Hi Pas, No worries, we have all done an accidental "Reply All" more than once! >I estimated ancestral (and tip) values for which I have real data via >BM assumption to see how good the fit is Can you clarify? Unless you have some a priori hypothesis to test about a particular tip (or set of tips, such as a whole clade), then why would you estimate their values and how would you do this? Did you just delete one at a time, crank the numbers (presumably yielding the same values as you would get from Garland and Ives, 2000), and see what you got? Whether it is a "tip" or a fossil taxon (which is just a tip with a branch that terminates before now), the confidence intervals on the predicted values will be hugely affected by how long the branch is to that taxon (the longer the branch, the wider the prediction intervals). And also by how many "close relatives" are attached to the node it comes from, and by how much phenotypic diversity exists in those "close relatives." >The bottom line is answering the question: how long should the branch >leading to that particular species be if it evolved at the same rate of its >sister species? That's an interesting way to look at it (a sort of inverse [perverse?] parameterization), but it does not give you any additional information beyond asking whether a taxon is an "outlier" via the tests we have discussed a bit ago. Or am I missing something? Cheers, Ted From: pasquale.r...@libero.it [pasquale.r...@libero.it] Sent: Friday, August 05, 2011 12:38 PM To: j...@gs.washington.edu Cc: dwba...@uchicago.edu; hu...@si.edu; Theodore Garland Jr; r-sig-phylo@r-project.org Subject: R: Re: R: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips
Folks, I was intending my most recent message to be off-list and didn't realize "r-sig-phylo@r-project.org" was in the CC field, which means I'm a fool. All kidding aside, yes Joe, I estimated ancestral (and tip) values for which I have real data via BM assumption to see how good the fit is. Actually, estimated values are very close to real values for some species, barely so for some others, and absolutely not for others still. The good news is that since there is a single mode of evolution tree wise, deviations from real values really mean that evolution is accelerated, or decelerated, either, in these particular lineages for which a significant deviation from the expected value is noticeable. What I', trying to do now is writing a R routine to back-calculate the "expected" branch lengths for the "unusual" critters, given the fitted ancestral values and tip values of the phenotypes, and assuming BM, in order to compare the actual branch lengths to the expected. The ratio of these ! lengths, if I'm not delusional and definitely lucky, is a per-lineage rate of phenotypic evolution. The bottom line is answering the question: how long should the branch leading to that particular species be if it evolved at the same rate of its sister species? Pas ----Messaggio originale---- Da: j...@gs.washington.edu Data: 05/08/2011 21.04 A: "pasquale.r...@libero.it"<pasquale.r...@libero.it> Cc: <dwba...@uchicago.edu>, <hu...@si.edu>, <theodore.garl...@ucr.edu>, "r-sig-phylo@r-project.org"<r-sig-phylo@r-project.org> Ogg: Re: R: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips Folks -- I was intending my most recent message to be apologetic -- that I was perhaps overreactive. Certainly Pas has not raised unreasonable objections or been obstructive with my grants! (Others have). Let me raise an issue so I understand him more clearly: Pas, are you saying that you see phenotypes in the fossils that seem incompatible with the Brownian Motion assumption? Joe ---- Joe Felsenstein j...@gs.washington.edu Dept of Genome Sciences and Dept of Biology, Univ. of Washington, Box 5065, Seattle Wa 98195-5065 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
