Research Publications

2011 Publication list




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.