Dear list, I am interested in determining how many times a trait was gained across a phylogeny. So I simulated the evolution of the trait (using simmap in phytools) and I can look at the mean number of gains across in the simulations, which in my case was ~20. However, I would also like to be able to point at the nodes where the trait was likely gained on my tree. For this, I simply rounded the posterior probability at each node to either 0 or 1. However, this only gives me 18 nodes where the trait was likely gained. I think I can see why there is a difference between those numbers; although there are 20 gains on average, since those gains aren’t always going to occur on the same nodes, then there aren’t going to be 20 nodes with a probability of gaining the trait >0.5.
My question is (1) is my logic right as to why that discrepancy exists, and (2) if I want to say “this trait likely evolved X number of times”, which is the more correct way to get that number? Should I report the mean/median (maybe with confidence intervals), or does it make more sense to look at the posterior probability at each node and get a number that way? Any input would be appreciated, phylogenetics is still pretty new to me! Thanks, Lucas — Lucas Eckert (he/him) www.lucaseckert.ca<http://www.lucaseckert.ca> MSc Student | McGill University Barrett and Bell Labs | Redpath Museum and Department of Biology [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
