[R-sig-phylo] R: Re: R: Re: R: ancestral state reconstruction for tips
Hi All, I'm happy I have stimulated some discussion about this subject matter. For some reason I can't imagine it looks this whole thing is going to be somehow personal and I have not posted this last e-mail to the list as a consequence. Joe, unfotunately I never attended a lecture of yours, and didn't raise trivial distinctions and objections to a grant proposal you submitted. My intention was not to be critical about BM or ICs, or whatever. I just wanted to point it out that things are sometimes a bit too complex and some unreliable predictions from our models may slip out unnoticed evey now and then, as I believe it is apparent reading the literature (including my own, of course). Having said that, my guess was that we *may* use the BM and computations at nodes to see where (in which lineages) do phenotypes appear very different from predictions. For instance, I think it could be somehow possible to use estimated ancestral charactes to see how much the inclusion of some fossil (or new) species changes the estimated value (e.g. by creating a polytomy by the inclusion of the new species), or even back-calculate branch lenghts (under BM assumption) for these unusual phenotypes to see how much evolution accelerates in these lineages (by comparison with real branch lengths). I hope I spoke my mind more clearly at this time. Pas Messaggio originale Da: dwba...@uchicago.edu Data: 05/08/2011 20.23 A: Joe Felsensteinj...@gs.washington.edu Cc: r-sig-phylo@r-project.orgr-sig-phylo@r-project.org Ogg: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips As the diversity of explicit models of trait evolution grow, it will be interesting to see if any consensus develops about which models hold most often in general and whether any insight is gained into which conditions predict appearance of different models. I think Joe is right that realizing a model is an inaccurate or imprecise description of reality should impel us to develop better models of the world around us, because this partly how science moves forward. However, I don't think pointing out that a model is deficient requires that that person must themselves develop an alternative. After all, an alternative model that capture a more realistic level of complexity may not be possible in some situations (it is certainly possible in trait evolution models, however.) Requiring such a thing would put too much pressure on scientific whistle-blowers, who play a very important role in reminding the rest of us that the world is more than the models we use to understand it and make our predictions. -Dave On Fri, Aug 5, 2011 at 10:51 AM, Joe Felsenstein j...@gs.washington.edu wrote: Pasquale Raia said: Of course Ted is right, but my problem with this computation, or with the simple exercise I was proposing is well another: as a paleontologist I often come across pretty exceptional phenotypes (dwarf hippos and elephants, huge flightless birds, to make a few examples). When you use methods like this (I mean Garland and Ives') and compare the output with those phenotypes, as I did, you immediately realize what the the bottom line is: no matter if they are nodes or tips, by using the expected (under BM) covariance the estimated phenotypes are dull, perfectly reasonable but very different from anything exceptional you may find yourself to work with. This is why I feel it is difficult to rely on those (unobserved) values to begin with. I think that what is being said is that Brownian Motion is too sedate a process and does not predict some of the large changes actually seen in the fossil record. That's a legitimate point but does put the onus on the maker of the point to propose some other stochastic process that is tractable and has these large changes (and that fits with known Mendelian and Darwinian mechanisms). Just complaining that the Brownian stochastic process is no good is insufficient. If we want to add the fossils to the calculation, then they will of course pressure the Brownian Motion process to change more in their vicinity, which may help some. Joe Joe Felsenstein j...@gs.washington.edu Dept of Genome Sciences and Dept of Biology, Univ. of Washington, Box 5065, Seattle Wa 98195-5065 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- David Bapst Dept of Geophysical Sciences University of Chicago 5734 S. Ellis Chicago, IL 60637 http://home.uchicago.edu/~dwbapst/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] R: Re: 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 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] R: Re: R: Re: R: ancestral state reconstruction for tips
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.itpasquale.r...@libero.it Cc: dwba...@uchicago.edu, hu...@si.edu, theodore.garl...@ucr.edu, r-sig-phylo@r-project.orgr-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
