[Taxacom] FW: Wrangling incongruence

[John Grehan]

First sentence of the abstract:

"Phylogenetic analyses have suggested that the everlasting daisy tribe
Gnaphalieae colonized the globe repeatedly and rapidly from southern
Africa."

The idea that a phylogenetic analysis generates information about
spatial movement is an often repeated claim, but it has no empirical
basis. A phylogeny based on biological form homologies cannot make
statements about spatial homologies. Instead, what is usually the case
is that the spatial arrangement of biological relationships is
interpreted based on a some theory (often through inventing centers of
origin based on the belief that they exist and can be identified) or
other that is external to the phylogeny.

John Grehan

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Rob Smissen
Sent: Thursday, May 12, 2011 7:22 AM
To: taxacom at mailman.nhm.ku.edu
Subject: [Taxacom] FW: Wrangling incongruence

Warning: what follows is shameless self promotion!

For an example of treating incongruence rather than dismissing it check
out

http://www.ingentaconnect.com/content/iapt/tax/pre-prints/11552smissen

Down with The One True Tree!

cheers
Rob
________________________________________
From: taxacom-bounces at mailman.nhm.ku.edu
[taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
[jfmate at hotmail.com]
Sent: Thursday, 12 May 2011 10:39 p.m.
To: Taxacom
Subject: Re: [Taxacom] Why Taxonomy does NOT matter

> Just as hard as wrangling your team members will be dealing with
incongruence and fitting it within your evolutionary picture. Who does
this now? Is there anyone who seriously examines incongruence, instead
of dismissing it as noise and an obstacle to discovering the One True
Tree?

> Regardless of what group is being studied, what I read in the
literature suggests that investigators are looking for evolutionary
'signal' in their data. The 'signal' is regarded as evolution, the rest
isn't. This is a very strange idea. Surely *all* the data reflect what's
happened during evolution?


One man's noise is another man's data, tt is noise if it doesn't apply
to the level you are looking at. When researchers speak of signal and
noise I don't think they are making the distinction between good/bad but
between useful (to me, now) and ''useless''. I think we all do this but
in the case of molecular data you have to deal with the numerous
characters which are simply not useful to you particular question.

 From what I have seen and in my limited experience the noise issue is
best dealt with through the
addition of taxa. And here lies a very important contribution that
classical taxonomists make. It is much more difficult to get the
material than sequencing; hence lab-based research is focused on more
data from the same taxa instead of closing gaps. Sometimes ''field''
taxonomists are approached by lab researchers for specimens. Often the
specimens are rare, have small distributions, narrow phenologies and
very specific ecologies, but the assumption out there is that one can
just go to the backyard and pick them up. So the idea that ''modern''
taxonomy doesn't need classical taxonomists is spurious. The simple
truth is that we give out our services for free and then are told that
our services have no value.

Jason

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