Evolutionary relationships among the eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA

Journal of Molecular Evolution

Volumn 45, Issue 6, 1997, Pages 619-630

  Van De Peer, Yves ^a   De Wachter, Rupert ^a  

^a UNIVERSITY OF ANTWERP   (Belgium)

Author keywords

18S rRNA; Eukaryotic crown taxa; Evolutionary distance; Substitution rate calibration

Indexed keywords

RIBOSOME RNA;

ARTICLE; EUKARYOTE; GENETIC DISTANCE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; RNA SEQUENCE; TAXONOMY;

ALGAE, GREEN; ALGAE, RED; ANIMALS; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FUNGI; MULTIGENE FAMILY; PHYLOGENY; PLANTS; PROTOZOA; RNA, RIBOSOMAL, 18S; VARIATION (GENETICS);

ALGAE; ALVEOLATA; ANIMALIA; APICOMPLEXA; BICOSOECIDA; CHOANOFLAGELLIDA; CILIOPHORA; DINOPHYCEAE; EMBRYOPHYTA; EUKARYOTA; FUNGI; HYPHOCHYTRIOMYCETES; LABYRINTHULIDA; OOMYCETES; RHODOPHYTA; STRAMENOPILES;

EID: 0031436828     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006266     Document Type: Article

References (87)

1. Adoutte A, Philippe H (1993) The major lines of Metazoan evolution: summary of traditional evidence and lessons from ribosomal RNA sequence analysis. In: Pichon Y (ed) Comparative molecular neurobiology. Birkhäuser Verlag, Basel, pp 1-30
2. Baldauf SL, Palmer JD (1993) Animals and fungi are each other's closest relatives: congruent evidence from multiple proteins. Proc Natl Acad Sci USA 90:11558-11562
3. Bhattacharya D, Medlin L (1995) The phylogeny of plastids: a review based on comparisons of small-subunit ribosomal RNA coding regions. J Phycol 31:489-498
4. Bhattacharya D, Helmchen T, Bibeau C, Melkonian M (1995a) Comparisons of nuclear-encoded small subunit ribosomal RNAs reveal the evolutionary position of the Glaucocystophyta. Mol Biol Evol 12:415-420
5. Bhattacharya D, Helmchen T, Melkonian M (1995b) Molecular evolutionary analyses of nuclear-encoded small subunit ribosomal RNA identify an independent Rhizopod lineage containing the Euglyphina and the Chlorarachniophyta. J Euk Microbiol 42:65-69
6. Boore JL, Brown WM (1994) Mitochondrial genomes and the phylogeny of mollusks. Nautilus 108(Suppl 2):61-78
7. Boore JL, Collins TM, Stanton D, Daehler L, Brown WM (1995) Deducing the pattern of arthropod phylogeny from mitochondrial DNA rearrangements. Nature 376:163-165
8. Cahill DM, Cope M, Hardham AR (1996) Thrust reversal by tubular mastgonemes: immunological evidence for a role of mastigonemes in forward motion of zoospores of Phytophthora cinnamoni. Protoplasma 194:18-28
9. Cavalier-Smith T (1992) The origin, losses and gains of chloroplasts. In: Lewin RA (ed) Origins of plastids. Chapman & Hall, New York, pp 291-348
10. Cavalier-Smith T (1993) Kingdom Protozoa and its 18 phyla. Microbiol Rev 57:953-994
11. Cavalier-Smith T (1995) Membrane heredity, symbiogenesis, and the multiple origins of algae. In: Arai R, Kato M, Doi Y (eds) Biodiversity and evolution. The National Science Museum Foundation, Tokyo, pp 75-114
12. Cavalier-Smith T, Chao EE (1996) Molecular phylogeny of the free-living Archezoan Trepomonas agilis and the nature of the first eukaryote. J Mol Evol 43:551-562
13. Cavalier-Smith T, Allsop MTEP, Chao EE (1994) Chimeric conundra: are nucleomorphs and chromists monophyletic or polyphyletic? Proc Natl Acad Sci USA 91:11368-11372
14. Christen R, Ratto A, Baroin A, Perasso R, Grell KG, Adoutte A (1991) An analysis of the origin of metazoans, using comparisons of partial sequences of the 28S RNA, reveals an early emergence of triploblasts. EMBO J 10:499-503
15. Cummings M, Otto S, Wakeley J (1995) Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol 12:814-822
16. De Rijk P, Van de Peer Y, Van den Broeck I, De Wachter R (1995) Evolution according to large ribosomal subunit RNA. J Mol Evol 41:366-375
17. De Rijk P, Van de Peer Y, De Wachter R (1997) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 25:117-123
18. Doolittle WF, Brown JR (1994) Tempo, mode, the progenote, and the universal root. Proc Natl Acad Sci USA 91:6721-6728
19. Douglas SE, Murphy CA, Spencer DF, Gray MW (1991) Cryptomonad algae are evolutionary chimaeras of two phylogenetically distinct unicellular eukaryotes. Nature 350:148-151
20. Erwin DH (1991) Metazoan phylogeny and the Cambrian radiation. Trends Ecol Evol 6:131-134
21. Eschbach S, Wolters J, Sitte P (1991) Primary and secondary structure of the nuclear small subunit ribosomal RNA of the cryptomonad Pyrenomonas salina as inferred from the gene sequence: evolutionary implications. J Mol Evol 32:247-252
22. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
23. Field GG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raff RA (1988) Molecular phylogeny of the animal kingdom. Science 239:748-753
24. Gajadhar AA, Marquardt WC, Hall R, Gunderson J, Ariztia-Carmona EV, Sogin ML (1991) Ribosomal RNA sequences of Sarcocystis muris, Theileria annulata, and Crythecodinium cohnii reveal evolutionary relationships among apicomplexans, dinoflagellates, and ciliates. Mol Biochem Parasitol 45:147-154
25. Goggin CL, Barker SC (1993) Phylogenetic position of the genus Perkinsus (Protista, Apicomplexa) based on small subunit ribosomal RNA. Mol Biochem Parasitol 60:65-70
26. Gouy M, Li W-H (1989) Molecular phylogeny of the kingdoms animalia, plantae, and fungi. Mol Biol Evol 6:109-122
27. Haase G, Sonntag L, Van de Peer Y, Uithof JMJ, Podbielski A, Melzer-Krick B (1995) Phylogenetic analysis of ten black yeast species using nuclear small subunit rRNA gene sequences. Antonie Van Leeuwenhoek 68:19-33
28. Hendriks L, De Baere R, Van de Peer Y, Neefs JM, Goris A, De Wachter R (1991) The evolutionary position of the rhodophyte Porphyra umbilicalis and the basidiomycete Leucosporidium scottii among other eukaryotes as deduced from complete sequences of small ribosomal subunit RNA. J Mol Evol 32:167-177
29. Hillis DM (1997) Inferring complex phylogenies. Nature 383:131
30. Jin L, Nei M (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 7:82-102
31. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HH (ed) Mammalian protein metabolism. Academic Press, New York, pp 21-132
32. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
33. Knoll AH (1992) The early evolution of eukaryotes: a geological perspective. Science 256:622-627
34. Kumar S, Rzhetsky A (1996) Evolutionary relationships of eukaryotic kingdoms. J Mol Evol 42:183-193
35. Lecointre G, Philippe H, Lê HLV, Le Guyader H (1993) Species sampling has a major impact on phylogenetic inference. Mol Phyl Evol 2:205-224
36. Leipe DD, Wainright PO, Gunderson JH, Porter D, Patterson DJ, Valois F, Himmerich S, Sogin ML (1994) The stramenopiles from a molecular perspective: 16S-like rRNA sequences from Labyrinthuloides minuta and Cafeteria roenbergensis. Phycologia 33:369-377
37. Lockhart PJ, Steel MA, Hendy MD, Penny D (1994) Recovering evolutionary trees under a more realistic model of sequence evolution. Mol Biol Evol 11:605-612
38. Mackey LY, Winnepenninckx B, De Wachter R, Backeljau T, Emschermann P, Garey JR (1996) 18S rRNA suggests that entoprocta are protostomes, unrelated to Ectoprocta. J Mol Evol 42:552-559
39. Maier UG, Hofmann CJB, Eschbach S, Wolters J, Igloi GL (1991) Demonstration of nucleomorph-encoded eukaryotic small ribosomal RNA in cryptomonads. Mol Gen Genet 230:155-160
40. McFadden GI, Gilson PR, Douglas SE (1994a) The photosynthetic endosymbiont in cryptomonad cells produces both chloroplast and cytoplasmic-type ribosomes. J Cell Sci 107:649-657
41. McFadden GI, Gilson PR, Hill DRA (1994b) Goniomonas: rRNA sequences indicate that this phagotrophic flagellate is a close relative of the host component of cryptomonads. Eur J Phycol 29:29-32
42. McFadden GI, Gilson PR, Hofmann CJB, Adcock GJ, Maier UW (1994c) Evidence that an amoeba acquired a chloroplast by retaining part of an engulfed eukaryotic alga. Proc Natl Acad Sci USA 91:3690-3694
43. McFadden GI, Gilson PR, Waller RF (1995) Molecular phylogeny of chlorarachniophytes based on plastid RNA and rbcL sequences. Arch Protistenkd 145:231-239
44. Milinkovitch MC, LeDuc RG, Adachi J, Farnir F, Georges M, Hasegawa M (1996) Effects of character weighting and species sampling on phylogeny reconstruction: a case study based on DNA sequence data in Cetaceans. Genetics 144:1817-1833
45. Nickrent DL, Soltis DE (1995) A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann Miss Bot Gard 82:208-234
46. Olsen GJ (1987) Earliest phylogenetic branchings: comparing rRNA-based evolutionary trees inferred with various techniques. Cold Spring Harb Symp Quant Biol LII:825-837
47. Otto SP, Cummings MP, Wakeley J (1996) Inferring phylogenies from sequence data: the effect of sampling. In: Harvey PH, Brown AJL, Maynard Smith J, Nee S (eds) New uses for new phylogenies. Oxford University Press, Oxford, pp 103-115
48. Palmer JD, Delwiche CF (1996) Second-hand chloroplasts and the case of the disappearing nucleus. Proc Natl Acad Sci USA 93:7432-7435
49. Patterson DJ (1989) Stramenopiles: chromophytes from a protistan perspective. In: Green JC, Leadbeater BSC, Diver WL (eds) The chromophyte algae: problems and perspectives. Clarendon, Oxford, pp 357-379
50. Patterson DJ, Sogin ML (1993) Eukaryote origins and protistan diversity. In: Hartman H, Matsuno K (eds) The origin and evolution of prokaryotic and eukaryotic cells. World Scientific, New Jersey, pp 13-46
51. Pawlowski J, Montoya-Burgos J-I, Fahrni JF, Wiiest J, Zaninetti L (1996) Origin of the Mesozoa inferred from 18S rRNA gene sequences. Mol Biol Evol 13:1128-1132
52. Philippe H, Chenuil A, Adoutte A (1994) Can the Cambrian explosion be inferred through molecular phylogeny? Development (Suppl): 15-25
53. Preisig HR, Anderson OR, Corliss JO, Moestrup O, Powell MJ, Roberson RW, Wetherbee R (1994) Terminology and nomenclature of protist cell surface structures. Protoplasma 181:1-28
54. Ragan MA, Gutell RR (1995) Are red algae plants? Bot J Linnean Soc 118:81-105
55. Reith M (1995) Molecular biology of rhodophyte and chromophyte plastids. Annu Rev Plant Physiol Plant Mol Biol 46:549-575
56. Rzhetsky A, Nei M (1994) Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites. J Mol Evol 38:295-299
57. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
58. Saunders GW, Potter D, Paskind MP, Andersen RA (1995) Cladistic analyses of combined traditional and molecular data sets reveal an algal lineage. Proc Natl Acad Sci USA 92:244-248
59. Sogin ML (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Am Zool 29:487-499
60. Stiller JW, Hall BD (1997) The origin of red algae: implications for plastid evolution. Proc Natl Acad Sci USA 94:4520-4525
61. Sullivan J, Holsinger KE, Simon C (1996) The effect of topology on estimation of among-site rate variation. J Mol Evol 42:308-312
62. Swofford DL, Olsen GJ, Waddell PJ, Hillis DM (1996) Phylogenetic inference. In: Hillis DM, Moritz C, Mable BK (eds) Molecular systematics. Sinauer, Sunderland, USA, pp 407-514
63. Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269-285
64. Tamura K, Nei M (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512-526
65. Tourasse NJ, Gouy M (1997) Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony. Mol Biol Evol 14:287-298
66. Turbeville JM, Field KG, Raff RA (1992) Phylogenetic position of the Nemertini, inferred from 18S rRNA sequences: molecular data as a test of morphological character homology. Mol Biol Evol 9:235-249
67. Van de Peer Y, De Wachter R (1994) TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569-570
68. Van de Peer Y, De Wachter R (1995) Investigation of fungal phylogeny on the basis of small ribosomal subunit RNA. In: Akkermans ADL, van Elsas JD, de Bruijn FJ (eds) Molecular microbial ecology manual. 3.3.4. Kluwer Academic Press, Dordrecht, pp 1-12
69. Van de Peer Y, De Wachter R (1997a) Construction of evolutionary distance trees with TREECON for Windows: accounting for variation in nucleotide substitution rate among sites. Comput Appl Biosci 13:227-230
70. Van de Peer Y, De Wachter R (1997b) Origin of the Mesozoa revisited. Mol Phyl Evol (submitted)
71. Van de Peer Y, Neefs J-M, De Rijk P, De Wachter R (1993a) Evolution of eukaryotes as deduced from small ribosomal subunit RNA sequences. Biochem Syst Ecol 21:43-55
72. Van de Peer Y, Neefs J-M, De Rijk P, De Wachter R (1993b) Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol 37:221-232
73. Van de Peer Y, Chapelle S, De Wachter R (1996a) A quantitative map of nucleotide substitution rates in bacterial ribosomal subunit RNA. Nuclei Acids Res 24:3381-3391
74. Van de Peer Y, Rensing S, Maier U-G, De Wachter R (1996b) Substitution rate calibration of small ribosomal subunit RNA identifies chlorarachniophyte endosymbionts as remnants of green algae. Proc Natl Acad Sci USA 93:7732-7736
75. Van de Peer Y, Van der Auwera G, De Wachter R (1996c) The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J Mol Evol 42:201-210
76. Van de Peer Y, Jansen J, De Rijk P, De Wachter R (1997) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res 25:111-116
77. Van der Auwera G, De Baere R, Van de Peer Y, De Rijk P, Van den Broeck I, De Wachter R (1995) The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. Mol Biol Evol 12:671-678
78. Vivier E, Desportes I (1989) Phylum Apicomplexa. In: Margulis L, Corliss JO, Melkonian M, Chapman DJ (eds) Handbook of Protoctista. Jones and Bartlett, Boston, pp 549-573
79. Wainright PO, Hinkle G, Sogin ML, Stickel SK (1993) Monophyletic origin of the Metazoa: an evolutionary link with fungi. Science 260:340-342
80. Wakeley (1993) Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA. J Mol Evol 37:613-623
81. Wilmotte A, Van de Peer Y, Goris A, Chapelle S, De Baere R, Nelissen B, Neefs J-M, Hennebert GL, De Wachter R (1993) Evolutionary relationships among higher fungi inferred from small ribosomal subunit RNA sequence analysis. System Appl Microbiol 16:436-444
82. Winnepenninckx B, Backeljau T, De Wachter R (1996) Investigation of Molluscan phylogeny on the basis of 18S rRNA sequences. Mol Biol Evol 13:1306-1317
83. Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221-271
84. Wolters J (1991) The troublesome parasites - molecular and morpho-logical evidence that Apicomplexa belong to the dinoflagellateciliate clade. Biosystems 25:75-83
85. Wray GA, Levinton JS, Shapiro LH (1996) Molecular evidence for deep precambrian divergences among metazoan phyla. Science 274:568-573
86. Yang Z (1996) Among-site rate variation and its impact on phylogenetic analyses. TREE 11:367-372
87. Zharkikh A (1994) Estimation of evolutionary distances between nucleotide sequences. J Mol Evol 39:315-329