Dear list members, I am grateful for any pointers related to the following problem:
I am trying to simulate extinct taxa "into" a completely sampled phylogeny of extant taxa. I can estimate lambda and mu for a phylogeny under the time-homogeneous birth-death model. I want to use these values to simulate trees that contain also the extinct taxa, but, here's the crux, the topology of the extant taxa needs to remain the same. (I only want to add branches that eventually go extinct, keeping the branching times among extant taxa unchanged. If I prune extinct taxa, the tree must be identical to the original tree.) I have been unsuccessful in finding a solution. Is there any function implemented that does this? Reason that I want to keep the original tree is that I want to do simulations for trees with multiple MEDUSA-style rate-partitions. I can disassamble the tree in into its rate partitions and simulate trees that satisfy lambda, mu, extant taxa and age of the partitions, but to correctly reassamble the tree, the topological relations among extant members of rate partitions should remain unchanged. Thanks in advance for any help! Juri -- Jurriaan M. de Vos, PhD Research Associate, Edwards Lab Dept. of Ecology and Evolutionary Biology Brown University Providence, RI, USA _______________________________________________ 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/
