A Short Glossary of Phylogenetics

Richard H. Zander

July 11, 2012

Res Botanica

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A SHORT GLOSSARY OF PHYLOGENETICS

 

In an effort to communicate the valid, scientific reasons for support of evolutionary systematics against phylogenetics, I have made, in the Modern Evolutionary Systematics Web site, every effort to eliminate in my comments on phylogenetics any risible observations, expressions of horror, or sardonic objurgations. Phylogenetics is, on the other hand, after 20 years of burgeoning growth, not just wrong but is knotted in a tendentious, logical bind that is not even internally consistent. The present glossary gives what I feel are clear definitions but is also crafted in a somewhat Biercean fashion to respond to past anonymous reviewers of my papers who kindly vouchsafed such solvent criticism as: “Zander should apologize to all cladists,” and “we [cladists] discussed and decided on all this back in the 1980s,” and similar comedy. Please accept these definitions, which I offer in a like spirit. Cladists who wish to remonstrate may write me email.

 

Alpha taxonomist – A “naïve” taxonomist, one who commonly works without benefit of interpretive software or white lab coat.

 

Apophyly – An apophyletic branch is that branch that comes out of a paraphyletic relationship on a cladogram; phylogenetic jargon for a descendant taxon in a cladistic context.

 

Astrology – A primitive form of mechanical knowledge in which unexplained, unnamed, unobservable processes as hidden causes affect understanding of the relationships of the stars and nature; see wrong.

 

Autapomorphy – A unique trait uninformative of sister-group relationships but which may be informative of unique evolutionary status or direction; a distinctive trait of no use in cladistic analysis but a major element of macroevolutionary transformation.

 

Bayesian analysis – A highly mathematical and statistical method of estimating phylogenetic relationships in terms of nested diagrams, using only data that is precise and amenable to the particular analysis; proper analysis is the Bayesian Solution, which includes the effect of all data, precise or imprecise, to give a probabilistic answer; see wrong.

 

Cladogram – An expanded diagram representing a set of nested parentheses.

 

Congruent – Two wrong cladograms that agree; see incongruent; see wrong.

 

Cognitive dissonance – An uncomfortable feeling had when something obviously wrong is nevertheless held as true, e.g. black is white, debt is good, polar bears are brown bears, traits evolve not taxa, or shared ancestors cannot be named, this psychic pain is much ameliorated by power, academic reputation, and generous funding.

 

Conciliate – To reconcile, to make compatible, to come half way; what is left on the field of battle after the clash of two paradigms.

 

Data – In evolutionary systematics, any information clustering specimens and revealing descent with modification, resulting often in annoyingly conflicting models that require scientific theory to conciliate. Phylogenetics: some selected information allowing the most precise evolutionary nesting of some specimens.

 

Evolutionary systematists – Unfunded, unappreciated scientists who agree with each other only in accepting paraphyly as a basis for classification; they rejoice, however, in being right, and, unlike others, know why they are right (paraphyly implies macroevolution); also, taxonomists who know when they are guessing.

 

Holophyly – Strict phylogenetic monophyly; all members of a clade of one name must derive from one shared ancestor, a classification “principle” of no scientific value. Thus good taxa are often lumped by phylogeneticists because they are apophyletic descendants of paraphyletic progenitors. As noted on Taxacom listserver, “Because of holophyly, phylogenetics has brought us: If it quacks like a duck and walks like a duck, it is a reptile; if it lives on the ice in the Arctic, has white fur and eats seals, it is a brown bear; if it grows in a desert, has fleshy stems, spines and no leaves to speak of, it is some kind of portulacca.”

 

Homoplasy – Trait similarity in cladogram lineages that lead back to different (cladistically unnameable, unobservable, unexplained, unparsimoniously invented superfluous) shared ancestors, in the context of holophyly.

 

Incongruent – Two wrong cladograms that disagree; see congruent; see wrong.

 

Lysenkoism – Less primitive than astrology, q.v., a form of mechanical knowledge in which unexplained, unnamed, unobservable processes as hidden causes affect understanding of the environment and heredity; see wrong.

 

Macroevolution – Descent with modification of taxa; series or successively branching sequences of taxa, not diagramable with cladograms therefore not important in phylogenetics; a word used in phylogenetics in place of microevolution.

 

Mapped taxon – Nodes on a molecular cladogram between certain separated exemplars representing inferred ancient ancestors of present-day taxa diagnosable at a particular taxonomic level (the lowest shared by the exemplars) through a kind of taxonomic uniformitarianism; the best information one can get from molecular systematic analysis.

 

Microevolution – Successive changes of traits mapped on a cladogram but never associated with changes from one taxon to another, only of one unnamed, unexplained, unobservable shared ancestor to another; atomized change perfectly amenable to “creation science.”

 

Node – Where two branches diverge in a cladogram; in phylogenetics, a locus tenens for an unnameable, unobserveable, unexplainable shared ancestor; in evolutionary taxonomy, an often nameable, inferrable  progenitor of one or more exemplars.

 

Paraphyly – Disparaging phylogenetic jargon for a cladogram’s representation of a progenitor in a macroevolutionary series; para- meaning faulty, wrong, amiss, recrementitious, or merely similar to the true form; see heterophyly. Some phylogeneticists do not insist on always modifying classification in the case of discovered molecular paraphyly, but ninety percent of phylogeneticists give the other ten percent a bad name.

 

Parsimony – A method of grouping taxa, which we all tend to use as a first pass from which to start analysis under the rubric that the simplest causal patterns should be examined first, in absence of other information; contrarily, the phylogenetic end of analysis; parsimony is defensible if evolutionarily fixed new simple changes have selective advantage over possibly adaptively more burdensome changes involving many traits..

 

Phylogenetics – An advanced form of mechanical knowledge in which unexplained, unnamed, unobservable processes as hidden causes explain the relationships of progenitors and descendants; evolution through descent of characters; see wrong.

 

Phylogeneticist – A well-funded scientist of power and prestige, who has found greater precision in modeling evolution by nested diagrams than by serial descent with modification.

 

Polyphyly – Evolutionary polyphyly is two lineages not reasonably derived from the same ancestral taxon. Phylogenetic polyphyly is two exemplars or lineages separated by two or more nodes; phylogenetic polyphyly can be either evolutionary polyphyly or simply extended paraphyly, with an implied ancestral taxon generative of two or more descendant lineages, or more commonly complex heterophyly involving two self-nesting ladders. Polyphyly is used by phylogeneticists as a bugaboo because of its double meaning, just as monophyly has a double meaning; see paraphyly; see wrong.

 

Primitive – First or nearly first in a series. A serial concept as opposed to pleisiomorphic, which is a nesting concept that includes taxa with primitive or those with advanced traits..

 

Pseudoextinction – A phylogenetically expected dichotomous tree with unnamed shared ancestors is conveniently generated if the shared ancestor dies out (or anagenetically changes beyond taxonomic recognition); see cognitive dissonance.

 

Tree, evolutionary – A branching representation of macroevolution, emphasizing serial, not nested, caulistic relationships.

 

Tree, phylogenetic – A cladogram of inferred nested evolutionary relationships; a set of nested parentheses; a view that is often highly astigmatic because it eliminates or minimizes one dimension in favor of another.

 

Wrong – Any mechanical knowledge generated by eliminating relevant but less imprecise data or theory that confounds the lazy; a quick fix; perfection simplified; see astrology, Lysenkoism, phylogenetics. “For every problem there is a solution—simple, neat and wrong.” H. L. Menken.