Gap Characters Research Articles

Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus).

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.

Uninode coding vs gene tree parsimony for phylogenetic reconstruction using duplicate genes

Two different methods of using paralogous genes for phylogenetic inference have been proposed: reconciled trees (or gene tree parsimony) and uninode coding. Gene tree parsimony suffers from 10 serious problems, including differential weighting of nucleotide and gap characters, undersampling which can be misinterpreted as synapomorphy, all of the characters not being allowed to interact, and conflict between gene trees being given equal weight, regardless of branch support. These problems are largely avoided by using uninode coding. The uninode coding method is elaborated to address multiple gene duplications within a single gene tree family and handle problems caused by lack of gene tree resolution. An example of vertebrate phylogeny inferred from nine genes is reanalyzed using uninode coding. We suggest that uninode coding be used instead of gene tree parsimony for phylogenetic inference from paralogous genes.

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Phylogenetic analysis of nucleotide and amino acid sequences requires the alignment of homologous sequences. The alignment procedure often requires the insertion of gaps, putatively corresponding to insertion or deletion events, which can be coded as phylogenetic characters. As a general class of phylogenetic characters, gaps have variously been suggested to be reliable (e.g., Lloyd and Calder, 1991; Van Dijk et al., 1999) or unreliable (e.g., Golenberg et al., 1993; Ford et al., 1995). This difference in opinion, coupled with the lack of a well-supported method for the coding of gaps, has led to a diversity of approaches by which gaps have been treated in, or excluded from, tree searches (Gonzalez, 1996). In an earlier paper we presented two methods, termed simple and complex indel coding, in which all gaps (excluding leading and trailing gaps, which are generally artifacts) can be coded from aligned sequence-based matrices (Simmons and Ochoterena, 2000). Simple indel coding, which is used in this study, is implemented by coding all gaps that have different 5' or 3' termini as separate presence/absence characters. Whenever a gap is being coded and the region it spans is completely included within the span of another gap, those sequences having the longer gap (i.e., one that extends to or beyond both the 5' and 3' termini of the gap being coded) are scored as inapplicable for the gap character being coded. Some have suggested on theoretical and empirical grounds that longer gaps are better phylogenetic characters than shorter gaps. Lloyd and Calder (1991) argued that multiresidue gaps are reliable phylogenetic characters because indels are unlikely to be repeated in the exact same position with the same length and sequence (for insertions); indels of different lengths at the same position are recognized as separate events. Similarly, van Ham et al. (1994) suggested that, based on the relative levels of homoplasy in the intergenic spacer between trnL and trnF, gaps longer than two positions are reliable phylogenetic characters. In this paper we assess the relative levels of homoplasy of gap and base characters from a selection of 38 published sequence-based matrices. We determine the potential phylogenetic information included in gap characters and the extent to which inclusion of gap characters alters the gene tree topology and branch support values. We also test the assertion that longer gaps are better phylogenetic characters than shorter gaps.

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

Incorporation, Relative Homoplasy, and Effect of Gap Characters in Sequence-Based Phylogenetic Analyses

A Molecular Phylogeny of the Tiger Beetles (Cicindelidae): Congruence of Mitochondrial and Nuclear rDNA Data Sets

As a basis for comparative studies in the family Cicindelidae (tiger beetles), a phylogenetic hypothesis for major groups was established based on molecular data, focusing on the taxa of the New World. Two markers, mitochondrial 16S rRNA and nuclear 18S rRNA, were sequenced for a total of 912 nucleotides and 30 taxa. All Cicindelidae were inferred to be a monophyletic group by the presence of a segment in the 5′ region of the 18S rDNA which is predicted to fold into a single stem-loop structure not present in the outgroup. The total number of variable and potentially informative positions was smaller in the 18S data set, but their higher internal consistency resulted in a strong phylogenetic signal. Inferred relationships were stable over a wide range of alignment parameters, but the inclusion of alignment-sensitive positions and presumptive gap characters added substantially to the resolution and overall support of the tree. Both data sets were in general congruence. The combined evidence suggests that relationships in Cicindelidae as currently recognized have to be reconsidered. No convincing evidence could be found for the traditional subdivision into two subfamilies, Cicindelinae and Collyrinae. The latter is embedded within the Cicindelinae and clearly not the sister to all other cicindelids. Most of the current tribes and subtribes, particularly in the Megacephalini, are paraphyletic groups, whereas monophyly of the large tribe Cicindelini is well supported by the molecular data.

Automatic generation of primary sequence patterns from sets of related protein sequences.

We have developed a computer algorithm that can extract the pattern of conserved primary sequence elements common to all members of a homologous protein family. The method involves clustering the pairwise similarity scores among a set of related sequences to generate a binary dendrogram (tree). The tree is then reduced in a stepwise manner by progressively replacing the node connecting the two most similar termini by one common pattern until only a single common "root" pattern remains. A pattern is generated at a node by (i) performing a local optimal alignment on the sequence/pattern pair connected by the node with the use of an extended dynamic programming algorithm and then (ii) constructing a single common pattern from this alignment with a nested hierarchy of amino acid classes to identify the minimal inclusive amino acid class covering each paired set of elements in the alignment. Gaps within an alignment are created and/or extended using a "pay once" gap penalty rule, and gapped positions are converted into gap characters that function as 0 or 1 amino acid of any type during subsequent alignment. This method has been used to generate a library of covering patterns for homologous families in the National Biomedical Research Foundation/Protein Identification Resource protein sequence data base. We show that a covering pattern can be more diagnostic for sequence family membership than any of the individual sequences used to construct the pattern.