Molecular Biology and Evolution 17:540-552 (2000)
© 2000 Society for Molecular Biology and Evolution
Regular Articles |
Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis
European Molecular Biology Laboratory, Heidelberg, Germany
Abstract
The use of some multiple-sequence alignments in phylogenetic analysis, particularly those that are not very well conserved, requires the elimination of poorly aligned positions and divergent regions, since they may not be homologous or may have been saturated by multiple substitutions. A computerized method that eliminates such positions and at the same time tries to minimize the loss of informative sites is presented here. The method is based on the selection of blocks of positions that fulfill a simple set of requirements with respect to the number of contiguous conserved positions, lack of gaps, and high conservation of flanking positions, making the final alignment more suitable for phylogenetic analysis. To illustrate the efficiency of this method, alignments of 10 mitochondrial proteins from several completely sequenced mitochondrial genomes belonging to diverse eukaryotes were used as examples. The percentages of removed positions were higher in the most divergent alignments. After removing divergent segments, the amino acid composition of the different sequences was more uniform, and pairwise distances became much smaller. Phylogenetic trees show that topologies can be different after removing conserved blocks, particularly when there are several poorly resolved nodes. Strong support was found for the grouping of animals and fungi but not for the position of more basal eukaryotes. The use of a computerized method such as the one presented here reduces to a certain extent the necessity of manually editing multiple alignments, makes the automation of phylogenetic analysis of large data sets feasible, and facilitates the reproduction of the final alignment by other researchers.
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S. A. Ramm, P. L. Oliver, C. P. Ponting, P. Stockley, and R. D. Emes Sexual Selection and the Adaptive Evolution of Mammalian Ejaculate Proteins Mol. Biol. Evol., January 1, 2008; 25(1): 207 - 219. [Abstract] [Full Text] [PDF]
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B. Cherif-Zahar, A. Durand, I. Schmidt, N. Hamdaoui, I. Matic, M. Merrick, and G. Matassi Evolution and Functional Characterization of the RH50 Gene from the Ammonia-Oxidizing Bacterium Nitrosomonas europaea J. Bacteriol., December 15, 2007; 189(24): 9090 - 9100. [Abstract] [Full Text] [PDF]
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J. M. Young and D.-C. Park Probable synonymy of the nitrogen-fixing genus Azotobacter and the genus Pseudomonas Int J Syst Evol Microbiol, December 1, 2007; 57(12): 2894 - 2901. [Abstract] [Full Text] [PDF]
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C. Meisinger-Henschel, M. Schmidt, S. Lukassen, B. Linke, L. Krause, S. Konietzny, A. Goesmann, P. Howley, P. Chaplin, M. Suter, et al. Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara J. Gen. Virol., December 1, 2007; 88(12): 3249 - 3259. [Abstract] [Full Text] [PDF]
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B. Hausdorf, M. Helmkampf, A. Meyer, A. Witek, H. Herlyn, I. Bruchhaus, T. Hankeln, T. H. Struck, and B. Lieb Spiralian Phylogenomics Supports the Resurrection of Bryozoa Comprising Ectoprocta and Entoprocta Mol. Biol. Evol., December 1, 2007; 24(12): 2723 - 2729. [Abstract] [Full Text] [PDF]
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A. Klevan, N. J. Tourasse, F. B. Stabell, A.-B. Kolsto, and O. A. Okstad Exploring the evolution of the Bacillus cereus group repeat element bcr1 by comparative genome analysis of closely related strains Microbiology, November 1, 2007; 153(11): 3894 - 3908. [Abstract] [Full Text] [PDF]
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R. Liu and H. Ochman Origins of Flagellar Gene Operons and Secondary Flagellar Systems J. Bacteriol., October 1, 2007; 189(19): 7098 - 7104. [Abstract] [Full Text] [PDF]
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