Monistic substantivalists believe that material objects and regions of space-time are not two distinct kinds of fundamental of entities. For the monist, objects either are identical with regions or are somehow derivative from them. Dualistic substantivalists view regions and objects as distinct kinds of fundamental entities. One virtue monists claim over dualists is that their view is more ideologically parsimonious than dualism because monists can do without a primitive notion of location. In this paper I provide an argument that undercuts some of the theoretical edge that monists claim over dualists. The assumption that the monist can provide a reduction of location unique to her position rests on a false assumption about the possible structures spacetime can have. If it is metaphysically possible for two distinct regions to coincide with respect to all their significant spatiotemporal properties and relations (call these 'coincident regions'), then analyses of location unique to monism will turn out to be inadequate. / Master of Arts

Phylogenetics is the research of ancestor-descendant relationships among different groups of organisms, for example, species or populations of interest. The datasets involved are usually sequence alignments of various subsets of taxa for various genes. A major task of phylogenetics is often to combine estimated gene trees from many loci sampled from the genes into an overall estimate species tree topology. Eventually, one can construct the tree of life that depicts the ancestor-descendant relationships for all known species around the world. If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated overall species tree topology. In this study, we assume that gene tree discordance is solely due to incomplete lineage sorting under the multispecies coalescent model (Degnan and Rosenberg, 2009). If there is missing data or incomplete sampling in the datasets, then supertree methods can be used to assemble gene trees with different subsets of taxa into an estimated species tree topology. In addition, we examine the performance of the most commonly used supertree method (Wilkinson et al., 2009), namely matrix representation with parsimony (MRP), to explore its statistical properties in this setting. In particular, we show that MRP is not statistically consistent. That is, an estimated species tree topology other than the true species tree topology is more likely to be returned by MRP as the number of gene trees increases. For some situations, using longer branch lengths, randomly deleting taxa or even introducing mutation can improve the performance of MRP so that the matching species tree topology is recovered more often. In conclusion, MRP is a supertree method that is able to handle large amounts of conflict in the input gene trees. However, MRP is not statistically consistent, when using gene trees arise from the multispecies coalescent model to estimate species trees.

In this thesis I focus on dismissivism in metaphysics. Some philosophers argue that at least some metaphysical disputes are not substantial, and as a consequence should be dismissed. In this work I restrict my attention to metaphysics and focus on debates about existence and grounding. In particular I am interested in finding out whether there is a difference between the possible options available for dismissing debates about what there is and the possible options available for dismissing debates about what grounds what. I will delve into this in two different steps. First of all I explore the possibility to dismiss debates about what there is, and as a case study I analyse the debate between three-dimensionalism and four-dimensionalism. Secondly I delve into whether it is possible to dismiss debates about what grounds what, thanks to the discussion of another case study, i.e. the debate between tropes ontologies and universals ontologies. It is worth exploring the nature of dismissivism, because it bears on the future of philosophy. If philosophy has to have a future, we have to make sure that at least some disagreements within it are substantial. My conclusions will be that metaphysical debates about what there is can be dismissed for a variety of reasons (semantic, epistemic, ...). I also argue there is no general formula to find out whether a specific debate should be dismissed. On the other hand I argue that debates about what grounds what should be dismissed. I offer two distinct arguments in favour of my claim. Firstly, I argue that disputants are having a verbal dispute when they talk about what grounds what, and thus their disagreement is non genuine. Secondly, I argue that the notion of grounding is underspecified, because it cannot be properly distinguished from causation.

<p>Coprophilous ascomycetes are a diverse group of saprobes, of which many belong to three families, Delitschiaceae, Phaeotrichaceae and Sporormiaceae, within the large order Pleosporales. The natural relationships and circumscription of these families are unclear, especially within the family Sporormiaceae, where the generic delimitation have been questioned. There is also a need to understand how different ecological processes affect species richness and occurrence of coprophilous ascomycetes in general. The aim of this thesis was therefore to test earlier classifications of coprophilous taxa within Pleosporales, using phylogenetic analyses of DNA sequences; and to study how the habitat, dung type and herbivores´ food choice may affect the species richness and species composition of coprophilous ascomycetes.</p><p>A phylogenetic study shows that coprophilous taxa have arisen several times within Pleosporales. Sporormiaceae and Delitschiaceae are separate monophyletic groups and should continue to be recognized as two distinct families within Pleosporales. Phaeotrichaceae forms a monophyletic group, and is, unexpectedly, a strongly supported sister-group to Venturiaceae, but if they belong to Pleosporales or not, remains unresolved. Testudinaceae and Zopfiaceae, which previously had an unclear position in Ascomycota, are shown to be members of Pleosporales and should be treated as two separate families. The genus <i>Eremodothis</i> is, however, not related to Testudinaceae, but is nested within Sporormiaceae and should be transferred to <i>Westerdykella</i>.</p><p>The natural relationships within Sporormiaceae are still not fully resolved and consequently, I suggest a rather conservative generic classification, accepting <i>Preussia, Sporormia, Westerdykella</i>, as well as <i>Sporormiella</i>, despite that the latter is not conclusively well supported as monophyletic. Characters previously used in the taxonomy and classification of Sporormiaceae, as choice of substrate, presence or absence of an ostiole, presence or absence of germ slits, and spore ornamentation, were all homoplastic and not very useful for circumscribing monophyletic groups.</p><p>Field-studies of moose (<i>Alces alces</i>), mountain hare (<i>Lepus timidus</i>) and roe deer (<i>Capreolus capreolus</i>) dung resulted in several new species records, which suggests that coprophilous ascomycetes in boreal Sweden are poorly known. Fungal species richness and occurrence on moose dung varied significantly between habitats. Species diversity was negatively associated with amount of insect attack, and insects feeding either on the dung and/or the fungi may be an important factor explaining the observed pattern. Species richness of coprophilous fungi varied also significantly between different dung types. A study of moose, mountain hare, and roe deer dung did not show any consistent patterns in respect to the animals´ digestive system. There was, however, a general strong positive relationship between the total number of ascomycete species and the number of plant species foraged by the three herbivores. Fungal species with large spores (≥ 50 µm) were over-represented on roe deer dung, and under-represented on moose dung, while the reverse was found for species with small spores (<10µm). This suggests that the foraging level of the herbivore, which in turn mirrors species-specific differences in spore dispersal of the fungi, may be an important factor in explaining species richness and diversity of the coprophilous community.</p>

Coprophilous ascomycetes are a diverse group of saprobes, of which many belong to three families, Delitschiaceae, Phaeotrichaceae and Sporormiaceae, within the large order Pleosporales. The natural relationships and circumscription of these families are unclear, especially within the family Sporormiaceae, where the generic delimitation have been questioned. There is also a need to understand how different ecological processes affect species richness and occurrence of coprophilous ascomycetes in general. The aim of this thesis was therefore to test earlier classifications of coprophilous taxa within Pleosporales, using phylogenetic analyses of DNA sequences; and to study how the habitat, dung type and herbivores´ food choice may affect the species richness and species composition of coprophilous ascomycetes. A phylogenetic study shows that coprophilous taxa have arisen several times within Pleosporales. Sporormiaceae and Delitschiaceae are separate monophyletic groups and should continue to be recognized as two distinct families within Pleosporales. Phaeotrichaceae forms a monophyletic group, and is, unexpectedly, a strongly supported sister-group to Venturiaceae, but if they belong to Pleosporales or not, remains unresolved. Testudinaceae and Zopfiaceae, which previously had an unclear position in Ascomycota, are shown to be members of Pleosporales and should be treated as two separate families. The genus Eremodothis is, however, not related to Testudinaceae, but is nested within Sporormiaceae and should be transferred to Westerdykella. The natural relationships within Sporormiaceae are still not fully resolved and consequently, I suggest a rather conservative generic classification, accepting Preussia, Sporormia, Westerdykella, as well as Sporormiella, despite that the latter is not conclusively well supported as monophyletic. Characters previously used in the taxonomy and classification of Sporormiaceae, as choice of substrate, presence or absence of an ostiole, presence or absence of germ slits, and spore ornamentation, were all homoplastic and not very useful for circumscribing monophyletic groups. Field-studies of moose (Alces alces), mountain hare (Lepus timidus) and roe deer (Capreolus capreolus) dung resulted in several new species records, which suggests that coprophilous ascomycetes in boreal Sweden are poorly known. Fungal species richness and occurrence on moose dung varied significantly between habitats. Species diversity was negatively associated with amount of insect attack, and insects feeding either on the dung and/or the fungi may be an important factor explaining the observed pattern. Species richness of coprophilous fungi varied also significantly between different dung types. A study of moose, mountain hare, and roe deer dung did not show any consistent patterns in respect to the animals´ digestive system. There was, however, a general strong positive relationship between the total number of ascomycete species and the number of plant species foraged by the three herbivores. Fungal species with large spores (≥ 50 µm) were over-represented on roe deer dung, and under-represented on moose dung, while the reverse was found for species with small spores (&lt;10µm). This suggests that the foraging level of the herbivore, which in turn mirrors species-specific differences in spore dispersal of the fungi, may be an important factor in explaining species richness and diversity of the coprophilous community.

I evaluate the methods of cladistic parsimony and maximum likelihood in phylogenetic systematics by their affinity to Popper‘s degree of corroboration. My work analyzes an important recent exchange between the proponents of the two methods. Until this exchange, only advocates of cladistic parsimony have claimed a basis for their method on epistemological grounds through corroboration. Advocates of maximum likelihood, on the other hand, have based the rational justification for their method largely on statistical grounds. In Part One I outline corroboration in terms of content, severity of test and explanatory power. In Part Two I introduce the two methods. In Part Three I analyze three important debates. The first involves the appropriate probability interpretation for phylogenetics. The second is about severity of test. The third concerns explanatory power. In Part Four I conclude that corroboration can decide none of these debates, and therefore cannot decide the debate between cladistic parsimony and maximum likelihood.

Despite decades of effort by molecular systematists, the trees of life of eukaryotic organisms still remain partly unresolved or in conflict with each other. An ever increasing number of fully-sequenced genomes of various eukaryotes allows to consider gene and species phylogenies at genome-scale. However, such phylogenomics-based approaches also revealed that more taxa and more and more gene sequences are not the ultimate solution to fully resolve these conflicts, and that there is a need for sequence-independent phylogenetic meta-characters that are derived from genome sequences. Spliceosomal introns are characteristic features of eukaryotic nuclear genomes. The relatively rare changes of spliceosomal intron positions have already been used as genome-level markers, both for the estimation of intron evolution and phylogenies, however with variable success. In this thesis, a specific subset of these changes is introduced and established as a novel phylogenetic marker, termed near intron pair (NIP). These characters are inferred from homologous genes that contain mutually-exclusive intron presences at pairs of coding sequence (CDS) positions in close proximity. The idea that NIPs are powerful characters is based on the assumption that both very small exons and multiple intron gains at the same position are rare. To obtain sufficient numbers of NIP character data from genomic and alignment data sets in a consistent and flexible way, the implementation of a computational pipeline was a main goal of this work. Starting from orthologous (or more general: homologous) gene datasets comprising genomic sequences and corresponding CDS transcript annotations, the multiple alignment generation is an integral part of this pipeline. The alignment can be calculated at the amino acid level utilizing external tools (e.g. transAlign) and results in a codon alignment via back-translation. Guided by the multiple alignment, the positionally homologous intron positions should become apparent when mapped individually for each transcript. The pipeline proceeds at this stage to output portions of the intron-annotated alignment that contain at least one candidate of a NIP character. In a subsequent pipeline script, these collected so-called NIP region files are finally converted to binary state characters representing valid NIPs in dependence of quality filter constraints concerning, e.g., the amino acid alignment conservation around intron loci and splice sites, to name a few. The computational pipeline tools provide the researcher to elaborate on NIP character matrices that can be used for tree inference, e.g., using the maximum parsimony approach. In a first NIP-based application, the phylogenetic position of major orders of holometabolic insects (more specifically: the Coleoptera-Hymenoptera-Mecopterida trifurcation) was evaluated in a cladistic sense. As already suggested during a study on the eIF2gamma gene based on two NIP cases (Krauss et al. 2005), the genome-scale evaluation supported Hymenoptera as sister group to an assemblage of Coleoptera and Mecopterida, in agreement with other studies, but contradicting the previously established view. As part of the genome paper describing a new species of twisted-wing parasites (Strepsiptera), the NIP method was employed to help to resolve the phylogenetic position of them within (holometabolic) insects. Together with analyses of sequence patterns and a further meta-character, it revealed twisted-wing parasites as being the closest relatives of the mega-diverse beetles. NIP-based reconstructions of the metazoan tree covering a broad selection of representative animal species also identified some weaknesses of the NIP approach that may suffer e.g. from alignment/ortholog prediction artifacts (depending on the depth of range of taxa) and systematic biases (long branch attraction artifacts, due to unequal evolutionary rates of intron gain/loss and the use of the maximum parsimony method). In a further study, the identification of NIPs within the recently diverged genus Drosophila could be utilized to characterize recent intron gain events that apparently involved several cases of intron sliding and tandem exon duplication, albeit the mechanisms of gain for the majority of cases could not be elucidated. Finally, the NIP marker could be established as a novel phylogenetic marker, in particular dedicated to complementarily explore the wealth of genome data for phylogenetic purposes and to address open questions of intron evolution.

I evaluate the methods of cladistic parsimony and maximum likelihood in phylogenetic systematics by their affinity to Popper‘s degree of corroboration. My work analyzes an important recent exchange between the proponents of the two methods. Until this exchange, only advocates of cladistic parsimony have claimed a basis for their method on epistemological grounds through corroboration. Advocates of maximum likelihood, on the other hand, have based the rational justification for their method largely on statistical grounds. In Part One I outline corroboration in terms of content, severity of test and explanatory power. In Part Two I introduce the two methods. In Part Three I analyze three important debates. The first involves the appropriate probability interpretation for phylogenetics. The second is about severity of test. The third concerns explanatory power. In Part Four I conclude that corroboration can decide none of these debates, and therefore cannot decide the debate between cladistic parsimony and maximum likelihood.

The Carex nardina complex is a group of one to three species (C. nardina, C. hepburnii, C. stantonensis) and six taxa of unispicate sedges (Cyperaceae), the taxonomy of which has been controversial since the 1800s. As initial DNA phylogenies suggested that the complex was nested within Carex section Filifoliae and sister to C. elynoides, a species often confused with C. nardina and sympatric with it in the western North American Cordillera, analyses were conducted to determine whether C. hepburnii, C. stantonensis and other infraspecific taxa could be the result of hybridization. Morphometric and molecular analyses found no substantial evidence for hybridization and supported the recognition of no taxon beyond C. nardina. Consequently, this study concludes that the complex comprises a single variable species, Carex nardina, distributed throughout arctic North America south through the western Cordillera to New Mexico with a minor portion of its range in northeastern Russia, northwestern Scandinavia and Iceland.

There is currently a large increase in the speed of production of DNA sequence data as next generation sequencing technologies become more widespread. As such there is a need for rapid computational techniques to functionally annotate data as it is generated. One computational method for the functional annotation of protein-coding genes is via detection of interaction partners. If the putative partner has a functional annotation then this annotation can be extended to the initial protein via the established principle of “guilt by association”. This work presents a method for rapid detection of functional interaction partners for proteins through the use of the comparative method. Functional links are sought between proteins through analysis of their patterns of presence and absence amongst a set of 54 eukaryotic organisms. These links can be either direct or indirect protein interactions. These patterns are analysed in the context of a phylogenetic tree. The method used is a heuristic combination of an established accurate methodology involving comparison of models of evolution the parameters of which are estimated using maximum likelihood, with a novel technique involving the reconstruction of ancestral states using Dollo parsimony and analysis of these reconstructions through the use of logistic regression. The methodology achieves comparable specificity to the use of gene coexpression as a means to predict functional linkage between proteins. The application of this method permitted a genome-wide analysis of the human genome, which would have otherwise demanded a potentially prohibitive amount of computational resource. Proteins within the human genome were clustered into orthologous groups. 10 of these proteins, which were ubiquitous across all 54 eukaryotes, were used to reconstruct a phylogeny. An application of the heuristic predicted a set of functional protein interactions in human cells. 1,142 functional interactions were predicted. Of these predictions 1,131 were not present in current protein-protein interaction databases.