I wanted to second Jacob Berv's suggestions about Bayes Factors for testing apriori hypotheses about tree topology. Here are two papers that show worked out examples of this approach, and discuss some of the checks you need to do before proceeding. For example, you want to be sure the character evolution model seems a pretty good fit before testing the topologies. Those types of concerns are mostly statistical, and so most would apply to genetic data equally as to the morphological characters these papers analyzed.
Matthews LJ, Tehrani JJ, Jordan FM, Collard M, Nunn CL. 2011. Testing for divergent transmission histories among cultural characters: a study using Bayesian phylogenetic methods and Iranian tribal textile data. PLoS One. 29;6(4):e14810. Dembo, M, NJ Matzke, AO Mooers, M Collard. 2015. Bayesian analysis of morphological supermatrix sheds light on controversial fossil hominin relationships. Proceedings of the Royal Society B. Volume 282 My best - Luke Matthews, Behavioral and Social Scientist, RAND Corporation -----Original Message----- From: R-sig-phylo [mailto:r-sig-phylo-boun...@r-project.org] On Behalf Of r-sig-phylo-requ...@r-project.org Sent: Wednesday, April 20, 2016 6:00 AM To: r-sig-phylo@r-project.org Subject: R-sig-phylo Digest, Vol 99, Issue 11 Send R-sig-phylo mailing list submissions to r-sig-phylo@r-project.org To subscribe or unsubscribe via the World Wide Web, visit https://stat.ethz.ch/mailman/listinfo/r-sig-phylo or, via email, send a message with subject or body 'help' to r-sig-phylo-requ...@r-project.org You can reach the person managing the list at r-sig-phylo-ow...@r-project.org When replying, please edit your Subject line so it is more specific than "Re: Contents of R-sig-phylo digest..." Today's Topics: 1. Fwd: Testing different topological hypotheses - based on taxonomic treatments (Chris Buddenhagen) 2. Re: Testing different topological hypotheses - based on taxonomic treatments (Jacob Berv) ---------------------------------------------------------------------- Message: 1 Date: Tue, 19 Apr 2016 07:06:45 -0400 From: Chris Buddenhagen <cbuddenha...@gmail.com> To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Fwd: Testing different topological hypotheses - based on taxonomic treatments Message-ID: <cad8oqpt+v-j77dqfsoorev6ko0gby6lfkgfgadaf60m1zjk...@mail.gmail.com> Content-Type: text/plain; charset="UTF-8" Dear all What is the best (statistically defensible) way to test different hypotheses regarding topology? I have data from hundreds of loci....concatenated alignment is approximately 200 kilobases. For example one taxonomist divided the tribe of plants I am working on into two main groups (presumably sister to each other). Also one genus is apparently embedded in the other, and was treated as separate. Another division in the taxonomic treatment identifies major groups above sections. Sincerely Chris Buddenhagen cbuddenha...@gmail.com [[alternative HTML version deleted]] ------------------------------ Message: 2 Date: Wed, 20 Apr 2016 01:54:58 -0400 From: Jacob Berv <jakeberv.r.sig.ph...@gmail.com> To: Chris Buddenhagen <cbuddenha...@gmail.com> Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Testing different topological hypotheses - based on taxonomic treatments Message-ID: <0f738896-8bd6-42c3-b086-6a5f11811...@gmail.com> Content-Type: text/plain; charset=utf-8 You could do a bayes factor test using MrBayes or BEAST, by applying topological constraints. This is an elegant solution for conducting explicit topological hypothesis tests. But you aren?t likely to get BEAST or MrBayes to run with 200kb. I?ve been thinking about doing this myself with data partitions generated from partition finder (For example). I think I once tried loading 500kb into MrBayes and it gave me some kind of warning that it can?t read alignments longer than ~90kb. Talk about a 21st century problem. Jake > On Apr 19, 2016, at 7:06 AM, Chris Buddenhagen <cbuddenha...@gmail.com> wrote: > > Dear all > > What is the best (statistically defensible) way to test different > hypotheses regarding topology? I have data from hundreds of > loci....concatenated alignment is approximately 200 kilobases. > > For example one taxonomist divided the tribe of plants I am working on > into two main groups (presumably sister to each other). Also one genus > is apparently embedded in the other, and was treated as separate. > Another division in the taxonomic treatment identifies major groups above > sections. > > Sincerely > > > Chris Buddenhagen > cbuddenha...@gmail.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/ ------------------------------ Subject: Digest Footer _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo ------------------------------ End of R-sig-phylo Digest, Vol 99, Issue 11 ******************************************* __________________________________________________________________________ This email message is for the sole use of the intended r...{{dropped:6}} _______________________________________________ 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/
