User:R. Eric Collins/MBL/Support

Branch Support and Tests

• Bootstrap
  • hat ^ signifies observed
  • not required to use majority-rule, sometimes 'rogue' taxa jump around and ruin support
  • tree/bootstrap as 'summary' of results (i.e. not the end all and be all)
  • asterisk * refers to boostrapped value

• CAN'T USE KH TEST TO COMPARE AN A PRIORI TREE TO YOUR BEST ML TREE
• SH test
  • if your model is too simple, you can overestimate branch support
  • in PAUP, include *all* trees for SHtest, not just 2 you're interested in because it takes all of them into account

p-value== how often do you get support for the alternate when the null hypothesis is true?

• • bootstrap proportion > 0.95 can sometimes be used as equivalence to 0.05 p-value
  • but... curved boundaries in treespace invalidate D ~ 1 - BP relationship
  • triple-point (star tree) corrected by Susko 2010
  • un-adjusted (Felsenstein) bootstraps tend to UNDERESTIMATE on a priori tree
  • for highly-supported branches (~ >70%), bootstrap proportions actually work quite well as estimates for p-values
  • things based on bootstraps are more robust to changes in model