Holobionts, hybrids, and cladistic classification

David P. Mindell assumes that incorporation of the holobionts (evolutionarily stable symbiotic complexes) and hybrids into phylogenetic trees necessarily distorts the hierarchical structure of cladistic classification, and must lead to reformulation of some basic cladistic concepts (BioSystems, 27, 53-62, 1992). He does not regard the Eukarya and Eubacteria as monophyletic taxa, the former being 'polyphyletic', the latter 'paraphyletic'. We attempt to show that the existence of holobionts/hybrids is not a cladistic problem. Cladistics is a systematic methodology, not a system of evolutionary hypotheses; cladograms are statements about distribution of shared characters (synapomorphies) and, consequently, the cladograms are always branching and hierarchically structured. A taxon is monophyletic if it has a single root in the cladogram, not a single ancestor 'in reality'. Cladistic methodology does not provide a clue for distinguishing whether a conflicting distribution of the potential synapomorphies is due to reticulation (e.g., symbiogenesis) or convergent evolution. Consequently, both Eubacteria and Eukarya either are or are not monophyletic taxa if they are or are not determined to be so during cladistic analysis.