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> 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 > > 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 > > > 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 > > 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 > > > > _______________________________________________ > 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/ > [[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/
