Just to follow off what Lucas said, but please note you cannot rescale branches of a phylogeny using an OU model when the tree is non-ultrametric (such as when it contains extinct, fossil taxa as tips). Slater (2014, MEE) discusses this more in a brief correction to Slater (2013).
I don't know if anyone in this conversation has a non-ultrametric tree, but I wanted to make that clear for anyone who stumbles on this thread n the future using a google search. -Dave On Sun, Jun 10, 2018 at 12:25 PM, Lucas Jardim <lucas.ljard...@gmail.com> wrote: > Hi Bruno, > > You can transform the branches of your phylogeny using the estimated > parameters of OU models. Then, if those models describe the observed data > adequatly, the transformed tree should model the observed data as a > Brownian motion model. So you can use an ancestral state reconstruction > based on Brownian motion model. However, I do not know if that is the best > approach as optimum values would not be included into the reconstruction > process. > > Best, > -- > Lucas Jardim > Doutor em Ecologia e Evolução > Bolsista do INCT-EECBio (Ecologia, Evolução e Conservação da > Biodiversidade) > Instituto de Ciências Biológicas > Laboratório de Ecologia Teórica e Síntese > Universidade Federal de Goiás > http://dinizfilho.wix.com/dinizfilholab > > [[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/ -- David W. Bapst, PhD Asst Research Professor, Geology & Geophysics, Texas A & M University https://github.com/dwbapst/paleotree Google Calendar: https://goo.gl/EpiM4J _______________________________________________ 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/
