<p>Population differentiation is both one of the central processes underlying the diversity that we observe in the natural world, and a mechanism that can be used to differentiate between evolutionary forces both at the level of the polymorphism, and at the level of the entire genome. Here, I use simulated evolution to analyze the statistical power to detect signals of selection in artificially selected laboratory populations, and use genomic data from wild populations of the clam shrimp Eulimnadia texana to identify genomic signals of selection in wild populations. Several loci in the wild populations appear to be under selection, and I analyze the types of genes that appear to contribute to differentiation of these populations. Additionally, I describe an analysis of genome assembly techniques that allowed for the creation of a highly contiguous genome assembly in the clam shrimp. I find that a pipeline that uses custom software to combine the results of several different genome assemblers is capable of producing genomes using long-read genomic sequencing data that are orders of magnitude more contiguous that pre-long-read methods. Simulations of experimental evolution indicated that extremely high levels of replication were necessary in order to achieve high power to detect signals of selection in experimental evolution. To this end, I describe a set of replicate experimentally evolved populations of E. texana that can be used to identify regions under selection with much higher power than could be accomplished with earlier experimental evolution schemes.

The philosophy of Friedrich Nietzsche was significantly influenced by the theory of evolution, though his interest was almost solely in relation to the human psyche. However, while many topics of his philosophy are similar to current topics of discussion in science, reflection on these thoughts is rare. The aim of this dissertation is to present Nietzsche's pivotal thoughts about the nature, function and evolution of human consciousness, with subsequent reflection on these thoughts and on their embedding in the broader context of current scientific discussion. From the standpoint of Nietzsche's philosophy, the main themes of this work are the conception of consciousness as "social instinct"; the critique of conception of consciousness as human essence and related topics; and, from the standpoint of current science, the question of the mechanism of the evolution of the human consciousness. The conclusion deals with cognitive archaeology and its attempt to reconstruct the evolutionary history of the human mind. The appendix is about Nietzsche's relation to Darwinism.

Recent advances in sequencing technology and computing power mean that we are in an unprecedented position to analyse large viral sequence datasets using state-of-the-art methods, with the aim of better understanding pathogen evolution and epidemiology. This thesis concerns the evolutionary analysis of rapidly evolving RNA viruses, with a focus on avian influenza and the use of Bayesian methodologies which account for uncertainty in the evolutionary process. As avian influenza viruses present an epidemiological and economic threat on a global scale, knowledge of how they are circulating and evolving is of substantial public health importance. In the first part of this thesis I consider avian influenza viruses of haemagglutinin (HA) subtype H7 which, along with H5, is the only subtype for which highly pathogenic influenza has been found. I conduct a comprehensive phylogenetic analysis of available H7 HA sequences to reveal global evolutionary relationships, which can help to target influenza surveillance in birds and facilitate the early detection of potential pandemic strains. I provide evidence for the continued distinction between American and Eurasian sequences, and suggest that the most likely route for the introduction of highly pathogenic H5N1 avian influenza to North America would be through the smuggling of caged birds. I proceed to apply novel methods to better understand the evolution of avian influenza. Firstly, I use an extension of stochastic mutational mapping methods to estimate the dN/dS ratio of H7 HA on different neuraminidase (NA) subtype backgrounds. I find dN/dS to be higher on the N2 NA background than on N1, N3 or N7 NA backgrounds, due to differences in selective pressure. Secondly, I investigate reassortment, which generates novel influenza strains and precedes human influenza pandemics. The rate at which reassortment occurs has been difficult to assess, and I take a novel approach to quantifying reassortment across phylogenies using discrete trait mapping methods. I also use discrete trait mapping to investigate inter-subtype recombination in early HIV-1 in Kinshasa, the epicentre of the HIV-1 group M epidemic. In the final section of the thesis, I describe a method whereby epidemiological parameters may be inferred from viral sequence data isolated from different infected individuals in a population. To conclude, I discuss the findings of this thesis in the context of other evolutionary and epidemiological studies, suggest future directions for avian influenza research and highlight scenarios in which the methods described in this thesis might find further application.

Many human behaviours are thought to depend upon cognitive capacities enriched with innate domain-specific knowledge. Underpinning this view is the hypothesis that evolution can shape cognition to include strong innate inductive biases. In this thesis, I re-examine that hypothesis with respect to a broad class of behaviours: those that we learn from other individuals. Taking human language as a test case, I present an analysis of the co-evolutionary process that underpins the formation of innate constraints on cognition for behaviours that are culturally transmitted through inductive inference. I derive a series of mathematical models of this process, built around Bayesian models of cognition and cultural transmission, and ask how they can inform our expectations about cognition in a cultural species. I argue that the traditional marriage of nativism and evolutionary reasoning is undermined by this process, as is the suggestion that cognitive adaptation to cultural behaviours is outright implausible. I explore the co-evolutionary dynamics induced by cultural transmission, and conclude that they can radically manipulate the evolution of cognition: culture can intervene in the formation of hard-wired knowledge, but nevertheless facilitate rapid cognitive adaptation. The analyses I report make strong, testable predictions about the nature of inductive biases for cultural behaviours, and offer solutions to a number of long-standing conundrums in the evolution of language.

Nematoda is a very diverse animal phylum. Within Nematoda, species display a multitude of life styles, different reproductive strategies and parasitism has arisen independently several times. Furthermore, morphological conservation and a high rate of homoplasy have impeded the resolution of nematode systematics. To address these issues, single gene (usually the nuclear ribosomal small subunit gene) and mitochondrial gene phylogenies have been used, but the information contained within the sequence of these genes is not enough to resolve the topological relationships between clades that emerged during rapid cladogenesis. Next generation sequencing data have been shown to produce high quality genomic and transcriptomic assemblies at low cost, as a result more and more nematode species are being sequenced. Sequences were gathered or generated for 53 nematode species from ESTs, gene predictions from full genome assemblies and transcripts from RNA-Seq experiments. These sequences were screened for orthologous gene clusters, which were concatenated into a supermatrix with thousands of aminoacid sites. The analysis of the supermatrix with maximum likelihood and Bayesian inference methods sheds light into the early splitting clades of the phylogenetic tree of nematodes and the derived clades III, IV and V. Furthermore, the phylogenetic relationships within the parastitic family Onchocercidae were resolved, unveiling the evolutionary history of these important taxa. Finally, data produced in this work will be useful for subsequent evolutionary studies of the phylum Nematoda.

Nietzsche comme Darwin envisagent la morale de manière évolutive, comme l'héritage temporaire de diverses sédimentations successives. Nietzsche comme Darwin remettent à plat toute une tradition antérieure, philosophique pour l'un, biologique et naturaliste pour l'autre. Tous deux poussent à voir la morale, certes comme un ensemble de règles et d'interdits structurant une société, mais comme un ensemble relatif, déterminé par des contextes, des environnements, des physiologies extra-morales. Le philosophe, comme le scientifique, eux mêmes inscrits dans une histoire et une évolution toujours inachevée à l'heure actuelle, font exploser les normes et les catégories morales anciennes, qu'elles soient métaphysiques, révélées, éternelles, fixes et définitives. Et tous deux, en observant, expliquant et critiquant la morale,provoquent une interrogation sur ses marges et son dépassement, par-delà d'ailleurs la science et la philosophie : qu'est-ce que l'individu pour le troupeau, qu'est-ce que l'homme pour son espèce ? / Nietzsche as Darwin are considering morality in an evolutionary way, as the legacy of various, impermanent and successive layers. Nietzsche as Darwin take a new look at an earlier tradition, one philosophical for the former, one biological and naturalist for the latter. Both evoke morals, indeed as a set of rules and prohibitions structuring a society, but morals as relative, determined by contexts, environments, extra-moral physiologies. The philosopher, like the scientist, whoare themselves enrolled in history and evolution which is yet incomplete, burst standards and old moral categories, whether metaphysical, revealed, eternal, fixed and final. And both, observing, explaining and criticizing the morality, are questionning its margins and its limits, beyond science and philosophy: what does the individual to the herd, what is the man for his species?

The threat superiority effect refers to an ability to quickly and efficiently detect threatening cues in one’s environment. Hence, ensuing and appropriate behavioral defense responses entail greater chances of survival for an organism. Some researchers argue that natural selection has led us to automatically prioritize threats that would have been salient during the period of evolutionary adaptation; as for example snakes. However, others have also argued that activation of our defense response system is more flexible, thus able to also be triggered to dangers of more recent age: such as guns or airplane crashes. The present study has sought to impact this debate, by measuring the electrodermal activity (EDA) – more specifically the skin conductance responses (SCRs) – of subjects who were visually presented with both evolutionary (snakes and spiders) and modern (guns and knives) fear-relevant stimuli. The results demonstrated no significant difference between the two categories within subjects, suggesting that both evolutionary and modern threatening cues activate the defense response system in a similar manner. Although the results are preliminary, and would need further verification in higher powered studies, they can be seen to favor the view that our defense response system is flexibly adaptive in relation to the age of a given threat.

Synaptonemal Komplexe (SC) sind evolutionär konservierte, meiosespezifische, proteinöse Strukturen, die maßgeblich an Synapsis, Rekombination und Segregation der homologen Chromosomen beteiligt sind. Sie zeigen eine dreigliedrige strickleiter-artige Organisation, die sich aus i) zwei Lateralelementen (LE), an die das Chromatin der Homologen angelagert ist, ii) zahlreichen Transversalfilamenten (TF), welche die LE in einer reißverschlussartigen Weise miteinander verknüpfen, und iii) einem zentralen Element (CE) zusammensetzt. Die Hauptproteinkomponenten der Säuger-SC sind das Transversalfilamentprotein SYCP1 und die Lateralelementproteine SYCP2 und SYCP3. Wie sich die SC-Struktur zusammenfügt war bisher nur wenig verstanden; es war nicht bekannt wie die TF innerhalb der LE-Strukturen verankert sind und dabei die homologen Chromosomen verknüpfen. Aufgrund dessen wurde die Interaktion zwischen den Proteinen SYCP1 und SYCP2 untersucht. Mit der Hilfe verschiedenster Interaktionssysteme konnte gezeigt werden, dass der C-Terminus von SYCP1 mit SYCP2 interagieren kann. Aufgrund der Bindungsfähigkeit zu beiden Proteinen, SYCP1 und SYCP3, kann angenommen werden, dass SYCP2 als Linker zwischen diesen Proteinen fungiert und somit möglicherweise das fehlende Bindungsglied zwischen den Lateralelementen und Transversalfilamenten darstellt. Obwohl die SC-Struktur in der Evolution hochkonserviert ist, schien dies nicht für seine Protein-Untereinheiten zuzutreffen. Um die Struktur und Funktion des SC besser verstehen zu können, wurde ein Vergleich zwischen den orthologen SYCP1 Proteinen der evolutionär entfernten Spezies Ratte und Medaka erstellt. Abgesehen von den erheblichen Sequenzunterschieden die sich in 450 Millionen Jahren der Evolution angehäuft haben, traten zwei bisher nicht identifizierte Sequenzmotive hervor, CM1 und CM2, die hochgradig konserviert sind. Anhand dieser Motive konnte in Datenbankanalysen erstmals ein Protein in Hydra vulgaris nachgewiesen werden, bei dem es sich um das orthologe Protein von SYCP1 handeln könnte. Im Vergleich mit dem SYCP1 der Ratte zeigten die Proteine aus Medaka und Hydra, neben den hoch konservierten CM1 und CM2, vergleichbare Domänenorganisationen und im heterologen System zudem sehr ähnliche Polymerisationseigenschaften. Diese Ergebnisse sprechen für eine evolutionäre Konservierung von SYCP1. / Synaptonemal complexes (SCs) are evolutionarily conserved, meiosis-specific proteinaceous structures critically involved in synapsis, recombination and segregation of homologous chromosomes. They show a tripartite ladder-like organization including i) two lateral elements (LEs), to which the chromatin of the homologs is attached, ii) numerous transverse filaments (TFs), that link the two lateral elements in a zipper-like way, and iii) a central element (CE). Major protein components of mammalian SCs are the transverse filaments protein SYCP1, and the lateral element proteins SYCP2 and SYCP3. How SCs become assembled was poorly understood; in particular it was not known how TFs assemble at the plane of LEs to interconnect the homologous chromosomes. Therefore, I have investigated possible interactions between SYCP1 and SYCP2. Using different interaction traps, I was able to show that the C-terminus of SYCP1 interacts with SYCP2. Because of its binding to both, SYCP1 and SYCP3, it can be proposed that SYCP2 acts as a linker between these proteins and therefore would be the missing connecting piece between LEs and TFs. Although the SC-structure is conserved in evolution this appears not to be the case for its protein components. For a better understanding of the conserved SC structure und function, I compared ortholog SYCP1 proteins of evolutionary distant species, namely rat and medaka fish. Despite of the sequence-differences that accumulated during 450 million years of evolution, sequence identity was highest at the level of two previously unidentified motifs (CM1 & CM2). Utilizing these motifs in a database analysis a protein of Hydra vulgaris could be found for the first time. It can be proposed that this protein is the orthologous of SYCP1. Besides the highly conserved motifs the proteins of medaka and hydra show quite similar domain organization and polymerization properties in comparison with rat SYCP1. These results suggest an evolutionary conservation of SYCP1.

Orientador: Cesar Martins / Abstract: One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of extra, non-essential karyotype elements, commonly known as supernumerary B chromosomes (Bs). Bs are present in diverse species of eukaryotes and their molecular characterization remains elusive for years. A distinguished feature that makes them different from the normal chromosomes (called A chromosomes) is their way of inheritance in irregular fashion. Over the last decades, their genetic composition, function and evolution have remained an unresolved query, although a few successful attempts have been made to address these phenomena. The non-Mendelian inheritance and unpairing/non-recombining abilities make the B chromosomes immensely interesting for genomics studies, thus arising different questions about their genetic composition, survival, maintenance and role inside the cell. This study aims to uncover these phenomena in different species. Here, we sequenced the genomes of three model organisms including fish species Astyanax mexicanus and Astyanax correntinus, and grasshopper Abracris flavolineata with (B+) and without Bs (B-) to identify the B-localized sequences, called B chromosome blocks (“B-blocks”). We established approaches for this analysis that comprised of steps such as comparative genomics analysis and annotation of B chromosomal genes and DNA repeat types. The next generation sequencing (NGS) analyses identified thousands of genes fragments as well as... (Complete abstract click electronic access below) / Doutor

Thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy at the University of the Witwatersrand, Johannesburg, 2017. / This thesis investigates in detail the structure of models of turbulent convec tion with phenomenological closures for the eddy-viscosity. It explores the merits of replacing the canonical Mixing Length Theory of stellar convection with more realistic models of fluid turbulence that take into account the full spectrum of eddy sizes. The author provides a detailed exposition of the fun damental assumptions and the modus operandi of various approaches to the treatment of convective energy-transfer in stars. He focuses in particular on spectral descriptions of the convective process. The structure of several clo sure models developed by various authors are investigated, and he identifies and elucidates those aspects of these closures that lead to an improved descrip tion of convective turbulence in the stellar interior. The author also develops an implementation within the public-domain code, called Modules for Experi ments in Stellar Astrophysics, of two of these models and reports and discusses the results of his numerical experiments. / XL2018