University of Tasmania, Australia

Phylogenetics is concerned with the problem of reconstructing the past evolutionary history of extant organisms from present day molecular data such as DNA. There is ongoing interest in further development of the mathematics that underlies computational phylogenetic methods. Hidden from view, in the software packages used by biologists, are algorithms performing statistical inference using Markov models on binary trees. The mathematics involved represents a wonderful confluence of stochastic methods and probability theory (Markov chain models), discrete mathematics (combinatorics of tree space), statistical inference (maximum likelihood and Bayesian methods) and, more recently, methods taken from algebraic geometry and the representation theory of finite and infinite (Lie) groups. There are many important theoretical problems that arise, such as statistical identifiability of models, consistency and convergence of methods. These problems can only be solved using a multi-disciplinary approach.

The Theoretical Phylogenetics Group is an umbrella group that encompasses several different funded projects in the area of phylogenetics. Current projects that we are working on include:

• Developing new mathematical phylogenetic methods to model hybrid evolution (ARC Future Fellowship, Holland)
• Mathematical modelling of microsatellite evolution (Human Frontier Science Programme, Lambert, Holland and Humphries)
• Markov invariants and phylogenetic tree reconstruction (ARC Discovery project, Sumner, Jarvis and Mitchell)

We run a monthly seminar series for anyone with phylogenetics interests – be they zoological, botanical, ecological or mathematical - across UTas and other Hobart based research institutes. To get on the mailing list for seminar announcements email Barbara.Holland@utas.edu.au

We also run an annual Theoretical Phyogenetics meeting – Phylomania

www.maths.utas.edu.au/phylomania/phylomania2011.htm

For further information on the Theoretical Phylogenetics group see our website at http://www.maths.utas.edu.au/People/Holland/theoreticalPhylogenetics.htm

Michael Woodhams, Dorothy A. Steane, Rebecca C. Jones, Dean Nicolle, Vincent Moulton, Barbara Holland. Novel Distances for Dollo Data. (preprint available at http://arxiv.org/pdf/1203.0072.pdf).

Saurabh, K., B.R. Holland G.C. Gibb, D. Penny. 2012. Gaps, an elusive source of phylogenetic information. Syst. Biol. (in press, accepted 18^th March, available online doi: 10.1093/sysbio/sys043).

Sumner, J., B. Kaine, M. Woodhams, J. Fernandez-Sanchez, P. Jarvis, B. R. Holland. 2012. Is the GTR model bad for phylogenetics? Syst. Biol. (in press, accepted 19^th March).

Eytan, R.I., Hastings, P.A., Holland, B., and Hellberg M.E. 2012. Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria). Molecular Phylogenetics and Evolution 62:159-173.

Johnson, K.A., B. R. Holland, M. M. Heslewood, D. M. Crayn. 2012. Supermatrices, supertrees and serendipitous scaffolding: Inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data. Molecular Phylogenetics and Evolution 62: 146–158.

Sumner, J.G., B.R. Holland, and P.D Jarvis. 2011. The algebra of the general Markov model on phylogenetic trees and networks. Bulletin of Mathematical Biology (published online 6 October 2011, DOI 10.1007/s11538-011-9691-z).

White, W.T.J and B.R. Holland. 2011. Faster Exact Maximum Parsimony Search with XMP. Bioinf. 27: 1359-1367.

P.D. Jarvis and J.G. Sumner. 2011. Markov invariants for phylogenetic rate matrices derived from embedded submodels. TCCB, accepted pending revision.

J.G. Sumner and M. A. Charleston. 2009. The Phylogenetic estimation with partial likelihood tensors. J. Theor. Biol., 262:413:424, 2009.

J.G. Sumnerand P.D. Jarvis, J. 2009. Markov invariants and the isotropy subgroup of a quartet. Theor. Biol., 258:302-310.

Members (External)

Dr Barbara Holland, ARC Future Fellow, Barbara.Holland@utas.edu.au

Dr Jeremy Sumner,  ARC Research Fellow, Jeremy.Sumner@utas.edu.au  

Dr Peter Jarvis, Reader, Peter.Jarvis@utas.edu.au