Direct optimization and multiple alignment of 28S D2?D3 rDNA sequences: problems with indels on the way to a molecular phylogeny of the cryptine ichneumon waSPS (Insecta: Hymenoptera)

Phylogenomics of Ichneumonoidea (Hymenoptera) and implications for evolution of mode of parasitism and viral endogenization

Ichneumonoidea is one of the most diverse lineages of animals on the planet with >48,000 described species and many more undescribed. Parasitoid wasps of this superfamily are mostly beneficial insects that attack and kill other arthropods and are important for understanding diversification and the evolution of life history strategies related to parasitoidism. Further, some lineages of parasitoids within Ichneumonoidea have acquired endogenous virus elements (EVEs) that are permanently a part of the wasp's genome and benefit the wasp through host immune disruption and behavioral control. Unfortunately, understanding the evolution of viral acquisition, parasitism strategies, diversification, and host immune disruption mechanisms, is deeply limited by the lack of a robust phylogenetic framework for Ichneumonoidea. Here we design probes targeting 541 genes across 91 taxa to test phylogenetic relationships, the evolution of parasitoid strategies, and the utility of probes to capture polydnavirus genes across a diverse array of taxa. Phylogenetic relationships among Ichneumonoidea were largely well resolved with most higher-level relationships maximally supported. We noted codon use biases between the outgroups, Braconidae, and Ichneumonidae and within Pimplinae, which were largely solved through analyses of amino acids rather than nucleotide data. These biases may impact phylogenetic reconstruction and caution for outgroup selection is recommended. Ancestral state reconstructions were variable for Braconidae across analyses, but consistent for reconstruction of idiobiosis/koinobiosis in Ichneumonidae. The data suggest many transitions between parasitoid life history traits across the whole superfamily. The two subfamilies within Ichneumonidae that have polydnaviruses are supported as distantly related, providing strong evidence for two independent acquisitions of ichnoviruses. Polydnavirus capture using our designed probes was only partially successful and suggests that more targeted approaches would be needed for this strategy to be effective for surveying taxa for these viral genes. In total, these data provide a robust framework for the evolution of Ichneumonoidea.

Checklist of British and Irish Hymenoptera - Ichneumonidae

BACKGROUND

The checklist of British and Irish Ichneumonidae is revised, based in large part on the collections of the Natural History Museum, London and the National Museums of Scotland, Edinburgh. Distribution records are provided at the country level.

NEW INFORMATION

Of the 2,447 species regarded as valid and certainly identified, 214 are here recorded for the first time from the British Isles. Neorhacodinae is considered to be a separate subfamily rather than a synonym of Tersilochinae. Echthrini is treated as a junior synonym of the tribe Cryptini, not Hemigastrini. Echthrus Gravenhorst and Helcostizus Förster are classified in Cryptini rather than, respectively, Hemigastrini and Phygadeuontini.

Species delimitation using morphology, morphometrics, and molecules: definition of the Ophionscutellaris Thomson species group, with descriptions of six new species (Hymenoptera, Ichneumonidae)

The diverse genus Ophion is almost entirely undescribed in the Nearctic region. In this paper we define the Ophionscutellaris species group. This species group is well-supported by analysis of DNA (ITS2, COI, and 28S D2-D3) and morphology. It includes the Palearctic species Ophionscutellaris and the Nearctic species Ophionidoneus. An integrative analysis of DNA, geometric wing morphometrics, classical morphometrics and qualitative morphology indicates that this species group contains a minimum of seven species in North America, although the full diversity of the group has likely not been sampled. Ophionclave Schwarzfeld, sp. n., Ophionaureus Schwarzfeld, sp. n., Ophionbrevipunctatus Schwarzfeld, sp. n., Ophiondombroskii Schwarzfeld, sp. n., Ophionkeala Schwarzfeld, sp. n. and Ophionimportunus Schwarzfeld, sp. n. are described, and a key to the known Nearctic species of the Ophionscutellaris group is provided.

Utility of the DNA barcoding gene fragment for parasitic wasp phylogeny (Hymenoptera: Ichneumonoidea): data release and new measure of taxonomic congruence

The enormous cytochrome oxidase subunit I (COI) sequence database being assembled from the various DNA barcoding projects as well as from independent phylogenetic studies constitutes an almost unprecedented amount of data for molecular systematics, in addition to its role in species identification and discovery. As part of a study of the potential of this gene fragment to improve the accuracy of phylogenetic reconstructions, and in particular, exploring the effects of dense taxon sampling, we have assembled a data set for the hyperdiverse, cosmopolitan parasitic wasp superfamily Ichneumonoidea, including the release of 1793 unpublished sequences. Of approximately 84 currently recognized Ichneumonoidea subfamilies, 2500 genera and 41,000 described species, barcoding 5'-COI data were assembled for 4168 putative species-level terminals (many undescribed), representing 671 genera and all but ten of the currently recognized subfamilies. After the removal of identical and near-identical sequences, the 4174 initial sequences were reduced to 3278. We show that when subjected to phylogenetic analysis using both maximum likelihood and parsimony, there is a broad correlation between taxonomic congruence and number of included sequences. We additionally present a new measure of taxonomic congruence based upon the Simpson diversity index, the Simpson dominance index, which gives greater weight to morphologically recognized taxonomic groups (subfamilies) recovered with most representatives in one or a few contiguous groups or subclusters.

The species of the Neotropical genus Fractipons Townes, 1970 (Hymenoptera, Ichneumonidae, Cryptinae)

In this paper, two new species of the Neotropical genus Fractipons Townes, 1970 (Hymenoptera, Ichneumonidae) are described. A new diagnosis for the genus, a re-description of Fractipons cincticornis Townes, 1970 and a key to known species are provided. New distribution records for the genus now include Argentina, Costa Rica, Panama and Peru.

An evaluation of phylogenetic informativeness profiles and the molecular phylogeny of diplazontinae (Hymenoptera, Ichneumonidae)

How to quantify the phylogenetic information content of a data set is a longstanding question in phylogenetics, influencing both the assessment of data quality in completed studies and the planning of future phylogenetic projects. Recently, a method has been developed that profiles the phylogenetic informativeness (PI) of a data set through time by linking its site-specific rates of change to its power to resolve relationships at different timescales. Here, we evaluate the performance of this method in the case of 2 standard genetic markers for phylogenetic reconstruction, 28S ribosomal RNA and cytochrome oxidase subunit 1 (CO1) mitochondrial DNA, with maximum parsimony, maximum likelihood, and Bayesian analyses of relationships within a group of parasitoid wasps (Hymenoptera: Ichneumonidae, Diplazontinae). Retrieving PI profiles of the 2 genes from our own and from 3 additional data sets, we find that the method repeatedly overestimates the performance of the more quickly evolving CO1 compared with 28S. We explore possible reasons for this bias, including phylogenetic uncertainty, violation of the molecular clock assumption, model misspecification, and nonstationary nucleotide composition. As none of these provides a sufficient explanation of the observed discrepancy, we use simulated data sets, based on an idealized setting, to show that the optimum evolutionary rate decreases with increasing number of taxa. We suggest that this relationship could explain why the formula derived from the 4-taxon case overrates the performance of higher versus lower rates of evolution in our case and that caution should be taken when the method is applied to data sets including more than 4 taxa.