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)

Elongation factor-1 alpha (EF-1 alpha) is a highly conserved nuclear coding gene that can be used to investigate recent divergences due to the presenc e of rapidly evolving introns. However, a universal feature of intron seque nces is that even closely related species exhibit insertion and deletion ev ents, which cause variation in the lengths of the sequences. Indels are fre quently rich in evolutionary information, but most investigators ignore sit es that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the ta xonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconi dae: Aphidiinae) using congruence as a criterion for assessing a range of m ethods for aligning such variable-length EF-1 alpha intron sequences. These methods included distance- and parsimony-based multiple-alignment programs (CLUSTAL W and MALIGN), direct optimization (POY), and two "by eye" alignm ent strategies. Furthermore, with one method (CLUSTAL W) we explored in det ail the robustness of results to changes in the gap cost parameters. Phenet ic-based alignments ("by eye" and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more de manding, methods. In general, all of our alignment and tree-building strate gies recovered the same basic topological structure, which means that an un derlying phylogenetic signal remained regardless of the strategy chosen. Ho wever, several relationships between clades were sensitive both to alignmen t and to tree-building protocol. Further alignments, considering only seque nces belonging to the same group, allowed us to infer a range of phylogenet ic relationships that were highly robust to tree-building protocol. By comp aring these topologies with those obtained by varying the CLUSTAL parameter s, we generated the distribution area of congruence and taxonomic compatibi lity. Finally, we present the first robust estimate of the European Pauesia phylogeny by using two EF-1 alpha introns and 38 taxa (plus 3 outgroups). This estimate conflicts markedly with the traditional subgeneric classifica tion. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.