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
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
It is possible to transform the branch lengths of a non-ultrametric tree to
make the OU process equivalent to a BM process (on the transformed branch
lengths), but there’s an extra correction needed at the tips (i.e. need to
transform the data too via a diagonal matrix). It makes likelihood
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
Simone, others,
Perhaps I misunderstand, but I believe Slater (2014) shows that there is no
correct branch length transformation for a non-ultrametric tree under an OU
process. The correct transformation that Slater applies is Hansen's, yes,
but to the VCV matrix. Slater does point out there is
It's a shame there aren't awards for great threads, because this is one!
The minor twist I would throw in is that it's difficult to make universal
generalizations about the quality of ancestral state estimation. If one is
interested in the ancestral state value at node N, it might be reasonably
Let me add more warnings to Marguerite and Thomas's excellent
responses. People may be tempted to infer ancestral states and then
treat those inferences as data (and also to infer ancestral
environments and then treat those inferences as data). In fact, I
wonder whether that is not the main use
Hi Marguerie, Simone and everyone,
Like Marguerie says there is no need to transform the OU process. If you have
fitted an OU process, then you know the joint distribution of all the the
species and nodes. It is a multivariate normal, and you can use standard
formulas for prediction of the
Hello all,
The package mvMORPH can also do ancestral state reconstruction of
continuous characters for some OU-related models, including OUM, but I
don't believe it has all the models Bruno is after. There's an example
given in one of the vignettes of using mvMORPH for reconstructing a
continuous
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
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
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
Prompted by Bruno's email, and similar requests by some students at the
Arnold & Felsenstein Evolutionary Quantitative Genetics course, we've
started adding ancestral state reconstruction to OUwie. It still needs
debugging and testing, but should be ready fairly soon. I do believe bayou
does
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
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
As far as I know, only the package bayou has a function to estimate
ancestral states using OU. Rphylopars also does it using OU with missing
data.
Best,
Diogo
--
Diogo B. Provete
Assistant Professor
Institute of Biosciences
Federal University of Mato Grosso do Sul
Campo Grande, Mato Grosso do
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