[Taxacom] Mapping traits

[Richard Zander]

Regarding "trial-fitting" (or mapping) of expressed traits on a
phylogenetic tree, there is plenty of study of how to reconstruct gene
trees (which are then seen as evolutionary relationships) based on
neutral or nearly neutral base changes, but little on that which is
mapped to them (the evolution part). (We use, I understand, neutral base
changes supposedly to avoid convergence and get large numbers of data
for statistical purposes.)

Consider a set of species, say a genus, one of which becomes another
species by a couple strongly expressed oddball genes. It is distinct at
the genus level. Later those couple expressed genes are disabled and a
third species is generated which looks much like the original group of
species, the old genus. Neutral base changes show a nice tree and the
third species, which looks like the old genus, is labeled massively
homoplasous, even though it is genetically sufficiently like the
original group of species to be included in that original genus. This is
parallelism that is somehow parleyed into major changes in higher taxa,
usually by resort to the artificial stricture of monophyly. 

How often does this happen? What are the assumptions about "that which
is mapped to a gene tree" that affect creation of a practical
classification? How often do major switches in evolutionary ecology
happen that are due to very few genes such that placing similar parallel
evolved taxa in the same genus is a better solution that splitting,
being more informative of genetics?

And it's not really a gene tree is it? It's a locus tree focusing on
presumably neutral base changes. A "gene tree" implies relationships of
expressed traits, which are only inferences in phylogenetics.

At least 80% (to as much as 97%) of genomes (ours anyway) is apparently
evolutionarily neutral genuine junk and does work to help track
phylogeny probabilistically, but because little attention is paid to
that which is mapped to phylogenies, phylogeny only approximates
sequential evolutionary relationships, but is not identical to evolution
itself. 

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Richard H. Zander 
Voice: 314-577-0276
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166-0299 USA
richard.zander at mobot.org
Web sites: http://www.mobot.org/plantscience/resbot/
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4344 Shaw Blvd.
St. Louis, MO 63110
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> -----Original Message-----
> From: Bob Mesibov [mailto:mesibov at southcom.com.au]
> Sent: Wednesday, June 20, 2007 6:08 PM
> To: TAXACOM; struwe at AESOP.Rutgers.edu; Richard Zander
> Subject: Re: [Taxacom] Geophylogeny
> 
> On Richard Zander's comment:
> 
> Of course evolutionary biologists are aware of geography, but they
forget
> about it as soon as they start constructing a hypothetical phylogeny.
It's
> only *after* the tree is built that time (dates, durations) and space
> (locations of terminal taxa, and of fossils in Kidd and Price's
> reconstruction) are trial-fitted to the space-free hypothesis.
> 
.