Comparative genomic studies have identified noncoding regions of the genome which are often more highly conserved between species than protein-coding sequences. One possible explanation for this conservation of non-coding sequences is some form of selective constraint since sequence conservation at great evolutionary depths is a preliminary indication of functional constraint. Here, I consider nearly 2500 putative regulatory elements, termed Conserved Noncoding Elements (CNEs), that are conserved across seven vertebrate species (human, macaque, mouse, chicken, frog, zebrafish and fugu). I distinguish between CNEs that show accelerated rates of evolution and those that have remained more constrained throughout evolution, and identify CNEs that show higher than expected substitution rates in the human lineage that may be potential candidates of adaptive evolution. However, it is not trivial to demonstrate the action of selection on such sequences. It is relatively easier in the case of protein-coding DNA, since selection would be predicted to result in different rates of substitution for synonymous and non-synonymous sites. Hence, I use the same seven species to define phylogenetically invariant positions in CNEs in contrast to those that have at least one substitution and analyse them independently to determine if there is a positive correlation between evolutionary conservation and the strength of purifying selection at individual sites. In the 1000 Genomes, but not the HapMap, data I find a significant excess of rare derived alleles in CNEs relative to coding sequences. This excess of rare alleles can be best explained if selection is relatively consistent across sites, with most mutations resulting in a similar reduction in fitness. Finally, I explore patterns of variation in the allele-frequencies within human populations, however do not detect any significant differences in the underlying distribution of negatively selected variants among human populations.

This paper considers the problem of language change. Linguists must explain not only how languages are learned but also how and why they have evolved along certain trajectories and not others. While the language learning problem has focused on the behavior of individuals and how they acquire a particular grammar from a class of grammars ${cal G}$, here we consider a population of such learners and investigate the emergent, global population characteristics of linguistic communities over several generations. We argue that language change follows logically from specific assumptions about grammatical theories and learning paradigms. In particular, we are able to transform parameterized theories and memoryless acquisition algorithms into grammatical dynamical systems, whose evolution depicts a population's evolving linguistic composition. We investigate the linguistic and computational consequences of this model, showing that the formalization allows one to ask questions about diachronic that one otherwise could not ask, such as the effect of varying initial conditions on the resulting diachronic trajectories. From a more programmatic perspective, we give an example of how the dynamical system model for language change can serve as a way to distinguish among alternative grammatical theories, introducing a formal diachronic adequacy criterion for linguistic theories.

Formalizing linguists' intuitions of language change as a dynamical system, we quantify the time course of language change including sudden vs. gradual changes in languages. We apply the computer model to the historical loss of Verb Second from Old French to modern French, showing that otherwise adequate grammatical theories can fail our new evolutionary criterion.

Hybrid zones are regions where genetically differentiated forms come together and exchange genes through hybrid offspring. The study of characters gradually changing across such zones (clines) can give insight into evolutionary processes, providing exceptionally sensitive estimates of the intensity of selection, and allowing the detection of loci that might be involved in reproductive isolation and speciation. The Alpine grasshopper Podisma pedestris has a hybrid zone in Southern France where two populations meet. They differ in their sex chromosome system, and strong selection against hybrids is observed. These distinct populations likely have split and re-joined several times during the Quaternary glacial cycles. A model explaining the selection observed against hybrids postulates hundreds of loci of small effect spread over two differentiated genomes meeting in secondary contact. Yet, over 50 years of study to-date non have been discovered. However, so far the study of P. pedestris has not made use of high-throughput sequencing data which provides an unprecedented resolution of molecular markers. I am aiming to close the gap with this thesis. I assemble the grasshopper's mitochondrial genome sequence and infer what proportion of its genome is made up by mitochondrial inserts (Numts). Using transcriptome data from two individuals, I then go on to fit demographic models, finding the populations split approximately 400 000 years ago and that the current-day population sizes are considerably smaller than the ancestral one. The final data chapter explores the genetic architecture of the hybrid zone using data from a targeted sequence capture of hundreds of loci covering some 10 000 polymorphic sites. Only two loci under selection are identified, which is surprising given the power of the analysis. Both loci are located on the X chromosome and are subject to weak selection (0.3% and 0.03%). This shows the power of hybrid zone analysis to infer targets of selection. The results are discussed in light of a theoretical chapter on the 'inexorable spread' phenomenon and lead to the proposal for further research into the causes of the reproductive isolation observed between the grasshopper populations.

The highlands in the northern Andes, which are known as the páramo, are recognized worldwide for their unique and species-rich flora. Many páramo plant groups underwent radiations, which have been shown to be very recent and outstandingly fast. These radiations have usually been linked to (1) the uplift of the northern Andes, which provided new ecological opportunities in the highlands that originated in this process, (2) Quaternary climate change that produced range shifts of the páramo, resulting in periods of páramo contraction and isolation, during cold periods, and periods of páramo expansion and connection, during warm periods (3) the Andean physiographical and ecological heterogeneity, which provides extent oppornuties for isolation and for ecological divergence. In spite of increasing research efforts to understand the evolution of the páramo flora, the actual processes underlying species diversification remain unclear. The main aim of this thesis is to contribute to the understanding of these processes. We use three different approaches in two different study systems: (1) A population genetics approach, which remains rare among páramo plant studies, focuses on three páramo Lupinus species (Lupinus alopecuroides, L. nubigenus, L. microphyllus). These species belong to one of the best...

The concept of a fitness landscape arose in theoretical biology, while that of effective fitness has its origin in evolutionary computation. Both have emerged as useful conceptual tools with which to understand the dynamics of evolutionary processes, especially in the presence of complex genotype-phenotype relations. In this contribution we attempt to provide a unified discussion of these two approaches, discussing both their advantages and disadvantages in the context of some simple models. We also discuss how fitness and effective fitness change under various transformations of the configuration space of the underlying genetic model, concentrating on coarse-graining transformations and on a particular coordinate transformation that provides an appropriate basis for illuminating the structure and consequences of recombination.

The G protein-coupled receptor 84 (GPR84) is found in immune cells and its expression is increased under inflammatory conditions. Activation of GPR84 by medium-chain fatty acids results in pro-inflammatory responses. Here, we screened available vertebrate genome data and found that GPR84 is present in vertebrates for more than 500 million years but absent in birds and a pseudogene in bats. Cloning and functional characterization of several mammalian GPR84 orthologs in combination with evolutionary and model-based structural analyses revealed evidence for positive selection of bear GPR84 orthologs. Naturally occurring human GPR84 variants are most frequent in Asian populations causing a loss of function. Further, we identified cis- and trans-2-decenoic acid, both known to mediate bacterial communication, as evolutionary highly conserved ligands. Our integrated set of approaches contributes to a comprehensive understanding of GPR84 in terms of evolutionary and structural aspects, highlighting GPR84 as a conserved immune cell receptor for bacteria-derived molecules.:1. ABBREVIATIONS (3) 2. INTRODUCTION (4) 2.1 Structure and signal transduction of G protein-coupled receptors (4) 2.2 The evolution of the GPCR protein superfamily (5) 2.3 GPR84, a receptor regulating immune functions (6) 2.4 Aim of the study (10) 3. PUBLICATION (11) 4. SUMMARY OF THE THESIS (37) 5. REFERENCES (40) 6. ANLAGEN (45) 6.1 Supplemental information (45) 6.2 Erklärung über die eigenständige Abfassung der Arbeit (58) 6.3 Darstellung des eigenen Beitrags (59)

This dissertation focuses on predictability problems regarding the behaviour of the professional librarians in public-, school- and research libraries in specific crucial situations. The material was obtained by observations/participations (over 10 years) in the daily work in Swedish libraries by non-structured interviews and “free” discussions with librarians and library visitors. Over 200 interviews with 87 librarians and over 300 discussions with 261 library visitors are the fundament of the empirical basis of my study. These findings build up a theoretical basis (a heuristic model) grounded in ideas of deterministic chaos and complexity theory. Deterministic means, that the current state is the consequence of its preceding states, in my terms, the corporate memory in organizations. Chaotic means the sensitivity of initial condition. Deterministic chaos describes behaviour which satisfies the conditions of determinism but even shows the characteristics of chaos. The study shows that differences between the behaviour of the librarians and the predictions of the behaviour in crucial situations from the political leadership are essentially grounded in ·The history of Swedish libraries (deterministic rationality and self-rationality). ·The asymmetric information between librarians and politicians. ·Self-organization of librarians in the daily work. ·The “free” will of librarians in crucial situations grounded in the philosophy of Kant. The behaviour I could observe was studied in the following situations: ·The demand of a law, which secures the existence of public- and school libraries. ·The selection, development and installation of appropriate computer based information systems in public- school- and research libraries. ·The GÖK- and KUR-projects, which was based on the assumption that new ways to work with the daily patterns in libraries should open the library for more visitors, book loaners and information seekers. The issues discussed in this dissertation gave the following results: ·That the long time, in many cases even short time, unpredictability of librarian behaviour in for the library crucial situations is not only understandable – but also necessary for the development of the library. ·That the deterministic chaotic behaviour of the librarians is generated by self-rationality, asymmetric information, and self-organization. ·That the library is not a chaotic organization but a deterministic chaotic organization. Further I could see tendencies for the same behaviour in other professional, knowledge based Non Profit Organizations like schools, universities and hospitals.