
Research Publications
2005 Publication list
Author/s |
Title |
Journal |
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. |