[Taxacom] Why Taxonomy does NOT matter

Thu May 12 11:19:17 CDT 2011

Weird how we talk past each other, Jason. The molecular data is fine for telling present-day relationships of exemplars, given the acknowledged problems of molecular analysis. Fine, fine. Do that. It is informative and of interest in contributing to classification.

What is not fine is basing classification on present-day relationships of taxa. Classification should be based on a theory that combines traditional taxonomy, morphological cladistics, and molecular analysis. Present-day relationships can be accurate but do not address the process of evolution. A theory of such process incorporates the differences between the different sets of information. 

For instance, 
1. Classical taxonomy distinguishes the polar bear from the brown bear by many unusual and apparently adaptive traits.
2. Morphological analysis says the two species are closely related.
3. Molecular analysis says ((polarbear, brownbearmol1) brownbearmol2)...
4. Dollo evaluation says the chance of an extinct molecular line of polar bears (differing in no expressed traits) below the brown bear lineages is near impossible, so the support values for molecular genetic continuity and series of isolation events are okay.

The theory is that one molecular line of brown bears was progenitor to the polar bears. No change in nomenclature is needed but understanding of evolution is advanced.

Phylogenetic dogma (but nobody has the nerve, yet) suggests we sink the polar bear into the brown bear species, or recognize three species. This is on the basis of a "principle" of classification (holophyly or strict phylogenetic monophyly) that is supposed to make classification simpler. 

Note to Bob Mesibov: I've already detailed on Taxacom recently a suggested method for conciliating (as best possible) the results of different approaches to taxonomic analysis and classification. Above is an example.

Note that I reserve a certain skepticism about support values for molecular clades. If more than half extant taxa have extant ancestors (Aldous, D. F., M. A. Krikun & L. Popovic. 2011. Five statistical questions about the Tree of Life. Syst. Biol. 60: 318-328. P. 322 says "...for about 63% of extant species, some ancestral species should be itself extant....") then there are doubtless many paraphyletic taxa that have one branch extinct and only appear to be monophyletic. Thus, half of "monophyletic" clades were actually paraphyletic in the past to the extent of generating a descendant line from one line of a split. If so, and the paraphyly was extended to two or more lineages of apophyletic taxa (common in the literature), then support of clade X at any one place in the molecular cladogram must be lowered because, although the clade itself may be well supported as a group, its position of origin is not. This can be studied and doubtless fixed, but phylogeneticists would need to examine information not in the data set. 

I think taxonomy is hard to do. Simplifying by hegemony of a particular method generating results that need conciliation with other information but don't get it is not the way to do science. Phylogenetics is not "to big to fail."

* * * * * * * * * * * *
Richard H. Zander
Missouri Botanical Garden, PO Box 299, St. Louis, MO 63166-0299 USAï¿½
Web sites: http://www.mobot.org/plantscience/resbot/ï¿½and http://www.mobot.org/plantscience/bfna/bfnamenu.htm
Modern Evolutionary Systematics Web site: http://www.mobot.org/plantscience/resbot/21EvSy.htm

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Jason Mate
Sent: Thursday, May 12, 2011 5:39 AM
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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