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Mol. Biol. Evol. 20(1):87-92. 2003
DOI: 10.1093/molbev/msg007
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Evolution and Phylogenetic Utility of Alignment Gaps Within Intron Sequences of Three Nuclear Genes in Bumble Bees (Bombus)

Atsushi Kawakita*, Teiji Sota{dagger},, John S. Ascher{ddagger}, Masao Ito§, Hiroyuki Tanaka|| and Makoto Kato*

* Graduate School of Human and Environmental Studies
{dagger} Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
{ddagger} Department of Entomology, Comstock Hall, Cornell University, Ithaca, New York
§ Sapporo Science and Technology College, Sapporo, Japan
|| Primate Research Institute, Kyoto University, Inuyama, Japan

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–1{alpha} (EF-1{alpha}) F2 copy genes. LW Rh intron had only a few uninformative gaps, ArgK intron had relatively long gaps that were easily aligned, and EF-1{alpha} 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-1{alpha} 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-1{alpha} 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.

Key Words: arginine kinase • elongation factor–1{alpha} • long-wavelength rhodopsin • intron • phylogeny • bumble bee


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