Diversity_and_Fitness

This file contains the relative fitness data and diversity data calculated as CV* for generations 500 and 100

Relative contributions of adaptation were larger than chance.

<p>Relative contributions of adaptation and chance to (A) fitness, (B) mean colony size and (C) colony size diversity. Error bars represent 95% confidence intervals. The effect of adaptation was measured as the difference between the mean trait value of the derived populations and the trait value of the ancestor. The effect of chance was calculated as the square root of the genetic variation among microcosms.</p

Trait Evolution of Fitness, Fitness Diversity, Mean Colony Size and Colony Size Diversity in 12 Independently Evolved Microcosms after 1000 Generations (Comparison between Ancestor and Derived).

a)<p>Relative Fitness as determined in competition with the ancestor, by definition the relative fitness of the ancestor is 1.</p>b)<p>Fitness variance determined as the CV* of relative fitness of individual colonies isolated from a microcosm.</p>c)<p>Colony size diversity is assessed as CV* of colony sizes within a microcosm.</p

Fitness and colony size diversity increased and mean colony size decreased over the course of the experiment.

<p>Trait evolution of (A) fitness, (B) mean colony size and (C) colony size diversity at generation 500 and 1000 (mean of twelve populations with 95% CI).</p

Analysis of the Rate of Change of the Microcosms over 1000 Generations.

a<p>Values are means and 95% confidence intervals based upon <i>t</i>-distribution with df  = 11.</p>b<p>Rate of change during the last 500 generations was calculated as twice the rate of change during 1000 generations minus the rate of change during the first 500 generations.</p>c<p>Difference calculated as rate of change during the first 500 generations minus the rate of change during the last 500 generations.</p>d<p>Null hypothesis is that the difference in slopes is equal to zero.</p>e<p>Two-tailed probability computed from the <i>t</i>-distribution with df  = 11.</p>f<p>In pixels.</p

Genetic Variation for Relative Fitness, Fitness Variation, Frequency Dependence, Mean Colony Size and Colony Size Diversity Among 12 Independently Derived Microcosms.

a<p>Microcosms: For frequency dependence, df  = 10, all other df  = 11.</p>b<p>Block: df  = 2.</p>c<p>Error in Single Factor ANOVA: For relative fitness at generation 1000 df  = 22; all other df  = 24.</p

Diverse colony morphologies evolved in all twelve microcosms.

<p>(A) Colony size diversity after 1000 generations of selection. Populations are grouped by arabinose marker (ara+ and ara−), with the ancestors 606 (ara−) and 607 (ara+) to the left and the derived populations on the right. (B) Colony size diversification of the 12 microcosms. Colony size diversity (H') was calculated for every population using the Shannon-Wiener index. Each point represents the mean of colony size diversity (H') of all 12 microcosms. Error bars represent 95% confidence intervals.</p

Parallel evolution suggests genes that may contribute to TGC resistance.

<p>Venn diagrams represent (A) the number of mutations, (B) nsSNPs, or (C) genes that were observed in the individual trials or combined (Trial 1, green; Trial 2 blue). (D) Genes mutated in both trials were plotted based on the number of mutations in the gene and the percentage of clones that contained at least one mutation in the gene. False noise was added to the number of mutations in each gene to separate the spots. <i>P</i> values were calculated using Fisher’s Exact Test. Genes with <i>p</i> values < 0.001 are labeled. Due to its role in TGC resistance, <i>rpsJ</i> was also labeled.</p

Frequencies of alleles associated with TGC resistance from Trial 1.

<p>Whole-genome sequencing data of mixed populations were collected every 24 hr. For clarity only mutations in the candidate genes <i>adeS</i>, <i>gna</i>, <i>rpsJ</i>, <i>rrf</i>, and <i>msbA</i> are shown. The mutations are grouped by gene. Each frequency is represented by the width (y-axis) of the colored object at the corresponding day (x-axis). The dashes on the left indicate a frequency of 20% and can be used as a scale to determine the frequency of a mutation on a specific day. Gray lines demark the different TGC concentrations in the culture.</p

<i>adeS</i> mutations increase TGC MIC, but not to the level detected in bioreactor isolates.

<p>Strains were cultured in MHBII with increasing amounts of TGC to measure the growth rate. The MIC of each strain is the point where the growth rate equals 0. Error bars represent the 95% confidence interval.</p