Hi Tom, One thing to keep in mind is the information content of the data relative to what you are trying to infer. Basically, you have data only at the tips, but are trying to infer the state of the root deep in the tree. So therefore there is actually very little information being brought to bear on this problem. In this case, whatever answer you get will very strongly reflect the assumptions of the model that you apply and the structure of the tree. Put another way, if you were to construct error bars around this character state estimate, you would see that they are huge (See Moers et al. 1997 in Evolution).
It sounds like you are expecting a linear parsimony reconstruction. Why not just use that? Your character does not change very much on the tree. This is basically what your ML answer is telling you anyway, more than 50% chance of red at the base. Marguerite On Jul 30, 2013, at 4:38 AM, Liam J. Revell <liam.rev...@umb.edu> wrote: > Hi Tom. > > There is no reason to expect that the marginal ancestral state > reconstructions at the root node (empirical Bayesian posterior probabilities) > should match your tip frequencies or prior probabilities. Imagine the > following scenario: you have one diverse clade comprising 50% of extant taxa > that all diverged recently from a common ancestor share state "B"; whereas > state "A" is found in all the other tips of the tree, some of which are in > clades originating near the root. We would not expect posterior probabilities > at the root node to mach the empirical frequencies of our state at the tips > (50:50). In fact, we might expect that our reconstructed state at the root of > the tree would be strongly "A". > > In your specific case, state "0" is found in three clades that originate > nearer to the root, whereas more nested clades are exclusively in state "1". > This is why - in spite of its relative rarity across the tips of the tree - > there is still some reasonable (PP~0.3) posterior probability under the model > that the root is in state "0". This is not an error that needs to be > corrected - it is just what your data, model, and tree tell us about the > ancestral node of the phylogeny. > > All the best, Liam > > Liam J. Revell, Assistant Professor of Biology > University of Massachusetts Boston > web: http://faculty.umb.edu/liam.revell/ > email: liam.rev...@umb.edu > blog: http://blog.phytools.org > > On 7/30/2013 6:10 AM, Tom Wenseleers wrote: >> Dear all, >> Many thanks for all your advice so far. I have now moved to using rayDISC in >> package corHMM to reconstruct marginal maximum likelihood ancestral state >> reconstructions, using the method of Maddison et al (2007) and FitzJohn et >> al (2009) to fix the prior probabilities at the root (setting it to the >> observed frequency at the tips doesn't change much). >> The code I have is >> >> library(ape) >> library(corHMM) >> tree=read.tree("http://www.kuleuven.be/bio/ento/temp/tree.tre";) >> data=read.csv(file="http://www.kuleuven.be/bio/ento/temp/data.csv";) >> rownames(data)=data[,1] >> ASR=rayDISC(tree,data,ntraits=1,charnum=1,model="ER",node.states="marginal",root.p="maddfitz") >> plot(tree, cex=0.6, show.tip.label=TRUE, ljoin=2,lend=2,label.offset=0.02) >> nodelabels(pie=ASR$states,piecol=c("white","red"), cex=0.45) >> tiplabels(pch = 22, bg = ifelse(data[tree$tip.label, ][,2],"red","white"), >> col="black",adj = c(0.51, 0.5), cex = 0.6) >> >> I still get unusually low marginal ML values for the trait being 1 at the >> basal nodes though (ca. 0.7, which is very low considering that 89% of my >> species have the trait). >> Would anyone be able to offer advice on why one could get the reconstructed >> root ML value to be so much lower than the actual observed frequency of the >> trait at the tips, and what could be a solution to obtaining a more >> realistic ML reconstruction? (I also tried diversitree and phangorn, but >> they all give similar results) >> >> Cheers, >> Tom >> >> >> >> -----Original Message----- >> From: Jack Viljoen [mailto:javilj...@gmail.com] >> Sent: 30 July 2013 10:23 >> To: Tom Wenseleers >> Subject: Re: [R-sig-phylo] Question on ace ML reconstruction of discrete >> binary character >> >> Hello, Tom. >> >> I was just wondering if the higher uncertainty at the basal nodes isn't >> expected, particularly given the long branches descended from them? >> >> Since this is an ML estimate and not a Bayesian one, surely the concept of >> priors does not apply? My understanding is that ace() actually only >> estimates the root node and that other methods are required to properly >> estimate the states at the other nodes. I'm basing this on these posts from >> Liam Revell earlier this year: >> http://blog.phytools.org/2013/03/conditional-scaled-likelihoods-in-ace.html >> http://blog.phytools.org/2013/03/a-little-more-on-ancestral-state.html >> >> I hope those links shed some light on the matter, or that someone who knows >> about this stuff has responded to you off-list as well. >> >> Good luck, >> Jack >> >> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Mon, 29 Jul 2013 16:00:28 +0000 >>> From: Tom Wenseleers <tom.wensele...@bio.kuleuven.be> >>> To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org> >>> Subject: [R-sig-phylo] Question on ace ML reconstruction of discrete >>> binary character >>> Message-ID: >>> >>> <37efc97028f3e44082acc5cbec00563011294...@icts-s-mbx7.luna.kuleuven.be >>>> >>> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Dear all, >>> >>> I just did some ancestral state reconstructions of binary characters >>> (screenshot attached) using ace (using an equal rate discrete character >>> reconstruction) . Everything seems to make sense to me, except the two >>> basal nodes, where I end up with quite low likelihoods for my red character >>> being 1 (cf. the pie charts), even though I get higher likelihoods at >>> practically all of the more shallow nodes in the tree. Any ideas why one >>> can get a result like this, and what I could potentially do about it, since >>> it doesn't seem quite right to me? >>> >>> >>> >>> Cheers, >>> >>> Tom >>> >>> ______________________________________________________________________ >>> _________________ >>> >>> Prof. Tom Wenseleers >>> * Lab. of Socioecology and Social Evolution >>> Dept. of Biology >>> Zoological Institute >>> K.U.Leuven >>> Naamsestraat 59, box 2466 >>> B-3000 Leuven >>> Belgium >>> * +32 (0)16 32 39 64 / +32 (0)472 40 45 96 >>> * tom.wensele...@bio.kuleuven.be >>> http://bio.kuleuven.be/ento/wenseleers/twenseleers.htm >>> >>> >>> >>> >>> >>> -------------- next part -------------- An HTML attachment was >>> scrubbed... >>> URL: >>> <https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20130729/609e4 >>> f89/attachment-0001.html> >>> -------------- next part -------------- A non-text attachment was >>> scrubbed... >>> Name: ace ML reconstruction.jpg >>> Type: image/jpeg >>> Size: 196149 bytes >>> Desc: ace ML reconstruction.jpg >>> URL: >>> <https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20130729/609e4 >>> f89/attachment-0001.jpg> >>> >>> ------------------------------ >>> >>> Message: 2 >>> Date: Mon, 29 Jul 2013 21:45:53 +0000 >>> From: Tom Wenseleers <tom.wensele...@bio.kuleuven.be> >>> To: "r-sig-phylo@r-project.org" <r-sig-phylo@r-project.org> >>> Subject: Re: [R-sig-phylo] Question on ace ML reconstruction of >>> discrete binary character >>> Message-ID: >>> >>> <37efc97028f3e44082acc5cbec00563011294...@icts-s-mbx7.luna.kuleuven.be >>>> >>> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> Dear all, >>> @Arne: yes I think it has to do something with the priors for the root. I'm >>> not sure what prior ace uses - I think equal, which in my case would not be >>> so appropriate given that nearly all species have the trait. Would anyone >>> know by any chance whether in ape it is possible to have ace use a prior >>> for the root which would reflect the frequency at the tips, and if so, how >>> one could specify this? >>> >>> Cheers, >>> Tom >>> >>> From: Arne Mooers [mailto:amoo...@sfu.ca] >>> Sent: 29 July 2013 20:10 >>> To: Tom Wenseleers >>> Subject: Question on ace ML reconstruction of discrete binary >>> character >>> >>> Hoi Tom, >>> >>> What is the default prior on the root in ace? Different approaches use >>> different priors (=observed frequency at tips, equal, equal to tested ratio >>> of q's, etc.) That has had a big affect on reconstructions I have done in >>> the past. >>> >>> Cheers, >>> >>> Arne Mooers >>> >>> >>> Begin forwarded message: >>> >>> From: Tom Wenseleers >>> <tom.wensele...@bio.kuleuven.be<mailto:tom.wensele...@bio.kuleuven.be> >>>> >>> Date: 29 July, 2013 9:00:28 AM PDT >>> To: "r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>" >>> <r-sig-phylo@r-project.org<mailto:r-sig-phylo@r-project.org>> >>> Subject: [R-sig-phylo] Question on ace ML reconstruction of discrete >>> binary character >>> >>> Dear all, >>> I just did some ancestral state reconstructions of binary characters >>> (screenshot attached) using ace (using an equal rate discrete character >>> reconstruction) . Everything seems to make sense to me, except the two >>> basal nodes, where I end up with quite low likelihoods for my red character >>> being 1 (cf. the pie charts), even though I get higher likelihoods at >>> practically all of the more shallow nodes in the tree. Any ideas why one >>> can get a result like this, and what I could potentially do about it, since >>> it doesn't seem quite right to me? >>> >>> Cheers, >>> Tom >>> >>> ______________________________________________________________________ >>> _________________ >>> >>> Prof. Tom Wenseleers >>> * Lab. of Socioecology and Social Evolution >>> Dept. of Biology >>> Zoological Institute >>> K.U.Leuven >>> Naamsestraat 59, box 2466 >>> B-3000 Leuven >>> Belgium >>> * +32 (0)16 32 39 64 / +32 (0)472 40 45 96 >>> * >>> tom.wensele...@bio.kuleuven.be<mailto:tom.wensele...@bio.kuleuven.be> >>> http://bio.kuleuven.be/ento/wenseleers/twenseleers.htm >>> >>> >>> >>> [cid:image001.jpg@01CE8CB5.C244A190]__________________________________ >>> _____________ R-sig-phylo mailing list - >>> R-sig-phylo@r-project.org<mailto: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/ >>> >>> _____________________________ >>> Dr. Arne Mooers >>> Biology, Simon Fraser University >>> 8888 University Drive., Burnaby BC V5A 1S6 Canada >>> amoo...@sfu.ca<mailto:amoo...@sfu.ca> >>> +1 778 782 3979 >>> skype: arnemooers >>> www.sfu.ca/~amooers<http://www.sfu.ca/~amooers> >>> www.sfu.ca/fabstar<http://www.sfu.ca/fabstar> >>> www.scientists-4-species.org<http://www.scientists-4-species.org> >>> hesp.irmacs.sfu.ca >>> 7billionandyou.org >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -------------- next part -------------- An HTML attachment was >>> scrubbed... >>> URL: >>> <https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20130729/d17a1 >>> 8f6/attachment.html> >>> -------------- next part -------------- A non-text attachment was >>> scrubbed... >>> Name: image001.jpg >>> Type: image/jpeg >>> Size: 159311 bytes >>> Desc: image001.jpg >>> URL: >>> <https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20130729/d17a1 >>> 8f6/attachment.jpg> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> 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 66, Issue 22 >>> ******************************************* >>> >>> >>> _______________________________________________ >>> 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/ _______________________________________________ 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/
