Wolbachia is a genus of bacterial endosymbionts that impacts the breeding systems of their hosts. Wolbachia can confuse the patterns of mitochondrial variation, including DNA barcodes, because it influences the pathways through which mitochondria are inherited. We examined the extent to which these endosymbionts are detected in routine DNA barcoding, assessed their impact upon the insect sequence divergence and identification accuracy, and considered the variation present in Wolbachia COI. Using both standard PCR assays (Wolbachia surface coding protein – wsp), and bacterial COI fragments we found evidence of Wolbachia in insect total genomic extracts created for DNA barcoding library construction. When >2 million insect COI trace files were examined on the Barcode of Life Datasystem (BOLD) Wolbachia COI was present in 0.16% of the cases. It is possible to generate Wolbachia COI using standard insect primers; however, that amplicon was never confused with the COI of the host. Wolbachia alleles recovered were predominantly Supergroup A and were broadly distributed geographically and phylogenetically. We conclude that the presence of the Wolbachia DNA in total genomic extracts made from insects is unlikely to compromise the accuracy of the DNA barcode library; in fact, the ability to query this DNA library (the database and the extracts) for endosymbionts is one of the ancillary benefits of such a large scale endeavor – for which we provide several examples. It is our conclusion that regular assays for Wolbachia presence and type can, and should, be adopted by large scale insect barcoding initiatives. While COI is one of the five multi-locus sequence typing (MLST) genes used for categorizing Wolbachia, there is limited overlap with the eukaryotic DNA barcode region.

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The internal phylogeny of the Ichneumonidae is investigated using parsimony analysis of a large data set including 1001 partial 28S ribosomal DNA sequences, 621 of which are newly reported, and a morphological data set of 162 characters scored variously at subfamily, tribe, genus group and genus levels and including only informative characters. The data set includes members of 630 named genera, representing all currently recognized subfamilies, all but four tribes and all but one of the taxa noted by Townes as being of uncertain placement. Sequences were aligned using clustal X, and a sensitivity analysis was performed varying gap-opening and gap-extension parameters. Alignments were appraised by reference to their ability to recover a range of traditional and morphologically recognized groups. Each alignment was analysed both independently and simultaneously with the morphological data set, and also with gap characters treated as both missing data and as informative. No single set of alignment parameters was found to be markedly better by this criterion, and different ranges of parameters led to the recovery of different recognized groups of taxa. Elision (combining all alignments into a single analysis) was therefore used, both with and without morphology and with both gap character treatments, to summarize the overall molecular signal. Analysis of the morphological matrix alone produced a number of results that are undoubtedly a consequence of convergence of morphological characters as the result of parallel evolution of similar life histories. Simultaneous analysis of the morphological data set with each of the 120 DNA alignments recovered most accepted subfamilies as monophyletic. Several currently recognized subfamilies are supported by most of the molecular analyses but some appear to be paraphyletic or polyphyletic. The Ctenopelmatinae are paraphyletic with respect to the Metopiinae. Robustly recovered results lead us to resurrect the Brachyscleromatinae to include Brachyschleroma and the Erythrodolius group of Phrudinae. The Neorhacodinae and the Phrudus group of Phrudinae are transferred to the Tersilochinae. Nonnus is transferred to the Nesomesochorinae. Hyperacmus is transferred to the Cylloceriinae. The major groupings of subfamilies that have recently been proposed (i.e. ichneumoniformes, pimpliformes and ophioniformes) were recovered as monophyletic, but their exact limits remain in question.

In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relationships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem‐based (total‐group) definition of Tetrapoda is preferred over apomorphy‐ and node‐based (crown‐group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differences between these trees concern: (1) the internal relationships of aistopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria crassidisca and Pholiderpeton scutigerum collapsed in a trichotomy with a clade formed by Anthracosaurus russelli and Pholiderpeton attheyi; (3) the internal relationships of derived dissorophoids, with four amphibamid species forming an unresolved node with a clade consisting of micromelerpetontids and branchiosaurids and a clade consisting of albanerpetontids plus basal crown‐group lissamphibians; (4) the position of albenerpetontids and Eocaecilia micropoda, which form an unresolved node with a trichotomy subtending Karaurus sharovi, Valdotriton gracilis and Triadobatrachus massinoti;(5) the branching pattern of derived diplocaulid nectrideans, with Batrachiderpeton reticulatum and Diceratosaurus brevirostris collapsed in a trichotomy with a clade formed by Diplocaulus magnicornis and Diploceraspis burkei. The results of the original parsimony run ‐ as well as those retrieved from several other treatments of the data set (e.g. exclusion of postcranial and lower jaw data;character reweighting; reverse weighting) ‐ indicate a deep split of early tetrapods between lissamphibian‐ and amniote‐related taxa. Colosteids, Crassigyrinus, Whatcheeria and baphetids are progressively more crownward stemtetrapods. Caerorhachis, embolomeres, gephyrostegids, Solenodonsaurus and seymouriamorphs are progressively more crownward stem‐amniotes. Eucritta is basal to temnospondyls, with crown‐lissamphibians nested within dissorophoids. Westlothiana is basal to Lepospondyli, but evidence for the monophyletic status of the latter is weak. Westlothiana and Lepospondyli form the sister group to diadectomorphs and crown‐group amniotes. Tuditanomorph and microbrachomorph microsaurs are successively more closely related to a clade including proximodistally: (1) lysorophids; (2) Acherontiscus as sister taxon to adelospondyls; (3) scincosaurids plus diplocaulids; (4) urocordylids plus aïstopods. A data set employing cranial characters only places microsaurs on the amniote stem, but forces remaining lepospondyls to appear as sister group to colosteids on the tetrapod stem in several trees. This arrangement is not significantly worse than the tree topology obtained from the analysis of the complete data set. The pattern of sister group relationships in the crownward part of the temnospondyl‐lissamphibian tree re‐emphasizes the important role of dissorophoids in the lissamphibian origin debate. However, no specific dissorophoid can be identiffed as the immediate sister taxon to crown‐group lissamphibians. The branching sequence of various stem‐group amniotes reveals a coherent set of internested character‐state changes related to the acquisition of progressively more terrestrial habits in several Permo‐Carboniferous forms.