Molecular Biology and Evolution, Vol 14, 428-441, Copyright © 1997 by Society for Molecular Biology and Evolution
DA Morrison and JT Ellis
The reconstruction of phylogenetic history is predicated on being able to
accurately establish hypotheses of character homology, which involves
sequence alignment for studies based on molecular sequence data. In an
empirical study investigating nucleotide sequence alignment, we inferred
phylogenetic trees for 43 species of the Apicomplexa and 3 of Dinozoa based
on complete small-subunit rDNA sequences, using six different
multiple-alignment procedures: manual alignment based on the secondary
structure of the 18S rRNA molecule, and automated similarity-based
alignment algorithms using the PileUp, ClustalW, TreeAlign, MALIGN, and SAM
computer programs. Trees were constructed using neighboring-joining,
weighted-parsimony, and maximum- likelihood methods. All of the multiple
sequence alignment procedures yielded the same basic structure for the
estimate of the phylogenetic relationship among the taxa, which presumably
represents the underlying phylogenetic signal. However, the placement of
many of the taxa was sensitive to the alignment procedure used; and the
different alignments produced trees that were on average more dissimilar
from each other than did the different tree-building methods used. The
multiple alignments from the different procedures varied greatly in length,
but aligned sequence length was not a good predictor of the similarity of
the resulting phylogenetic trees. We also systematically varied the gap
weights (the relative cost of inserting a new gap into a sequence or
extending an already-existing gap) for the ClustalW program, and this
produced alignments that were at least as different from each other as
those produced by the different alignment algorithms. Furthermore, there
was no combination of gap weights that produced the same tree as that from
the structure alignment, in spite of the fact that many of the alignments
were similar in length to the structure alignment. We also investigated the
phylogenetic information content of the helical and nonhelical regions of
the rDNA, and conclude that the helical regions are the most informative.
We therefore conclude that many of the literature disagreements concerning
the phylogeny of the Apicomplexa are probably based on differences in
sequence alignment strategies rather than differences in data or
tree-building methods.
ORIGINAL ARTICLE
Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa
Molecular Parasitology Unit, University of Technology Sydney, NSW, Australia. davidm@bio.uts.edu.au
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  K. M. Wong, M. A. Suchard, and J. P. Huelsenbeck Alignment Uncertainty and Genomic Analysis Science, January 25, 2008; 319(5862): 473 - 476. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Landan and D. Graur Heads or Tails: A Simple Reliability Check for Multiple Sequence Alignments Mol. Biol. Evol., June 1, 2007; 24(6): 1380 - 1383. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kumar and A. Filipski Multiple sequence alignment: In pursuit of homologous DNA positions Genome Res., February 1, 2007; 17(2): 127 - 135. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Lassmann and E. L. L. Sonnhammer Automatic assessment of alignment quality Nucleic Acids Res., December 16, 2005; 33(22): 7120 - 7128. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Hollich, L. Milchert, L. Arvestad, and E. L. L. Sonnhammer Assessment of Protein Distance Measures and Tree-Building Methods for Phylogenetic Tree Reconstruction Mol. Biol. Evol., November 1, 2005; 22(11): 2257 - 2264. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. J. Gillespie, J. B. Munro, J. M. Heraty, M. J. Yoder, A. K. Owen, and A. E. Carmichael A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 for Chalcidoid Wasps (Hymenoptera: Chalcidoidea) Mol. Biol. Evol., July 1, 2005; 22(7): 1593 - 1608. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. M. Gottlieb, G. C. Giberti, and L. Poggio Molecular analyses of the genus Ilex (Aquifoliaceae) in southern South America, evidence from AFLP and ITS sequence data Am. J. Botany, February 1, 2005; 92(2): 352 - 369. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Madern, X. Cai, M. S. Abrahamsen, and G. Zhu Evolution of Cryptosporidium parvum Lactate Dehydrogenase from Malate Dehydrogenase by a Very Recent Event of Gene Duplication Mol. Biol. Evol., March 1, 2004; 21(3): 489 - 497. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. N. Martin and P. W. Tooley Phylogenetic relationships among Phytophthora species inferred from sequence analysis of mitochondrially encoded cytochrome oxidase I and II genes Mycologia, March 1, 2003; 95(2): 269 - 284. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. A. Kelchner Group II introns as phylogenetic tools: structure, function, and evolutionary constraints Am. J. Botany, October 1, 2002; 89(10): 1651 - 1669. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H.-Y. Wang and S.-C. Lee Secondary Structure of Mitochondrial 12S rRNA Among Fish and Its Phylogenetic Applications Mol. Biol. Evol., February 1, 2002; 19(2): 138 - 148. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Palacios, I. Casas, A. Tenorio, and C. Freire Molecular Identification of Enterovirus by Analyzing a Partial VP1 Genomic Region with Different Methods J. Clin. Microbiol., January 1, 2002; 40(1): 182 - 192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Sanchis, J. M. Michelena, A. Latorre, D. L. J. Quicke, U. Gärdenfors, and R. Belshaw The Phylogenetic Analysis of Variable-Length Sequence Data: Elongation Factor-1{{alpha}} Introns in European Populations of the Parasitoid Wasp Genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) Mol. Biol. Evol., June 1, 2001; 18(6): 1117 - 1131. [Abstract] [Full Text]
|
|
|
|
|
|
N. B. Mugridge, D. A. Morrison, T. Jakel, A. R. Heckeroth, A. M. Tenter, and A. M. Johnson Effects of Sequence Alignment and Structural Domains of Ribosomal DNA on Phylogeny Reconstruction for the Protozoan Family Sarcocystidae Mol. Biol. Evol., December 1, 2000; 17(12): 1842 - 1853. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. D. M. Page Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching Nucleic Acids Res., October 15, 2000; 28(20): 3839 - 3845. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Billoud, M.-A. Guerrucci, M. Masselot, and J. S. Deutsch Cirripede Phylogeny Using a Novel Approach: Molecular Morphometrics Mol. Biol. Evol., October 1, 2000; 17(10): 1435 - 1445. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. E. Hickson, C. Simon, and S. W. Perrey The Performance of Several Multiple-Sequence Alignment Programs in Relation to Secondary-Structure Features for an rRNA Sequence Mol. Biol. Evol., April 1, 2000; 17(4): 530 - 539. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Castresana Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis Mol. Biol. Evol., April 1, 2000; 17(4): 540 - 552. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Zhu, M. J. Marchewka, and J. S. Keithly Cryptosporidium parvum appears to lack a plastid genome Microbiology, February 1, 2000; 146(2): 315 - 321. [Abstract] [Full Text]
|
|