Pied oystercatchers (Haematopus longirostris) at Ben Boyd National Park
Selected publications - see Google Scholar button above for more
Mammal evolution
Phillips, M.J. & Zakaria (2021) Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal mammals. Molecular Phylogenetics and Evolution 158, 107082.
Viacava, P., Baker, A.M., Blomberg, S.P., Phillips, M.J. & Weisbecker, V. (2021) Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (genus Antechinus). Zoological Journal of the Linnean Society, zlab048..
Celik, M., Cascini, M., Haouchar, D., Van Der Burg, C., Dodt, W., Evans, A. R., ... & Phillips, M. J. (2019). A molecular and morphometric assessment of the systematics of the Macropus complex clarifies the tempo and mode of kangaroo evolution. Zoological Journal of the Linnean Society, 186(3), 793-812.
Cascini, M., Mitchell, K. J., Cooper, A., & Phillips, M. J. (2018). Reconstructing the evolution of giant extinct kangaroos: comparing the utility of DNA, morphology, and total evidence. Systematic biology, 68(3), 520-537.
Travouillon K.J. & Phillips M.J. (2018). Total evidence analysis of the phylogenetic relationships of bandicoots and bilbies (Marsupialia: Peramelemorphia): reassessment of two species and description of a new species. Zootaxa
Fruciano, C., Celik, M.A., Butler, K., Dooley, T., Weisbecker, V. and Phillips, M.J., 2017. Sharing is caring? Measurement error and the issues arising from combining 3D morphometric datasets. Ecology and evolution, 7(17), pp.7034-7046.
Phillips, M.J. (2016) Geomolecular Dating and the Origin of Placental Mammals. Systematic Biology 65, 546-557.
Mitchell, K.J., Pratt, R.C., Watson, L.N, Gibb, G.C., Llamas, B., Kasper, M., Edson, J., Hopwood, B., Male, D, Armstrong K, Meyer, M., Hofreiter, M., Austin, J., Donnellan, S.C., Lee, M.S.Y., Phillips, M.J., Cooper, A. (2014) Molecular phylogeny, biogeography, and habitat preference evolution of marsupials. Molecular Biology & Evolution. 31, 2322-2330.
Phillips, M.J., Haouchar, D., Pratt, R.C., Gibb, G.C., Bunce, M. (2013) Inferring kangaroo phylogeny from incongruent nuclear and mitochondrial genes. PLoS ONE 8, e57745.
Phillips, M.J., Bennett, T.H. and Lee, M.S.Y. (2009) Molecules, morphology and ecology indicate a recent, amphibious origin for echidnas. Proceedings of the National Academy of Sciences USA. 106 17089-17094.
Penny, D. & Phillips, M.J. (2007) Mass survivals. Nature 446, 501-502.
Phillips, M. J., Lin, Y.-H., Harrison, G. L. & Penny, D. (2001) Mitochondrial genomes of a bandicoot and a brushtail possum confirm the monophyly of australiadelphian marsupials. Proceedings of the Royal Society of London B 268, 1533-1538.
Molecular dating and fossil calibration
Lartillot, N., Phillips, M.J., and Ronquist, F. (2016) A mixed relaxed clock model. Philosophical Transactions of the Royal Society B: Biological Sciences 371, 20150136.
Ronquist, F., Lartillot, N., and Phillips, M.J. (2016) Closing the gap between rocks and clocks using total-evidence dating. Philosophical Transactions of the Royal Society B: Biological Sciences 371, 20150132.
Ksepka, D.T, Parham, J.F., Allman, J.F., Benton, M.J., Carrano, M.T., Cranston, K.A., Donoghue, P.C.J., Head, J.J., Hermsen, E.J., Irmis, R.B., Joyce, W.G., Kohli, M., Lamm, K.S., Leehr, D., Patané, J.S.L., Polly, P.D, Phillips, M.J., Smith, N.A., Smith, N.D., van Tuinen, M., Ware, J.L., Warnock, R.C.M. (2015) The fossil calibration database, a resource for divergence dating. Systematic Biology 64, 853-859.
Phillips, M.J. (2015) Four mammal fossil calibrations: balancing competing palaeontological and molecular considerations. Palaeontologia Electronica 18.1.5FC, 1-16.
Phillips, M.J., Page, T.J., de Bruyn, M., Huey, J., Humphreys, W., Hughes, J., Santos, S., Schmidt, D., Waters, J. (2013) The linking of plate tectonics and evolutionary divergence. Current Biology 23, R603-R605.
Ho, S.Y.W., Lanfear, R., Phillips, M.J., Barnes, I. & Shapiro, B (2011) Bayesian estimation of substitution rates from ancient DNA sequences with low information content. Systematic Biology 60, 366-375.
Ho, S.Y.W., Lanfear, R., Bromham, L., Phillips, M.J., Soubrier, J., Rodrigo, A.G., and Cooper, A. (2011) Time-dependent rates of molecular evolution. Molecular Ecology 20, 3087-3101.
Ho, S.Y.W and Phillips, M.J. (2009) Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times. Systematic Biology 58, 367 – 380.
Phillips, M.J. (2009) Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny. Gene 44, 132-140.
Drummond, A.J., Phillips, M.J., Ho, S.Y.W. & Rambaut, A. (2006) Relaxed phylogenetics and dating with confidence. PLoS Biology 4, 699-710.
Ho, S.Y.W., Phillips, M.J., Cooper, A., and Drummond, A.J. (2005) Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times. Molecular Biology and Evolution 22, 1561-1568.
Phylogenetics
Phillips, M.J., Westerman, M. & Cascini, M. (2021) The value of updating GenBank accessions for supermatrix phylogeny: the case of the New Guinean marsupial carnivore genus Myoictis. Molecular Phylogenetics and Evolution 106, 107328.
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.
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.
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.
Delsuc F., Phillips M.J. & Penny, D. (2003) Comment on "Hexapod origins: Monophyletic or paraphyletic?" Science 301, 1482.
Avian evolution
Grealy, A., Phillips, M.J., Miller, G., Gilbert, M.T.P., Rouillard, J.-M., Lambert, D., Bunce, M., and Haile, J. (2017) Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird (Aepyornis sp.) eggshell. Molecular Phylogenetics and Evolution 109, 151-163.
Mitchell, K.J., Cooper, A., and Phillips, M.J. (2015) Comment on “Whole-genome analyses resolve early branches in the tree of life of modern birds”. Science 349, 1460-1460.
White, N.E., Phillips, M.J., Gilbert, T.P., Alfaro-Núñez, A., Willerslev, E., Mawson, P.R., Spencer, P.B.S. & Bunce, M. (2011) The evolutionary history of cockatoos (Aves: Psittaciformes: Cacatuidae). Molecular Phylogenetics and Evolution 59, 615-622.
Phillips, M.J., Gibb, G.C., Crimp, E.A., Penny, D. (2010) Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. Systematic Biology 59, 90-107.
Bunce, M., Worthy, T. H., Phillips, M. J., Holdaway, R. N., Willerslev, E., Haile, J, Shapiro, B., Scofield, P., Drummond, A., Kamp, P., and Cooper, A. (2009) The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proceedings of the National Academy of Sciences USA. 106, 20646-20651.
Pratt, R.C., Gibb, G.C., Morgan-Richards, M., Phillips, M.J., Hendy, M.D. & Penny, D. (2009) Towards resolving Neoaves phylogeny: data, signal enhancement and priors. Molecular Biology and Evolution 26, 313-326.
Pratt, R.C., Gibb, G.C., Morgan-Richards, M., Phillips, M.J., Hendy, M.D. & Penny, D. (2009) Towards resolving Neoaves phylogeny: data, signal enhancement and priors. Molecular Biology and Evolution 26, 313-326.
Palaeobiology / ancientDNA
Butler, K., Travouillon, K.J., Price, G. J., Archer, M. and Hand, S. J. In Press. Revision of Oligo-Miocene kangaroos, Ganawamaya and Nambaroo (Marsupialia: Macropodiformes, Balbaridae), Palaeontologia Electronica.
Butler, K., Travouillon, K.J., Price, G. J., Archer, M. and Hand, S. J. 2017. Species abundance, richness and body size evolution of kangaroos (Marsupialia: Macropodiformes) throughout the Oligo-Miocene of Australia, Palaeontology Palaeoclimatology, Palaeoecology, 487, 25 – 36.
Bishop, P.J., Walmsley, C.W., Phillips, M.J., Quayle, M.R., Boisvert, C.R., McHenry, C.R. (2015) Oldest Pathology in a Tetrapod Bone Illuminates the Origin of Terrestrial Vertebrates. PloS ONE 10, e0125723.
Haouchar, D., Haile, J., McDowell, M.C., Murray, D.C., White, N.E., Allcock, R.J.N., Phillips, M.J., Prideaux, G.J. & Bunce, M. (2014) Thorough assessment of DNA preservation from fossil bone and sediments excavated from a late Pleistocene Holocene cave deposit on Kangaroo Island, South Australia. Quaternary Science Reviews. 84, 56-64.
Hebsgaard, M.B., Phillips, M.J. & Willerslev, E. (2005) Geologically ancient DNA: fact or artefact. Trends in Microbiology. 13, 212-220.
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.
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.
Bromham, L., Phillips, M. J. & Penny, D. (1999) Growing up with dinosaurs: molecular dates and the mammalian radiation. Trends in Ecology and Evolution 14, 113-118.
