That sounds pretty different from doing ancestral reconstruction with some fossil data, and hoping the resulting node estimates will reflect reality, because fossil data is now involved. Look, I think every method has its uses; I'm just railing against the idea that the concerns of any particular method go away by tapping into the fossil record.
Personally I have a work-in-progess myself that involves parsimony ancestral state reconstruction of some very slow-evolving discrete traits in a fossil-rich group. I think in that particular case, I can defend my approach, but I don't think it'd be applicable in many other cases, even with other fossil-rich groups. Cheers, -Dave On Thu, Jun 14, 2018 at 11:08 AM, Jacob Berv <jakeberv.r.sig.ph...@gmail.com > wrote: > What about situations in which fossil calibrations are used as priors to > inform reconstructions for uncalibrated important/interesting nodes? Sure, > there is great uncertainty, but that doesn’t necessarily imply we should > entirely abandon hypothesis testing using this approach, does it? I like > the idea of using priors to constrain different scenarios and then using > model testing to compare alternative histories (though one’s model ranking > may change depending on the underlying models too, I guess). > > Jake > > > > On Jun 14, 2018, at 9:32 AM, David Bapst <dwba...@tamu.edu> wrote: > > > > Simone, Marguerite, others, > > > > I'll also add that I think there's a great deal to be skeptical of > > ancestral trait reconstruction even when large amounts of fossil data is > > available. You can try the exercise yourself: simulate pure BM on a > > non-ultrametric tree with lots of 'extinct' tips, and you'll still find > > pretty large confidence intervals on the estimates of the trait values. > > What does it mean to do ancestral trait reconstruction, if our > calculations > > of uncertainty are that broad? > > > > That said, in the era of sampled-ancestor phylogenetics for fossil data, > > the ability to examine quantitative support for ancestor-descendant > > relationships among fossil taxa may allow alternative routes to > considering > > this issue. > > > > Cheers, > > -Dave > > > > On Tue, Jun 12, 2018 at 2:43 AM, Simone Blomberg <s.blombe...@uq.edu.au> > > wrote: > > > >> I would add an extra caveat to Marguerite’s excellent post: Most > >> researchers work with extant taxa only, ignoring extinction. This > causes a > >> massive ascertainment bias, and the character states of the extinct taxa > >> can often be very different to the ancestral state reconstructions, > >> particularly if the evolutionary model is wrong. Eg. there has been an > >> evolutionary trend for example. Ancestral state reconstructions based > only > >> on extant taxa should be treated as hypotheses to be tested with fossil > >> data. I wouldn’t rely on them for much more. > >> > >> Cheers, > >> Simone. > >> > >> Sent from my iPhone > >> > >> On 12 Jun 2018, at 4:59 pm, Marguerite Butler <mbutler...@gmail.com> > >> wrote: > >> > >> Aloha all, > >> > >> There is no requirement for an ultra metric tree in the formulae > reported > >> in Butler-King 2004. Interested investigators should in particular read > the > >> supplementary materials where the mathematical details are worked out. > >> > >> We do generally use ultrametric trees because as comparative biologists, > >> it is more straightforward to think about evolution in units of time > rather > >> than in terms of mutational units, etc. However this is by choice, not > any > >> methodological limitation. > >> > >> Once the model parameters are found, the phylogenetic > variance-covariance > >> matrix defined by the alpha, thetas, and sigmas can be used to compute > >> ancestral states using a weighted least squares reconstruction method > >> (instead of the typical BM var-cov matrix). The mapping of the alphas, > >> thetas, and sigmas onto the tree are incorporated into this V-COV > matrix, > >> so that accounts for the OU model. > >> > >> NOTES: > >> 1) without knowing why you are doing this, I do feel compelled to warn > you > >> that it is unclear why one would want to estimate ancestral states for > >> poorly-fitting models. Be careful! > >> > >> 2) I hope you realize that ancestral states are in general poorly > >> estimated, even assuming the “correct” model. This is because there is > less > >> and less information to anchor the values as you get farther from the > tips, > >> similar to the root estimation problem described below. This issue was > >> clearly exposed in Schluter et al 1997 (and less famously so in Butler > and > >> Losos 1997). These depressing results were among the motivations for > >> developing model-fit approaches in the first place. > >> > >> 3) In 2008/2009 the algorithms in OUCH, SLOUCH, and possibly other > methods > >> have changed in the estimation of the value of the root state (X0) > which is > >> an internal calculation in fitting the model. Ho and Ane 2013, and > Hansen > >> et al 2008 both reported that the root state X0 is ill-defined (unless > >> there are fossil data to anchor the value). This makes sense > intuitively, > >> as all of the information is from the tips, and the root is very far > down > >> the tree. A reasonable assumption is that it is distributed according to > >> the stationary distribution of the OU process (X0 ~ N(theta(0), > >> sigma^2/2*alpha) and this assumption is what these methods now employ. > >> > >> 4) Whatever you end up doing, do check for the robustness of your > results > >> with parametric bootstrap on your fitted models (a la Boettinger et al > >> 2012). As many investigators have reported, these parameters can have > large > >> confidence intervals, and can covary with one another (being on a > >> likelihood ridge, etc.). But do note that even when parameters may not > be > >> uniquely identifiable, it may still be possible to have robust model > >> selection (see Cressler et al 2015). So perhaps you want to fit > ancestral > >> states to see if the different models give you the same states? IDK? > >> > >> So in short, yes, you can do it, with any number of methods. But why? If > >> you can answer your biological question with methods that do not involve > >> estimation of a parameter that is inherently fraught with error, it > might > >> be better to go another way. Bottom line - use caution and be > thoughtful! > >> > >> I am sure if I have made any errors Aaron, Clay, or Thomas will help. > >> > >> Hope this helps > >> > >> Marguerite > >> > >> Schluter, D., T. Price, A. O. Mooers, and D. Ludwig. 1997. Likelihood of > >> ancestor states in adaptive radiation. Evolution 51:1699–1711. > >> > >> Butler, M. A., and J. B. Losos. 1997. Testing for unequal amounts of > >> evolution in a continuous character on dif- ferent branches of a > >> phylogenetic tree using linear and squared-change parsimony: an example > >> using Lesser Antillean Anolis lizards. Evolution 51:1623–1635. > >> > >> Hansen T.F., Pienaar J., Orzack S.H. 2008. A comparative method for > >> studying adaptation to a randomly evolving environment. Evolution > >> 62:1965–1977. > >> > >> Ho L.S.T., Ané C.. 2014. Intrinsic inference difficulties for trait > >> evolution with Ornstein-Uhlenbeck models. Methods Ecol. Evol. > 2:1133–1146. > >> > >> Cressler C., Butler M.A., and King A. A. (2015) Detecting adaptive > >> evolution in phylogenetic comparative analysis using the > Ornstein-Uhlenbeck > >> model. Sys. Bio. 64(6):953-968. DOI: 10.1093/sysbio/syv043 > >> > >> Boettiger C., Coop G., Ralph P. 2012. Is your phylogeny informative? > >> Measuring the power of comparative methods. Evolution 66: 2240–2251. > >> ____________________________________________ > >> Marguerite A. Butler > >> Professor > >> > >> Department of Biology > >> 2538 McCarthy Mall, Edmondson Hall 216 > >> Honolulu, HI 96822 > >> > >> Office: 808-956-4713 > >> Dept: 808-956-8617 > >> Lab: 808-956-5867 > >> FAX: 808-956-4745 > >> http://butlerlab.org > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__butlerlab.org&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm- > Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=wCJc2Wt5C_3_9p68keEdKURQw1DgMPgzYSroUns4EgU&e=> > >> http://manoa.hawaii.edu/biology/people/marguerite-butler > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__manoa.hawaii.edu_biology_people_marguerite-2Dbutler&d=DwMGaQ&c=ODFT- > G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=kjcIRTrUHxUQV36VKJBe2PFbPgsjX97DHi6mXwRRy_8&e=> > >> http://www2.hawaii.edu/~mbutler > >> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www2.hawaii.edu_- > 7Embutler&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm- > Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58-9Xpxcc2aQgYVVI&s= > a0SwA8yTo1qWJZLpuWR9cVHuO_cxYqknynO9BdyATbs&e=> > >> > >> > >> On Jun 11, 2018, at 7:33 PM, Simone Blomberg <s.blombe...@uq.edu.au> > >> wrote: > >> > >> 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 > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__dinizfilho.wix.com_dinizfilholab&d=DwMGaQ&c=ODFT- > G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=hmSpj_Jqi4ORoecbP03Rbwo9Rev08deDEcSe7sCS0ts&e=> > >> > >> [[alternative HTML version deleted]] > >> > >> _______________________________________________ > >> R-sig-phylo mailing list - R-sig-phylo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> <https://urldefense.proofpoint.com/v2/url?u=https- > 3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwMGaQ&c=ODFT- > G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=AZL0t-pN5FCe9zTEubB331r_pQAK6cyHrXnkBzG_Xws&e=> > >> Searchable archive at http://www.mail-archive.com/r- > >> sig-ph...@r-project.org/ > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject. > org_&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ > ImxCh5QSrmEwsVni8p58-9Xpxcc2aQgYVVI&s=z8NuJWTJpoo2fEjoToX0ve70Xl5YoB > Swilz7-WuZ9ys&e=> > >> > >> > >> > >> > >> -- > >> David W. Bapst, PhD > >> Asst Research Professor, Geology & Geophysics, Texas A & M University > >> https://github.com/dwbapst/paleotree > >> <https://urldefense.proofpoint.com/v2/url?u=https- > 3A__github.com_dwbapst_paleotree&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm- > Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58-9Xpxcc2aQgYVVI&s=- > TR5K67uraveHhfMrWG1shHuRwD7joTQwcrQ1mN91Fk&e=> > >> Google Calendar: https://goo.gl/EpiM4J > >> <https://urldefense.proofpoint.com/v2/url?u=https- > 3A__goo.gl_EpiM4J&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm- > Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=YuE9V-1l-MXDZZ9nf7UNuuevqjl1h28dnySDV3X3QqU&e=> > >> > >> _______________________________________________ > >> R-sig-phylo mailing list - R-sig-phylo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> <https://urldefense.proofpoint.com/v2/url?u=https- > 3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwMGaQ&c=ODFT- > G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=AZL0t-pN5FCe9zTEubB331r_pQAK6cyHrXnkBzG_Xws&e=> > >> Searchable archive at http://www.mail-archive.com/r- > >> sig-ph...@r-project.org/ > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject. > org_&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ > ImxCh5QSrmEwsVni8p58-9Xpxcc2aQgYVVI&s=z8NuJWTJpoo2fEjoToX0ve70Xl5YoB > Swilz7-WuZ9ys&e=> > >> > >> _______________________________________________ > >> R-sig-phylo mailing list - R-sig-phylo@r-project.org > >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >> <https://urldefense.proofpoint.com/v2/url?u=https- > 3A__stat.ethz.ch_mailman_listinfo_r-2Dsig-2Dphylo&d=DwMGaQ&c=ODFT- > G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ImxCh5QSrmEwsVni8p58- > 9Xpxcc2aQgYVVI&s=AZL0t-pN5FCe9zTEubB331r_pQAK6cyHrXnkBzG_Xws&e=> > >> Searchable archive at http://www.mail-archive.com/r- > >> sig-ph...@r-project.org/ > >> <https://urldefense.proofpoint.com/v2/url?u=http- > 3A__www.mail-2Darchive.com_r-2Dsig-2Dphylo-40r-2Dproject. > org_&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=bm-Cvhz5zv2wG5pZT4ATCg&m=XIxoaHi_ > ImxCh5QSrmEwsVni8p58-9Xpxcc2aQgYVVI&s=z8NuJWTJpoo2fEjoToX0ve70Xl5YoB > Swilz7-WuZ9ys&e=> > >> > >> > >> > > > > > > -- > > David W. Bapst, PhD > > Asst Research Professor, Geology & Geophysics, Texas A & M University > > Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville > > https://github.com/dwbapst/paleotree > > Google Calendar: https://goo.gl/EpiM4J > > > > [[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-ph...@r-project.org/ > > -- David W. Bapst, PhD Asst Research Professor, Geology & Geophysics, Texas A & M University Postdoc, Ecology & Evolutionary Biology, Univ of Tenn Knoxville https://github.com/dwbapst/paleotree Google Calendar: https://goo.gl/EpiM4J [[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/
