This sounded wrong to me, as the OU process should be agnostic to the dataset: There are no restrictions inherent in the OU process that apply particularly to phylogenetic data, whether the tree is ultrametric or not. I re-read Slater 2014 and it is clear that you can use branch length transformations with OU, so long as you use the (correct) Hansen formula, not the Butler-king formula, which does indeed require an ultrametric tree.
Cheers, Simone. Sent from my iPhone > On 12 Jun 2018, at 8:01 am, David Bapst <dwba...@tamu.edu> wrote: > > 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/ _______________________________________________ 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/
