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-phylo@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-phylo@r-project.org/
