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

Abstract

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.

Phylogeny, historical biogeography, and character evolution in bumble bees (Bombus: Apidae) based on simultaneous analysis of three nuclear gene sequences

“…1; strict consensus of 72 trees of 2240 steps; Consistency Index excluding uninformative characters ¼ 0.49; Retention Index ¼ 0.76). Monophyly of Fervidobombus and Separatobombus were not verified, as anticipated by morphological (Ito, 1985;Williams, 1994) and molecular data (Kawakita et al, 2003;Koulianos and SchmidHempel, 2000). The basal placement of Mendacibombus, Bombias, and Kallobombus is consistent with previous phylogenetic studies (Kawakita et al, 2003;Pedersen, 2002;Williams, 1994).…”

“…Methods of DNA sequencing and phylogenetic analyses are described in Kawakita et al (2003). As in our previous assessment (Kawakita et al, 2003), we conducted simultaneous parsimony analysis of exon + intron data for three nuclear gene fragments (LW Rh,ArgK, including appropriately coded indel nucleotides and gap q Supplementary data associated with this article can be found, in the online version, at doi: 10. 1016/j.ympev.2003.12.003characters; this approach allows all relevant data from our nuclear sequences to contribute to the resolution of Bombus phylogeny.…”

“…Our recent work (Kawakita et al, 2003) has recovered robust phylogenetic relationships among most major Bombus lineages based on three nuclear genes, long-wavelength rhodopsin (LW Rh), arginine kinase (ArgK), and elongation factor-1a F2 copy . This study also showed that these genes contain gaps within introns that can reinforce results obtained from base substitutions.…”

A multi-gene phylogeny of aquiline eagles (Aves: Accipitriformes) reveals extensive paraphyly at the genus level

“…Indels, therefore, provide an independent source of evidence that can reinforce conclusions derived from nucleotide substitutions. This approach has been successfully applied in diverse organisms (e.g., Bapteste and Philippe, 2002;Kawakita et al, 2003;Venkatesh et al, 2001) including birds (Ericson et al, 2000;Prychitko and Moore, 2003).…”

An integrative approach identifies a new species of bumblebee (Hymenoptera: Apidae: Bombini) from northeastern Brazil

“…Also, the large ribosomal RNA subunit (16S ) region was amplified according to the same authors. We amplified exons and introns from two nuclear genes, arginine kinase (ArgK) (Kawakita et al 2003) and elongation factor -1 α (EF -1 α) (Hines et al 2006), to test for mitochondrial introgression and to improve our phylogenetic analyses. All PCR amplifications were according to the articles cited above and performed in a Mastercycler Pro (Eppendorf, Germany).…”