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Publications

Lind, P. A., Farr, A.D. & P. B. Rainey (2015). Experimental evolution reveals hidden diversity in evolutionary pathways. eLife 10.7554/eLife.07074. DOI: http://dx.doi.org/10.7554/eLife.07074.

Rainey, P. B. (2015). Precarious development: the uncertain social life of cellular slime molds. Proceedings of the National Academy of Sciences, USA 112, 2639-2640. DOI: 10.1073/pnas.1500708112.

Gallie, J., Libby, E., Bertels, F., Remigi, P., Jendresen, C. B., Ferguson, G. C., Desprat, N., Buffing, M. F., Sauer, U., Beaumont, H. J. E., Martinussen, J., Kilstrup, M. & Rainey, P. B. (2015). Bistability in a metabolic network underpins the de novo evolution of colony switching in Pseudomonas fluorescens. PLoS Biology, 13(3): e1002109. DOI:10.1371/journal.pbio.1002109.

Liu, Y., Rainey, P. B. & Zhang, X.-X. (2014). Mini-Tn7 vectors for studying post-transcriptional gene expression in Pseudomonas. Journal of Microbiological Methods 107, 182-185.

Hammerschmidt, K., Rose, C., Kerr, B & Rainey, P. B. (2014). Life cycles, fitness decoupling and the evolution of multicellularity. Nature, in press. DOI: 10.1038/nature13884.

Ritchie, S. R., Thomas, M. G. & Rainey, P. B. (2014). Genetic structure of Staphylococcus aureus from the Southwest Pacific. PLoS One, DOI: 10.1371/journal.pone.0100300.

Yildirim, Y., Patel, S., Millar, C. D. & Rainey, P. B. (2014). Microsatellite development for a tetrodotoxin-containing sea slug (Pleurobranchaea maculata). Biochemical Systematics and Ecology, DOI: 10.1016/j.bse.2014.04.001.

Whiteson, K. L., Bailey, B., Bergkessel, M., Conrad, D., Delhaes, L., Felts, B., Harris, J. K., Hunter, R., Lim Y.-W., Maughan, H., Quinn, R., Salamon, P., Sillivan, J., Wagner, B. D. & Rainey, P. B. (2014). The upper respiratory tract as a microbial source for pulmonary infections in cystic fibrosis: parallels from island biogeography. American Journal of Respiratory and Critical Care Medicine, 189, 1309-1315.

Alsohim, A. S., Taylor, T. B., Barrett, G. A., Gallie, J., Zhang, X.-X., Johnson, L. J., Altamirano-Junqueira, A. E., Rainey, P. B. & Jackson, R. W. (2014). The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 mediates in vitro spreading motility and plant growth promotion. Environmental Microbiology, DOI: 10.1111/1462-2920.12469.

Rainey, P. B., Desprat, N., Driscoll, W. W. & Zhang, X.-X. (2014). Microbes are not bound by sociobiology: response to Kümmerli and Ross-Gillespie (2013). Evolution, DOI: 10.1111/evo.12508.

De Monte, S., & Rainey, P. B. (2014). Nascent multicellular organisms and the evolution of individuality. Journal of Biosciences. 39, 237-248. DOI: 10.1007/s12038-014-9420-5.

Bertels, F., Silander, O. K., Pachkov, M., Rainey, P. B. & van Nimwegen, E. (2014). Automated reconstruction of whole genome phylogenies from short sequence reads. Molecular Biology and Evolution. 31, 1077-1088. DOI: 10.1093/molbev/msu088.

Rainey, P. B. & De Monte, S. (2014). Resolving conflicts during the transition to multicellular life. Annual Review of Ecology Evolution and Systematics, DOI: 10.1146/annurev-ecolsys-120213-091740.

Zhang, X.-X., Ritchie, S., Rainey, P. B. (2014). Urocanate as a potential signaling molecule for bacterial recognition of eukaryotic hosts. Cell and Molecular Life Sciences. 71, 541-547. DOI: 10.1007/s00018-013-1527-6.

Flohr, R. C. E., Blom, C., Rainey, P. B. & Beaumont, H. J. E. Founder niche constrains evolutionary adaptive radiation. (2013). Proceedings of the National Academy of Sciences, USA. 110, 20663-20668. DOI: 10.1073/pnas.1310310110.

Libby, E. & Rainey, P. B. Eco-evolutionary feed-back and the tuning of proto-developmental life cycles. (2013). PLoS One, DOI: 10.1371/journal.pone.0082274.

Ferguson, G. C. Bertels, F. & Rainey, P. B. (2013). Adaptive divergence in experimental populations of Pseudomonas fluorescens. V. Insight into the niche specialist fuzzy spreader compels revision of the model Pseudomonas radiation. Genetics, doi:10.1534/genetics.113.154948.

Bailey, S., Dettman, J. R., Rainey, P. B. & Kassen, R. (2013). Competition both drives and impedes diversification in a model adaptive radiation. Proceedings of the Royal Society (London) B. 280: 20131253. DOI: 10.1098/rspb.2013.1253.

Zhang, X.-X. & Rainey, P. B. (2013). Exploring the social biology of pyoverdin-producing Pseudomonas. Evolution. 67, 3161-3174. DOI: 10.1111/evo.12183.

McCann, H., Rikkerink, E. H., Bertels, F. Fiers, M., Lu, A., Rees-George, J., Andersen, M. T., Gleave, A. P., Haubold, B., Wohlers, Guttman, D. S., Wang, P., Vanneste, J., Rainey, P. B*. & Templeton, M. D*. (2013). Genomic analysis of the kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insights into the origins of an emergent plant disease. PLoS Pathogens 9(7): e1003503. DOI:10.1371/journal.ppat.1003503. *Joint senior authors.

Libby, E. & Rainey, P. B. (2013). A conceptual framework for the evolutionary origins of multicellularity. Physical Biology 10, 035001. DOI: 10.1088/1478-3975/10/3/035001.

Frean, M. Rainey, P. B. & Traulsen, A. (2013). The effect of population structure on the rate of evolution. Proceedings of the Royal Society (London) B. 280 DOI: 10.1098/rspb.2013.0211.

Conrad, D., Haynes, M., Salamon, P., Rainey, P. B. Youle, M. & Rohwer, F. (2012). Cystic fibrosis therapy: a community ecology perspective. American Journal of Respiratory and Critical Care Medicine. 48, 150-156. DOI: 10.1165/rcmb.2012-0059PS.

Kidd, T. J., Ritchie, S. R., Ramsay, K. A., Grimwood, K., Bell, S. C. & Rainey, P. B. (2012). Genetic structure of clinical and environmental Pseudomonas aeruginosa reveals a freely recombining population and a lack of correspondence between genotype and source. PLoS One, 7(9): e44199. doi:10.1371/journal.pone.0044199.

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. & Rival, R. (2012). Genome sequence of the biocontrol strain Pseudomonas fluorescens F113. Journal of Bacteriology. 194, 1273-1274. DOI: 10.1128/ JB.06601-11

Gerth, M. L., Ferla, M. P. & Rainey, P. B. (2012). The origin and ecological significance of multiple branches for histidine utilisation in Pseudomonas aeruginosa PAO1. Environmental Microbiology. 14, 1929-1940. DOI: 10.1111/j.1462-2920.2011.02691.x.

Zhang, X.-X., Chang, H., Tran, S., L., Gauntlett, J. C., Cook, G. M. & Rainey, P. B. (2012). Variation in transporter genes explains polymorphism of histidine and urocanate utilisation in natural populations of Pseudomonas. Environmental Microbiology. 14, 1941-1951. DOI: 10.1111/j.1462-2920.2011.02692.x.

Willner, D., Haynes, M. R., Furlan, M., Hanson, N., Kirby, B., Lim, Y.-W., Rainey, P. B., Schmieder, R., Yule, M., Conrad, D. & Rohwer, F. (2012). 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. & Conrad, D. (2012). Spatial distribution of microbial communities in the cystic fibrosis lung. ISME Journal. 6, 471-474. doi:10.1038/ismej.2011.104.

Bertels, F. & Rainey, P. B. (2011). Curiosities of REPINs and RAYTs. Mobile Genetic Elements. 1(4), 1-7.

Rainey, P. B., Beaumont, H. J. E., Ferguson, G. C., Gallie, J., Kost, C., Libby, E. & Zhang, X.-X. (2011). The evolutionary emergence of stochastic phenotype switching. BMC Microbial Cell Factories 10(Suppl 1):S14.

Bertels, F. & Rainey, P. B. (2011). Within genome evolution of REPINs: A new family of miniature mobile DNA in bacteria. PLoS Genetics, 7(6): e1002132.

Libby, E. & Rainey, P. B. (2011). 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.

Kidd, T. J., Ramsay, K. A., Grimwood, K., Rainey, P. B. & Bell, S. C. (2011). 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.

Ritchie, S. R., Fraser, J. D., Libby, E., Morris, A. J., Rainey, P. B. & Thomas, M. G. (2011). Demographic variation in community-based MRSA skin and soft tissue infection in Auckland, New Zealand. The New Zealand Medical Journal 124, 21-30.

Best, N, Fraser, J. D., Rainey, P. B., Roberts, S. A., Thomas, M. G. & Ritchie, S. R. (2011). Nasal carriage of Staphylococcus aureus in healthy Aucklanders. The New Zealand Medical Journal 124, 31-39.

McDonald, M. J., Cooper, T. F., Beaumont, H. J. E. & Rainey, P. B. (2011). The distribution of fitness effects of new mutations in Pseudomonas fluorescens. Biology Letters. 7, 98-100.

Rainey, P. B. and Kerr, B. (2010). Cheats as first propagules: A new hypothesis for the evolution of individuality during the transition from single cells to multicellularity. BioEssays 32, 872-880.

Zhang, X.-X., Liu, Y.-H. & Rainey P. B. (2010). CbrAB-dependent regulation of pcnB, a poly(A) polymerase gene involved in polyadenylation of RNA in Pseudomonas fluorescens. Environmental Microbiology 12, 1674-1683.

Refardt, D. & Rainey, P. B. (2010). Tuning a genetic switch: experimental evolution and natural variation of prophage induction. Evolution. 64, 1086-1097.

Knight, C. G., Zhang, X.-X., Gunn, A., Brenner, T., Jackson, R. W., Giddens, S. R., Sripardi, P., Zitzmann, N. & Rainey, P. B. (2010). Testing temperature induced proteomic changes in the plant associated bacterium Pseudomonas fluorescens SBW25. Environmental Microbiology Reports 2, 396-402.

Beaumont, H. J. E., Gallie, J., Kost, C., Ferguson, G. C. & Rainey, P. B. (2009). Experimental evolution of bet-hedging. Nature 462, 90-93.

McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X.-X. & Rainey, P. B. (2009). Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints guide evolutionary trajectories in a parallel adaptive radiation. Genetics 183, 1041-1053.

Silby, M. W., Cerdeno-Tarranga, A. M., Vernikos, G., Giddens, S. R., Jackson, R. W., Preston, G. M., Zhang, X.-X., Moon, C. D., Gehrig, S. M., Godfrey, S. A. C., Knight, C. G., Malone, J. G., Robinson, Z., Spiers, A. J., Harris, S., Challis, G. L., Yaxley, A. M., Harris, D., Seeger, K., Murphy, L., Rutter, S., Squares, R., Quail, M. A., Saunders, E., Anderson, I., Mavromat, K., Brettin, T. S., Bentley, S., Hothersall, J., Stephens, E., Thomas, C. M., Parkhill, J., Levy, S. B., Rainey, P. B. & Thomson, N. R. (2009). Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biology 10, R51.

Zhang, X.-X. & Rainey, P. B. (2008). The regulation of copper homeostasis in Pseudomonas fluorescens SBW25. Environmental Microbiology, 10, 3284-3294.

Moon, C. D., Zhang, X.-X., Matthijs, S. Schäfer, M, Budzikiewicz, H. & Rainey, P. B. (2008).
Pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium, Pseudomonas
fluorescens SBW25. BMC Microbiology 8, 7.

Zhang X.-X. & Rainey, P. B. (2008). Dual involvement of CbrAB and NtrBC in the regulation of histidine utilization in Pseudomonas fluorescens SBW25. Genetics 178, 185-195.

Zhang X.-X., Scott, K. Meffin, R. & Rainey, P. B. (2008). Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BMC Microbiology 7, 114.

Giddens, S. R., Jackson, R. W., Moon, C. D., Jacobs, M. A., Zhang, X.-X., Gehrig, S. M. & Rainey, P.B. (2007). 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.

Zhang X.-X. & Rainey, P. B. (2007). Construction and validation of a neutrally marked strain of Pseduomonas fluorescens SBW25. Journal of Microbiological Methods 71, 78-81.

Zhang X.-X. & Rainey, P. B. (2007). Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25. Genetics 176, 2165-2176.

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. & Bailey, M. J. (2007). 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.

Bantinaki, E., Kassen, R., Knight, C. G., Robinson, Z. & Spiers, & Rainey, P. B. (2007). Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 176, 441-453.

Rainey, P. B. (2007). Unity from conflict. Nature 446, 616.

Fukami, T, Beaumont, H. J. E. & Zhang, X.-X. Rainey, P. B. Immigration history controls diversification in experimental adaptive radiation. Nature 446, 436-439.

Malone, J. G., Williams, R., Christen, M., Jenal, U., Spiers, A. J. & Rainey, P. B. (2007). The structure- function relationship of WspR; a Pseudomonas fluorescens response regulator with a GGDEF output domain. Microbiology 153, 980-994.

Zhang, X.-X. & Rainey, P. B. (2007). Biological and ecological significance of a plant-inducible copper-transporting P1-type ATPase from Pseudomonas fluorescens SBW25. Molecular Plant- Microbe Interactions 20, 581-588.

Kirkelund Hansen, S., Rainey, P. B., Haagensen, J. A. J & Molin, S. (2007). Evolution of species interactions in a biofilm community. Nature 445, 533-536.

Buckling, A., Brockhurst, M. A., Travisano, M. & Rainey, P. B. (2007). Experimental adaptation to high and low quality environments under different scales of temporal variation. Journal of Evolutionary Biology, 20, 296-300.
Brockhurst, M. A., Fenton, A., Roulston, B. & Rainey, P. B. (2006). The impact of phages on interspecific competition in experimental populations of bacteria. BMC Ecology 6, 19 doi:
10.1186/1472-6785-6-19.

Knight, C. G., Zitzmann, N, Prabhakar, S, Antrobus, R, Dwek, R, Hebestreit, H., & Rainey, P. B. (2006). Unravelling adaptive evolution: how a single point mutation affects the protein co- regulation network. Nature Genetics 38, 1015-1022.

Goymer, P., Kahn, S. G., Malone, J. G., Gehrig, S. M., Spiers, A. J. & Rainey, P. B. (2006). Adaptive divergence in experimental populations of Pseudomonas fluorecens. II. Role of the GGDEF regulator, WspR, in evolution and development of the wrinkly spreader phenotype. Genetics,
173, 515-526.

Zhang, X.-X., George, A., Bailey, M. J. & Rainey, P. B. (2006). The histidine uptake and degradation operon (hut) of Pseudomonas fluorescens SBW25 is active on plant surfaces, but is not required for colonisation of sugar beet seedlings. Microbiology, 152, 1867-1875.

Brockhurst, M. A., Buckling, A. & Rainey, P. B. (2006). Spatial heterogeneity and the stability of host- parastie coexistence. Journal of Evolutionary Biology, 19, 374-379.

Jackson, R. J., Preston G. M. & Rainey, P. B. (2005) Genetic characterisation of Pseudomonas fluorescens SBW25 rsp gene expression in the phytosphere and in vitro. Journal of Bacteriology 187, 8477-8488.

Arcus, V. L., Rainey, P. B. & Turner, S. J. (2005). The PIN-domain toxin-antitoxin array in mycobacteria. Trends in Microbiology 13, 360-365.

Spiers, A. J. & Rainey, P. B. (2005). The Pseudomonas fluorescens SBW25 wrinkly spreader A-L biofilm requires attachment factor, cellulose fibre and LPS interactions to maintain strength and integrity. Microbiology 151 2829-2839.

Cooper, T. F., Beaumont, H. J. E. & Rainey, P. B. (2005). Biofilm diversity as a test of the insurance hypothesis. Microbiology 151, 2815-2816.

Brockhurst, M. A., Buckling, A. & Rainey, P. B. (2005). The effect of a bacteriophage on diversification of the opportunisitic bacterial pathogen Pseudomonas aeruginosa. Proceedings of the Royal Society (London) B 272, 1385-1391.

Rediers, H., Rainey, P. B., Vanderleyden, J. & De Mot, R. (2005). Unravelling the secret lives of bacteria: IVET and DFI promoter traps as tools for exploring niche-specific gene expression. Microbiology and Molecular Biology Reviews 69, 217-261.

Zhang, X.-X., Lilley, A. K., Bailey, M. J. & Rainey, P. B. (2004). The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes including three putative helicases. FEMS Microbiology Ecology, 51, 9-17.

Kassen, R., Llewellyn, M. & Rainey, P. B. (2004). Ecological constraints in a model adaptive radiation, Nature 431, 984-988.

Zhang, X.-X., Lilley, A. K., Bailey, M. J. & Rainey, P. B. (2004). Functional and phylogenetic analysis of a plant-inducible oligoribonuclease (orn) gene from an indigenous Pseudomonas plasmid. Microbiology 150, 2889-2898.

Knight, C. G., Kassen, R, Hebestreit, H. & Rainey, P. B. (2004) Global analysis of predicted proteomes: functional adaptation and physical properties. Proceedings of the National Academy of Sciences USA 101, 8390-8395.

MacLean, C. Bell, G. & Rainey, P. B. (2004) The evolution of a pleiotropic fitness tradeoff in
Pseudomonas fluorescens. Proceedings of the National Academy of Sciences USA 101,
8072-8077.

Silby, M. W. Rainey, P. B. & Levy, S. B. (2004). IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150,
518-520.

Kassen, R & Rainey, P. B. (2004). The ecology and genetics of microbial diversity. Annual Review of
Microbiology 58, 207-231

Rainey, P. B. & Cooper, T. F (2004). Evolution of bacterial diversity and the origins of modularity.
Research in Microbiology (special issue on genome plasticity dedicated to the memory of
Michel Blot) 155, 370-375.

Jessup, C. M., Kassen, R., Forde, S. E., Kerr, B., Buckling, A., Rainey, P. B. & Bohannan, B. J. M. (2004) Big questions, small worlds: Microbial model systems in ecology. Trends in Ecology and Evolution 19, 189-197.

Brockhurst, M. A., Rainey, P. B. & Buckling, A. (2004). The effect of spatial heterogeneity and parasites on the evolution of host diversity. Proceedings of the Royal Society 271, 107-111.

Rediers, H., Bonnecarrere, V., Rainey, P. B., Hamonts, K., Vanderleyden, J. & De Mot, R. (2003).
Development and application of a dapB-based IVET system to study colonization of rice by
the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15. Applied and
Environmental Microbiology 69, 6864-6874.

Spiers, A. J., Bohannon, J., Gehrig, S. M. & Rainey, P. B. (2003). Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Molecular Microbiology, 50, 15-27.

Gal, M., Preston, G. M., Massey, R. M., Spiers, A. J. & Rainey, P. B. (2003). Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Molecular Ecology, 12, 3109-3121.

Brockhurst, M. A., Morgan, A. D., Rainey, P. B. & Buckling, A. (2003). Population mixing accelerates coevolution. Ecology Letters 6, 975-979.

Rainey, P. B. & Rainey. K. (2003). Evolution of co-operation and conflict in experimental bacterial populations. Nature 425, 72-74.

Aldrige, P., Paul, R., Goymer, P. J., Rainey, P. B. & Jenal, U. (2003). Role of the GGDEF regulator
PleD in polar development of Caulobacter crescentus. Molecular Microbiology 47,
1695-1708.

Buckling, A. & Rainey, P. B. (2002). The role of parasites on sympatric and allopatric diversification of hosts. Nature 420, 496-499.

Hodgson, D., Rainey, P. B. & Buckling A (2002). Mechanisms linking, productivity and invasibility in experimental bacterial communities. Proceedings of the Royal Society (London) B 269,
2277-2283.

D’Argenio, D. A., Calfee, M. W., Rainey, P. B. & Pesci, E. C. (2002) Autolysis and autoaggregation in
Pseudomonas aeruginosa colony morphology mutants. Journal of Bacteriology 184,
6481-6489.

Buckling, A & Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage. Proceedings of the Royal Society (London) B 269, 931-936.

Spiers, A. J., Kahn, S. G., Bohannon, J., Travisano, M. & Rainey, P. B. (2002). Adaptive divergence in experimental populations of Pseudomonas fluorescens. 1. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 161, 33-46.

Preston, G. M. Bertrand, N. & Rainey, P. B. (2001). Type III (Hrp) secretion in plant growth- promoting Pseudomonas fluorescens SBW25. Molecular Microbiology 41, 999-1014.

Spiers, A. J., Field, D., Bailey, M. J. & Rainey, P. B. (2001). Notes on designing a partial genomic database: The PfSBW25 Encyclopaedia, a sequence database for Pseudomonas fluorescens SBW25. Microbiology 147, 247-249.

Buckling, A. Kassen, R. Bell, G. & Rainey, P. B. (2000). Diversity and disturbance in experimental microcosms. Nature, 408, 961-964.

Spiers, A. J., Buckling, A. & Rainey, P. B. (2000). The causes of Pseudomonas diversity.
Microbiology, 146, 2345-2350.

Rainey, P. B. & Preston, G. M. (2000). IVET strategies: valuable tools for biotechnology. Current
Opinion in Biotechnology 11, 440-444.

Travisano, M. & Rainey, P. B. (2000). Studies of adaptive radiation using model microbial systems.
American Naturalist, 156, S35-S44.

Kassen, R. Buckling, A. Bell, G. & Rainey, P. B. (2000) Diversity peaks at intermediate productivity in a laboratory microcosm. Nature, 406, 508-512.

Rainey, P. B. & Moxon, E. R. (2000). When being hyper keeps you fit. Science 288: 1186-1187.

Rainey, P. B., Buckling, A., Kassen, R. & Travisano, M. (2000). The emergence and maintenance of diversity: Insights from experimental microbial populations. Trends in Ecology and Evolution, 15, 243-247.

Massey, R. M., Rainey, P. B., Keane, O., Sheehan, B. & Dorman, C. J. (1999). Environmentally constrained mutation and adaptive evolution in Salmonella. Current Biology 9, 1477-1480.

Rainey, P. B. (1999). Economics of mutation. Current Biology 9, R371-R373.

Rainey, P. B. (1999). Adaptation of Pseudomonas fluorescens to the plant rhizosphere.
Environmental Microbiology 1, 243-258.

Haubold, B., Travisano, M., Rainey, P. B. & Hudson, R. R. (1998). Testing linkage equilibrium in bacterial populations. Genetics 150, 1342-1348.

Preston, G. M., Haubold, B. & Rainey, P. B. (1998) Bacterial genomics and adaptation to life on plants: Implications for the evolution of pathogenicity and symbiosis. Current Opinion in Microbiology 1, 589-597.
Rainey, P. B. & Travisano, M. (1998) Adaptive radiation in a heterogeneous environment. Nature
394, 69-72.

Rainey, P. B., Heithoff, D. & Mahan, M. (1997). Single-step conjugative cloning of gene fusions involved in microbial-host interactions. Molecular and General Genetics 256, 84-87.

Appleby, B. M., Petty, S. J., Blakey, J. K., Rainey, P. B. & MacDonald, D. W. Does variation of sex ratio enhance reproductive success of offspring in tawny owls (Strix aluco)? Proceedings of the Royal Society, London Series B 264, 1111-1116.

Ebert, D., Rainey, P. B., Embley, M. & Scholz, D. (1996). Development, life cycle, ultrastructure and phylogenetic position of Pasteuria ramosa Metchnikoff 1888:rediscovery of an obligate endoparasite of Daphnia magna Straus. Philosophical Transactions of the Royal Society, London B 351, 1689-1701.

Haubold, B. & Rainey, P. B. (1996). Genetic and ecotypic structure of a fluorescent Pseudomonas
population. Molecular Ecology 5, 747-761.

Rainey, P. B. & Bailey, M. J. (1996). Physical and genetic map of the Pseudomonas fluorescens
SBW25 chromosome. Molecular Microbiology 19, 521-533.

Bailey, M. J., Lilley, A. K., Thompson, I. P., Rainey, P. B. & Ellis, R. J. (1995). Site-directed chromosomal marking of a fluorescent pseudomonad isolated from the phytosphere of sugar beet: stability and potential for marker gene transfer. Molecular Ecology 4, 755-763.

Thompson, I. P., Bailey, M. J., Ellis, R. J., Lilley, A. K., McCormack, P. J., Purdy, K. J., & Rainey, P. B. (1995). Short-term community dynamics in the phyllosphere microbiology of field-grown sugar beet. FEMS Microbiology Ecology 16, 205-212.

Livesley, M. A., Thompson, I. P., Rainey, P. B. & Nuttall, P. A. (1995). Comparison of Borrelia isolated from UK foci of Lyme disease. FEMS Microbiology Letters 130, 151-158.

Rainey, P. B., Bailey, M. J. & Thompson, I. P. (1994). Phenotypic and genotypic diversity of fluorescent pseudomonads isolated from the phyllosphere of sugar beet. Microbiology 140,
2315-2331.

Rainey, P. B., Thompson, I. P. & Palleroni, N. J. (1994). Genome and fatty acid analysis of Pseudomonas stutzeri. International Journal of Systematic Bacteriology 44, 54-61.

Moxon, E. R., Rainey, P. B., Nowak, M. & Lenski, R. E (1994). Adaptive evolution of highly mutable loci in pathogenic bacteria. Current Biology 4, 24-33.

Rainey , P. B., Brodey, C. L. & Johnstone, K. (1993). Identification of a gene cluster encoding three high molecular weight proteins which is required for synthesis of tolaasin by the mushroom pathogen Pseudomonas tolaasii. Molecular Microbiology 8, 643-652.

Rainey, P. B. & Moxon, E. R. (1993). Unusual mutational mechanisms and evolution. Science 260, 1958.

Thompson, I. P., Bailey, M. J. Fenlon, J. S., Fermor, T. R., Lilley, A., K., Lynch, J. M., McCormack, P., McQuilken, M. P., Purdy, K. P., Rainey, P. B. and Whipps, J. (1993). Quantitative and qualitative seasonal changes in the microbial community from the phyllosphere of sugar beet (Beta vulgaris). Plant and Soil 150, 177-191.
Han, F.S., Mortishire-Smith, R. J., Rainey, P. B. & Williams, D. H. (1992). Structure of the white line inducing principle from Pseudomonas reactans. Acta Crystalographia 48C, 1965-1969.

Rainey, P. B. (1991). Phenotypic variation of Pseudomonas putida and P. tolaasii affects attachment to Agaricus bisporus mycelium. Journal of General Microbiology. 137, 2769-2779.

Rainey, P. B., Brodey, C. L. & Johnstone. K. (1991). Biological properties and spectrum of activity of tolaasin, a lipodepsipeptide toxin produced by the mushroom pathogen, Pseudomonas tolaasii. Physiological and Molecular Plant Pathology. 39, 57-70.

Rainey, P. B. (1991). Effect of Pseudomonas putida on hyphal growth of Agaricus bisporus.
Mycological Research. 95, 699-704.

Brodey, C. L., Rainey, P. B., Tester, M. & Johnstone, K. (1991). Bacterial blotch disease of the cultivated mushroom is caused by an ion-channel forming lipodepsipeptide toxin. Molecular Plant-Microbe Interactions. 4, 407-411.

Grewal, S. I. S. & Rainey, P. B. (1991). Phenotypic variation of Pseudomonas putida and P. tolaasii affects the chemotactic response toward Agaricus bisporus mycelial exudate. Journal of General Microbiology. 137, 2761-2768.

Mortishire-Smith, R. J., Nutkins, J., Packman, L., Brodey, C. L., Rainey, P. B., Johnstone, K. & Williams, D. H. (1991). Determination of the structure of an extracellular peptide produced by the mushroom saprotroph, Pseudomonas reactans. Tetrahedron 47, 3645-3654.

Nutkins, J., Mortishire-Smith, R. J., Packman, L., Brodey, C. L., Rainey, P. B., Johnstone, K. & Williams, D. H. (1991). Structure determination of tolaasin, an extracellular toxin produced by the mushroom pathogen Pseudomonas tolaasii. Journal of the American Chemical Society
113, 2621-2627.

Rainey, P. B., Cole, A. L. J., Fermor, T. R. & Wood, D. A. (1990). A model system for determining the effect of bacteria on basidiome initiation of Agaricus bisporus. Mycological Research 94,
191-195.

Rainey, P. B. (1989). A new laboratory medium for the cultivation of Agaricus bisporus. New Zealand Natural Sciences 16, 109-112.

Rainey, P. B. & Cole, A. L. J. (1988). A new bacterial disease of the cultivated mushroom, Agaricus bisporus. Transactions of the British Mycological Society 90, 122-125.

Invited papers, chapters, articles

Rainey, P. B. (2012). Section Editor: Evolutionary / Population Genetics. In Encyclopedia of Genetics
2nd edition (Editors-in-Chief Maloy, S. & Hughes, K.) Elsevier, Oxford. (forthcoming).

Rainey, P. B. (2011). Advances in evolution by convergence. New Zealand Science Teacher 126, 12-13.

Rainey, P. B. & Kerr, B. (2011). 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, in press.

Rainey, P. B. (2011). Adaptive radiation, the evolution of diversity and the emergence of rules governing phenotypic evolution. In Microbes and the Origin of Species. (eds Kolter, R. & Maloy, S.). American Society for Microbiology Press, in press.

Zhang, X.-X. & Rainey, P. B. (2010). Bet hedging in the underworld. Genome Biology 11, 137
Rainey, P. B. (2010). The de novo evolution of cooperation: an unlikely event. In Social Behaviour: Genes, Ecology and Evolution. (eds Szekely, T., Moore, A. & Komdeur, J.), Cambridge University Press, pp 357-359.

Rainey, P. B. (2009). Arrythmia in tempo and mode (News & Views). Nature, 461, 1219-1221.

Rainey, P. B. (2007). Using molecules to connect organisms, populations and communities. Proceedings of the Royal Society (London) B 274, 2221.

De Weert, S., Kuiper, I., Eijkemans, K., Kamilova F. D., Preston, G. M., Mulders, I. H. M., Rainey, P. B., Bloemberg, G. V., Tikhonovich, I., Kravchenko, L., Wifjes, A. H. M., Azarova, T. & Lugtenberg, B. J. J. (2007). The role of competitive root tip colonization in the biological control of tomato foot and root rot. In Biological Control of Plant Diseases. (eds Chincholkar, S. B. & Mukerji, K. G.) Hawthorn Press, pp. 103-122.

Beaumont, H. J. E., Gehrig, S. M., Kassen, R., Knight, C., Malone, J., Spiers, A. J. & Rainey, P. B. (2006). The genetics of phenotypic innovation. In Prokaryotic Diversity: Mechanisms and Significance (ed Logan, N.), Cambridge University Press, pp. 91-104.

Rainey, P. B., Brockhurst, M., Buckling, A., Hodgson, D. & Kassen, R. (2005). The causes and consequences of microbial diversity. In Biological Diversity and Function in Soils. (eds Bardgett, R., Hopkins, D & Usher, M.). Cambridge University Press, pp. 83-99.

Rainey, P. B. (2005). Bacteria evolve and function within communities: observations from experimental Pseudomonas populations. In The Influence of Cooperative Bacteria on Animal Host Biology. (ed. McFail-Ngai, M., Henderson, B., Ruby, N). Cambridge University Press, pp.
83-102.

Rainey, P. B. (2004). Bacteria adapt – genetically, by natural selection – even in the lab! Microbiology Today 31, 160-162.

Rainey, P. B. (2003). Big questions in evolution. New Scientist. 14th june 2003 issue (article featured on front cover).

Preston G, Spiers A, Zhang X-X, Jackson R, Gal M, Knight C, Gehrig S, Malone J, Moon C, Godfrey S, Robinson Z, Bertrand N, Field D and Rainey P. B. (2003). The secret life of Pseudomonas fluorescens SBW25. In Pseudomonas syringae and related pathogens. (eds Iacobellis N.S., Collmer A., Hutcheson S.W., Mansfield J.W., Morris C.E., Murillo J., Schaad N.W., Stead D.E., Surico G., and Ullrich M.S.) Kluwer Academic Publishers. Dordrecht, The Netherlands. pp
347-353.

Rainey, P. B. (2003). Mutation rate evolution and implications for Pseudomonas aeruginosa in cystic fibrosis. In Antibiotic Riesistance in Cystic Fibrosis – an Emerging Crisis? (ed. Pitt, T.) Royal Society of Medicine Press. pp 23-28.

Bailey, M. J., Rainey, P. B., Zhang, X.-X., & Lilley, A. K. (2002). Population dynamics, gene transfer and gene expression in plasmids, the role of the horizontal gene pool in local adaptation at
the plant surface. In Phyllosphere Microbiology (eds Lindow, S. E., Hecht-Poinar, E. I. & Elliot, V. J.) American Phytopathological Society Press. pp 173-192.

Rainey, P. B. (1999). A sense of science. Time Higher Education Supplement, February 99; and yearly reviews of biology texts for THES until 2005).

Moxon, E. R, Lenski, R. E. & Rainey, P. B. (1998). Perspectives in Biology and Medicine 42, 154-155.

Rainey, P. B. (1997) Contributor of definitions and short articles for Encyclopaedia of Ecology and
Environmental Management. Blackwell Science.
Haubold, B. & Rainey, P. B. (1997). Toward an understanding of the population genetics of plant- colonizing bacteria. Advances in Botanical Research Incorporating Advances in Plant Pathology. Academic Press 24, 335-351.

Moxon, E. R. & Rainey, P. B. (1995). Pathogenic bacteria; the wisdom of their genes. In Ecology of Pathogenic Bacteria: Molecular and Evolutionary Aspects. Proceedings of the 1995 Royal Netherlands Academy of Arts and Sciences Symposium. pp 255-268.

Rainey, P. B. & Beckman, K. (1994). Plant Pathology. In Encyclopaedia of Molecular Biology. (ed. J. Kendrew) Blackwell Scientific Publications. pp 838-843.

Rainey, P. B. (1994) Contributor of definitions on bacterial genetics for Encyclopaedia of Molecular Biology. (ed. J. Kendrew). Blackwell Scientific Publications.

Rainey, P. B., Moxon, E. R. & Thompson, I. P. (1993) Intraclonal polymorphism in bacteria.
Advances in Microbial Ecology Vol 13, pp. 263-300. Plenum Press.

Rainey, P. B., Brodey, C. L. & Johnstone, K. (1992). Biology of Pseudomonas tolaasii, cause of brown blotch disease of mushrooms. Advances in Plant Pathology. 8, 95-117. Academic Press.