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
estimated if it is nested high up within the phylogeny, if the rates of
change aren't high, etc. And (local) trends etc might well be reliably
inferred.  We are pretty confident that the common ancestor of humans and
chimps was larger than many deeper primate ancestors, for instance. If N is
the root of your available phylogeny, however, you have to be much more
cautious.

Cheers,
Nick


On Wed, Jun 13, 2018 at 6:57 AM, Joe Felsenstein <j...@gs.washington.edu>
wrote:

> 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 people make of these
> inferences.
>
> But not only are those inferences very noisy, they are correlated with
> each other.  So if you infer the ancestral state for the clade (Old
> World Monkeys, Apes) and also the ancestral state for the clade (New
> World Monkeys, (Old World Monkeys, Apes)) the two will typically not
> only be error-prone, but will also typically be subject to strongly
> correlated errors.  Using them as data for further inferences is very
> dubious.  It is better to figure out what your hypothesis is and then
> test it on the data from the tips of the tree, without the
> intermediate step of taking ancestral state inferences as
> observations.
>
> The popular science press in particular demands a fly-on-the-wall
> account of what happened in evolution, and giving them the ancestral
> state inferences as if they were known precisely is a mistake.
>
> Joe
> ----
> Joe Felsenstein         j...@gs.washington.edu
>  Department of Genome Sciences and Department of Biology,
>  University of Washington, Box 355065, Seattle, WA 98195-5065 USA
>
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