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Evolutionary biology
Evolutionary biology
Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes
Published:03 June 2008https://doi.org/10.1098/rsbl.2008.0224
Abstract
Advances in molecular phylogeny of eukaryotes have suggested a tree composed of a small number of supergroups. Phylogenomics recently established the relationships between some of these large assemblages, yet the deepest nodes are still unresolved. Here, we investigate early evolution among the major eukaryotic supergroups using the broadest multigene dataset to date (65 species, 135 genes). Our analyses provide strong support for the clustering of plants, chromalveolates, rhizarians, haptophytes and cryptomonads, thus linking nearly all photosynthetic lineages and raising the question of a possible unique origin of plastids. At its deepest level, the tree of eukaryotes now receives strong support for two monophyletic megagroups comprising most of the eukaryotic diversity.
References
-
Andersson J.O& Roger A.J . 2002 A cyanobacterial gene in nonphotosynthetic protists—an early chloroplast acquisition in eukaryotes?. Curr. Biol. 12, 115–119.doi:10.1016/S0960-9822(01)00649-2. . Crossref, PubMed, ISI, Google Scholar -
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.doi:10.1093/molbev/msi023. . Crossref, PubMed, ISI, Google Scholar -
Bhattacharya D, Archibald J.M, Weber A.P& Reyes-Prieto A . 2007 How do endosymbionts become organelles? Understanding early events in plastid evolution. Bioessays. 29, 1239–1246.doi:10.1002/bies.20671. . Crossref, PubMed, ISI, Google Scholar -
Burki F, Shalchian-Tabrizi K, Minge M, Skjaeveland A, Nikolaev S.I, Jakobsen K.S& Pawlowski J . 2007 Phylogenomics reshuffles the eukaryotic supergroups. PLoS One. 2, e790 doi:10.1371/journal.pone.0000790. . Crossref, PubMed, ISI, Google Scholar -
Cavalier-Smith T . 2002 The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. Int. J. Syst. Evol. Microbiol. 52, 297–354. Crossref, PubMed, ISI, Google Scholar -
Hackett J, Yoon H, Li S, Reyes-Prieto A, Rümmele S& 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.doi:10.1093/molbev/msm089. . Crossref, PubMed, ISI, Google Scholar -
Jobb G, von Haeseler A& Strimmer K . 2004 Treefinder: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol. Biol. 4, 18 doi:10.1186/1471-2148-4-18. . Crossref, PubMed, ISI, Google Scholar -
Katoh K, Misawa K, Kuma K& Miyata T . 2002 MAFFT version 5.25: multiple sequence alignment program. Nucl. Acids Res. 30, 3059–3066.doi:10.1093/nar/gkf436. . Crossref, PubMed, ISI, Google Scholar -
Keeling P.J, Burger G, Durnford D.G, Lang B.F, Lee R.W, Pearlman R.E, Roger A.J& Gray M.W . 2005 The tree of eukaryotes. Trends Ecol. Evol. 20, 670–676.doi:10.1016/j.tree.2005.09.005. . Crossref, PubMed, ISI, Google Scholar -
Kim E, Simpson A.G& Graham L.E . 2006 Evolutionary relationships of apusomonads inferred from taxon-rich analyses of 6 nuclear encoded genes. Mol. Biol. Evol. 23, 2455–2466.doi:10.1093/molbev/msl120. . Crossref, PubMed, ISI, Google Scholar -
Lane C.E& Archibald J.M . 2008 The eukaryotic tree of life: endosymbiosis takes its TOL. Trends Ecol. 23, 268–275.doi:10.1016/j.tree.2008.02.004. . Crossref, PubMed, ISI, Google Scholar -
Lartillot N& Philippe H . 2004 A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol. Biol. Evol. 21, 1095–1109.doi:10.1093/molbev/msh112. . Crossref, PubMed, ISI, Google Scholar -
Lartillot N, Brinkmann H& Philippe H . 2007 Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evol. Biol. 7, Suppl. 1, S4 doi:10.1186/1471-2148-7-S1-S4. . Crossref, PubMed, ISI, Google Scholar -
McFadden G.I& van Dooren G.G . 2004 Evolution: red algal genome affirms a common origin of all plastids. Curr. Biol. 14, R514–R516.doi:10.1016/j.cub.2004.06.041. . Crossref, PubMed, ISI, Google Scholar -
Nosaki H . 2005 A new scenario of plastid evolution: plastid primary endosymbiosis before the divergence of the “Plantae”, emended. J. Plant Res. 111, 247–255.doi:10.1007/s10265-005-0219-1. . Crossref, ISI, Google Scholar -
Richards T.A& Cavalier-Smith T . 2005 Myosin domain evolution and the primary divergence of eukaryotes. Nature. 436, 1113–1118.doi:10.1038/nature03949. . Crossref, PubMed, ISI, Google Scholar -
Rodríguez-Ezpeleta N, Brinkmann H, Burger G, Roger A.J, Gray M.W, Philippe H& Lang B.F Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans. Curr. Biol. 17, 2007a 1420–1425.doi:10.1016/j.cub.2007.07.036. . Crossref, PubMed, ISI, Google Scholar -
Rodríguez-Ezpeleta N, Brinkmann H, Roure B, Lartillot N, Lang B.F& Philippe H Detecting and overcoming systematic errors in genome-scale phylogenies. Syst. Biol. 56, 2007b 389–399.doi:10.1080/10635150701397643. . Crossref, PubMed, ISI, Google Scholar -
Roure B, Rodriguez-Ezpeleta N& Philippe H . 2007 SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics. BMC Evol. Biol. 7, Suppl. 1, S2 doi:10.1186/1471-2148-7-S1-S2. . Crossref, PubMed, ISI, Google Scholar -
Sakaguchi M, Inagaki Y& Hashimoto T . 2007 Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes. Gene. 405, 47–54.doi:10.1016/j.gene.2007.09.003. . Crossref, PubMed, ISI, Google Scholar -
Shalchian-Tabrizi K, 2006 Telonemia, a new protist phylum with affinity to chromist lineages. Proc. R. Soc. B. 273, 1833–1842.doi:10.1098/rspb.2006.3515. . Link, ISI, Google Scholar -
Stamatakis A . 2006 RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22, 2688–2690.doi:10.1093/bioinformatics/btl446. . Crossref, PubMed, ISI, Google Scholar -
Stechmann A& Cavalier-Smith T Phylogenetic analysis of eukaryotes using heat-shock protein Hsp90. J. Mol. Evol. 57, 2003a 408–419.doi:10.1007/s00239-003-2490-x. . Crossref, PubMed, ISI, Google Scholar -
Stechmann A& Cavalier-Smith T The root of the eukaryote tree pinpointed. Curr. Biol. 13, 2003b R665–R666.doi:10.1016/S0960-9822(03)00602-x. . Crossref, PubMed, ISI, Google Scholar -
Yang Z . 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13, 555–556. PubMed, Google Scholar
