Research Publications

2009 Publication list




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.