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
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>
>
> 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
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> --
> David W. Bapst, PhD
> Asst Research Professor, Geology & Geophysics, Texas A & M University
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-- 
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
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