Protists – A textbook example for a paraphyletic taxon

Protists constitute a paraphyletic taxon since the latter is based on the plesiomorphic character of unicellularity and does not contain all descendants of the stem species. Multicellularity evolved several times independently in metazoans, higher fungi, heterokonts, red and green algae. Various hypotheses have been developed on the evolution and nature of the eukaryotic cell, considering the accumulating data on the chimeric nature of the eukaryote genome. Subsequent evolution of the protists was further complicated by primary, secondary, and even tertiary intertaxonic recombinations. However, multi-gene sequence comparisons and structural data point to a managable number of such events. Several putative monophyletic lineages and a gross picture of eukaryote phylogeny are emerging on the basis of those data. The Chromalveolata comprise Chromista and Alveolata (Dinoflagellata, Apicomplexa, Ciliophora, Perkinsozoa, and Haplospora). Major lineages of the former ‘amoebae’ group within the Heterolobosa, Cercozoa, and Amoebozoa. Cercozoa, including filose testate amoebae, chlorarachnids, and plasmodiophoreans seem to be affiliated with foraminiferans. Amoebozoa consistently form the sister group of the Opisthokonta (including fungi, and with choanoflagellates as sister group of metazoans). A clade of ‘plants’ comprises glaucocystophytes, red algae, green algae, and land vascular plants. The controversial debate on the root of the eukaryote tree has been accelerated by the interpretation of gene fusions as apomorphic characters. In the more traditional view, based on sequence comparisons using archaebacteria as outgroup representatives, parabasaleans and diplomonads branch off first, rendering the biflagellate eukaryotes paraphyletic. In sharp contrast, the root is placed between Bikonta and Opisthokonta plus Amoebozoa on the argument of a single enzyme gene fusion which is postulated to have occurred in the stem species of the Bikonta, and of a double enzyme gene fusion weighed as a synapomorphy of the Opisthokonta and Amoebozoa. We conclude that the paraphyletic taxon ‘protists’ may be maintained for practical reasons. However, introduction of new, clearly recognizable paraphyletic taxa should be avoided.