期刊
MOLECULAR BIOLOGY AND EVOLUTION
卷 18, 期 6, 页码 1117-1131出版社
SOC MOLECULAR BIOLOGY EVOLUTION
DOI: 10.1093/oxfordjournals.molbev.a003882
关键词
phylogenetics; variable-length sequences; alignment strategies; tree-building methods; aphidiinae; Pauesia; EF-1 alpha introns; elongation factor-1 alpha
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 presence of rapidly evolving introns. However, a universal feature of intron sequences is that even closely related species exhibit insertion and deletion events, which cause variation in the lengths of the sequences. Indels are frequently rich in evolutionary information, but most investigators ignore sites that fall within these variable regions, largely because the analytical tools and theory are not well developed. We examined this problem in the taxonomically problematic parasitoid wasp genus Pauesia (Hymenoptera: Braconidae: Aphidiinae) using congruence as a criterion for assessing a range of methods 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 alignment strategies. Furthermore, with one method (CLUSTAL W) we explored in detail the robustness of results to changes in the gap cost parameters. Phenetic-based alignments (by eye and CLUSTAL W) appeared, under our criterion, to perform as well as more readily defensible, but computationally more demanding, methods. In general, all of our alignment and tree-building strategies recovered the same basic topological structure, which means that an underlying phylogenetic signal remained regardless of the strategy chosen. However, several relationships between clades were sensitive both to alignment and to tree-building protocol. Further alignments, considering only sequences belonging to the same group, allowed us to infer a range of phylogenetic relationships that were highly robust to tree-building protocol. By comparing these topologies with those obtained by varying the CLUSTAL parameters, we generated the distribution area of congruence and taxonomic compatibility. 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 classification. We recommend that this classification be abandoned, and we propose a series of monophyletic species groups.
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