Additional file 4.
Table S1: Parameters and example calculations utilized in divergence age estimates. (Top table) Summary of age estimates for Dehalococcoides-related genetic divergence utilizing four different models for rate of evolution: (1) estimated universal bacterial rate of evolution in nature , (2) in vitro E. coli empirically derived rate of evolution , (3) empirical Dehalococcoides rate based on observed mutations in the whole genomes of strain 195 and its resequenced variant in the DONNA2 sister culture (see Methods), and (4) the 16S rRNA gene clock model. For ages based on the first two rates of evolution, we further considered six different values for doubling time that span a range relevant to Dehalococcoides, including four published values for Dehalococcoides growth in laboratory culture [4,6,88,96], other anaerobic bacterial growth rates , and values derived from environmental anaerobic systems [48,49], as well as one arbitrarily large value (130 days) intended to represent general substrate-limited conditions. The left two columns indicate the divergence being considered and the tree calculation method, respectively. Ages are presented in units of 1 million years. (Middle Two Tables) Referenced summary of growth rates utilized for the age estimate calculations. (Bottom Table) Sample calculation for length of time to a single mutation, given rates of evolution taken from literature and the averaged Dehalococcoides growth rate.
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McMurdie et al. BMC Genomics 2011 12:287 doi:10.1186/1471-2164-12-287