title: The impact of spatial structure on viral genomic diversity generated during adaptation to thermal stress.
abstract: BACKGROUND
  Most clinical and natural microbial communities live and evolve in spatially structured environments. When changes in environmental conditions trigger evolutionary responses, spatial structure can impact the types of adaptive response and the extent to which they spread. In particular, localized competition in a spatial landscape can lead to the emergence of a larger number of different adaptive trajectories than would be found in well-mixed populations. Our goal was to determine how two levels of spatial structure affect genomic diversity in a population and how this diversity is manifested spatially.
  
  
  RESULTS
  We serially transferred bacteriophage populations growing at high temperatures (40°C) on agar plates for 550 generations at two levels of spatial structure. The level of spatial structure was determined by whether the physical locations of the phage subsamples were preserved or disrupted at each passage to fresh bacterial host populations. When spatial structure of the phage populations was preserved, there was significantly greater diversity on a global scale with restricted and patchy distribution. When spatial structure was disrupted with passaging to fresh hosts, beneficial mutants were spread across the entire plate. This resulted in reduced diversity, possibly due to clonal interference as the most fit mutants entered into competition on a global scale. Almost all substitutions present at the end of the adaptation in the populations with disrupted spatial structure were also present in the populations with structure preserved.
  
  
  CONCLUSIONS
  Our results are consistent with the patchy nature of the spread of adaptive mutants in a spatial landscape. Spatial structure enhances diversity and slows fixation of beneficial mutants. This added diversity could be beneficial in fluctuating environments. We also connect observed substitutions and their effects on fitness to aspects of phage biology, and we provide evidence that some substitutions exclude each other.
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America ; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Dilara
authors.initials: D
authors.lastname: Ally
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America ; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Valorie R
authors.initials: VR
authors.lastname: Wiss
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America ; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America ; Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, United States of America.
authors.forename: Gail E
authors.initials: GE
authors.lastname: Deckert
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Danielle
authors.initials: D
authors.lastname: Green
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America ; Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Pavitra
authors.initials: P
authors.lastname: Roychoudhury
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America ; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Holly A
authors.initials: HA
authors.lastname: Wichman
authors.affiliation: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America ; Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Celeste J
authors.initials: CJ
authors.lastname: Brown
authors.affiliation: Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho, United States of America ; Department of Mathematics, University of Idaho, Moscow, Idaho, United States of America.
authors.forename: Stephen M
authors.initials: SM
authors.lastname: Krone
mesh_terms: D000064:Acclimatization / Q000235:genetics*; D001435:Bacteriophages / Q000235:genetics* / Q000502:physiology; D016000:Cluster Analysis; D004777:Environment; D004926:Escherichia coli / Q000821:virology; D014644:Genetic Variation; D016679:Genome, Viral; D005838:Genotype; D006358:Hot Temperature; D009154:Mutation; D009841:Oligonucleotides / Q000737:chemistry; D010641:Phenotype; D017422:Sequence Analysis, DNA
chemical_list: D009841:Oligonucleotides