diversification analysis

[felipe lamarca]

Hi, I am trying to do a diversification analysis in BAMM and my tree result shows model 0, no rate changes, with only an evolving rate dynamic and the plot shows this.
I don't know if it is my data that really shows no rate changes or if it is some error.

Here are the files I am using. 

[pasca...@gmail.com]

Hi,

Can you please share your control file as well? I can take a look.

Thanks,

-Pascal

[felipe lamarca]

[pasca...@gmail.com]

Hi,

It may be true that BAMM finds no evidence for notable rate shifts in this tree. But one thing you should be doing is setting some of the priors to values calculated with the setBAMMpriors() function in BAMMtools. The values calculated with your tree are substantially different from the default values.

When I do this, I get more variability in the posterior than you do. There are occasionally one or two shifts sampled in the posterior.

-Pascal

[felipe lamarca]

Thank you for answer.
What do I need to change in the analysis because I don't have an estimate of the extinction rate? Does this affect the analysis?

[pasca...@gmail.com]

In the R package BAMMtools, you need to run the function setBAMMpriors with your tree. It will generate some parameter values that you can use in your BAMM controlfile. See this page on the BAMM website and look for the section that starts with "One other block of parameters can be critical to BAMM performance: the priors". The values you get will replace the default value that are in the standard control file. You don't need an estimate of extinction rate. This will affect your analyses.