Please see Nick Gardiner’s comment and my reply below, as he attempts to discredit this day’s theme with traditional thinking and I reply with an explanation of my niche in paleontology by following this day’s theme.
Grandcolas et al. 2001 push for the use of
“as many characters as possible should be included in the cladistic analysis.” The risk, as seen by Grandcolas et al. not to do so is to, “bias the analysis.” The risk in my opinion is you’ll never run the analysis if you keep looking for more and more characters. Their number, if not infinite, is certainly some multiple factor of legion. In certain circles we call this sort of encouragement snipe hunting.
The authors’ wish/suggestion/push runs counter to my arguments
for the large reptile tree (LRT), and its overlapping satellites, the large pterosaur tree (LPT) and the therapsid skull tree (TST). I have argued that the minimum number of characters and character states should be employed that will separate each and every taxon and each and every node apart from one another, with high Bootstrap scores. After all, the goal of every analysis is to model and replicate actual evolutionary events to the best of our ability, given our detachment from taxa in deep time and the reduction of data to only skeletons or partial crushed, and broken skeletons in most cases. If most of the characters used are general in nature and are set in place before the addition of any included taxon, then no a priori bias can be said to exist with regard to included characters. Case in point: the LRT has successfully used intended generalized reptile traits to nest birds, mammals and fish with high resolution.
Frankly, the authors’ arguments go over my head throughout
as they argue semantics, possibilities and a priori issues; nothing specific. They point out many theoretical errors reported by prior authors. Thankfully they sum it all up neatly with a statement near the conclusion, “Not to use available and logically suitable characters is like suppressing evidence.”
On that note, the authors should have remembered
that every judicial case has a court date, a moment in time when evidence is no longer sought and gathered, but used. Theory is one thing. Practice is another. At one point or another, you simply have to run the analysis.
The authors conclude,
“Phylogenetics must propose refutable hypotheses: characters should not be included or excluded from the analysis because of a priori ideas regarding their evolution.” I think we can all agree to that.
However, let’s remember, we all lead busy lives.
Seeking characters ad infinitum sooner or later leads to decreasing value for the incremental and extended effort. Seeking just enough characters to recover a fully resolved tree that documents a gradual accumulation of derived traits at every node will still leave you time to eat, sleep, drive, work and brush your teeth.
is still the best way to add value to a phylogenetic analysis if the LRT, LPT and TST are any indication. All use a large enough character list with variations within to separate virtually all taxa from one another in a way that appears to echo micro-evolutionary processes in deep time from jawless fish to blog readers.
Thanks to Neil for bringing this paper to my attention.
Grandcolas P, Deleporte P, Desutter-Grandcolas L and Daugeron C 2001. Phylogenetics and Ecology: As many characters as possible should be included in the cladistic analysis. Cladistics 17:104–110.