I've read the hOUwie paper, but it wasn't clear to me that it allowed estimating the *order* of changes.
Thanks, -Rafa *--* *Rafael S. Marcondes, Ph.D.* *https://www.rafaelmarcondes.com/ <https://www.rafaelmarcondes.com/>* Faculty Fellow in EEB Department of BioSciences Rice University Houston TX 77005 Pronouns: he/him *"Eu quase que nada não sei. Mas desconfio de muita coisa"* *"I almost don't know nothing. But I suspect many things"* -João Guimarães Rosa, Brazilian novelist (Portuguese original and free English translation by me) On Fri, Feb 2, 2024 at 12:42 PM O'Meara, Brian C <bome...@utk.edu> wrote: > Isn’t that what houwie does (which is fairly recently published)? > https://doi.org/10.1093/evolut/qpad002 > > > > Note my conflict of interest as a coauthor. > > > > Best, > Brian > > > > _________________________________________ > > > > Brian O’Meara > > He/Him > > Professor, Dept. of Ecology & Evolutionary Biology > > University of Tennessee, Knoxville > > > > > > *From: *R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of > Rafael S Marcondes <raf.marcon...@gmail.com> > *Date: *Friday, February 2, 2024 at 1:06 PM > *To: *r-sig-phylo <r-sig-phylo@r-project.org> > *Subject: *Re: [R-sig-phylo] Determining Order of Trait Evolution > > Hi all, > > This is a reply to an ancient thread that I pasted below. My question is > the same as the original one: how to determine the relative order of > changes between a discrete and a continuous traits. I came up with the > approach I describe below (inspired by Heath Blackmon in the original > thread), but I don't feel great about it. So I was wondering if anything > better has been developed since, or if anyone has any better ideas. > > Here's what I've got: > > Next, we will test hypothesis 3, that transitions in [discrete trait] occur > proximate in time to changes in [continuous trait]. To do that, we will > adapt the approach from Blackmon et al. (2015). Briefly, we will first > conduct ancestral state estimation of the discrete trait using stochastic > character mapping (Huelsenbeck et al. 2003) in phytools, and separately an > ancestral state estimation of each continuous trait using the function ace > in the package ape (Paradis et al 2023). We will then assess whether the > continuous trait displayed a tendency of change either before or after each > discrete transition: we will extract the value of the continuous trait at > each discrete trait transition, as well as in the immediate parent and > ancestral nodes, and calculate the difference between the latter trait > values and the value at the transition. We will also generate a null > distribution by doing the same based on points sampled randomly along the > tree. The overlap between distribution of continuous trait value-changes > immediately before/after a transition and the continuous trait > value-changes immediately before/after random points will determine if the > two characters tend to change near each other in time. For example, if the > distribution of continuous trait value-changes immediately before a > discrete transition shows little overlap with the random distribution, that > would indicate that changes in [redacted continuous-valued] morphology tend > to precede changes in [redacted discrete valued ecology]. Likewise, if the > distribution of continuous trait value-changes immediately after a discrete > transition shows little overlap with the random distribution, that would > indicate that changes in [redacted continuous-valued] morphology tend > instead to follow changes in [redacted discrete valued ecology]. > > Thanks! > > -Rafa > > *--* > *Rafael S. Marcondes, Ph.D.* > *https://www.rafaelmarcondes.com/ <https://www.rafaelmarcondes.com/>* > Faculty Fellow in EEB > Department of BioSciences > Rice University > Houston TX 77005 > > Pronouns: he/him > > > *"Eu quase que nada não sei. Mas desconfio de muita coisa"* > *"I almost don't know nothing. But I suspect many things"* > -João Guimarães Rosa, Brazilian novelist > (Portuguese original and free English translation by me) > > Heath Blackmon > < > https://www.mail-archive.com/search?l=r-sig-phylo@r-project.org&q=from:%22Heath+Blackmon%22 > > > Mon, 04 Apr 2016 13:26:02 -0700 > < > https://www.mail-archive.com/search?l=r-sig-phylo@r-project.org&q=date:20160404 > > > > An alternative that doesn't require discretization of the continuous trait > would be an approach I used > inhttp://onlinelibrary.wiley.com/doi/10.1111/evo.12792/abstract. > Briefly you > do standard ASR of both traits (continuous = ML brownian motion; discrete = > stochastic mappings) independently. Then extract the continuous trait value > distribution at inferred transition points & compare to a null generated by > simulating the discrete trait. If your interested in doing this email me > off list and I can give you the latest version of the code for doing this > using phytools stochastic mapping results. > > Cheers > > Heath > > On Monday, April 4, 2016, Alejandro Gonzalez Voyer > <alejandro.gonza...@iecologia.unam.mx> wrote: > > > Hello Gavin, > > > > You could have a look at the method for evolutionary contingency, which > > works only for binary traits (meaning you’d have to transform your > > continuous trait into a binary one). See Pagel and Meade 2006 (Bayesian > > Analysis of Correlated Evolution of Discrete Characters by > Reversible-Jump > > Markov Chain Monte Carlo in Am Nat) for details on the method. > > Note that it will provide information on whether evolutionary transitions > > in trait state for one of the traits is contingent on the state of the > > second one. You can infer the probable history of transitions from the > > results. However, you should be careful as the method is sensitive to > > trait-state distribution. > > > > Cheers > > > > Alejandro > > > > > > > > _______________________________________________ > > Dr Alejandro Gonzalez Voyer > > > > Laboratorio de Conducta Animal > > Instituto de Ecología > > Circuito Exterior S/N > > Ciudad Universitaria > > Universidad Nacional Autónoma de México > > México, D.F. > > 04510 > > México > > > > Tel: +52 55 5622 9044 > > E-mail: alejandro.gonza...@iecologia.unam.mx <javascript:;> > > Web: www.alejandrogonzalezvoyer.com > > > > > El 04/04/2016, a las 13:37, Gavin McLean Leighton <gm...@cornell.edu > > <javascript:;>> escribió: > > > > > > Hi all, > > > > > > > > > I have 500 trees of 80 species downloaded from birdtree.org and am > > primarily interested in two traits. I have used PGLS to determine the > > traits are related but would ideally like to test if there is an order to > > trait evolution. To complicate matters one trait (Trait A) is continuous > > while the second (Trait B) is presence/absence. I was hoping someone > could > > direct me to methods (assuming they exist) that would allow me to > determine > > the estimated value of Trait A before a gain of Trait B evolves in a > > lineage. > > > > > > > > > Thank you, > > > > > > Gavin > > > > > > > > > Gavin Leighton > > > NSF Postdoctoral Fellow > > > Cornell University > > > Cornell Laboratory of Ornithology > > > 159 Sapsucker Woods Road > > > Ithaca, NY > > > http://www.gavinmleighton.com/ > > > > > [[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/ > [[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/
