1. Send me a PDF or screenshot of your MAP tree (you can open it in FigTree)
Primates_MAP_tree

Primates_MAP_tree

  1. Take a look at your log file in tracer. Does it look like your analysis has converged? Name two or more ways you could alter your MCMC to improve it.

It does not look like this analysis has converged. ESS scores are very low. This could have been improved by running the analysis for more generations (searching more tree space), or by introducing a more informative prior.

  1. Figure out how to alter the script such that effective population size is fixed across the tree. Rerun the analyses with your new script. What is your estimate for effective population size? Do you believe the estimate? Why or why not?

The ESS values were also terrible (incredibly low) with fixed populations. I would not trust these estimates. The lack of convergence shows the lack of sufficient searching of an accurate value.

  1. BONUS: What does it mean to “run the analysis under the prior?” Why would this make # the analysis run faster? Try it, and tell me how much time it saved you.