Other perspectives

Dans le document A phylogenomic contribution to the eukaryotic tree of life (Page 139-162)

Our work has contributed to a more accurate picture for the eukaryote evolution. But some key lineages, such as the apusomonads, collodictyonids, or radiolarians have not yet been placed within this new framework. Thank to new mass sequencing technologies, it has recently become cheaper to generate genomic data so it is to be expected that most of these orphan species will rapidly be under investigation (if not already in the pipeline of various laboratories).

Similarly, questions regarding phylogenetic uncertainties of higher taxonomic levels are likely to be soon addressed as more species are being massively sequenced. This switch to

‘within clades’ phylogenomics will for example concern the relationships among the mem-bers of the CCTH group we described in chapter 6, the relationships among Amoebozoa or within Rhizaria where many doubts remain (see our paper “Untangling the Phylogeny of

These are only some directions but obviously the possibilities are endless. Yes it is a promising time for studying evolution, in particular to reconstruct the tree of life.

Chapter 8: Literature cited

Abascal, F, Zardoya, R Posada, D. 2005. ProtTest: selection of best-fit models of protein evolution.

Bioinformatics. 21:2104-2105.

Abu, SM, Li, G Asiegbu, FO. 2004. Identification of Heterobasidion annosum (S-type) genes expressed during initial stages of conidiospore germination and under varying culture conditions. FEMS Micro-biol Lett. 233:205-213.

Adachi, J Hasegawa, M. 1996. MOLPHY version 2.3: Programs for molecular phylogenetics based on maximum likelihood. Comp Sci Monographs. 28:1-150.

Adl, SM et al. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol. 52:399-451.

Altschul, SF, Gish, W, Miller, W, Myers, EW Lipman, DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.

Andersson, JO Roger, AJ. 2002. A cyanobacterial gene in nonphotosynthetic protists--an early chloro-plast acquisition in eukaryotes? Curr Biol. 12:115-119.

Archibald, JM. 2009. The puzzle of plastid evolution. Curr Biol. 19:R81-88.

Archibald, JM Keeling, PJ. 2004. Actin and ubiquitin protein sequences support a

cerco-zoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J Eukaryot Microbiol. 51:113-118.

Archibald, JM, Longet, D, Pawlowski, J Keeling, PJ. 2003a. A novel polyubiquitin structure in Cer-cozoa and Foraminifera: evidence for a new eukaryotic supergroup. Mol Biol Evol. 20:62-66.

Archibald, JM, Rogers, MB, Toop, M, Ishida, K Keeling, PJ. 2003b. Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans.

Proc Natl Acad Sci USA. 100:7678-7683.

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

Armbrust, E et al. 2004. The genome of the diatom Thalassiosira pseudonana: ecology, evolution, and metabolism. Science. 306:79-86.

Atkins, MS, Teske, AP Anderson, OR. 2000. A survey of flagellate diversity at four deep-sea hydro-thermal vents in the Eastern Pacific Ocean using structural and molecular approaches. J Eukaryot Microbiol. 47:400-411.

Bachvaroff, TR, Sanchez Puerta, MV Delwiche, CF. 2005. Chlorophyll c-Containing Plastid Relation-ships Based on Analyses of a Multigene Data Set with All Four Chromalveolate Lineages. Mol Biol Evol. 22:1772-1782.

Baldauf, SL. 1999. A Search for the Origins of Animals and Fungi: Comparing and Combining Mo-lecular Data. Am Nat. 154:S178-S188.

Baldauf, SL. 2003. The deep roots of eukaryotes. Science. 300:1703-1706.

Baldauf, SL Doolittle, WF. 1997. Origin and evolution of the slime molds (Mycetozoa). Proc Natl Acad Sci USA. 94:12007-12012.

Baldauf, SL Palmer, JD. 1993. Animals and fungi are each other's closest relatives: congruent evi-dence from multiple proteins. Proc Natl Acad Sci USA. 90:11558-11562.

Baldauf, SL, Roger, AJ, Wenk-Siefert, I Doolittle, WF. 2000. A kingdom-level phylogeny of eukaryo-tes based on combined protein data. Science. 290:972-977.

Bapteste, E et al. 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc Natl Acad Sci USA. 99:1414-1419.

Bapteste, E Philippe, H. 2002. The potential value of indels as phylogenetic markers: position of trichomonads as a case study. Mol Biol Evol. 19:972-977.

Barker, S, Higgins, JA Elderfield, H. 2003. The future of the carbon cycle: review, calcification re-sponse, ballast and feedback on atmospheric CO2. Philos Trans R Soc Lond A. 361:1977-1998; discus-sion 1998-1979.

Bass, D, Moreira, D, López-García, P, Polet, S, Chao, EE, von der Heyden, S, Pawlowski, J Cava-lier-Smith, T. 2005. Polyubiquitin insertions and the phylogeny of Cercozoa and Rhizaria. Protist.


Beiko, RG Ragan, MA. 2008. Detecting lateral genetic transfer : a phylogenetic approach. Methods Mol Biol. 452:457-469.

Benton, MJ Donoghue, PC. 2007. Paleontological evidence to date the tree of life. Mol Biol Evol.


Berney, C Pawlowski, J. 2003. Revised small subunit rRNA analysis provides further evidence that Foraminifera are related to Cercozoa. J Mol Evol. 57 Suppl 1:S120-127.

Berney, C Pawlowski, J. 2006. A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record. Philos Trans R Soc Lond B Biol Sci. 273:1867-1872.

Bhattacharya, D, Archibald, JM, Weber, AP Reyes-Prieto, A. 2007. How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays. 29:1239-1246.

Bhattacharya, D, Helmchen, T Melkonian, M. 1995. Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent Rhizopod lineage containing the Euglyphida and the Chlorarachniophyta. J Eukaryot Microbiol. 42:65-69.

Bodyl, A. 2005. Do plastid-related characters support the chromalveolate hypothesis? J Phycol.


Bodyl, A, Stiller, JW P., M. 2009. Chromalveolate plastids: direct descent or multiple endosymbio-ses? Trends Ecol Evol. 24:119-121.

Bowler, C et al. 2008. The Phaeodactylum genome reveals the evolutionary history of diatom ge-nomes. Nature. 456:239-244.

Bown, P. 1998. Calcareous Nannofossil Biostratigraphy.

Bown, P, Dunkley Jones, T Young, J. 2007. Umbilicosphaera jordanii Bown, 2005 from the Paleogene of Tanzania: confirmation of generic assignment and a Paleocene origination for the Family Calcidis-caceae. J Nannoplankton Res. 29:25-30.

Breuker, R. 1997. Cytoskelettenkomponenten des plasmodialen Rhizopoden Reticulomyxa filosa. Dis-sertation. Ruhr-Universität, Bochum, Germany.

Brinkmann, H Philippe, H. 1999. Archaea sister group of Bacteria? Indications from tree reconstruc-tion artifacts in ancient phylogenies. Mol Biol Evol. 16:817-825.

Brinkmann, H, van der Giezen, M, Zhou, Y, Poncelin de Raucourt, G Philippe, H. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol. 54:743-757.

Bui, ET, Bradley, PJ Johnson, PJ. 1996. A common evolutionary origin for mitochondria and hydro-genosomes. Proc Natl Acad Sci USA. 93:9651-9656.

Burki, F, Berney, C Pawlowski, J. 2002. Phylogenetic position of Gromia oviformis Dujardin inferred from nuclear-encoded small subunit ribosomal DNA. Protist. 153:251-260.

Burki, F, Nikolaev, SI, Bolivar, I, Guiard, J Pawlowski, J. 2006. Analysis of expressed sequence tags from a naked foraminiferan Reticulomyxa filosa. Genome. 49:882-887.

Burki, F Pawlowski, J. 2006. Monophyly of Rhizaria and multigene phylogeny of unicellular bikonts.

Mol Biol Evol. 23:1922-1930.

Burki, F, Shalchian-Tabrizi, K, Minge, MA, Skjaeveland, A, Nikolaev, SI, Jakobsen, KS Pawlowski, J. 2007. Phylogenomics reshuffles the eukaryotic supergroups. PLoS ONE. 2:e790.

Burki, F, Shalchian-Tabrizi, K Pawlowski, J. 2008. Phylogenomics reveals a new 'megagroup' includ-ing most photosynthetic eukaryotes. Biol Lett. 4:366-369.

Castresana, J. 2000. Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylo-genetic Analysis. Mol Biol Evol. 17:540-552.

Cavalier-Smith, T. 1989. Molecular phylogeny. Archaebacteria and Archezoa. Nature. 339:l00-101.

Cavalier-Smith, T. 1993. Kingdom protozoa and its 18 phyla. Microbiol Rev. 57:953-994.

Cavalier-Smith, T. 1996-1997. Amoeboflagellates and mitochondrial cristae in eukaryotic evolution:

megasystematics of the new protozoan subkingdoms Eozoa and Neozoa. Arch Protistenkd. 147:237-258.

Cavalier-Smith, T. 1998a. A revised six-kingdom system of life. Biol Rev Camb Philos Soc. 73:203-266.

Cavalier-Smith, T. 1998b. A revised six-kingdom system of life. Biol Rev Camb Philos Soc. 73:203-266.

Cavalier-Smith, T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: eugle-noid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. J Eukaryot Micro-biol. 46:347-366.

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

Cavalier-Smith, T. 2003. Protist phylogeny and the high-level classification of Protozoa. Eur J Pro-tistol. 39:338-348.

Cavalier-Smith, T. 2009. Megaphylogeny, cell body plans, adaptive zones: causes and timing of eu-karyote basal radiations. J Eukaryot Microbiol. 56:26-33.

Cavalier-Smith, T. 2004. Chromalveolate diversity and cell megaevolution: interplay of membranes, genomes and cytoskeleton. In Organelles, Genomes and Eukaryotic Evolution, London: Taylor and Francis.

Cavalier-Smith, T Chao, E. 2003a. Phylogeny and classification of phylum Cercozoa (Protozoa).

Protist. 154:341-358.

Cavalier-Smith, T Chao, EE. 1995. The Opalozoan Apusomonas is Related to the Common Ancestor of Animals, Fungi, and Choanoflagellates. Philos Trans R Soc Lond B Biol Sci. 261:1-6.

Cavalier-Smith, T Chao, EE. 1996-1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny, and the origin of euglyphid amoebae. Arch Protistenkd. 147:227-236.

Cavalier-Smith, T Chao, EE. 1997. Sarcomonad ribosomal RNA sequences, rhizopod phylogeny and the origin of euglyphid amoebae. Arch Protistenkd. 147:227-236.

Cavalier-Smith, T Chao, EE. 2003b. Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss. J Mol Evol. 56:387-396.

Cavalier-Smith, T Chao, EE. 2003c. Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution. J Mol Evol. 56:540-563.

Cavalier-Smith, T Chao, EE. 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). J Mol Evol. 62:388-420.

Cavalier-Smith, T, Lewis, R, Chao, EE, Oates, B Bass, D. 2008. Morphology and phylogeny of Sainouron acronematica sp. n. and the ultrastructural unity of Cercozoa. Protist. 159:591-620.

Cavalier-Smith, T von der Heyden, S. 2007. Molecular phylogeny, scale evolution and taxonomy of centrohelid heliozoa. Mol Phylogenet Evol. 44:1186-1203.

Chu, KH, Qi, J, Yu, ZG Anh, V. 2004. Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. Mol Biol Evol. 21:200-206.

Clark, CG Roger, AJ. 1995. Direct evidence for secondary loss of mitochondria in Entamoeba histo-lytica. Proc Natl Acad Sci USA. 92:6518-6521.

Copeland, HF. 1938. The Kingdoms of Organisms. Q Rev Biol. 13:383-420.

Cox, CJ, Foster, PG, Hirt, RP, Harris, SR Embley, TM. 2008. The archaebacterial origin of eu-karyotes. Proc Natl Acad Sci U S A.

Culver, SJ. 1991. Early Cambrian Foraminifera from West Africa. Science. 254:689-691.

Cuvelier, ML, Ortiz, A, Kim, E, Moehlig, H, Richardson, DE, Heidelberg, JF, Archibald, JM Wor-den, AZ. 2008. Widespread distribution of a unique marine protistan lineage. Environ Microbiol.


de Koning, A, Tartar, A, Boucias, D Keeling, P. 2005. Expressed sequence tag (EST) survey of the highly adapted green algal parasite, Helicosporidium. Protist. 156:181-190.

de Vargas, C, Zaninetti, L, Hilbrecht, H Pawlowski, J. 1997. Phylogeny and rates of molecular evolu-tion of planktonic foraminifera: SSU rDNA sequences compared to the fossil record. J Mol Evol.


Delsuc, F, Brinkmann, H, Chourrout, D Philippe, H. 2006. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature. 439:965-968.

Delsuc, F, Brinkmann, H Philippe, H. 2005. Phylogenomics and the reconstruction of the tree of life.

Nat Rev Genet. 6:361-375.

Deschavanne, PJ, Giron, A, Vilain, J, Fagot, G Fertil, B. 1999. Genomic signature: characterization and classification of species assessed by chaos game representation of sequences. Mol Biol Evol.


Douzery, EJ, Snell, EA, Bapteste, E, Delsuc, F Philippe, H. 2004. The timing of eukaryotic evolution:

does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A. 101:15386-15391.

Driskell, AC, Ané, C, Burleigh, JG, McMahon, MM, O'meara, BC Sanderson, MJ. 2004. Prospects for building the tree of life from large sequence databases. Science. 306:1172-1174.

Edwards, SV, Fertil, B, Giron, A Deschavanne, PJ. 2002. A genomic schism in birds revealed by phylogenetic analysis of DNA strings. Syst Biol. 51:599-613.

Eisen, JA. 1998. Phylogenomics: improving functional predictions for uncharacterized genes by evolu-tionary analysis. Genome Res. 8:163-167.

Eisen, JA Fraser, CM. 2003. Phylogenomics: intersection of evolution and genomics. Science.


Embley, TM Hirt, RP. 1998. Early branching eukaryotes? Curr Opin Genet Dev. 8:624-629.

Embley, TM Martin, W. 2006. Eukaryotic evolution, changes and challenges. Nature. 440:623-630.

Ewing, B, Hillier, L, Wendl, MC Green, P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.

Fahrni, JF, Bolivar, I, Berney, C, Nassonova, E, Smirnov, A Pawlowski, J. 2003. Phylogeny of lo-bose amoebae based on actin and small-subunit ribosomal RNA genes. Mol Biol Evol. 20:1881-1886.

Falquet, L, Bordoli, L, Ioannidis, V, Pagni, M Jongeneel, CV. 2003. Swiss EMBnet node web server.

Nucleic Acids Res. 31:3782-3783.

Fast, NM, Kissinger, JC, Roos, DS Keeling, PJ. 2001. Nuclear-Encoded, Plastid-Targeted Genes Suggest a Single Common Origin for Apicomplexan and Dinoflagellate Plastids. Mol Biol Evol.


Fast, NM, Logsdon, JM Doolittle, WF. 1999. Phylogenetic analysis of the TATA box binding protein (TBP) gene from Nosema locustae: evidence for a microsporidia-fungi relationship and spliceosomal intron loss. Mol Biol Evol. 16:1415-1419.

Fast, NM, Xue, L, Bingham, S Keeling, P. 2002. Re-examining alveolate evolution using multiple protein molecular phylogenies. J Eukaryot Microbiol. 49:30-37.

Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively mislead-ing. Syst Zool. 27:401-410.

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 17:368-376.

Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution.


Felsenstein, J. 2004. PHYLIP (phylogeny inference package), version 3.6, University of Washington, Seattle.

Fensome, RA, MacRae, RA, Moldowan, JM, Taylor, FJR Williams, GL. 1996. The early Mesozoic radiation of dinoflagellates. Paleobiology. 22:329-338.

Fitz-Gibbon, ST House, CH. 1999. Whole genome-based phylogenetic analysis of free-living microor-ganisms. Nucleic Acids Res. 27:4218-4222.

Fitzpatrick, DA, Logue, ME, Stajich, JE Butler, G. 2006. A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol. 6:99.

Flakowski, J, Bolivar, I, Fahrni, J Pawlowski, J. 2005. Actin phylogeny of foraminifera. Pp. 93-102.

J Foramin Res.

Foster, PG. 2004. Modeling compositional heterogeneity. Syst Biol. 53:485-495.

Foyn, B. 1934. Lebenszyklus, cytology und sexualitat der Chlorophyceae Cladopora subriana Kützing.

Arch Protistenkd. 83:1-56.

Friedman, S, Debrunner-Vossbrinck, BA Woese, CR. 1987. Ribosomal RNA sequence suggests mi-crosporidia are extremely ancient eukaryotes. Nature. 326:411-414.

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

Gee, H. 2003. Evolution: ending incongruence. Nature. 425:782.

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

Gooday, AJ. 2002. Organic-walled allogromiids: Aspects of their occurrence, diversity and ecology in marine habitats. Pp. 384-399. J Foramin Res.

Gould, SB, Waller, RF McFadden, GI. 2008. Plastid evolution. Annu Rev Plant Biol. 59:491-517.

Graybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol. 47:9-17.

Green, P. 1996. PHRAP documentation.

Gu, X Zhang, H. 2004. Genome phylogenetic analysis based on extended gene contents. Mol Biol Evol.


Gubler, U Hoffman, BJ. 1983. A simple and very efficient method for generating cDNA libraries.

Gene. 25:263-269.

Guindon, S Gascuel, O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.

Habura, A, Pawlowski, J, Hanes, SD Bowser, SS. 2004. Unexpected foraminiferal diversity revealed by small-subunit rDNA analysis of Antarctic sediment. J Eukaryot Microbiol. 51:173-179.

Habura, A, Wegener, L, Travis, JL Bowser, SS. 2005. Structural and functional implications of an unusual foraminiferal beta-tubulin. Mol Biol Evol. 22:2000-2009.

Hackett, JD, Scheetz, TE, Yoon, HS, Soares, MB, Bonaldo, MF, Casavant, TL Bhattacharya, D.

2005. Insights into a dinoflagellate genome through expressed sequence tag analysis. BMC Genomics.


Hackett, JD, Yoon, HS, Li, S, Reyes-Prieto, A, Rümmele, SE 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.

Haeckel, EHPA. 1866. Generelle Morphologie der Organismen: Allgemeine Grundzüge der organischen Formen-wissenschaft, …. books.google.com.

Hagopian, JC, Reis, M, Kitajima, JP, Bhattacharya, D de Oliveira, MC. 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.

Hall, T. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser. 41:95-98.

Hampl, V, Horner, DS, Dyal, P, Kulda, J, Flegr, J, Foster, PG Embley, TM. 2005. Inference of the Phylogenetic Position of Oxymonads Based on Nine Genes: Support for Metamonada and Excavata.

Mol Biol Evol. 22:2508-2518.

Hampl, V, Hug, LA, Leigh, JW, Dacks, JB, Lang, BF, Simpson, AG Roger, AJ. 2009. Phylogenomic Analyses Support the Monophyly of Excavata and Resolve Relationships among Eukaryotic “Super-groups”. Proc Natl Acad Sci U S A. in press.

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

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

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

Hendy, MD Penny, D. 1989. A framework for the quantitative study of evolutionary trees. Syst Zool.


Hirt, RP, Logsdon, JM, Healy, B, Dorey, MW, Doolittle, WF Embley, TM. 1999. Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci USA. 96:580-585.

Ho, SY Jermiin, L. 2004. Tracing the decay of the historical signal in biological sequence data. Syst Biol. 53:623-637.

Holzmann, M, Habura, A, Giles, H, Bowser, SS Pawlowski, J. 2003. Freshwater foraminiferans re-vealed by analysis of environmental DNA samples. J Eukaryot Microbiol. 50:135-139.

Holzmann, M Pawlowski, J. 2002. Freshwater foraminiferans from Lake Geneva: Past and present. J Foramin Res. 32:344-350.

Hoppenrath, M Leander, BS. 2006. Ebriid phylogeny and the expansion of the Cercozoa. Protist.


House, CH Fitz-Gibbon, ST. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J Mol Evol. 54:539-547.

Howe, CJ, Barbrook, AC, Nisbet, RE, Lockhart, PJ Larkum, AW. 2008. The origin of plastids. Phi-los Trans R Soc Lond B Biol Sci. 363:2675-2685.

Huelsenbeck, JP. 1997. Is the Felsenstein zone a fly trap? Syst Biol. 46:69-74.

Huelsenbeck, JP, Ronquist, F, Nielsen, R Bollback, JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science. 294:2310-2314.

Hug, LA Roger, AJ. 2007. The impact of fossils and taxon sampling on ancient molecular dating analyses. Mol Biol Evol. 24:1889-1897.

Hülsmann, N. 1984. Biology of the genus Reticulomyxa (Rhizopoda). J Protozool. 31:55A.

Iida, K, Takishita, K, Ohshima, K Inagaki, Y. 2007. Assessing the monophyly of chlorophyll-c con-taining plastids by multi-gene phylogenies under the unlinked model conditions. Mol Phylogenet Evol.


Jeffroy, O, Brinkmann, H, Delsuc, F Philippe, H. 2006. Phylogenomics: the beginning of incongru-ence? Trends Genet. 22:225-231.

Jermiin, L, Ho, SY, Ababneh, F, Robinson, J Larkum, AW. 2004. The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. Syst Biol. 53:638-643.

Jobb, G, von Haeseler, A Strimmer, K. 2004. TREEFINDER: a powerful graphical analysis environ-ment for molecular phylogenetics. BMC Evol Biol. 4:18.

Jouannic, S, Argout, X, Lechauve, F, Fizames, C, Borgel, A, Morcillo, F, Aberlenc-Bertossi, F, Duval, Y Tregear, J. 2005. Analysis of expressed sequence tags from oil palm (Elaeis guineensis). FEBS Lett.


Katoh, K, Misawa, K, Kuma, K Miyata, T. 2002. MAFFT: a novel method for rapid multiple se-quence alignment based on fast Fourier transform. Nucleic Acids Res. 30:3059-3066.

Keeling, P Palmer, J. 2001. Lateral transfer at the gene and subgenic levels in the evolution of eu-karyotic enolase. Proc Natl Acad Sci USA. 98:10745-10750.

Keeling, PJ. 1998. A kingdom's progress: Archezoa and the origin of eukaryotes. Pp. 87-95. Bioes-says.

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

Keeling, PJ. 2004. Diversity and evolutionary history of plastids and their hosts. Pp. 1481-1493. Am J Bot.

Keeling, PJ, Burger, G, Durnford, DG, Lang, BF, Lee, RW, Pearlman, RE, Roger, AJ Gray, MW.

2005. The tree of eukaryotes. Trends Ecol Evol. 20:670-676.

Keeling, PJ Doolittle, WF. 1996. Alpha-tubulin from early-diverging eukaryotic lineages and the evo-lution of the tubulin family. Mol Biol Evol. 13:1297-1305.

Keeling, PJ Palmer, JD. 2008. Horizontal gene transfer in eukaryotic evolution. Nat Rev Genet.


Keon, J, Antoniw, J, Rudd, J, Skinner, W, Hargreaves, J Hammond-Kosack, K. 2005. Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici). Fungal Genet Biol. 42:376-389.

Khan, H, Parks, N, Kozera, C, Curtis, BA, Parsons, BJ, Bowman, S Archibald, JM. 2007. Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny. Mol Biol Evol. 24:1832-1842.

Kim, E Graham, LE. 2008. EEF2 analysis challenges the monophyly of Archaeplastida and Chromal-veolata. PLoS ONE. 3:e2621.

Kim, E, Simpson, AG Graham, LE. 2006. Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol Biol Evol. 23:2455-2466.

Klaveness, D, Shalchian-Tabrizi, K, Thomsen, HA, Eikrem, W Jakobsen, KS. 2005. Telonema antarc-ticum sp. nov., a common marine phagotrophic flagellate. Int J Syst Evol Microbiol. 55:2595-2604.

Knoll, AH. 1992. The Early Evolution of Eukaryotes: A Geological Perspective. Science.622-627.

Kolaczkowski, B Thornton, JW. 2004. Performance of maximum parsimony and likelihood phyloge-netics when evolution is heterogeneous. Nature. 431:980-984.

Kooistra, WH Medlin, LK. 1996. Evolution of the diatoms (Bacillariophyta). IV. A reconstruction of their age from small subunit rRNA coding regions and the fossil record. Mol Phylogenet Evol. 6:391-407.

Koonce, M Schliwa, M. 1985. Bidirectional organelle transport can occur in cell processes that contain single microtubules. J Cell Biol. 100:322-326.

Korbel, JO, Snel, B, Huynen, MA Bork, P. 2002. SHOT: a web server for the construction of genome

Koski, L, Gray, M, Lang, BF Burger, G. 2005. AutoFACT: An Automatic Functional Annotation and Classification Tool %U http://www.biomedcentral.com/1471-2105/6/151. BMC Bioinformatics.


Koski, LB Golding, GB. 2001. The closest BLAST hit is often not the nearest neighbor. J Mol Evol.


Kuhn, S, Lange, M Medlin, LK. 2000. Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist. 151:337-345.

Kuhn, S, Lange, M Medlin, LK. 2000. Phylogenetic position of Cryothecomonas inferred from nuclear-encoded small subunit ribosomal RNA. Protist. 151:337-345.

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