Research Publications


2008 Publication list

Author/s

Title

Journal

     
Allendorf, F.W., England, P.R., Luikart, G., Ritchie, P.A. and Ryman, N.  Genetic effects of harvest on wild animal populations.  Trends in Ecology & Evolution 23:327-337.
     
Ashton G.V., Stevens M.I., Hart M.C., Green D.H., Burrows M.T., Cook E.J. and Willis, K.J. Mitochondrial DNA reveals multiple northern hemisphere introductions of Caprella mutica (Crustacea, Amphipoda).  Molecular Ecology 17: 1293-1303.
     
Atkinson, Q. D., Gray, R.D. and Drummond, A.J. MtDNA variation predicts population size in humans and reveals a major southern Asian chapter in human prehistory.  Molecular Biology and Evolution 25:468-474.
     
Boessenkool, S., King, T.M., Seddon, P.J. and Waters, J.M. Isolation and characterization of microsatellite loci from the yellow-eyed penguin (Megadyptes antipodes).  Molecular Ecology Resources 8:1043-1045.
     
Bordewich, M., Rodrigo, A. and Semple, C. Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution.  Systematic Biology 57:825-834.
     
Bordewich, M. and Semple, C. Nature reserve selection problem: A tight approximation algorithm. Ieee-Acm Transactions on Computational Biology and Bioinformatics 5:275-280.
     
Bruen, T. C. and Bryant, D. A subdivision approach to maximum parsimony.  Annals of Combinatorics 12:45-51.
     
Bruen, T. C. and Bryant, D. Parsimony via consensus.  Systematic Biology 57:251-256.
     
Buckley, T. R., Attanayake,D., Park, D., Ravindran, S., Jewell, T.R. and  Normark, B.B. Investigating hybridization in the parthenogenetic New Zealand stick insect Acanthoxyla (Phasmatodea) using single-copy nuclear loci.  Molecular Phylogenetics and Evolution 48:335-349.
     
Burridge, C. P., Craw, D., Jack, D.C., King, T.M. and Waters, J. Does fish ecology predict dispersal across a river drainage divide?  Evolution 62:1484-1499.
     
Burridge, C. P., Craw, D., Fletcher, D. and Waters, J.M. Geological dates and molecular rates: Fish DNA sheds light on time dependency.  Molecular Biology and Evolution 25:624-633.
     
Chapple, D. G., Daugherty, C.H. and Ritchie, P.A. Comparative phylogeography reveals pre-decline population structure of New Zealand Cyclodina (Reptilia: Scincidae) species.  Biological Journal of the Linnean Society 95:388-408.
     
Chapple, D. G., Patterson, G.B., Gleeson, D.M., Daugherty, C.H. and Ritchie, P.A. Taxonomic revision of the marbled skink (Cyclodina oliveri, Reptilia : Scincidae) species complex, with a description of a new species.  New Zealand Journal of Zoology 35:129-146.
     
Chapple, D. G., Patterson, G.B., Bell, T. and Daugherty, C.H. Taxonomic revision of the New Zealand Copper Skink (Cyclodina aenea : Squamata : Scincidae) species complex, with descriptions of two new species.  Journal of Herpetology 42:437-452.
     
Chapple, D. G., Hutchinson, M.N., Maryan, B., Plivelich, M., Moore, J.A. and Keogh, J.S. Evolution and maintenance of colour pattern polymorphism in Liopholis (Squamata : Scincidae).  Australian Journal of Zoology 56:103-115.
     
Chen, X. S., White,W.T.,  Collins, L. and Penny, D. Computational Identification of Four Spliceosomal snRNAs from the Deep-Branching Eukaryote Giardia intestinalis.  Public Library of Science ONE 3:e3106.
     
Collins, L. J. and Schoenfeld, B. Next Generation Sequencing in New Zealand.  New Zealand BioScience 17:12-15.
     
Collins, L. J., Biggs, P.J., Voelckel, C. and Joly, S. An approach to transcriptome analysis of non-model organisms using short-read sequences.  Genome Informatics 21:3-14.
     
Convey, P., J. Gibson, A.E., Hillenbrand, C.D., Hodgson, D.A., Pugh, P.J.A., Smellie, J.L. and Stevens, M.I. Antarctic terrestrial life - challenging the history of the frozen continent?  Biological Reviews 83:103-117.
     
Corin, S. E., Ritchie, P.A. and Lester, P.J. Introduction Pathway Analysis Into New Zealand Highlights a Source Population 'Hotspot' in the Native Range of the Red imported Fire Ant (Solenopsis invicta).  Sociobiology 52:129-143.
     
Craw, D., Burridge, C., Norris, R. and Waters, J. Genetic ages for Quaternary topographic evolution: a new dating tool.  Geology 36:19-22.
     
Craw, D., Burridge, C.P., Upton, P.,  Rowe, D.L. and Waters, J.M. Evolution of biological dispersal corridors through a tectonically active mountain range in New Zealand.  Journal of Biogeography 35:1790-1802.
     
Daugherty, C.H. and Cree, A. A survivor from the dinosaur age.  In The Awa Book of New Zealand Science. R. Priestley, ed. Wellington, Awa Press 291-301 [ISBN 9780958262996] [Reprinted excerpt from popular article by Daugherty and Cree 1990 New Zealand Geographic No. 6: 66-86].
     
Faller, B., Pardi, F. and Steel, M. Distribution of phylogenetic diversity under random extinction. Journal of Theoretical Biology 251:286-296.
     
Fischer, M. and Steel, M. Expected anomolies in the fossil record.  Evolutionary bioinformatics online 4: 61-67.
     
Gernhard, T. New analytic results for speciation times in neutral models.  Bulletin of Mathematical Biology 70:1082-1097.
     
Gernhard, T. The conditioned reconstructed process. Journal of Theoretical Biology 253:769-778.
     
Gernhard, T., Hartmann, K. and Steel, M. Stochastic properties of generalised Yule models, with biodiversity applications.  Journal of Mathematical Biology 57:713-735.
     
Gill, J., Linusson, S., Moulton, V. and Steel, M. A regular decomposition of the edge-product space of phylogenetic trees.  Advances in Applied Mathematics. 158-176.
     
Gluckman, P. D., Hanson, M.A., Beedle, A.S. and Spencer, H.G. Predictive adaptive responses in perspective.  Trends in Endocrinology and Metabolism 19:109-110.
     
Godfrey, S. S., Bull, C.M. and Nelson, N.J. Seasonal and spatial dynamics of ectoparasite infestation of a threatened reptile, the tuatara (Sphenodon punctatus). Medical and Veterinary Entomology 22:374-385.
     
Goldberg, J., Trewick, S.A. and Paterson, A.M. Evolution of New Zealand's terrestrial fauna: a review of molecular evidence. Philosophical Transactions of the Royal Society B-Biological Sciences 363:3319-3334.
     
Greaves, S. N. J., Chapple, D.G., Daugherty, C.H., Gleeson, D.M. and Ritchie, P.A. Genetic divergences pre-date Pleistocene glacial cycles in the New Zealand speckled skink, Oligosoma infrapunctatum.  Journal of Biogeography 35:853-864.
     
Greenslade, P., Melbourne, B., Davies, K. and Stevens, M.I. The status of two exotic terrestrial Crustacea on subantarctic Macquarie Island. Polar Record 44:15-23.
     
Grueber, C. E., King, T.M., Waters, M. and Jamieson, I.J. Isolation and characterization of microsatellite loci from the endangered New Zealand takahe (Gruiformes; Rallidae; Porphyrio hochstetteri).  Molecular Ecology Resources 8:884-886.
     
Gruenheit, N., Lockhart, P.J., Steel, M. and Martin, W. Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites.  Molecular Biology and Evolution 25:1512-1520.
     
Grunewald, S., Huber, K.T., Moulton, V. and Semple,C. Encoding phylogenetic trees in terms of weighted quartets.  Journal of Mathematical Biology 56:465-477.
     
Grunewald, S., Humphries, P.J. and Semple,  C.  Quartet compatibility and the quartet graph.  Electronic Journal of Combinatorics 15.
     
Hare, K.M., Pledger, S. and Daugherty, C.H. Low incubation temperatures negatively influence locomotor performance and behaviour of the nocturnal lizard Oligosoma suteri (Lacertidae: Scincidae). Copeia 2008(1): 16-22.
     
Hare, K.M., Daugherty, C.H. and Chapple, D.G. Comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O suteri; Reptilia: Scincidae) in northeastern New Zealand. Molecular Phylogenetics and Evolution 46: 303-315.
     
Hartnup, K., Huynen, L., Te Kanawa, R., Shepherd, L.D., Millar, C.D. and Lambert, D. A molecular study of a unique Maori cloak. in M. Haslam, ed. Archaeological Science Under A Microscope: Studies in Honour of Thomas H. Loy.  Australian National University Press, Canberra, Australia.
     
Hay, J. M. and Lambert, D.M. Microsatellite DNA loci identify individuals and provide no evidence for multiple paternity in wild tuatara (Sphenodon : Reptilia).  Conservation Genetics 9:1039-1043.
     
Hay, J. M., Subramanian, S., Millar,C.D.,  Mohandesan, E. and Lambert, D. Rapid Molecular Evolution in a Living Fossil.  Trends in Genetics 24:106-109.
     
Hayward, J. J. and Rodrigo, A.G. Recombination in feline immunodeficiency virus from feral and companion domestic cats.  Virology Journal 5.
     
Hendy, M. D. and Snir, S. Hadamard conjugation for the Kimura 3ST model: Combinatorial proof using path sets. Ieee-Acm Transactions on Computational Biology and Bioinformatics 5:461-471.
     
Holland, B. R., Clarke, A.C. and Meudt, H.M. Optimizing automated AFLP scoring parameters to improve phylogenetic resolution.  Systematic Biology 57:347-366.
     
Holland, B. R., Benthin, S., Lockhart, P.J., Moulton, V. and Huber, K.T. Using supernetworks to distinguish hybridization from lineage-sorting.  Bmc Evolutionary Biology 8.
     
Hon, C. C., Lam, T.Y., Shi, Z.L., Drummond, A.J., Yip, C.W., Zeng,F.,  Lam, P.Y. and Leung, F.C.C. Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus.  Journal of Virology 82:1819-1826.
     
Horrocks, A., Grant-Mackie, J. and Matisoo-Smith, E. Introduced taro (Colocasia esculenta) and yams (Dioscorea spp.) in Podtanean (2700-1800 years BP) deposits from Mé Auré Cave (WMD007), Moindou, New Caledonia.  Journal of Archaeological Science 35:169-180.
     
Howe, C. J., Barbrook, A.C., Nisbet, R.E.R., Lockhart, P.J. and Larkum, A.W.D. The origin of plastids.  Philosophical Transactions of the Royal Society B-Biological Sciences 363:2675-2685.
     
Irimia, M.,  Rukov, J.L., Penny, D., Garcia-Fernandez, J., Vinther, J. and Roy, S.W. Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis. Molecular Biology and Evolution 25:375-382.
     
Irimia, M., Rukov, J.L., Penny, D., Vinther, J., Garcia-Fernandez, J. and Roy, S.W. Origin of introns by "intronization' of exonic sequences. Trends in Genetics 24:378-381.
     
Jamieson, I. G., Grueber, C.E., Waters,J.M.  and Gleeson, D.M.  Managing genetic diversity in threatened populations: a New Zealand perspective.  New Zealand Journal of Ecology 32:130-137.
     
Kneip, C., Voss, C., Lockhart, P.J. and Maier, U.G. The cyanobacterial endosymbiont of the unicellular algae Rhopalodia gibba shows reductive genome evolution.  Bmc Evolutionary Biology 8.
     
Landis, C. A., Campbell, H.J., Begg, J.G., Mildenhall, D.C., Paterson, A.M. and Trewick, S.A. The Waipounamu Erosion Surface: Questioning the Antiquity of the New Zealand Land Surface and Terrestrial Fauna and Flora.  Geological Magazine 145:173-197.
     
Lawrence, H. A., Millar, C.D., Taylor, G.A., Macdonald, L.D. and Lambert, D.M. Excess of unpaired males in one of the World's most endangered seabirds, the Chatham Island taiko Pterodroma magentae.  Journal of Avian Biology 39:359-363.
     
Lawrence, H. A., Taylor, G.A., Millar, C.D. and Lambert, D.M. High mitochondrial and nuclear genetic diversity in one of the world's most endangered seabirds, the Chatham Island Taiko (Pterodroma magentae). Conservation Genetics 9:1293-1301.
     
Lawrence, H. A., Taylor, G.A., Crockett, D.E., Millar, C.D. and Lambert, D.M. New Genetic Approach to Detecting Individuals of Rare and Endangered Species.  Conservation Biology 22:1267-1276.
     
Lawrence, H. A., Scofield, R.P., Crockett, D.E., Millar, C.D., and Lambert, D.M. Ancient genetic variation in one of the world's rarest seabirds.  Heredity 101:543-547.
     
Lemey, P., Pond, S.L.K., Drummond, A.J., Pybus, O.G., Shapiro, B., Barroso, H., Taveira, N. and Rambaut, A. Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.  Infection Genetics and Evolution 8:S15-S16.
     
Leschen, R. A. B., Buckley, T.R., Harman, H.M. and Shulmeister, J. Determining the origin and age of the Westland beech (Nothofagus) gap, New Zealand, using fungus beetle genetics.  Molecular Ecology 17:1256-1276.
     
Li, G., Steel, M. and Zhang, L. More taxa are not necessarily better for the reconstruction of ancestral character states.  Systematic Biology 57(4):647--653.
     
Liggins, L., Chapple, D.G., Daugherty, C.H. and Ritchie, P.A. Origin and post-colonization evolution of the Chatham Islands skink (Oligosoma nigriplantare nigriplantare).  Molecular Ecology 17: 3290-3305.
     
Liggins, L., Chapple, D.G., Daugherty, C.H. and Ritchie, P.A. A SINE of restricted gene flow across the Alpine Fault: phylogeography of the New Zealand common skink (Oligosoma nigriplantare polychroma). Molecular Ecology 17:3668-3683.
     
Matisoo-Smith, E., Roberts, K., Welikala, N., Tannock, G., Chester, P., Feek, D. and Flenley, J. Recovery of DNA and pollen from New Zealand lake sediments.  Quartnary International 184:139-149.
     
Matsen, F. A., Mossel, E. and Steel, M. Mixed-up trees: The structure of phylogenetic mixtures.  Bulletin of Mathematical Biology 70:1115-1139.
     
McCallum, J., Thomson, S., Pither-Joyce,M.,  Kenel, F., Clarke, A.C. and Havey, M.J. Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tag-simple sequence repeat markers. Journal of the American Society for Horticultural Science 133:810-818.
     
McGaughran, A., Hogg, .ID. and Stevens, M.I. Patterns of population genetic structure for springtails and mites in southern Victoria Land, Antarctica.  Molecular Phylogenetics and Evolution 46: 606-618.
     
Michel, C., Hicks B.J., Stölting, K.N., Clarke, A.C., Stevens, M..I, Tana, R., Meyer, A. and van den Heuvel, M.R. Distinct migratory and landlocked ecotypes in a New Zealand eleotrid (Gobiomorphus cotidianus) – implications for incipient speciation and the origin of island freshwater fish species.  BMC Evolutionary Biology 8:49.
     
Millar, C. D., Dodd, A., Anderson, J., Gibb, G.C., Ritchie, P.A., Baroni, C., Woodhams, M.D., Hendy, M.D. and Lambert, D.M. Mutation and Evolutionary Rates in Adelie Penguins from the Antarctic.  Plos Genetics 4: 1-9.
     
Millar, C. D., Huynen, L.J., Subramanian,S.,  Mohandesan, E. and Lambert, D. New developments in ancient genomics.  Trends in Ecology & Evolution 23:386-393.
     
Miller, H. C., Miller, K.A. and Daugherty, C.H. Reduced MHC variation in a threatened tuatara species. Animal Conservation 11:206-214.
     
Miller, H.C., Moore, J.A., Allendorf, F.A. and Daugherty, C.H. The evolutionary rate of tuatara revisited.  Trends in Genetics 25(1): 13-15.
     
Mitchell, N.J., Kearney, M.R., Nelson, N.J. and Porter, W.P. Predicting the fate of a living fossil: how will global warming affect sex determination and hatching phenology in tuatara? Proceedings of the Royal Society B 275(1648): 2185-2193.
     
Mohandesan, E., Mowla, S.J., H.N.A. and Hofreiter, M. Ancient DNA from Human and Animal Remains from North-West Iran.  Journal of Sciences, Islamic Republic of Iran 19:3-8.
     
Moore, J.A., Miller, H.C., Daugherty, C.H. and Nelson, N.J. Fine-scale genetic structure of a long-lived reptile reflects recent habitat modification.  Molecular Ecology 17:4630-4641.
     
Moore, J. A., Nelson, N.J., Keall, S.N., and Daugherty, C.H. Implications of social dominance and multiple paternity for the genetic diversity of a captive-bred reptile population (tuatara).  Conservation Genetics 9(5):1243-1251.
     
Moore, J.A., Bell, B.D. and Linklater, W.L. The debate on behavior in conservation: New Zealand integrates theory with practice.  Bioscience 58 (5): 454-459.
     
Morgan-Richards, M., Trewick, S.A., Bartosch-Haerlid, A., Kardailsky, O., Phillips, M.J., McLenachan, P.A. and Penny, D. Bird evolution: testing the Metaves clade with six new mitochondrial genomes.  Bmc Evolutionary Biology 8.
     
Morgan-Richards, M., Trewick, S.A. and Dunavan, S. When is it coevolution? The case of ground weta and fleshy fruits in New Zealand.  New Zealand Journal of Ecology 32:108-112. New Zealand Journal of Ecology 32:108-112.
     
Neall, V.E. and Trewick, S.A. The age and origin of the Pacific islands: a geological overview.  Philosophical Transactions of the Royal Society B-Biological Sciences 363:3293-3308.
     
Nelson, N.J., Keall, S.N., Gaze, P. and Daugherty, C.H. Re-introduction of tuatara (Reptilia) as part of an ecological restoration project on Wakatere-papanui Island, Marlborough Sounds, New Zealand.  Chapter in “Reintroduction Specialist Group Book”, IUCN.
     
O’Neill, S.B., Chapple, D.G., Daugherty, C.H. and Ritchie, P.A. Phylogeography of two New Zealand lizards: McCann’s skink (Oligosoma maccanni) and the brown skink (O. zelandicum).  Molecular Phylogenetics and Evolution 48: 1168-1177.
     
Oxley, J., Semple, C. and Whittle, G. Wild triangles in 3-connected matroids. Journal of Combinatorial Theory Series B 98:291-323.
     
Oxley, J., Semple, C. and Whittle, G. A chain theorem for matroids.  Journal of Combinatorial Theory, Series B, 98, 447-483.
     
Oxley, J., Semple, C., and Whittle, G. Maintaining 3-connectivity relative to a fixed basis.  Advances in Applied Mathematics, 41, 1-9.
     
Paul, D.B. and Spencer, H.G. It’s Ok, We’re Not Cousins by Blood: The Cousin Marriage Controversy in Historical Perspective.  PLoS 6: 2627-2630.
     
Penny, D. Molecular Evolution: Introduction.  Encyclopedia of Life Sciences. John Wiley & Sons, Ltd, Chichester.
     
Penny, D., White, W.T., Hendy, M.D., and  Phillips, M.J. A Bias in ML Estimates of Branch Lengths in the Presence of Multiple Signals.  Molecular Biology and Evolution 25:239-242.
     
Phillips, M. J. and Pratt, R.C. Family-level relationships among the Australasian marsupial "herbivores" (Diprotodontia : Koala, wombats, kangaroos and possums).  Molecular Phylogenetics and Evolution 46:594-605.
     
Poss, M., and Ross, H. Evolution of the long terminal repeat and accessory genes of feline immunodeficiency virus genomes from naturally infected cougars.  Virology 370:55-62.
     
Poss, M., Ross, H., Rodrigo, A., Terwee, J., VandeWoude, S. and Biek, R. The molecular biology and evolution of feline immunodeficiency viruses of cougars.  Veterinary Immunology and Immunopathology 123:154-158.
     
Pratt, R. C., Morgan-Richards, M., and Trewick, S.A. Diversification of New Zealand weta (Orthoptera : Ensifera : Anostostomatidae) and their relationships in Australasia.  Philosophical Transactions of the Royal Society B-Biological Sciences 363:3427-3437.
     
Refsnider, J.M., Moore, J.A. and Streby, H.   Sphenodon punctatus (Common tuatara): Prey detection.   Herpetological Review 39(3): 347-348.
     
Robins, J. H., McLenachan, P.A., Phillips,M.J., Craig, L., Ross, H.A., and Matisoo-Smith, E. Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes.  Molecular Phylogenetics and Evolution 49:460-466.
     
Rodrigo, A., Bertels, F., Heled, J.,  Noder, R., Shearman, H. and Tsai, P. The perils of plenty: what are we going to do with all these genes?  Philosophical Transactions of the Royal Society B-Biological Sciences 363:3893-3902.
     
Ross, H.A.,  Murugan, S. and Li, W.L.S. Testing the reliability of genetic methods of species identification via simulation.  Systematic Biology 57:216-230.
     
Semple, C. and Welsh, D. Negative correlation in graphs and matroids.  Combinatorics, Probability and Computing, 17, 423-435.
     
Shavit Grievink, L., Penny, D., Hendy, M.D., and Holland, B.R. LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites.  BMC Evolutionary Biology 8:317.
     
Shepherd, L. D., and Lambert, D.M. Ancient DNA and conservation: lessons from the endangered kiwi of New Zealand.  Molecular Ecology 17:2174-2184.
     
Shepherd, L. D., Holland, B.R. and Perrie, L.R. Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns.  Molecular Phylogenetics and Evolution 48:176-187.
     
Shepherd, L. D., Zuccarello, G.C., and Perrie, L.R. Microsatellite markers for Pseudopanax trees and their cross-species amplification in the Araliaceae.  Conservation Genetics 9:1687-1689.
     
Shepherd, L.D.,  Perrie, L.R. and Brownsey, P.J. Low-copy nuclear DNA sequences reveal a predominance of allopolyploids in a New Zealand Asplenium fern complex.  Molecular Phylogenetics and Evolution 49:240-248.
     
Smith, A.M., Taylor, P.D. and Spencer, H.G. Resolution of taxonomic issues in the Horneridae (Bryozoa: Cyclostomata).  Annals of Bryozoology 2: 359-411.
     
Star, B., Trotter, M.V. and Spencer, H.G. Evolution of fitnesses in structured populations with correlated environments.  Genetics 179:1469-1478.
     
Steel, M. and Rodrigo, A. Maximum likelihood supertrees.  Systematic Biology 57:243-250.
     
Stoffels, R. J. and Spencer, H.G. An asymmetric model of heterozygote advantage at major histocompatibility complex genes: Degenerate pathogen recognition and intersection advantage.  Genetics 178:1473-1489.
     
Storey, A. A., Quiroz, D., Ramirez, J.M., Beavan-Athfield, N., Addison, D.J., Walter, R., Hunt, T., Athens, J.S., Huynen, L. and Matisoo-Smith, E.A. Pre-Colombian chickens, dates, isotopes, and mtDNA.  Proceedings of the National Academy of Sciences of the United States of America 105:E99-E99.
     
Storey, A. A., Ladefoged, T. and Matisoo-Smith, E.A. Counting your chickens: Density and distribution of chicken remains in archaeological sites of Oceania.  International Journal of Osteoarchaeology 18:240-261.
     
Subramanian, S., Hay, J.M., Mohandesan, E., Millar, C.D. and Lambert, D.M. Molecular and morphological evolution in tuatara are decoupled.  Trends in Genetics 25:16-18.
     
Terezow, M. G., Nelson, N.J., and Markwell, T.J. Circadian emergence and movement of captive juvenile tuatara (Sphenodon spp.).  New Zealand Journal of Zoology 35:205-216.
     
Thatte, B. D., and Steel, M. Reconstructing pedigrees: A stochastic perspective.  Journal of Theoretical Biology 251:440-449.
     
Thierer, T., Bryant, D., and Steel, M. Counting ancestral reconstructions in a fixed phylogeny.  Annals of Combinatorics 12:123-132.
     
Trewick, S. A. DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera : Acrididae).  Cladistics 24:240-254.
     
Trewick, S. A., and Cowie, R.H. Introduction. Evolution on Pacific islands: Darwin's legacy.  Philosophical Transactions of the Royal Society B-Biological Sciences 363:3289-3291.
     
Trewick, S. A., Walker, K.J., and Jordan, C.J. Taxonomic and conservation status of a newly discovered giant landsnail from Mount Augustus, New Zealand.  Conservation Genetics 9:1563-1575.
     
Trewick, S. A., Morgan-Richards, M., and Collins, L.J. Are you my mother? Phylogenetic analysis reveals orphan hybrid stick insect genus is part of a monophyletic New Zealand clade.  Molecular Phylogenetics and Evolution 48:799-808.
     
Trewick, S., and Morris, S. Diversity and taxonomic status of some New Zealand grasshoppers. DOC Research & Development Series #290. Wellington, New Zealand.
     
Trotter, M. V., and Spencer, H.G. The Generation and Maintenance of Genetic Variation by Frequency-Dependent Selection: Constructing Polymorphisms Under the Pairwise Interaction Model. Genetics 180:1547-1557.
     
Voelckel, C., Heenan, P.B., Janssen, B., Reichelt, M., Ford, K., Hofmann, R., and Lockhart, P.J. Transcriptional and biochemical signatures of divergence in natural populations of two species of New Zealand alpine Pachycladon.  Molecular Ecology 17:4740-4753.
     
Walker, K.J., Trewick, S.A., and Barker, G.M. A new species of Powelliphanta (Mollusca: Pulmonata: Rhytididae) land snail from the Stockton Plateau, New Zealand.  Journal of the Royal Society of New Zealand 38: 163–186.
     
Wang, Y. L.,  Joly, S., and Morse, D. Phylogeny of dinoflagellate plastid genes recently transferred to the nucleus supports a common ancestry with red algal plastid genes.  Journal of Molecular Evolution 66:175-184.
     
Waters, J. M. Driven by the West Wind Drift? A synthesis of southern temperate marine biogeography, with new directions for dispersalism.  Journal of Biogeography 35:417-427.
     
Waters, J. M. Marine biogeographical disjunction in temperate Australia: historical landbridge, contemporary currents, or both?  Diversity and Distributions 14:692-700.
     
Waters, J. M., and Craw, D. Evolution and biogeography of New Zealand's longjaw galaxiids (Osmeriformes : Galaxiidae): the genetic effects of glaciation and mountain building.  Freshwater Biology 53:521-534.
     
Waugh, J., Huynen, L., Millar, .CD., and Lambert, D.M. DNA barcoding in animal species.  BioEssays 30:92-93.
     
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