Missouri Botanical Garden

Department Member, Science and Conservation

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Phylogenetic systematics seeks to eliminate macroevolution from classification, while creationism wants to eliminate macroevolution from the classroom; the difference is that creationism has failed.

Phylogenetics deals only with clades in systematics, namely groups of terminal taxa (as exemplars). Lineages, as concatenated series of nodes in a cladogram, are not named because to do so would violate the phylogenetic principle of classification by holophyly (strict phylogenetic monophyly). This is a principle or axiom, maxim or slogan, designed to simplify classification, not a scientific fact or theory. Phylogeneticists thus reject paraphyly, a group from which other taxa - at the same taxonomic rank or higher - are derived as seen in molecular cladograms. Modern evolutionary systematists celebrate paraphyly, however, as "good" or natural taxa demonstrably the ancestors of other taxa. A paraphyletic taxon plus its derived taxon is a example of evolutionary monophyly, but is not phylogenetic monophyly. When a phylogeneticist encourages one to follow "monophyly," this does not mean evolutionary monophyly, which is a real scientific theory not an a priori "principle."

The practice of following the principle of holophyly (strict phylogenetic monophyly) with molecular cladograms is now resulting in taxonomic outrages, such as the sinking or threatened sinking of Aves into Reptilia, the Cactaceae into Portulacaceae, and polar bears into brown bears, because the second of each pair would be paraphyletic if recognized separately.

A cladogram may be totally represented by placing the terminal taxa into a nested set of parentheses. Thus, the clades are given as sister groups and commonly named, but lineages are not represented or named, even though they could be by recognition of paraphyletic taxa. A phylogenetic Tree of Life is much the same as a Nested Parentheses of Life.

This researcher and others of reasonable thought ask members of Academia.edu to seriously consider the ramifications. Words are needed for real things in nature. If words are eliminated for the products of macroevolution, how can one discuss them or use them in scientific research? If evolutionists, ecologists, biogeographers, and others use recent phylogenetic classifications, a serious distortion in the results of their research will be inevitable. In my opinion, phylogenetic systematics involving molecularly based cladograms is proving a disaster for western science.

Molecular cladograms commonly tout highly supported branches. But, though such branches are well supported, what about the effect of the possibility of extinct lineages, particularly those involved in paraphyly, on the accuracy of retrodiction of the sequence of macroevolutionary branching?

(1) Clades are taxa that exist at a point in time, while lineages are taxa in stasis or changing through time. (2) Paraphyly (and extended paraphyly) infers a natural taxon through some stretch of time (as a kind of evolutionary uniformitarianism), and the taxon may be in two (or more) lineages. (3) Natural taxa inferred as one or more nodes on a cladogram make for better evolutionary classification. (4) At any point in time, paraphyletic groups may differ due to extinction of old lineages and "budding" of new daughter lineages from an ancestral group. (5) The proportion of extant paraphyletic taxa in any one group may prove a guide to the proportion of past, different paraphyletic groups. (6) Thus, any extant sister-group molecular lineage has a certain chance of having an extinct lineage of its natural taxon below or beyond that molecular split on the cladogram.

Although in groups with little paraphyly of natural groups that chance may be small, every sister group on a molecular cladogram has that same chance of actually being a paraphyletic group with an extinct branch, and therefore the ancestor of its opposite sister group on the molecular tree, or even the ancestor of two or more different lineages. This is a additional and quite significant contribution to lowering of accuracy in molecular systematic analysis. Ignoring it, as is presently common, leads to aleatory classification but apparently that is preferable to acknowledging that natural taxa can occur in two or more lineages and this makes molecular cladograms inaccurate. The actual limit of resolution depends on the judgment of the scientist on the reasonable patristic distance (e.g. number of nodes) as a measure of phylogenetic constraint among which two or more lineages of a natural taxon might be separated by splits leading to other taxa. It is on this criterion that one should evaluate the actual advances contributed to systematics by molecular parsimony, maximum likelihood, or Bayesian analyses. For instance, a taxon found be greatly misplaced, perhaps because of extreme reduction in morphology, and in fact belongs to another large group may be reasonably moved to that group. Wholesale renaming of lineages just to preserve strict phylogenetic monophyly is, however, largely an exercise in empty precision.

A paper uploaded to Academia.edu called "Structuralism in Phylogenetic Systematics" is commended to the concerned reader.

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