Abstract
Evolutionary trees were constructed, by distance methods, from an alignment of 225 complete large subunit (LSU) rRNA sequences, representing Eucarya, Archaea, Bacteria, plastids, and mitochondria. A comparison was made with trees based on sets of small subunit (SSU) rRNA sequences. Trees constructed on the set of 172 species and organelles for which the sequences of both molecules are known had a very similar topology, at least with respect to the divergence order of large taxa such as the eukaryotic kingdoms and the bacterial divisions. However, since there are more than ten times as many SSU as LSU rRNA sequences, it is possible to select many SSU rRNA sequence sets of equivalent size but different species composition. The topologies of these trees showed considerable differences according to the particular species set selected.
The effect of the dataset and of different distance correction methods on tree topology was tested for both LSU and SSU rRNA by repetitive random sampling of a single species from each large taxon. The impact of the species set on the topology of the resulting consensus trees is much lower using LSU than using SSU rRNA. This might imply that LSU rRNA is a better molecule for studying wide-range relationships. The mitochondria behave clearly as a monophyletic group, clustering with the Proteobacteria. Gram-positive bacteria appear as two distinct groups, which are found clustered together in very few cases. Archaea behave as if monophyletic in most cases, but with a low confidence.
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Abbreviations
- LSU rRNA:
-
large subunit ribosomal RNA
- SSU rRNA:
-
small subunit ribosomal RNA
- JC:
-
Jukes and Cantor
- JN:
-
Jin and Nei
References
Baroin-Tourancheau A, Delgado P, Perasso R, Adoutte A (1992) A broad molecular phylogeny of ciliates: identification of major evolutionary trends and radiations within the phylum. Proc Natl Acad Sci USA 89:9764–9768
Cedergren G, Gray MW, Abel Y, Sankoff D (1988) The evolutionary relationships among known life forms. J Mol Evol 28:98–112
Clark CG, Tague BW, Ware VC, Gerbi SA (1984) Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications. Nucleic Acids Res 12:6197–6220
De Rijk P, De Wachter R (1993) DOSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 9:735–740
De Rijk P, Van de Peer Y, Chapelle S, De Wachter R (1994) Database on the structure of large ribosomal subunit RNA. Nucleic Acids Res 22:3495–3501
Dickerson R (1980) Evolution and gene transfer in purple photosynthetic bacteria. Nature 283:210–212
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Field KG, Olsen GJ, Lane DJ, Giovannoni SJ, Ghiselin MT, Raff EC, Pace NR, Raft' RA (1988) Molecular phylogeny of the animal kingdom. Science 239:748–753
Golding GB (1983) Estimates of DNA and protein sequence divergence: an examination of some assumptions. Mol Biol Evol 1:125–142
Hassouna N, Michot B, Bachellerie J-P (1984) The complete nucleotide sequence of mouse 28S rRNA gene. Implications for the process of size increase of the large subunit rRNA in higher eukaryotes. Nucleic Acids Res 12:3563–3583
Hendriks L, Van Broeckhoven C, Vandenberghe A, Van de Peer Y, De Wachter R (1988) Primary and secondary structure of the 18S ribosomal RNA of the bird spider Eurypelma califomica and evolutionary relationships among eukaryotic phyla. Eur J Biochem 177:15–20
Iwabe N, Kuma K-I, Hasegawa M, Osawa S, Miyata T (1989) Evolutionary relationship of archaebacteria, eubacteria, and eukaryotes inferred from phylogenetic trees of duplicated genes. Proc Natl Acad Sci USA 86:9355–9359
Jin L, Nei M (1990) Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol Biol Evol 7:82–102
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Muntu HN (ed) Mammalian protein metabolism, vol 111. Academic press, New York
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
Lake JA (1988) Origin of the eukaryotic nucleus determined by rateinvariant analysis of rRNA sequences. Nature 331:184–186
Nei M (1991) Relative efficiencies of different tree-making methods for molecular data. In: Miyamoto MM, Cracraft JL (eds) Recent advances in phylogenetic studies of DNA sequences. Oxford University press, Oxford
Olsen GJ (1987) Earliest phylogenetic branchings: comparing rRNAbased evolutionary trees inferred with various techniques. Cold Spring Harbor Symp Quant Biol 52:825–837
Olsen GJ, Woese CR, Overbeek R (1994) The winds of (evolutionary) change: breathing new life into microbiology. J Bacteriol 176:1–6
Roise D, Maduke M (1994) Import of a mitochondrial presequence into P. denitrificans. Insight into the evolution of protein transport. FEBS Lett 337:9–13
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
Saitou N, Imanishi T (1989) Relative efficiencies of the Fitch-Margoliash, Maximum-Parsimony, Maximum-Likelihood, Minimum-Evolution, and Neighbour-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6: 514–525
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sogin ML (1989) Evolution of eukaryotic microorganisms and their small subunit ribosomal RNAs. Am Zool 29:487–499
Van de Peer Y, De Wachter R (1993) TREECON: a software package for the construction and drawing of evolutionary trees. Comput Applic Biosci 9:177–182
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
Van de Peer Y, Neefs J-M, De Rijk P, De Vos P, De Wachter R (1994a) About the order of divergence of the major bacterial taxa during evolution. System Appl Microbiol 17:32–38
Van de Peer Y, Van den Broeck I, De Rijk P, De Wachter R (1994b) Database on the structure of small ribosomal subunit RNA. Nucleic Acids Res 22:3488–3494
Van de Peer Y, Neefs J-M, 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
Van de Peer Y, Neefs J-M, De Wachter R (1990) Small ribosomal subunit RNA sequences, evolutionary relationships among different life forms, and mitochondrial origins. J Mol Evol 30:463–476
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 innerred from small ribosomal subunit RNA sequence analysis. System Appl Microbiol 16:436–444
Woese CR (1987) Bacterial evolution. Microbiol Rev 51:221–271
Yang D, Oyaizu Y, Oyaizu H, Olsen GJ, Woese CR (1985) Mitochondrial origins. Proc Natl Acad Sci USA 82:4443–4447
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Correspondence to: R. De Wachter
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De Rijk, P., Van de Peer, Y., Van den Broeck, I. et al. Evolution according to large tribosomal subunit RNA. J Mol Evol 41, 366–375 (1995). https://doi.org/10.1007/BF00186549
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DOI: https://doi.org/10.1007/BF00186549