Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.

An earliest Triassic age for Tasmaniolimulus and comments on synchrotron tomography of Gondwanan horseshoe crabs

Constraining the timing of morphological innovations within xiphosurid evolution is central for understanding when and how such a long-lived group exploited vacant ecological niches over the majority of the Phanerozoic. To expand the knowledge on the evolution of select xiphosurid forms, we reconsider the four Australian taxa: Austrolimulus fletcheri, Dubbolimulus peetae, Tasmaniolimulus patersoni, and Victalimulus mcqueeni. In revisiting these taxa, we determine that, contrary to previous suggestion, T. patersoni arose after the Permian and the origin of over-developed genal spine structures within Austrolimulidae is exclusive to the Triassic. To increase the availability of morphological data pertaining to these unique forms, we also examined the holotypes of the four xiphosurids using synchrotron radiation X-ray tomography (SRXT). Such non-destructive, in situ imaging of palaeontological specimens can aid in the identification of novel morphological data by obviating the need for potentially extensive preparation of fossils from the surrounding rock matrix. This is particularly important for rare and/or delicate holotypes. Here, SRXT was used to emphasize A. fletcheri and T. patersoni cardiac lobe morphologies and illustrate aspects of the V. mcqueeni thoracetronic doublure, appendage impressions, and moveable spine notches. Unfortunately, the strongly compacted D. peetae precluded the identification of any internal structures, but appendage impressions were observed. The application of computational fluid dynamics to high-resolution 3D reconstructions are proposed to understand the hydrodynamic properties of divergent genal spine morphologies of austrolimulid xiphosurids.

Total-evidence dating and morphological partitioning: a novel approach to understand the phylogeny and biogeography of augochlorine bees (Hymenoptera: Apoidea)

Augochlorini comprise 646 described bee species primarily distributed in the Neotropical region. According to molecular and morphological phylogenies, the tribe is monophyletic and subdivided into seven genus groups. Our main objective is to propose a revised phylogeny of Augochlorini based on a comprehensive data set including fossil species as terminals and new characters from the internal skeleton. We also aim to develop a total-evidence framework incorporating a morphological-partitioned homoplasy approach and molecular data and propose a detailed biogeographic and evolutionary scenario based on ancestor range estimation. Our results recovered Augochlorini and most genus groups as monophyletic, despite some uncertainties about monophyly of the Megalopta and Neocorynura groups. The position of the cleptoparasite Temonosoma is still uncertain. All analyses recovered Augochloropsis s.l. as related to the Megaloptidia group. Internal characters from the head, mesosoma and sting apparatus provided important synapomorphies for most internal nodes, genus groups and genera. Augochlorini diversification occurred in the uplands of the Neotropical region, especially the Brazilian Plateau. Multiple dispersals to Amazonia, Central America and North America with returns to the Atlantic endemism area were recovered in our analysis. Total evidence, including morphological partitioning, was shown to be a reliable approach for phylogenetic reconstruction.

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.

Contribution to understanding the evolution of holometaboly: transformation of internal head structures during the metamorphosis in the green lacewing Chrysopa pallens (Neuroptera: Chrysopidae)

BACKGROUND

Metamorphosis remains one of the most complicated and poorly understood processes in insects. This is particularly so for the very dynamic transformations that take place within the pupal sheath of holometabolous insects. Only few studies address these transformations especially with regard to cranial structures of those holometabolous species where the larval and adult forms have a similar diet. It thus remains unclear to what extent the internal structures undergo histolysis and rebuilding. Here, the development of the brain and skeleto-muscular system of the head of Chrysopa pallens (Rambur, 1838) is studied. This species is a predator of aphids in the larval and adult stage.

RESULTS

We used micro-computed-tomography (μ-CT) to study the transformations of the larval, prepupal and pupal head within the cocoon. We first assessed the morphological differences and similarities between the stages. We then determined the point in time when the compound eyes appear and describe the re-orientation of the head capsule which transforms the prognathous larva into a hypognathous adult. The internal head muscles are distinctly more slender in larvae than adults. In addition, the adults have a significantly larger brain which is likely needed for the processing of the signals obtained by the adults vastly expanded sensory organs that are presumably needed for dispersal and mating. Our study shows that the histolysis and modification of the inner muscles and skeletal elements take place within the prepupa. The central nervous system persists throughout metamorphosis but its morphology changes significantly.

CONCLUSION

Our study reveals that not only the inner structures, but also the outer morphology continues to change after the final larval moult. The adult cuticle and internal structures form gradually within the cocoon. The histolysis and rebuilding begin with the skeletal elements and is followed by changes in the central nervous system before it concludes with modifications of the musculature. This order of events is likely ancestral for Holometabola because it is also known from Hymenoptera, Diptera, Mecoptera, and Coleoptera.

Evolutionary transformation of mouthparts from particle-feeding to piercing carnivory in Viper copepods: Review and 3D analyses of a key innovation using advanced imaging techniques

BACKGROUND

Novel feeding adaptations often facilitate adaptive radiation and diversification. But the evolutionary origins of such feeding adaptations can be puzzling if they require concordant change in multiple component parts. Pelagic, heterorhabdid copepods (Calanoida) exhibit diverse feeding behaviors that range from simple particle feeding to a highly specialized form of carnivory involving piercing mouthparts that likely inject venom. We review the evolutionary history of heterorhabdid copepods and add new high-resolution, 3D anatomical analyses of the muscular system, glands and gland openings associated with this remarkable evolutionary transformation.

RESULTS

We examined four heterorhabdid copepods with different feeding modes: one primitive particle-feeder (Disseta palumbii), one derived and specialized carnivore (Heterorhabdus subspinifrons), and two intermediate taxa (Mesorhabdus gracilis and Heterostylites longicornis). We used two advanced, high-resolution microscopic techniques - serial block-face scanning electron microscopy and two-photon excitation microscopy - to visualize mouthpart form and internal anatomy at unprecedented nanometer resolution. Interactive 3D graphical visualizations allowed putative homologues of muscles and gland cells to be identified with confidence and traced across the evolutionary transformation from particle feeding to piercing carnivory. Notable changes included: a) addition of new gland cells, b) enlargement of some (venom producing?) glands, c) repositioning of gland openings associated with hollow piercing fangs on the mandibles, d) repurposing of some mandibular-muscle function to include gland-squeezing, and e) addition of new muscles that may aid venom injection exclusively in the most specialized piercing species. In addition, live video recording of all four species revealed mandibular blade movements coupled to cyclic contraction of some muscles connected to the esophagus. These behavioral and 3D morphological observations revealed a novel injection system in H. subspinifrons associated with piercing (envenomating?) carnivory.

CONCLUSIONS

Collectively, these results suggest that subtle changes in mandibular tooth form, and muscle and gland form and location, facilitated the evolution of a novel, piercing mode of feeding that accelerated diversification of the genus Heterorhabdus. They also highlight the value of interactive 3D animations for understanding evolutionary transformations of complex, multicomponent morphological systems.

A comparative study of the pharyngeal plate of Apoidea (Hymenoptera: Aculeata), with implications for the understanding of phylogenetic relationships of bees

The pharyngeal plate is a morphological complex with extensive anatomical variation among bees and, therefore, potential as a source of phylogenetic information. The pharyngeal plate of bees is divided into four morphologically distinct regions: sitophore, hypopharyngeal lobe, pharyngeal rods, and median oral plate. In this work we illustrate and document in detail for the first time the pharyngeal plate of 43 bee species, providing descriptions of the morphological variation and contrasting these findings with representatives of apoid wasps (Crabronidae and Sphecidae). We evaluate and discuss the potential of this structure as a rich source of morphological information in the context of bee phylogeny and any research potentially impacted by comparative morphological data. The shape of the hypopharyngeal lobe is highly variable among suprageneric taxa of bees and can be readily employed to characterise taxa at various levels. We argue that the global patterns in the variation of the pharyngeal plate can provide information for phylogenetic inference within bees and constructed and coded 10 characters that encompass the most noticeable morphological differences discussed herein.

The effect of automated landmark identification on morphometric analyses

Morphometric analysis of anatomical landmarks allows researchers to identify specific morphological differences between natural populations or experimental groups, but manually identifying landmarks is time-consuming. We compare manually and automatically generated adult mouse skull landmarks and subsequent morphometric analyses to elucidate how switching from manual to automated landmarking will impact morphometric analysis results for large mouse (Mus musculus) samples (n = 1205) that represent a wide range of 'normal' phenotypic variation (62 genotypes). Other studies have suggested that the use of automated landmarking methods is feasible, but this study is the first to compare the utility of current automated approaches to manual landmarking for a large dataset that allows the quantification of intra- and inter-strain variation. With this unique sample, we investigated how switching to a non-linear image registration-based automated landmarking method impacts estimated differences in genotype mean shape and shape variance-covariance structure. In addition, we tested whether an initial registration of specimen images to genotype-specific averages improves automatic landmark identification accuracy. Our results indicated that automated landmark placement was significantly different than manual landmark placement but that estimated skull shape covariation was correlated across methods. The addition of a preliminary genotype-specific registration step as part of a two-level procedure did not substantially improve on the accuracy of one-level automatic landmark placement. The landmarks with the lowest automatic landmark accuracy are found in locations with poor image registration alignment. The most serious outliers within morphometric analysis of automated landmarks displayed instances of stochastic image registration error that are likely representative of errors common when applying image registration methods to micro-computed tomography datasets that were initially collected with manual landmarking in mind. Additional efforts during specimen preparation and image acquisition can help reduce the number of registration errors and improve registration results. A reduction in skull shape variance estimates were noted for automated landmarking methods compared with manual landmarking. This partially reflects an underestimation of more extreme genotype shapes and loss of biological signal, but largely represents the fact that automated methods do not suffer from intra-observer landmarking error. For appropriate samples and research questions, our image registration-based automated landmarking method can eliminate the time required for manual landmarking and have a similar power to identify shape differences between inbred mouse genotypes.

Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Systematic Review of Applications, Tools, and Protocols

Background

The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians.

Objective

The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology.

Methods

A systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art.

Results

The search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface.

Conclusions

The use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.

Systematics of the ant genus Proceratium Roger (Hymenoptera, Formicidae, Proceratiinae) in China - with descriptions of three new species based on micro-CT enhanced next-generation-morphology

The genus Proceratium Roger, 1863 contains cryptic, subterranean ants that are seldom sampled and rare in natural history collections. Furthermore, most Proceratium specimens are extremely hairy and, due to their enlarged and curved gaster, often mounted suboptimally. As a consequence, the poorly observable physical characteristics of the material and its scarcity result in a rather challenging alpha taxonomy of this group. In this study, the taxonomy of the Chinese Proceratium fauna is reviewed and updated by combining examinations of traditional light microscopy with x-ray microtomography (micro-CT). Based on micro-CT scans of seven out of eight species, virtual 3D surface models were generated that permit in-depth comparative analyses of specimen morphology in order to overcome the difficulties to examine physical material of Proceratium. Eight Chinese species are recognized, of which three are newly described: Proceratium bruelheidei Staab, Xu & Hita Garcia, sp. n. and P. kepingmaisp. n. belong to the P. itoi clade and have been collected in the subtropical forests of southeast China, whereas P. shoheisp. n. belongs to the P. stictum clade and it is only known from a tropical forest of Yunnan Province. Proceratium nujiangense Xu, 2006 syn. n. is proposed as a junior synonym of P. zhaoi Xu, 2000. These taxonomic acts raise the number of known Chinese Proceratium species to eight. In order to integrate the new species into the existing taxonomic system and to facilitate identifications, an illustrated key to the worker caste of all Chinese species is provided, supplemented by species accounts with high-resolution montage images and still images of volume renderings of 3D models based on micro-CT. Moreover, cybertype datasets are provided for the new species, as well as digital datasets for the remaining species that include the raw micro-CT scan data, 3D surface models, 3D rotation videos, and all light photography and micro-CT still images. These datasets are available online (Dryad, Staab et al. 2018, http://dx.doi.org/10.5061/dryad.h6j0g4p).

A 3D anatomical atlas of appendage musculature in the chelicerate arthropod Limulus polyphemus

Limulus polyphemus, an archetypal chelicerate taxon, has interested both biological and paleontological researchers due to its unique suite of anatomical features and as a useful modern analogue for fossil arthropod groups. To assist the study and documentation of this iconic taxon, we present a 3D atlas on the appendage musculature, with specific focus on the muscles of the cephalothoracic appendages. As L. polyphemus appendage musculature has been the focus of extensive study, depicting the muscles in 3D will facilitate a more complete understanding thereof for future researchers. A large museum specimen was CT scanned to illustrate the major exoskeletal features of L. polyphemus. Micro-CT scans of iodine-stained appendages from fresh, non-museum specimens were digitally dissected to interactively depict appendage sections and muscles. This study has revealed the presence of two new muscles: one within the pushing leg, located dorsally relative to all other patella muscles, and the other within the male pedipalp, located in the modified tibiotarsus. This atlas increases accessibility to important internal and external morphological features of L. polyphemus and reduces the need for destructive fresh tissue dissection of specimens. Scanning, digitally dissecting, and documenting taxa in 3D is a pivotal step towards creating permanent digital records of life on Earth.

Entomological Collections in the Age of Big Data

With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.

Malagasy Conostigmus (Hymenoptera: Ceraphronoidea) and the secret of scutes

We revise the genus Conostigmus Dahlbom 1858 occurring in Madagascar, based on data from more specimens than were examined for the latest world revision of the genus. Our results yield new information about intraspecific variability and the nature of the atypical latitudinal diversity gradient (LDG) observed in Ceraphronoidea. We also investigate cellular processes that underlie body size polyphenism, by utilizing the correspondence between epidermal cells and scutes, polygonal units of leather-like microsculpture. Our results reveal that body size polyphenism in Megaspilidae is most likely related to cell number and not cell size variation, and that cell size differs between epithelial fields of the head and that of the mesosoma. Three species, Conostigmus ballescoracas Dessart, 1997, C. babaiax Dessart, 1996 and C. longulus Dessart, 1997, are redescribed. Females of C. longulus are described for the first time, as are nine new species: C. bucephalus Mikó and Trietsch sp. nov., C. clavatus Mikó and Trietsch sp. nov., C. fianarantsoaensis Mikó and Trietsch sp. nov., C. lucidus Mikó and Trietsch sp. nov., C. macrocupula, Mikó and Trietsch sp. nov., C. madagascariensis Mikó and Trietsch sp. nov., C. missyhazenae Mikó and Trietsch sp. nov., C. pseudobabaiax Mikó and Trietsch sp. nov., and C. toliaraensis Mikó and Trietsch sp. nov. A fully illustrated identification key for Malagasy Conostigmus species and a Web Ontology Language (OWL) representation of the taxonomic treatment, including specimen data, nomenclature, and phenotype descriptions, in both natural and formal languages, are provided.

The rapidly changing landscape of insect phylogenetics

Insect phylogenetics is being profoundly changed by many innovations. Although rapid developments in genomics have center stage, key progress has been made in phenomics, field and museum science, digital databases and pipelines, analytical tools, and the culture of science. The importance of these methodological and cultural changes to the pace of inference of the hexapod Tree of Life is discussed. The innovations have the potential, when synthesized and mobilized in ways as yet unforeseen, to shine light on the million or more clades in insects, and infer their composition with confidence. There are many challenges to overcome before insects can enter the 'phylocognisant age', but because of the promise of genomics, phenomics, and informatics, that is now an imaginable future.

Mesoscale morphology at nanoscale resolution: serial block-face scanning electron microscopy reveals fine 3D detail of a novel silk spinneret system in a tube-building tanaid crustacean

Background

The study of morphology is experiencing a renaissance due to rapid improvements in technologies for 3D visualization of complex internal and external structures. But 3D visualization of the internal structure of mesoscale objects — those in the 10–1000 μm range — remains problematic. They are too small for microCT, many lack suitable specific fluorescent markers for confocal microscopy, or they require labor-intensive stacking and smoothing of individual TEM images. Here we illustrate the first comprehensive morphological description of a complete mesoscale biological system at nanoscopic resolution using ultra-modern technology for 3D visualization — serial block-face scanning electron microscopy (SBF-SEM). The SBF-SEM machine combines an in-chamber ultramicrotome, which creates a serial array of exposed surfaces, with an SEM that images each surface as it is exposed. The serial images are then stacked automatically by 3D reconstruction software. We used SBF-SEM to study the spinneret (thread-producing) system of a small, tube-dwelling crustacean that weaves tubes of silk. Thread-producing ability is critical for the survival of many small-bodied animals but the basic morphology of these systems remains mysterious due to the limits of traditional microscopy.

Results

SBF-SEM allowed us to describe — in full 3D — well-resolved components (glands, ducts, pores, and associated nerves and muscles) of the spinneret system in the thoracic legs and body segments of Sinelobus sp. (Crustacea, Peracarida, Tanaidacea), a tube-building tanaid only 2 mm in body length. The 3D reconstruction by SBF-SEM revealed at nanoscale resolution a unique structure to the gland and duct systems: In each of three thread-producing thoracic segments, two separate ducts, derived from two separate glands located in the body, run through the entire leg and merge at the leg tip just before the spinneret pore opening. We also resolved nerves connecting to individual setae, spines and pores on the walking legs, and individual muscles within each leg segment.

Conclusions

Our results significantly expand our understanding of the diversity of spinneret systems in the Crustacea by providing the first well-resolved view of spinneret components in the peracarid crustacean order, Tanaidacea. More significantly, our results reveal the great power of SBF-SEM technology for comprehensive studies of the morphology of microscopic animals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12983-016-0146-0) contains supplementary material, which is available to authorized users.

The need for data standards in zoomorphology

eScience is a new approach to research that focuses on data mining and exploration rather than data generation or simulation. This new approach is arguably a driving force for scientific progress and requires data to be openly available, easily accessible via the Internet, and compatible with each other. eScience relies on modern standards for the reporting and documentation of data and metadata. Here, we suggest necessary components (i.e., content, concept, nomenclature, format) of such standards in the context of zoomorphology. We document the need for using data repositories to prevent data loss and how publication practice is currently changing, with the emergence of dynamic publications and the publication of digital datasets. Subsequently, we demonstrate that in zoomorphology the scientific record is still limited to published literature and that zoomorphological data are usually not accessible through data repositories. The underlying problem is that zoomorphology lacks the standards for data and metadata. As a consequence, zoomorphology cannot participate in eScience. We argue that the standardization of morphological data requires i) a standardized framework for terminologies for anatomy and ii) a formalized method of description that allows computer-parsable morphological data to be communicable, compatible, and comparable. The role of controlled vocabularies (e.g., ontologies) for developing respective terminologies and methods of description is discussed, especially in the context of data annotation and semantic enhancement of publications. Finally, we introduce the International Consortium for Zoomorphology Standards, a working group that is open to everyone and whose aim is to stimulate and synthesize dialog about standards. It is the Consortium's ultimate goal to assist the zoomorphology community in developing modern data and metadata standards, including anatomy ontologies, thereby facilitating the participation of zoomorphology in eScience.