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Research Publications
2003 Publication list
Author/s |
Title |
Journal |
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. |