Investigating Evolutionary Rate Variation in Bacteria

Abstract

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. However, our study, with only 34 species, is likely to lack power to detect anything but large effects. We suggest that much of the rate variation may be explained by differences between species in the generation time in the wild.

Keywords: Accumulation rate; Bacteria; Evolutionary rate; Mutation.

Fig.  1

Distribution of accumulation rate estimates for 34 species of bacteria

Fig.  2

The accumulation rate vs sampling time. Yersinia pestis and Mycobacterium leprae are highlighted as outliers

Fig.  3

The accumulation rate vs sampling time split for the 12 species for which we have multiple estimates

Fig.  4

The expected relationship between the accumulation rate at selected sites relative to neutral sites and sampling time. In panels A and B, the shape parameter of the gamma distribution is varied 0.25 (top line), 0.50 (middle) and 0.75 (bottom); in panels C and D the mean strength of selection, multiplied by N, is varied from 10 (top), 100 (middle) and 1000 (bottom). Panels A and C show the relative accumulation rate over the first 0.1 N generations, panels B and D over the first 4 N generations

Fig.  5

a The accumulation rate vs genome size (Buchnera aphidicola is highlighted as an outlier). b phylogenetic independent contrasts for the accumulation rate vs genome size

Fig.  6

a The accumulation rate vs GC content (Buchnera aphidicola is highlighted as an outlier). b phylogenetic independent contrasts for the accumulation rate vs GC content