[R-sig-phylo] R: Re: R: ancestral state reconstruction for tips

Theodore Garland Jr theodore.garland at ucr.edu
Fri Aug 5 21:35:40 CEST 2011


>Having said that, my guess was that we *may* use the BM and
>computations at nodes to see where (in which lineages) do
>phenotypes appear very different from predictions.
>For instance, I think it could be somehow possible to use
>estimated ancestral charactes to see how much the inclusion
>of some fossil (or new) species changes the estimated value
>(e.g. by creating a polytomy by the inclusion of the new species),
>or even back-calculate branch lengths (under BM assumption)
>for these unusual phenotypes to see how much evolution
>accelerates in these lineages (by comparison with real branch lengths).

Yes, I think that is an excellent way to proceed.

Cheers,
Ted

From: pasquale.raia at libero.it [pasquale.raia at libero.it]
Sent: Friday, August 05, 2011 12:00 PM
To: dwbapst at uchicago.edu; joe at gs.washington.edu; HuntE at si.edu; Theodore Garland Jr
Cc: r-sig-phylo at r-project.org
Subject: R: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips

Hi All,

I'm happy I have stimulated some discussion about this subject matter. For
some reason I can't imagine it looks this whole thing is going to be somehow
personal and I have not posted this last e-mail to the list as a consequence.
Joe, unfotunately I never attended a lecture of yours, and didn't raise trivial
distinctions and objections to a grant proposal you submitted. My intention was
not to be critical about BM or ICs, or whatever. I just wanted to point it out
that things are sometimes a bit too complex and some unreliable predictions
from our models may slip out unnoticed evey now and then, as I believe it is
apparent reading the literature (including my own, of course). Having said
that, my guess was that we *may* use the BM and computations at nodes to see
where (in which lineages) do phenotypes appear very different from predictions.
For instance, I think it could be somehow possible to use estimated ancestral
charactes to see how much the inclusion of some fossil (or new) species changes
the estimated value (e.g. by creating a polytomy by the inclusion of the new
species), or even back-calculate branch lenghts (under BM assumption) for these
unusual phenotypes to see how much evolution accelerates in these lineages (by
comparison with real branch lengths).
I hope I spoke my mind more clearly at this time.
Pas





>----Messaggio originale----
>Da: dwbapst at uchicago.edu
>Data: 05/08/2011 20.23
>A: "Joe Felsenstein"<joe at gs.washington.edu>
>Cc: "r-sig-phylo at r-project.org"<r-sig-phylo at r-project.org>
>Ogg: Re: [R-sig-phylo] R: Re: R: ancestral state reconstruction for tips
>
>As the diversity of explicit models of trait evolution grow, it will
>be interesting to see if any consensus develops about which models
>hold most often in general and whether any insight is gained into
>which conditions predict appearance of different models.
>
>I think Joe is right that realizing a model is an inaccurate or
>imprecise description of reality should impel us to develop better
>models of the world around us, because this partly how science moves
>forward. However, I don't think pointing out that a model is deficient
>requires that that person must themselves develop an alternative.
>After all, an alternative model that capture a more realistic level of
>complexity may not be possible in some situations (it is certainly
>possible in trait evolution models, however.) Requiring such a thing
>would put too much pressure on scientific whistle-blowers, who play a
>very important role in reminding the rest of us that the world is more
>than the models we use to understand it and make our predictions.
>
>-Dave
>
>
>
>
>On Fri, Aug 5, 2011 at 10:51 AM, Joe Felsenstein <joe at gs.washington.edu>
wrote:
>>
>> Pasquale Raia said:
>>
>>> Of course Ted is right, but my problem with this computation, or
>>> with the
>>> simple exercise I was proposing is well another: as a
>>> paleontologist I often
>>> come across pretty exceptional phenotypes (dwarf hippos and
>>> elephants, huge
>>> flightless birds, to make a few examples). When you use methods
>>> like this (I
>>> mean Garland and Ives') and compare the output with those
>>> phenotypes, as I did,
>>> you immediately realize what the the bottom line is: no matter if
>>> they are
>>> nodes or tips, by using the expected (under BM) covariance the
>>> estimated
>>> phenotypes are dull, perfectly reasonable but very different from
>>> anything
>>> exceptional you may find yourself to work with. This is why I feel
>>> it is
>>> difficult to rely on those (unobserved) values to begin with.
>>
>> I think that what is being said is that Brownian Motion is too sedate
>> a process
>> and does not predict some of the large changes actually seen in the
>> fossil
>> record.
>>
>> That's a legitimate point but does put the onus on the maker of the
>> point to
>> propose some other stochastic process that is tractable and has these
>> large
>> changes (and that fits with known Mendelian and Darwinian mechanisms).
>> Just complaining that the Brownian stochastic process is no good is
>> insufficient.
>>
>> If we want to add the fossils to the calculation, then they will of
>> course
>> pressure the Brownian Motion process to change more in their vicinity,
>> which may help some.
>>
>> Joe
>> ----
>> Joe Felsenstein      joe at gs.washington.edu
>>  Dept of Genome Sciences and Dept of Biology, Univ. of Washington,
>> Box 5065, Seattle Wa 98195-5065
>>
>>
>>        [[alternative HTML version deleted]]
>>
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>
>
>
>--
>David Bapst
>Dept of Geophysical Sciences
>University of Chicago
>5734 S. Ellis
>Chicago, IL 60637
>http://home.uchicago.edu/~dwbapst/
>
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