Hi Jurriaan- I've been thinking about this after your email and my sense is that such a simulation would be very difficult. Just dropping onto the tree branching events on the extant tree that only produced one living daughter might not be too difficult under a homogenous birth-death model. However, some of those extinct lineages coming off those nodes could actually be clades of considerable size, and you'd still have to condition in the simulation on those clades going extinct before the modern... which sounds difficult to me. In addition, the probability of getting an unobserved node and the size of the unseen, extinct clades would vary the closer you get to the modern (the branch length probabilities in Mooers et al., 2012, Syst. Biol. might be useful here). Someone else on the list might know better and know of an elegant way around these issues.
My suggestion is that there might be easier ways to get whatever it is you'd like from these simulations. For example, if you'd like to estimate the expected number of total number of extinct and surviving lineages for some surviving lineage, the appendix for Raup (1985) provides some equations that might be useful for you. -Dave On Mon, Sep 30, 2013 at 2:05 PM, Jurriaan de Vos <jurriaan_de...@brown.edu> wrote: > 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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
