• Chiococca grandiflora (Rubiaceae), a new species from Northern Mexico

      Lorence, David H.; Van Devender, Thomas R.; Ferguson, George M.; Univ Arizona Herbarium (PENSOFT PUBL, 2018-03-02)
      The new species Chiococca grandiflora Lorence & T.Van Devender from Sinaloa and Sonora, Mexico differs from its congeners by its larger, showy white flowers in compact cymes of 3-9, and infundibuliform corollas 16-20 mm long with tubes 13-17 mm long and lobes 3-3.5 mm long. Its distribution, habitat, and relationships are outlined. The conservation status for this species is estimated to be Endangered (EN) based on IUCN Red List Criteria.
    • Developing a vocabulary and ontology for modeling insect natural history data: example data, use cases, and competency questions

      Stucky, Brian; Balhoff, James; Barve, Narayani; Barve, Vijay; Brenskelle, Laura; Brush, Matthew; Dahlem, Gregory; Gilbert, James; Kawahara, Akito; Keller, Oliver; et al. (PENSOFT PUBL, 2019-03-13)
      Insects are possibly the most taxonomically and ecologically diverse class of multicellular organisms on Earth. Consequently, they provide nearly unlimited opportunities to develop and test ecological and evolutionary hypotheses. Currently, however, large-scale studies of insect ecology, behavior, and trait evolution are impeded by the difficulty in obtaining and analyzing data derived from natural history observations of insects. These data are typically highly heterogeneous and widely scattered among many sources, which makes developing robust information systems to aggregate and disseminate them a significant challenge. As a step towards this goal, we report initial results of a new effort to develop a standardized vocabulary and ontology for insect natural history data. In particular, we describe a new database of representative insect natural history data derived from multiple sources (but focused on data from specimens in biological collections), an analysis of the abstract conceptual areas required for a comprehensive ontology of insect natural history data, and a database of use cases and competency questions to guide the development of data systems for insect natural history data. We also discuss data modeling and technology-related challenges that must be overcome to implement robust integration of insect natural history data.
    • Modifier Ontologies for frequency, certainty, degree, and coverage phenotype modifier

      Endara, Lorena; Thessen, Anne E; Cole, Heather A; Walls, Ramona; Gkoutos, Georgios; Cao, Yujie; Chong, Steven S; Cui, Hong; Univ Arizona (PENSOFT PUBL, 2018-11-28)
      Background: When phenotypic characters are described in the literature, they may be constrained or clarified with additional information such as the location or degree of expression, these terms are called "modifiers". With effort underway to convert narrative character descriptions to computable data, ontologies for such modifiers are needed. Such ontologies can also be used to guide term usage in future publications. Spatial and method modifiers are the subjects of ontologies that already have been developed or are under development. In this work, frequency (e.g., rarely, usually), certainty (e.g., probably, definitely), degree (e.g., slightly, extremely), and coverage modifiers (e.g., sparsely, entirely) are collected, reviewed, and used to create two modifier ontologies with different design considerations. The basic goal is to express the sequential relationships within a type of modifiers, for example, usually is more frequent than rarely, in order to allow data annotated with ontology terms to be classified accordingly. Method: Two designs are proposed for the ontology, both using the list pattern: a closed ordered list (i.e., five-bin design) and an open ordered list design. The five-bin design puts the modifier terms into a set of 5 fixed bins with interval object properties, for example, one_level_more/less_frequently_than, where new terms can only be added as synonyms to existing classes. The open list approach starts with 5 bins, but supports the extensibility of the list via ordinal properties, for example, more/less_frequently_than, allowing new terms to be inserted as a new class anywhere in the list. The consequences of the different design decisions are discussed in the paper. CharaParser was used to extract modifiers from plant, ant, and other taxonomic descriptions. After a manual screening, 130 modifier words were selected as the candidate terms for the modifier ontologies. Four curators/experts (three biologists and one information scientist specialized in biosemantics) reviewed and categorized the terms into 20 bins using the Ontology Term Organizer (OTO) (http://biosemantics.arizona.edu/OTO). Inter-curator variations were reviewed and expressed in the final ontologies. Results: Frequency, certainty, degree, and coverage terms with complete agreement among all curators were used as class labels or exact synonyms. Terms with different interpretations were either excluded or included using "broader synonym" or "not recommended" annotation properties. These annotations explicitly allow for the user to be aware of the semantic ambiguity associated with the terms and whether they should be used with caution or avoided. Expert categorization results showed that 16 out of 20 bins contained terms with full agreements, suggesting differentiating the modifiers into 5 levels/bins balances the need to differentiate modifiers and the need for the ontology to reflect user consensus. Two ontologies, developed using the Protege ontology editor, are made available as OWL files and can be downloaded from https://github.com/biosemantics/ontologies. Contribution: We built the first two modifier ontologies following a consensus-based approach with terms commonly used in taxonomic literature. The five-bin ontology has been used in the Explorer of Taxon Concepts web toolkit to compute the similarity between characters extracted from literature to facilitate taxon concepts alignments. The two ontologies will also be used in an ontology-informed authoring tool for taxonomists to facilitate consistency in modifier term usage.
    • A new species of Euchaetes Harris from southern Arizona (Erebidae, Arctiinae)

      Nagle, Raymond B; Schmidt, B Christian; Univ Arizona, Dept Pathol (PENSOFT PUBL, 2018-10-08)
      Euchaetes nancyae sp. n. is described from southeastern Arizona. Although superficially similar to species of Pygarctia Grote, structural and molecular variation shows it to be most closely related to Euchaetes helena (Cassino). Adults, genitalic structure, e s, and first instar larvae are described and illustrated. The larval host plant remains unknown. Euchaetes helena is confirmed as occurring in Mexico.
    • A new species of Hypoprepia from the mountains of central Arizona (Lepidoptera, Erebidae, Arctiinae, Lithosiini)

      Palting, John Douglas; Ferguson, Douglas C; Moore, Wendy; Univ Arizona, Grad Interdisciplinary Program Entomol & Insect S; Univ Arizona, Dept Entomol (PENSOFT PUBL, 2018-10-08)
      A new firefly-mimicking lichen moth of the genus Hypoprepia, H.lampyroides Palting & Ferguson, sp. n., is described from the mountains of east-central Arizona and the Sierra Madre Occidental of Mexico. Hypoprepia Hübner, 1831 is a North American genus of lithosiine tiger moths, previously consisting of five species: H.fucosa Hübner, 1831 and H.miniata (Kirby, 1837), both of eastern and central North America; H.cadaverosa Strecker, 1878 from the Rocky Mountains into New Mexico and west Texas; H.inculta H. Edwards, 1882, a widespread western USA species and H.muelleri Dyar, 1907 from the vicinity of Mexico City. The latter is herein synonymized under H.inculta (= H.muellerisyn. n.), resulting in the total number of taxa in the genus unchanged at five.
    • Provenance of invaders has scale-dependent impacts in a changing wetland ecosystem

      Amatangelo, Kathryn L.; Stevens, Lee; Wilcox, Douglas A.; Jackson, Stephen T.; Sax, Dov F.; Amatangelo, Kathryn L.; Stevens, Lee; Wilcox, Douglas A.; Jackson, Stephen T.; Sax, Dov F.; et al. (PENSOFT PUBL, 2019-11-19)
      Exotic species are associated with a variety of impacts on biodiversity, but it is unclear whether impacts of exotic specks differ from those of native species with similar growth forms or native species invading disturbed sites. We compared presence and abundance of native and exotic invaders with changes in wetland plant species diversity over a 28-year period by re-surveying 22 ponds to identify factors correlated with observed changes. We also compared communities found within dense patches of native and exotic emergent species with similar habits. Within patches, we found no categorical diversity differences between areas dominated by native or exotic emergent species. At the pond scale, the cover of the exotic grass Phragmites australis best predicted change in diversity and evenness over time, likely owing to its significant increase in coverage over the study period. These changes in diversity and evenness were strongest in younger, less successionally-advanced ponds. Changes associated with cover of P. australis in these ponds were not consistent with expected diversity decreases, but instead with a dampening of diversity gains, such that the least-invaded ponds increased in diversity the most over the study period. There were more mixed effects on evenness, ranging from a reduction in evenness gains to actual losses of evenness in the ponds with highest invader cover. In this wetland complex, the habit, origin and invasiveness of species contribute to diversity responses in a scale- and context-dependent fashion. Future efforts to preserve diversity should focus on preventing the arrival and spread of invaders that have the potential to cover large areas at high densities, regardless of their origin. Future studies should also investigate more thoroughly how changes in diversity associated with species invasions are impacted by other ongoing ecosystem changes.
    • Resolving "orphaned" non-specific structures using machine learning and natural language processing methods

      Xu, Dongfang; Chong, Steven S; Rodenhausen, Thomas; Cui, Hong; Univ Arizona (PENSOFT PUBL, 2018-08-10)
      Scholarly publications of biodiversity literature contain a vast amount of information in human readable format. The detailed morphological descriptions in these publications contain rich information that can be extracted to facilitate analysis and computational biology research. However, the idiosyncrasies of morphological descriptions still pose a number of challenges to machines. In this work, we demonstrate the use of two different approaches to resolve meronym (i.e. part-of) relations between anatomical parts and their anchor organs, including a syntactic rule-based approach and a SVM-based (support vector machine) method. Both methods made use of domain ontologies. We compared the two approaches with two other baseline methods and the evaluation results show the syntactic methods (92.1% F1 score) outperformed the SVM methods (80.7% F1 score) and the part-of ontologies were valuable knowledge sources for the task. It is notable that the mistakes made by the two approaches rarely overlapped. Additional tests will be conducted on the development version of the Explorer of Taxon Concepts toolkit before we make the functionality publicly available. Meanwhile, we will further investigate and leverage the complementary nature of the two approaches to further drive down the error rate, as in practical application, even a 1% error rate could lead to hundreds of errors.
    • The smallest 'true chameleon' from Madagascar: a new, distinctly colored species of the Calumma boettgeri complex (Squamata, Chamaeleonidae)

      Prötzel, David; Lambert, Shea M.; Andrianasolo, Ginah Tsiorisoa; Hutter, Carl R.; Cobb, Kerry A.; Scherz, Mark D.; Glaw, Frank; Univ Arizona, Dept Ecol & Evolut Biol (PENSOFT PUBL, 2018-10-19)
      On a recent expedition to eastern Madagascar, we discovered a distinct new species of the genus Calumma that we describe here using an integrative approach combining morphology, coloration, osteology and molecular genetics. Calumma roaloko sp. n. has a dermal rostral appendage and occipital lobes, and belongs to the C. boettgeri complex, within the Madagascar-endemic phenetic C. nasutum species group. It is readily distinguished from other species of the C. boettgeri complex by a characteristic two-toned body coloration and small body size with a snout-vent length of 45.6 mm in an adult male. The osteology of the skull, with a prominent maxilla and broad parietal, is similar to the closest related species, C. uetzi. Analysis of uncorrected genetic distances within the C. nasutum group using the mitochondrial gene ND2 shows a minimum pairwise distance of 11.98% to C. uetzi from the Sorata massif and Marojejy National Park >500 km north of the type locality of C. roaloko sp. n.. Given an apparently small range (potentially <300 km(2)), located entirely outside of any nationally-protected areas, we recommend this new species be classified as Endangered under criterion B1ab(iii) of the IUCN Red List. The discovery of clearly distinct species like C. roaloko sp. n. in an area of Madagascar that is comparatively thoroughly surveyed highlights the critical role of continued field surveys for understanding the true extent of Madagascar's spectacular biodiversity.