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Berkeley MCELLBI 140 - Hedgehog signalling controls eye degeneration in blind cavefish

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AnalysesWe determined the population size of the bacteriophage by adding 30ml of chloroform to a1 ml subsample of each chemostat (to remove bacteria) and plating 100ml of the purifiedsubsample of bacteriophage with 300ml of an overnight culture of bacteria in 3 ml of softagar. We counted the number of plaques (spots cleared of bacteria by the bacteriophage)after 24 h. Becau se the bacteriophage were well mixed before plating, each plaque waspresumed to result from a single viral particle. A lawn of ancestral bacteria (B0) was used todetermine the total size of the bacteriophage population and a lawn of resistant bacteria(B1) was used to calculate the number of host-range mutants (T71) in the bacteriophagepopulation.We determined the population size of the bacteria by plating 100ml of a subsample(without chloroform treatment) and counting the number of bacterial colonies presentafter 24 h of incubation. To determine the size of the B1population, we plated the bacteriawith an equal volume of ancestral bacteriophage.To investigate local adaptation in the bacteriophage through time, we isolated two tothree colonies of B1from the same day (day 9, 13 and 19) from each treatment during eachrun of the experiment. For each adaptation assay, overnight cultures of the colonies weregrown up in 1 mg ml21glucose media. We plated replicate samples of T71from each timepoint on a lawn of sympatric (from the same chemostat) and allopatric (from a differentchemostat, but at the same productivity level) B1from the overnight culture. We used the‘efficiency of plating’ (the number of plaques on each host) as a measure of bacteriophageinfectivity.We calculate d adaptation as the ratio of the number of plaques formed by thenumerically dominant bacteriophage on the dominant sympatric host to the number ofplaques formed on the allopatric host. Ratios of the number of plaques formed on thebacterial isolates from each replicate run of the experiment were averaged to give a meanratio for each run. Only one replicate run of the experiment was used in assays of theclosed/high productivity community due to contamination. There were often no plaqueson allopatric hosts, therefore we coded the data by adding one to bo th the numerator andthe denominator to allow calculation of a ratio. A value above one indicates localadaptation and a number below one indicates local maladaptation (that is, the number ofplaques was higher on the allopatric host than on the sympatric host). All ratios were log-transformed before analysis.Variation in adaptation was assessed by calculating the coefficient of variation of theadaptation ratios. Significance was tested using an F-test, with a sequential Bonferronicorrection for five pairwise comparisons25. Inspecting the data in detail showed that thereversed pattern for the open and closed intermediate productivity communities wasdriven by one of the two replicate runs of the experiment. Thus, we did not include datafrom the intermediate productivity communities in the analyses.Received 3 July; accepted 30 July 2004; doi:10.1038/nature02906.1. Thompson, J. N. The Coevolutionary Process (Univ. of Chicago Press, Chicago, 1994).2. Brodie, E. D. Jr, Ridenhour, B. J. & Brodie, E. D. III The evolutionary response of predators todangerous prey: hotspots and coldspots in the geographic mosaic of coevolution between gartersnakes and newts. Evolution 56, 2067–2082 (2002).3. Burdon, J. J. & Thrall, P. H. Spatial and temporal patterns in coevolving plant and pathogenassociations. Am. Nat. 153, S15–S33 (2002).4. Zangerl, A. R. & Berenbaum, M. R. Phenotype matching in wild parsnip and parsnip webworms:causes and consequences. Evolution 57, 806–815 (2003).5. Thompson, J. N. & Cunningham, B. M. Geographic structure and dynamics of coevolutionaryselection. Nature 417, 735–738 (2002).6. Benkman, C. W., Parchman, T. L., Favis, A. & Siepielski, A. M. Reciprocal selection causes acoevolutionary arms race between crossbills and lodgepole pine. Am. Nat. 162, 182–194 (2003).7. Nuismer, S. L., Thompson, J. N. & Gomulkiewicz, R. Gene flow and geographically structuredcoevolution. Proc. R. Soc. Lond. B 266, 605–609 (1999).8. Hochberg, M. & van Baalen, M. Antagonistic coevolution over productivity gradients. Am. Nat. 152,620–634 (1998).9. Chao, L., Levin, B. R. & Stewart, F. M. A complex community in a simple habitat: an experimentalstudy with bacteria and phage. Ecology 58, 369–378 (1977).10. Lenski, R. E. & Levin, B. R. Constraints on the coevolution of bacteria and virulent phage: amodel, some experiments, and predictions for natural communities. Am. Nat. 125, 585–602(1985).11. Shrag, S. J. & Mittler, J. E. Host–parasite coexistence: the role of spatial refuges in stabilizing bacteria-phage interactions. Am. Nat. 148, 348–377 (1996).12. Bohannan, B. J. M. & Lenski, R. E. The relative importance of competition and predation varies withproductivity in a model system. Am. Nat. 156, 329–340 (2000).13. Buckling, A. & Rainey, P. B. Antagonistic coevolution between a bacterium and a bacteriophage. Proc.R. Soc. Lond. B 269, 931–936 (2002).14. Thompson, J. N. The evolution of species interactions. Science 284, 2116–2118 (1999).15. Bohannan, B. J. M. & Lenski, R. E. The effect of resource enrichment on a chemostat community ofbacteria and phage. Ecology 78, 2303–2315 (1997).16. Gandon, S. Local adaptation and the geometry of host–parasite coevolution. Ecol. Lett. 5, 246–256(2002).17. Gandon, S. & Michalakis, Y. Local adaptation, evolutionary potential and host–parasite coevolution:interactions between migration, mutation, population size and generation time. J. Evol. Biol. 15,451–462 (2002).18. Gomulkiewicz, R., Thompson, J. N., Holt, R. D., Nuismer, S. L. & Hochberg, M. E. Hot spots, coldspots and the geographic mosaic theory of coevolution. Am. Nat. 156, 156–174 (2000).19. Slatkin, M. Gene flow in natural populations. Annu. Rev. Ecol. Syst. 16, 393–430 (1985).20. Futuyma, D. J. Evolutionary Biology, 3rd edn (Sinauer Associates Inc., Sunderland, 1998).21. Gandon, S., Capowiez, Y., Dubios, Y., Michalakis, Y. & Olivieri, I. Local adaptation and gene-for-genecoevolution in a metapopulation model. Proc. R. Soc. Lond. B 263, 1003–1009 (1996).22. Buckling, A., Wills, M. A. & Colegrave, N. Adaptation limits diversification of experimental bacterialpopulations. Science 302, 2107–2109 (2003).23. Brockhurst, M. A., Morgan, A. D., Rainey, P. B. & Buckling, A. Population mixing


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