A simple test to infer mode of selection in metagenomics time series of evolving asexual populations

ABSTRACTWe introduce a simple test to infer mode of selection (STIMS) in metagenomic time series of evolving asexual populations. STIMS compares the tempo of molecular evolution for a gene set of interest against a null distribution that is bootstrapped on random gene sets. We test STIMS on metagenomic data spanning 62,750 generations of Lenski’s long-term evolution experiment with E. coli (LTEE). Our method successfully recovers signals of purifying selection and positive selection on gold standard sets of genes. We then use STIMS to study the evolution of genetic modules in the LTEE. We find strong evidence of ongoing positive selection on key regulators of the E. coli gene regulatory network. Key regulatory genes show evidence of positive selection over the entire time series, even in some hypermutator populations. By contrast, we found no signal of selection on the genetic modules that show the strongest transcriptional responses to changes in growth conditions. In addition, the cis-regulatory regions of key regulators are evolving faster than the cis-regulatory regions of their downstream regulatory targets. These results indicate that one mechanistic cause for ongoing fitness gains in the LTEE is ongoing fine-tuning of the gene regulatory network.