Skip to main content
SpringerLink
Log in

The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree

  • Chapter
Eukaryotic Membranes and Cytoskeleton

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 607))

Abstract

More than 15 years ago, on the basis of phylogenetic analyses of a handful of anciently duplicated genes and of rRNA, Carl Woese proposed both a eubacterial rooting of the Tree of Life and a stepwise evolution of the eukaryotic cell. An important part of Woese’s paradigm was the assumption that the so-called Archezoa were considered to be genuinely primitive because they were lacking mitochondria and several other organelles characteristic for most eukaryotes. Since then, enormous progress have been accomplished in sequencing technology and in phylogenetic reconstruction. In particular, it is now clear that a tree reconstruction artefact, known as Long Branch Attraction, is responsible for the early emergence of the fast evolving Archezoa in the eukaryotic tree. The corollary hypothesis that all extant eukaryotes are ancestrally mitochondrial is strongly supported by the discovery of rudimentary mitochondrial organelles in all analysed Archezoa. Today a consensus that divides the extant eukaryotes into six major groups is replacing Woese’s paradigm, which needs, however, further confirmation. Recendy, a molecular dating study based on a large phylogenomic dataset with a relaxed molecular clock and multiple time intervals yielded in a surprisingly recent time estimate of 1085 Mya for the origin of the extant eukaryotic diversity. Therefore, extant eukaryotes seem to be the product of a massive radiation that happened rather late, at least in terms of prokaryotic diversity. In multiple cases evolution has proceeded via secondary simplification of a complex ancestor, instead of the constant march towards rising complexity generally assumed. Therefore it is time to reevaluate the origin and evolution of eukaryotes, in light of the newly established phylogeny, by further integrating secondary simplification as an equal partner to complexification.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Woese CR, Kandier O, Wheelis ML. Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87(12):4576–4579.

    Article  PubMed  CAS  Google Scholar 

  2. Sogin ML, Elwood HJ, Gunderson JH. Evolutionary diversity of eukaryotic small-subunit rRNA genes. Proc Natl Acad Sci USA 1986; 83(5): 1383–1387.

    Article  PubMed  CAS  Google Scholar 

  3. Knoll AH. The early evolution of eukaryotes: A geological perspective. Science 1992; 256(5057):622–627.

    Article  PubMed  CAS  Google Scholar 

  4. Sogin ML. Early evolution and the origin of eukaryotes. Curr Opin Genet Dev 1991; l(4):457–463.

    Article  Google Scholar 

  5. Cavalier-Smith T. Molecular phylogeny. Archaebacteria and Archezoa. Nature 1989; 339(6220):100–101.

    Article  Google Scholar 

  6. Bekker A, Holland HD, Wang PL et al. Dating the rise of atmospheric oxygen. Nature 2004; 427(6970):117–120.

    Article  PubMed  CAS  Google Scholar 

  7. Mereschkowski C. Ueber Natur und Ursprung der Cromatophoren im Pflanzenreiche. Biologisches Centralblatt 1905; 25:593–604.

    Google Scholar 

  8. Margulis L. Origin of Eukaryotic cells. New Haven: Yale University Press, 1970.

    Google Scholar 

  9. Tomioka N, Sugiura M. The complete nudeotide sequence of a 16S ribosomal RNA gene from a blue-green alga, Anacystis nidulans. Mol Gen Genet 1983; 191(l):46–50.

    Article  PubMed  CAS  Google Scholar 

  10. Yang D, Oyaizu Y, Oyaizu H et al. Mitochondrial origins. Proc Natl Acad Sci USA 1985; 82(13):4443–4447.

    Article  PubMed  CAS  Google Scholar 

  11. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proc Natl Acad Sci USA 1977; 74(11):5088–5090.

    Article  PubMed  CAS  Google Scholar 

  12. Iwabe N, Kuma K, Hasegawa M et al. Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 1989; 86(23):9355–9359.

    Article  PubMed  CAS  Google Scholar 

  13. Gogarten JP, Kibak H, Dittrich P et al. Evolution of the vacuolar H+-ATPase: Implications for the origin of eukaryotes. Proc Natl Acad Sci USA 1989; 86(17):6661–6665.

    Article  PubMed  CAS  Google Scholar 

  14. Baldauf SL, Palmer JD, Doolittle WF. The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny. Proc Natl Acad Sci USA 1996; 93(15):7749–7754.

    Article  PubMed  CAS  Google Scholar 

  15. Brown JR, Doolittle WF. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc Natl Acad Sci USA 1995; 92(7):2441–2445.

    Article  PubMed  CAS  Google Scholar 

  16. Lawson FS, Charlebois RL, Dillon JA. Phylogenetic analysis of carbamoylphosphate synthetase genes: Complex evolutionary history includes an internal duplication within a gene which can root the tree of life. Mol Biol Evol 1996; 13(7):970–977.

    PubMed  CAS  Google Scholar 

  17. Gribaldo S, Cammarano P. The root of the universal tree of life inferred from anciently duplicated genes encoding components of the protein-targeting machinery. J Mol Evol 1998; 47(5):508–516.

    Article  PubMed  CAS  Google Scholar 

  18. Charlebois RL, Sensen CW, Doolittle WF et al. Evolutionary analysis of the hisCGABdFDEHI gene cluster from the archaeon Sulfolobus solfataricus P2. J Bacteriol 1997; 179(13):4429–4432.

    PubMed  CAS  Google Scholar 

  19. Gupta RS, Singh B. Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus. Curr Biol 1994; 4(12): 1104–1114.

    Article  PubMed  CAS  Google Scholar 

  20. Zillig W. Eukaryotic traits in Archaebacteria. Could the eukaryotic cytoplasm have arisen from archaebacterial origin? Ann NY Acad Sci 1987; 503:78–82.

    Article  PubMed  CAS  Google Scholar 

  21. Martin W, Müller M. The hydrogen hypothesis for the first eukaryote. Nature 1998; 392(6671):37–41.

    Article  PubMed  CAS  Google Scholar 

  22. Moreira D, Löpez-Garcfa P. Symbiosis between methanogenic archaea and delta-Proteobacteria as the origin of eukaryotes: The syntrophic hypothesis. J Mol Evol 1998; 47(5):517–530.

    Article  PubMed  CAS  Google Scholar 

  23. Olsen G. Earliest phylogenetic branching: Comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb symp Quant Biol 1987; LII:825–837.

    Google Scholar 

  24. Hendy MD, Penny D. A framework for the quantitative study of evolutionary trees. Syst Zool 1989; 38:297–309.

    Article  Google Scholar 

  25. Lecointre G, Philippe H, Le HLV et al. Species sampling has a major impact on phylogenetic inference. Mol Phylogenet Evol 1993; 2(3):205–224.

    Article  PubMed  CAS  Google Scholar 

  26. Woese CR, Achenbach L, Rouviere P et al. Archaeal phylogeny: Reexamination of the phylogenetic position of Archaeoglobus fulgidus in light of certain composition-induced artifacts. Syst Appl Microbiol 1991; 14(4):364–371.

    PubMed  CAS  Google Scholar 

  27. Embley TM, Thomas RH, Williams RAD. Reduced thermophilic bias in the 16S rDNA sequence from Thermus ruber provides further support for a relationship between Thermus and Deinococcus. Syst Appl Microbiol 1992; 16:25–29.

    Google Scholar 

  28. Galtier N, Lobry JR. Relationships between genomic G + C content, RNA secondary structures, and optimal growth temperature in prokaryotes. J Mol Evol 1997; 44(6):632–636.

    Article  PubMed  CAS  Google Scholar 

  29. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 1978; 27:401–410.

    Article  Google Scholar 

  30. Delsuc F, Brinkmann H, Philippe H. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet 2005; 6(5):361–375.

    Article  PubMed  CAS  Google Scholar 

  31. Philippe H, Laurent J. How good are deep phylogenetic trees? Curr Opin Genet Dev 1998; 8(6):616–623.

    Article  PubMed  CAS  Google Scholar 

  32. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17(6):368–376.

    Article  PubMed  CAS  Google Scholar 

  33. Huelsenbeck JP. Is the Felsenstein zone a fly trap? Syst Biol 1997; 46(l):69–74.

    Article  PubMed  CAS  Google Scholar 

  34. Brinkmann H, Giezen M, Zhou Y et al. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol 2005; 54(5):743–757.

    Article  PubMed  Google Scholar 

  35. Jukes TH, Cantor CR. Evolution of protein molecules. In: Munro HN, ed. Mammalian Protein Metabolism. New York: Academic Press, 1969:21–132.

    Google Scholar 

  36. Lanave C, Preparata G, Saccone C et al. A new method for calculating evolutionary substitution rates. J Mol Evol 1984; 20(1):86–93.

    Article  PubMed  CAS  Google Scholar 

  37. Whelan S, Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001; 18(5):691–699.

    PubMed  CAS  Google Scholar 

  38. Yang Z. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 1993; 10(6):1396–l401.

    PubMed  CAS  Google Scholar 

  39. Lartillot N, Philippe H. A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol 2004; 21(6):1095–1109.

    Article  PubMed  CAS  Google Scholar 

  40. Pagel M, Meade A. A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data. Syst Biol 2004; 53(4):571–581.

    Article  PubMed  Google Scholar 

  41. Galtier N, Gouy M. Inferring pattern and process: Maximum-likelihood implementation of a nonhomogeneous model of DNA sequence evolution for phylogenetic analysis. Mol Biol Evol 1998; 15(7):871–879.

    PubMed  CAS  Google Scholar 

  42. Yang Z, Roberts D. On the use of nucleic acid sequences to infer early branchings in the tree of life. Mol Biol Evol 1995; 12(3):451–458.

    PubMed  CAS  Google Scholar 

  43. Foster PG. Modeling compositional heterogeneity. Syst Biol 2004; 53(3):485–495.

    Article  PubMed  Google Scholar 

  44. Philippe H, Delsuc F, Brinkmann H et al. Phylogenomics. Annu Rev Ecol Evol Syst 2005; 36:541–562.

    Article  Google Scholar 

  45. Felsenstein J. Inferring phylogenies. Sunderland, MA, USA: Sinauer Associates Inc., 2004.

    Google Scholar 

  46. Lockhart PJ, Larkum AW, Steel M et al. Evolution of chlorophyll and bacteriochlorophyll: The problem of invariant sites in sequence analysis. Proc Natl Acad Sci USA 1996; 93(5): 1930–1934.

    Article  PubMed  CAS  Google Scholar 

  47. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431(7011):980–984.

    Article  PubMed  CAS  Google Scholar 

  48. Hillis DM. Inferring complex phylogenies. Nature 1996; 383(6596):130–131.

    Article  PubMed  CAS  Google Scholar 

  49. Kim J. General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa. Syst Biol 1996; 45(3):363–374.

    Article  Google Scholar 

  50. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 1998; 47(1):9–17.

    Article  PubMed  CAS  Google Scholar 

  51. Philippe H, Douzery E. The pitfalls of molecular phylogeny based on four species, as illustrated by the Cetacea/Artiodactyla relationships. Journal of Mammalian Evolution 1994; 2:133–152.

    Article  Google Scholar 

  52. Mitchell A, Mitter C, Regier JC. More taxa or more characters revisited: Combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Syst Biol 2000; 49(2):202–224.

    Article  PubMed  CAS  Google Scholar 

  53. Lin YH, McLenachan PA, Gore AR et al. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Mol Biol Evol 2002; 19(12):2060–2070.

    PubMed  CAS  Google Scholar 

  54. Aguinaldo AM, Turbeville JM, Linford LS et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 1997; 387(6632):489–493.

    Article  PubMed  CAS  Google Scholar 

  55. Field KG, Olsen GJ, Lane DJ et al. Molecular phylogeny of the animal kingdom. Science 1988; 239(4841 Pt l):748–753.

    Article  PubMed  CAS  Google Scholar 

  56. Madsen O, Scally M, Douady CJ et al. Parallel adaptive radiations in two major clades of placental mammals. Nature 2001; 409(6820):610–614.

    Article  PubMed  CAS  Google Scholar 

  57. Murphy WJ, Eizirik E, Johnson WE et al. Molecular phylogenetics and the origins of placental mammals. Nature 2001; 409(6820):614–618.

    Article  PubMed  CAS  Google Scholar 

  58. Qiu YL, Lee J, Bernasconi-Quadroni F et al. The earliest angiosperms: Evidence from mitochondrial, plastid and nuclear genomes. Nature 1999; 402(6760):404–407.

    Article  PubMed  CAS  Google Scholar 

  59. Soltis PS, Soltis DE, Chase MW. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 1999; 402(6760):402–404.

    Article  PubMed  CAS  Google Scholar 

  60. Wolf YI, Rogozin IB, Koonin EV. Coelomata and not ecdysozoa: Evidence from genome-wide phylogenetic analysis. Genome Res 2004; 14(l):29–36.

    PubMed  CAS  Google Scholar 

  61. Blair JE, Ikeo K, Gojobori T et al. The evolutionary position of nematodes. BMC Evol Biol 2002; 2(1):7.

    Article  PubMed  Google Scholar 

  62. Philip GK, Creevey CJ, McInerney JO. The Opisthokonta and the Ecdysozoa may not be clades: Stronger support for the grouping of plant and animal than for animal and fungi and stronger support for the Coelomata than Ecdysozoa. Mol Biol Evol 2005; 22(5):1175–1184.

    Article  PubMed  CAS  Google Scholar 

  63. Philippe H, Lartillot N, Brinkmann H. Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia. Mol Biol Evol 2005; 22(5):1246–1253.

    Article  PubMed  CAS  Google Scholar 

  64. Dopazo H, Dopazo J. Genome-scale evidence of the nematode-arthropod clade. Genome Biol 2005; 6(5):R41.

    Article  PubMed  CAS  Google Scholar 

  65. Jeffroy O, Brinkmann H, Delsuc F et al. Phylogenomics: The beginning of incongruence? Trends in Genetics, (in press).

    Google Scholar 

  66. Delsuc F, Phillips MJ, Penny D. Comment on “Hexapod origins: Monophyletic or paraphyletic?” Science 2003; 301(5639):1482, (author reply 1482).

    Article  PubMed  CAS  Google Scholar 

  67. Hrdy I, Hirt RP, Dolezal P et al. Trichomonas hydrogenosomes contain the NADH dehydrogenase module of mitochondrial complex I. Nature 2004; 432(7017):618–622.

    Article  PubMed  CAS  Google Scholar 

  68. Steel M. Should phylogenetic models be trying to’ fit an elephant’? Trends Genet 2005; 21(6):307–309.

    Article  PubMed  CAS  Google Scholar 

  69. Brown JR, Robb FT, Weiss R et al. Evidence for the early divergence of tryptophanyl-and tyrosyl-tRNA synthetases. J Mol Evol 1997; 45(1):9–16.

    Article  PubMed  CAS  Google Scholar 

  70. Philippe H, Forterre P. The rooting of the universal tree of life is not reliable. J Mol Evol 1999; 49(4):509–523.

    Article  PubMed  CAS  Google Scholar 

  71. Lopez P, Forterre P, Philippe H. The root of the tree of life in the light of the covarion model. J Mol Evol 1999; 49:496–508.

    Article  PubMed  CAS  Google Scholar 

  72. Brinkmann H, Philippe H. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol 1999; 16(6):817–825.

    PubMed  CAS  Google Scholar 

  73. Yap VB, Speed T. Rooting a phylogenetic tree with nonreversible substitution models. BMC Evol Biol 2005; 5(1):2.

    Article  PubMed  Google Scholar 

  74. Caetano-Anolles G. Evolved RNA secondary structure and the rooting of the universal tree of life. J Mol Evol 2002; 54(3):333–345.

    PubMed  CAS  Google Scholar 

  75. Philippe H, Germot A, Moreira D. The new phylogeny of eukaryotes. Curr Opin Genet Dev 2000; 10(6):596–601.

    Article  PubMed  CAS  Google Scholar 

  76. Philippe H, Lopez P, Brinkmann H et al. Early-branching or fast-evolving eukaryotes? An answer based on slowly evolving positions. Proc R Soc Lond BS 2000; 267(1449):1213–1221.

    Article  CAS  Google Scholar 

  77. Philippe H, Adoutte A. The molecular phylogeny of Eukaryota: Solid facts and uncertainties. In: Coombs G, Vickerman K, Sleigh M, Warren A, eds. Evolutionary Relationships Among Protozoa. Dordrecht: Kluwer, 1998:25–56.

    Google Scholar 

  78. Baldauf SL, Roger AJ, Wenk-Siefert I et al. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 2000; 290(5493):972–977.

    Article  PubMed  CAS  Google Scholar 

  79. Roger AJ. Reconstructing early events in eukaryotic evolution. Am Nat 1999; 154:S146–S163.

    Article  PubMed  Google Scholar 

  80. Embley TM, Hirt RP. Early branching eukaryotes? Curr Opin Genet Dev 1998; 8(6):624–629.

    Article  PubMed  CAS  Google Scholar 

  81. Silberman JD, Clark CG, Diamond LS et al. Phylogeny of the genera Entamoeba and Endolimax as deduced from small-subunit ribosomal RNA sequences. Mol Biol Evol 1999; 16(12):1740–1751.

    PubMed  CAS  Google Scholar 

  82. Keeling PJ, Fast NM. Microsporidia: Biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 2002; 56:93–116.

    Article  PubMed  CAS  Google Scholar 

  83. Clark CG, Roger AJ. Direct evidence for secondary loss of mitochondria in Entamoeba histolytica. Proc Natl Acad Sci USA 1995; 92(14):6518–6521.

    Article  PubMed  CAS  Google Scholar 

  84. Roger AJ, Clark CG, Doolittle WF. A possible mitochondrial gene in the early-branching amitochondriate protist Trichomonas vaginalis. Proc Natl Acad Sci USA 1996; 93(25): 14618–14622.

    Article  PubMed  CAS  Google Scholar 

  85. Germot A, Philippe H, Le Guyader H. Presence of a mitochondrial-type 70-kDa heat shock protein in Trichomonas vaginalis suggests a very early mitochondrial endosymbiosis in eukaryotes. Proc Natl Acad Sci USA 1996; 93(25):14614–14617.

    Article  PubMed  CAS  Google Scholar 

  86. Germot A, Philippe H, Le Guyader H. Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Mol Biochem Parasitol 1997; 87(2):159–168.

    Article  PubMed  CAS  Google Scholar 

  87. Roger AJ, Svard SG, Tovar J et al. A mitochondrial-like chaperonin 60 gene in Giardia lamblia: Evidence that diplomonads once harbored an endosymbiont related to the progenitor of mitochondria. Proc Natl Acad Sci USA 1998; 95(1):229–234.

    Article  PubMed  CAS  Google Scholar 

  88. Bui ET, Bradley PJ, Johnson PJ. A common evolutionary origin for mitochondria and hydrogenosomes. Proc Natl Acad Sci USA 1996; 93(18):9651–9656.

    Article  PubMed  CAS  Google Scholar 

  89. Tovar J, Fischer A, Clark CG. The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol Microbiol 1999; 32(5): 1013–1021.

    Article  PubMed  CAS  Google Scholar 

  90. Williams BA, Hirt RP, Lucocq JM et al. A mitochondrial remnant in the microsporidian Trachipleistophora hominis. Nature 2002; 418(6900):865–869.

    Article  PubMed  CAS  Google Scholar 

  91. Tovar J, Leon-Avila G, Sanchez LB et al. Mitochondrial remnant organelles of Giardia function in iron-sulphur protein maturation. Nature 2003; 426(6963): 172–176.

    Article  PubMed  CAS  Google Scholar 

  92. Boxma B, de Graaf RM, van der Staay GW et al. An anaerobic mitochondrion that produces hydrogen. Nature 2005; 434(7029):74–79.

    Article  PubMed  CAS  Google Scholar 

  93. Keeling PJ, Burger G, Durnford DG et al. The tree of eukaryotes. Trends in Ecology and Evolution 2005; 20(12):670–676.

    Article  PubMed  Google Scholar 

  94. Adl SM, Simpson AG, Farmer MA et al. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 2005; 52(5):399–451.

    Article  PubMed  Google Scholar 

  95. Simpson AG, Roger AJ. The real ‘kingdoms’ of eukaryotes. Curr Biol 2004; 14(17):R693–696.

    Article  PubMed  CAS  Google Scholar 

  96. Patterson DJ. The diversity of eukaryotes. Am Nat 1999; 154:S96–S124.

    Article  PubMed  Google Scholar 

  97. Rokas A, Holland PW. Rare genomic changes as a tool for phylogenetics. Trends in Ecology and Evolution 2000; 15(11):454–459.

    Article  PubMed  Google Scholar 

  98. Baldauf SL, Palmer JD. Animals and fungi are each other’s closest relatives: Congruent evidence from multiple proteins. Proc Natl Acad Sci USA 1993; 90(24):l 1558–11562.

    Article  Google Scholar 

  99. Baldauf SL. A search for the origins of animals and fungi: Comparing and combining molecular data. Am Nat 1999; 154:S178–S188.

    Article  PubMed  Google Scholar 

  100. Rodriguez-Ezpeleta N, Brinkmann H, Burey SC et al. Monophyly of primary photosynthetic eukaryotes: Green plants, red algae, and glaucophytes. Current Biology 2005; 15(14): 1325–1330.

    Article  PubMed  CAS  Google Scholar 

  101. Steenkamp ET, Wright J, Baldauf SL. The protistan origins of animals and fungi. Mol Biol Evol 2005.

    Google Scholar 

  102. Philippe H, Snell EA, Bapteste E et al. Phylogenomics of eukaryotes: Impact of missing data on large alignments. Mol Biol Evol 2004; 21(9):1740–1752.

    Article  PubMed  CAS  Google Scholar 

  103. Palmer JD. The symbiotic birth and spread of plastids: Hows many times and whodunit? J Phycol 2003; 39:4–11.

    Article  CAS  Google Scholar 

  104. Rodriguez-Ezpeleta N, Brinkmann H, Burey S et al. Monophyly of primary photosynthetic eukaryotes: Green plants, red algae and glaucophytes. Current Biology 2005.

    Google Scholar 

  105. Marin B, EC MN, Melkonian M. A plastid in the making: Evidence for a second primary endosymbiosis. Protist 2005; 156(4):425–432.

    Article  PubMed  CAS  Google Scholar 

  106. Lonergan KM, Gray MW. Expression of a continuous open reading frame encoding subunits 1 and 2 of cytochrome c oxidase in the mitochondrial DNA of Acanthamoeba castellanii. J Mol Biol 1996; 257(5):1019–1030.

    Article  PubMed  CAS  Google Scholar 

  107. Bapteste E, Brinkmann H, Lee JA et al. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA 2002; 99(3):1414–1419.

    Article  PubMed  CAS  Google Scholar 

  108. Cavalier-Smith T. Principles of protein and lipid targeting in secondary symbiogenesis: Euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote familly tree. J Eukaryot Microbiol 1999; 46(4):347–366.

    Article  PubMed  CAS  Google Scholar 

  109. Harper JT, Keeling PJ. Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol Biol Evol 2003; 20(10):1730–1735.

    Article  PubMed  CAS  Google Scholar 

  110. Patron NJ, Rogers MB, Keeling PJ. Gene replacement of fructose-1,6-bisphosphate aldolase supports the hypothesis of a single photosynthetic ancestor of chromalveolates. Eukaryot Cell 2004; 3(5):1169–1175.

    Article  PubMed  CAS  Google Scholar 

  111. Petersen J, Teich R, Brinkmann H et al. A “Green” phosphoribulokinase in complex algae with red plastids: Evidence for a single secondary endosymbiosis leading to haptophytes, cryptophytes, heterokonts and dinoflagellates. Journal of molecular evolution 2005; 60, (in press).

    Google Scholar 

  112. Harper JT, Waanders E, Keeling PJ. On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int J Syst Evol Microbiol 2005; 55(Pt l):487–496.

    Article  PubMed  CAS  Google Scholar 

  113. Yoon HS, Hackett JD, Ciniglia C et al. A molecular timeline for the origin of photosynthetic eukaryotes. Mol Biol Evol 2004; 21(5):809–818.

    Article  PubMed  CAS  Google Scholar 

  114. Martin W, Rujan T, Richly E et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 2002; 99(19): 12246–12251.

    Article  PubMed  CAS  Google Scholar 

  115. Simpson AG, Roger AJ, Silberman JD et al. Evolutionary history of “early-diverging” eukaryotes: The excavate taxon Carpediemonas is a close relative of Giardia. Mol Biol Evol 2002; 19(10):1782–1791.

    PubMed  CAS  Google Scholar 

  116. Cavalier-Smith T. The excavate protozoan phyla Metamonada Grasse emend. (Anaeromonadea, Parabasalia, Carpediemonas, Eopharyngia) and Loukozoa emend. (Jakobea, Malawimonas): Their evolutionary affinities and new higher taxa. Int J Syst Evol Microbiol 2003; 53(Pt 6): 1741–1758.

    Article  PubMed  CAS  Google Scholar 

  117. Nikolaev SI, Berney C, Fahrni JF et al. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes. Proc Natl Acad Sci USA 25 2004; 101(21):8066–8071.

    Article  CAS  Google Scholar 

  118. Arisue N, Hasegawa M, Hashimoto T. Root of the Eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 2005; 22(3):409–420.

    Article  PubMed  CAS  Google Scholar 

  119. Bass D, Moreira D, Lopez-Garcia P et al. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist 2005; 156(2):149–161.

    Article  PubMed  CAS  Google Scholar 

  120. Simpson AG. Cytoskeletal organization, phylogenetic affinities and systematics in the contentious taxon Excavata (Eukaryota). Int J Syst Evol Microbiol 2003; 53(Pt 6):1759–1777.

    Article  PubMed  Google Scholar 

  121. Hampl V, Horner DS, Dyal P et al. Inference of the phylogenetic position of oxymonads based on nine genes: Support for metamonada and excavata. Mol Biol Evol 2005; 22(12):2508–2518.

    Article  PubMed  CAS  Google Scholar 

  122. Cavalier-Smith T. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002; 52(Pt 2):297–354.

    PubMed  CAS  Google Scholar 

  123. Keeling PJ, Palmer JD. Parabasalian flagellates are ancient eukaryotes. Nature 2000; 405(6787):635–637.

    Article  PubMed  CAS  Google Scholar 

  124. Bapteste E, Philippe H. The potential value of indels as phylogenetic markers: Position of trichomonads as a case study. Mol Biol Evol 2002; 19(6):972–977.

    PubMed  CAS  Google Scholar 

  125. Keeling PJ. Polymorphic insertions and deletions in parabasalian enolase genes. J Mol Evol 2004; 58(5):550–556.

    Article  PubMed  CAS  Google Scholar 

  126. Stechmann A, Cavalier-Smith T. Rooting the eukaryote tree by using a derived gene fusion. Science 2002; 297(5578):89–91.

    Article  PubMed  CAS  Google Scholar 

  127. Nara T, Hshimoto T, Aoki T. Evolutionary implications of the mosaic pyrimidine-biosynthetic pathway in eukaryotes. Gene 2000; 257(2):209–222.

    Article  PubMed  CAS  Google Scholar 

  128. Stechmann A, Cavalier-Smith T. The root of the eukaryote tree pinpointed. Curr Biol 2003; 13(17):R665–666.

    Article  PubMed  CAS  Google Scholar 

  129. Richards TA, Cavalier-Smith T. Myosin domain evolution and the primary divergence of eukaryotes. Nature 2005; 436(7054):1113–1118.

    Article  PubMed  CAS  Google Scholar 

  130. Cermakian N, Ikeda TM, Miramontes P et al. On the evolution of the single-sub unit RNA polymerases. J Mol Evol 1997; 45(6):671–681.

    Article  PubMed  CAS  Google Scholar 

  131. Hedges SB, Blair JE, Venturi ML et al. A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol 2004; 4:2.

    Article  PubMed  Google Scholar 

  132. Douzery EJ, Snell EA, Bapteste E et al. The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 2004, (10 19).

    Google Scholar 

  133. Graur D, Martin W. Reading the entrails of chickens: Molecular timescales of evolution and the illusion of precision. Trends Genet 2004; 20(2):80–86.

    Article  PubMed  CAS  Google Scholar 

  134. Bromham L, Penny D. The modern molecular clock. Nat Rev Genet 2003; 4(3):216–224.

    Article  PubMed  CAS  Google Scholar 

  135. Sanderson MJ. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol Biol Evol 1997; 14(12):1218–1231.

    CAS  Google Scholar 

  136. Thorne JL, Kishino H, Painter IS. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 1998; 15(12):1647–1657.

    PubMed  CAS  Google Scholar 

  137. Huelsenbeck JP, Larget B, Swofford D. A compound poisson process for relaxing the molecular clock. Genetics 2000; 154(4):1879–1892.

    PubMed  CAS  Google Scholar 

  138. Bromham L, Penny D, Rambaut A et al. The power of relative rates tests depends on the data. J Mol Evol 2000; 50(3):296–301.

    PubMed  CAS  Google Scholar 

  139. Philippe H, Adoutte A. What can phylogenetic patterns tell us about the evolutionary processes generating biodiversity? In: Hochberg M, Clobert J, Barbault R, eds. Aspects of the Genesis and Maintenance of Biological Diversity. Oxford University Press, 1996:41–59.

    Google Scholar 

  140. Wiegmann BM, Yeates DK, Thorne JL et al. Time flies, a new molecular time-scale for brachyceran fly evolution without a clock. Syst Biol 2003; 52(6):745–756.

    Article  PubMed  Google Scholar 

  141. Springer MS, Murphy WJ, Eizirik E et al. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci USA 2003; 100(3):1056–1061.

    Article  PubMed  CAS  Google Scholar 

  142. Javaux EJ, Knoll AH, Walter MR. Morphological and ecological complexity in early eukaryotic ecosystems. Nature 2001; 412(6842):66–69.

    Article  PubMed  CAS  Google Scholar 

  143. Javaux EJ, Knoll AH, Walter M. Recognizing and interpreting the fossils of early eukaryotes. Orig Life Evol Biosph 2003; 33(l):75–94.

    Article  PubMed  CAS  Google Scholar 

  144. Brocks JJ, Logan GA, Buick R et al. Archean molecular fossils and the early rise of eukaryotes. Science 1999; 285(5430):1033–1036.

    Article  PubMed  CAS  Google Scholar 

  145. Rohde DL, Olson S, Chang JT. Modelling the recent common ancestry of all living humans. Nature 2004; 431(7008):562–566.

    Article  PubMed  CAS  Google Scholar 

  146. Zhaxybayeva O, Gogarten JP. Cladogenesis, coalescence and the evolution of the three domains of life. Trends Genet 2004; 20(4): 182–187.

    Article  PubMed  CAS  Google Scholar 

  147. Canfield DE, Teske A. Late proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies. Nature 1996; 382:127–132.

    Article  PubMed  CAS  Google Scholar 

  148. Dacks JB, Doolittle WF. Reconstructing/deconstructing the earliest eukaryotes: How comparative genomics can help. Cell 2001; 107(4):419–425.

    Article  PubMed  CAS  Google Scholar 

  149. Mitchell DR. Speculations on the evolution of 9 + 2 organelles and the role of central pair microtubules. Biol Cell 2004; 96(9):691–696.

    Article  PubMed  CAS  Google Scholar 

  150. Lwoff A. L’évolution physiologique. Étude des pertes de fonctions chez les microorganismes. Paris: Hermann et Cie, 1943.

    Google Scholar 

  151. Gould SJ. Full house: The spread of excellence from plato to darwin. Harmony Books, 1996.

    Google Scholar 

  152. Jacob F. Evolution and tinkering. Science 1977; 196(4295):1161–1166.

    Article  PubMed  CAS  Google Scholar 

  153. Forterre P, Philippe H. Where is the root of the universal tree of life? BioEssays 1999; 21:871–879.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Hervé Philippe—Canadian Institute for Advanced Research, Evolutionary Biology Program, Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Succursale CentreVille, 2900 Edouard Montpetit, Montréal, Québec, H3C3J7, Canada

    Henner Brinkmann & Hervé Philippe

Authors
  1. Henner Brinkmann
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hervé Philippe
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hervé Philippe .

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Landes Bioscience and Springer Science+Business Media

About this chapter

Cite this chapter

Brinkmann, H., Philippe, H. (2007). The Diversity Of Eukaryotes And The Root Of The Eukaryotic Tree. In: Eukaryotic Membranes and Cytoskeleton. Advances in Experimental Medicine and Biology, vol 607. Springer, New York, NY. https://doi.org/10.1007/978-0-387-74021-8_2

Download citation

Publish with us

Policies and ethics

Search

Navigation