Fig. 2: Substitution rate variation in Y. pestis.
From: Plagued by a cryptic clock: insight and issues from the global phylogeny of Yersinia pestis
A A root-to-tip regression on mean sampling age using all genomes from the maximum likelihood phylogeny. B A root-to-tip regression on mean sampling age by population. The distance to the population MRCA was calculated using subtrees extracted from the maximum likelihood phylogeny. C Bayesian substitution rates within and between populations. For each branch in the maximum clade credibility (MCC) trees, we extracted the estimated substitution rate (subs/site/year) and converted this to subs/year based on an alignment of 4,229,098 genomic sites.
