WHITHER MOLECULAR PHYLOGENETIC SYSTEMATICS?
Richard H. Zander
Res Botanica, a Missouri Botanical Garden Web Site
July 16, 2005
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WHITHER MOLECULAR PHYLOGENETIC SYSTEMATICS?
(An essay)

A long discussion raged on the listserver Taxacom in early to mid 2005 about whether the orangutan or the chimpanzee was mankind's little brother. Morphological evidence apparently favored the man-orangutan while molecular evidence favored man-chimp. The discussions are archived at http://listserv.nhm.ku.edu/archives/taxacom.html.

Given the statistically strongly supported molecular tree of (((man chimp) gorilla) orangutan, gibbon), most discussants, including myself, poo-pooed the morphological evidence as contradictory and doubtless convergent.

After that discussion, I've had second thoughts, and here is my slightly edited comment on contradictory morphological and molecular results, and the immediate future of molecular phylogenetic analysis:

I've been looking in the evo-devo literature recently (e.g. the journal Evolution and Development, and in fact there is some (not much, but some) evidence that evolution commonly involves large gene complexes regulated (e.g. turned off and on) by non-coding regulatory genes.

This makes for a sloppy evolutionary tree because the silenced gene complexes can travel the lineage byways for up to 10 million years before being degraded.  The problem is that some major morphological complexes are greatly split by molecular systematics.

Although statistically the molecular split is well supported, that split statistically contravenes Dollo's Law that it is not to be expected by chance alone that two taxa sharing many complex morphological characters should separately exactly re-evolve (by gradual accumulation of traits).  Molecular systematics, in my opinion, tracks reproductive splits assuming a Biological Species Concept (iffy for plants for which there is much evidence of gene-permeable species barriers), which mainly also does reflect evolutionary changes (to the extent it matches expectations from morphological analysis), but instances of apparent massive homoplasy can be mediated by identical or little changed shared gene complexes turned on by selection on regulatory genes.

This re-activation of a gene complex is the only explanation of such homoplasy, and it builds on Darwinian thinking.  The human-chimp relationship is statistically supported by molecular studies as a sister group, but we share too many critical morphological traits with the patristically more distant orangutan not to suspect some kind or degree of direct shared genetic past, a deep homology.  If demonstrably shared evolution is more important to systematics and classification than tree-like segregation of gradually accumulated changes in introns and junk DNA, and if evolution may not be recovered in at least some salient cases of apparent improbable convergence by molecular systematics, then careful examination of morphology is a major clue to evolutionary relationships.

So, dust off your 1970's phenetic techniques! Morphology will rule again!