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Contrasts between paraphyletic (ancestral) and polyphyletic groups. (a) The special case used by Hennig (1974) to claim that there is no cladistic difference between them because both have the same common ancestor (A) and an identical ancestral branching pattern. (b) A more realistic case where the three black-circle taxa do not have the same last common ancestor as the white-circle group, but have a different last common ancestor (B) which also has a different phenotype (black square) from A and from themselves. Case (b) shows that Hennig's claim for cladistic equivalence between paraphyletic and polyphyletic taxa lacks generality and rested on a cunningly chosen exceptional example. A paraphyletic group includes its last common ancestor and a polyphyletic one does not, a key fact partially concealed by Hennig misleadingly putting the same-sized box around both groups; to have correctly represented paraphyly the lower box should have included A, as it does in (b), where the obvious monophyly (single origin) of the paraphyletic white-circle taxon is much clearer than in Hennig's tendentious figure. The figure on the right also more strongly makes the point that the difference between polyphyly and paraphyly lies in the shared defining character (white circle) of the paraphyletic group having had a single origin, whereas the shared defining character of the polyphyletic group had three separate origins, i.e. a strongly contrasting phylogenetic history. Moreover, in (b) taxa 1 and 2 evolved black circleness in parallel from separate but phenotypically similar white-circle ancestors, whereas taxon 3 evolved it convergently from a cladistically and phenotypically more distinct black-square ancestor. It should be obvious that classifying white-circle taxa together is phylogenetically sound, i.e. they have a shared white-circle history, whereas classifying the black-circle ones together is unsound—being strongly contradicted by the lack of shared black-circle history. Unlike (a), (b) is a proper phylogeny with all ancestors and phenotypes shown; ignoring ancestral phenotypes makes nonsense of phylogeny. Cladistic aversion to paraphyletic groups, and lumping of paraphyly and polyphyly as ‘non-monophyly’, are logically flawed and anti-evolutionary (see also Cavalier-Smith (1998) which explains that clades, grades and taxa are all useful but non-equivalent kinds of group and that all taxa need not be clades and all clades need not be taxa).
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RSTB20090161F2: Contrasts between paraphyletic (ancestral) and polyphyletic groups. (a) The special case used by Hennig (1974) to claim that there is no cladistic difference between them because both have the same common ancestor (A) and an identical ancestral branching pattern. (b) A more realistic case where the three black-circle taxa do not have the same last common ancestor as the white-circle group, but have a different last common ancestor (B) which also has a different phenotype (black square) from A and from themselves. Case (b) shows that Hennig's claim for cladistic equivalence between paraphyletic and polyphyletic taxa lacks generality and rested on a cunningly chosen exceptional example. A paraphyletic group includes its last common ancestor and a polyphyletic one does not, a key fact partially concealed by Hennig misleadingly putting the same-sized box around both groups; to have correctly represented paraphyly the lower box should have included A, as it does in (b), where the obvious monophyly (single origin) of the paraphyletic white-circle taxon is much clearer than in Hennig's tendentious figure. The figure on the right also more strongly makes the point that the difference between polyphyly and paraphyly lies in the shared defining character (white circle) of the paraphyletic group having had a single origin, whereas the shared defining character of the polyphyletic group had three separate origins, i.e. a strongly contrasting phylogenetic history. Moreover, in (b) taxa 1 and 2 evolved black circleness in parallel from separate but phenotypically similar white-circle ancestors, whereas taxon 3 evolved it convergently from a cladistically and phenotypically more distinct black-square ancestor. It should be obvious that classifying white-circle taxa together is phylogenetically sound, i.e. they have a shared white-circle history, whereas classifying the black-circle ones together is unsound—being strongly contradicted by the lack of shared black-circle history. Unlike (a), (b) is a proper phylogeny with all ancestors and phenotypes shown; ignoring ancestral phenotypes makes nonsense of phylogeny. Cladistic aversion to paraphyletic groups, and lumping of paraphyly and polyphyly as ‘non-monophyly’, are logically flawed and anti-evolutionary (see also Cavalier-Smith (1998) which explains that clades, grades and taxa are all useful but non-equivalent kinds of group and that all taxa need not be clades and all clades need not be taxa).

Mentions: In marked evolutionary contrast to the polyphyletic fungoids, the shared common features of an ancestral (paraphyletic) group like Protozoa evolved once only and were inherited continuously from a common ancestry, making their similarity much more fundamental and unified. The naked phagotrophic lifestyle and often flagellate and/or amoeboid motility of most members of kingdom Protozoa evolved once only in their last common ancestor, as part of an extremely complex set of over 60 major innovations, the most radical in the history of life (Cavalier-Smith 2009b). Thus, the evolutionary status of polyphyletic groups such as fungoids and paraphyletic ones such as protozoa differs radically; recognition of the important contrast between them (figure 2) depends on correctly deducing the phenotype of common ancestors. Even fungoids ultimately had a last common ancestor (but one of non-fungoid phenotype); it so happens that it was also the common ancestor of all four derived (holophyletic) eukaryotic kingdoms and the paraphyletic subkingdom Sarcomastigota of the paraphyletic kingdom Protozoa. An analogous purely hypothetical example of shared common ancestry led Hennig (1974) to assert that there is therefore ‘no difference’ between paraphyletic and polyphyletic groups ‘in the structure of their genealogical relationships’ (figure 2a). His implication that distinguishing paraphyly and polyphyly is therefore unimportant for systematics or arbitrary does not remotely follow; it merely underlines the casual neglect of actual ancestors and their phenotypes, and differing degrees of phenotypic change generally, by Hennigian cladistic philosophy. There being in these instances a shared common ancestor between a paraphyletic and a polyphyletic group does not ify the importance of the distinction, which depends entirely on the historical phenotypes along the stems of the phylogenetic tree (figure 2), and not on the branching order. I am repeatedly irritated when indoctrinees of Hennig's narrow, biased viewpoint assert that they have shown a taxon to be ‘non-monophyletic’ (they mean non-holophyletic); this umbrella term conflates paraphyly and polyphyly—evolutionarily very different and of contrasting taxonomic implications. Polyphyletic taxa must be split into monophyletic ones; a paraphyletic one already is monophyletic in phylogenetic origin and need not necessarily be abandoned or radically revised, though sometimes this is advisable if it is excessively heterogeneous. Non-monophyletic conceals information, contrary to Hennig's wish to make terminology more informative and precise.

Deep phylogeny, ancestral groups and the four ages of life

Cavalier-Smith T - Philos. Trans. R. Soc. Lond., B, Biol. Sci. (2010)

Bottom Line: It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum.Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth.Accidents and organizational constraints are as important as adaptiveness in body plan evolution.

Affiliation: Department of Zoology, University of Oxford, Oxford, UK. tom.cavalier-smith@zoo.ox.ac.uk

ABSTRACT
Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.

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