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/
