Keith M. Bayless

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.

The evolution and biogeography of the austral horse fly tribe Scionini (Diptera: Tabanidae: Pangoniinae) inferred from multiple mitochondrial and nuclear genes.

Phylogenetic relationships within the Tabanidae are largely unknown, despite their considerable medical and ecological importance. The first robust phylogenetic hypothesis for the horse fly tribe Scionini is provided, completing the systematic placement of all tribes in the subfamily Pangoniinae. The Scionini consists of seven mostly southern hemisphere genera distributed in Australia, New Guinea, New Zealand and South America. A 5757 bp alignment of 6 genes, including mitochondrial (COI and COII), ribosomal (28S) and nuclear (AATS and CAD regions 1, 3 and 4) genes, was analysed for 176 taxa using both Bayesian and maximum likelihood approaches. Results indicate the Scionini are strongly monophyletic, with the exclusion of the only northern hemisphere genus Goniops. The South American genera Fidena, Pityocera and Scione were strongly monophyletic, corresponding to current morphology-based classification schemes. The most widespread genus Scaptia was paraphyletic and formed nine strongly supported monophyletic clades, each corresponding to either the current subgenera or several previously synonymised genera that should be formally resurrected. Molecular results also reveal a newly recognised genus endemic to New Zealand, formerly placed within Scaptia. Divergence time estimation was employed to assess the global biogeographical patterns in the Pangoniinae. These analyses demonstrated that the Scionini are a typical Gondwanan group whose diversification was influenced by the fragmentation of that ancient land mass. Furthermore, results indicate that the Scionini most likely originated in Australia and subsequently radiated to New Zealand and South American by both long distance dispersal and vicariance. The phylogenetic framework of the Scionini provided herein will be valuable for taxonomic revisions of the Tabanidae.

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.

Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera): Diptera evolution and supermatrix

Early diverging brachyceran fly lineages underwent a rapid radiation approximately 180 Ma, coincident in part with the origin of flowering plants. This region of the fly tree includes 25 000 described extant species with diverse ecological roles such as blood‐feeding (haematophagy), parasitoidism, predation, pollination and wood‐feeding (xylophagy). Early diverging brachyceran lineages were once considered a monophyletic group of families called Orthorrhapha, based on the shared character of a longitudinal break in the pupal skin made during the emergence of the adult. Yet other morphological and molecular evidence generally supports a paraphyletic arrangement of ‘Orthorrhapha’, with strong support for one orthorrhaphan lineage – dance flies and relatives – as the closest relative to all higher flies (Cyclorrhapha), together called Eremoneura. In order to establish a comprehensive estimate of the relationships among orthorrhaphan lineages using a thorough sample of publicly available data, we compiled and analysed a dataset including 1217 taxa representing major lineages and 20 molecular markers. Our analyses suggest that ‘Orthorrhapha’ excluding Eremoneura is not monophyletic; instead, we recover two main lineages of early brachyceran flies: Homeodactyla and Heterodactyla. Homeodactyla includes Nemestrinoidea (uniting two parasitic families Acroceridae + Nemestrinidae) as the closest relatives to the large SXT clade, comprising Stratiomyomorpha, Xylophagidae and Tabanomorpha. Heterodactyla includes Bombyliidae with a monophyletic Asiloidea (exclusive of Bombyliidae) as the closest relatives to Eremoneura. Reducing missing data, modifying the distribution of genes across taxa, and, in particular, removing rogue taxa significantly improved tree resolution and statistical support. Although our analyses rely on dense taxonomic sampling and substantial gene coverage, our results pinpoint the limited resolving power of Sanger sequencing‐era molecular phylogenetic datasets with respect to ancient, hyperdiverse radiations.

Exoskeletons and economics: indoor arthropod diversity increases in affluent neighbourhoods

In urban ecosystems, socioeconomics contribute to patterns of biodiversity. The ‘luxury effect’, in which wealthier neighbourhoods are more biologically diverse, has been observed for plants, birds, bats and lizards. Here, we used data from a survey of indoor arthropod diversity (defined throughout as family-level richness) from 50 urban houses and found that house size, surrounding vegetation, as well as mean neighbourhood income best predict the number of kinds of arthropods found indoors. Our finding, that homes in wealthier neighbourhoods host higher indoor arthropod diversity (consisting of primarily non-pest species), shows that the luxury effect can extend to the indoor environment. The effect of mean neighbourhood income on indoor arthropod diversity was particularly strong for individual houses that lacked high surrounding vegetation ground cover, suggesting that neighbourhood dynamics can compensate for local choices of homeowners. Our work suggests that the management of neighbourhoods and cities can have effects on biodiversity that can extend from trees and birds all the way to the arthropod life in bedrooms and basements.

New data, same story: phylogenomics does not support Syrphoidea (Diptera: Syrphidae, Pipunculidae): Syrphoidea are not supported by new data

The Syrphoidea (families Pipunculidae and Syrphidae) has been suggested to be the sister group of the Schizophora, the largest species radiation of true flies. A major challenge in dipterology is inferring the phylogenetic relationship between Syrphoidea and Schizophora in order to understand the evolutionary history of flies. Using newly sequenced transcriptomic data of Syrphidae, Pipunculidae and closely related lineages, we were able to fully resolve phylogenetic relationships of Syrphoidea using a supermatrix approach with more than 1 million amino acid positions derived from 3145 genes, including 19 taxa across nine families. Platypezoidea were inferred as a sister group to Eumuscomorpha, which was recovered monophyletic. While Syrphidae were also found to be monophyletic, the superfamily Syrphoidea was not recovered as a monophyletic group, as Pipunculidae were inferred as sister group to Schizophora. Within Syrphidae, the subfamily Microdontinae was resolved as sister group to the remaining taxa, Syrphinae and Pipizinae were placed as sister groups, and the monophyly of Eristalinae was not recovered. Although our results are consistent with previously established hypotheses on Eumuscomorphan evolution, our approach is new to dipteran phylogeny, using larger‐scale transcriptomic data for the first time for this insect group.

The Habitats Humans Provide: Factors affecting the diversity and composition of arthropods in houses

The indoor biome is a novel habitat which recent studies have shown exhibit not only high microbial diversity, but also high arthropod diversity. Here, we analyze findings from a survey of 50 houses (southeastern USA) within the context of additional survey data concerning house and room features, along with resident behavior, to explore how arthropod diversity and community composition are influenced by physical aspects of rooms and their usage, as well as the lifestyles of human residents. We found that indoor arthropod diversity is strongly influenced by access to the outdoors and carpeted rooms hosted more types of arthropods than non-carpeted rooms. Arthropod communities were similar across most room types, but basements exhibited more unique community compositions. Resident behavior such as house tidiness, pesticide usage, and pet ownership showed no significant influence on arthropod community composition. Arthropod communities across all rooms in houses exhibit trophic structure—with both generalized predators and scavengers included in the most frequently found groups. These findings suggest that indoor arthropods serve as a connection to the outdoors, and that there is still much yet to be discovered about their impact on indoor health and the unique ecological dynamics within our homes.