The mean substitution rate estimates for MSV and SSRV are between 2.0 × 10-4 and 3.5 × 10-4 subs/site/year. For the six-year MSV-B and MSV-F and the 32-year SSRV evolution experiments, substitution rate estimates made using a range of demographic and molecular clock models are presented. Whereas black squares indicate the most probable substitution rates, vertical bars indicate the 95% highest probability density of the substitution rate estimates. Red squares indicate rates estimated using the best fit demographic and clock models (determined using Bayes factor tests; Additional file 1). Stars indicates the models that returned the highest likelihood. When more than one red square is shown for a particular dataset this indicates that neither demographic model provided better support for the data. For purposes of comparison, previous estimates of substitution rates are presented (in the grey area) for both MSV (full genome sequences sampled during shorter term evolution experiments lasting between 2 months and 5 years; [9, 22] from individual plants) and the begomoviruses, TYLCV (full genome sequences sampled from nature over 19 years ), East African cassava mosaic virus (EACMV, full genome sequences sampled from nature over 8 years ), Tomato yellow leaf curl China virus (TYLCCV, partial genome sequences sampled over 1 to 2 months from individual plants ) and TYLCV (full genome sequences sampled over 1 month from individual plants).