Cladistic equivalence of nested parentheses and ckadogram

R. H. Zander

Res Botanica,

A Missouri Botanical Garden Web site

April 18, 2011

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Cladistic equivalence of nested parentheses and cladogram

R. H. Zander, Missouri Botanical Garden

 

 

 

 

Diagramming the nesting of exemplar taxa on a cladogram. Upper left is standard cladistic parenthetical Newick formula, lower right is cladogram coded by this formula, and between are conceptual gradations. Clearly, a dendrogram is just an aid to visualizing nestings. For scientific realism the cladogram requires identification of nodes as diagnosable ancestral taxa, not just referred to uniformly as “shared ancestors.” Nodes reified as speciation events and internodes as taxa different from the exemplars are unwarranted assumptions because there are theoretical alternatives.

 

Adding scientific realism to the cladogram with caulistic explanation of phylogenetic paraphyly and polyphyly. Left: A paraphyletic cluster of exemplars representing the same taxon implies a shared ancestor A* of that taxon, with the extraneous taxon (B) as descendant. Right: Phylogenetic polyphyly is theoretically simply evolutionary monophyly if the phylogenetically distant exemplars (A) of the same taxon are, after re-examination, are definitely of that phenotypic taxon (a “natural” group with respect to biogeography, ecology, population biology, chromosome number, sexuality), and a deep shared ancestor (A*) is implied, with all intermediate lineages (B, C, D, E) as descendants.  This provides a theoretical alternative to the usual phylogenetic explanation of heterophyly as convergence.