Limitations of metazoan 18s rRNA sequence data: Implications for reconstructing a phylogeny of the animal kingdom and inferring the reality of the cambrian explosion

Journal of Molecular Evolution

Volumn 47, Issue 4, 1998, Pages 394-405

  Abouheif, Ehab ^a   Zardoya, Rafael ^a,b   Meyer, Axel ^a,c  

^a STONY BROOK UNIVERSITY   (United States)

^b MUSEO NACIONAL DE CIENCIAS NATURALES   (Spain)

^c UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

18S rRNA; Among site rate variation; Cambrian explosion; Metazoan phylogeny; Molecular phylogeny

Indexed keywords

RNA 18S;

ARTICLE; FOSSIL; METAZOON; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; TAXONOMY; UNINDEXED SEQUENCE;

ANIMALS; EVOLUTION, MOLECULAR; FOSSILS; HUMANS; INVERTEBRATES; MAMMALS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PHYLOGENY; REGRESSION ANALYSIS; RNA, RIBOSOMAL, 18S; VERTEBRATES;

ANIMALIA; METAZOA; PROTOZOA;

EID: 0031691532     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006397     Document Type: Article

References (51)

1. Aguinaldo AMA, Turbeville JM, Linford LS, Rivera MC, Garey JR, Ralf RA, Lake JA (1997) Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387:489-493
2. Bowring SA, Grotzinger JP, Isachsen CE, Knoll AH, Pelechaty SM, Kolosov P (1993) Calibrating rates of early Cambrian evolution. Science 261:1293-1298
3. Brusca RC, Brusca GJ (1990) Invertebrates. Sinauer, Sunderland, MA
4. Conway Morris S (1993) The fossil record and the early evolution of the Metazoa. Nature 361:219-225
5. Conway Morris S (1994) Why molecular biology needs paleontology. Development 120 (Suppl):1-13
6. Desalle R, Freedman T, Prager EM, Wilson AC (1987) Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J Mol Evol 26:157-164
7. Doolittle RF, Feng DF, Tsang S, Cho G, Little E (1996) Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271:470-477
8. Erwin DH (1991) Metazoan phylogeny and the Cambrian radiation. Trends Ecol Evol 6:131-134
9. Felsenstein J (1981) A likelihood approach to character weighting and what it tells us about parsimony and compatibility. Biol J Linn Soc 16:183-196
10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
11. Felsenstein J (1989) Phylogenetic inference programs (PHYLIP). University of Washington, Seattle, and University Herbarium, University of California, Berkeley
12. Field KG, 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
13. Fortey RA, Briggs DEG, Wills MA (1997) The Cambrian evolutionary "explosion" recalibrated. BioEssays 19:429-434
14. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Caruthers MH, Neilson T, Turner DH (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc Natl Acad Sci USA 83:9373-9377
15. Friedrich M, Tautz D (1997) An episodic change of rDNA nucleotide substitution rate has occurred during the emergence of the insect order Diptera. Mol Biol Evol 14:644-653
16. Gutell RR (1994) Collection of small subunit (16S and 16S like) ribosomal RNA structures. Nucleic Acids Res 22:3502-3507
17. Gutell RR, Weiser B, Woese CR, Noller HF (1985) Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res Mol Biol 32:155-216
18. Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411-453
19. Kuhner MK, Felsenstein J (1994) A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol Biol Evol 11:459-468
20. Li CW, Chen J-Y, Hua T-E (1998) Precambrian sponges with cellular structures. Science 279:879-882
21. Maddison WP, Maddison DR (1992) MacClade. Sinauer, Sunderland, MA
22. Maley LE, Marshall CR (1998) The coming age of molecular systematics. Science 279:505-506
23. Marshall CR (1992) Substitution bias, weighted parsimony, and amniote phylogeny as inferred from 18S rRNA sequences. Mol Biol Evol 9:370-373
24. McClintock Turbeville J, Schulz JR, Raff RA (1994) Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology. Mol Biol Evol 11:648-655
25. Nielsen C (1995) Animal evolution. Oxford University Press, Oxford, UK
26. Nielsen R (1997) Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst Biol 46:346-353
27. Nikoh N, Iwabe N, Kuma K, Ohno M, Sugiyama T, Watanabe Y, Yasui K, Shi-cui Z, Hori K, Shimura Y, Miyata T (1997) An estimate of divergence time of Parazoa and Fumetazoa and that of Cephalochordala and Vertebrata by Aldolase and triose phosphate isomerase clocks. J Mol Evol 45:97-106
28. Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113-123
29. Orti G, Petry P, Porto JIR, Jégu M, Meyer A (1996) Patterns of nucleotide change in mitochondrial ribosomal RNA genes and phylogeny of piranhas. J Mol Evol 42:169-182
30. Philippe H, Chenuil A, Adoutte A (1994) Can the Cambrian explosion be inferred through molecular phylogeny? Development 120 (Suppl):15-25
31. Raff RA, Marshall CR, Turbeville JM (1994) Using DNA sequences to unravel the Cambrian radiation of the animal phyla. Annu Rev Ecol Syst 25:351-375
32. Runegar B (1982) A molecular clock date for the origin of the animal phyla. Lethaia 15:199-205
33. Sanderson MH, Donoghue M (1996) The relationship between homoplasy and confidence in a phylogenetic tree. In: Sanderson MJ, Hufford L (eds) Homoplasy: the recurrence of similarity in evolution. Academic Press, San Diego, pp 67-89
34. Signor PW (1990) The geologic history of diversity. Annu Rev Ecol Syst 21:509-539
35. Smith AB (1989) RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution. Cladistics 5:321-344
36. Sokal RR, Rohlf FJ (1995) Biometry, 3rd ed. Freedman, New York
37. Swofford DL (1993) PAUP: phylogenetic analysis using parsimony. Illinois Natural History Survey, Champaign
38. Swofford DL (1997) PAUP*: phylogenetic analysis using parsimony (* and other methods). Version d55. Sinauer Associates, Sunderland, MA
39. Tateno Y, Takezaki N, Nei M (1994) Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum parsimony methods when substitution rate varies with site. Mol Biol Evol 11:261-277
40. Valentine JW, Erwin DH, Jablonski D (1996) Developmental evolution of metazoan body plans: the fossil evidence. Dev Biol 173:373-381
41. Van de Peer Y, Neefs JM, De Rijk P, De Wachter R (1993) Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: calibration of the molecular clock. J Mol Evol 37:221-232
42. Van de Peer Y, De Wachter R (1997) Evolutionary relationships among the Eukaryotic crown taxa taking into account site-to-site rate variation in 18S rRNA. J Mol Evol 45:619-630
43. Vawter L, Brown WM (1993) Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597-608
44. Wada H, Satoh N (1994) Details of the evolutionary history from invertebrates to vertebrates, as deduced from sequences of 18S rDNA. Proc Natl Acad Sci USA 91:1801-1804
45. Wheeler WC, Honeycutt RL (1988) Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol 5:90-96
46. Wray GA, Levinton JS, Shapiro LH (1996) Molecular evidence for deep Precambrian divergences among metazoan phyla. Science 274:568-573
47. Xiao S, Zhang Y, Knoll AH (1998) Three dimensional preservation of algae and animal embryos in a Neoproterozoic phosphorite. Nature 391:553-558
48. Yang Z (1995) Evaluation of several methods for estimating phylogenetic trees when substitution rates differ over nucleotide sites. J Mol Evol 40:689-697
49. Yang Z (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol Evol 11:367-372
50. Yang Z, Kumar S (1996) Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol Biol Evol 13:650-659
51. Zardoya R, Meyer A (1996) Evolutionary relationships of the coelacanth, lungfishes, and tetrapods based on the 28S ribosomal RNA gene. Proc Natl Acad Sci USA 93:5449-5454