| Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus). | |
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MedLine Citation:
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PMID: 12519910 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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To test whether gaps resulting from sequence alignment contain phylogenetic signal concordant with those of base substitutions, we analyzed the occurrence of indel mutations upon a well-resolved, substitution-based tree for three nuclear genes in bumble bees (Bombus, Apidae: Bombini). The regions analyzed were exon and intron sequences of long-wavelength rhodopsin (LW Rh), arginine kinase (ArgK), and elongation factor-1alpha (EF-1alpha) F2 copy genes. LW Rh intron had only a few uninformative gaps, ArgK intron had relatively long gaps that were easily aligned, and EF-1alpha intron had many short gaps, resulting in multiple optimal alignments. The unambiguously aligned gaps within ArgK intron sequences showed no homoplasy upon the substitution-based tree, and phylogenetic signals within ambiguously aligned regions of EF-1alpha intron were highly congruent with those of base substitutions. We further analyzed the contribution of gap characters to phylogenetic reconstruction by incorporating them in parsimony analysis. Inclusion of gap characters consistently improved support for nodes recovered by substitutions, and inclusion of ambiguously aligned regions of EF-1alpha intron resolved several additional nodes, most of which were apical on the phylogeny. We conclude that gaps are an exceptionally reliable source of phylogenetic information that can be used to corroborate and refine phylogenies hypothesized by base substitutions, at least at lower taxonomic levels. At present, full use of gaps in phylogenetic reconstruction is best achieved in parsimony analysis, pending development of well-justified and generally applicable methods for incorporating indels in explicitly model-based methods. |
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Authors:
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Atsushi Kawakita; Teiji Sota; John S Ascher; Masao Ito; Hiroyuki Tanaka; Makoto Kato |
Publication Detail:
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Type: Journal Article; Research Support, Non-U.S. Gov't |
Journal Detail:
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Title: Molecular biology and evolution Volume: 20 ISSN: 0737-4038 ISO Abbreviation: Mol. Biol. Evol. Publication Date: 2003 Jan |
Date Detail:
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Created Date: 2003-01-09 Completed Date: 2004-01-09 Revised Date: 2006-11-15 |
Medline Journal Info:
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Nlm Unique ID: 8501455 Medline TA: Mol Biol Evol Country: United States |
Other Details:
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Languages: eng Pagination: 87-92 Citation Subset: IM |
Affiliation:
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Graduate School of Human and Environmental Studies, Graduate School of Science, Kyoto University, Kyoto, Japan. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Animals Base Sequence Bees / classification, genetics* Evolution, Molecular Introns* Molecular Sequence Data Mutation* Phylogeny Sequence Alignment Sequence Analysis, DNA |
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