EVOLUTION OF THE EUKARYOTIC SUPERTREE

Determination of the evolutionary relationships between major eukaryotic groups has been the Holy Grail of phylogenetics since the demise of the Plant-Animal dichotomy of the old Aristotelian 2-Kingdom system. Through the latter half of the 20th Century, structural and ultrastructural evidences, together with a growing support for the theory of the endosymbiotic origin of eukaryotes, brought about a general acceptance of the 5-Kingdom system, both of which were energetically championed by Lynn Margulis. The immediate results were the realizations that protozoa and algae were ecological concepts rather than taxonomic realities and occupied the Kingdom Protista (or Protochtista). Otherwise, early attempts to resolve eukaryotic relationships promised some successes but were slow to deliver.

THE ERA OF SET

Taylor (1976) created a phylogeny of flagellated eukaryotes based on ultrastructure within a 5-Kingdom paradigm. His phylogeny suffered from the assumption that non-flagellated taxa were primitive, and, therefore, rooted his tree on the red algae (also, they were photosynthetic with pigments and storage products very similar to those of the Cyanobacteria). Nevertheless, Taylor (1976) was one of the first to attempt such an analysis (in cladistic format) based on numerous ultrastructural and cytological characters. His tree made some very prescient statements such as the relationship between the ciliates and the dinoflagellates and the interrelationships between taxa of the chrysophyte complex (a group that later was called the stramenopiles or heterokonts).

The analysis of Dodge (1973) was predicated on the assumption that the dinoflagellates were the most primitive of the algae because of their nucleus with numerous condensed chromosomes that lacked histones (a condition that he called mesokaryotic). He compared all of the photosynthetic eukaryotic microbial groups on the basis of cell covering, flagella, storage products, chlorophylls, etc. (many of the same characters that Taylor, 1976 used later). His numerical taxonomic study confirmed the primitive nature of the dinoflagellate (the initial assumption of the analysis), but was otherwise an uninformative jumble of taxa.

Round (1980) cautioned that the endosymbiotic theory would make any search for the relationships between higher taxa of eukaryotes very difficult especially if all major organelles (mitochondria, chloroplasts, etc.) were acquired through uptake of the appropriate symbionts. Thus, he concluded that the distinct nature of major eukaryotic groups was a consequence of non-Darwinian mix-and-match endosymbiotic events around the time of the origin of eukaryotes, which eliminated any solid evidence of lateral relationships and made the concept of Protista unusable. He concluded, therfore, that we should just return to the Plant-Animal dichotomy.

The Theory of Serial Endosymbiosis (SET; Taylor, 1974), that eukaryotes evolved from a singular line of nuclear taxa, which then acquired mitochondrial endosymbiotes of several different types (those with tubular, flattened, or discoid cristae) seemed to respond to the warning of Round (1980). Ultrastructural work confirmed that such groups of eukaryotes existed and helped to define major groups of eukaryotic protists as platycristate, discicristate, tubulocristate, and amitochondrial. Margulis (Margulis and Schwartz 1982, 1988, 1998, 2001) further defined lines of eukaryotes based on the occurrences of flagella and their orientations. She interpreted the flagellum as a spirochete that entered into an endosymbiotic relationship with a nuclear host, and, thus, the lines of eukaryotic evolution could be defined as having anteriorly-directed, posteriorly-directed, or no flagella. That the clusters of major groups with particular types of flagella also had similar kinds of mitochondria tended to confirm her position. However, for her, the flagellum (she called the eukaryotic flagellum an undulapodium) loomed as the single most important defining character for any major line of eukaryotes (e.g. Margulis and Schwartz, 1982, 1988, 1998, 2001; and Margulis et al., 1990).

THE ARCHEZOA HYPOTHESIS AND CHAOS

Cavalier-Smith (1983) devised the Archezoa Hypothesis as a more precise explanation for SET. In this view, the prenuclear protoeukaryote evolved from a bacterium that had developed the ability to construct a microtubular cytoskeleton. A flagellum was just the outward manifestation of the ability to make organized clusters of microtubules in the earliest group of eukaryote, a group that he called the Archezoa. Thus, he began the search for living members of the Archezoa and used his theory to explain the diversity of eukaryotes at the highest level.

In the meantime, molecular phylogenetics led to the discovery of the Archaea as a separate domain of life and promised to provide the key to the elucidation of eukaryotic diversity. The methods that molecular phylogenetics used compared presumably conserved and universal biopolymers (e.g. small subunit rRNA, actin, etc.). The earliest molecular analyses tended to be too sparsely branched to provide adequate information on whole groups. After a time, however, enough sequences could be compared to generate a tree that had a few deeply branched taxa with a collection of well-defined groups at its crown. The deeply-branched taxa like Giardia, Pelomyxa, and Microsporidia seemed to fit well into the Archezoa Hypothesis because they were amitochondriate. Margulis (1982, 1988) also used the molecular tree to confirm her theory that a primitive eukaryote without flagella or mitochondria was at the root of the tree. Pelomyxa seemed to fit that requirement perfectly well.

Through the decade of the 1990’s more and more molecular analyses began to be used and uncover relationships that were poorly understood, especially among the crown eukaryotes. Thus, the Heterokonts, Alveolates, Discicristates, and the Opisthokonts (animals + fungi) came together confirmed by molecular evidence and ultrastructural synapomorphies. The same methods, however, began to dismember the tree that had grown. Molecular genetics and ultrastructural studies showed that all of the deeply branched “primitive” taxa had mitochondrial genes in their nuclear genomes. Almost all of the deeply branched taxa were either parasites or symbiotes with concomitant structural and molecular simplification. Furthermore, even Pelomyxa had an internal flagellum. So, both the Archaezoan Hypothesis and the Margulis version of SET were overturned. Rather than the creation of a definitive tree, the work of the 1990’s produced 71 separate sisterless taxa (Patterson, 1999), and, by the end of the decade, eukaryotic systematics at the highest level was in chaos. Evidence of such phylogenetic confusion could be seen in Tudge (2000) where single genera like Giardia and Entamoeba were given kingdom-level status!

SUPERTREES AND SUPERGROUPS

Fortunately, a new powerful method called supertree analysis had been pioneered with bacteria (Daubin et al., 2002). According to Baldauf (2003a), supertrees employed:

combined multigene datasets
recognition of common patterns (consensus)
a better understanding of long branch attraction, an artifact of molecular comparisons that tends to produce false relationships between quite disparate groups.

Soon, the same methods were applied to major groups of eukaryotes and served to mitigate the problems to which analyses of single molecular sequences were prone (particularly to that of long branch attraction). Quickly, the orphaned groups began to be assembled into larger groups. Simpson and Roger (2002) summarized the changes from 1993-2002 in which the Archaezoa disappeared and the tree of life changed from being tree-like with a crown of advanced taxa to a shrub of major clusters of taxa. Baldauf (2003a) showed them combined into 8 clades while Keeling (2004) reduced them into 5 clades. The power of supertree analysis allowed for the assembly of many of the orphaned or sisterless taxa into a previously unrecognized kingdom called the Cercozoae. Thus, supertree analysis gave new life to the tree of life, one of Darwin’s favorite metaphors. Curiously though, rather than adopting the appearance of a tree, the supertrees of Baldauf (2003) and Keeling (2004) emerged as large clades from a common root, much like the petals of a flower. Perhaps a different botanical metaphor should be applied.

I have adopted the supertree of Keeling (2004) as the template for the following system (Table 1). Furthermore, I accept the difference between animals and fungi to be a kingdom-level difference. Thus, I interpret his 5 supergroups as superkingdoms, four of which contain more than one kingdom. In all, in this system, the eukaryotes occupy 11 kingdoms, only one of which (the Eukaryomonadae) likely is artificial, although the details for all of the kingdoms and the eukaryotic clades that they represent have yet to be ironed out.

TABLE 1. Higher-Level Classification of the Eukaryota, which includes the eukaryotic supergroups and their kingdoms with representative higher taxa.
SUPERGROUP	KINGDOM	REPRESENTATIVE TAXA
UNIKONTA	ANIMALIA	METAZOA, MYXOZOA, CHOANOZOA, NUCLEARIID AMOEBAE, ICHTHYOSPORIDS.
	FUNGI	FUNGI, CHYTRIDS, MICROSPORIDS.
	AMOEBOZOAE	PELOBIONTS, PROTOSTELID SLIME MOLDS, PLASMODIAL SLIME MOLDS, DICTYOSTELID SLIME MOLDS, LOBOSE AMOEBAS, APUSOZOA?
EXCAVATA	EUEXCAVATAE	DIPLOMONADS, PARABASALIDS, RETORTOMONADS, OXYMONADS, JAKOBODS?
EXCAVATA	DISCICRISTATAE	EUGLENOIDS, TRYPANOSOMES + LEISHMANIAS, VAHLKAMPHID AMOEBAS, ACRASID SLIME MOLDS.
CHROMALVEOLATA	HETEROKONTAE	ALL HETEROKONTAE (ALSO CALLED STRAMENOPILES), ACTINOPHRYDIAN HELIOZOANS.
	EUKARYOMONADAE	HAPTOMONADS, CRYPTOMONADS, CENTROHELID HELIOZOANS.
	ALVEOLATAE	DINOFLAGELLATES, CILIATES, APICOMPLEXANS.
RHIZARIA	CERCOZOAE	RADIOLARIANS, EUGLIPHID AMOEBAS, FORAMINIFERANS, CERCOMONADS, CHLORARACHNIOPHYTES, PLASMODIOPHORIDS, HAPLOSPORIDS.
PLANTA	VIRIDIPLANTAE	GREEN ALGAE, EMBRYOPHYTES
PLANTA	RHODOPHYTAE	RED ALGAE, GLAUCOPHYTES

LITERATURE CITED

Baldauf, S. L. 2003a. The deep roots of eukaryotes. Science. 300 (5626): 1701-1703.

Cavalier-Smith, T. 1983. A six-kingdom classification and a unified phylogeny. In: Schenk, H.E.A. and W.S. Schwemmler, eds. Endocytobiology II. de Gruyter , Berlin . pp. 1027-1034.

Daubin, V. M. Gouy, and G. Perrière. 2001. Bacterial molecular phylogeny using supertree approach. Genome Informatics. 12: 155-164.

Dodge, J. D. 1973. The fine structure of algal cells. Academic Press. New York.

Keeling P. J. 2004 The diversity and evolutionary history of plastids and their hosts. American Journal of Botany. 91(10): 1481-1493.

Margulis, L. and K. Schwartz. 1982. Five kingdoms, an illustrated guide to the phyla of life on earth. W.H. Freeman and Co. New York.

Margulis, L. and K. Schwartz. 1988. Five kingdoms, an illustrated guide to the phyla of life on earth. 2nd Edition. W.H. Freeman and Co. New York.

Margulis, L. and K. Schwartz. 1998. Five kingdoms, an illustrated guide to the phyla of life on earth. 3rd Edition. W. H. Freeman and Company. New York.

Margulis, L., J. O. Corliss, M. Melkonian, and D. J. Chapman, eds. 1990. Handbook of the Protoctista; the structure, cultivation, habits and life histories of the eukaryotic microorganisms and their descendants exclusive of animals, plants and fungi. Jones and Bartlett Publishers. Boston.

Patterson, D. J. 1999. The diversity of eukaryotes. American Naturalist. 154 (Suppl.): S96–S124.

Round, F. E. 1980. The evolution of pigmented and unpigmented unicells – a reconsideration of the Protista. BioSystems. 12: 61-69.

Simpson, A. G. B., and A. J. Roger. 2002. Eukaryotic evolution: getting to the root of the problem: Current Biology. 12 R691–RR693.

Taylor, F. J. R. 1974. Implications and extensions of the serial endosymbiosis theory of the origin of eukaryotes. Taxon. 23: 229–258.

Taylor, F. J. R. 1976. Flagellate Phylogeny: A Study in Conflicts. Journal of Protozoology. 23(1):28-40.

Tudge, C. 2000. The Variety of Life, A Survey and a Celebration of all the Creatures That Have Ever Lived. Oxford University Press. New York.

By Jack R. Holt. Last revised: 02/15/2009

EVOLUTION OF THE EUKARYOTIC SUPERTREE

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