DOI: 10.5061/dryad.53n0rf5
title: Data from: Parallel genetic adaptation across environments differing in mode of growth or resource availability

description: 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.
description: 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