Research Publications

2010 Publication list




Addison, D.J. and Matisoo-Smith, E. Rethinking Polynesians origins: a West-Polynesia Triple-I Model. Archaeology in Oceania, 45, 1-12.
Allibone, R., David, B., Hitchmough, R., Jellyman, D., Ling, N., Ravsenscroft, P. and Waters, J. Conservation status of New Zealand freshwater fish. Journal of Marine and Freshwater Research doi: 10.1080/00288330.2010.514346.
Allwood, J.,  Gleeson, D.M., Mayer,G.,  Daniels, S., Beggs, J.   and  Buckley, T.R. Support for vicariant origins of the New Zealand Onychophora. Journal of Biogeography, 37: 669–681.
Benschop, J., Spencer, S., Alban, L., Stevenson, M., and French, N.  Bayesian zero-inflated predictive modelling of herd-level Salmonella prevalence for risk-based surveillance.  Zoonoses Public Health 57 Suppl 1, 60-70.
Boessenkool, S., Star, B., Scofield, R.P., Seddon, P.J., and Waters, J.M.   Lost in translation or deliberate falsification? Genetic analyses reveal erroneous museum data for historic penguin specimens. Proceedings of the Royal Society B 277:1057-1064.
Boessenkool, S., Star, B., Seddon, P.J., and Waters, J.M.    Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin. Conservation Genetics 11:539-546.
Bredeweg, E.M. and Nelson, N.J.   Sphenodon punctatus (Tuatara). Frugivory. Herpetological Review 41(2): 211-212.
Buckley, T.R., and Bradler, S. Tepakiphasma ngatikuri, a new genus and species of stick insect (Phasmatodea) from the Far North of New Zealand. New Zealand Entomologist, 33: 118-126.
Buckley, T.R., Attanayake, D., Nylander, J.A.A., and Bradler, S.  The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea). Systematic Entomology. 35:207–225.
Buckley, T.R., Marske, K., and Attanayake, D.  Phylogeography and ecological niche modelling of the New Zealand stick insect Clitarchus hookeri (White) support survival in multiple coastal refugia. Journal of Biogeography, 37: 682–695.
Collins, C.J., Fraser, C.I., Ashcroft, A., and Waters, J.M. Asymmetric dispersal of southern bull-kelp (Durvillaea antarctica) adults in coastal New Zealand: testing an oceanographic hypothesis. Molecular Ecology 19:4572-4580.
Crow, S.K., Closs, G.P., Waters, J.M., Booker, D.J., and Wallis, G.P. Niche partitioning and the effect of interspecific competition on microhabitat use by two sympatric galaxiid stream fishes. Freshwater Biology 55:967-982. 
Dagan, T, Roettger, M. Bryant, D. and Martin, W.   Genome network roots the tree of life between prokaryotic domains. Genome Biology and Evolution. 2:379-392.
Di-Poi, N., Montoya-Burgos, J.I., Miller, H.C., Pourquie, O., Milinkovitch, M.C. and  Duboule, D. Changes in Hox genes' structure and function during the evolution of the squamate body plan.   Nature, 464, 99-103.
Dress, A.W.M., Moulton, V., Steel, M. and Wu, T.  Species, clusters and the `Tree of Life': A graph-theoretic perspective. Journal of Theoretical Biology 265(4): 535-542.
Drummond, A.J. and Suchard, M.A. Bayesian random local clocks, or one rate to rule them all. BMC Biology 8:114. doi:10.1186/1741-7007-8-114
Fraser, C.I., Nikula, R., and Waters, J.M.  Oceanic rafting of a coastal community. Proceedings of the Royal Society B doi: 10.1098/rspb.2010.1117.
Fraser, C.I., Thiel, M., Spencer, H.G., and  Waters, J.M. Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp.  BMC Evolutionary Biology 10: 203.
Fraser, C.I., Winter, D.J., Spencer, H.G., and Waters, J.M. Multigene phylogeny of the southern bull-kelp genus   Durvillaea (Phaeophyceae: Fucales). Molecular Phylogenetics and Evolution 57:1301-1311.
Gascuel, O. and Steel, M.  Inferring ancestral sequences in taxon-rich phylogenies. Mathematical Biosciences, 227: 125-135.
Godfrey, S.S., Moore, J.A., Nelson, N.J. and Bull, C.M.  Social network structure and parasite infection patterns in a territorial reptile, the tuatara (Sphenodon punctatus). International Journal for Parasitology 40: 1575-1585. doi:10.1016/j.ijpara.2010.06.002
Gray, R.D., Greenhill, S.J., and Bryant, D.  On the shape and fabric of human history. Philosophical Transactions of The Royal Society London 365:3923-3933.
Grove-White, D.H., Leatherbarrow, A.J., Cripps, P.J., Diggle, P.J., and French, N.P. Temporal and farm-management-associated variation in the faecal-pat prevalence of Campylobacter jejuni in ruminants. Epidemiol Infect 138, 549-558.
Grove-White, D.H., Leatherbarrow, A.J.H., Cripps, P.J., Diggle, P.J. and French N.P. Temporal and farm management associated variation in the faecal pat prevalence of Campylobacter jejuni in ruminants in three zones in Lancashire. Epidemiol Infect, 2010 138:549-558.
Grueber, C.E., Waters, J.M., and Jamieson,  I.G.  The imprecision of heterozygosity-fitness correlations hinders the detection inbreeding and inbreeding depression in a threatened species. Molecular Ecology 20:67-79.
Hare, K.M. and Miller, K.A.   Frequency of tail loss does not reflect innate predisposition in temperate New Zealand lizards. Naturwissenschaften 97: 197-203.   DOI 10.1007/s00114-00009-00628-00114.
Hare, K.M., Pledger, S., Thompson, M.B., Miller, J.H. and Daugherty, C.H.   Nocturnal lizards from a cool-temperate environment have high metabolic rates at low temperatures.  Journal of Comparative Physiology B 180: 1173-1181.
Hay, J.M., Sarre, S.D., Lambert, D.M., Allendorf, F.W. and Daugherty, C.H.   Genetic diversity and taxonomy: a reassessment of species designation in tuatara (Sphenodon: Reptilia).   Conservation Genetics 11: 1063-1081.
Herrel, A., Moore, J.A., Bredeweg, E.M. and Nelson, N.J.  Sexual dimorphism, body size, bite force, and male mating success in tuatara.  Biological Journal of the Linnean Society 100: 287-292.
Holland, B.A., Spencer, H.G., Worthy, T.H., and Kennedy, M.   Identifying cliques of convergent characters: concerted evolution in the cormorants and shags.  Systematic Biology 59: 433-445.
Hordijk, W., Hein, J. and Steel, M.  Autocatalytic Sets and the Origin of Life. Entropy 12(7): 1733-1744.
Hotter, G.S., Li I.H. and French N.P. Binary genomotyping using lipooligosaccharide biosynthesis genes distinguishes between Campylobacter jejuni isolates within poultry-associated multilocus sequence type.  Epidemiol Infect, 2010 138:992-1003.
Huynen, L., Gill, B.J., Millar, C.D. and Lambert,  D.M.  Exogenous ancient DNA unscrambles eggs from New Zealand’s extinct moa. Proceedings of the National Academy of Science 107: 16201-16206.
Igic, B., Leuschner, N., Parker, K.A., Ismar,  S.M.H., Gill, B.J., Lovegrove, T.G., Millar,  C.D., and Hauber,  M.E. Size dimorphism and avian-perceived sexual dichromatism in a New Zealand endemic bird, the whitehead (Mohoua albicilla). Journal of Morphology 271: 697–704.
Ingram, T. and Steel, M.  Modelling the unpredictability of biodiversity in ecological networks. Journal of Theoretical Biology 264: 1047-1056.
Ismar, S.M.H., Baird, K., Patel, S., Millar, C.D., and Hauber, M.E. Morphology of the recently re–classified masked booby (Sula dactylatra tasmani) breeding on the Kermadec Islands. Marine Ornithology 38:105–109.
John, K., Fitzpatrick, J., French, N., Kazwala, R., Kambarage, D.,  Mfinanga, G.S., MacMillan, A.  and Cleaveland, S. Quantifying risk factors for human brucellosis in rural northern Tanzania. PLoS One 2010 5:e9968.
Keall, S.N., Nelson, N.J. and Daugherty, C.H.  Securing the future of threatened tuatara populations with artificial incubation.   Herpetological Conservation and Biology 5(3): 555-562.
Knapp, M. and Hofreiter, M. (2010.  Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes, 1, 227-243.
Knapp, M.; Finstermeier, K.; Horn, S.;Stiller, M.; Hofreiter, M.   Neue PCR-Technologien für alte DNA Biospektrum 05.10, 531-535.
Knight, C. G., Zhang, X.-X., Gunn, A., Brenner, T., Jackson, R. W., Giddens, S. R., Sripardi, P., Zitzmann, N. and Rainey, P. B.  Testing temperature induced proteomic changes in the plant associated bacterium Pseudomonas fluorescens SBW25.  Environmental Microbiology Reports 2, 396-402.
La Flamme, A.C., de Thierry, D., O'Neill, S., and Miller, H.C.  Toll-like receptor responses in tuatara. New Zealand Journal of Zoology, 37: 235-242.
Lambert, D., Millar, C., Swaminathan, S., and Baroni, C.  Evolution on a frozen continent. American Scientist 98: 386–393.
Linz, S., Semple, C., and Stadler, T.  Analyzing and reconstructing reticulation networks under timing constraints. Journal of Mathematical Biology, 61, 715–737.
Lockhart, C. Y., Stevenson, M.A., Rawdon, T.G., Gerber, N., and French, N.P. Patterns of contact within the New Zealand poultry industry. Prev Vet Med 2010 95:258-266.
Magnuson-Ford, K., Mooers, A., Rioux Paquette, S., and Steel, M.  Comparing strategies to preserve evolutionary diversity. Journal of Theoretical Biology 266(1): 107-116.
Masters, B. C., Fan, V., and Ross, H.A.  Species Delimitation - a Geneious plugin for the exploration of species boundaries. Molecular Ecology Resources 11:154-157.
Matisoo-Smith, E. and Ramirez, J-M.  Human skeletal evidence of Polynesian presence in South America? Metric analyses of six crania from Mocha Island. Chile. Journal of Pacific Archaeology, 1, 1, 76-88.
McCulloch, G.A., Wallis, G.P., and Waters, J.M.  Onset of glaciation drove simultaneous vicariant isolation of alpine insects in New Zealand. Evolution 64:2033-2043.
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. doi: 10.1098/rsbl.(2010).0547.
Mihaescu, R. and Steel, M.  Logarithmic bounds on the posterior divergence time of two sequences.  Applied Mathematics Letters 23: 975-979.
Miller, H.C., Allendorf, F.W., and Daugherty, C.H.  Genetic diversity and differentiation at MHC genes in island populations of tuatara (Sphenodon spp.). Molecular Ecology, 19: 3894-3908. DOI: 10.1111/j.1365-294X.2010.04771.x
Miller K.A., Hare, K.M., and Nelson, N.J. Do alternate escape tactics provide a means of compensation for impaired performance ability?   Biological Journal of the Linnean Society 99: 241-249.
Miller, K.A., Gruber, M.A.M., Keall, S.N., Blanchard, B. and Nelson, N.J.  Changing taxonomy and the need for supplementation in the management of re-introductions of Brothers Island tuatara in Cook Strait, New Zealand.  In Global Re-introduction Perspectives: Additional case studies from around the globe. Soorae, P.S. (ed.). IUCN/SSC Re-introduction Specialist Group, Abu Dhabi, UAE, pp. 93-97.
Mitchell, N.J., Allendorf, F.W.,  Keall, S.N., Daugherty, C.H., and Nelson, N.J.   Demographic effects of temperature-dependent sex determination: will tuatara survive global warming?   Global Change Biology 16: 60-72. doi: 10.1111/j.1365-2486.2009.01964.x
Moore, J.A., Grant, T., Brown, D., Keall, S.N. and Nelson, N.J.  Mark-recapture accurately estimates census for tuatara, a burrowing reptile.   Journal of Wildlife Management 74(4): 897-901.
Morgan-Richards, M., Trewick,S.A.,  and Stringer, I.A.N.  Geographic parthenogenesis and the common tea-tree stick insect of New Zealand.  Molecular Ecology 19:1227-1238. doi: 10.1111/j.1365-294X.(2010).04542.x
Mullner, P., Collins-Emerson, J.M., Midwinter, A.C, Carter, P., Spencer, S.E.F., van der Logt, P., Hathaway, S. and French, N.P. Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry. Appl Environ Microbiol, 2010 76:2145-2154.
Mullner, P., Collins-Emerson, J.M., Midwinter, A.C., Carter, P., Spencer, S.E., van der Logt, P., Hathaway, S., and French, N.P.  Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.  Microbiol 76, 2145-2154.
Mullner, P., Shadbolt, T., Collins-Emerson, J.M., Midwinter, A.C., Spencer, S., Marshall, J., Carter, P.,  Campbell, D., Wilson, D.J., Hathaway, S., Pirie, R., and French, N.P. Molecular and spatial epidemiology of human campylobacteriosis - source association and genotype-related risk factors. Epidemiol Infect 2010 138:1372-1383.  
Mullner, P., Shadbolt, T., Collins-Emerson, J.M., Midwinter, A.C., Spencer, S.E., Marshall, J., Carter, P.E., Campbell, D.M., Wilson, D.J., Hathaway, S., Pirie, R., and French, N.P.  Molecular and spatial epidemiology of human campylobacteriosis: source association and genotype-related risk factors.  Epidemiol Infect 138, 1372-1383.
Nelson, N.J., Moore, J.A., Pillai, S. and Keall, S.N.  Thermosensitive period for sex determination in the tuatara. Herpetological Conservation and Biology 5(2): 324-329.
Nikula, R., Fraser, C.I.,  Spencer, H.G., and Waters, J.M.    Circumpolar dispersal by rafting in two subantarctic kelp-dwelling crustaceans.  Marine Ecology Progress Series 405: 221-230.
O'Meally, D., Miller, H.C., Patel, H.R., Marshall Graves, J.A., and Ezaz, T.   The first cytogenetic map of the tuatara. Sphenodon punctatus. Cytogenetics and Genome Research 127: 213-223 (DOI: 10.1159/000300099) (This issue actually came out in April 2010, but the journal has it listed as 2009).
Patel, S., Waugh, J., Millar, C.D., and Lambert, D.M.  Conserved primers for DNA barcoding historical and modern avian samples. Molecular Ecology Resources 10:431–438.
Patterson, I.P., Baillie, S.M., Brunton, D.H., Ritchie, P.A. and Benton, P.  Twelve new microsatellite loci for the Korimako (New Zealand bellbird), Anthornis melanura. Conservation Genetics Resources 2: 257-259.
Phillips, M.J., G.C. Gibb, E.A. Crimp, and D. Penny.  Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight Among Ratites. Systematic Biology 59:90-107. doi:10.1093/sysbio/syp079.
Phiri, B.J.,, Benschop,  J. and French, N.P.   Systematic review of causes and factors associated with morbidity and mortality on smallholder dairy farms in Eastern and Southern Africa. Prev Vet Med, 2010  94:1-8.  
Pleydell, E. J., L. Rogers, E. Kwan, and French, N.P. Low levels of antibacterial drug resistance expressed by Gram-negative bacteria isolated from poultry carcasses in New Zealand.  N Z Vet J 2010 58:229-236.
Pleydell, E., Rogers, L., Kwan, E., and French, N.  Evidence for the clustering of antibacterial resistance phenotypes of enterococci within integrated poultry companies.  Microb Ecol 59, 678-688.
Pleydell, E.J., Rogers, L., Kwan, E., and French, N.P.  Low levels of antibacterial drug resistance expressed by Gram-negative bacteria isolated from poultry carcasses in New Zealand, NZ. Vet J 58, 229-236.
Prost, S., Knapp, M., Flemming, J., Hufthammer, A.K., Kosintev, P., Stiller, M., and Hofreiter, M.  A phantom extinction? New insights into extinction dynamics of the Don-hare Lepus tanaiticus. Journal of Evolutionary Biology (early online: doi:10.1111/j.1420-9101.2010.02062.x)
Prost, S., Smirnov, N., Fedorov, V. B., Sommer, R. S., Stiller, M., Nagel, D., Knapp, M., and Hofreiter, M.   Influence of Climate Warming on Arctic Mammals? New Insights from Ancient DNA. Studies of the Collared Lemming Dicrostonyx torquatus. PLoS ONE 5, e10447.
Rainey, P.B. and Kerr, B.  Conflicts among levels of selection as fuel for the evolution of individuality.  In The Major Transitions Revisited: The Evolution of Individuality. (eds Calcott, B. & Sterelny K.).  The Vienna Series in Theoretical Biology, MIT Press, 
Rainey, P.B. and Kerr, B.   Cheats as first propagules: A new hypothesis for the evolution of individuality during the transition from single cells to multicellularity. BioEssays, doi: 10.1002/bies. 2010 00039.
Ramstad, K.M.,  Woody, C.A. and Allendorf, F.W. Recent local adaptation of sockeye salmon to glacial spawning habitats. Evolutionary Ecology 24:391-411.
Ramstad, K.M., Pfunder, M., Robertson, H.A., Colbourne, R.M., Allendorf, F.W. and Daugherty, C.H.  Fourteen microsatellite loci cross-amplify in all five kiwi species (Apteryx spp.) and reveal extremely low genetic variation in little spotted kiwi (A. owenii). Conservation Genetics Resources 2: 333-336.  doi:10.1007/s12686-010-9233-2.
Ramstad, K.M and Faulkner, L. Tikanga & technology: a new net goes fishing. Pages 248-254 in JS Te Rito & S Healy (eds.), Proceedings of the Traditional Knowledge Conference 2008 – “Te tatau pounamu: The greenstone door, Traditional knowledge and gateways to balanced relationships”, University of Auckland, New Zealand.
Refardt, D. and Rainey, P.B.    Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution. 64, 1086-1097.
Refsnider, J.M., Daugherty, C.H., Keall, S.N. and Nelson, N.J.  Nest-site choice and fidelity in tuatara on Stephens Island, New Zealand.   Journal of Zoology 280: 396-402.
Rioux Paquette, S., Louis Jr. E.E., and Lapointe, F.-J.  Microsatellite analyses provide evidence of male-biased dispersal in the radiated tortoise Astrochelys radiata (Chelonia: Testudinidae). Journal of Heredity 101(4): 403-412.
Robins, J. H., McLenachan, P.A., Phillips, M.J.,  McComish, B.J., Matisoo-Smith, E., and Ross, H.A. Evolutionary relationships and divergence times among the native rats of Australia.  BMC Evolutionary Biology 10:375.
Sanderson, M.J., McMahon, M.M. and Steel, M.  Phylogenomics with incomplete taxon coverage: the limits to inference. BMC Evolutionary Biology 10: 155.
Sangaralingam, A., Susko, E., Bryant, D., and Spencer, M.  On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. 2010 BMC Evolutionary Biology 10:343
Spencer, H.G. and Willan, R.C. Neotaenioglossa (Gastropoda, Mollusca).   Pages 354-387 in New Zealand Coastal Marine Invertebrates: An Illustrated Guide, Volume 1, S.deC. Cook (ed.).  University of Canterbury Press, Christchurch, New Zealand.
Spencer, H.G. and Willan, R.C. Heterostropha (Gastropoda, Mollusca). Page 421 in New Zealand Coastal Marine Invertebrates: An Illustrated Guide, Volume 1, S.deC. Cook (ed.). University of Canterbury Press, Christchurch, New Zealand.
Spencer, H.G., and Willan, R.C.  Neogastropoda (Gastropoda, Mollusca).   Pages 387-420 in New Zealand Coastal Marine Invertebrates: An Illustrated Guide. Volume 1, S. deC. Cook (ed.). University of Canterbury Press, Christchurch NZ.
Steel, M. and Mooers, A.  Expected length of pendant and interior edges of a Yule tree. Applied Mathematics Letters 23(11): 1315-1319
Steel, M. and Penny, D.  Origins of life: Common ancestry put to the test. Nature 465: 168-169.
Steel, M. and Sanderson, M.J.  Characterizing phylogenetically decisive taxon coverage. Applied Mathematics Letters 23, 82-86.
Subramanian, S., Huynen, L., Millar, C.D., and Lambert, D.M.  Next generation sequencing and analysis of a conserved transcriptome of New Zealand’s kiwi. BMC Evolutionary Biology 20: 387.
Summerhayes, G.R., Matisoo-Smith, E., Mandui, H., Allen, J., Specht, J., Hogg, N. and McPherson, S.   Tamuarawai (EQS): An early Lapita site on Emirau, New Ireland, PNG. Journal of Pacific Archaeology, 1, 1, 62-75
Teh, K. H., Flint, S.,  and French, N.  Biofilm formation by Campylobacter jejuni in controlled mixed-microbial populations. Int J Food Microbiol 2010 143:118-124.
Trewick S.A., and Gibb, G.C. Vicars, Tramps and the Assembly of New Zealand Avifauna – A review of molecular phylogenetic evidence. Ibis 152: 226-253. doi:10.1111/j.1474-919X.(2010).01018.x
van Iersel, L., Semple, C., and Steel, M.  Locating a tree in a phylogenetic network.  Information Processing Letters, 110, 1037–1043.
van Iersel, L., Semple, C., and Steel, M.  Quantifying the extent of lateral gene transfer required to advert a ‘Genome of Eden’. Bulletin of Mathematical Biology, 72, 1783–1798.
Voelckel, C., Borevitz, J., and Hodges, S.A. Within and between whorls: Comparative profiling of Aquilegia and Arabidopsis. Within and between whorls: Comparative profiling of Aquilegia and Arabidopsis. PLoS ONE 5(3): e9735. doi:10.1371/journal.pone.0009735
Voelckel, C., Mirzai, M., Reichelt, M., Luo, L., Pascovici, D., Heenan, P.B., Schmidt, S., Janssen, B., Haynes, P.A., and Lockhart, P.J.  Transcript and protein profiling identify candidate gene sets of potential adaptive significance in New Zealand alpine Pachycladon. BMC Evolutionary Biology 10:151 (20 May 2010).
Waters, J.M., Rowe, D.L., Burridge, C.P., and Wallis, G.P. Gene trees versus species trees: reassessing life-history evolution in a freshwater fish radiation. Systematic Biology 59:504-517.
Waters, J.M., Wernberg, T., Connell, S.D., Thomsen, M.S., Zuccarello, G.C., Kraft, G.T., Sanderson, J.C., West, J.A., and Gurgel, C.F. Australia's marine biogeography revisited: back to the future? Austral Ecology 35:998-992.
Waugh J, Evans MW, Millar CD, Lambert DM.  Birdstrikes and barcoding: can DNA methods help make the airways safer? Molecular Ecology Resources (available online).
Whitworth, J., Zhang, Y., Bono, J., Pleydell, E., French, N. and Besser, T. Diverse Genetic Markers Concordantly Identify Bovine-origin Escherichia coli O157 Genotypes Under-represented in Human Disease.  Appl Environ Microbiol, 2010 76: 361-5.
Williams, S.T, Donald,K.M.,  Spencer H.G., and Nakano, T.   Molecular systematics of the marine gastropod families Trochidae and Calliostomatidae (Superfamily Trochoidea).   Molecular Phylogenetics and Evolution 54: 783-809. doi:10.1016/j.ympev.2009.11.008
Winnebeck, E.C., Millar, C.D., and Warman, G.R.  Why does insect RNA look degraded? Journal of Insect Science 10: Article 170.
Zhang, X.-X., Liu, Y.-H. and Rainey P.B.  CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environmental Microbiology 12, 1674-1683.