Re: Polytomies in cladistics: Good, Bad, or Ugly?

[David Marjanovic <david.marjanovic@gmx.at>]

----- Original Message -----
From: "Phil Bigelow" <bigelowp@juno.com>
Sent: Thursday, September 15, 2005 4:50 PM
Subject: Polytomies in cladistics: Good, Bad, or Ugly?

> In cladistics, are polytomies (3 or more branches from one node)
> considered to be a valid working hypothesis, or are they instead viewed
> as an artefact of a limited data set, weaknesses in the algorithm, or a
> bad choice of test parameters?

They are never seen as the result of weaknesses in the algorithm.

This leaves three possible interpretations of polytomies:

(1) The true simultaneous split of a population into several. (In principle 
this is easy to imagine -- for example, take the classic model of allopatric 
speciation and suppose that two or more barriers arise instead of one.)
(2) A very fast succession of two (or more) dichotomies -- so fast that no 
detectable apomorphies had time to evolve between the first and the second 
(and so on).
(3) A mere lack of data. (Like (2), but replace "detectable" with 
"detected".)

The third is by far the most common assumption. After all, it is very easy 
to make a too small data matrix!

One famous polytomy was widely thought to be a case of (1) or (2): the split 
between humans, chimpanzees and gorillas. For 20 years or something most 
molecular studies found a trichotomy, while others found all three possible 
resolutions.* Then people turned to longer sequences of faster-evolving 
genes, and it turned out to be a case of (3).

What do you mean by "bad choice of test parameters"? Things like maximum 
parsimony vs Bayes*? Indeed some methods are less sensitive to artifacts 
like long-branch attraction than others, and some or all of those artifacts 
can produce polytomies. But this is actually a case of (3) -- more robust 
methods simply need fewer data to get a resolved tree.

* I'm not sure if any molecular study found chimps and gorillas as 
sistergroups, but morphology did anyway.
** There is a paper on Bayesian inference for morphology (applied to 
trilobites) in the latest Systematic Paleontology. I haven't read it yet.