Re: [R-sig-phylo] Unexpected behaviour: all.equal.phylo(), unique.multiPhylo(), and un/rerooting phylo objects
Hi David, It's a follow-up on your message. David Williams wrote on 22/06/2011 07:31: Dear R users and phylogeneticists, I've been manipulating some phylo objects mostly with ape functions but also with some phangorn functions. I'm a bit confused with some effects of rerooting and the output of various functions. Any help would be greatly appreciated! R code: ## Rerooting seems to fail sometimes: library(ape) tree - read.tree(text=G:1,H:1)g:1,(((A:1,B:1)c:1,(C:1,D:1)d:1)b:1,(E:1,F:1)e:1)a:1)f:1,K:1)h:1,I:1,J:1)i;) clan - list(c(G,H),c(A,B,C,D,E,F))[[2]] layout(matrix(c(1,2), 1, 2), width = c(1, 1)) plot(tree,'u');nodelabels() treeR - root(tree, outgroup = c(I,J,K), resolve.root = F) plot(treeR,'u');nodelabels() treeR$edge[1] reorder(treeR)$edge[1] ## the root node of treeR is unchanged and within the requested ## outgroup :-( This was a bug which is now fixed: https://svn.mpl.ird.fr/ape/dev/ape/R/root.R plot(tree,'u');nodelabels() treeR - root(tree, outgroup = c(G,H), resolve.root = F)# put the root elsewhere temporarily treeR - root(treeR, outgroup = c(I,J,K), resolve.root = F) plot(treeR,'u');nodelabels() treeR$edge[1] reorder(treeR)$edge[1] ## the root node of treeR is now at the base of the outgroup as ## expected :-) but an additional rerooting was necessary. That was indeed a work-around. ## all.equal.phylo() and therefore unique.phylo() are sensitive to edge ## order in the edge matrix in unrooted trees: clado1 - read.tree(text=((:1,(:1,:1):1):1,:1,((:1,:1):1,((:1,:1):1,:1):1):1);) clado2 - read.tree(text=((:1,(:1,:1):1):1,(:1,:1):1,(:1,((:1,:1):1,:1):1):1);) plot(clado1,'u');tiplabels();nodelabels() plot(clado2,'u');tiplabels();nodelabels() ## I would say these are topologically identical is.rooted(clado1)# FALSE is.rooted(clado2)# FALSE ## confirm these phylo objects are not rooted all.equal.phylo(clado1,clado2,use.tip.label=F,use.edge.length=F)# FALSE The difficulty is that these trees have empty strings as tip labels, so the algorithm used by all.equal.phylo does not work in this situation. However, this affects only the unrooted trees as you noted. I'm going to add a warning in the help page to mention this fact. Thanks for the report (and your patience). Cheers, Emmanuel ## all.equal.phylo thinks they are different . . . . length(unique(c(clado1,clado2)))# 2 ## things are as expected if a root is added in equivalent places: library(phangorn) plot(midpoint(clado1),'u');tiplabels();nodelabels() plot(midpoint(clado2),'u');tiplabels();nodelabels() ## I would say these are topologically identical ## all.equal.phylo agrees this time all.equal.phylo(unroot(midpoint(clado1)),unroot(midpoint(clado2)),use.tip.label=F,use.edge.length=F) # TRUE length(unique(c(midpoint(clado1),midpoint(clado2#1 ## if the phylo objects are topologically identical, I would expect ## a Robinson-Foulds distance of 0 RF.dist(clado1,clado2)# 4 RF.dist(reorder(clado1),reorder(clado2))# 4 RF.dist(reorder(midpoint(clado1)),reorder(midpoint(clado2)))# 6 RF.dist(midpoint(clado1),midpoint(clado2))# 6 Thanks! -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] R: ancestral state reconstruction for tips
Hi Morgan, this is just stuff for thought, and remember, this is wrong anyway. But you may try something like this: 1. compute pics, 2. take the pic value at the ancestral node subtending to your unknown tip, 3. pretend one of the two tips the pic was originally computed on is in fact your unknown species, 4. modify the square of the summed branch lengths of the two species by using the new bl, 5. use the formula for pics (standardized) to derive your unknown tip value by using the other (real) species tip value and the new square of summed branch lengthts but again, remember this is wrong, because contrasts were computed without your unknown species. With ace everything turns out to be much more complicated because ancestral value estimations are 'optimized' by taking the entire tree and distribution of values at once, so to speak. Messaggio originale Da: morgan.g.i.langi...@gmail.com Data: 05/08/2011 14.15 A: r-sig-phylo@r-project.org Ogg: [R-sig-phylo] ancestral state reconstruction for tips I was wondering if there is a way to get ancestral state reconstructions not for nodes within the tree but for tips that I don't know the trait of. I could do this somewhat manually, by taking the ancestral state resconstruction from the parent and child nodes surrounding where my unknown tip branches off from the tree and averaging those results (weighted by the branch length). This approach seems kind of clunky, so I was hoping there was something better. Morgan Langille ___ 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: ancestral state reconstruction for tips
Also, the issue of predicting values for unknown tips using data from other species in the tree is considered in this reference: Garland, T., and A. R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155(3):346-364. Best, Gene On 8/5/11 11:31 AM, pasquale.r...@libero.it pasquale.r...@libero.it wrote: Hi Morgan, this is just stuff for thought, and remember, this is wrong anyway. But you may try something like this: 1. compute pics, 2. take the pic value at the ancestral node subtending to your unknown tip, 3. pretend one of the two tips the pic was originally computed on is in fact your unknown species, 4. modify the square of the summed branch lengths of the two species by using the new bl, 5. use the formula for pics (standardized) to derive your unknown tip value by using the other (real) species tip value and the new square of summed branch lengthts but again, remember this is wrong, because contrasts were computed without your unknown species. With ace everything turns out to be much more complicated because ancestral value estimations are 'optimized' by taking the entire tree and distribution of values at once, so to speak. Messaggio originale Da: morgan.g.i.langi...@gmail.com Data: 05/08/2011 14.15 A: r-sig-phylo@r-project.org Ogg: [R-sig-phylo] ancestral state reconstruction for tips I was wondering if there is a way to get ancestral state reconstructions not for nodes within the tree but for tips that I don't know the trait of. I could do this somewhat manually, by taking the ancestral state resconstruction from the parent and child nodes surrounding where my unknown tip branches off from the tree and averaging those results (weighted by the branch length). This approach seems kind of clunky, so I was hoping there was something better. Morgan Langille ___ 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 -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm ___ 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: ancestral state reconstruction for tips
The methods in the Garland and Ives (2000) paper are in our package of DOS PDAP programs, and should also be functional in the PDAP module of Mesquite. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Hunt, Gene [hu...@si.edu] Sent: Friday, August 05, 2011 8:35 AM To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] R: ancestral state reconstruction for tips Also, the issue of predicting values for unknown tips using data from other species in the tree is considered in this reference: Garland, T., and A. R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155(3):346-364. Best, Gene On 8/5/11 11:31 AM, pasquale.r...@libero.it pasquale.r...@libero.it wrote: Hi Morgan, this is just stuff for thought, and remember, this is wrong anyway. But you may try something like this: 1. compute pics, 2. take the pic value at the ancestral node subtending to your unknown tip, 3. pretend one of the two tips the pic was originally computed on is in fact your unknown species, 4. modify the square of the summed branch lengths of the two species by using the new bl, 5. use the formula for pics (standardized) to derive your unknown tip value by using the other (real) species tip value and the new square of summed branch lengthts but again, remember this is wrong, because contrasts were computed without your unknown species. With ace everything turns out to be much more complicated because ancestral value estimations are 'optimized' by taking the entire tree and distribution of values at once, so to speak. Messaggio originale Da: morgan.g.i.langi...@gmail.com Data: 05/08/2011 14.15 A: r-sig-phylo@r-project.org Ogg: [R-sig-phylo] ancestral state reconstruction for tips I was wondering if there is a way to get ancestral state reconstructions not for nodes within the tree but for tips that I don't know the trait of. I could do this somewhat manually, by taking the ancestral state resconstruction from the parent and child nodes surrounding where my unknown tip branches off from the tree and averaging those results (weighted by the branch length). This approach seems kind of clunky, so I was hoping there was something better. Morgan Langille ___ 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 -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm ___ 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
[R-sig-phylo] R: Re: R: ancestral state reconstruction for tips
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. Any opinion? Pas Messaggio originale Da: theodore.garl...@ucr.edu Data: 05/08/2011 18.24 A: Hunt, Genehu...@si.edu, r-sig-phylo@r-project.orgr-sig-phylo@r- project.org Ogg: Re: [R-sig-phylo] R: ancestral state reconstruction for tips The methods in the Garland and Ives (2000) paper are in our package of DOS PDAP programs, and should also be functional in the PDAP module of Mesquite. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Home Phone: (951) 328-0820 Facsimile: (951) 827-4286 = Dept. office (not confidential) Email: tgarl...@ucr.edu http://www.biology.ucr.edu/people/faculty/Garland.html Experimental Evolution: Concepts, Methods, and Applications of Selection Experiments Edited by Theodore Garland, Jr. and Michael R. Rose http://www.ucpress.edu/book.php?isbn=9780520261808 (PDFs of chapters are available from me or from the individual authors) From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Hunt, Gene [hu...@si.edu] Sent: Friday, August 05, 2011 8:35 AM To: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] R: ancestral state reconstruction for tips Also, the issue of predicting values for unknown tips using data from other species in the tree is considered in this reference: Garland, T., and A. R. Ives. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic comparative methods. American Naturalist 155(3):346-364. Best, Gene On 8/5/11 11:31 AM, pasquale.r...@libero.it pasquale.r...@libero.it wrote: Hi Morgan, this is just stuff for thought, and remember, this is wrong anyway. But you may try something like this: 1. compute pics, 2. take the pic value at the ancestral node subtending to your unknown tip, 3. pretend one of the two tips the pic was originally computed on is in fact your unknown species, 4. modify the square of the summed branch lengths of the two species by using the new bl, 5. use the formula for pics (standardized) to derive your unknown tip value by using the other (real) species tip value and the new square of summed branch lengthts but again, remember this is wrong, because contrasts were computed without your unknown species. With ace everything turns out to be much more complicated because ancestral value estimations are 'optimized' by taking the entire tree and distribution of values at once, so to speak. Messaggio originale Da: morgan.g.i.langi...@gmail.com Data: 05/08/2011 14.15 A: r-sig-phylo@r-project.org Ogg: [R-sig-phylo] ancestral state reconstruction for tips I was wondering if there is a way to get ancestral state reconstructions not for nodes within the tree but for tips that I don't know the trait of. I could do this somewhat manually, by taking the ancestral state resconstruction from the parent and child nodes surrounding where my unknown tip branches off from the tree and averaging those results (weighted by the branch length). This approach seems kind of clunky, so I was hoping there was something better. Morgan Langille ___ 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 -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm ___ 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 ___ 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: ancestral state reconstruction for tips
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
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
Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips
David Bapst wrote: 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. As a theoretician, I am perhaps oversensitive to the folks who, after a lecture in which I present a simple model, triumphantly declare but you didn't include predator satiation. Then they walk away looking very pleased with themselves. There is a similar problem with the quibblers who inhabit grant review panels, and are always asking me to do much more complicated models that are impossibly hard (and they are not aware how hard they are). Just understand, when you raise legitimate concerns, that us model-analyzers are also used to getting a lot of these unreasonable demands too, and may be grumpy as a result. 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: ancestral state reconstruction for tips
Hello everyone. I just wanted to say thank you for all of the responses so far and have thoroughly enjoyed the discussion. Just for reference I thought I would explain what I am doing in more detail and why I asked my original question. I am interested in developing a practical method for using 16s sequences to infer function. This is to hopefully aid in metagenomic experiments where we would like to compare the observed functions (quantity of a particular protein family) in a metagenomic sample to what we would expect based on the species that we believe are present in the sample based on 16s sequences (or possibly some other marker down the road). The current pipeline starts with a 16s reference tree for all Archaea and Bacteria completed genomes (~1400 species). We know the functions within these genomes so I would like to leverage that information along with the tree to predict (as best as possible) what the functions would be for a newly placed species on that tree. One method would be simply to take the nearest neighbour (the species with minimum 16s branch length) to the new species and use the functions encoded in that genome as a representative. However, this is very naive. I then turned to ancestral state reconstruction and current methods (if any) for predicting characters for species that we don't have information on for those traits. I realize that caution has to be used for predicting these functions, as mentioned below by Pasquale, but I am mostly searching for some best practices to use in my current situation. The results should be interesting since I will be testing how well the method does across ~1 functions (e.g. PFAMs). Many of these are not predictable at all since their phylogenetic signal is basically nill due to horizontal gene transfer. However, I am optimistic that many functions will be reliably predictable. Sincerely, Morgan Langille On Fri, Aug 5, 2011 at 2:51 PM, 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 ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[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: Re: R: ancestral state reconstruction for tips
Pas said: 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? Good way to approach it. If you can calculate the likelihood of trees, one way would be to not bother fitting any ancestral values: just try different lengths for the branch that connects the fossil to the tree, and see which one maximizes the likelihood. 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
