|dc.description.abstract||Though molecular phylogenetics has been very successful in reconstructing the
evolutionary history of species, some phylogenies, particularly those involving ancient
events, have proven difficult to resolve. One approach to improving the resolution of
deep phylogenies is to increase the amount of data by including multiple genes
assembled from public sequence databases. Using modern phylogenetic methods and
abundant computing power, the vast amount of sequence data available in public
databases can be brought to bear on difficult phylogenetic problems.
In this thesis I outline the motivation for assembling large multigene datasets and lay
out the obstacles associated with doing so. I discuss the various methods by which
these obstacles can be overcome and describe a bioinformatics solution, TaxMan, that
can be used to rapidly assemble very large datasets of aligned genes in a largely
automated fashion. I also explain the design and features of TaxMan from a biological
standpoint and present the results of benchmarking studies. I illustrate the use of
TaxMan to assemble large multigene datasets for two groups of taxa – the subphylum
Chelicerata and the superphylum Lophotrochozoa.
Chelicerata is a diverse group of arthropods with an uncertain phylogeny. When a set
of mitochondrial genes is used to analyse the relationships between the chelicerate
orders, the conclusions are highly dependent upon the evolutionary model used and are
affected by the presence of systematic compsitional bias in mitochondrial genomes.
Lophotrochozoa is a recently-proposed group of protostome phyla. A number of
distinct phylogenetic hypotheses concerning the relationships between
lophotrochozoan phyla have been proposed. I compare the phylogenetic conclusions
given by analysis of nuclear and mitochondrial protein-coding and rRNA genes to
evaluate support for some of these hypotheses.||en