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 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 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
> > 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
> >> 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
