Thanks, Liam! That was really helpful. But what would be an alternative to estimate evolutionary rates in those cases? Simply the sigsq estimate under a white noise model? (which I assume is simply the variance in the original data?)
Karla On Wed, Sep 23, 2020 at 10:23 PM Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Karla. > > > I just wanted to make sure that the estimate of sigma^2 in a BM model > > in fitContinuous is a meaningful measure of the rate of evolution of > > the trait even if its phylogenetic signal is low. > > I would say that the answer to this question (if it were posed as one) > is 'no.' Another way to put this is that sigma^2 is probably not a > meaningful measure of the rate of evolution for your character if > Brownian motion is a (very) poor fit to your data. > > It's kind of equivalent to saying 'is the slope of a fitted linear > regression a good measure of the rate of change in y as a function of x > if a linear model is a very poor fit to my data?' (That is, you can > still find a value of the slope that maximizes the probability of your > data under a linear model, and this slope accurately give the mean > effect of x on y over the range of your observations for x - but it may > not mean a whole lot about how x & y genuinely co-vary.) > > All the best, Liam > > Liam J. Revell > University of Massachusetts Boston > Universidad Católica de la Ssma Concepción > web: http://faculty.umb.edu/liam.revell/, http://www.phytools.org > > Academic Director UMass Boston Chile Abroad: > https://www.umb.edu/academics/caps/international/biology_chile > > On 9/23/2020 9:36 PM, Karla Shikev wrote: > > **[EXTERNAL SENDER] > > > > Dear All, > > > > Thanks for your fantastic feedback. Just a bit more background: I'm > > interested both in the phylogenetic signal and the evolutionary rate. I > > just wanted to make sure that the estimate of sigma^2 in a BM model in > > fitContinuous is a meaningful measure of the rate of evolution of the > > trait even if its phylogenetic signal is low. > > > > thanks again! > > > > Karla > > > > On Wed, Sep 23, 2020 at 8:45 PM Theodore Garland > > <theodore.garl...@ucr.edu <mailto:theodore.garl...@ucr.edu>> wrote: > > > > Carla, I can also suggest looking at some of the papers on this, > > such as: > > > > Blomberg, S. P., T. Garland, Jr., and A. R. Ives. 2003. Testing for > > phylogenetic signal in comparative data: behavioral traits are more > > labile. Evolution 57:717–745. > > > > > > Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species > > variation and measurement error in phylogenetic comparative methods. > > Systematic Biology 56:252–270. > > > > > > Revell, L., L. Harmon, and D. Collar. 2008. Phylogenetic signal, > > evolutionary process, and rate. Systematic Biology 57:591–601. > > > > > > Hardy, O. J., and S. Pavoine. 2012. Assessing phylogenetic signal > > with measurement error: a comparison of Mantel tests, Blomberg et > > al.’s K, and phylogenetic distograms. Evolution 66:2614–2621. > > > > > > Cheers, > > > > Ted Garland > > > > > > > > > > On Wed, Sep 23, 2020 at 4:33 PM Liam J. Revell <liam.rev...@umb.edu > > <mailto:liam.rev...@umb.edu>> wrote: > > > > Dear Karla. > > > > What do you want to use fitContinuous to do? > > > > fitContinuous fits multiple models, some of which will result in > > low > > values of lambda in a test of phylogenetic signal. In fact, this > is > > really the main point of fitContinuous: to compare alternative > > models > > for trait evolution. If you just want to estimate the > > most-likely rate > > of evolution assuming a Brownian evolutionary process, you could > > just > > compute the mean squared PIC value (this is the REML estimate of > > sigma^2). > > > > fitContinuous can also take into account sampling error in the > > estimation of species means, which can be a cause for low > measured > > values of phylogenetic signal. > > > > Hope this is of some help Karla. > > > > All the best, Liam > > > > Liam J. Revell > > University of Massachusetts Boston > > Universidad Católica de la Ssma Concepción > > web: http://faculty.umb.edu/liam.revell/, > > http://www.phytools.org > > < > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.phytools.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732071994&sdata=L7HXU2Ljrj89dZ5ql%2FRWMB7ddrReMWnZxdufzJQ2Nvs%3D&reserved=0 > > > > > > Academic Director UMass Boston Chile Abroad: > > https://www.umb.edu/academics/caps/international/biology_chile > > > > On 9/23/2020 8:21 PM, Karla Shikev wrote: > > > [EXTERNAL SENDER] > > > > > > Dear friends, > > > > > > I guess this is as much a philosophical question as it is > > methodological. I > > > want to estimate the rate of evolution of a trait (e.g. using > the > > > fitContinuous function), but the trait has low phylogenetic > > signal (e.g. > > > lambda close to 0). Does it make sense to use fitContinuous > > on a trait > > > evolving like that? > > > > > > Thanks for your input. > > > > > > Karla > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > <mailto:R-sig-phylo@r-project.org> > > > > > > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653&sdata=4u7Q9SP0M9b0l07P13q6zruhfqyMW0AEVIqa%2FT9p1Ko%3D&reserved=0 > > < > https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732071994&sdata=atomHLOjHR5zPxx0gZmRKhpJoKaUq6E0opPN3HZ00ws%3D&reserved=0 > > > > > Searchable archive at > > > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C238f2a4ce92f4b62411f08d86017813f%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365001363567653&sdata=sKb4MeniYVOo5pQSEUtWRIpz%2BAGHt6wccZ%2B5mPQl7qU%3D&reserved=0 > > < > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732081987&sdata=o23UtSdhUFuHhXKbc2xNwgcVQldnCRD6pyoDn%2F0w5cs%3D&reserved=0 > > > > > > > > > _______________________________________________ > > 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://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylo&data=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732081987&sdata=%2BxIZJ84p0Ll311wu9i%2Fl843%2B2ixOwG5zD9yhQ0znY9Y%3D&reserved=0 > > > > Searchable archive at > > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > < > https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.mail-archive.com%2Fr-sig-phylo%40r-project.org%2F&data=02%7C01%7Cliam.revell%40umb.edu%7C4b3649722f5c4a9bb0f508d86021d687%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637365045732091986&sdata=UH5%2B76Tdem3lTl4eUW%2BQE1D%2F6MfrKFVNaBDmvjLnrnA%3D&reserved=0 > > > > > [[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/
