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Research Publications

2005 Publication list




Albach, Dirk C., Heidi M. Meudt, and Oxelman, Bengt. Piecing together the “new” Plantaginaceae. American Journal of Botany. 92: 297-315. 
Barker, A.J., Huynen, L.J., Haddrath, O., Millar, C.D., and Lambert, D.M. Reconstructing the tempo and mode of evolution in an extinct clade of birds with ancient DNA: The giant moas of New Zealand. PNAS: vol 102 (23): 8257-8262.
Burnham, D.K., Keall, S.N., Nelson, N.J., and Daugherty, C.H. T-cell function in tuatara (Sphenodon punctatus).  Comparative Immunology, Microbiology and Infectious Diseases 28: 213-222.
Campbell, C.J., K.A. Horsburgh and E. Matisoo-Smith. A genetic analysis of group relatedness in free-ranging black-handed spider monkeys (Ateles geoffroyi). American Journal of Physical Anthropology S40:83.
Chan, C., Ballantyne, K.N., Lambert, D.M. and Chambers, G.K. Characterization of variable microsatellite loci in Forbes’ parakeet (Cyanoramphus forbesi) and their use in other parrots. Conservation Genetics 6: 651-654.
Chan, Z.S., Kasabov, N., and Collins, L. A hybrid genetic algorithm and expectation maximization method for global gene trajectory clustering. J Bioinf & Comp Biol 3:1227-1242.
Collins, L.J. and Penny, D. Complex Spliceosomal Organization Ancestral to Extant Eukaryotes. Mol. Biol. Evol. 22(4):1053–1066.
Donald, K. M., Kennedy, M., and Spencer, H. G. Cladogenesis as the result of long-distance rafting events in South Pacific topshells (Gastropoda, Trochidae). Evolution 59(8), pp. 1701–1711.
Donald, K.M., Kennedy, M. and Spencer, H.G.  The phylogeny and taxonomy of austral monodontine topshells (Mollusca: Gastropoda: Trochidae), inferred from DNA sequences. Mol Phylo Evol 37: 474-483.
Dress, A., Holland, B.R., K. Huber, J. H. Koolen, V. Moulton, and Weyer-Menkhoff, J. Delta-additive metrics and ?-ultrametric maps, Gromov’s trees and the Farris transform. Discrete Applied Mathematics 146: 51-73.
Erickson, D.L., Smith, B.D., Clarke, A.C., Sandweiss, D.H. and Tuross, N. An Asian origin for a 10,000-year-old domesticated plant in the Americas. Proceedings of the National Academy of Science, USA 102(51): 18315-18320.
Gartrell, B. and Hare, K.M. Mycotic dermatitis with digital gangrene and osteomyelitis, and protozoal intestinal parasitism in Marlborough green geckos (Naultinus manukanus). New Zealand Veterinary Journal 53(5): 363-367.
Gluckman, P.D., Hanson, M.A., and Spencer, H.G. Predictive adaptive responses and human evolution. Trends in Ecology and Evolution 20: 527-533.
Gluckman, P.D., Hanson, M.A., Spencer, H.G. and Bateson, P. Environmental influences and their later consequences for health and disease: implications for the interpretation of empirical studies. Proc. R. Soc. B. 272: 671-677.
Goremykin, V. V., B. Holland, K. I. Hirsch-Ernst, and Hellwig, F.H. Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Molecular Biology and Evolution22: 1813-1822.
Hare, K.M. and Cree, A. Natural history of Hoplodactylus stephensi (Reptilia: Gekkonidae) on Stephens Island, Cook Strait, New Zealand.  New Zealand Journal of Ecology 29(1): 137-142.
Hare, K.M. and Hoare, J.M.   Hoplodactylus maculatus (Common Gecko) aggregations. Herpetological Review 36(2): 179.
Hare, K.M., Daugherty, C.H., and Miller, J.H.   Do nocturnal lizards have cold-adapted enzymes? (abstract) New Zealand Journal of Zoology 32: 223 
Hare, K.M., Miller, J.H., Clark, A.G. and Daugherty, C.H. Total lactate dehydrogenase activity of tail muscle is not cold-adapted in nocturnal lizards from cool-temperate habitats. Comparative Biochemistry and Physiology, Part B 142(4): 438-444.
Hoare, J.M. Book Review.  Flight of the Huia: Ecology and conservation of New Zealand's frogs, reptiles, birds and mammals.   Pacific Conservation Biology 11(2): 147-148.
Hoare, J.M., Nelson, N.J., and Daugherty, C.H.   Does the naïve behaviour of New Zealand lizards threaten their future? (abstract) New Zealand Journal of Zoology 32: 224-225 
Hoare, J.M., Stephens, C.L., Daugherty, C.H., and Phillpot. P.M.S. Oligosoma lineoocellatum (Spotted skink) longevity, site fidelity.  Herpetological Review 36(2): 181.
Holland, B.R., F. Delsuc, and Moulton, V. Visualising conflicting evolutionary hypotheses in large collections of trees using consensus networks. Syst. Biol. 54(1):66–76
Holland, B.R., K.T. Huber, D. Penny, and Moulton, V. The MinMax Squeeze: Guaranteeing a minimal tree for population data. Mol. Biol. Evol. 22:235-242.
Holland, B. and Schmid, J. Selecting representative model strains. BMC Microbiology 5: 26.
Hörandl, E., Paun, O., Johansson, J.T., Lehnebach, C., Armstrong, T., Chen, L. and Lockhart, P.J. Phylogenetic relationships and evolutionary traits in Ranunculus s.l. (Ranunculaceae) inferred from ITS sequence analysis. Mol Phyl Evol 36: 305-327.
Huber, K.T. Moulton, V., Semple, M.C. and Steel, M. Recovering a phylogenetic tree using pairwise closure operations. Applied Mathematics Letters 18(3): 361-366.
Huber, K., Moulton, V. and Steel, M. Four characters suffice to convexly define a phylogenetic tree.  SIAM Journal on Discrete Mathematics 18(4): 835-843
Huson, D., Kloepper, T., Lockhart, P.J. and Steel, M.A. Reconstruction of Reticulate Networks from Gene Trees In Proceedings of the ninth international conference in computational molecular biology. (RECOMB): 233-249.
Kennedy, M., B. R. Holland, R. D. Gray, and Spencer, H.G. Untangling Long Branches: Identifying Conflicting Phylogenetic Signals a priori using Spectral Analysis, Neighbor-Net, and Consensus Networks. Systematic Biology 54:620-633.
Knapp, M., Stöckler, K., Havell, D., Delsuc, F., Sebastiani, F. and Lockhart, P.J. Relaxed Molecular Clock Provides Evidence for Long-Distance Dispersal of Nothofagus (Southern Beech) PLoS Biology 3, 38-43
Larson, G., K. Dobney, U. Albarella, M. Fang, E. Matisoo-Smith, J. Robins, S. Lowden, H. Finlayson, T. Brand, E. Willerslev, P. Rowley-Conwy, L. Andersson and Cooper, A. Worldwide phylogeography of wild boar reveals multiple centres of pig domestication. Science307:1618-1621.
Larson, G., Dobney, K., Albarella, U., Matisoo-Smith, E., Robins, J., Lowden, S., Rowley-Conwy, P., Andersson, L. and Cooper, A. Response to Domesticated Pigs in Eastern Indonesia.  Science 309:381.
Lambert, D.M., Baker, A., Huynen, L., Haddrath. O., Hebert, P.D.N., Millar, C.D. Is a large-scale DNA-based taxonomy of ancient life possible?  Journal of Heredity 96: 279-284.
Lockhart, P., et al. Dispersal or Drift? More to Plant Biodiversity Than Meets the Eye.  PLoS Biol 3(1): e43.
Lockhart, P.J., Novis, P., Milligan, B.G., Riden, J., Rambaut, A. and Larkum, A.W.D. Heterotachy and Tree Building: A Case Study with Plastids and Eubacteria.  Mol Biol Evol 23: 40-45.
Lockhart, P.J. and Penny, D. The place of Amborella in the radiation of angiosperms. Trends Plant Sci.10: 201-202.
Lockhart, P. and Steel, M. A tale of two processes.  Systematic Biology, 54(6): 948-951.
Matisoo-Smith, E. The Rat Path - Tracing Polynesian migration through rat DNA. Wild California The magazine of the California Academy of Science. 58(2):16-19.
Meintjes, P. and Rodrigo, A. G. Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1.  Journal of Bioinformatics and Computational Biology.3:157-168.
Miller, H.C., Belov, K. and Daugherty, C.H. Characterisation of MHC class II genes from an ancient reptile lineage, Sphenodon (tuatara).  Immunogenetics 57: 883-891.
Miller, H.C., Belov, K., Edwards, S.V., and Daugherty, C.H. Unravelling the reptile MHC. (abstract) New Zealand Journal of Zoology 32: 227 
Mitchell, N.J., Nelson, N.J., and Daugherty, C.H.   Tuatara take a year to hatch – and 15 years to reveal their gender: the heat is on for survival of this living fossil La Trobe University Bulletin, June: 1-2.
Morgan-Richards, M. Chromosome rearrangements are not accompanied by expected genome size change in the tree weta Hemideina thoracica (Orthoptera, Anostostomatidae).  Journal of Orthoptera Research, 14(2): 143-148.
Morgan-Richards, M., Trewick, S. A. Hybrid origin of a parthenogenetic genus? Molecular Ecology 14, 2133-2142.
Morison, I.M., Ramsay, J.P., and Spencer, H.G. A census of mammalian imprinting. TRENDS in Genetics 21(8): 457-465
Mossel, E. and Steel, M. Random biochemical networks and the probability of self-sustaining autocatalysis.  Journal of Theoretical Biology 233(3), 327-336.
Nelson, N.J. News from the Australasian section of the Society for Conservation Biology. Pacific Conservation Biology 11(2): 79.
Nelson, N.J. Conservation-biased research on a New Zealand treasure, the tuatara. (abstract) New Zealand Journal of Zoology 32: 228.
Olshen, A. B., Cosman, P. C., Rodrigo, A. G., Bickel, P. J., and Olshen, R. A. Vector quantization of amino acids: analysis of the HIV V3 loop region.  Journal of Statistical Planning and Inference.130:277-298.
Ovidiu, P., Lehnebach, C., Johansson, J.T., Lockhart, P.J. and Hörandl, E. Phylogenetic relationships and biogeography of Ranunculus and allied genera (Ranunculaceae) in the Mediterranean region and in the European Alpine System.  Taxon 54: 911-930.
Penny, D. An interpretive review of the origin of life research.  Biology and Philosophy20:633–671.
Penny, D. Relativity for Molecular Clocks. NATURE(436): 183-184.
Perrie, L.R., Shepherd. L.D. and Brownsey, P.J. Asplenium xlucrosum nothosp. Nov.: a sterile hybrid widely and erroneously cultivated as “Aspelium bulbiferum”.  Plant Syst Evol250:243-257.
Shepherd, L.D. and Lambert, D.M. Mutational drive in penguin microsatellite DNA. Journal of Heredity 96(5): 566-571.
Shepherd, L.D., Millar, C.D., Ballard, G., Ainley, D.G., Wilson, P.R., Haynes, G.D., Baroni, C. and Lambert, D.M Microevolution and mega-icebergs in the Antarctic.  Proceedings of the National Academy of Sciences USA 102: 16717-16722.
Spencer, H.G., and Feldman, M.W. Adaptive dynamics, game theory and evolutionary population genetics.  Journal of Evolutionary Biology 18: 1191-1193.
Steel, M., Should phylogenetic models be trying to `fit an elephant'?  Trends in Genetics21(6), 307-309.
Trewick, S. A., Morgan-Richards, M. After the deluge: mitochondrial DNA indicates Miocene radiation and Pliocene adaptation of tree and giant weta (Orthoptera: Anostostomatidae).  Journal of Biogeography, 32: 295-309.
Waters, J.W., King, T.M., O’Loughlin, P.M., and Spencer, H.G. Phylogeographical disjunction in abundant high-dispersal littoral gastropods.  Mol. Ecol 14: 2789 – 2802.
Winkworth, R.C., Bryant, D., Lockhart, P.J., Havell, D., and Moulton, V. Biogeographic interpretation of split graphs: least squares optimization of branch lengths.  Sys Biol 54: 56-65.
Winkworth, R.C., Wagstaff, S.J., Glenny, D. and Lockhart P.J. Evolution of the New Zealand alpine flora: origins, diversification and dispersal.  Org. Divers. Evol. 5: 237-247
Winsor, L. and Stevens, M.I. Terrestrial flatworms (Platyhelminthes: Tricladida: Terricola) from sub-Antarctic Macquarie Island.  Kanunnah 1: 17-32.
Woo, K.L., Hunt, M., Harper, D., Nelson, N.J., Daugherty, C.H., and Bell, B.D. Acquisition of a learned operant and critical flicker-fusion rate in tuatara (Sphenodon). (abstract) New Zealand Journal of Zoology 32: 232.