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.2013 Aug 2;8(8):e69344.
doi: 10.1371/journal.pone.0069344. Print 2013.

The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data

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The hymenopteran tree of life: evidence from protein-coding genes and objectively aligned ribosomal data

Seraina Klopfstein et al. PLoS One..

Abstract

Previous molecular analyses of higher hymenopteran relationships have largely been based on subjectively aligned ribosomal sequences (18S and 28S). Here, we reanalyze the 18S and 28S data (unaligned about 4.4 kb) using an objective and a semi-objective alignment approach, based on MAFFT and BAli-Phy, respectively. Furthermore, we present the first analyses of a substantial protein-coding data set (4.6 kb from one mitochondrial and four nuclear genes). Our results indicate that previous studies may have suffered from inflated support values due to subjective alignment of the ribosomal sequences, but apparently not from significant biases. The protein data provide independent confirmation of several earlier results, including the monophyly of non-xyelid hymenopterans, Pamphilioidea + Unicalcarida, Unicalcarida, Vespina, Apocrita, Proctotrupomorpha and core Proctotrupomorpha. The protein data confirm that Aculeata are nested within a paraphyletic Evaniomorpha, but cast doubt on the monophyly of Evanioidea. Combining the available morphological, ribosomal and protein-coding data, we examine the total-evidence signal as well as congruence and conflict among the three data sources. Despite an emerging consensus on many higher-level hymenopteran relationships, several problems remain unresolved or contentious, including rooting of the hymenopteran tree, relationships of the woodwasps, placement of Stephanoidea and Ceraphronoidea, and the sister group of Aculeata.

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Conflict of interest statement

Competing Interests:The authors have declaared that no competing interests exist.

Figures

Figure 1
Figure 1. Saturation plots of the different genes and codon positions.
Uncorrected p-distances are shown on the y-axis, while the x-axis represents the pairwise distances as inferred on the tree recovered from the single-gene analyses. “CO1 12” indicates the combined first and second codon position of the CO1 gene, and so forth.
Figure 2
Figure 2. Bayesian tree recovered from the analysis of the two ribosomal genes under the MAFFT alignment.
Support values next to the nodes are Bayesian posterior probabilities obtained from the MAFFT and the BAli-Phy alignments, respectively. Asterisks stand for maximal support. Taxa identified as rogues are shown on dashed branches. Very long branches leading to some of the outgroup taxa were compressed in this figure.
Figure 3
Figure 3. Bayesian tree recovered from the analysis of first and second codon positions of the combined protein-coding genes.
Support values next to the nodes are Bayesian posterior probabilities obtained from first and second and from all three codon positions of the nuclear genes, respectively. Asterisks stand for maximal support. Taxa identified as rogues are shown on dashed branches.
Figure 4
Figure 4. Outgroups and symphytan part of the Bayesian total-evidence tree obtained from the BAli-Phy based alignment.
Support values next to nodes indicate the support obtained under either of the two alignment approaches (BAli-Phy and MAFFT) and with morphology included (total evidence, TE), versus the molecular data only, again under both alignment approaches. Asterisks represent maximal support. Symbols indicate support from partitions of the molecular data (see legend). Superfamilies that were not recovered as monophyletic are shown in grey.
Figure 5
Figure 5. Vespina part of the Bayesian total-evidence tree obtained from the BAli-Phy based alignment.
See legend of Figure 4 for details.
Figure 6
Figure 6. Simplified total-evidence tree based on the combined molecular and morphological data contrasted with the tree obtained from the molecular data alone.
Support values are in both cases given for both the BAli-Phy-based and the MAFFT alignment of the rRNA genes, with asterisks representing maximal support. Taxa which assume conflicting positions are shown in grey.
Figure 7
Figure 7. Schematic representation of controversial relationships in high-level phylogenetics of Hymenoptera.
Numbers next to nodes and superscripts in the text indicate nodes for which the consensus trees obtained in specific analyses are in conflict with the diagram (see these for details). Numbers next to taxon names stand for non-monophyly of the group. Besides hypotheses derived from our data, we also show selected results from the literature. If a dataset or publication does not appear in one of the cases, then it did not provide any resolution for the relationships in question. In the Heraty et al. (2011) analysis, we refer to the by-eye alignment.
See this image and copyright information in PMC

References

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