
Research Publications
2011 Publication list
Author/s |
Title |
Journal |
Allibone, R., David, B., Hitchmough, R., Jellyman, D., Ling, N., Ravenscroft, P. and Waters, J. | Reply to Chisholm (2011), Conservation status of New Zealand freshwater fish. | New Zealand Journal of Marine and Freshwater Research 45:303-305. |
Bertels, F. and Rainey, P.B. | Curiosities of REPINs and RAYTs. | Mobile Genetic Elements. 1(4), 1-7. |
Bertels, F. and Rainey, P.B. | Within genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. | PLoS Genetics, 7(6): e1002132. |
Bertels, F. and Rainey, P.B. | Within-Genome Evolution of REPINs: a New Family of Miniature Mobile DNA in Bacteria. | Plos Genetics. June 2011 Vol. 7. Issue 6. E1002132. |
Best, N., Fraser, J.D., Rainey, P.B., Roberts, S.A., Thomas, M.G. and Ritchie, S.R. | Nasal carriage of Staphylococcus aureus in healthy Aucklanders. | The New Zealand Medical Journal 124, 31-39. |
Biggs, P.J., Fearnhead, P., Hotter, G., Mohan, V., Collins-Emerson, J., Kwan, E., Besser, T.E., Cookson, A., Carter, P.E. and French, N.P. | Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage. | PLoS One 6, e27121. |
Bradler, S. and Buckley, T.R. | Stick insect on unsafe ground: Does a fossil from the Early Eocene of France really link Mesozoic taxa to the extant crown group of Phasmatodea? | Systematic Entomology, 36: 218-222. |
Buckley, T.R., James, S., Allwood, J., Bartlam. S., Howitt, R. and Prada, D. | Phylogenetic analysis of New Zealand earthworms (Oligochaeta: Megascolecidae) reveals ancient clades and cryptic taxonomic diversity. | Molecular Phylogenetics and Evolution, 58: 85-96. |
Buckley, T.R., Stringer, I., Gleeson, D., Howitt,R., Attanayake, D., Parish, R., Sherley, G., and Rohan, M. | A revision of the New Zealand Placostylus land snails using mitochondrial DNA and shell morphometric analyses, with implications for conservation. | New Zealand Journal of Zoology, 38: 55-81. |
Burridge, C.P., McDowall, R.M., Craw, D., Wilson, M.V.H. and Waters, J.M. | Marine dispersal as a pre‐requisite for Gondwanan vicariance among elements of the galaxiid fish fauna. | Journal of Biogeography 39:306-321. |
Chapple, D.G., Bell, T.P, Chapple, S.N.J., Miller, K.A., Daugherty, C.H. and Patterson, G.B. | Phylogeography and taxonomic revision of the New Zealand cryptic skink (Oligosoma inconspicuum; Reptilia: Scincidae) species complex. | Zootaxa 2782: 1-33. |
Collins, J., Linz, S. and Semple, C. | Quantifying hybridization in realistic time. | Journal of Computational Biology, 18, 1305–1318. |
Donald, K.M., Keeney, D.B. and Spencer, H.G | Contrasting population makeup of two intertidal gastropod species that differ in dispersal opportunities. | Journal of Experimental Marine Biology and Ecology 396: 224-232 |
Faller, B., Semple, C. and Welsh, D. | Optimizing phylogenetic diversity with ecological constraints. | Annals of Combinatorics, 15, 255–266. |
Garden, C., Craw, D., Waters, J.M. and Smith, A. | Rafting rocks reveal marine biological dispersal: A case study using clasts from beach-cast macroalgal holdfasts. | Estuarine, Coastal and Shelf Science 95:388-394. Journal of Wildlife Diseases 47(1): 126-139. |
Gillespie, R.G., Baldwin, B.G., Waters, J.M., Fraser, C.I., Nikula, R. and Roderick, G.K. | Long-distance dispersal: a framework for hypothesis testing. | Trends in Ecology and Evolution 27:52-61. |
Godfrey, S.S., Nelson, N.J. and Bull, C.M. | Microhabitat choice and host-seeking behaviour of the tuatara tick, Amblyomma sphenodonti (Acari:Ixodidae). | New Zealand Journal of Ecology 35(1): 52-60. |
Godfrey, S.S., Nelson, N.J. and Bull, C.M. | Ecology and dynamics of the blood parasite, Hepatozoon tuatarae (Apicomplexa), in tuatara (Sphenodon punctatus) on Stephens Island. | Journal of Wildlife Diseases 47(1): 126-139. |
Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J. and French, N.P. | Molecular epidemiology and genetic diversity of Campylobacter jejuni in ruminants. | Epidemiol Infect 139, 1661-1671 |
Grueber, C.E., Waters, J.M. and Jamieson, I.G. | The imprecision of heterozygosity-fitness correlations hinders the detection of inbreeding and inbreeding depression in a threatened species. | Molecular Ecology 20:67-79. |
Hartnup, K., Huynen, L., Te Kanawa, R., Shepherd, .LD., Millar, C.D. and Lambert, D.M. | Ancient DNA recovers the origins of Mãori feather cloaks. | Molecular Biology Evolution 28: 2741–2750. |
Heled, J. and Drummond, A.J. | Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation. | Systematic Biology. doi:10.1093/sysbio/syr087 |
Hepworth, P.J., Ashelford, K.E., Hinds, J., Gould, K.A., Witney, A.A., Williams, N.J., Leatherbarrow, H., French, N.P., Birtles, R.J., Mendonca, C., Dorrell, N., Wren, B.W., Wigley, P., Hall, N. and Winstanley, C. | Genomic variations define divergence of water/wildlife-associated Campylobacter jejuni niche specialists from common clonal complexes. | Environ Microbiol 13, 1549-1560. |
Höhna, S. and Drummond, A.J. | Guided Tree Topology Proposals for Bayesian Phylogenetic Inference. | Systematic Biology. doi:10.1093/sysbio/syr074. |
Holder, M.T. and Steel, M. | Estimating phylogenetic trees from pairwise likelihoods and posterior probabilities of substitution counts. | Journal of Theoretical Biology 280: 159-166. |
Jones T.L., Clarke, A.C., Cordero, M-A., Green, R.C., Irwin, G., Klar, K.A., Matisoo-Smith, E.A., Quiroz, D., Ramirez-Aliaga, J.M., Scaglion, R., Storey, A.A. and Weisler, M.I. | Summary and Conclusions. | Chapter 14 in T.L. Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramirez-Aliaga (eds). Polynesians in America: Pre-Columbian Contacts with the New World. Atamira Press. |
Jones, T.L., Storey, A.A., Matisoo-Smith, E.A. and Ramirez-Aliaga, J.M. | Polynesians in America: Pre-Columbian Contacts with the New World. | Atamira Press. |
Kidd, T.J., Ramsay, K.A., Grimwood, K., Rainey, P.B. and Bell, S.C. | Comparison of pulsed-field gel electrophoresis and multi-locus sequence typing of Pseudomonas aeruginosa isolates in cystic fibrosis sputum. | Journal of Clinical Microbiology 49, 263-268. |
Kieser, J.A., He, L-H., Dean, M.C., Jones, M.E.H., Duncan, W.J., Swain, M.V. and Nelson, N.J | Structure and compositional characteristics of caniniform dental enamel in the tuatara Sphenodon punctatus (Lepidosauria: Rhynchocephalia). | New Zealand Dental Journal 107, No. 2: 44-50. |
Knapp, M., Clarke, A., Horsburgh, K.A. and Matisoo-Smith, E. | Setting the Stage: what is needed to build an ancient DNA cleanroom. | Annals of Anatomy, special issue “ancient DNA” doi:10.1016/j.aanat.2011.03.008 |
Kühnert, D., Wu, C.H. and Drummond, A.J. | Phylogenetic and epidemic modeling of rapidly evolving infectious diseases. | Infection Genetics and Evolution. doi:10.1016/j.meegid.2011.08.005. |
Lambert. D., Millar. C., Swaminathan. S. and Baroni. C. | Evolution on a frozen continent. | Printed in Le Scienze 510 February: 80–87, the Italian edition of Scientific American. |
Lee, K., French, N.P., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H. and Kumagai, S. | Multivariate analyses revealed distinctive features differentiating human and cattle isolates of Shiga toxin-producing Escherichia coli O157 in Japan. | J Clin Microbiol 49, 1495-1500. |
Leschen, R.A., Butler, B., Buckley, T.R. and Ritchie. P. | Biogeography of the New Zealand subantarctics: phylogenetics of Pseudhelops (Coleoptera: Tenebrionidae). | New Zealand Entomologist, 43: 12-26. |
Li, W.L.S. and Drummond, A.J. | Model averaging and Bayes factor calculation of relaxed molecular clocks in Bayesian phylogenetics. | Molecular Biology and Evolution. doi:10.1093/molbev/msr232 |
Libby, E. and Rainey, P.B. | Exclusion rules, population bottlenecks, and the evolution of stochastic switching. | Proceedings of the Royal Society (London) B 278, 3574-3583. doi:10.1098/rspb.2011.0146. |
Linz, S. and Semple, C. | A cluster reduction for computing the subtree distance between phylogenies. | Annals of Combinatorics, 15, 465–484. |
Marske, K.A., Leschen, R.A.B. and Buckley, T.R. | Reconciling phylogeography and ecological niche models for New Zealand beetles: Looking beyond glacial refugia. | Molecular Phylogenetics and Evolution, 59: 89-102. |
Matisoo-Smith, E.A. | Human Biological Evidence for Polynesian Contacts with the Americas – Finding maui on mocha? | Chapter 11 in T.L. Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramirez-Aliaga (eds). Polynesians in American: Pre-Columbian Contacts with the New World. Atamira Press |
McDonald, M.J., Cooper, T.F., Beaumont, H.J.E. and Rainey, P.B. | The distribution of fitness effects of new mutations in Pseudomonas fluorescens. | Biology Letters. 7, 98-100. |
Millar, C.D., Waugh, J. and Lambert, D.M. | Are BOLD searches scientific? A response to Federhen. | Molecular Ecology Resources 11: 939–940. |
Miller, H.C., Bowker-Wright, G., Kharkang, M. and Ramstad, K. | Characterisation of class II B MHC genes from a ratite bird, the little spotted kiwi (Apteryx owenii). | Immunogenetics 63: 223-233. |
Miller, K.A., Towns, D.R., Allendorf, F.W., Ritchie, P.A. and Nelson, N.J. | Genetic structure and individual performance following a recent founding event in a small lizard. | Conservation Genetics 12: 461-473. |
Minh, P., Stevenson, M., Jewell, C., French, N. and Schauer, B., | Spatio-temporal analyses of highly pathogenic avian influenza H5N1 outbreaks in the Mekong River Delta, Vietnam, 2009. | Spatial and Spatio-temporal Epidemiology 2, 49-57. |
Mirzai, M., Pascovici, D., Keighley, T., George, I., Voelckel, C., Heenan, P.B. and Haynes, P.A. | Shotgun proteomic profiling of five species of New Zealand Pachycladon. | Proteomics 11:166-171. |
Mooers, A., Gascuel, O., Stadler, T., Li, H. and Steel, M. | Branch lengths on Yule trees and the expected loss of phylogenetic diversity. | Systematic Biology 61(2): 195-203 |
Moulton, V. and Steel, M. | The 'Butterfly effect' in Cayley graphs, and its relevance to evolutionary genomics. | Journal of Mathematical Biology (in press) |
Muellner, P., Marshall, J.C., Spencer, S.E., Noble, A.D., Shadbolt, T., Collins-Emerson, J.M., Midwinter, A.C., Carter, P.E., Pirie, R., Wilson, D.J., Campbell, D.M., Stevenson, M.A. and French, N.P. | Utilizing a combination of molecular and spatial tools to assess the effect of a public health intervention. | Prev Vet Med 102, 242-253. |
Muellner, P., Zadoks, R., Perez, A., Spencer, S., Schukken, Y. and French, N. | The integration of molecular tools into veterinary and spatial epidemiology. | Spatial and Spatio-temporal Epidemiology 2, 173-183. |
Nielsen, S.V., Bauer, A.M., Jackman, T.R., Hitchmough, R.A. and Daugherty, C.H. | New Zealand geckos (Diplodactylidae): Cryptic diversity in a post-Gondwanan lineage with trans-Tasman affinities. | Molecular Phylogenetics and Evolution 59: 1-22. |
Nikula, R., Spencer, H.G. and Waters, J.M. | Evolutionary consequences of microhabitat: population-genetic structuring in kelp- versus rock-associated chitons. | Molecular Ecology 20:4915-4924. |
Nikula, R., Spencer, H.G. and Waters, J.M. | Comparison of population-genetic structuring in congeneric kelp- versus rock-associated snails: a test of a dispersal-by-rafting hypothesis. | Ecology and Evolution 1:169-180. |
Patel, S. and Millar, C. | A rapid DNA extraction method for avian blood samples. | ZyGEM Application Note Z01074. |
Prost, S. and Anderson, C.N.K. | TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data. | Methods in Ecology and Evolution, 2011 British Ecological Society. doi: 10.1111/j.2041-210X.2011.00129.x |
Rainey, P.B., Beaumont, H.J.E., Ferguson, G.C., Gallie, J., Kost, C., Libby, E. and Zhang, X-X. | The evolutionary emergence of stochastic phenotype switching. | BMC Microbial Cell Factories 10(Suppl 1):S14. |
Ritchie, S.R., Fraser, J.D., Libby, E., Morris, A.J., Rainey, P.B. and Thomas, M.G. | Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand. | The New Zealand Medical Journal 124, 21-30. |
Rose, C.J., Chapman, J.R., Marshall, S. G., Lee. S,F., Batterman, P., Ross, H.A. and Newcomb, R.D. | Selective Sweeps at the Organophosphorus Insecticide Resistance Locus, Rop-1, Have Affected Variation across and beyond the alpha-Esterase Gene Cluster in the Australian Sheep Blowfly, Lucilia cuprina. | Mol. Biol. Evol. 28:1835-1846. |
Sanderson, M.J., McMahon, M.M. and Steel, M. | Terraces in phylogenetic tree space. | Science 333: 448-450. |
Santure, A.W. and Spencer, H.G. | Quantitative Genetics of Genomic Imprinting: A Comparison of Simple Variance Derivations, the Effects of Inbreeding, and Response to Selection G3 Genes. | Genomes,Genetics. 131-142. |
Sears, A., Baker, M.G., Wilson, N., Marshall, J., Muellner, P., Campbell, D.M., Lake, R.J. and French, N.P. | Marked campylobacteriosis decline after interventions aimed at poultry, new zealand. | Emerg Infect Dis 17, 1007-1015. |
Shapiro, B., Ho, S. Y. W., Drummond, A.J., et al. | A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages. | Molecular Biology and Evolution 28:879-887. |
Spencer, S., Marshall, J., Pirie, R., Campbell, D. and French, N. | The detection of spatially localised outbreaks in campylobacteriosis notification data. | Spatial and Spatio-temporal Epidemiology 2, 159-171. |
Spencer, S., Marshall, J., Pirie, R., Campbell, D. and French, N. | The detection of spatially localised outbreaks in campylobacteriosis notification data. | Spatial and Spatio-temporal Epidemiology 2, 159-171. |
Stadler, T., Kouyos, R., Von Wyl, V., Yerly, S., Böni, J., Bürgisser, P., Klimkait, T., Joos, B., Rieder, P., Xie, D., Günthard, H., Drummond, A.J., Bonhoeffer, S. & The Swiss HIV Cohort Study. | Estimating the basic reproductive number from viral sequence data. | Mol Biol Evol. doi:10.1093/molbev/msr217 |
Steel, M. | Can we avoid 'SIN' in the House of 'No Common Mechanism'? | Systematic Biology 60(1): 96-109. |
Steel, M. | Can maths help us glimpse the future? | NZ Science Teacher 126: 6-7 (non-peer reviewed) |
Storey, A.A., Clarke, A.C. and Matisoo-Smith, E. | Identifying Contact with the Americas: A Commensal-Based Approach. | Chapter 7 in T.L.Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramirez-Aliaga (eds). Polynesians in American: Pre-Columbian Contacts with the New World. Atamira Press |
Storey, A.A., Quiroz. D. and Matisoo-Smith, E. | A Reappraisal of the Evidence for Pre-Columbian Introduction of Chickens to the Americas. | Chapter 8 in T.L.Jones, A.A. Storey, E.A. Matisoo-Smith and J.M. Ramirez-Aliaga (eds). Polynesians in American: Pre-Columbian Contacts with the New World. Atamira Press |
Tooman, L.K., Rose, C.J., Carraher, C., Suckling, D.M., Paquette, S., Ledezma, L.A., Gilligan, T.M., Epstein, M., Barr, N.B. and Newcomb, R.D. | Patterns of Mitochondrial Haplotype Diversity in the Invasive Pest Epiphyas postvittana (Lepidoptera: Tortricidae). | Journal of Economic Entomology 104: 920-932. |
Waters, J.M. | Competitive exclusion: phylogeography’s ‘elephant in the room’? | Molecular Ecology 20:4388-4394. |
Waugh, J., Evans, M.W., Millar, C.D. and Lambert, D.M. | Birdstrikes and barcoding: can DNA methods help make the airways safer? | Molecular Ecology Resources 11: 38–45. |
Williams, N.J., Sherlock, C., Jones, T.R., Clough, H.E., Telfer, S.E., Begon, M., French, N., Hart, C.A. and Bennett, M. | The prevalence of antimicrobial-resistant Escherichia coli in sympatric wild rodents varies by season and host. | J Appl Microbiol 110, 962-970. |
Wu, C-H. and Drummond, A.J. | Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo. | Genetics 188:151-U254 |
Yogeeswaran, K., Voeckel, C., Joly, S. and Heenan, P.B. | Pachycladon. In Wild Crop Relatives: Genomic and Breeding Resources. | Vol 3: Wild Relatives of Oilseeds (ed. Kole) Springer-Verlag, Tokyo pp. 227-249. |
Zhong, B., Deusch, O., Goremykin, V.V., Penny, D., Biggs, P.J., Atherton, R.A., Nikiforova, S.V. and Lockhart, P.J. | Systematic Error in Seed Plant Phylogenomics. | Genome Biol. Evol. 3:1340-1348. Doi10: 1093/gbe/evr105 |
Zhu, S., Degnan, J.H. and Steel, M. | Clades clans and reciprocal monophyly under neutral evolutionary models. | Theoretical Population Biology 79: 220-227. |