Matthew A. Bertone

Episodic radiations in the fly tree of life

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation—lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)—and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y.

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.

Phylogenetic analysis and temporal diversification of mosquitoes (Diptera: Culicidae) based on nuclear genes and morphology

BackgroundPhylogenetic analyses provide a framework for examining the evolution of morphological and molecular diversity, interpreting patterns in biogeography, and achieving a stable classification. The generic and suprageneric relationships within mosquitoes (Diptera: Culicidae) are poorly resolved, making these subjects difficult to address.ResultsWe carried out maximum parsimony and maximum likelihood, including Bayesian, analyses on a data set consisting of six nuclear genes and 80 morphological characters to assess their ability to resolve relationships among 25 genera. We also estimated divergence times based on sequence data and fossil calibration points, using Bayesian relaxed clock methods. Strong support was recovered for the basal position and monophyly of the subfamily Anophelinae and the tribes Aedini and Sabethini of subfamily Culicinae. Divergence times for major culicid lineages date to the early Cretaceous.ConclusionsDeeper relationships within the family remain poorly resolved, suggesting the need for additional taxonomic sampling. Our results support the notion of rapid radiations early in the diversification of mosquitoes.

Phylogenetics and temporal diversification of the earliest true flies (Insecta: Diptera) based on multiple nuclear genes

Abstract Relationships among families of the lower Diptera (formerly suborder ‘Nematocera’) have been exceptionally difficult to resolve. Multiple hypotheses based on morphology have been proposed to identify the earliest lineages of flies and place the phylogenetic origin of the higher flies (Brachycera), but convincing support is limited. Here we resolve relationships among the major groups of lower Diptera using sequence data from four nuclear markers, including both ribosomal (28S rDNA) and protein‐coding (CAD, TPI and PGD) genes. Our results support both novel and traditional arrangements. Most unexpectedly, the small, highly‐specialized family Deuterophlebiidae appears to be sister to all remaining Diptera. Other results include the resolution of the traditional infra‐orders Culicomorpha (including a novel superfamily Simulioidea = Thaumaleidae + Simuliidae), Tipulomorpha (Tipulidae sensu lato + Trichoceridae) and Bibionomorpha sensu lato. We find support for a limited Psychodomorpha (Blephariceridae, Tanyderidae and Psychodidae) and Ptychopteromorpha (Ptychopteridae), whereas the placement of several enigmatic families (Nymphomyiidae, Axymyiidae and Perissommatidae) remains ambiguous. According to genetic data, the infra‐order Bibionomorpha is sister to the Brachycera. Much of the phylogenetic signal for major lineages was found in the 28S rDNA gene, whereas protein‐coding genes performed variably at different levels. In addition to elucidating relationships, we also estimate the age of major lower dipteran clades, based on molecular divergence time estimates using relaxed‐clock Bayesian methods and fossil calibration points.

Phylogenetic synthesis of morphological and molecular data reveals new insights into the higher-level classification of Tipuloidea (Diptera)

Tipuloidea, the crane flies, are a diverse lineage of true flies (Insecta: Diptera) whose phylogenetic classification and taxonomy remain a challenge. Here we present the results of a quantitative phylogenetic analysis of Tipuloidea based on combined morphological characters (adult, larvae and pupae) and nuclear gene sequence data (28S rDNA and CAD). Forty‐five species, from 44 genera and subgenera, were sampled, representing the four putative families of Tipuloidea (Cylindrotomidae, Limoniidae, Pediciidae and Tipulidae sensu stricto). Analyses of individual datasets, although differing in overall topology, support the monophyly of several major lineages within Tipuloidea. Parsimony and Bayesian analyses using individual morphological and molecular datasets resulted in incongruent topologies. Increased resolution and tree support was obtained when both datasets (morphology and genes) were combined, in both combined evidence parsimony and Bayesian analyses, than when analysed separately. The recovered consensus phylogeny was not consistent with any previously proposed Tipuloidea classification, with previous importance assigned to character states shown here to represent losses and reversals seen as a major factor influencing erroneous classification. The results provided here, together with evidence from previous analyses, were used to append the Tipuloidea classification to supported evolutionary lineages. Tipuloidea is presented as two families: Pediciidae and Tipulidae. Pediciidae is recovered as the sister group to all remaining Tipuloidea. Our current phylogenetic hypothesis is not consistent with the existing subfamilial classification of the ‘Limoniidae’, which is paraphyletic with respect to a well‐supported Tipulinae + Cylindrotominae clade, whereas the three ‘limoniid’ subfamilies are para‐ or polyphyletic. The recognition of ‘Limoniidae’ as a valid monophyletic family is discouraged and the subfamilies of ‘Limoniidae’ are amended and placed within Tipulidae. A revised phylogenetic classification is proposed for the crane flies based on a synthesis of evidence from multiple genes and morphology.

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.

Results and insights from the NCSU Insect Museum GigaPan project.

Abstract Pinned insect specimens stored in museum collections are a fragile and valuable resource for entomological research. As such, they are usually kept away from viewing by the public and hard to access by experts. Here we present a method for mass imaging insect specimens, using GigaPan technology to achieve highly explorable, many-megapixel panoramas of insect museum drawers. We discuss the advantages and limitations of the system, and describe future avenues of collections research using this technology.

Arthropods of the great indoors: characterizing diversity inside urban and suburban homes

Although humans and arthropods have been living and evolving together for all of our history, we know very little about the arthropods we share our homes with apart from major pest groups. Here we surveyed, for the first time, the complete arthropod fauna of the indoor biome in 50 houses (located in and around Raleigh, North Carolina, USA). We discovered high diversity, with a conservative estimate range of 32–211 morphospecies, and 24–128 distinct arthropod families per house. The majority of this indoor diversity (73%) was made up of true flies (Diptera), spiders (Araneae), beetles (Coleoptera), and wasps and kin (Hymenoptera, especially ants: Formicidae). Much of the arthropod diversity within houses did not consist of synanthropic species, but instead included arthropods that were filtered from the surrounding landscape. As such, common pest species were found less frequently than benign species. Some of the most frequently found arthropods in houses, such as gall midges (Cecidomyiidae) and book lice (Liposcelididae), are unfamiliar to the general public despite their ubiquity. These findings present a new understanding of the diversity, prevalence, and distribution of the arthropods in our daily lives. Considering their impact as household pests, disease vectors, generators of allergens, and facilitators of the indoor microbiome, advancing our knowledge of the ecology and evolution of arthropods in homes has major economic and human health implications.

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. Database URL: http://purl.obolibrary.org/obo/hao/2012-07-18/arthropod-mappings.obo