Oops. Sorry the citation is Schluter, Price, Mooers, Ludwig 1997. Likelihood of ancestor states in adaptive radiation. Evolution 51:1699-1711. This issue has been known for a long time.
On Jul 30, 2013, at 6:51 AM, Marguerite Butler <mbutler...@gmail.com> wrote: > 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/
