Michael Woodhams

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Michael Woodhams

University Associate

Room 323 , Maths & Physics

+61 3 6226 2729 (phone)

Michael Woodhams trained in astronomy and computer programming before moving into mathematics applied to molecular phylogenetics.


Michael studied physics and computer science at the University of Auckland (MSc thesis on cosmic rays from SN1987a) followed by a PhD from Princeton University (submillimetre radio telescope observations of mass loss from evolved stars.) He worked for five years as a computer programmer for Peace Software in Auckland, and then moved into phylogenetics, with postdoctoral appointments at Massey University (Palmerston North, New Zealand), the University of Sydney and the University of Tasmania.

Career summary


DegreeThesis TitleUniversityCountryDate of Award
PhDSubmillimeter observations of mass loss from evolved starsPrinceton UniversityUSA1998
MA Princeton UniversityUSA1992
DipCompSci University of AucklandNew Zealand1990
MScScintillator Data Analysis for the JANZOS ArrayUniversity of AucklandNew Zealand1989
BSc University of AucklandNew Zealand1987


Phylogenetics, molecular evolution, bioinformatics, continuous time Markov processes, Monte Carlo simulation, maximum likelihood, Java, Mathematica, R, Perl.

View more on Dr Michael Woodhams in WARP


  • Applied Mathematics
  • Bioinformatics
  • Evolutionary Biology

Research Themes

Michael's research is in molecular phylogenetics – the use of molecular sequencing data (DNA or protein sequences) to determine the evolutionary relationships between species. He uses Java, Mathematica and R programming to test new mathematical models developed in collaboration with Jeremy Sumner and others. One important strand of work is investigating model misspecification: when a complex evolutionary process (e.g. rates of various mutation events vary over time and lineage) is analysed as if it were simpler (e.g. assuming rates of mutations are constant over time and lineage) what effect does this have on our analysis? Are some analysis methods more robust to model misspecification than others? The primary tool for studying these questions is Monte Carlo simulations, where we generate realistic simulated data from the complex model and analyse it with the simpler model.

Fields of Research

  • Biological mathematics (490102)
  • Plant physiology (310806)
  • Phylogeny and comparative analysis (310410)

Research Objectives

  • Expanding knowledge in the mathematical sciences (280118)
  • Expanding knowledge in the biological sciences (280102)
  • Expanding knowledge in the physical sciences (280120)


Total publications


Journal Article

(8 outputs)
2020Holland BR, Ketelaar-Jones S, O'Mara AR, Woodhams MD, Jordan GJ, 'Accuracy of ancestral state reconstruction for non-neutral traits', Scientific Reports, 10, (1) Article 7644. ISSN 2045-2322 (2020) [Refereed Article]

DOI: 10.1038/s41598-020-64647-4 [eCite] [Details]

Citations: Scopus - 8Web of Science - 9

Co-authors: Holland BR; Ketelaar-Jones S; O'Mara AR; Jordan GJ


2020Jordan GJ, Carpenter RJ, Holland BR, Beeton NJ, Woodhams MD, et al., 'Links between environment and stomatal size through evolutionary time in Proteaceae', Proceedings of the Royal Society of London. Biological Sciences, 287, (1919) Article 20192876. ISSN 0962-8452 (2020) [Refereed Article]

DOI: 10.1098/rspb.2019.2876 [eCite] [Details]

Citations: Scopus - 5Web of Science - 5

Co-authors: Jordan GJ; Carpenter RJ; Holland BR; Beeton NJ; Brodribb TJ


2018Sumner JG, Woodhams MD, 'Lie-Markov models derived from finite semigroups', Bulletin of Mathematical Biology, 81, (2) pp. 361-383. ISSN 0092-8240 (2018) [Refereed Article]

DOI: 10.1007/s11538-018-0455-x [eCite] [Details]

Citations: Scopus - 2Web of Science - 2

Co-authors: Sumner JG


2016Woodhams MD, Lockhart PJ, Holland BR, 'Simulating and summarizing sources of gene tree incongruence', Genome Biology and Evolution, 8, (5) pp. 1299-1315. ISSN 1759-6653 (2016) [Refereed Article]

DOI: 10.1093/gbe/evw065 [eCite] [Details]

Citations: Scopus - 8Web of Science - 7

Co-authors: Holland BR


2015Fernandez-Sanchez J, Sumner JG, Jarvis PD, Woodhams MD, 'Lie Markov models with purine/pyrimidine symmetry', Journal of Mathematical Biology, 70, (4) pp. 855-891. ISSN 0303-6812 (2015) [Refereed Article]

DOI: 10.1007/s00285-014-0773-z [eCite] [Details]

Citations: Scopus - 17Web of Science - 14

Co-authors: Sumner JG; Jarvis PD


2015Woodhams MD, Fernandez-Sanchez J, Sumner JG, 'A new hierarchy of phylogenetic models consistent with heterogeneous substitution rates', Systematic Biology, 64, (4) pp. 638-650. ISSN 1063-5157 (2015) [Refereed Article]

DOI: 10.1093/sysbio/syv021 [eCite] [Details]

Citations: Scopus - 20Web of Science - 19

Co-authors: Sumner JG


2013Woodhams M, Steane DA, Jones RC, Nicolle D, Moulton V, et al., 'Novel distances for Dollo data', Systematic Biology, 62, (1) pp. 62-77. ISSN 1063-5157 (2013) [Refereed Article]

DOI: 10.1093/sysbio/sys071 [eCite] [Details]

Citations: Scopus - 23Web of Science - 21

Co-authors: Steane DA; Jones RC; Holland BR


2012Sumner JG, Jarvis PD, Fernandez-Sanchez J, Kaine BT, Woodhams MD, et al., 'Is the general time-reversible model bad for molecular phylogenetics?', Systematic Biology, 61, (6) pp. 1069-1074. ISSN 1063-5157 (2012) [Refereed Article]

DOI: 10.1093/sysbio/sys042 [eCite] [Details]

Citations: Scopus - 33Web of Science - 32

Co-authors: Sumner JG; Jarvis PD; Kaine BT; Holland BR