Investigating evolutionary rate variation in bacteria

Rates of molecular evolution are known to vary between species and across all kingdoms of life. Here we explore variation in the rate at which bacteria accumulate mutations (accumulation rates) in their natural environments over short periods of time. We have compiled estimates of the accumulation rate for over 34 species of bacteria, the majority of which are pathogens evolving either within an individual host or during outbreaks. Across species we find that accumulation rates vary by over 3700- fold. We investigate whether accumulation rates are associated to a number potential correlates including genome size, GC content, measures of the natural selection and the time-frame over which the accumulation rates were estimated. After controlling for phylogenetic non-independence, we find that the accumulation rate is not significantly correlated to any factor. Furthermore, contrary to previous results we find that it is not impacted by the time-frame of which the estimate was made. We conclude that much of the rate variation is probably explained by variation in the generation time. We attempt to estimate doubling times of bacteria in the wild using a new method. We estimate the DT for five species of bacteria for which we have both an accumulation and a mutation rate estimate. We also infer the distribution of DTs across all bacteria from the distribution of the accumulation and mutation rates. Both analyses suggest that DTs for bacteria in the wild are substantially greater than those in the laboratory, that they vary by orders of magnitude between different species of bacteria and that a substantial fraction of bacteria double very slowly in the wild.