[Taxacom] Integrative taxonomy, bacterial phyla, and a Two Domain classification

[Richard Zander]

My own take on the integrative taxonomy paper is that it is an extremely detailed method for combining precise but very inaccurate results. Although I agree that a pluralistic methodology is best in taxonomy, surely the hyperprecise cladistic methods cannot be dealt with as generating results that do not need more massaging and interpretation.
 
E.g.: morphological cladistics is based on "which two of three taxa are more closely related based on shared ancestry" yet this fails for a significant proportion of cladistic nodes that are actually mother-daughter relationships, i.e. ((AB)C)D... where B and C are species generated by species A. You get good resolution if B and C differ in numbers of traits from their ancestor A. An evaluation of which traits respond to neutral and to joint selective presures will help solve this problem. Who will do this? Hint: neutral traits are found in different species in different environments for a particular bauplan. Hint: traits that are fixed as a package are those characteristically found in the same environments in different species. Let's go!
 
E.g.: molecular cladistics works pretty much because all splits are theoretically based on gradualistic change in traits as opposed to stasis being common in expressed traits of surviving ancestors. But this works only for the individual specimens analyzed. If a specimen occurs in a tree apart from other specimens of the same taxon, well you just rename the wayward specimen and that solves the problem. This is nonsense. Will molecular systematists continue this practice?
 
E.g.: cladistics results in an evoluation of relationships of extant taxa in a slice of time. Macroevolution (one taxon generating another at the same or higher rank) is ignored or suppressed through strict phylogenetic monophyly. A cladogram is just a set of parentheses and the "tree" is just a helpful way to visualize the nesting of the parentheses. A lineage has no line (i.e., a pedigree as in a genealogy) but is really a parentheage. The idea that evolutionary theory must follow the tree is nonsense in that there is no tree.
 
I submit that both morphological and molecular cladistics require additional use of brains to figure out what the results really mean given evolutionary theory. We have to gird ourselves to make sense of the new techniques, and that means abandoning the balkanization of systematics into classical taxonomy, morphological cladistics, and molecular systematics. 
 
The integrative taxonomy paper, I repeat, fails to address the fully understandable inaccuracies of present methods and continues the pretense that mathematically non-trivial methods must surely provide both precise AND accurate results.
 
_______________________
Richard H. Zander
Missouri Botanical Garden
PO Box 299
St. Louis, MO 63166 U.S.A.
richard.zander at mobot.org