Such expressions as that famous one of Linnæus, and which we often meet with in a more or less concealed form, that the characters do not make the genus, but that the genus gives the characters, seem to imply that something more is included in our classification, than mere resemblance. I believe that something more is included; and that propinquity of descent,—the only known cause of the similarity of organic beings,—is the bond, hidden as it is by various degrees of modification, which is partially revealed to us by our classifications (Darwin, 1859, p. 413f).

Tuesday, 23 October 2007

The Great Phenetic Revival 1: Stratophenetics

Phenetics haunts us again in what appears to be a great revival in molecular systematics and paleontology - two fields that are linked not by their data but by a common world view.

The molecular clock and all that is associated with it, mainly a belief in a new empirical attempt to date nodes on trees, is an old idea that stems back to stratophenetics, a term coined by P.D. Gingerich in 1979. The practice of stratophenetics is simple. Taxa that share similarities that can be clustered either as phenograms (or on graphs) and together with their respective fossil dates can be compared directly to existing hypotheses of classification (i.e. phylogenies). The practice of assigning dates to taxa as well as to nodes (i.e. ancestors or events) is the underlying principle. In short, the ingredients for the stratophenetic recipe are:

  • Any taxic hierarchy (i.e. phenograms, cladograms, area cladograms etc.).

  • The oldest known fossil date for each taxon.

  • Interpreting nodes as either ancestors or events and cladograms and phenograms as explicit ancestor-descendant relationships.

This then can be turned into molecular clocks, stratocladistics or any other recent attempt at dating nodes (Wagner 1995, Hunn & Upchurch 2001, Donoghue & Moore 2003, Makovicky in press). Given the number of times that stratophenetics pops up in systematics and biogeography, many would be under the impression that it is a good idea. We beg to differ.

Stratophenetics like stratocladistics tests existing phylogenetic hypotheses based existing classifications (see Wagner, 1995). The test adds in the extra stratigraphical data (i.e. age of fossil taxa) to any given ancestor-descendant lineage. The better the stratigraphy the better rates of speciation can be retrodicted - something like a fossil clock. Unlike molecular clocks however stratophenetics and stratocladistics goes further. They use the fossil clock to test if the lineage is correct. If for instance the clock tells us that taxa A is the oldest followed by B, C and D sequentially, it would contradict a hypothesis that related A closer to D than to either B or C (if the lineage follows chronological order, namely A=>B=>C=>D). If we were to interpret phenograms and cladograms as real phylogenetic trees (rather than overall classifications) we could interpret the tree (AD)(BC) as the node that unites B and C (herein node X) to be older and therefore more ancestral than A. Many would go one step further and identify node X as an ancestor that is older than A but not necessarily older than the node that unites A and D. Molecular clocks do not go that far, only adopting the oldest known age as the "minimal" age for any given node.

Where both molecular systematics and paleontology share a common world view is that the oldest node of a group (e.g. Node X) is a real taxon or event - most likely an ancestor or radiation. Gingerich (1979) thought the same and would after some careful consideration also be the father of not only stratopehentics, but molecular clocks as well.

Donoghue, M. J. and B. R. Moore. 2003. Toward an integrative historical biogeography. Integrative and Comparative Biology 43: 261-270.
Gingerich, P. D. 1979. The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. In J. Cracraft and N. Eldredge (eds.), Phylogenetic Analysis and Paleontology, Columbia University Press, New York, pp. 41-77.
Hunn, C. A. & Upchurch, P. 2001 The importance of. time/space in diagnosing the causality of phylogenetic events: Towards a "Chronobiogeographical" paradigm? Systematic Biology 50:391-407.
Makovicky, P.J. In press. Telling time from fossils: a phylogeny-based approach to chronological ordering of paleobiotas. Cladistics.
Wagner, P.J. 1995. Stratigraphic tests of cladistic hypotheses. Paleobiology 21:153-178.

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