Research Publications

2007 Publication list




Abbott, K.L, Greaves, S.N.J., Ritchie, P.A. and Lester, P.J.   Behaviourally and genetically distinct populations of an invasive ant provide insight into invasion history and impacts on a tropical ant community.  Biological Invasions 9: 453-463.
Bantinaki, E., Kassen, R., Knight, C. G., Robinson, Z. & Spiers, and Rainey, P. B Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity.  Genetics 176, 441-453.
Bordewich, M., and Semple, C.  Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable.  Ieee-Acm Transactions on Computational Biology and Bioinformatics 4:458-466.
Bordewich, M., and Semple, C.  Computing the minimum number of hybridization events for a consistent evolutionary history.  Discrete Applied Mathematics 155:914-928.
Bruneau, A., Starr, J.R., and Joly, S.  Phylogenetic relationships in the genus Rosa: New evidence from chloroplast DNA sequences and an appraisal of current knowledge. Systematic Botany 32:366-378.
Buckling, A., Brockhurst, M. A., Travisano, M. and Rainey, P. B.  Experimental adaptation to high and low quality environments under different scales of temporal variation.  Journal of Evolutionary Biology, 20, 296-300.
Chapple, D.G. and Patterson, G.B.   A new skink species (Oligosoma taumakae sp. nov.; Reptilia: Scincidae) from the Open Bay Islands, New Zealand.   New Zealand Journal of Zoology 34: 347-357.
Chan, Z.S.H., Collins, L, and Kasabov, N.  Bayesian learning of sparse gene regulatory networks.  Biosystems 87:299-306.
Chen, X., Rozhdestvensky, T.S.,Collins, L. J. , Schmitz, J., and Penny. D.  Combined experimental and computational approach to identify non-protein-coding RNAs in the deep-branching eukaryote Giardia intestinalis.  Nucleic Acids Research, Vol. 35, No. 14 4619–4628
Chor, B., Hendy, M.D., and Penny, D.  Analytic solutions for three taxon ML trees with variable rates across sites.  Discrete Applied Mathematics 155:750-758.
Convey, P. and Stevens, M.I.  Ecology: Antarctic Biodiversity.  Science 28(317): 1877 - 1878.
Convey, P., Gibson, J.A.E., Hodgson, D.A., Pugh, P.J.A. and Stevens, M.I.  New terrestrial biological constraints for Antarctic glaciation  Online Proceedings of the 10th ISAES, edited by A. K. Cooper & C. R. Raymond et al., USGS Open-File Report 2007-1047, Extended Abstract 053, 4 p.
Corin, S.E., Lester, P.J., Abbott, K.L. and Ritchie, P.A.   Inferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New Zealand.  Diversity & Distributions 13: 510-518.
Corin, S.E., Abbott, K.L., Ritchie, P.A. and Lester, P.J.   Large scale unicoloniality: the population and colony structure of the invasive Argentine ant (Linepithema humile) in New Zealand. Insectes Sociaux 54: 275-282.
Donald, K., Sijnja, A., and Spencer, H.  Species assignation amongst morphologically cryptic larval Digenea isolated from New Zealand topshells (Gastropoda: Trochidae). Parasitology Research 101:433-441.
Dress A, and Steel, M.  Phylogenetic diversity over an abelian group. Annals of Combinatorics 11:143-160.
Gartrell, B.D., Youl, J.M., King, C.M., Bolotovski, I., McDonald, W.L., and Nelson, N.J.   Failure to detect Salmonella species in a population of wild tuatara (Sphenodon punctatus). New Zealand Veterinary Journal 55(3): 134-136.
Fukami, T, Beaumont, H. J. E. & Zhang, X.-X., and Rainey, P. B.  Immigration history controls diversification in experimental adaptive radiation.  Nature 446, 436-439.
Gibb, G.C., Kardailsky, O., Kimball, R.T., Braun, E.L., and Penny, D.  Mitochondrial Genomes and Avian Phylogeny: Complex Characters and Resolvability without Explosive Radiations.  . Biol. Evol. 24(1):269-280. 
Gleeson, D.M., Birkett, A., Berry, O. and Chapple, D.G.   Population genetic structure of Oligosoma otagense (Otago skink) with comparisons to O. grande (grand skink) populations and the long-term genetic management of both species. (abstract) New Zealand Journal of Zoology 34: 263.
Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. and Rainey, P. B.  Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex enviroment. Proceedings of the National Academy of Sciences, USA 104, 18247-18252.
Goode, M.G,, and Rodrigo, A.G.  SQUINT: a multiple alignment program and editor. Bioinformatics 23:1553-1555.
Greaves, S.N.J., Chapple, D.G., Gleeson, D.M., Daugherty, C.H., and Ritchie, P.A.  Phylogeography of the spotted skink (Oligosoma lineoocellatum) and green skink (O. chloronoton) species complex (Lacertilia: Scincidae) in New Zealand reveals pre-Pleistocene divergence.  Molecular Phylogenetics and Evolution 45: 729-739.
Greenslade, P., Stevens, M.I., and Edwards, R.  Invasion of two exotic terrestrial flatworms to subantarctic Macquarie Island.  Polar Biology 30:961–967.
Grunewald, S., Steel, M., and Swenson, M.S.  Closure operations in phylogenetics. Mathematical Biosciences 208:521-537.
Hall, R., Oxley, J., and Semple, C.  The structure of 3-connected matroids of path width three.  European Journal of Combinatorics 28:964-989.
Hare, K.M.   Physiology does not always reflect ecology: a plea for natural history data. (abstract) New Zealand Journal of Zoology 34: 264.
Hare, K.M., Hoare, J.M. and  Hitchmough, R.A.   Investigating natural population dynamics of Naultinus manukanus to inform conservation management of New Zealand's cryptic diurnal geckos. Journal of Herpetology 41(1): 81-93.
Hare, K.M., Pledger S., Thompson, M.B., Miller, J.H., and Daugherty, C.H.  Low cost of locomotion in lizards that are active at low temperatures. Physiological and Biochemical Zoology 80(1): 46-58.
Hayward ,J., Taylor, J., and Rodrigo, A.  Phylogenetic Analysis of Feline Immunodeficiency Virus in Domestic Feral and Companion Cats of New Zealand.  Journal of Virology 81:2999-3004.
Hoare, J.M., Adams, L.K., Bull, L.S., and Towns, D.R.   Attempting to manage complex predator-prey interactions fails to avert imminent extinction of a threatened New Zealand skink population.   The Journal of Wildlife Management 71(5): 1576-1584.
Hoare, J.M., Pledger, S. and Nelson, N.J.  Chemical discrimination of food, conspecifics and predators by apparently visually-oriented diurnal geckos, Naultinus manukanus. Featured Article for June 2007 Herpetologica 63(2): 184-192.
Hoare, J.M., Pledger, S., Nelson, N.J., and Daugherty, C.H.  Avoiding aliens: Behavioural plasticity in habitat use enables large, nocturnal geckos to survive Pacific rat invasions. Biological Conservation 136: 510-519.
Holland, B., Conner, G.,  Huber, K., and  Moulton, V. Imputing supertrees and supernetworks from quartets.  Systematic Biology 56:57-67. 
Hughes, J., Kennedy, M., Johnson, K.P., Palma, R.L, and Page, R.D.M.  Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice. Systematic Biology 56:232-251.
Huynen L.  Revealing the histories of Maori cloaks using DNA. New Zealand. Science Teacher 116:19.
Irimia, M., Maeso, I., Penny, D., Garcia-Ferna`ndez, J., and Roy, S.W.  Rare Coding Sequence Changes are Consistent with Ecdysozoa, not Coelomata. Mol. Biol. Evol. 24(8):1604–1607.
Irimia, M., Penny, D., and Roy, S.W.  Coevolution of genomic intron number and splice sites.  TRENDS in Genetics Vol.23 No.7, 321-325. 
Irimia, M., Rukov, J.L., Penny, D., and Roy, S.W.  Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evolutionary Biology 2007, 7:188.
Jansen van Vuuren, B., Mortimer, E.,Stevens, M.I., Marshall, D.J., Convey, P., Daniels, S.R., and Chown, S.L.  Molecular data can help to unveil biogeographic complexities since the Miocene: lessons from ameronothroid mites and isotomid springtails.  Online Proceedings of the 10th ISAES, edited by A.K. Cooper and C.R. Raymond et al., USGS Open-File Report 2007-1047, Extended Abstract 008, 4 p.
Joly S, and Bruneau A.  Delimiting species boundaries in Rosa sect. Cinnamomeae (Rosaceae) in eastern North America.  Systematic Biology 32:819-836.
Joly S, Stevens MI, and van Vuuren BJ.  Haplotype networks can be misleading in the presence of missing data.  Systematic Biology 56:857-862
Kirkelund Hansen, S., Rainey, P. B., Haagensen, J. A. J and Molin, S.  Evolution of species interactions in a biofilm community.  Nature 445, 533-536.
Knapp M, Mudaliar R, Havell D, Wagstaff SJ, and Lockhart P.  The Drowning of New Zealand and the problem of Agathis.  Systematic Biology 56:862-870.
Kneip C, Lockhart P, Voss C, and Maier UG.  Nitrogen fixation in eukaryotes - New models for symbiosis.  BMC Evolutionary Biology 7: 55.
Kurland CG, Collins LJ, and Penny D.  The evolution of eukaryotes - Response.  Science316:543-543.
Lambert D.  How fast is evolution?  New Zealand Science Teacher 116:14-15.
Larkum A, Lockhart P, and Howe C.  The origin of plastids: A shopping bag model. Photosynthesis Research 91:272-272.
Larson G, Cucchi T, Fujita M, Matisoo-Smith E, et al.  Phylogeny and ancient DNA of Sus provides insights into neolithic expansion in island southeast Asia and Oceania. Proceedings of the National Academy of Sciences of the United States of America 104:4834-4839.
Lehnebach CA, Cano A, Monsalve C, McLenachan P, Horandl E, and Lockhart P.  Phylogenetic relationships of the monotypic Peruvian genus Laccopetalum (Ranunculaceae). Plant Systematics and Evolution 264:109-116.
Liggins, L., Chapple, D.G., Ritchie, P.A., and Daugherty, C.H. Phylogeography of the New Zealand common skink, Oligosoma nigriplantare polychroma. (abstract) New Zealand Journal of Zoology 34: 267.
Lim SG, Cheng Y, Guindon S et al.  Viral Quasi-Species Evolution During Hepatitis Be Antigen Seroconversion. Gastroenterology 133:951-958.
Longson, C.G., Hare, K.M., and Daugherty, C.H.  Fluctuating asymmetry does not reflect environmental stress during incubation in an oviparous lizard. New Zealand Journal of Zoology 34: 91-96.
Love DR, Lan, C.C., Dodd, A., Shelling, A.N., McNabb, W.C., Ferguson, L.R.  Modeling inflammatory bowel disease: the zebrafish as a way forward.  Expert Review of Molecular Diagnostics 7(2): 177-193
MacAvoy, E.S., McGibbon, L.M., Sainsbury,J.P., Lawrence, H., Wilson, C.A., Daugherty, C.H., and Chambers, G.K.  Genetic variation in island populations of tuatara (Sphenodon spp.) inferred from microsatellite markers.  Conservation Genetics Online 8:305–318 DOI 10.1007/s10592-006-9170-5
Malone, J. G., Williams, R., Christen, M., Jenal, U., Spiers, A. J. and Rainey, P. B.  The structure-function relationship of WspR; a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153, 980-994.
Martin, W., Roettger, M., and Lockhart, P.J.  A reality check for alignments and trees. Trends in Genetics 23:478-480.
Matsen, F.A., and Steel, M.  Phylogenetic mixtures on a single tree can mimic a tree of another topology.  Systematic Biology 56:767-755.
McDowall, R.M. and Stevens, M.I.  Taxonomic status of the Tarndale bully Gobiomorphus alpinus (Teleostei: Eleotridae), revisited - again.  Journal of the Royal Society of New Zealand 37: 15-29 
Meudt, H.M., and Clarke, A.C.  Almost Forgotten or Latest Practice? AFLP applications, analyses and advances.  Trends in Plant Science 12: 106-117.
Miller, H.C. and Daugherty, C.H.   A tale of two islands: MHC variation in tuatara (Sphenodon). (abstract) New Zealand Journal of Zoology 34: 267-268.
Miller, H.C., Andrews-Cookson, M.A., and Daugherty, C.H.   Two patterns of variation among MHC class I loci in tuatara (Sphenodon punctatus).  Journal of Heredity 98: 666-677. 
Miller, H.C., Conrad, A.M., Barker, S.C., and Daugherty, C.H.  Distribution and phylogenetic analyses of an endangered tick, Amblyomma sphenodonti. New Zealand Journal of Zoology 34: 97-105.
Miller, K.A.   Taking the plunge Forest and Bird 326 November 2007: 20-22
Miller, K.A. and Nelson, N.J.   Genetic differentiation between disjunct populations and implications for the conservation of Whitaker’s skink (Cyclodina whitakeri). (abstract) New Zealand Journal of Zoology 34: 268.
Moore, J.A., Hoare, J.M., Daugherty, C.H., and Nelson, N.J.  Waiting reveals waning weight: Monitoring over 54 years shows a decline in body condition of a long-lived reptile (tuatara, Sphenodon punctatus).  Biological Conservation 135: 181-188.
Morely, C.G., McLenachan, P., and Lockhart, P. Evidence for the presence of a second species of mongoose inthe Fiji Islands.  Pacific Conservation Biol.13:29-34.
Moulton, V., Semple, C. and Steel, M.  Optimizing phylogenetic diversity under constraints.  Journal of Theoretical Biology 246, 186-194.
Nakano, T., and Spencer, H.  Simultaneous polyphenism and cryptic species in an intertidal limpet from New Zealand.  Molecular Phylogenetics and Evolution 45:470-479.
Nolan, L., Hogg, .ID., Sutherland, D.L., Stevens, M,I., and Schnabel, K.E.  Allozyme and mitochondrial DNA variability within the New Zealand damselfly genera Xanthocnemis, Austrolestes, and Ischnura (Odonata).  New Zealand Journal of Zoology 34:371-380.
Oxley, J., Semple, C., and Whittle, G.  The structure of the 3-separations of 3-connected matroids II. European Journal of Combinatorics 28:1239-1261.
Penny, D.  Charles Darwin, evolution simple and testable.  NZ Science Teacher (116): 23-27 
Penny, D., and Phillips, M.J.  Evolutionary biology - Mass survivals Nature 446:501-502.
Perrie, L.R., Bayly, M.J., Lehnebach, C.A., Brownsey, P.J.  Molecular phylogenetics and molecular dating of the New Zealand Gleicheniaceae.  Brittonia 59: 129-141.
Pledger, S., Geange, S., Hoare, J.M., and Perez Matus, A. Resource Selection : Tests and estimation using null models. Wellington, Victoria University of Wellington, 22pp.
Poole, A. and Penny, D.  Engulfed by speciation.  Nature 447:913.
Poole, A.M., and Penny, D.  Evaluating hypotheses for the origin of eukaryotes. Bioessays29:74-84.
Poole, A.M., and Penny, D.  Response to Dagan and Martin.  Bioessays 29:611-614.
Poss, M., Idoine, A., Ross, H.A., Terwee, J.A., VandeWoude, S., and Rodrigo, A.  Recombination in feline lentiviral genomes during experimental cross-species infection. Virology 359:146-151.
Rainey, P. B.  Unity from conflict Nature 446, 616.
Ramstad, K.M., Nelson, N.J., Paine, G., Beech, D., Paul, A., Paul, P., Allendorf, F.W. and Daugherty, C.H.  Māori traditional ecological knowledge complements science in conservation of tuatara (Sphenodon). (abstract) New Zealand Journal of Zoology 34: 269-270.
Ramstad, K.M., Nelson, N.J., Paine, G., Beech, D., Paul, A., Paul, P., Allendorf, F.W., and Daugherty, C.H. Tuatara: our living ancient taonga.   Mana Magazine 76: 18-21.
Ramstad, K.M., Nelson, N.J., Paine, G., Beech, D., Paul, A., Paul, P., Allendorf, F.W., and Daugherty, C.H.  Species and cultural conservation in New Zealand: Maori traditional ecological knowledge of tuatara.  Conservation Biology 21(2): 455-464.
Refsnider, J.M., Nelson, N.J. and Keall, S.N. Manipulative females: intra-sexual interactions in nest site choice, nest guarding, and nest defence in tuatara. (abstract) New Zealand Journal of Zoology 34: 270-271
Robins, J.H., Hingston, M., Matisoo-Smith, E., and Ross, H.A.  Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes 7:717-729.
Roy, S.W. and Penny, D Patterns of intron loss and gain in plants: intro loss-dominated evolution and a genome-wide comparison of O. sativa and A. thaliana.  Mol Biol Evol 24, 171-81.
Roy, S.W. and Penny, D.  Intron length distributions and gene prediction.  Nucleic Acids Research, Vol. 35, No. 14 4737–4742
Roy, S.W. and Penny, D.  On the Incidence of Intron Loss and Gain in Paralogous Gene Families. Mol. Biol. Evol. 24(8):1579–1581.
Roy, S.W. and Penny, D.  A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain.  Mol. Biol. Evol.24(7):1447–1457.
Roy, S.W., and Penny, D.  Widespread Intron Loss Suggests Retrotransposon Activity in Ancient Apicomplexans.  Molecular Biology and Evolution 24:1926-1933.
Roy, S.W., Penny, D., and Neafsey, D.E.  Evolutionary conservation of UTR intron boundaries in Cryptococcus.  Molecular Biology and Evolution 24:1140-1148.
Shavit, L., Penny, D., Hendy, M.D., and Holland, B.R.  The Problem of Rooting Rapid Radiations.  Molecular Biology and Evolution 24:2400-2411.
Shepherd, L.D., and Lambert, D.M.  The relationships and origins of the New Zealand wattlebirds (Passeriformes, Callaeatidae) from DNA sequence analyses.  Molecular Phylogenetics and Evolution 43:480-492.
Slack, K.E, Delsuc, F., Mclenachan, P.A., Arnason, U., and Penny, D.  Resolving the root of the avian mitogenomic tree by breaking up long branches.  Molecular Phylogenetics and Evolution 42:1-13. 
Spencer, H.G., Waters, J.M. and Eichorst, T.E.  Taxonomy and nomenclature of black nerites (Gastrpoda:Neritimorpha:Nerita) from the South Pacific. Invert Syst 21:229-237. 
Star B, Stoffels RJ, and Spencer HG.  Evolution of Fitnesses and Allele Frequencies in a Population With Spatially Heterogeneous Selection Pressures.  Genetics 177:1743-1751.
Star, B., Stoffels, R.J., and Spencer, H.G.  Single-Locus Polymorphism in a Heterogeneous Two-Deme Model.  Genetics 176: 1625–1633
Steel M, and Szekely LA.  Teasing apart two trees.  Combinatorics, Probability and Computing 16:903-922.
Steel M, Mimoto A, and Mooers A.  Hedging Our Bets: The Expected Contribution of Species to Future Phylogenetic Diversity.  Evolutionary Bioinformatics 3:237-244.
Steel, M. and Matsen, E.  The Bayesian `star paradox' persists for long finite sequences. Molecular Biology and Evolution. 24(4):1075-1079; doi:10.1093/molbev/msm028 
Stevens, M.I., Frati, F., McGaughran, A., Spinsanti, G., and Hogg, I.D.  Phylogeographic structure suggests multiple glacial refugia in northern Victoria Land for the endemic Antarctic springtail Desoria klovstadi, (Collembola, Isotomidae).  Zoologica Scripta 36: 201-212 
Stevens, M.I., Hogendoorn, K., and Schwarz, M.P.  Evolution of sociality by natural selection on variances in reproductive fitness: evidence from a social bee.  BMC Evolutionary Biology7:153.
Stevens, M.I., Hunger, S.A., Hills, S.F.K., and Gemmill, C.E.C.  Phantom hitch-hikers mislead estimates of genetic variation in Antarctic mosses. Plant Systematics and Evolution263: 191-201 
Stevens, M.I., McCartney, J., and Stringer, I.A.N.  New Zealand’s forgotten biodiversity: new techniques reveal new records for ‘giant’ springtails.  New Zealand Entomologist 30: 79-84.
Stevens, M.I., Winter, D., Morris, R., McCartney, J., and Greenslade, P.  New Zealand's giant Collembola: new information on distribution and morphology for Holacanthella Börner, 1906 (Neanuridae: Uchidanurinae).  New Zealand Journal of Zoology 34: 63-78 
Storey, A.A., Ramirez, J.M., Quiroz, D., Burley, D.V., Addison, D.J., Walter, R., Anderson, A.J., Hunt, T.L., Athens, J.S., Huynen, L., and Matisoo-Smith, E.A.  Radiocarbon and DNA evidence for a pre-Columbian introduction of Polynesian chickens to Chile.  Proceedings of the National Academy of Sciences 104:10335-10339.
Tang, R., Dodd, A., Lai, D., McNabb, W.C., and Love D.R.  Validation of Zebrafish (Danio rerio) Reference Genes for Quantitative Real-time RT-PCR Normalization.  Acta Biochim Biophys Sin (Shanghai), 39(5): 384-390
Tett, A., Spiers, A. J., Crossman, L. C., Aagar, D., Ciric, L., Dow, M., Fry, J., Harris, D., Lilley, A. K., Parkhill, J., Quail, M. A., Seeger, K., Squares, R., Snyder, L., Saunders, N., Rainey, P. B., Thomas, C., Turner, S. L., Zhang, X.-X., Field, D. and Bailey, M. J.  Sequence-based analysis of pQBR103, a representative of a unique, transfer proficient mega plasmid resident in the microbial community of sugar beet The ISME Journal 1, 331-340.
Thatte, B.D.  A correct proof of the McMorris-Powers' theorem on the consensus of phylogenies. Discrete Applied Mathematics 155(3): 423-427
Trewick, S.A.  Stick insects.  Te Ara - the Encyclopedia of New Zealand.
Trewick, S.A., Paterson, A.M., and Campbell, H.J.  Hello New Zealand Journal of Biogeography 34:1-6.
Trotter, M.V., and Spencer, H.G.  Frequency-Dependent Selection and the Maintenance of Genetic Variation: Exploring the Parameter Space of the Multiallelic Pairwise Interaction Model.  Genetics 176: 1729–1740
Van den Heuvel, M.R., Michel, C., Stevens, M.I., Clarke, A.C., Stölting, K.N., Hicks, B.J., and Tremblay, L.A.  Monitoring the effects of pulp and paper effluent is restricted in genetically distinct populations of common bully (Gobiomorphus cotidianus). Environmental Science & Technology 41: 2602-2608. 
Van Vuuren, B.J., Mortimer, E., Stevens, M.I., Marshall, D.J., Convey, P., Daniels, S.R., and Chown, S.L.  Molecular data can help to unveil biogeographic complexities since the Miocene: lessons from ameronothroid mites and isotomid springtails.  Pp. Extended Abstract 008 in Cooper, AK, and Raymond, CR, eds. Online Proceedings of the 10th ISAES. USGS OFR 2007-1047.
Votier, S.C., Kennedy, M., Bearhop, S., Newell, R.G., Griffiths, K., Whitaker, H., Ritz, M.S., and Furness, R.W.  Supplementary DNA evidence fails to confirm presence of Brown Skuas Stercorarius antarctica in Europe: a retraction of Votier et al. (2004).  Ibis 149:619-621.
Waugh, J.  DNA barcoding in animal species: progress, potential and pitfalls.  BioEssays 29:188-197. 
Waugh, J.  DNA barcoding of animal species - response to De salle.  BioEssays 29: 1-2.
White, W., Hills S., Gaddam, R., Holland, B., and Penny, D.  Treeness Triangles: Visualizing the Loss of Phylogenetic Signal. Molecular Biology and Evolution 24:2029-2039.
Whitfield, J.B., and Lockhart, P.J.  Deciphering ancient rapid radiations.  Trends in Ecology and Evolution 22:258-265.
Woodhams, M., Stadler, P., Penny, D., and Collins, L.  RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evolutionary Biology 7:S13.
Zhang X.-X. and Rainey, P. B.  Construction and validation of a neutrally marked strain of Pseduomonas fluorescens SBW25.  Journal of Microbiological Methods 71, 78-81.
Zhang X.-X. and Rainey, P. B.  Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Journal of Microbiological Methods 71, 78-81.
Zhang, X.-X. and Rainey, P. B.  Biological and ecological significance of a plant-inducible copper-transporting P1-type ATPase from Pseudomonas fluorescens SBW25 Molecular Plant-Microbe Interactions 20, 581-588.