergence occurring between the Mediterranean populations and, in particular, to assess the presence of any barrier (geographic, hydrogeological and biological) to gene flow for this species. Different statistical approaches were performed to reach this aim evaluating both the genetic diversity (nucleotide diversity, allelic richness, observed and expected heterozygosity and Hardy-Weinberg equilibrium test) and the population differentiation patterns (pairwise Fst estimated and population structure analysis). The results obtained from the analysis of the microsatellite dataset suggest a geographic and genetic separation between the starry ray populations of the Mediterranean basin into three or four distinct groups: Western and Eastern Mediterranean basins and Sicilian coast always clustering as an independent group and Algeria which could be or not considered another separate group. The data were discussed from both an evolutionary and a conservation point of view and in relation to previous results obtained by the analysis of mitochondrial marker. A comparison with other Mediterranean demersal skate species was performed in order to better contextualise our results. Finally, our results could offer useful information to protect vulnerable species as R. asterias and developing effective conservation plans in the Mediterranean.

Genetic dynamics across early life stages in the tropical tree Prunus africana (Rosaceae)

In many plant species, the genetic template of early life-stages is formed by animal-mediated pollination and seed dispersal and has profound impact on further recruitment and population dynamics. Understanding the impact of pollination and seed dispersal on genetic patterns is a central issue in plant population biology. In my thesis, I investigated (i) contemporary dispersal and gene flow distances as well as (ii) genetic diversity and spatial genetic structure (SGS) across subsequent recruitment stages in a population of the animal-pollinated and dispersed tree Prunus africana in Kakamega Forest, West Kenya. Using microsatellite markers and parentage analyses, I inferred distances of pollen dispersal (father-to-mother), seed dispersal/maternal gene flow (mother-to-offspring) as well as paternal gene flow (father-to-offspring) for four early life stages of the species (seeds and fruits, current year seedlings, seedlings ≤ 3yr, seedlings > 3yr). Distances of pollen and seed dispersal as well as paternal gene flow were significantly shorter than expected from the spatial arrangement of trees and sampling plots. They were not affected by the density of conspecific trees in the surrounding. At the propagule stage, mean pollen dispersal distances were considerably (23-fold) longer than seed dispersal distances, and paternal gene flow distances exceeded maternal gene flow by a factor of 25. Seed dispersal distances were remarkably restricted, potentially leading to a strong initial SGS. The initial genetic template created by pollination and seed dispersal was extensively altered during later recruitment stages. Potential Janzen-Connell effects led to markedly increasing distances between offspring and both parental trees in older life stages. This showed that distance and density-dependent mortality factors are not exclusively related to the mother tree, but also to the father. Across subsequent recruitment stages, the pollen to seed dispersal ratio and the paternal to maternal gene flow ratio dropped to 2.1 and 3.4, respectively, in seedlings > 3yr. The relative changes in effective pollen dispersal, seed dispersal, and paternal gene flow distances across recruitment stages elucidate the mechanisms affecting the contribution of the two processes pollen and seed dispersal to overall gene flow. Using the same six microsatellite loci, I analyzed genetic diversity and SGS across five life stages, from seed rain to adults. Levels of genetic diversity within the studied P. africana population were comparable to other Prunus species and did not vary across life stages. In congruence with the short seed dispersal distances, I found significant SGS in all life stages. SGS decreased from seed and early seedling stages to older juvenile stages, and it was higher in adults than in late juveniles of the next generation. A comparison of the data with direct assessments of contemporary gene flow patterns indicate that distance- or density-dependent mortality, potentially due to Janzen-Connell effects, led to the initial decrease in SGS. Intergeneration variation in SGS could have been driven by variation in demographic processes, the effect of overlapping generations, and local selection processes. Overall, my study showed that complex sequential processes during recruitment contribute to the spatial genetic structure of tree populations. It highlights the importance of a multistage perspective for a comprehensive understanding of the impact of animal-mediated pollen and seed dispersal on spatial population dynamics and genetic patterns of trees.

Landscape ecology and genetics of the wolf in Italy

This PhD Thesis includes five main parts on diverse topics. The first two parts deal with the trophic ecology of wolves in Italy consequently to a recent increase of wild ungulates abundance. Data on wolf diet across time highlighted how wild ungulates are important food resource for wolves in Italy. Increasing wolf population, increasing numbers of wild ungulates and decreasing livestock consume are mitigating wolf-man conflicts in Italy in the near future. In the third part, non-invasive genetic sampling techniques were used to obtain genotypes and genders of about 400 wolves. Thus, wolf packs were genetically reconstructed using diverse population genetic and parentage software. Combining the results on pack structure and genetic relatedness with sampling locations, home ranges of wolf packs and dispersal patterns were identified. These results, particularly important for the conservation management of wolves in Italy, illustrated detailed information that can be retrieved from genetic identification of individuals. In the fourth part, wolf locations were combined with environmental information obtained as GIS-layers. Modern species distribution models (niche models) were applied to infer potential wolf distribution and predation risk. From the resulting distribution maps, information pastures with the highest risk of depredation were derived. This is particularly relevant as it allows identifying those areas under danger of carnivore attack on livestock. Finally, in the fifth part, habitat suitability models were combined with landscape genetic analysis. On one side landscape genetic analyses on the Italian wolves provided new information on the dynamics and connectivity of the population and, on the other side, a profound analysis of the effects that habitat suitability methods had on the parameterization of landscape genetic analyses was carried out to contributed significantly to landscape genetic theory.

Genetic and morphological variation and differentiation of Raja clavata populations in the European seas: marker development and preliminary data

In this study the population structure and connectivity of the Mediterranean and Atlantic Raja clavata (L., 1758) were investigated by analyzing the genetic variation of six population samples (N = 144) at seven nuclear microsatellite loci. The genetic dataset was generated by selecting population samples available in the tissue databases of the GenoDREAM laboratory (University of Bologna) and of the Department of Life Sciences and Environment (University of Cagliari), all collected during past scientific surveys (MEDITS, GRUND) from different geographical locations in the Mediterranean basin and North-east Atlantic sea, as North Sea, Sardinian coasts, Tuscany coasts and Cyprus Island. This thesis deals with to estimate the genetic diversity and differentiation among 6 geographical samples, in particular, to assess the presence of any barrier (geographic, hydrogeological or biological) to gene flow evaluating both the genetic diversity (nucleotide diversity, observed and expected heterozygosity, Hardy- Weinberg equilibrium analysis) and population differentiation (Fst estimates, population structure analysis). In addition to molecular analysis, quantitative representation and statistical analysis of morphological individuals shape are performed using geometric morphometrics methods and statistical tests. Geometric coordinates call landmarks are fixed in 158 individuals belonging to two population samples of Raja clavata and in population samples of closely related species, Raja straeleni (cryptic sibling) and Raja asterias, to assess significant morphological differences at multiple taxonomic levels. The results obtained from the analysis of the microsatellite dataset suggested a geographic and genetic separation between populations from Central-Western and Eastern Mediterranean basins. Furthermore, the analysis also showed that there was no separation between geographic samples from North Atlantic Ocean and central-Western Mediterranean, grouping them to a panmictic population. The Landmark-based geometric morphometry method results showed significant differences of body shape able to discriminate taxa at tested levels (from species to populations).

Is hatchery stocking a help or harm? Evidence, limitations and future directions in ecological and genetic surveys

Hatchery fish stocking for stock enhancement has been operated at a massive and global scale. However, the use of hatchery fish as a means of stock enhancement is highly controversial, and little is known about its effects on wild stock and consequences for stock enhancement. Here we review the scientific literature on this subject in order to address a fundamental - question is hatchery stocking a help or harm for wild stock and stock enhancement? We summarized 266 peer-reviewed papers that were published in the last 50 years, which describe empirical case studies on ecology and genetics of hatchery stocks and their effects on stock enhancement. Specifically, we asked whether hatchery stock and wild stock differed in fitness and the level of genetic variation, and whether stocking affected population abundance. Seventy studies contained comparisons between hatchery and wild stocks, out of which 23 studies showed significantly negative effects of hatchery rearing on the fitness of stocked fish, and 28 studies showed reduced genetic variation in hatchery populations. None of these studies suggested a positive genetic effect on the fitness of hatchery-reared individuals after release. These results suggest that negative effects of hatchery rearing are not just a concern but undeniably present in many aquaculture species. In a few cases, however, no obvious effect of hatchery rearing was observed, and a positive contribution of hatchery stock to the abundance of fish populations was indicated. These examples suggest that there is a chance to improve hatchery practices and mitigate the negative effects on wild stocks, although scientific data supporting the positive effect on stock enhancement are largely missing at this moment. Technically, microsatellite-based parentage assignments have been proven as a useful tool for the evaluation of reproductive fitness in natural settings, which is a key for stock enhancement by hatchery-based stocking. We discuss implications of these results, as well as their limitations and future directions. (C) 2010 Elsevier B.V. All rights reserved.

Paternity of subordinates raises cooperative effort in cichlids

Background In cooperative breeders, subordinates generally help a dominant breeding pair to raise offspring. Parentage studies have shown that in several species subordinates can participate in reproduction. This suggests an important role of direct fitness benefits for cooperation, particularly where groups contain unrelated subordinates. In this situation parentage should influence levels of cooperation. Here we combine parentage analyses and detailed behavioural observations in the field to study whether in the highly social cichlid Neolamprologus pulcher subordinates participate in reproduction and if so, whether and how this affects their cooperative care, controlling for the effect of kinship. Methodology/Principal Findings We show that: (i) male subordinates gained paternity in 27.8% of all clutches and (ii) if they participated in reproduction, they sired on average 11.8% of young. Subordinate males sharing in reproduction showed more defence against experimentally presented egg predators compared to subordinates not participating in reproduction, and they tended to stay closer to the breeding shelter. No effects of relatedness between subordinates and dominants (to mid-parent, dominant female or dominant male) were detected on parentage and on helping behaviour. Conclusions/Significance This is the first evidence in a cooperatively breeding fish species that the helping effort of male subordinates may depend on obtained paternity, which stresses the need to consider direct fitness benefits in evolutionary studies of helping behaviour.

Selection on floral traits through male fertility in a natural plant population

Most studies on selection in plants estimate female fitness components and neglect male mating success, although the latter might also be fundamental to understand adaptive evolution. Information from molecular genetic markers can be used to assess determinants of male mating success through parentage analyses. We estimated paternal selection gradients on floral traits in a large natural population of the herb Mimulus guttatus using a paternity probability model and maximum likelihood methods. This analysis revealed more significant selection gradients than a previous analysis based on regression of estimated male fertilities on floral traits. There were differences between results of univariate and multivariate analyses most likely due to the underlying covariance structure of the traits. Multivariate analysis, which corrects for the covariance structure of the traits, indicated that male mating success declined with distance from and depended on the direction to the mother plants. Moreover, there was directional selection for plants with fewer open flowers which have smaller corollas, a smaller anther-stigma separation, more red dots on the corolla and a larger fluctuating asymmetry therein. For most of these traits, however, there was also stabilizing selection indicating that there are intermediate optima for these traits. The large number of significant selection gradients in this study shows that even in relatively large natural populations where not all males can be sampled, it is possible to detect significant paternal selection gradients, and that such studies can give us valuable information required to better understand adaptive plant evolution.

A 19-Mb de novo deletion on BTA 22 including MITF leads to microphthalmia and the absence of pigmentation in a Holstein calf.

Mutations in MITF lead to a large variety of phenotypes in human, mice and other species. They mostly affect pigmentation and hearing, whereas in mice, they may additionally cause microphthalmia and osteopetrosis. In this study, we report a single case of a Holstein calf with lack of pigmentation and microphthalmia born to healthy parents. Mendelian analysis of high-density SNP genotypes reveals a large number of parentage errors showing missing paternal alleles in the offspring, indicating a deletion encompassing 19 Mb on BTA 22. The genomic deletion affects the paternal allele and includes MITF and 131 other annotated genes. As the calf shows only one copy of the BTA 22 segment, the observed phenotype is probably caused by haploinsufficiency of the genes in that genomic region. Both the observed lack of skin pigmentation and reduced eye size can most likely be explained by a lack of MITF function.

Chemical and isotopic compositions of volcanics from ODP Hole 210-1276

Site 1276, Leg 210 of the Ocean Drilling Program, was located on the Newfoundland margin in a seismically-defined ~128 Ma "transitional" crust just west of the presumed oceanic crust, and the M3 magnetic anomaly. The goal of drilling on this non-volcanic margin was to study the rifting, nature of basement, and post-rift sedimentation in the Newfoundland-Iberia rift. Drilling of this 1739 m hole was terminated 90-160 m above basement, in the lower of a doublet of alkaline diabase sills. We have carried out geochemical studies of the sill complex, in the hopes that they will provide proxy information regarding the nature of the underlying basement. Excellent 40Ar/39Ar plateau ages were obtained for the two sills: upper sill ~105.3 Ma; lower sill ~97.8 Ma. Thus the sills are substantially younger than the presumed age of the seafloor at site 1276 (~128 Ma), and were intruded beneath substantial sediment overburden (250 m for the upper, older sill, and 575 m for the lower younger sill). While some of the geochemistry of the sills has been compromised by alteration, the "immobile" trace elements show these sills to be hawaiites, differentiated from an enriched alkaline or basanitic parentage. Sr, Nd and Pb isotopes are suggestive of an enriched hotspot/plume mantle source, with a possible "added" component of continental material. These sills unequivocally were not derived from typical MORB (asthenospheric) upper mantle.

Formless as Water, Flaming as a Fire-Some observations on the Theory and Practice of Self-Determination

The concept of national self-determination is a highly contested concept from very outset. It is partly due to its dual parentage, namely nationalism and liberalism. Prior to 1945 it was only a political concept without legal binding. With the incorporation of the principle in the UN Charter it was universalized and legalized. However, there were two competing interpretations at the UN based on de-colonization and representative government. How to define self and what really determined remain highly controversial. How to reconcile the international norm of sovereignty of state and self determination of people became more complex problem with the tide of secessionist movements based on ethno-nationalism. The concept of internal self-determination came as a compromise; but it is also very vague and harbors a wide range of interpretations.

MALAQUIAS, MENSAGEIRO DA JUSTIÇA:UM ESTUDO A PARTIR DO QUARTO ORÁCULO (2,17-3,5)

O livro de Malaquias apresenta oráculos que conservam informações relevantes do período pós exílico sob o domínio da Pérsia e, especialmente, os problemas religiosos focalizando a displicência dos sacerdotes no cumprimento de suas funções e os problemas sociais apontando para um amplo movimento de opressão externa e interna. Esta pesquisa buscou verificar, no primeiro capítulo, como a mensagem de Malaquias através de sua forma e conteúdos visava aplacar as insatisfações internas dos grupos que habitavam o território de Judá. Neste capítulo, foram abordadas as discussões histórico-literárias sobre data, autoria, destinatários, forma do anúncio. Ainda procurou-se realizar levantamentos históricos verificando o sistema e as estruturas de opressão dos persas no território de Judá e também as faces da reorganização da sociedade de Judá. O segundo capítulo enfatizou, mais propriamente, o trabalho exegético no quarto oráculo (2,17-3,5). Neste pode-se verificar uma síntese dos temas centrais da mensagem de Malaquias: O juízo divino que viria pela negligência religiosa e que exigia compromissos com a justiça prática na vida do povo. A partir das discussões exegéticas buscou-se verificar como o profeta apresentou ao povo e aos sacerdotes quais seriam os agentes e as ações transformadoras que Javé promoveria para restaurar a justiça e o culto purificado. O terceiro capítulo apresenta um tema recorrente nos oráculos do livro de Malaquias: a justiça. Para isso, foram analisadas três perícopes que tratam o tema da justiça enfocadamente, as influências do sistema judicial persa na prática da justiça cotidiana em Judá e a realidade de opressão nos sistema de parentesco entre as famílias (clãs) que habitavam o território de Judá - (2,10-16; 2,17-3,5 e 3,13-21). A pesquisa de Malaquias aponta para um profeta engajado política e socialmente. O Mensageiro manteve os ideais proféticos e desejou reacender os valores da aliança entre o povo e fortalecer a confiança na ação de Javé que restauraria a justiça na prática cotidiana.(AU)