Molecular Phylogenetics of Mammals

In this thesis, the phylogenetic relationships of the Mammalia have been studied at various levels. Different sources of genetic information have been evaluated and used as phylogenetic markers. These include the well-known mitochondrial genome, cDNA from housekeeping genes and expressed sequence tags from nuclear genes. Applying RT-PCR on mRNA from nuclear genes is a new approach for collecting nuclear gene data for studying the phylogeny of Placentalia. The sequence analysis of eight housekeeping genes found Glires as sister group to the remaining Placentalia. The evaluation of previously suggested phylogenetic hypotheses requires large amounts of data that cannot be collected from individually selected genes. Whole genome sequencing projects have made the sequence data from numerous placental mammals available. The data from an appropriate outgroup to root the placental mammal tree was initially missing. Therefore expressed sequence tag from a marsupial mouse was made. This increased the amount of sequence data for phylogenetic analysis a hundredfold compared to methods that select individual genes. Phylogenetic analysis recovered a monophyletic Euarchontoglires and Boreoeutheria, thus contradicting the results from the housekeeping gene dataset. Mammalia contains three subgroups: Prototheria, Metatheria and Eutheria. The analysis of genomic and EST sequence data supported a sister group relationship between Eutheria and Metatheria in accordance with the Theria hypothesis. Molecular estimates of their divergence times suggest a basal divergence of Theria at ?138 MYA and the basal divergences of Mammalia was estimated to 167 ? 178 MYA. Mitogenomics has been used to study divergences of Caniformia, the dog like carnivores. Phylogenetic analysis revealed a basal divergence between dogs and the remaining caniforms. Within the caniforms, seals and musteloids are sister taxa. Molecular evidence clearly identifies the giant panda as belonging to the bear lineage. The lesser panda is associated with the musteloids making ?panda? a paraphyletic construction