Dear Brian This is extremely useful. Many thanks for taking your time to write this for me.
Best wishes, Shinichi _____________________________________________________________ Dr Shinichi Nakagawa (Associate Professor / ARC Future Fellow) Deputy Director of Research, Evolution & Ecology Research Centre, EERC (Visiting Scientist at Garvan Institute of Medical Research) Room 568, Biological Sciences Building (D26) School of Biological, Earth and Environmental Sciences, BEES The University of New South Wales Randwick NSW 2052, Sydney, Australia Mobile: 0422 655 854 Office : 0293 859 138 Website: http://www.i-deel.org/ On Mon, Oct 31, 2016 at 1:42 AM, Brian O'Meara <omeara.br...@gmail.com> wrote: > Emmanuel's way is the most general and quickest (well, other than just > making up branch lengths entirely, using ape::compute.brlen() -- that's > even faster!). However, the original question was "best and most general" > for making ultrametric trees for phylogenetic comparative analysis. For an > analysis where branch lengths matter, as in many comparative methods > (ancestral state estimation, independent contrasts, diversification > analyses, etc), the *best* method probably involves data. Getting a tree > with branch lengths proportional to time uses calibrations, often from > fossils, and this is non trivial (requires substantial expertise in the > groups, can take some time to run, etc.). A few solutions here: > > 1) Start with chronograms: TreeBase initially prohibited trees with branch > lengths, so it probably isn't the best place to go. However, OpenTree does > have trees with branch lengths, with metadata on whether the branch lengths > represent time. You can access that using the rotl package and only pull > trees that are chronograms from its tree store. The datelife package ( > https://github.com/phylotastic/datelife: note COI that I'm lead author on > that) has a dataset of all OpenTree chronograms stored already, which makes > it even easier to get them, and you can use a function there to pull in an > updated list. It's often better to start with expert-calibrated chronograms > rather than do your own, especially if all you need is a set of trees. Note > that OpenTree has a bit over a hundred chronograms (anyone reading: > please add yours > <https://github.com/OpenTreeOfLife/opentree/wiki/Submitting-phylogenies-to-Open-Tree-of-Life> > -- you'll help advance science [and get more citations]); TimeTree.org has > thousands, but I believe they're not available for download and reuse. > However, you could reach out to the TimeTree authors for a potential > collaboration and perhaps access them that way. > > 2) Date yourself: take the trees from treebase, find calibrations from > other papers, and then use other programs (Beast, r8s, pathd8, treepl [COI: > coauthor], revbayes, etc.) to convert them into chronograms. You could wrap > these program in an R interface to do this. > > 3) Stretch: use geiger::congruify() to stretch your treebase trees to > other calibrated trees. This works for a pair of trees at a time; the > datelife package does this for your tree and all the trees in OpenTree with > overlapping taxa (but it's still alpha-level software, so use at your own > risk (and let me know if there are issues)). > > If you need ultrametric trees for some quick and dirty examples for using > comparative methods, the above is overkill; if you care about biological > results that are sensitive to branch lengths (and the degree to which > methods are sensitive to branch length errors does vary by method) you > might need to invest in the harder analyses. > > Best, > Brian > > > _______________________________________________________________________ > Brian O'Meara, http://www.brianomeara.info, especially Calendar > <http://brianomeara.info/calendars/omeara/>, CV > <http://brianomeara.info/cv/>, and Feedback > <http://brianomeara.info/teaching/feedback/> > > Associate Professor, Dept. of Ecology & Evolutionary Biology, UT Knoxville > Associate Head, Dept. of Ecology & Evolutionary Biology, UT Knoxville > Associate Director for Postdoctoral Activities, National Institute for > Mathematical & Biological Synthesis <http://www.nimbios.org> (NIMBioS) > Communication Director, Society of Systematic Biologists > > On Sat, Oct 29, 2016 at 10:09 PM, Shinichi Nakagawa < > s.nakag...@unsw.edu.au> wrote: > >> Dear Emmanuel and Alejandro >> >> Many thanks for your replies. >> >> Emmanuel, I understand what you said if I use vcv(nonultrametric_tree, >> cor=FALSE) in a phylogenetic comparative method (PCM). But if I use >> vcv(nonultrametric_tree, cor=TRUE), isn't this the same as assuming a >> ultrametric tree? I may be missing something here? >> >> Note that vcv(nonultrametric_tree, cor=TRUE) is different from >> vcv(chronoMPL(nonultrametric_tree), cor = TRUE), which is relates to my >> previous question (which one is preferred?) >> >> Many thanks >> >> Shinichi >> >> On Sun, Oct 30, 2016 at 9:53 AM, Alejandro Gonzlaez Voyer < >> alejandro.gonza...@iecologia.unam.mx> wrote: >> >> > Hi, >> > >> > I would venture in adding that with an additive tree the differences in >> > evol rates among species are determined by the genes used to estimate >> the >> > tree, given differences in substitution rates among genes. I do think >> its >> > important to bear in mind. >> > >> > Cheers >> > >> > Alejandro >> > >> > Alejandro Gonzalez Voyer >> > Instituto de Ecologia >> > UNAM >> > >> > >> > >> > >> > > On Oct 29, 2016, at 2:45 PM, Emmanuel Paradis < >> emmanuel.para...@ird.fr> >> > wrote: >> > > >> > > Sure they are different. I forgot to mention that. >> > > >> > > In comparative analyses, the expected quantity of trait change (= the >> > variance in the VCV matrix) is given by the product of the rate of >> > evolution of the trait with branch length. So using a non-ultrametric >> tree >> > is a way to assume different rates of evolution for each branch. With an >> > ultrametric tree, you somehow assume a "clock-like" trait evolution >> (i.e., >> > the quantity of change from the root of the tree to the tips is the >> same). >> > > >> > > BTW, the first command you give below should be (misplaced right >> > parenthesis): >> > > >> > > vcv(chronoMPL(nonultrametric_tree), cor = TRUE) >> > > >> > > Best, >> > > >> > > Emmanuel >> > > >> > >> Le 29/10/2016 à 13:12, Shinichi Nakagawa a écrit : >> > >> Dear Emmanuel >> > >> >> > >> Many thanks for your swift reply. >> > >> >> > >> If we get a correlation matrix, via chronoMPL [i.e. >> > >> vcv(chronoMPL(nonultrametric_tree,cor=T))], this correlation matrix >> is >> > >> different from a correlation matrix obtained directly from vcv [i.e. >> > >> vcv(nonultrametric_tree, cor=T)]. >> > >> >> > >> Could you enlighten me about differences and why chronoMPL method >> might >> > >> be preferred? >> > >> >> > >> Best wishes and thanks in advance. >> > >> >> > >> Shinichi >> > >> >> > >> On Sat, Oct 29, 2016 at 8:50 PM, Emmanuel Paradis >> > >> <emmanuel.para...@ird.fr <mailto:emmanuel.para...@ird.fr>> wrote: >> > >> >> > >> Dear Shinichi, >> > >> >> > >> A fast solution is provided by the function chronoMPL in ape; it >> does >> > >> not require calibration points (see the references in the help >> page >> > of >> > >> this function for the assumptions). The function chronos (also in >> > ape) >> > >> is another possibility but it needs at least one calibration point >> > >> (though this can be fixed to unity at the root). >> > >> >> > >> Note that a correlation matrix can be calculated from a >> > non-ultrametric >> > >> tree: see the function vcv. >> > >> >> > >> Best, >> > >> >> > >> Emmanuel >> > >> >> > >> Le 29/10/2016 à 05:26, Shinichi Nakagawa a écrit : >> > >> > Dear List >> > >> > >> > >> > We would like make several non-ultrametic trees (based on >> > >> molecular data; >> > >> > downloaded from treeBASE) into ultrametric trees using R. Could >> > >> you advice >> > >> > us what is the best and the most general way of doing this >> please? >> > >> > >> > >> > We would like to use resultant ultrametric trees in >> phyologenetic >> > >> > comparative analysis (by turning into correlation matrices). >> > >> > >> > >> > Best wishes, >> > >> > >> > >> > Shinichi Nakagawa >> > >> > >> > >> > [[alternative HTML version deleted]] >> > >> > >> > >> > _______________________________________________ >> > >> > R-sig-phylo mailing list - R-sig-phylo@r-project.org >> > >> <mailto:R-sig-phylo@r-project.org> >> > >> > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> > >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> > >> > Searchable archive at >> > >> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> > >> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> >> > >> > >> > >> > >> > >> > Pour nous remonter une erreur de filtrage, veuillez vous rendre >> > >> ici : http://f.security-mail.net/301dITcFgNy >> > >> <http://f.security-mail.net/301dITcFgNy> >> > >> > >> > >> > >> > >> >> > >> >> > >> >> > >> >> > > >> > > _______________________________________________ >> > > 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-ph...@r-project.org/ >> > >> > _______________________________________________ >> > 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-ph...@r-project.org/ >> > >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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-ph...@r-project.org/ >> > > [[alternative HTML version deleted]] _______________________________________________ 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/
