Research Publications

2012 Publication list




Abdelkrim, J., Hunt, G.R., Gray, R.D. and Gemmell, N.J. Fine-scale population structure and maintenance of local behaviours in New Caledonian crows. PLoS ONE 7(5): e36608.
Albre, J., Liénard, M., Sirey, T., Schmidt, S., Tooman, L., Carraher, C., Greenwood, D.R., Löfstedt, C., and Newcomb, R.D Sex pheromone evolution in leafroller moths by differential regulation of a desaturase gene.  PLoS Genetics 8: e1002489.
Anderson-Lederer, R.M., Linklater, W.L. and Ritchie, P.A.  Limited mitochondrial DNA variation within South Africa’s black rhino (Diceros bicornis minor) population and implications for management.  African Journal of Ecology doi: 10.1111/j.1365-2028.2012.01333.x
Besson, A.A., Nelson, N.J., Nottingham, C.M. and Cree, A. Is cool egg incubation temperature a limiting factor for the translocation of tuatara to southern New Zealand?  New Zealand Journal of Ecology 36(1): 90-99. 
Bordewich, M., Semple, C. Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems.  Journal of Mathematical Biology, 64, 69-85.
Bryant, D. and Steel, M.  Bureaucratic' set systems, and their role in phylogenetics. Applied Mathematics Letters 25: 1148-1152.
Carreher, C., Authier, A., Steinwender, S. and Newcomb, R.D.  Sequence comparisons of odorant receptors among tortricid moths reveal different rates of molecular evolution among family members.  PLoS One 7: e38391.
Chapple, D.G., Birkett, A., Miller, K.A., Daugherty, C.H. and Gleeson, D.M Phylogeography of the endangered Otago skink, Oligosoma otagense: population structure, hybridisation and genetic diversity in captive populations.   PLoS One 7(4):e34599. 
Cheeseman J.F., Winnebeck E.C., Millar C.D., Kirkland L.S., Sleigh J., Goodwin M., Pawley M.D.M., Bloch G., Lehmann K., Menzel R., and Warman G.R. General anesthesia alters time-perception by phase shifting the circadian clock.  Proceedings of the National Academy of Science 109: 7061–7066.
Collins, J., Linz, S., and Semple, C. Quantifying hybridization in realistic time.  Journal of Computational Biology, 18, 1305–1318.
Donald, K.M., Preston, J., Williams, S.T., Reid, D.G., Winter, D., Alvarez, R., Buge, B., Hawkins, S.J., Templado, J., and Spencer, H.G Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea.   Molecular Phylogenetics and Evolution. 62 (2012) 35-45.
Dress, A.W.M., Huber, K.T. and Steel, M.  'Lassoing' a phylogenetic tree I: Basic properties, shellings, and covers.  Journal of Mathematical Biology 65(1): 77-105.
Faller, B. and Steel, M.  Trait-dependent extinction leads to greater expected biodiversity loss. SIAM Journal on Discrete Mathematics 26(2): 472-482.
Faller, B., Semple, C., and Welsh, D. Optimizing phylogenetic diversity with ecological constraints.  Annals of Combinatorics, 15, 255–266.
Fouquet, A., Noonan, B.P., Rodrigues, M.T., Pech, N., Gilles, A., Gemmell, N.J. Multiple Quaternary refugia in the Eastern Guiana Shield revealed by comparative phylogeography of 12 Frogs Species.  Systematic Biology 61:461-489.
Fraser, C.I., Spencer, H.G. and Waters, J.M. Durvillaea poha sp. nov. (Fucales, Phaeophyceae): a buoyant southern bull-kelp species endemic to New Zealand.  Phycologia (2012) Volume 51 (2), 151-156.
Geoghegan, J.L., and Spencer, H.G. Population-epigenetic models of selection.  Theoretical Population Biology 81 (2012) 232-242.
Gerth, M. L., Ferla, M. P. and Rainey, P. B.  The origin and ecological significance of multiple branches for histidine utilisation in Pseudomonas aeruginosa PAO1.  Environmental Microbiology. DOI: 10.1111/j.1462-2920.2011.02691.x.
Gruber, M.A.M., Hoffmann, B.D., Ritchie, P.A. and Lester, P.J Recent behavioural and population genetic divergence of an invasive ant in a novel environment.  Diversity and Distributions 18: 323-333.
Harlow. G.E., Summerhayes. G.R., Davies. H.L. and Matisoo-Smith. L. A jade gouge from Emirau Island, Papua New Guinea (Ealy Lapita context, 3300 BP); a unique jadeitite.  European Journal of Mineralogy 24:391-399.
Hegg, D., Greaves, G., Maxwell, J.M., MacKenzie, D.I., and Jamieson, I.G. Demography of takahe (Porphyrio hochstetteri) in Fiordland: environmental factors and management affect survival and breeding success.  NZ Journal of Ecology 36(1):75-89 
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. 
Irshad, H., Cookson, A., Hotter, G., Besser, T., On, S., and French, N.  Epidemiology of Shiga toxin-producing Escherichia coli O157 in very young calves in the North Island of New Zealand, NZ.  Vet J 60, 21-26.
Jamieson, I.G and Lacy, R.C. Managing genetic issues in reintroduction biology In Reintroduction Biology: Integrating Science and Management. First Edition. Edited by John G. Ewen, Doug P. Armstrong, Kevin A. Parker and Philip J. Seddon. Blackwell Publishing Ltd., Oxford, UK. [ISBN: 978-1-4051-8674-2]
Johnson, S. L., and Gemmell, N. J Are old males still good males and can females tell the difference?  BioEssays. First published online: 11 May 2012. DOI: 10.1002/bies.201100157
Jones, G., Johnson, W.O., Vink, W.D., and French, N.  A Framework for the Joint Modeling of Longitudinal Diagnostic Outcome Data and Latent Infection Status: Application to Investigating the Temporal Relationship between Infection and Disease.  Biometrics.
Kidd, T. J., Ritchie, S. R., Ramsay, K. A., Grimwood, K., Bell, S. C. and Rainey, P. B.  Genetic structure of clinical and environmental Pseudomonas aeruginosa reveals a freely recombining population and a lack of correspondence between genotype and source.   PLoS One, in press.
Lal, A., Baker, M.G., French, N.P., Dufour, M., and Hales, S. The epidemiology of human salmonellosis in New Zealand, 1997-2008.  Epidemiol Infect, 1-10.
Lal, A., Baker, M.G., French, N.P., Dufour, M., and Hales, S. The epidemiology of human salmonellosis in New Zealand, 1997-2008.  Epidemiol Infect, 1-10.
Lee, K., French, N.P., Jones, G., Hara-Kudo, Y., Iyoda, S., Kobayashi, H., Sugita-Konishi, Y., Tsubone, H., and Kumagai, S.  Variation in stress-resistance patterns among stx genotypes and genetic lineages in Shiga toxin-producing Escherichia coli O157.  Applied and Environmental Microbiology in press, available on-line.
Ludin N.M., Rescan M., Cheeseman J.F., Millar C.D., and Warman G.R A honey bee (Apis mellifera) light phase response curve.  Chronobiology International 29: 523–526.
Marske, K.A.,  Leschen, R.A.B. and. Buckley. T.R. Concerted versus independent evolution and the search for multiple refugia: comparative phylogeography of four forest beetles.  Evolution, 66: 1862-1877.
Matisoo-Smith, E. and Daugherty, C. The longest journey: Africa to Aotearoa.  Journal of the Royal Society of New Zealand 42(2):87-92.
Newcomb, R.D., Xia, M. and Reed, D.R.  Heritable differences in chemosensory ability among humans. Flavour 1: 9.
Pleydell, E., Souphavanh, K., Hill, K., French, N., and Prattley, D.  Descriptive epidemiological study of the use of antimicrobial drugs by companion animal veterinarians in New Zealand.  New Zealand Veterinary Journal.
Ramstad, K.M., Moore, J.A. and Refsnider, J.M.   Intrasexual aggression in tuatara: males and females respond differently to same-sex intruders.  Herpetological Review 43(1): 19-21.
Redondo-Niece, M., Barret, M., Morrisey, J., Germaine, K., Martinez-Garner, F., Brahman, E., Navazo, A., Sanchez-Contraries, M., Moynihan, J. A., Giddens, S. R., Coppoolse, E. R., Muriel, C., Stiekema, W. J., Rainey, P. B., Dowling, D., O’Hare, F., Martin, M. and Rival, R Genome sequence of the biocontrol strain Pseudomonas fluorescens F113. Journal of Bacteriology. 194, 1273-1274. DOI: 10.1128/ JB.06601-11
Sawaya, S.M., Lennon, D., Buschiazzo, E., Gemmell, N., and Minin, V,N. Minin Measuring microsatellite conservation in mammalian evolution with a phylogenetic birth-death model. Genome Biology and Evolution First published online: 16 May 2012, DOI: 10.1093/gbe/evs050.
Sebastien, A., Gruber, M.A.M. and Lester, P.J.  Prevalence and genetic diversity of three bacterial endosymbionts (Wolbachia, Arsenophonus, and Rhizobiales) associated with the invasive yellow crazy ant (Anoplolepis gracilipes). Insectes Sociaux 59(1): 33-40
Spencer, S.E., Marshall, J., Pirie, R., Campbell, D., Baker, M.G., and French, N.P. The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001-2007.  Epidemiol Infect, 1-15.
Stadler, T. and Steel, M.  Distribution of branch lengths and phylogenetic diversity under homogeneous speciation models.  Journal of Theoretical Biology. 297: 33-40.
Willner, D., Haynes, M. R., Furlan, M., Hanson, N., Kirby, B., Lim, Y.-W., Rainey, P. B., Schmieder, R., Yule, M., Conrad, D. and Rohwer, F. Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung.  American Journal of Respiratory Cell and Molecular Biology. 46, 127-131. doi:10.1165/2011-0253OC.
Willner, D., Haynes, M. R., Furlan, M., Schmieder, R., Lim, J.-W., Rainey, P. B., Rohwer, F. and Conrad, D.  Spatial distribution of microbial communities in the cystic fibrosis lung.  ISME Journal. 6, 471-474. doi:10.1038/ismej.2011.104.
Yu, S., Fearnhead, P., Holland, B., Biggs, P., Maiden, M., and French, N.  Estimating the relative roles of recombination and point mutation to the generation of single locus variants in Campylobacter jejuni and Campylobacter coliEstimating the relative roles of recombination and point mutation to the generation of single locus variants in Campylobacter jejuni and Campylobacter coli. Journal of Molecular Evolution in press.
Zhao, Z. Li, D.  and Buckley. T.R. Analysis of primary structure of Hairpin 35 and 48 loops of SSU rRNA gene of Nematoda: further evidence that the genera Tripylina Brzeski, 1963, Trischistoma Cobb, 1913 and Rhabdolaimus de Man, 1880 are members of Enoplida.   Zootaxa, 3208: 41-57.
Zhang, X.-X., Chang, H., Tran, S., L., Gauntlett, J. C., Cook, G. M. and Rainey, P. B.   Variation in transporter genes explains polymorphism of histidine and urocanate utilisation in natural populations of Pseudomonas.  Environ Microbiol. (8):1941-51.