10.5061/DRYAD.53N0RF5
Turner, Caroline B.
University of Pittsburgh
Marshall, Christopher W.
University of Pittsburgh
Cooper, Vaughn S.
University of Pittsburgh
Data from: Parallel genetic adaptation across environments differing in
mode of growth or resource availability
Dryad
dataset
2018
Burkholderia cenocepacia
Parallel evolution
2018-07-11T14:03:30Z
2018-07-11T14:03:30Z
en
https://doi.org/10.1002/evl3.75
180829 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Evolution experiments have demonstrated high levels of genetic parallelism
between populations evolving in identical environments. However, natural
populations evolve in complex environments that can vary in many ways,
likely sharing some characteristics but not others. Here we ask whether
shared selection pressures drive parallel evolution across distinct
environments. We addressed this question in experimentally evolved
populations founded from a clone of the bacterium Burkholderia
cenocepacia. These populations evolved for 90 days (approximately 600
generations) under all combinations of high or low carbon availability and
selection for either planktonic or biofilm modes of growth. Populations
that evolved in environments with shared selection pressures (either level
of carbon availability or mode of growth) were more genetically similar to
each other than populations from environments that shared neither
characteristic. However, not all shared selection pressures led to
parallel evolution. Genetic parallelism between low-carbon biofilm and
low-carbon planktonic populations was very low despite shared selection
for growth under low-carbon conditions, suggesting that evolution in
low-carbon environments may generate stronger tradeoffs between biofilm
and planktonic modes of growth. For all environments, a population’s
fitness in a particular environment was positively correlated with the
genetic similarity between that population and the populations that
evolved in that particular environment. Although genetic similarity was
low between low-carbon environments, overall, evolution in similar
environments led to higher levels of genetic parallelism and that genetic
parallelism, in turn, was correlated with fitness in a particular
environment.
Breseq output with verificationTab delimited data file listing mutations
observed in evolved populations. Includes a column labeling whether a
given mutation is included in the Bray-Curtis analysis. This file is used
by the R scripts for Bray-Curtis and NMDS
analysis.Breseq_Output_with_verification.txtBray-Curtis calculations R
scriptThis script uses Breseq_Output_with_verification.txt data file. It
tests whether there is a significant difference in mutation number between
treatments, calculates the Bray-Curtis pairwise similarity between each
pair of populations, and conducts randomization tests.Bray-Curtis
Calculations.RBray-Curtis similarity matrixContains the Bray-Curtis
similarity between each pair of evolved populations. This file is produced
by the Bray-Curtis calculations R
script.braycurtis_similarity_matrix.csvTreatment listComma delimited file
with list of treatments by freezer label. Needed for NMDS R
script.Treatment_list.csvNMDS calculationsR script for calculating NMDS
used in figure 2B. Uses Treatment_list.csv and
breseq_output_with_verification.txtFitness versus similarityFitness and
similarity values used in Figure 3.FitnessSimilaritySummary.csvKendall
correlation- Similarity versus fitnessCalculates the correlation between
fitness of populations in a given environment and the similarity of the
populations to populations that evolved in that environment. Uses
FitnessSimilaritySummary.csvKendallCorrelationSimilarityVFitness.RPopulation sizePopulation size data for figure S1S1_Population_Size_Ancestral.txtS1 Population size R scriptANOVA of population size by treatment. Uses S1_Population_Size_Ancestral.txt.S1_Population_Size_ancestral.RFitnessFitness data for figure S2. Fitness of each population relative to the ancestor in its evolutionary environment.S2_Fitness.csvBiofilm productionBiofilm production data for Figure S3.S3_Biofilm_Production.txtBiofilm analysis scriptANOVA of biofilm production by treatment.S3_BiofilmANOVA.R