Classified in the Lissamphibia, modern amphibians are the only non-amniote tetrapods living today. They consist of three morphologically distinct groups: the tailless frogs and toads (Anura), the limbless caecilians (Gymnophiona), and the tailed salamanders and newts (Urodela). With 205 species, the caecilians are highly specialized worm-like forms that live a fossorial lifestyle, with a relatively narrow distribution in the tropic rainforests of South America, Africa and Asia (Duellman and Trueb, 1994; Amphibiaweb, 2015). Salamanders, with 683 species, are widely distributed in the North America, Asia and Europe, with a few plethodontids extending to Central and South America (Duellman and Trueb, 1994; Amphibiaweb, 2015). Frogs are the most diverse amphibian groups, with 6644 species distributed over all continents except Antarctica (Duellman and Trueb, 1994; Amphibiaweb, 2015). Both frogs and salamanders develop a wide array of lifestyles, ranging from terrestrial, aquatic, fossorial to aboreal lifestyles (Duellman and Trueb, 1994). During ontogeny, amphibian larvae usually undergo a drastic post-embryonic shift into an adult form, a term known as metamorphosis. In salamanders, another developmental pathway – neoteny – also occurs, in which the larval morphology is retained in sexually mature adults (Duellman and Trueb, 1994; Rose, 2003). Because of the diverse lifestyles and developmental pathways, frogs and salamanders are often used as model systems in many fields of biology (e.g., evo-devo). Over a century, but especially in the past two decades, a wealth of frog and salamander fossils has been discovered from the Mesozoic and Cenozoic of East Asia (e.g., Noble, 1924; Young, 1936; Borsuk-Bialynicka, 1978; Gao, 1986; Dong and Wang, 1998; Gao and Shubin, 2001, 2003, 2012; Gao and Wang, 2001; Gao and Chen, 2004; Wang and Rose, 2005; Wang and Evans, 2006b; Zhang et al., 2009; Chen et al., 2016; this study). Some of these fossils represent the earliest members of many crown clades, including the earliest crown salamanders from the Middle Jurassic (~165 Ma, Gao and Shubin, 2003), the earliest salamandroid from the Late Jurassic, the earliest sirenid from the Late Jurassic (this study), and the earliest spadefoot toads from the late Paleocence (Chen et al., 2016). Other fossils also bear important anatomical, temporal and geographical information in understanding their evolution. Unfortunately, the importance of many of these fossils remains obscure in a phylogenetic context. For example, an early-middle Oligocene Mongolian spadefoot toad Macropelobates osborni (Noble, 1924) was discovered outside the current distribution of spadefoot toads, yet its phylogenetic position and its implication on spadefoot toad biogeography remain not well understood. A major reason for the poor understanding of these fossils can be attributed to a trend of dichotomy between morphological and molecular phylogenies on amphibians. Whereas morphologists and paleontologists sometimes use a relatively small morphological dataset to reconstruct relationships (e.g., Gao and Shubin, 2012; Henrici, 2013), large-scale phylogenies are almost always conducted with molecular data with only living taxa (e.g., Roelants and Bossuyt, 2005; Pyron and Wiens, 2011). Very few studies on amphibian phylogeny have combined morphological and molecular data together, and even fewer also combined fossils. Because of this, the positions of many important fossils remains unclear, and the evolutionary scenarios inferred from only living species can sometimes be inconsistent with fossil evidence. In this thesis, I adopt a total-evidence approach to understand the evolution of amphibians, especially frogs and salamanders. I will incorporate information from fossils, morphology and molecules together to reconstruct the relationships. Compared with studies with each individual datasets, this approach incorporates all available data in a single analysis, with a goal to reach robust and congruent results that allow further discussions on character evolution and biogeographic reconstruction. The inclusion of fossils directly into the combined analysis provides the time dimension that is independent from molecular data (Norell, 1992). The anatomical combination of fossils can represent intermediate forms that help to solve the “long branch” problems caused by highly specialized modern taxa. The morphological dataset, despite its much smaller size with molecular data, is the only link between fossils and modern taxa. The inclusion of key morphological characters in both reconstructing phylogenetic hypotheses and examining character evolution provide consistent results that allow discussion on the homology/homoplasy of a certain character without ambiguity. The molecular sequence data provides overwhelmingly large data on modern taxa for phylogenetic reconstructions compared with morphological data, which helps to reach a robust hypothesis. Although fossils contain no molecular data, the inclusion of molecular sequence data into the combined analysis does have an effect on the positions of fossil taxa. By altering the relationship “framework” of modern taxa, the character optimization of fossils and other taxa of a combined analysis also varies compared with results of morphology-only analysis, thus changing the positions of fossils. In the following five chapters, I will describe a number of fossil amphibian species, reconstruct three combined phylogenies, and use the results for discussions on character evolution and biogeography. In Chapter 1 and Chapter 2, I focus on a frog clade called spadefoot toads (Anura: Pelobatoidea). In Chapter 1, I provide descriptions on three important fossil spadefoot toads from the Cenozoic of East Asia and North America: Macropelobates osborni from the early-middle Oligocene of Mongolia, Prospea holoserisca from the latest Paleocene of Mongolia, and Scaphiopus skinneri from the middle Oligocene of the United States. In Chapter 2, I conduct a combined phylogenetic analysis of archaeobatrachian frogs, and discuss the evolution of the bony spade and the historical biogeography of spadefoot toads based on the results of the phylogeny. In Chapter 3, I describe a new fossil frog from the Early Cretaceous of Inner Mongolia, China. The unique morphology of the new fossil is distinct from previous Early Cretaceous frogs from the Jehol Biota of China. Results of the combined analysis show that the new frog represents a basal member of the Pipanura. Comparisons between the Early Cretaceous frogs from China, Spain and Brazil show a high diversity of species coupled with a high degree of endemism during the Early Cretaceous. I discuss in the phylogenetic context how early frogs gradually reach their postcranial body plan with a shortened vertebral column, loss of ribs, and specialized pelvic regions. In Chapter 4, I provide a brief review of Mesozoic fossil salamanders from northern China, and describe a new fossil from the Late Jurassic of Liaoning Province, China. I conduct a combined phylogeny of higher-level relationships of salamanders. The new fossil, despite its general-looking appearance, represents a basal member of the highly specialized eel-like neotenic family Sirenidae on the cladogram. I discuss character evolutions in the Sirenidae, and how the neotenic developmental pathway evolved in early salamanders. In Chapter 5, I conduct a combined phylogenetic analysis of the salamander suborder Cryptobranchoidea, consisting of the neotenic giant salamanders (Cryptobranchidae) and the metamorphic Asiatic salamanders (Hynobiidae). The new morphological matrix includes new characters that were previously less sampled in the hynobranchial region. The monophyly of the Hynobiidae are confirmed by the new analysis, and four unequivocal synapomorphies are found for the clade. An S-DIVA biogeographic reconstruction is conducted to disscuss the distributional patterns of the Hynobiidae.

This study lends strong support to the idea that members of Bromeliaceae have undergone a recent adaptive radiation, and therefore show that, at least in part, diversity in the tropics is due to a fast speciation rate and that the tropics can be a "cradle" for new diversification and exploitation of varying ecological niches through the diversification of ecophysiological traits within a lineage.

Darwinian Evolutionary system - a system satisfying the abstract conditions: reproduction with heritable variation, in a finite world, giving rise to Natural Selection encompasses a complex and subtle system of interrelated theories, whose substantive transplantation to any artificial medium let it be mathematical model or computational model - will be very far from easy. There are two motives in bringing Darwinian evolution into computational frameworks: one to understand the Darwinian evolution, and the other is to view Darwinian evolution - that carries out controlled adaptive-stochastic search in the space of all possible DNA-sequences for emergence and improvement of the living beings on our planet - as an optimization process, which can be simulated in appropriate frameworks to solve some intractable problems. The first motive led to emerging field of study commonly referred to as Artificial Life, and other gave way to emergence of Evolutionary Computation, which is speculated to be the only practical path to the development of ontogenetic machine intelligence. In this thesis we touch upon all the above aspects. Natural selection is the central concept of Darwinian evolution and hence capturing natural selection in computational frameworks which maintains the spirit of Darwinian evolution in the sense of conventional, terrestrial and biological perspectives is essential. Naive models of evolution define natural selection as a process which brings in differential reproductive capabilities in organisms of a population, and hence, most of the evolutionary simulations in Artificial Life and Evolutionary Computation implement selection by differential reproduction: the Attest members of the population are reproduced preferentially at the expense of the less fit members of the population. Formal models in evolutionary biology often subdivide selection into components called 'episodes of selection' to capture the different complex mechanisms of nature by which Darwinian evolution can occur. In this thesis we introduce the concept of 'episodes of selection' into computational frameworks of Darwinian evolution by means of A Conceptual Evolutionary model (ACE-model). ACE-model is proposed to be simple and yet it captures the essential features of modern evolutionary perspectives in evolutionary computation framework. ACE-model is rich enough to offer abstract and structural framework for evolutionary computation and can serve as a basic model for evolutionary algorithms. It captures selection in two episodes in two phases of evolutionary cycle and it offers various parameters by which evolutionary algorithms can control selection mechanisms. In this thesis we propose two evolutionary algorithms namely Malthus evolutionary algorithms and Malthus Spencer evolutionary algorithms based on the ACE-model and we discuss the relevance of parameters offered by ACE-model by simulation studies. As an application of ACE-model to artificial life we study misconceptions involved in defining fitness in evolutionary biology, and we also discuss the importance of introducing fitness landscape in the theories of Darwinian evolution. Another important and independent contribution of this thesis is: A Mathematical Abstraction of Evolutionary process. Evolutionary process is characterized by Evolutionary Criteria and Evolutionary Mechanism which are formalized by classical mathematical tools. Even though the model is in its premature stage to develop any theory based on it, we develop convergence criteria of evolutionary process based on this model.

In der vorliegenden Arbeit soll zum Thema Geschichtsphilosophie die Frage nach einem Ende der Geschichte, wie es 1989 von Francis Fukuyama in seinem viel beachteten Aufsatz „The End of History?“ postuliert wurde, diskutiert werden. Dazu werden zu Beginn die Vordenker oder Ideengeber, auf deren Werk Fukuyama seine Argumentation aufbaut, vorgestellt. Den Hauptteil der Arbeit bildet die Vorstellung und Analyse der 1992 erschienenen Monographie „Das Ende der Geschichte – Wo stehen wir?“ von Francis Fukuyama. Im letzten Teil der Arbeit werden eine Reihe im weitesten Sinne philosophischer Fragen und Kritiken zum Werk Fukuyamas thematisiert.

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Appropriate recognition of parasites is crucial for effective immune response, ensuring activation of adequate defence mechanisms. In vertebrates, it has frequently been demonstrated that genes encoding proteins involved in pathogen recognition by an adaptive immune system are often subject to intense selection pressures. On the contrary, much less information has been provided on the evolution of recognition mechanisms of innate immunity. The aim of this thesis is to describe the pattern of natural variation of innate immunity genes involved in pathogen recognition in rodents and to analyze the mechanisms of their evolution. We used murine rodents (subfamily Murinae) as a principal model group because they are potential reservoirs of various pathogens dangerous to humans. First, we studied the intraspecific variability of five bacterial sensing Toll-like receptors (TLR1, TLR2, TLR4, TLR5, and TLR6) in inbred strains derived from two subspecies of the house mouse (M. m. musculus, hereafter abbreviated as Mmm and Mus musculus domesticus, Mmd). Wild-derived inbred strains are suitable tools for studying variation of immunity genes because they provide information about alleles that occur in natural populations, and at the same time they occur at homozygous state. The most significant results include the findings of a stop codon in exon 2 of the Tlr5 gene in one Mmm strain and no variability in Tlr4 of Mmd. Following these results we decided to check whether the absence of Tlr4 polymorphism in Mmd reflects the pattern found in natural populations, or whether it is a consequence of insufficient sampling or subsequent breeding. We therefore sequenced Tlr4 in both subspecies across a large part of the Western Palearctic region (in total 39 Mmm and 62 Mmd individuals), then we compared these results with variability on mitochondrial DNA (cytochrome b). The result confirmed our prediction that observed variability in Mmd is strongly reduced also in free-living populations (compared to Mmm), probably due to strong purifying selection by pathogens with which they met during the westward colonization. However, the influence of random evolutionary processes (e.g. drift during bottlenecks) cannot be excluded based on our data. At the intraspecific level, we could not find any sign of positive selection. The last part of my dissertation is devoted to interspecific comparison of two receptors, TLR4 and TLR7. These two TLRs differ in the exposure and the ligands detection. TLR4 is an extracellular receptor detecting mainly bacterial ligands (especially lipopolysaccharides), while TLR7 is located inside the cell and detects ssRNA viruses. The aim of this part of the thesis was to describe variability of both receptors at the interspecific level and to reveal selection forces acting on TLRs in longer evolutionary time scale. In total we analyzed 23 rodent species of the subfamily Murinae in Europe, Asia and Africa. Our results suggest that purifying selection has been a dominant force in evolution of the Tlr4 and Tlr7 genes, but we also demonstrated that episodic diversifying selection has shaped the present species-specific variation in rodent Tlrs. Sites under positive selection were concentrated mainly in the extracellular domain of both receptors, which is responsible for ligand binding. The comparison between two TLRs lead us to the conclusion that the intracellular TLR7 is under much stronger negative selection pressure, presumably due to its interaction with viral nucleic acids.

Sexual selection has long been a working explanation for the elaboration of appreciable traits in plants and animals, but the idea that it is an equally potent agent of change at the level of individual molecules is relatively recent. Indications that genes associated with reproductive biology evolve especially rapidly planted this notion, but many details about the genomics of sex remain elusive. Numerous studies have characterized rapid sequence and expression divergence of sex-related molecules, but few if any have demonstrated convincingly that these patterns exist as a result of sexual selection. This dissertation describes several genome-scale studies related to reproduction and the sexes in teleost fishes, a group of animals underexploited in regard to this topic. Using commercial microarrays I measured the extent of sexually dimorphic gene expression in the zebrafish, Danio rerio. Sex-biased patterns of gene expression in this species are similar to those described in other animals. A number of genes expressed at high levels in ovaries and testes relative to the body were identified as a product of the study, and these data may be useful for future studies of reproductive genes in Danio fishes. In a second study, the recent advent of high throughput cDNA pyrosequencing was leveraged to characterize the relationships between tissue-, sex-, and species-specific expression patterns of genes and rates of sequence evolution in swordtail fishes (Xiphophorus). I discovered ample evidence for expression biases of all three types, and a generally positive but idiosyncratic relationship between the magnitude of expression bias and rates of protein-coding sequence evolution. Pyrosequencing of cDNA was also used to explore the possibility that postcopulatory sexual selection drives the rapid evolution of male pregnancy genes, a novel class of reproductive molecules unique to syngnathid fishes (seahorses and pipefishes). Genes differentially expressed in the male brooding tissues as a function of pregnancy status evolve more rapidly at the amino acid level than genes exhibiting static expression. Brooding tissue genes expressed during male pregnancy have evolved especially rapidly in polyandrous lineages, a finding that supports the hypothesized relationship between postcopulatory sexual selection and the adaptive evolution of reproductive molecules.

Darwin's (1859) theory of evolution by natural selection accounts for the adaptations of organisms, but, as Fisher (1930) famously said, 'natural selection is not evolution.' Evolutionary theory has two major components: i) natural selection, which involves the underlying dynamics of populations; and ii) adaptive evolutionary change, which involves the optimisation of phenotypes for fitness maximisation. Many of the traditional theoretical frameworks in evolutionary theory have focussed on studying optimisation processes that generate biological adaptations. In recent years, however, a number of evolutionary theorists have turned to using frameworks such as the 'replicator dynamics' or 'eco-evolutionary dynamics', to explore the dynamics of natural selection. There has, however, been little attempt to explore how these dynamical systems frameworks relate to more traditional frameworks in evolutionary theory or how they incorporate the principles that embody the process of evolution by natural selection, namely, phenotypic variation, differential reproductive success, and heritability. In this thesis, I use these principles to provide the formal foundations of a general framework - a mathematical synthesis - in which the future state of an evolutionary system can be predicted from its present state; what I will call a 'dynamical systems theory of natural selection.' Given the state of an existing biological system, and a set of assumptions about how individuals within the system interact, the job of the dynamical systems theory of natural selection is no less than to predict the future in its entirety.

Language is arguably one of the most salient features that distinguish humans from other animal species. However, despite the existence of a large body of relevant theoretical and empirical research, there is currently no consensus as to why language emerged exclusively in the human species or how it evolved its unique communicative structure. In this thesis, I therefore take a multi-pronged approach to analysing and testing several different hypotheses for the biological function and evolution of language. In Chapter I, I review the evidence and theoretical arguments for each of these proposals and provide, in place, a synthetic perspective which integrates or eliminates each of these ostensibly competing hypotheses for the biological function of language. In Chapter II, I employ the first experimental test of the interdependence hypothesis: the unique proposal offered to explain the emergence and potential coevolution of language and cooperation in the human species. In pursuit of this experiment, I employed a cooperative social foraging task using small and large groups to determine what factors enable individuals to make sense of information from others and converge upon a group consensus. In Chapter III, I take an experimental approach to determine whether aspects of human language can be characterised in terms of honest signalling theory. In this respect, I test several different proposals predicted by the sexual selection and deception hypotheses for human language function. In Chapter IV, I divert attention away from biological function to focus more closely on language structure. More specifically, I take an experimental approach to the problem of how and indeed whether recursive syntax evolved to be a consistent feature of human language. In pursuit of this experiment, I utilized the Imposing Memory Task (IMT) and a recursive syntax measure, to determine relative performance on each of these cognitive tasks, thereby testing whether recursive syntax may have evolved in tandem with higher-order intentionality (also known as embedded mindreading). Finally, in Chapter V, I discuss the results and implications of these experiments, and possible suggestions for future studies.

Despite being observed since the XVIIIth century, Algol systems and related objects are<p>still rather poorly understood. We know that they are composed by a generally B-A main sequence<p>star and a lighter but more evolved companion star. This paradox is explained by the transfer of mass<p>between the two stars, but new problems arose. In particular, I studied the mass-transfer driven spin-<p>up of the accreting star that drives the star to critical rotation and the puzzling, indirectly observed, non-conservative evolution. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished