Eukaryotes - Comprehensive List of References

Patrick Keeling, Brian S. Leander, and Alastair Simpson


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Archibald, J.M., Longet, D., Pawlowski, J. and Keeling, P.J. (2002) A novel polyubiquitin structure in Cercozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol. Biol. Evol., 20, 62-66.

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Bass, D., Moreira, D., Lopez-Garcia, P., Polet, S., Chao, E.E., von der Heyden, S., Pawlowski, J. and Cavalier-Smith, T. (2005) Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist, 156, 149-161.

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Budin, K. and Philippe, H. (1998) New insights into the phylogeny of eukaryotes based on Ciliate Hsp70 sequences. Molecular Biology and Evolution, 15, 943-956.

Burki, F. and Pawlowski, J. (2006) Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts. Molecular Biology and Evolution, 23(10), 1922-1930.

Burki, F., Shalchian-Tabrizi, K., Minge, M., Skjaeveland, A., Nikolaev, S.I., Jakobsen, K.S. and Pawlowski, J. (2007) Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE, 2, e790.

Burki, F., Shalchian-Tabrizi, K. and Pawlowski, J. (2008) Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol. Lett., 4(4), 366-369.

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

Cavalier-Smith, T. (2002) The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Sys. Evol. Microbiol., 52, 297-354.

Cavalier-Smith, T. (2003) Protist phylogeny and the high-level classification of Protozoa. Eur. J. Protistol., 39, 338-348.

Cavalier-Smith, T. (2004) Chromalveolate diversity and cell megaevolution: interplay of membranes, genomes and cytoskeleton. In Hirt, R.P. and Horner, D. (eds.), Organelles, Genomes and Eukaryotic Evolution. Taylor and Francis, London, pp. 71-103.

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Cavalier-Smith, T. and Chao, E.E. (2003) Phylogeny and classification of phylum Cercozoa (Protozoa). Protist, 154, 341-358.

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Edlind, T.D. (1998) Phylogenetics of protozoan tubulin with reference to the amitochondriate eukaryotes. Pages 91-108 in Evolutionary Relationships Among Protozoa (Coombs, G.H., Vickerman, K., Sleigh, M.A. and Warren, A., eds.) Chapman & Hall, London.

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Fast, N.M., Logsdon, J.M., and Doolittle, W.F. (1999) Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a microsporidia-fungi relationship and spliceosomal intron loss. Molecular Biology and Evolution, 16, 1415-1419.

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Germot, A., Philippe, H., and Le Guyader, H. (1997) Evidence for loss of mitochondria in Microsporidia from a mitochondrial-type HSP70 in Nosema locustae. Molecular and Biochemical Parasitology, 87, 159-168.

Gogarten, J.P. (2003) Gene transfer: Gene swapping craze reaches eukaryotes. Curr Biol., 13, R53–54.

Gogarten, J.P., Kiblak, H., Dittrich, P., Taiz, L., Bowman, E.J., Bowman, B.J., Manolson, N.F., Poole, R.J., Date, T., Oshima, T., Konishi, J., Denda, K. and Yoshida, M. (1989) Evolution of the vacuolar H+-ATPase: inplications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA, 86, 6661-6665.

Golding, G.B. and Gupta, R. S. (1995) Protein-based phylogenies support a chimeric origin for the eukaryotic genome. Molecular Biology and Evolution, 12, 1-6.

Gould, S.B., Waller, R.F. and McFadden, G.I. (2008) Plastid evolution. Annu. Rev. Plant. Biol., 59, 491-517.

Gray, M.W., Burger, G. and Lang, B.F. (1999) Mitochondrial evolution. Science, 283, 1476-1481.

Gray, M.W. and Doolittle, W.F. (1982) Has the endosymbiont hypothesis been proven? Microbiol Rev., 46, 1-42.

Gray, M.W., Lang, B.F. and Burger, G. (2004) Mitochondria of protists. Annu. Rev. Genet., 38, 477-524.

Grosberg, R.K. and Strathmann, R.R. (2007) The evolution of multicellularity: a minor major transition? Annual Review of Ecology, Evolution, and Systematics, 38, 621-654.

Hackett, J.D., Yoon, H.S., Li, S., Reyes-Prieto, A., Rummele, S.E. and Bhattacharya, D. (2007) Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. Mol. Biol. Evol., 24, 1702-1713.

Hagopian, J.C., Reis, M., Kitajima, J.P., Bhattacharya, D. and de Oliveira, M.C. (2004) Comparative analysis of the complete plastid genome sequence of the red alga Gracilaria tenuistipitata var. liui provides insights into the evolution of rhodoplasts and their relationship to other plastids. J. Mol. Evol., 59, 464-477.

Hampl, V., Horner, D.S., Dyal, P., Kulda, J., Flegr, J., Foster, P.G., and Embley, T.M. (2005) Inference of the phylogenetic position of oxymonads based on nine genes: Support for Metamonada and Excavata. Molecular Biology and Evolution, 22(12), 2508-2518.

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Harper, J.T. and Keeling, P.J. (2003) Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. Mol. Biol. Evol., 20, 1730-1735.

Hashimoto, T., Nakamura, Y., Kamaishi, T., and Hasegawa, M. (1997) Early evolution of eukaryotes inferred from protein phylogenies of translation elongation factors 1 alpha and 2. Archiv für Protistenkunde, 148, 287-295.

Herrmann, K.M. and Weaver, L.M. (1999) The Shikimate Pathway. Annu. Rev. Plant Physiol. Plant Mol. Biol., 50, 473-503.

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Hirt, R.P. and Horner, D. (eds.) (2004) Organelles, Genomes and Eukaryote Evolution. Taylor & Francis, London.

Hirt, R.P., Logsdon, Jr., J.M., Healy, B., Dorey, M.W., Doolittle, W.F., and Embley, T.M. (1999) Microsporidia are related to fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proceedings of the National Academy of Sciences (USA), 96, 580-585.

Hoppenrath, M. and Leander, B.S. (2006) Dinoflagellate, euglenid or cercomonad? The ultrastructure and molecular phylogenetic position of Protaspis grandis n. sp. J. Eukaryot. Microbiol., 53, 327-342.

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Katz, L.A. (1998) Changing perspectives on the origin of eukaryotes. Trends Ecol. Evol., 13, 493-497.

Katz, L.A. (1999) The tangled web: gene genealogies and the origin of eukaryotes. American Naturalist, 154(suppl.), S137-S145.

Keeling, P.J. (1998) A kingdom's progress: Archezoa and the origin of eukaryotes. BioEssays, 20, 87-95.

Keeling, P.J. (2001) Foraminifera and Cercozoa are related in actin phylogeny: two orphans find a home? Mol. Biol. Evol., 18, 1551-1557.

Keeling, P.J. (2004) The diversity and evolutionary history of plastids and their hosts. Am. J. Bot., 91, 1481-1493.

Keeling, P.J. (2009) Chromalveolates and the evolution of plastids by secondary endosymbiosis. J. Eukaryot Microbiol., in press.

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. and Gray, M.W. (2005) The tree of eukaryotes. Trends Ecol. Evol., 20, 670-676.

Keeling, P.J. and Doolittle, W.F. (1996) Alpha-tubulin from early-diverging eukaryotic lineages and the evolution of the tubulin family. Molecular Biology and Evolution, 13, 1297-1305.

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Keeling, P.J. and Palmer, J.D. (2000) Phylogeny - Parabasalian flagellates are ancient eukaryotes. Nature, 405, 635-637.

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About This Page

Patrick Keeling
The University of British Columbia, Vancouver, British Columbia, Canada

Brian S. Leander
The University of British Columbia, Vancouver, British Columbia, Canada

Alastair Simpson
Dalhousie University, Halifax, Nova Scotia, Canada

Correspondence regarding this page should be directed to Patrick Keeling at , Brian S. Leander at , and Alastair Simpson at

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