The Molecular History of Eukaryotic Life Introduction
David Nelson Dec. 9, 2000 modified Jan. 11, 2001 The history of life is more than the history of eukaryotic life, so some explanation must be given for limiting this effort just to eukaryotes. Why not include the evolution of photosynthesis, oxidative phosphorylation and the ATP synthase in bacteria as well as the evolution of the various cytochromes, other pigments and cofactors? Surely, these are worthy of consideration. They are also so ancient that their origins are probably lost in the distant past. The recent appreciation of the impact of lateral gene transfer between early prokaryotes (1,2) has dampened hopes of following evolution back to the last common ancestor and on to the 3.85 billion year age of the Isua rock belt C12/C13 biomarker(3,4). The network nature of genome phylogeny in these early prokaryotes may mean that there were no species as we now think of them until a kind of genomic phase transition occurred and the lateral transfer of fundamental genes became limited. This restriction of rampant gene swapping allowed independent lineages to exist without being blended completely into a universal gene pool. The base of the three Domain tree of life probably represents this point in time(5,6). Once a dichotomous branching pattern became dominant, evolutionary history could be preserved in each lineage. However, lateral gene transfer did not stop abruptly. Prokaryotic genomes, have many genes that appear to be transfered, especially the metabolic genes(7). Thermotoga maritima, a bacteria, exhibits extensive lateral gene transfer with archaea(8). The continued transfer of genes between Domains will make unravelling the early history of life complicated. The magnitude of this effect should be much reduced by the time eukaryotes appeared about 2.1 billion years ago. These considerations have caused me to limit the discussions of these pages to the molecular history of eukaryotic life. What are we really talking about when we say eukaryotic life? What does that include? This is a matter of higher level taxonomy, which becomes almost philosophical and subject to debate. The higher level taxonomy of life is constantly being revised, as it should be to accomodate new data, especially the new genome sequence data. However, there appears to be a convergence on an accepted core grouping of organisms. This will probably continue until a firm consensus is reached. I give three examples, two from 1998(9,10) and one from Nov. 2000(11), based on the most current sequence data. First is the five kingdom classification of Margulis and Schwartz (9). This system places all prokaryotes in the Superkingdom Prokarya, with one Kingdom Bacteria. Archaea and Eubacteria are Subkingdoms. The eukaryotes are treated as the Superkingdom Eukarya and are placed in four Kingdoms: Protoctista(30 phyla), Fungi(3 phyla), Plantae(12 phyla) and Animalia(37 phyla). There are a total of 96 phyla in this system. Protoctista is the catch-all Kingdom for all eukaryotes that do not fit in the other three Kingdoms. The six kingdom system of Cavalier-Smith(10) also treats Archaea as an infrakingdom of the Kingdom Bacteria. This is in agreement with Margulis and Schwartz and with Ernst Mayr, who sees the fundamental division of life as prokaryote vs. eukaryote. This is in sharp contrast to Woese who argues for his own three Domain system based on small subunit rRNA sequence trees. The eukaryotes are divided into five kingdoms in Cavalier-Smith’s system: Protozoa(13 phyla), Chromista(? phyla) Plantae(? phyla) Fungi(4 phyla) and Animalia(23 phyla). There are a total of 60 phyla in the Cavalier-Smith system. The new results from Baldauf and Doolittle are completely based on molecular data(11). These results only deal with eukaryotes. The organisms are sorted into 14-15 main groups which seemingly would all have to be treated as Kingdoms, since they do include the classical Kingdoms of Plantae, Animalia and Fungi. A few of these larger groups have high bootstrap support for even larger supergroups. This would reduce the number of kingdom level taxa to eight or nine (1. Fungi + Microsporidia; 2. Metazoa; 3. Amoebozoa = Mycetozoa + Lobosa; 4. Plantae = Viridiplantae + Rhodophyta + Glaucophyta; 5. Heterokonta; 6. Alveolata = Ciliophora + Apicomplexa; 7. Discicristata = Euglenozoa + Heterolobosea; 8. Diplomonadida; 9. Parabasala). The latter two could be united in a group called Archezoa as done by Cavalier-Smith. This is actually a satisfying result that escapes from the catch-all categories created by the Protoctista and the Protozoa. This molecular based phylogeny may be a better reflection of the real evolution of these groups. It should be mentioned that the system of Cavalier-Smith with its Chromista Kingdom was already moving in this direction. One aspect of Baldauf and Doolittle’s tree is the many phyla that are missing. In Margulis and Schwartz’s system, there are 30 protoctist phyla. 18 of them are not in the Doolittle tree. These phyla are numbered PR# where # = 1 to 30. PR4, 5, 7, 10, 13, 14, 15, 16, 18, 19, 21, 22, 23, 24, 26, 27, 29 and 30 are absent. Many of these will fit into the tree in existing groups, like PR4 (foraminifera) and PR7 (dinoflagellates) that are part of Alveolata. PR13 to PR21 are identified by Margulis and Schwartz as part of the Stramenopiles. The Heterokonta from Doolittle’s tree includes two members of this group PR17 and PR20. Presumably the others would also sort into the Heterokonta in this tree. PR22 Haplospora is categorized as Alveolata in GenBank. PR24 Myxospora is classified as Metazoa in GenBank. PR26 Gamophyta is classified in the Viridiplantae in GenBank. PR29 Chytridiomycota is classified as Fungi in GenBank. These placements may be convenient, but they need to be verified. PR5 Xenophyophora is completely absent from Genbank. The remaining four phyla PR10 Haptomonada, PR23 Paramyxa, PR27 Actinopoda (radiolarians) and PR30 Zoomastigota are given their own classifications in GenBank. These and PR5 are not present on the Baldauf and Doolittle tree. It is not clear where they belong, but this needs to be established. For a cross-referenced table of Protist taxonomy and numbers of sequence entries in Genbank see Protist Sequence Space What’s Out There? The group of phyla that are called Stramenopiles by Sogin (12), Chromista by Cavalier- Smith, or Heterokonta by Doolittle are overlapping but not exacly the same sets of phyla in each case. This should be clarified by more sequence data and perhaps by the discovery of unique insertions or deletions shared by this set of eukaryotes. According to the web page Evolution: A Molecular Point of View (13) Heterokonta is included in the Kingdom Chromista. The current data on the eukaryotic phyla, with emphasis on the new concatenated protein tree of Baldauf and Doolittle, provide a starting point in the quest for uncovering the true relationships of the eukaryotic phyla. As a statement of the problem, there are eight main divisions on the tree as listed above. These are reasonably well supported groups that can tentatively be accepted as accurate. The other 5 phyla (PR5 Xenophyophora; PR10 Haptomonada; PR23 Paramyxa; PR27 Actinopoda (radiolarians); PR30 Zoomastigota) that do not fit in existing locations on the tree must be added in for a total of 13 branches. The task ahead is to discern how these 13 branches truely diverged from one another over time. The SSU rRNA trees that have become the norm for placement of phyla cannot be assumed to be correct for the deep time branches. This has been demonstrated by the movement of the Microsporidia from a very deep branch location into the fungi. This adjustment was a dramatic change on the rRNA tree and dealt a blow to the dependence on rare structural features like the lack of mitochondria as a reliable guide in assigning phylogenetic position. The molecular feature that did support the joining of Microsporidia with animals and Fungi was an insertion in the EF1 alpha protein sequence. This 12 amino acid insertion was present in animals, fungi (and later, microsporidians, follow the link below to the synapomorphies for an alignment) and no other eukaryote or prokaryote phyla(14). The same was also true for three short deletions in enolase. These are synapomorphies that define a clade. The structure of the cells is not important, and in this case it was misleading. My proposition in these pages is that synapomorphies of this nature, a diagnostic insertion or deletion, must be found to define the relationships of these 13 eukaryotic branches. Once such an indel is found the chance that it came from a lateral gene transfer must be evaluated and ruled out. With 13 branches to join, 12 synapomorphies need to be found. We already know of two. Go to The Synapomorphies. Return to index References 1. Doolittle W.F. Phylogenetic classification and the universal tree. Science 284, 2124-2128 1999 2. Doolittle W.F. Uprooting the tree of life. Sci Am. 282, 90-95 2000 3. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CR. Evidence for life on Earth before 3,800 million years ago. Nature. 1996 Nov 7;384(6604):55-9. 4. Rosing MT. 13C-Depleted carbon microparticles in >3700-Ma sea-floor sedimentary rocks from west greenland. Science. 1999 Jan 29;283(5402):674-6. 5. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576-9. 6. Woese CR. Interpreting the universal phylogenetic tree. Proc Natl Acad Sci U S A. 97, 8392-8396 2000 7. Jain R, Rivera MC, Lake JA. Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3801-6. 8. Nelson KE, Paulsen IT, Heidelberg JF, Fraser CM. Status of genome projects for nonpathogenic bacteria and archaea. Nat Biotechnol. 18, 1049-54 2000 9. Margulis, L. and Schwartz, K.V. Five Kingdoms an illustrated guide to the phyla of life on earth. Freeman, New York 1998 10. Cavalier-Smith T. A revised six kingdom system of life. Biol. Rev. Camb. Philos. Soc. 73, 203-266 1998 11. Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 2000 Nov 3;290(5493):972-7. 13. 14. Hirt RP, Logsdon JM Jr, Healy B, Dorey MW, Doolittle WF, Embley TM. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A. 1999 Jan 19;96(2):580-5. Additional references and notes Cavalier-Smith, T. Kingdom Protozoa and Its 18 Phyla" Microbiol. Rev. 57:953-994 note from The University of California Museum of Paleontology web site concerning Chromista. "There is also considerable variation in the application of names to this group and the vaious subgroups in the literature. The group, which we here call the Chromista, is sometimes called Stramenopiles, Heterokonta, and Chromobionta, among others. Each of these terms has at times been used for a more restricted group however, so we follow Cavalier-Smith (1997) in using the term Chromista."