On the Evolution of Kangaroos and Their Kin (Family Macropodidae) Using Retrotransposons, Nuclear Genes and Whole Mitochondrial Genomes
ON THE EVOLUTION OF KANGAROOS AND THEIR KIN (FAMILY MACROPODIDAE) USING RETROTRANSPOSONS, NUCLEAR GENES AND WHOLE MITOCHONDRIAL GENOMES William George Dodt B.Sc. (Biochemistry), B.Sc. Hons (Molecular Biology) Principal Supervisor: Dr Matthew J Phillips (EEBS, QUT) Associate Supervisor: Dr Peter Prentis (EEBS, QUT) External Supervisor: Dr Maria Nilsson-Janke (Senckenberg Biodiversity and Research Centre, Frankfurt am Main) Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy Science and Engineering Faculty Queensland University of Technology 2018 1 Keywords Adaptive radiation, ancestral state reconstruction, Australasia, Bayesian inference, endogenous retrovirus, evolution, hybridization, incomplete lineage sorting, incongruence, introgression, kangaroo, Macropodidae, Macropus, mammal, marsupial, maximum likelihood, maximum parsimony, molecular dating, phylogenetics, retrotransposon, speciation, systematics, transposable element 2 Abstract The family Macropodidae contains the kangaroos, wallaroos, wallabies and several closely related taxa that occupy a wide variety of habitats in Australia, New Guinea and surrounding islands. This group of marsupials is the most species rich family within the marsupial order Diprotodontia. Despite significant investigation from previous studies, much of the evolutionary history of macropodids (including their origin within Diprotodontia) has remained unclear, in part due to an incomplete early fossil record. I have utilized several forms of molecular sequence data to shed
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