What does the tree prior mainly shape in a dated analysis?

• The file format of the alignment
• Node ages through expectations about speciation and extinction
• The number of bootstrap replicates to run

What does a posterior probability of 0.95 on a clade mean?

• The clade appears in 95 percent of the posterior trees
• The clade was resampled in 95 percent of bootstrap replicates
• The clade covers 95 percent of the sequence length

A posterior probability and a bootstrap proportion answer the same question about a clade.

Your chain shows a low effective sample size and a trace that drifts upward. What do you do?

• Quote the posteriors with extra decimals
• Lengthen the run and check independent runs before quoting anything
• Delete the drifting part and publish the rest silently

Your dates swing widely when you try reasonable alternative priors. What should you conclude?

• The chain has converged and the dates are firm
• The sequences are long enough to ignore priors
• The priors are carrying the conclusion, not the data

Two independent runs give very different posteriors for the same clade. What does that mean?

• The runs disagree, so the chain has not converged
• The runs prove the clade is absent from the tree
• The runs show the prior was uniform

You move from a strict clock to a relaxed clock prior. What changes in your model?

• Rates may now vary freely across branches instead of staying shared
• Node ages become fixed and immune to the tree prior
• Bootstrap replicates replace the posterior distribution

A colleague quotes 0.99 from one short chain with no convergence checks as proof of a clade. What is the flaw?

• High posterior values never need any checks
• Only bootstrap values above 0.99 count as proof
• An unconverged sampler can report strong support that means nothing yet