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The excellent penguin fossil record is temporally long, among the oldest of modern birds, and contains fossils on every Gondwanan continent except India. However, most of fifty-nine named taxa are isolated skeletal elements, many of which are noncomparable. Fossil diversity is highest in New Zealand, with additional Antarctic and Patagonian faunas and fewer remains from Australia and South Africa. Phylogenetic hypotheses place penguins within Aves and Neornithes, but further relationships remain contentious. Recent work clarified living species' phylogeny, but none examined all fossil taxa. I describe penguin skeletal anatomy using CT scans and museum specimens, providing the first such description for all living and extinct species in an explicitly phylogenetic framework. All elements are phylogenetically variable, intergeneric variation is large, and extinct taxa are more variable than extant. I recommend that future systematic works include all elements for extinct species diagnoses, osteology for living species, and discussions of intraspecific variation. This description grounds my phylogenetic analysis, based on a 503-character matrix of osteological, myological, integumentary, and behavioral characters. This greatly expands previous datasets, and allows recovery of a highly resolved phylogeny, including monophyly of two extinct clades and the crown-group. Data partitions support different levels of relationship, whereas missing data and outgroup choice drastically affect recovered topology. Incorporating the maximum amount of data gives the highest resolution by recovering all relevant character states. I propose the first formal phylogenetic nomenclature for sphenisciforms, and define and diagnose previously used terms such as Panspheniscidae (total group), Sphenisciformes (known penguins), Spheniscidae (crown-group), Palaeeudyptidae and Paraptenodytidae (two extinct clades). I coin Spheniscoidea (Spheniscidae + Paraptenodytidae) and Australodyptinae (Aptenodytes + Pygoscelis). After calibration with geologic time, I calculate the completeness of the pencuin record and determine confidence intervals to estimate a Cretaceous origin and an Eocene crown-clade origin. These dates and the derived phylogenetic placement of penguins suggest that numerous extant bird lineages may also have Cretaceous origins. I recover a New Zealand origin for penguins and a West Antarctic origin for the crown-group and extinct clades. Correlating penguins with tectonic and climatic data indicates an Eocene adaptive radiation, probably related to latest-stage Gondwanan breakup and associated global cooling.

<p> The larval nutritional mode of marine invertebrates is an important life history trait that has strong effects on their ecology and evolution. Increases in egg size and transitions from feeding to nonfeeding larvae have happened repeatedly. In Spiralia, a change in cytoplasm allocated to macromeres at the 8-cell stage (that could delay the development of a functional gut) may accompany these transitions. The first part of this thesis describes the development of the gastropod <i>Crepidula williamsi</i> and compares it to the closely related <i>C. fornicata,</i> with a focus on changes in allocation to macromeres and the development of a functional gut. The second part is a phylogenetic comparison of egg size and allocation to macromeres in 44 species of spiralians, which revealed a significant correlation between the two. A phylogenetic comparison like this one has not previously been done on the development of such diverse marine invertebrate taxa.</p>

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Cyanobacteria are globally widespread and ecologically highly significant photoautotrophic microorganisms, with diverse geno- and phenotypic characters unprecedented among prokaryotes. This phylum embraces representatives with an exclusive adaptability in highly specialized environments, from oligotrophic ocean waters to the interior of cells in symbiotic plants, the most extreme being the chloroplasts. Insertion sequences (ISs) are short (~1000 bp) mobile genetic elements prevalent in microbial genomes, potentially representing potent adaptive forces. In this thesis, hypotheses tested that ISs play significant roles in both reductive and adaptive evolution in physiologically versatile cyanobacteria, using two model systems. First, the genome of an obligate plant (Azolla) symbiont, the cyanobacterium ‘Nostoc azollae 0708’, was sequenced, which led to the discovery of a highly ‘eroding’ genome (5,48 Mbp), loaded with ISs covering 14% of the genome, a situation likely caused by the relaxed selection pressure within the plant. The ISs were located in close proximity to the extremely numerous pseudogenes identified, although genes with key functions in a symbiotic context escaped IS mediated erosion (e.g. nitrogen fixation and differentiation genes). Some ISs were shown to have transposed short distances within the genome (‘local hoping’), and to be likely causative agents in pseudogene formation, and thus pivotal actors in the reductive evolution discovered. To widen the scope of ISs further, additionally 66 phylogenetically diverse microorganisms with a variety of life styles (free-living, symbionts, pathogens) were examined in regards to ISs influence. The data verified their over-all importance in shaping microbial genomes. Finally, natural microbial populations in the Baltic Sea, a semi-enclosed geologically young (~10,000 years) brackish water body offering steep gradients in salinity and nutrient loads, were examined using metatranscriptomics and metagenomics. A large proportion of the metagenome was devoted to ISs and most importantly a large fraction of the metatranscriptome consisted of IS transcripts (~1%), which may be suggestive of a high IS activity. These phenomena were most apparent in cyanobacteria in central parts of the Baltic Sea. The presence of an especially rich abundance of ISs in brackish waters was further substantiated by their low frequency (&lt; 0.1%) in microbes of marine waters. Hence, ISs may facilitate both adaptations (short term) and adaptive evolution (long term) in microbes entering brackish water, otherwise unable to cross the distinct limnic-to-marine salinity-divide. Together, the data reveal high genomic loads of ISs in cyanobacteria subject to highly demanding conditions and stress the importance of locally migrating ISs (and pseudogenization) as important facilitators in adaptation and evolution, being a more rapid process than hitherto expected. The findings strongly support current theories stating a crucial role of ISs in shaping microbial genomes to render fitness. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

The groups with which we associate influence our actions. This is often the case even when they are not deliberately organised but rather based on social categories, such as sex and skin colour, or cultural homogeneity, such as common language or customs. Group membership can cause widespread phenomena such as ingroup favouritism, polarisation of opinion and competition. Previous experiments have shown that these effects can be triggered by even completely arbitrary distinctions between groups. This thesis uses mathematical models to investigate under what circumstances these phenomena can arise. Using a game theoretical approach, the first three papers address the evolution of ingroup favouritism. Previous models have focused on the prisoners’ dilemma, interactions where the socially optimal behaviour is to co-operate, but where it is in the individual’s self-interest not to. The results presented here suggest that co-ordination problems may have been more important than those of co-operation in the evolution of an ingroup bias. In particular, this applies to common goals that require trust. It is also demonstrated in a behavioural experiment that such trust is most common within groups, but that it can emerge between groups through group reputation. The fourth paper focuses on a model on how cultural groups in contact can develop common norms, rather than polarise into different norm groups, by assuming a confirmation bias. The model is empirically tested on demographic and linguistic data from Mauritian Creole, a natural language developed from the mixing of parent languages. In the fifth paper, the group is defined by common preferences (e.g. for pop songs), which are transmitted in a random copying model. The competitive success of the groups, with respect to their size, is recorded on a toplist, the turnover rate of which is derived. In the final paper, people match up in pairs between groups according to their preferences, and all stable matchings are found under a specific assumption of bounded rationality, when people’s individual behaviour may be affected by the consequences for fellow group members.

Although population genetics has a long history and firm theoretical basis, until recently little data was available for empirical hypothesis testing. The unprecedented growth of sequencing methodologies has transformed the discipline from data-poor and theory rich field into one virtually unlimited by the available of suitable data. In this thesis, we develop bioinformatic methods to address a variety of longstanding questions in the field of evolutionary genetics. Specifically, we use data derived from model organisms to study the evolution of inversion polymorphisms, segregation distorters and fitness epistasis. In the first chapter, we develop methods for detecting chromosomal inversions using next-generation sequencing data. Subsequently, we show that chromosomal inversions in Drosophila melanogaster are evolutionarily young, and at least one has likely achieved polymorphic frequencies via sex-ratio segregation distortion. In the third chapter, we develop a method of surveying the genome for segregation distortion in an unbiased manner, and show that segregation distortion does not contribute to hybrid male sterility in one pair of house mouse populations. Finally, we show that contrary to expectations, gene-gene interactions are widespread within species, which challenges a central paradigm of speciation research.

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