Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the eastern South Atlantic Ocean

The deep-sea environments of the South Atlantic Ocean are less studied in comparison to the North Atlantic and Pacific Oceans. With the aim of identifying the deep-sea bacteria in this less known ocean, 70 strains were isolated from eight sediment samples (depth range between 1905 to 5560 m) collected in the eastern part of the South Atlantic, from the equatorial region to the Cape Abyssal Plain, using three different culture media. The strains were classified into three phylogenetic groups, Gammaproteobacteria, Firmicutes and Actinobacteria, by the analysis of 16s rRNA gene sequences. Gammaproteobacteria and Firmicutes were the most frequently identified groups, with Halomonas the most frequent genus among the strains. Microorganisms belonging to Firmicutes were the only ones observed in all samples. Sixteen of the 41 identified operational taxonomic units probably represent new species. The presence of potentially new species reinforces the need for new studies in the deep-sea environments of the South Atlantic.

Phylogenetic relationships of the genus Sibynophis (Serpentes: Colubroidea)

We present the results of the first molecular analysis of the phylogenetic affinities of the Asian colubroid genus Sibynophis. We recovered a sister-group relationship between Sibynophis and the New World Scaphiodontophis. Although Liophidium sometimes is associated with these genera, the relationship is distant. Morphological characters that Liophidium shares with Sibynophis and Scaphiodontophis are resolved as homoplasies that probably reflect the similarities of their specialized feeding habits. The traditional subfamily Sibynophiinae is elevated to the family-level, and Scaphiodontophiinae is placed in its synonymy.

Molecular phylogeny, morphology and their implications for the taxonomy of Eriocaulaceae

The pantropical family Eriocaulaceae includes ten genera and c. 1,400 species, with diversity concentrated in the New World. The last complete revision of the family was published more than 100 years ago, and until recently the generic and infrageneric relationships were poorly resolved. However, a multi-disciplinary approach over the last 30 years, using morphological and anatomical characters, has been supplemented with additional data from palynology, chemistry, embryology, population genetics, cytology and, more recently, molecular phylogenetic studies. This led to a reassessment of phylogenetic relationships within the family. In this paper we present new data for the ITS and trnL-F regions, analysed separately and in combination, using maximum parsimony and Bayesian inference. The data confirm previous results, and show that many characters traditionally used for differentiating and circumscribing the genera within the family are homoplasious. A new generic key with characters from various sources and reflecting the current taxonomic changes is presented.

Phylogenetic relation among bovine rabies cases from Minas Gerais and Sao Paulo States, Brazil: a possible common origin

Acknowledgements: CAPES, FAPESP process number 2011/06236-0

Essays on Bayesian Inference for Social Networks

This thesis presents Bayesian solutions to inference problems for three types of social network data structures: a single observation of a social network, repeated observations on the same social network, and repeated observations on a social network developing through time. A social network is conceived as being a structure consisting of actors and their social interaction with each other. A common conceptualisation of social networks is to let the actors be represented by nodes in a graph with edges between pairs of nodes that are relationally tied to each other according to some definition. Statistical analysis of social networks is to a large extent concerned with modelling of these relational ties, which lends itself to empirical evaluation. The first paper deals with a family of statistical models for social networks called exponential random graphs that takes various structural features of the network into account. In general, the likelihood functions of exponential random graphs are only known up to a constant of proportionality. A procedure for performing Bayesian inference using Markov chain Monte Carlo (MCMC) methods is presented. The algorithm consists of two basic steps, one in which an ordinary Metropolis-Hastings up-dating step is used, and another in which an importance sampling scheme is used to calculate the acceptance probability of the Metropolis-Hastings step. In paper number two a method for modelling reports given by actors (or other informants) on their social interaction with others is investigated in a Bayesian framework. The model contains two basic ingredients: the unknown network structure and functions that link this unknown network structure to the reports given by the actors. These functions take the form of probit link functions. An intrinsic problem is that the model is not identified, meaning that there are combinations of values on the unknown structure and the parameters in the probit link functions that are observationally equivalent. Instead of using restrictions for achieving identification, it is proposed that the different observationally equivalent combinations of parameters and unknown structure be investigated a posteriori. Estimation of parameters is carried out using Gibbs sampling with a switching devise that enables transitions between posterior modal regions. The main goal of the procedures is to provide tools for comparisons of different model specifications. Papers 3 and 4, propose Bayesian methods for longitudinal social networks. The premise of the models investigated is that overall change in social networks occurs as a consequence of sequences of incremental changes. Models for the evolution of social networks using continuos-time Markov chains are meant to capture these dynamics. Paper 3 presents an MCMC algorithm for exploring the posteriors of parameters for such Markov chains. More specifically, the unobserved evolution of the network in-between observations is explicitly modelled thereby avoiding the need to deal with explicit formulas for the transition probabilities. This enables likelihood based parameter inference in a wider class of network evolution models than has been available before. Paper 4 builds on the proposed inference procedure of Paper 3 and demonstrates how to perform model selection for a class of network evolution models.

Indagini in Deep Inference

La tesi è uno studio di alcuni aspetti della nuova metodologia “deep inference”, abbinato ad una rivisitazione dei concetti classici di proof theory, con l'aggiunta di alcuni risultati originali orientati ad una maggior comprensione dell'argomento, nonché alle applicazioni pratiche. Nel primo capitolo vengono introdotti, seguendo un approccio di stampo formalista (con alcuni spunti personali), i concetti base della teoria della dimostrazione strutturale – cioè quella che usa strumenti combinatoriali (o “finitistici”) per studiare le proprietà delle dimostrazioni. Il secondo capitolo focalizza l'attenzione sulla logica classica proposizionale, prima introducendo il calcolo dei sequenti e dimostrando il Gentzen Hauptsatz, per passare poi al calcolo delle strutture (sistema SKS), dimostrando anche per esso un teorema di eliminazione del taglio, appositamente adattato dall'autore. Infine si discute e dimostra la proprietà di località per il sistema SKS. Un percorso analogo viene tracciato dal terzo ed ultimo capitolo, per quanto riguarda la logica lineare. Viene definito e motivato il calcolo dei sequenti lineari, e si discute del suo corrispettivo nel calcolo delle strutture. L'attenzione qui è rivolta maggiormente al problema di definire operatori non-commutativi, che mettono i sistemi in forte relazione con le algebre di processo.

Mitochondrial Genomics: structure, inheritance and phylogenetic utility of the Mitochondrial genome in Bivalvia and Insecta

This PhD Thesis is the result of my research activity in the last three years. My main research interest was centered on the evolution of mitochondrial genome (mtDNA), and on its usefulness as a phylogeographic and phylogenetic marker at different taxonomic levels in different taxa of Metazoa. From a methodological standpoint, my main effort was dedicated to the sequencing of complete mitochondrial genomes, and the approach to whole-genome sequencing was based on the application of Long-PCR and shotgun sequences. Moreover, this research project is a part of a bigger sequencing project of mtDNAs in many different Metazoans’ taxa, and I mostly dedicated myself to sequence and analyze mtDNAs in selected taxa of bivalves and hexapods (Insecta). Sequences of bivalve mtDNAs are particularly limited, and my study contributed to extend the sampling. Moreover, I used the bivalve Musculista senhousia as model taxon to investigate the molecular mechanisms and the evolutionary significance of their aberrant mode of mitochondrial inheritance (Doubly Uniparental Inheritance, see below). In Insects, I focused my attention on the Genus Bacillus (Insecta Phasmida). A detailed phylogenetic analysis was performed in order to assess phylogenetic relationships within the genus, and to investigate the placement of Phasmida in the phylogenetic tree of Insecta. The main goal of this part of my study was to add to the taxonomic coverage of sequenced mtDNAs in basal insects, which were only partially analyzed.

Mediterranean brachiopods: morphological, ecological and phylogenetic aspects

The Brachiopoda of the Marine Protected Area “Secche di Tor Paterno”, Central Tyrrhenian Sea, have been investigated in order to give a first glance of the diversity of the brachiopods of this area and provide a new report on the Mediterranean Brachiopod fauna. Four species were reported: Novocrania anomala (Müller, 1776), Megathiris detruncata (Gmelin, 1790), Joania cordata (Risso,1826) and Argyrotheca cuneata (Risso,1826). For all the four species a morphological analysis was carried out. For the two most abundant species, J.cordata and A. cuneata, a morphometric study, based on thickness/width and length/width scattergrams, was carried out, in order to investigate their variability. Size-frequency distributions relative to the three dimensions of the shell were also computed, aimed at a evaluation of population dynamics of these two species. The results showed that, for both species, the parameters which most determine the rise of the shell during the growth of animal are width and length and that frequency distributions are mainly bi- or plurymodal and that they are difficult to interpret, as reported by other studies. Analysis of drill holes found on the shell of some specimens of the two same species revealed a predatory origin and that three different predators are responsible for them. Partial sequences of two different genetic markers, the Internal Transcribed Spacer 1 (ITS1) and the cytochrome oxidase subunit 1 (COI), were used to investigate the phylogenetic relationship between two populations of the eurybathic brachiopod species Gryphus vitreus (Born,1778) across the strait of Gibraltar. This represents the first genetic population study on brachiopods. Results from AMOVA and Bayesian analysis performed on 31 specimens highlighted no genetic differentiation indicating a likely panmixia, dispite the lecitotrophic development of the species.

A revision of Askeptosaurus italicus and other thalattosaurs from the European Triassic, the interrelationships of thalattosaurs, and their phylogenetic position within diapsid reptiles (Amniota, Eureptilia)

Zusammenfassung: Thalattosaurier sind eine rein auf die Trias beschränkte Grupper mariner Diapsiden, die derzeit aus Nordamerika, Europa und China bekannt ist. Die europäischen Formen sind über längere Zeit vernachlässigt worden, was speziell für Askeptosaurus italicus aus der Mitteltrias des Monte San Giorgio gilt. Die hier durchgeführte anatomische Revision des Taxons ergibt einige Korrekturen im dorsalen Schädeldach, und ermöglicht erstmalig eine detaillierte Darstellung des ventralen Teils von Gaumen und Gehirnkapsel. Im postcranialen Skelett ergeben sich ebenfalls wichtige Korrekturen, so fehlt z. B. im Gegensatz zu bisherigen Annahmen ein Thyroidfenster im Becken. Weiterhin zeigt die Hand von Askeptosaurus eine intraspezifische Variation in der Verknöcherung. Das aquatische Reptil Endennasaurus acutirostris aus dem Nor der Lombardei wird ebenfalls neu untersucht, speziell im Hinblick auf eine potenzielle Zugehörigkeit zu Thalattosauriern. Letzteres wird bestätigt, zudem werden einige Korrekturen im Schädel durchgeführt, so ist z.B. der für Thalattosaurier typische Prämaxillare/Frontale-Kontakt vorhanden. Im Postcranium wird u.a. erstmals die vollständige Phalangenformel für die Hand ermittelt. Zwei weitere aquatische Trias-Reptilien werden ebenfalls untersucht. Zum einen ein bisher unbeschriebenes Postcranium eines relativ kleinen, hochschwänzigen Thalattosauriers aus der Obertrias von Österreich, der sehr viele Ähnlichkeiten mit dem chinesischen Xinpusaurus zeigt, und zum anderen die nur an Hand von Wirbeln bekannte Form Blezingeria ichthyospondyla aus dem Muschelkalk/Lettenkeuper der Germanischen Trias. Trotz einiger anatomischer Gemeinsamkeiten mit Thalattosauriern kann eine definitive Zugehörigkeit zu dieser Gruppe nicht bestätigt werden. Zur Klärung der verwandtschaftlichen Position der Thalattosaurier innerhalb der diapsiden Reptilien wird eine computergestützte phylogenetische Analyse basaler Diapsiden unter der Verwendung von 182 Merkmalen und 31 Taxa durchgeführt. Thalattosaurier gruppieren sich hierbei außerhalb der Sauria, und zeigen zudem ein gewisses Signal zu einer Monophylie mit Ichthyosauriern. Weitere Ergebnisse sind eine Gruppierung von Schildkröten mit Lepidosauriern, ein Schwestergruppenverhältnis von Drepanosauriern und Kuehneosauriern außerhalb der Sauria, sowie der Verlust des unteren Schläfenbogens in der frühen Evolution der Diapsiden und dessen sekundäre Aquirierung innerhalb der Archo- und Lepidosauromorpha. Eine Innengruppen-Analyse der Thalattosaurier ergibt auf der Basis von 35 Merkmalen eine basale Dichotomie, die Endennasaurus und die monophyletischen Askeptosaurus/Anshunsaurus von den übrigen Thalattosauriern abgrenzt. Die Monte San Giorgio-Taxa Hescheleria und Clarazia sind ebenfalls monophyletisch und zudem die Schwestergruppe zu Thalattosaurus. Die verbleibenden Thalattosaurier sind basal zu diesen drei Taxa positioniert, wobei der chinesische Xinpusaurus und der kalifornische Nectosaurus monophyletisch sind, und die Einbeziehung des österreichischen Thalattosauriers diesen innerhalb letzterer Taxa gruppiert. Auf der Basis dieser Ergebnisse wird ein vorläufiges biogeographisch-evolutives Szenario entworfen. Eine Kiefermuskelrekonstruktion von Askeptosaurus ergibt eine eher plesiomorphe, von posterodorsal nach anteroventral verlaufende Schläfen-Muskulatur. Zusammen mit weiteren osteologischen Merkmalen resultiert daraus eine Konfiguration, die die effektivste Beißkaft bei nur gering geöffneten Kiefern erlaubt. Die lange Schnauze, der flache Kopf und der bewegliche Hals legen eine Jagdstrategie nahe, bei der die wahrscheinlich aus kleinen bis mittelgroßen Wirbeltieren bestehende Beute durch schnelle Seitwärtsbewegungen des Kopfes gefangen wurde. Die übrige aquatische Fortbewegung des Taxons bestand aus einer subundulatorischen Lokomotion ohne Beteiligung der Extremitäten. Im Gegensatz zu Askeptosaurus bevorzugte der vollständig zahnlose Endennasaurus vermutlich nur Invertebraten und kleine Wirbeltiere als Beute, und schien seine Extremitäten im Rahmen eines paraxialen 'Pectoropelvical-Ruderns' explizit mitbenutzt zu haben.

Inference on copula-based correlation structures

We propose an extension of the approach provided by Kluppelberg and Kuhn (2009) for inference on second-order structure moments. As in Kluppelberg and Kuhn (2009) we adopt a copula-based approach instead of assuming normal distribution for the variables, thus relaxing the equality in distribution assumption. A new copula-based estimator for structure moments is investigated. The methodology provided by Kluppelberg and Kuhn (2009) is also extended considering the copulas associated with the family of Eyraud-Farlie-Gumbel-Morgenstern distribution functions (Kotz, Balakrishnan, and Johnson, 2000, Equation 44.73). Finally, a comprehensive simulation study and an application to real financial data are performed in order to compare the different approaches.

Partial reconstruction of the trajectories of a discretely observed branching diffusion with immigration and an application to inference

In this treatise we consider finite systems of branching particles where the particles move independently of each other according to d-dimensional diffusions. Particles are killed at a position dependent rate, leaving at their death position a random number of descendants according to a position dependent reproduction law. In addition particles immigrate at constant rate (one immigrant per immigration time). A process with above properties is called a branching diffusion withimmigration (BDI). In the first part we present the model in detail and discuss the properties of the BDI under our basic assumptions. In the second part we consider the problem of reconstruction of the trajectory of a BDI from discrete observations. We observe positions of the particles at discrete times; in particular we assume that we have no information about the pedigree of the particles. A natural question arises if we want to apply statistical procedures on the discrete observations: How can we find couples of particle positions which belong to the same particle? We give an easy to implement 'reconstruction scheme' which allows us to redraw or 'reconstruct' parts of the trajectory of the BDI with high accuracy. Moreover asymptotically the whole path can be reconstructed. Further we present simulations which show that our partial reconstruction rule is tractable in practice. In the third part we study how the partial reconstruction rule fits into statistical applications. As an extensive example we present a nonparametric estimator for the diffusion coefficient of a BDI where the particles move according to one-dimensional diffusions. This estimator is based on the Nadaraya-Watson estimator for the diffusion coefficient of one-dimensional diffusions and it uses the partial reconstruction rule developed in the second part above. We are able to prove a rate of convergence of this estimator and finally we present simulations which show that the estimator works well even if we leave our set of assumptions.

Molecular phylogenetic inferences on the position of the Mollusca within the Lophotrochozoa

Die phylogenetische Position der Mollusken innerhalb der Trochozoa sowie die interne Evolution der Klassen der Mollusca sind weitgehend unbekannt und wurden in meiner Arbeit anhand molekularer Merkmale untersucht. Phylogenomische Analysen zeigten in der Vergangenheit eine gute Auflösung für ursprüngliche Speziationsereignisse. Daher wurden hier drei neue EST Datensätze generiert: für Sipunculus nudus (Sipuncula), Barentsia elongata (Kamptozoa) und Lepidochitona cinerea, (Polyplacophora, Mollusca). Zusätzlich wurden gezielt Gene verschiedener Mollusken mittels RT-PCR amplifiziert. rnSowohl Kamptozoen als auch Sipunculiden wurden aufgrund morphologischer Kriterien bisher als mögliche Schwestergruppe der Mollusken gehandelt, aber die hier erzielten Ergebnisse zur Evolution der Hämerythrine, Gen-Anordnungen der mitochondrialen Genome und phylogenetische Analysen der ribosomalen und der mitochondriellen Proteine stützen diese Hypothese nicht. Die Position der Kamptozoa erwies sich hier generell als unbeständig; phylogenomische Analysen deuten eine Nähe zu den Bryozoen an, aber diese Position wird stark durch die Auswahl der Taxa beeinflusst. Dagegen weisen meine Analysen klar auf eine nähere Beziehung zwischen Annelida und Sipuncula hin. Die ribosomalen Proteine zeigen Sipuncula (und Echiura) sogar als Subtaxa der Anneliden. Wie den Mollusken fehlt den Sipunculiden jegliche Segmentierung und meine Ergebnisse legen hier die Möglichkeit des Verlusts dieses Merkmals innerhalb der Anneliden bei den Sipunculiden nahe. Innerhalb der Mollusken wurden die Solenogastren bereits als Schwestergruppe aller rezenten Mollusken vorgeschlagen. Im Rahmen meiner Arbeit wurden von drei verschiedenen Solenogastren-Arten die ersten zuverlässigen 18S rRNA-Sequenzen ermittelt, und es zeigte sich, dass alle bisher veröffentlichten 18S-Sequenzen dieser Molluskenklasse höchst unvollständig oder fehlerhaft sind. rnRibosomale Proteine sind gute phylogenetische Marker und hier wurden die Auswahl und Anzahl dieser Gene für phylogenetische Analysen optimiert. Über Sonden-basierte Detektion wurde eine sampling-Strategie getestet, die im Vergleich mit standard-phylogenomischen Ansätzen zukünftige molekulare Stammbaumrekonstruktionen mit größerem Taxonsampling ermöglicht.rn

Phage therapy: A software system for phage quantification and kinetic model inference.

One of the most serious problems of the modern medicine is the growing emergence of antibiotic resistance among pathogenic bacteria. In this circumstance, different and innovative approaches for treating infections caused by multidrug-resistant bacteria are imperatively required. Bacteriophage Therapy is one among the fascinating approaches to be taken into account. This consists of the use of bacteriophages, viruses that infect bacteria, in order to defeat specific bacterial pathogens. Phage therapy is not an innovative idea, indeed, it was widely used around the world in the 1930s and 1940s, in order to treat various infection diseases, and it is still used in Eastern Europe and the former Soviet Union. Nevertheless, Western scientists mostly lost interest in further use and study of phage therapy and abandoned it after the discovery and the spread of antibiotics. The advancement of scientific knowledge of the last years, together with the encouraging results from recent animal studies using phages to treat bacterial infections, and above all the urgent need for novel and effective antimicrobials, have given a prompt for additional rigorous researches in this field. In particular, in the laboratory of synthetic biology of the department of Life Sciences at the University of Warwick, a novel approach was adopted, starting from the original concept of phage therapy, in order to study a concrete alternative to antibiotics. The innovative idea of the project consists in the development of experimental methodologies, which allow to engineer a programmable synthetic phage system using a combination of directed evolution, automation and microfluidics. The main aim is to make “the therapeutics of tomorrow individualized, specific, and self-regulated” (Jaramillo, 2015). In this context, one of the most important key points is the Bacteriophage Quantification. Therefore, in this research work, a mathematical model describing complex dynamics occurring in biological systems involving continuous growth of bacteriophages, modulated by the performance of the host organisms, was implemented as algorithms into a working software using MATLAB. The developed program is able to predict different unknown concentrations of phages much faster than the classical overnight Plaque Assay. What is more, it gives a meaning and an explanation to the obtained data, making inference about the parameter set of the model, that are representative of the bacteriophage-host interaction.