I have selected representative strains from each cluster in my Maximum Likelihood tree for divergence dates estimation but I made sure I covered the entire time period of detection of these strains (1975-2012). Will my exclusion of some of the strains affect my estimated evolutionary rate and times of divergence at the nodes after BEAST analysis?
Sorry, but that's question is way beyond my understanding of Bayesian Analysis.
Since it is a bayesian method, anything related to the data influence the output. Excluding some taxa should not influence so much the estimate, but the distribution of them across the years may do. If you have more taxa from a specific range of time, this may drive the estimate towards one direction rather than another. The punctual estimate may not change, but then you can have a broader 95% HPD.
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