WCO-Lite version 1.1: an online nomenclatural catalogue of harvestmen of the world (Arachnida, Opiliones) curated in TaxonWorks.

The "World Catalogue of Opiliones" (WCO) is a collaborative effort to comprehensively index the Earth's species of harvestmen. This paper announces one component of the WCO, "WCO-Lite" a website available at https://wcolite.com/. WCO-Lite provides a graphic user interface for a second component of the WCO, "Opiliones of the World", a database on the taxonomy of the harvestmen curated in TaxonWorks (TW). WCO-Lite interfaces include: (1) a checklist of all valid taxa of the arachnid Opiliones, exhaustive up to December 2018; (2) a taxonomic tree; (3) a search engine comprising two modules; and (4) a counter of species diversity for each taxon. An e-Book companion was launched simultaneously with WCO-Lite version 1.1 on September 12, 2020 to account for the formal publication of mandatory nomenclatural changes and availability of taxonomic names. The collective components of the WCO are also being summarized in a forthcoming conventional paper-form catalogue, currently in manuscript stage.

Transforming the study of organisms: Phenomic data models and knowledge bases.

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem.

Folding wings like a cockroach: a review of transverse wing folding ensign wasps (Hymenoptera: Evaniidae: Afrevania and Trissevania).

We revise two relatively rare ensign wasp genera, whose species are restricted to Sub-Saharan Africa: Afrevania and Trissevania. Afrevania longipetiolata sp. nov., Trissevania heatherae sp. nov., T. hugoi sp. nov., T. mrimaensis sp. nov. and T. slideri sp. nov. are described, males and females of T. anemotis and Afrevania leroyi are redescribed, and an identification key for Trissevaniini is provided. We argue that Trissevania mrimaensis sp. nov. and T. heatherae sp. nov. populations are vulnerable, given their limited distributions and threats from mining activities in Kenya. We hypothesize that these taxa together comprise a monophyletic lineage, Trissevaniini, tr. nov., the members of which share the ability to fold their fore wings along two intersecting fold lines. Although wing folding of this type has been described for the hind wing of some insects four-plane wing folding of the fore wing has never been documented. The wing folding mechanism and the pattern of wing folds of Trissevaniini is shared only with some cockroach species (Blattodea). It is an interesting coincidence that all evaniids are predators of cockroach eggs. The major wing fold lines of Trissevaniini likely are not homologous to any known longitudinal anatomical structures on the wings of other Evaniidae. Members of the new tribe share the presence of a coupling mechanism between the fore wing and the mesosoma that is composed of a setal patch on the mesosoma and the retinaculum of the fore wing. While the setal patch is an evolutionary novelty, the retinaculum, which originally evolved to facilitate fore and hind wing coupling in Hymenoptera, exemplifies morphological exaptation. We also refine and clarify the Semantic Phenotype approach used in previous taxonomic revisions and explore the consequences of merging new with existing data. The way that semantic statements are formulated can evolve in parallel, alongside improvements to the ontologies themselves.

Monograph of the Afrotropical species of Scelio Latreille (Hymenoptera, Platygastridae), egg parasitoids of acridid grasshoppers (Orthoptera, Acrididae).

The genus Scelio is a cosmopolitan and speciose group of solitary parasitoids of the eggs of short-horned grasshoppers (Orthoptera: Acrididae). A number of these hosts are important pests, including plague locusts of the genus Schistocerca. Species of Scelio are recognized as potentially important biological control agents, but this possibility has yet to be fully realized, in part because the species-level taxonomy is still incompletely developed. The species of the pulchripennis group have been recently revised. As a continuation of this effort, here we revise the Afrotropical species of Scelio, excluding the pulchripennis species group. Sixty two (62) species are treated, 48 of which are new. Species are classified into the following species groups: ernstii (12 species, 9 new), howardi (23 species, 19 new), ipomeae (6 species, 5 new), irwini (4 species, 3 new), simoni (3 new species) and walkeri (12 species, 9 new). Keys to species groups and to the species within each group are provided. New species described are: S. albatus Yoder, sp. n., S. aphares Yoder, sp. n., S. apospastos Yoder, sp. n., S. ardelio Yoder, sp. n., S. aurantium Yoder, sp. n., S. balo Valerio & Yoder, sp. n., S. bayanga Yoder, sp. n., S. bubulo Yoder, sp. n., S. cano Yoder, sp. n., S. clypeatus Yoder, sp. n., S. concavus Yoder, sp. n., S. copelandi Yoder, sp. n., S. crepo Yoder, sp. n., S. destico Yoder, sp. n., S. dupondi Yoder, sp. n., S. effervesco Yoder, sp. n., S. erugatus Yoder, sp. n., S. exophthalmus Yoder, sp. n., S. fremo Valerio & Yoder, sp. n., S. gemo Yoder, sp. n., S. grunnio Yoder, sp. n., S. harinhalai Yoder, sp. n., S. igland Yoder, sp. n., S. impostor Yoder, sp. n., S. irwini Yoder, sp. n., S. janseni Yoder, sp. n., S. latro Yoder, sp. n., S. memorabilis Yoder, sp. n., S. modulus Yoder, sp. n., S. mutio Yoder, sp. n., S. ntchisii Yoder, sp. n., S. parkeri Yoder, sp. n., S. phaeoprora Yoder, sp. n., S. pilosilatus Yoder, sp. n., S. pipilo Yoder, sp. n., S. quasiclypeatus Yoder, sp. n., S. retifrons Yoder, sp. n., S. ructo Yoder, sp. n., S. scomma Yoder, sp. n., S. simoni Yoder, sp. n., S. simonolus Yoder, sp. n., S. somaliensis Yoder, sp. n., S. susurro Yoder, sp. n., S. tono Yoder, sp. n., S. transtrum Yoder, sp. n., S. tritus Yoder, sp. n., S. ululo Yoder, sp. n., S. vannoorti Valerio & Yoder, sp. n. The following species are redescribed: S. afer Kieffer, S. chapmani Nixon, S. howardi Crawford, S. ipomeae Risbec, stat. n., S. mauritanicus Risbec, S. philippinensis Ashmead, S. remaudierei Ferrière, S. striatus Priesner,S. taylori Nixon, and S. zolotarevskyi Ferrière. The genus Lepidoscelio Kieffer is treated as a junior synonym of Scelio Latreille, syn. n.; its type species, Lepidoscelio fuscipennis Kieffer, 1905 is transferred to Scelio, renamed Scelio obscuripennis Johnson, nom. n. (preoccupied by Scelio fuscipennis Ashmead, 1887), and redescribed. The following additional species are transferred from Lepidoscelio to Scelio: S. cayennensis (Risbec), comb. n., S. insularis Ashmead, rev. comb., S. luteus (Cameron), comb. n., S. thoracicus Ashmead, rev. comb. Lectotypes are designated for S. africanus Risbec, S. ipomeae Risbec, S. mauritanicus Risbec, S. remaudierei Ferrière, S. sudanensis Ferrière, and S. zolotarevskyi Ferrière. Scelio gaudens Nixon is a junior synonym of Scelio striatus Priesner, syn. n.; Scelio africanus Risbec and Scelio clarus Fouts are both junior synonyms of Scelio afer Kieffer, syn. n.; Scelio sudanensis Ferrière and Scelio cheops Nixon are both junior synonyms of Scelio zolotarevskyi Ferrière, syn. n.; Scelio cahirensis Priesner is a junior synonym of Scelio mauritanicus Risbec, syn. n. The name Scelio chapmanni Nixon is an incorrect original spelling, requiring an emendation to S. chapmani. Digital versions of the identification keys are available at http://www.waspweb.org/Platygastroidea/Keys/index.htm.

A semantic model for species description applied to the ensign wasps (hymenoptera: evaniidae) of New Caledonia.

Taxonomic descriptions are unparalleled sources of knowledge of life's phenotypic diversity. As natural language prose, these data sets are largely refractory to computation and integration with other sources of phenotypic data. By formalizing taxonomic descriptions using ontology-based semantic representation, we aim to increase the reusability and computability of taxonomists' primary data. Here, we present a revision of the ensign wasp (Hymenoptera: Evaniidae) fauna of New Caledonia using this new model for species description. Descriptive matrices, specimen data, and taxonomic nomenclature are gathered in a unified Web-based application, mx, then exported as both traditional taxonomic treatments and semantic statements using the OWL Web Ontology Language. Character:character-state combinations are then annotated following the entity-quality phenotype model, originally developed to represent mutant model organism phenotype data; concepts of anatomy are drawn from the Hymenoptera Anatomy Ontology and linked to phenotype descriptors from the Phenotypic Quality Ontology. The resulting set of semantic statements is provided in Resource Description Framework format. Applying the model to real data, that is, specimens, taxonomic names, diagnoses, descriptions, and redescriptions, provides us with a foundation to discuss limitations and potential benefits such as automated data integration and reasoner-driven queries. Four species of ensign wasp are now known to occur in New Caledonia: Szepligetella levipetiolata, Szepligetella deercreeki Deans and Mikó sp. nov., Szepligetella irwini Deans and Mikó sp. nov., and the nearly cosmopolitan Evania appendigaster. A fifth species, Szepligetella sericea, including Szepligetella impressa, syn. nov., has not yet been collected in New Caledonia but can be found on islands throughout the Pacific and so is included in the diagnostic key.

Utilizing descriptive statements from the biodiversity heritage library to expand the Hymenoptera Anatomy Ontology.

Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the 'Proofer', as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction.

Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.

Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each ontology or gaps in representing each group's anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process.

Nearly complete rRNA genes from 371 Animalia: updated structure-based alignment and detailed phylogenetic analysis.

This study presents a manually constructed alignment of nearly complete rRNA genes from most animal clades (371 taxa from ~33 of the ~36 metazoan phyla), expanded from the 197 sequences in a previous study. This thorough, taxon-rich alignment, available at http://www.wsu.edu/~jmallatt/research/rRNAalignment.html and in the Dryad Repository (doi: http://dx.doi.org/10.5061/dryad.1v62kr3q), is based rigidly on the secondary structure of the SSU and LSU rRNA molecules, and is annotated in detail, including labeling of the erroneous sequences (contaminants). The alignment can be used for future studies of the molecular evolution of rRNA. Here, we use it to explore if the larger number of sequences produces an improved phylogenetic tree of animal relationships. Disappointingly, the resolution did not improve, neither when the standard maximum-likelihood method was used, nor with more sophisticated methods that partitioned the rRNA into paired and unpaired sites (stem, loop, bulge, junction), or accounted for the evolution of the paired sites. For example, no doublet model of paired-site substitutions (16-state, 16A and 16B, 7A-F, or 6A-C models) corrected the placement of any rogue taxa or increased resolution. The following findings are from the simplest, standard, ML analysis. The 371-taxon tree only imperfectly supported the bilaterian clades of Lophotrochozoa and Ecdysozoa, and this problem remained after 17 taxa with unstably positioned sequences were omitted from the analysis. The problem seems to stem from base-compositional heterogeneity across taxa and from an overrepresentation of highly divergent sequences among the newly added taxa (e.g., sequences from Cephalopoda, Rotifera, Acoela, and Myxozoa). The rogue taxa continue to concentrate in two locations in the rRNA tree: near the base of Arthropoda and of Bilateria. The approximately uncertain (AU) test refuted the monophyly of Mollusca and of Chordata, probably due to long-branch attraction of the highly divergent cephalopod and urochordate sequences out of those clades. Unlikely to be correct, these refutations show for the first time that rRNA phylogeny can support some 'wrong' clades. Along with its weaknesses, the rRNA tree has strengths: It recovers many clades that are supported by independent evidence (e.g., Metazoa, Bilateria, Hexapoda, Nonoculata, Ambulacraria, Syndermata, and Thecostraca with Malacostraca) and shows good resolution within certain groups (e.g., in Platyhelminthes, Insecta, Cnidaria). As another strength, the newly added rRNA sequences yielded the first rRNA-based support for Carnivora and Cetartiodactyla (dolphin+llama) in Mammalia, for basic subdivisions of Bryozoa ('Gymnolaemata+Stenolaemata' versus Phylactolaemata), and for Oligostraca (ostracods+branchiurans+pentastomids+mystacocarids). Future improvement could come from better sequence-evolution models that account for base-compositional heterogeneity, and from combining rRNA with protein-coding genes in phylogenetic reconstruction.

On dorsal prothoracic appendages in treehoppers (Hemiptera: Membracidae) and the nature of morphological evidence.

A spectacular hypothesis was published recently, which suggested that the "helmet" (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the "helmet" was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the "helmet" could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the "helmet"-wing homology, the relationship of the "helmet" to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the "helmet"-wing homology hypothesis as originally conceived: 1) the "helmet" actually represents T1 (excluding the fore legs); 2) the "T1 tergum" is actually the anterior dorsal area of T2; 3) the putative articulation between the "helmet" and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies.

Time to change how we describe biodiversity.

Taxonomists are arguably the most active annotators of the natural world, collecting and publishing millions of phenotype data annually through descriptions of new taxa. By formalizing these data, preferably as they are collected, taxonomists stand to contribute a data set with research potential that rivals or even surpasses genomics. Over a decade of electronic innovation and debate has initiated a revolution in the way that the biodiversity is described. Here, we opine that a new generation of semantically based digital scaffolding, presently in various stages of completeness, and a commitment by taxonomists and their colleagues to undertake this transformation, are required to complete the taxonomic revolution and critically broaden the relevance of its products.

A gross anatomy ontology for hymenoptera.

Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology, phylogenetic, taxonomic, and morphological research can be actualized. Inherent mechanisms for feedback and content delivery demonstrate the effectiveness of remote, collaborative ontology development and facilitate future refinement of the HAO.

Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction.

This study (1) uses nearly complete rRNA-gene sequences from across Metazoa (197 taxa) to reconstruct animal phylogeny; (2) presents a highly annotated, manual alignment of these sequences with special reference to rRNA features including paired sites (http://purl.oclc.org/NET/rRNA/Metazoan_alignment) and (3) tests, after eliminating as few disruptive, rogue sequences as possible, if a likelihood framework can recover the main metazoan clades. We found that systematic elimination of approximately 6% of the sequences, including the divergent or unstably placed sequences of cephalopods, arrowworm, symphylan and pauropod myriapods, and of myzostomid and nemertodermatid worms, led to a tree that supported Ecdysozoa, Lophotrochozoa, Protostomia, and Bilateria. Deuterostomia, however, was never recovered, because the rRNA of urochordates goes (nonsignificantly) near the base of the Bilateria. Counterintuitively, when we modeled the evolution of the paired sites, phylogenetic resolution was not increased over traditional tree-building models that assume all sites in rRNA evolve independently. The rRNA genes of non-bilaterians contain a higher % AT than do those of most bilaterians. The rRNA genes of Acoela and Myzostomida were found to be secondarily shortened, AT-enriched, and highly modified, throwing some doubt on the location of these worms at the base of Bilateria in the rRNA tree--especially myzostomids, which other evidence suggests are annelids instead. Other findings are marsupial-with-placental mammals, arrowworms in Ecdysozoa (well supported here but contradicted by morphology), and Placozoa as sister to Cnidaria. Finally, despite the difficulties, the rRNA-gene trees are in strong concordance with trees derived from multiple protein-coding genes in supporting the new animal phylogeny.

Predicted secondary structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): impact on sequence alignment and phylogeny estimation.

We utilize the secondary structural properties of the 28S rRNA D2-D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450-477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.

A secondary structural model of the 28S rRNA expansion segments D2 and D3 for Chalcidoid wasps (Hymenoptera: Chalcidoidea).

We analyze the secondary structure of two expansion segments (D2, D3) of the 28S ribosomal (rRNA)-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are composed of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction or regions of slipped-strand compensation. Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.