Nina Laurenne

A thousand and one wasps: a 28S rDNA and morphological phylogeny of the Ichneumonidae (Insecta: Hymenoptera) with an investigation into alignment parameter space and elision

Abstract 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.

Revision of the Agathidinae (Hymenoptera: Braconidae) with comparisons of static and dynamic alignments

The phylogeny of the Agathidinae (Insecta: Hymenoptera: Braconidae) is investigated based on morphological and sequence data from the D2–3 regions of 28S rDNA. Morphology and molecular data were run simultaneously and separately and the molecular and combined data sets were analyzed using both static, Clustal W, and dynamic, POY, alignments. Both alignments were conducted under a variety of gap costs and results are compared. Sixty‐two ingroup exemplars representing 22 genera and six outgroup taxa representing two subfamilies and five genera were included. Numerous taxa at the generic and tribal levels were tested for monophyly and the evolutionary history of several characters is discussed. The tribe Agathidini s.s. is found to be a derived member of the Microdini and the two are synonymized under the older name, Agathidini s.l. Support is substantial for the tribes Cremnoptini and Disophrini and Earinini but equivocal for the Agathidini s.l. At the generic level, Bassus is found to be polyphyletic. Numerous new synonymies and combinations are proposed.

Biological names and taxonomies on the semantic web: managing the change in scientific conception

Biodiversity management requires the usage of heterogeneous biological information from multiple sources. Indexing, aggregating, and finding such information is based on names and taxonomic knowledge of organisms. However, taxonomies change in time due to new scientific findings, opinions of authorities, and changes in our conception about life forms. Furthermore, organism names and their meaning change in time, different authorities use different scientific names for the same taxon in different times, and various vernacular names are in use in different languages. This makes data integration and information retrieval difficult without detailed biological information. This paper introduces a meta-ontology for managing the names and taxonomies of organisms, and presents three applications for it: 1) publishing biological species lists as ontology services (ca. 20 taxonomies including more than 80,000 names), 2) collaborative management of the vernacular names of vascular plants (ca. 26,000 taxa), and 3) management of individual scientific name changes based on research results, covering a group of beetles. The applications are based on the databases of the Finnish Museum of Natural History and are used in a living lab environment on the web.

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.

Suspended mummies in Aleiodes species (Hymenoptera: Braconidae: Rogadinae) with descriptions of six new species from western Uganda based largely on DNA sequence data

A group of species of the rogadine braconid genus Aleiodes are shown to produce a distinctive mummy, which is “J”‐shaped and is formed after the host larva, in all cases an ennomine geometrid moth, has dropped from a plant suspended in midair by a silk thread. The group includes one described species, A. buzurae He & Chen from China, and a species complex from tropical Africa (W. Uganda). All the African specimens reared from suspended mummies looked morphologically virtually indistinguishable, though there was considerable colour variation that segregated the specimens into five groups. Three gene fragments (nuclear 28S D2‐3 rDNA, the nuclear ITS2 region and part of the mitochondrial cytochrome oxidase 1 gene (CO1)) were sequenced to assess if these specimens represented a single variable species or a complex of morphologically cryptic species. Results show variation in all three gene fragments, with strong signal in the CO1 gene, parsimony analysis of which revealed six well supported groups corresponding to the colour variants, except that two specimens with nearly identical colour differed considerably in their CO1 sequences. Large, and difficult to align, variation was found in the ITS2 fragments, which by eye also supported the same six groupings. Limited variation was found in the 28S fragment, but one position supported monophyly of the two specimens belonging to one of the species circumscribed by the other genes. These groups are considered to correspond to separate species, which are described as new: A. barnardae Quicke & Shaw, A. basutai Quicke & Shaw, A. kanyawarensis Quicke & Shaw, A. kasenenei Quicke & Shaw, A. mubfsi Quicke & Shaw and A. trevelyanae Quicke & Shaw. The possible function of the specialised mummification behaviour is discussed and some observations on rates of hyperparasitism are presented.

Molecular phylogeny and historical biogeography of the bee genus Colletes Latreille, 1802 (Hymenoptera: Apiformes: Colletidae), based on mitochondrial COI and nuclear 28S sequence data

A phylogenetic analysis of the intrageneric relationships within the bee genus Colletes using a combined data set of the mitochondrial cytochrome oxidase 1 (COI) and 28S sequences is presented and its implications for historical biogeography are investigated. We analyzed 91 out of 469 described Colletes species (19.4%) from the entire range of distribution and 25 outgroup taxa representing all colletid subfamilies closely related to Colletinae. Eight different combinations of alignment parameters were used for the 28S data, and our combined data set comprised between 1801 and 1845 aligned nucleotides with COI contributing 339 informative bases and 28S between 318 and 360 informative sites. Our results corroborate the monophyly of about half of the Old World subgenera and show the need for a taxonomic re-delimitation of other groups currently accepted. The phylogenetic results confirm the South American origin of Colletes and multiple faunal exchange events between North America and Eurasia. The last continent colonized was Africa south of the Sahara, which experienced at least two independent invasions.

The parasitic wasp genera Skiapus, Hellwigia, Nonnus, Chriodes, and Klutiana (Hymenoptera, Ichneumonidae): Recognition of the Nesomesochorinae stat. rev. and Nonninae stat. nov. and transfer of Skiapus and Hellwigia to the Ophioninae

The ichneumonid wasp genera Skiapus Morley, Hellwigia Gravenhorst, Nonnus Cresson, Chriodes Förster, and Klutiana Betrem are each formally removed from the Campopleginae on the basis of morphological, molecular, and simultaneous analyses using PAUP* and the optimization alignment program POY. Skiapus and Hellwigia are shown to form a monophyletic group with the Ophioninae to which they are transferred. Nonnus is treated as comprising the Nonninae stat. nov. and Chriodes and Klutiana (sometimes treated as a junior synonym of Chriodes) are treated as comprising the Nesomesochorinae stat. rev. The status of Nesomesochorinae and Nonninae is not fully resolved as they are not consistently recovered as separate groups, forming a single clade in some analyses. We keep them separate because of this uncertainty. Molecular synapomorphies within the D2–3 expansion region of the 28S rDNA gene show the utility of this gene region in determining subfamily‐level placement within the higher Ophioniformes.

Making species checklists understandable to machines - a shift from relational databases to ontologies.

BackgroundThe scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications.ResultsWe introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time.ConclusionsThe use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more “intelligent” biological applications and services.

The Birds of the World Ontology AVIO

We present an ontology for managing the scientific and common names of birds. The ontology is based on the TaxMeOn meta-ontology model for biological names. The ontology is in use as an ontology service and it has been applied in a bird watching system.

ENVIROFI - Bringing Biodiversity to the Future Internet

In order to meet the requirements for observational biodiversity data, new sources of data must be enabled; for this purpose, new tools will be required. In order to effectively implement such tools, standardized building blocks such as the enablers defined by the FI will be very valuable. Thus, it is of utmost urgency that the requirements posed by the biodiversity sector are clearly structured and made available for implementation of environmental enablers within the FI. The ENVIROFI project has gone to great lengths so provide these requirements for various environmental domains; of specific relevant to this paper being the biodiversity domain. We hope to successfully contribute to the future of e-Environment in this manner.