Research Publications

2003 Publication list




Anderson, J.P., Learn, G.H., Rodrigo, A.G., He, X., Wang, Y., Weinstock, H., Kalish, M.L., Robbins, K.E., Hood, L. and Mullins, J.I. Predicting Demographic Group Structures Based on DNA Sequence Data. Molecular Biology and Evolution 20: 1168-1180
Bininda-Emonds, O.R.P., Gittleman, J.L. and Steel, M. The (super) tree of life: procedures, probems and prospects. Annual Review of Ecology and Systematics 33: 265-289. 
Bromham, L. and Penny. D. The Modern Molecular Clock. Nature Reviews - Genetics4:216-224.
Collins, L.J., Poole, A.M. and Penny, D. Using ancestral sequences to uncover potential gene homologs. Applied Bioinformatics 2, S85-S95.
Daugherty, C.H. Understanding the past – discovering a future: how learning more about tuatara and its chequered past is helping to shape the future of New Zealand. New Zealand Science Review 60(4): 141-142.
Delsuc, F., Phillips, M.J. and Penny, D. Comment on "Hexapod Origins: Monophyletic or Paraphyletic?" Science 12 301: 1482-1483.
Edvardsson, S, Gardner, P.P., Poole, A.M., Hendy, M.D., Penny, D, and Moulton, V. A Search for H/ACA SnoRNAs in Yeast Using Predicted MFE Secondary Structures. BioInformatics 19: 865-873.
Gardner, P.P., Holland, B.R., Moulton, V., Hendy, M.D. and Penny, D. On the optimal number of nucleotides in an RNA-world. Proceedings of the Royal Society, London, Series B270:1177-1182.
Gascuel, O., Hendy, M.D., Jean-Marie, A. and McLachlan, R. The combinatorics of tandem duplication trees. Systematic Biology 52:110-118.
Hay, J.M., Daugherty, C.H., Cree, A. and Maxson, L.R.   Low genetic divergence obscures phylogeny amongst populations of Sphenodon, remnant of an ancient reptile lineage. Molecular Phylogenetics and Evolution 29(1): 1-19.
Holland, B.R., Penny, D. and Hendy, M.D.  Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock - A Simulation Study. Systematic Biology. 52(2): 229-238.
Hurles, M.E., Matisso-Smith, E., Gray, R.D., and Penny, D. Untangling Oceanic settlement: the edge of the knowable. Trends in Ecology and Evolution 18(10): 531-540.
Huynen, L., Lambert, D.M., McLennan, J.A., Rickard, C., and Robertson, H.A. A DNA test for sex assignment in kiwi. (Apteryx spp.). Notornis 50(4): 231-233.
Huynen, L., Millar, C.D., Scofield, R.P. and Lambert, D.M. Nuclear DNA sequences detect species limits in ancient moa. Nature 425: 175 -178.
Kleine, T., Lockhart, P. and Batschauer, A. An Arabidopsis protein closely related to Synechocystis cryptochrome is targeted to organelles. The Plant Journal. 35 (1): 93-103.
Markwell, T.J. and Daugherty, C.H. Variability in *15N,  *13C and Kjeldahl nitrogen of soils from islands with and without seabirds in the Marlborough Sounds, New Zealand. New Zealand Journal of Ecology 27: 25-30.
McBreen, K., Lockhart, P.J., McLenachan, P., Scheele, S., and Robertson, A.W. The use of molecular techniques to resolve relationships among traditional weaving cultivars of Phormium. The use of molecular techniques to resolve relationships among traditional weaving cultivars of Phormium. NZ J Bot. 41:301-310
Miller, H.C. and Lambert, D.M. An evaluation of methods of blood preservation for RT-PCR from endangered species. Conservation Genetics 4: 651-654.
Miller, H.C., Lambert, D.M., Millar, C.D., Robertson, B.C., and Minot. E.O. Minisatellite DNA profiling detects lineages and parentage in the endangered kakapo (Strigops habroptilus) despite low microsatellite DNA variation.  Conservation Genetics 4: 265-274.
Morgan-Richards, M. and Wallis, G.P. Degree of cytogenetic differentiation fails to predict hybrid zone width in the weta Hemideina thoracica (Orthoptera: Anostostomatidae). Evolution 57: 849-861
Nelson, N.J. Implications of global warming for tuatara conservation.   2003 Annual Report of the Center for Reproduction of Endangered Species, Zoological Society of San Diego
Nickle, D.C., Jensen, M.A., Gottlieb, G.S., Shriner, D., Learn, G.H., Rodrigo, A.G., and Mullins.J.I. Consensus and ancestral state HIV vaccines. Science 299: 1515-1518.
Ota, R. and Penny, D. Estimating changes in mutational mechanisms of evolution. Journal of Molecular Evolution 57:1-8.
Penny, D. and Poole, A.M. Lateral gene transfer: some theoretical aspects. New Zealand Bio Science. 12: 32-35.
Penny, D., Hendy, M. and Poole, A. Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 223(3): 377-385.
Perrie, L.R., Brownsey, P.J., Lockhart, P.J. and Large, M.F. Evidence for an allopolyploid complex in New Zealand Polystichum (Dryopteridaceae). New Zealand Journal of Botany 41: 189-215.
Perrie, L.R., Brownsey, P.J., Lockhart, P.J. and Large, M.F. Morphological and genetic diversity in the New Zealand fern Polystichum vestitum (Dryopteridaceae), with special reference to the Chatham Islands. New Zealand Journal of Botany 41: 581-602.
Perrie, L.R., Brownsey, P.J., Lockhart, P.J., Brown, E.A. and Large, M.F. Biogeography of temperate Australasian Polystichum ferns as inferred from chloroplast sequence and AFLP. Journal of Biogeography 30: 1729-1736 .
Phillips, M.J. and Penny D. The root of the mammalian tree inferred from whole mitochondrial genomes. Molecular Phylogenetics and Evolution 28(2):171-85
Poole, A.M., Phillips, M.J., and Penny, D. Prokarote and eukaryote evolvability. BioSystems 69: 163-185.
Ritchie, P.A., Anderson, I.A. and Lambert, D.M. Evidence for specificity of psittacine beak and feather disease viruses among avian hosts. Virology 306: 109-115
Robins, J.H., Matisoo-Smith, E., Ross, H. The origins of the feral pigs on the Auckland Islands. Journal of the Royal Society of New Zealand 33(2): 561-569.
Rodrigo, A.G., Goode, M., Forsberg, R., Ross, H.A. and Drummond, A. Inferring evolutionary rates using serially sampled sequences from several populations. Mol. Biol. Evol., 20:2010–2018
Ross, H. A., G. M. Lento, M. L. Dalebout, M. Goode, G. Ewing, P. McLaren, A. G. Rodrigo, S. Lavery, and C. S. Baker. DNA Surveillance: Web-based molecular identification of whales, dolphins and porpoises. Journal of Heredity 94(2): 111-114.
Slack, K.E., Janke, A., Penny, D. and Arnason. U. Two new avian mitochondrial genomes (penguin and goose) and a summary of bird and reptile mitogenomic features. Gene302:43-52.
Smissen, R., Breitwieser, I., Ward, J., McLenachan, P. and Lockhart, P.J. Use of ISSR profiles and ITS sequences to study the biogeography alpine cushion in the genus Raoulia. Plant Systematics and Evolution 239: 79-94.
Spencer, H.G. Further properties of Gavrilets’s one-locus two-allele model of maternal selection. Genetics 164: 1689-1692.
Stevens, M.I., and Hogg, I.D. Long-term isolation and recent range expansion revealed for the endemic springtail Gomphiocephalus hodgsoni from southern Victoria Land, Antarctica. Molecular Ecology 12: 2357-2369.
Watson, E.E. and Penny, D. DNA and people: From East Africa to Aotearoa New Zealand. New Zealand Science Review 60: 29-35.
Weisstein, A.E., and Spencer, H.G. The evolution of genomic imprinting via variance minimization: An evolutionary genetic model. Genetics 165: 205-222.