
Research Publications
2009 Publication list
Author/s |
Title |
Journal |
Ahmed I, Islam M, Arshad W, Mannan A, Ahmad W, and Mirza B. | High-quality plant DNA extraction for PCR: an easy approach. | Journal of Applied Genetics, 50(2): 105-107. |
Beaumont H.J.E., Gallie, J., Kost, C., Ferguson, G.C. and Rainey, P.B. | Experimental evolution of bet hedging. | Nature 462: 90-93. |
Bordewich, M., Semple, C., and Spillner, A. | Optimizing phylogenetic diversity across two trees. | Applied Mathematics Letters, 22, 638-641. |
Bryant, D. and Steel, M. | Computing the distribution of a tree metric. | IEEE/ACM Transactions in Computational Biology and Bioinformatics 16(3): 420-426. |
Buckley, T.R., Attanayake, D., and Bradler, S. | Extreme convergence in stick insect evolution: phylogenetic placement of the Lord Howe Island tree lobster. | Proceedings of the Royal Society B, 276: 1055-1062. |
Buckley, T.R., K. Marske, and D. Attanayake. | Identifying glacial refugia in a geographic parthenogen using palaeoclimate modeling and phylogeography: the New Zealand stick insect Argosarchus horridus (White). | Molecular Ecology, 18: 4650-4663. |
Chapple, D.G. and Hitchmough, R.A. | Taxonomic instability of reptiles and frogs in New Zealand: information to aid the use of Jewell (2008) for species identification. | New Zealand Journal of Zoology 36: 59-71. |
Chapple, D.G., Ritchie, P.A. and Daugherty, C.H. | Origin, diversification and systematics of the New Zealand skink fauna (Reptilia: Scincidae). | Molecular Phylogenetics and Evolution 52: 470-487. |
Chen, X., Collins, L.J., Biggs, P.J. and Penny, D. | High throughput genome-wide survey of small RNAs from the parasitic protists Giardia intestinalis and Trichomonas vaginalis. | Genome Biol and Evol doi:10.1093/gbe/evp017. |
Collins L.J., Kurland C.G., Biggs P., and Penny, D. | The modern RNP world of eukaryotes. | Journal of Heredity 2009 Sep-Oct;100(5):597-604. Epub 2009 Jul 30. Review. |
Collins, L.J. and Penny, D. | The RNA infrastructure: dark matter of the eukaryotic cell? | Trends in Genetics 25:120-128. |
Cox, M.P., Morales, D.A., Woerner, A.E., Sozanski, J., Wall,J.D. and Hammer, M.F. | Autosomal Resequence Data Reveal Late Stone Age Signals of Population Expansion in Sub-Saharan African Foraging and Farming Populations. | PLoS One 4:e6366. |
de Nooijer, S., Holland, B.R. and Penny, D. | The Emergence of Predators in Early Life: There was No Garden of Eden. | PLoS 4:e5507. |
Fischer, M. and Steel, M. | Sequence length bounds for resolving a deep phylogenetic divergence. | Journal of Theoretical Biology 256: |
Fraser, C.I., Hay, C.H., Spencer, H.G. and Waters, J.M. | Genetic and morphological analyses of the southern bull kelp Durvillaea antractica (Phaeophyceae: Durvillaeales) in New Zealand reveal cryptic species. | J Phycol 45: 436-443. |
Fraser, C.I., Nikula, R., Spencer, H.G. and Waters, J.M. | Kelp genes reveal effects of subantarctic sea ice during the Last Glacial Maximum. | Proceedings of the National Academy of Sciences, USA 106: 3249-3253. |
Fraser, C.I., Spencer, H.G. and Waters, J. | Glacial oceanographic contrasts explain phylogeography of Australian bull kelp. | Mol Ecol 18:2287-2296. |
French, N., Midwinter, A., Holland, B., Collins-Emerson, J., Pattison, R., and Carter, P. | Molecular epidemiology of Campylobacter jejuni isolated from wild bird faecal material in children’s play areas. | Applied and Environmental Microbiology 75:779-783. |
Godfrey S.S., Moore, J.A., Nelson, N.J. and Bull, C.M. | Unravelling causality from correlations: revealing the impacts of endemic ectoparasites on a protected species (tuatara). | Parasitology 137(2):275-286. |
Grunewald, S., Huber, K. T., Moulton, V., Semple, C., and Spillner, A. | Characterizing weak compatibility in terms of weighted quartets. | Advances in Applied Mathematics, 42, 329-341. |
Hare, K.M. and Miller, K.A. | What dives beneath: diving as a measure of performance in lizards. | Herpetologica 65(3): 227-236. |
Heled J. and Drummond A..J. | Bayesian inference of species trees from multilocus data. | Molecular Biology and Evolution. doi:10.1093/ molbev/msp274. |
Hendy, M.D., Woodhams, M.D. and Dodd, A. | Modelling mitochondrial site polymeorphisms to infer the number of segregating units and mutation rate. | Biol Lett. |
Humphries, P. J. and Semple, C. | Note on the hybridization number and subtree distance in phylogenetics. | Applied Mathematics Letters, 22, 611-615. |
Huson, D., Moulton, V. and Steel, M. | Special Section: Phylogenetics. | IEEE/ACM Transactions in computational biology andbioinformatics 6(1): 4-6. ISSN: 1545-5963. |
Kieser, J.A., Tkatchenko, T., Dean, C., Jones, M.E.H., Duncan, W. and Nelson, N.J. | Microstructure of dental hard tissues and bone in the tuatara dentary, Sphenodon punctatus (Diapsida: Lepidosauria: Rhynchocephalia). | In Comparative Dental Morphology, Koppe, T., Meyer, G, Alt, K.W. (eds.), Front Oral Biol. Basel, Karger. Vol 13, pp80-85. |
Kennedy, M., Valle, C.A. and Spencer, H.G | The phylogenetic position of the Galápagos Cormorant. | Mol Phylo Evol 53:94-98. |
Lambert D.M., Shepherd L.D., Huynen L., Beans-Picón G., Walter G., and Millar C.D. | The molecular ecology of the extinct New Zealand Huia. | PLoS ONE 4:e8019. |
Langhoff, P., Authier, A., Buckley, T.R., Dugdale, J.S., Rodrigo, A. and Newcomb, R.D. | DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix . | Mol Ecol Res 9: 691-698. |
Lansing, J.S., M.P. Cox, S.S. Downey, M.A. Janssen, and Schoenfelder, J.W. | A Robust Budding Model of Balinese Water Temple Networks. | World Archaeology 41:112-133. |
Lawrence H.A., Millar C.D., Imber M.J., Crockett D.E., Robins J.H., Scofield R.P., Taylor G.A., Lambert D.M. | Molecular evidence for the identity of the Magenta Petrel. | Molecular Ecology Resources 9: 458–461 |
Leschen, R.A.B., Buckley, T.R. and Hoare, R. | The use of tag names and New Zealand taxonomy. | New Zealand Entomologist, 32: 85-87. |
Leung, T.L.F., Donald, K.M., Keeney D.B., Koehler, A.V., Peoples, R.C. and Poulin, R. | Trematode parasites of Otago Harbour (New Zealand) soft-sediment intertidal ecosystems: life cycles, ecological roles and DNA barcodes. | NZ J Marine & Freshwater Res 43:857-865. |
Linz, S. and Semple, C. | Hybridization in non-binary trees. | IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 30-45. |
Marshall, D.C., Hill, K.B.R., Buckley, T.R., Fontainek K. and Simon, C. | Glacial refugia in a maritime temperate climate: cicada (Kikihia subalpina) mtDNA phylogeography in New Zealand. | Molecular Ecology, 18: 1995-2009. |
Matisoo-Smith, E. | The Commensal Model for Human Settlement of the Pacific 10 Years On: What can we say and where to now? | Journal of Coastal and Island Archaeology, Special Issue, 4:151-163. |
Matisoo-Smith, E. and Robins, J.H. | Mitochondrial DNA evidence for the spread of Pacific rats through Oceania. | Biological Invasions, 11:1521-1527. |
Matisoo-Smith, E., Hingston, M., Summerhayes, G., Robins, J., Ross, H.A. and Hendy, M. | On the Rat Trail in Near Oceania: Applying the Commensal Model to the Question of the Lapita Colonization. | Pacific Science 63:465–475. |
McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X. and Rainey, P. B. | Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. | Genetics 183, 1041-1053. |
McGaughran, A., Redding, G.P.P., Stevens, M.I., and Convey, P. | Temporal metabolic rate variation in a continental Antarctic springtail. | Journal of Insect Physiology, 55, 129-134. |
Meudt, H.M., Lockhart, P.J. and Bryant, D. | Species delimitation and phylogeny of a New Zealand plant species radiation. | BMC Evolutionary Biology 9, 111. |
Miller, H.C., Moore, J.A., Nelson, N.J. and Daugherty, C.H. | Influence of major histocompatibility complex genotype on mating success in a free-ranging reptile population. | Proc. R. Soc. Lond. B. 276: 1695-1704. |
Miller, K.A., Chapple, D.G., Towns, D.R., Ritchie, P.A. and Nelson, N.J. | Assessing genetic diversity for conservation management: a case study of a threatened reptile. | Animal Conservation 12: 163-171. |
Miller, K.A., Nelson, N.J., Smith, H.G. and Moore, J.A. | How do reproductive skew and founder group size affect genetic diversity in reintroduced populations? | Molecular Ecology 18:3792-3802. (Featured article in “News and Views: Perspective”: Keogh, J.S. 2009. Evolutionary, behavioural and molecular ecology must meet to achieve long-term conservation goals. Molecular Ecology 18: 3761-3762). |
Moore, J.A., Daugherty, C.H. and Nelson, N.J. | Large male advantage: phenotypic and genetic correlates of territoriality in tuatara. | Journal of Herpetology 43(4): 570-578. |
Moore, J.A., Daugherty, C.H., Godfrey, S.S. and Nelson, N.J. | Seasonal monogamy and multiple paternity in a wild population of a territorial reptile (tuatara). | Biological Journal of the Linnean Society, 98: 161-170. |
Morgan-Richards, M., Smissen, R.D., Shepherd, L.D., Wallis, G.P., Hayward, J.J., Chan, C., Chambers, G.K. and Chapman, H.M. | A review of genetic analyses of hybridisation in New Zealand. | J Royal Soc NZ 39:15-34. |
Mossel, E., Roch, S. and Steel, M. | Shrinkage effect in ancestral maximum likelihood. | IEEE/ACM Transactions in computational biology and bioinformatics 6(1): 126-133. ISSN: 1545-5963 |
Nakano, T., Marshall, B.A., Kennedy, M. and Spencer, H.G. | The phylogeny and taxonomy of New Zealand Notoacmea and Patelloida species (Mollusca: Patellogastropoda: Lottiidae) inferred from DNA sequences. | Molluscan Research (29):33-59. |
O'Meally, D., Miller, H.C., Patel, H.R., Marshall Graves, J.A. and Ezaz, T. | The first cytogenetic map of the tuatara, Sphenodon punctatus. | Cytogenetics and Genome Research 127: 213-223. |
O’Neill, S.B., Buckley, T.R., Jewell,T.R. and Ritchie. P.A. | Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci. | Molecular Phylogenetics and Evolution, 53: 523–536. |
Penny, D. | Charles Darwin as a scientist. | NZ Science Review 66:87-92. |
Penny, D. | Charles Darwin as a theoretical biologist in the mechanistic tradition. | Trends Evol Biol 1:e1. |
Penny, D., Hoeppner, M.P., Poole, A.M. and Jeffares, D.C. | An Overview of the Introns-First Theory. | J Mol Evol 69:527-540. |
Perrie, L.R. and Shepherd, L.D. | Reconstructing the species phylogeny of Pseudopanax(Araliaceae), a genus of hybridising trees. | Mol Phylo and Evol 52: 774-83. doi:10.1016/j.ympev.2009.05.030. |
Pratt, R.C., Gibb, G.C., Morgan-Richards, M., Phillips, M.J., Hendy, M.D., and Penny, D. | Toward Resolving Deep Neoaves Phylogeny: Data, Signal Enhancement, and Priors. | Molecular Biology and Evolution 26:313-326. |
Ramstad, K.M., Paine, G., Dunning, D.L., Geary, A.F., Keall, S.N. and Nelson, N.J. | Effective partnerships between universities and indigenous communities: a case study in tuatara conservation in Aotearoa. | Journal of the Royal Society of New Zealand 39(4): 229-231. |
Refsnider, J.M., Keall, S.N., Daugherty, C.H. and Nelson, N.J. | Does nest-guarding in female tuatara (Sphenodon punctatus) decrease nest-destruction by conspecific females? | Journal of Herpetology 43(2): 294-299. |
Rioux Paquette, S., and Lapointe, F.-J. | A statistical procedure to assess the significance level of barriers to gene flow. | Journal of Genetics and Genomics 36: 685-693. |
Semple, C. and Steel, M. | Mathematical aspects of the 'Tree of life'. | Math Horizons. |
Shepherd, L.D., de Lange, P.J and Perrie, L.R. | Multiple colonizations of a remote oceanic archipelago by one species: how common is long-distance dispersal? | J Biogeog. Shepherd et al 2009.pdf (177 KB) |
Silby, M. W., Cerdeno-Tarranga, A. M., Vernikos, G., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X.-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T. S., Bentley, S., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. and Thomson, N. R | Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. | Genome Biology 10, R51. |
Spencer, H.G. | Effects of genomic imprinting on quantitative traits. | Genetica 136:285-293. Spencer Genetica 2009.pdf (313 KB) |
Spencer, H.G., Marshall, B.A. and Waters, J. | Systematics and phylogeny of a new cryptic species of Diloma philippi (Mollusca: Gastropoda: Trochidae) from a novel habitat, the bull kelp holdfast communities of southern New Zealand. | Invert Syst 23:19-25. Spencer et al InvertSyst 2009.pdf (439 KB) |
Steel, M. | A basic limitation on inferring phylogenies by pairwise sequence comparisons. | Journal of Theoretical Biology 256: 467-472. Steel basic.pdf (231 KB) |
Steel, M. | The `Penny Ante': Mathematical biology or biological mathematics?. | New Zealand Science Review 66(1): 11-12. Steel penny_ante.pdf (305 KB) |
Steel, M. and Faller, B. | Markovian log-supermodularity, and its applications in phylogenetics. | Applied Mathematics Letters 22 (7): 1141--1144. Steel Markovian.pdf (397 KB) |
Steel, M., Szekely, L. and Mossel, E. | Phylogenetic information complexity: Is testing a tree easier than finding it? | Journal of Theoretical Biology 258: 95--102. Steel Phylogenetic.pdf (452 KB) |
Stiller, M., Knapp, M., Stenzel, U., Hofreiter, M., and Meyer, M. | Direct multiplex sequencing (DMPS): a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. | /Genome Research/ 19, 1843–1848. |
Subramanian S., Denver D.R., Millar C.D., Heupink T., Aschrafi A., Emslie S.D., Baroni C., David M., and Lambert D.M. | Mitogenomic rates for the study of recent evolutionary events. | Trends in Genetics 25: 482–486. |
Trotter, M.V., and Spencer, H.G. | Complex dynamics occur in a single-locus, multiallelic model of frequency dependent selection. | Theoretical Population Biology 76: 292-298. |
Waddell, P.J., Ota, R. and Penny, D. | Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests. | J Mol Evol 69:289-299. |
Whyte, A.L.H., Bell, J.J., Ramstad, K.M., and Gardner, J.P.A. | An indigenous-led community challenge to fisheries management in New Zealand: the revival of regional scale management practices? | Pacific Conservation Biology 14:248-249. |
Woo, K.L., Hunt, M., Harper, D., Nelson, N.J., Daugherty, C.H., and Bell, B.D | Discrimination of flicker frequency rates in the reptile tuatara (Sphenodon). | Naturwissenschaften 96(3): 415-419. |
Wu, T., Moulton, V., and Steel, M. | Refining phylogenetic trees given additional data: Algorithms based on parsimony. | IEEE/ACM Transactions in computational biology and bioinformatics 6(1): 118-125. ISSN: 1545-5963. |
Yeates, G.W., and Buckley, T.R. | First records of mermithid nematodes (Nematoda: Mermithidae) parasitising stick insects (Insecta: Phasmatodea). | New Zealand Journal of Zoology, 36: 35-39. |
Zeng, Q.Z., and Buckley, T.R. | Phylogenetic analysis of nematode nuclear 18S rDNA sequences indicates the Genus Tripylina Brzeski, 1964 (Nematoda: Tripylidae de Man, 1876) should be placed in Enoplida. | Zootaxa, 2238: 25-32. |
Zhang, M., Upritchard, J.E., Holland, B., Fenton, L.E., Ferguson, M.M., Cannon,R.D. and Schmid, J. | Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes. | Infection Genetics and Evolution 9:493-500. |