Genome-scale rates of evolutionary change in bacteria

摘要: Estimating the rates at which bacterial genomes evolve is critical to understanding major evolutionary and ecological processes such as disease emergence, long-term host-pathogen associations, short-term transmission patterns. The surge in genomic data sets provides a new opportunity estimate these reveal factors that shape dynamics. For many organisms estimates of rate display an inverse association with time-scale over are sampled. However, this relationship remains unexplored bacteria due difficulty estimating genome-wide rates, impacted by extent temporal structure prevalence recombination. We collected 36 whole genome sequence from 16 species pathogens systematically compare their assess absence majority (28/36) possessed sufficient clock-like robustly rates. some reliable were not possible even “ancient DNA” sampled centuries, suggesting they very slowly or extensive variation among lineages. estimated spanned several orders magnitude, 10-6 10-8 nucleotide substitutions site-1 year-1. This was largely attributable sampling time, strongly negatively associated best described exponential decay curve. To avoid potential estimation biases time-dependency should be considered when inferring time-scales bacteria.