Dr Matt Phillips ARC Postdoctoral Fellow Phone: 61 2 6125 9138 Fax: 61 2 6125 5573 Email: matt.phillips@anu.edu.au Bromham Lab: http://www.tempoandmode.com

Background
Having started postgraduate work with Honours in Botany at the University of Queensland, I switched disciplines and countries and went on to complete a PhD in Evolutionary Biology (on mammals) at Massey University, New Zealand. Subsequent activity has included postdoctoral research at Oxford University and Massey University, as well as travelling and cycle touring. In 2007 I returned to Australia to join the Centre for Macroevolution and Macroecology at the School of Botany and Zoology.

Research Interests
Most of my research has been concerned with reconstructing the evolutionary history of mammals. I am currently pursuing the following studies:

• Inferring the phylogentic interrelations (=family tree) of marsupials using DNA sequences.
• Exploring the influence of historical constraints and competition in determining the ecological and evolutionary trajectories of marsupials.
• Monotreme evolution. What are the phylogenetic affinities of these egg-laying mammals to extinct mammal groups and are their characteristics definitively mammalian, "primitive reptilian retentions" or more recent adaptations associated with their peculiar ecological habits?
• The role of extraterrestrial impact and competition with birds (and mammals) in the extinction of dinosaurs and other land vertebrates during the Late Cretaceous.

Beyond mammalian evolution specifically, I have recently worked on phylogenetic inference methodology and molecular dating techniques with data from sources as varied as yeast, plants, arthropods, birds and ancient DNA from extinct cats.

Possible Honours Projects
Research projects are available for studying the evolution of Australia's mammal fauna. Possible areas to focus on include:

• Testing hypotheses on the evolution of the pygmy possums (Burramyidae), including inferring their relationships to other marsupials, using DNA sequences.
• Exploring models of species and ecological diversification for the early evolution of Australian marsupials. Here, a moderate level of computer modelling or programming skills would be helpful.

I am open to other projects involving the evolution of vertebrates.

Current Funding
Environmental Futures Network, Early Career Researchers Grant (2008-2009)
Australian Postdoctoral Fellowship, including discovery project funding (July 2007-July 2010)
ANU Faculty of Science research equipment small grant (2007)

Software
Site strip search: A Perl program for noise reduction (signal enhancement) in DNA sequence datasets - developed by myself and Warwick Allen
NicheSim: A C++ program for simulating and optimizing reconstruction of ecological niche, or morphological evolution on phylogenetic trees - developed by myself and Tim white.

download program
download documentation

Journal Articles (2004-2009)
Phillips, M.J. 2009. Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 441: 132-140.

Phillips, M.J. 2009. Mammalian and avian survival across the Cretaceous- Tertiary boundary. New Zealand Science Review 66(1): 34-38.

Pratt, R.C., Gibb, G.C., Morgan-Richards, M., Phillips, M.J., Hendy, M.D., Penny, D. 2009. Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors. Molecular Biology and Evolution 26(2): 313-326.

Gibbs, A.J., Ohshima, K., Phillips, M.J., Gibbs, M.J. 2008. The Prehistory of Potyviruses: Their Initial Radiation Was during the Dawn of Agriculture. PLoS ONE 3(6): e2523.

Morgan-Richards, M., Trewick, S.A., Bartosch-Härlid, A., Kardailsky, O., Phillips, M.J., McLenachan, P.A., Penny, D. 2008. Bird evolution: testing the Metaves clade with six new mitochondrial genomes. BMC Evolutionary Biology 8, 20.

Penny, D., White, W.T., Hendy, M.D., Phillips, M.J. 2008. A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals. Molecular Biology and Evolution 25(2), 239-242.

Phillips, M.J., Pratt, R.C. 2008. Family-level relationships among the Australasian marsupial "herbivores" (Diprotodontia: Koala, wombats, kangaroos and possums). Molecular Phylogenetics and Evolution 46, 594-605.

Robins, J.H., McLenachan, P.A., Phillips, M.J., Craig, L., Ross, H.A., Matisoo-Smith, E. 2008. Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Molecular Phylogenetics and Evolution 49, 460-466.

Penny, D. & Phillips, M. J. (2007) Mass survivals. Nature 446, 501-502.

Ho, S. Y. W., Shapiro, B., Phillips, M. J., Cooper, A. & Drummond, A. J. (2007) Evidence for time dependency of molecular rate estimates. Systematic Biology 56, 515-522.

Phillips, M. J. (2006) Sympathy for the devil. Nature 440, 1115-1115.

Trewick, S. R. & Phillips, M. J. (2006) Geology and Genes III. Geological Society of New Zealand, Wellington, New Zealand.

Penny, D. & Phillips, M. J. (2006) "Nothing exists for one cause": putting biology back into evolution. In Geology and Genes III (S. A. Trewick and M. J. Phillips, eds.), pp. 30-31. Geological Society of New Zealand, Wellington.

Phillips, M. J., McLenachan, P. A., Down, C., Gibb, G. C. & Penny, D. (2006) Combined mitochondrial and nuclear DNA sequences resolve the interrelations of the major Australasian marsupial radiations. Systematic Biology 55, 122-137.

Drummond, A. J., Phillips, M. J., Ho, S. Y. W. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology 4, 699-710.

Barnett, R., Barnes, I., Phillips, M. J., Martin, L. D., Harrington, C. R., Leonard, J. A. & Cooper, A. (2005) Evolution of the extinct sabretooths and the American cheetah-like cat. Current Biology 15, R589-R590.

Ho, S. Y. W., Phillips, M. J., Drummond, A. J. & Cooper, A. (2005) Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation. Molecular Biology and Evolution 22, 1355-1363.

Phillips, M. J. (2005) Telling the Evolutionary Time: Molecular Clocks and the Fossil Record - Book review. Systematic Biology 54, 174-176.

Ho, S. Y. W., Phillips, M. J., Cooper, A. & Drummond, A. J. (2005) Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Molecular Biology and Evolution 22, 1561-1568.

Hebsgaard, M . B., Phillips, M. J. & Willerslev, E. (2005) Geologically ancient DNA: fact or artefact. Trends in Microbiology . 13, 212-220.

Phillips M. J., Delsuc, F. D., and Penny, D. (2004) Genome-scale phylogeny and the detection of systematic biases.   Molecular Biology and Evolution 21, 1455-1458.

Penny, D. & Phillips, M. J. (2004) The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution. Trends in Ecology and Evolution 19, 516-522.

Harrison, G. L., McLenachan, P. A., Phillips M. J., Slack, K. L. & Penny, D. (2004) Four new avian mitochondrial genomes help get to basic evolutionary questions in the late Cretaceous. Molecular Biology and Evolution 21, 974-983 .

Jeffares, D. C., Phillips, M. J., Moore, S. & Veit, B. (2004) A description of the Mei2-like protein family; structure, phylogenetic distribution and biological context. Development Genes and Evolution 214, 149-158.