Phylogenomics

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One major focus of the lab is understanding the phylogeny and evolutionary history of bees and related wasps (Aculeata).

We use cutting-edge methods, including targeted enrichment of ultra-conserved elements (UCEs), to develop large molecular data sets for resolving phylogenetic relationships at a variety of taxonomic levels. We are currently involved in a collaborative project on the phylogeny of the aculeate wasps and bees using ultra-conserved elements (UCEs). This project involves a collaboration with Sean Brady (Smithsonian Institution), James Pitts (Utah State University), and Robert Ross (Paleontological Research Institute). The project is entitled “Phylogeny and diversification of the stinging Hymenoptera (Aculeata) using targeted enrichment of ultra-conserved elements” (NSF-DEB 1555905).

Current Projects

The lab has recently embarked on a new collaborative project on the phylogeny of the aculeate wasps and bees using ultra-conserved elements (UCEs). This project involves a collaboration with Sean Brady (Smithsonian Institution), James Pitts (Utah State University), and Robert Ross (Paleontological Research Institute). The project is entitled “Phylogeny and diversification of the stinging Hymenoptera (Aculeata) using targeted enrichment of ultra conserved elements” (NSF-DEB 1555905).

One universal feature of life on earth is that diversification rates vary widely among lineages and over time. Key innovations, such as changes in life history, may be one explanation for dramatic shifts in diversification. In insects, shifts in diet, sociality, and mode of parasitism have all been implicated in diversification rate shifts. Few lineages of insects include species that exhibit all of these life history traits, making it difficult to compare the impact of these factors on diversification within a closely related group of organisms. The ants, wasps and bees (Aculeata) represent one such lineage because aculeate species exhibit a diversity of life histories and multiple shifts in life history. This project will focus on reconstructing the evolutionary relationships among the 65,000 described aculeate species using novel methods of high-throughput, genomic-scale sequencing. These results will provide important insights into the evolution and diversification of the most sophisticated social organisms on earth (the ants, vespid wasps [hornets and yellow jackets], and corbiculate bees [including honey bees and bumblebees]) and the most economically important lineage of pollinating insects (the bees).

We will take advantage of new technological innovations in DNA sequencing to generate massive data sets for resolving aculeate relationships. Using highly conserved regions of the genome (ultraconserved elements, or UCEs) we will enrich genomic libraries for genes of interest. These enriched libraries will then be sequenced using the Illumina Hi-Seq platform. Using bioinformatics tools, the data sets will be assembled, aligned, and analyzed in order to reconstruct the evolutionary relationships among aculeate taxa and determine where and when shifts in diversification took place.

This project will contribute significantly to the development of scientific expertise and improved infrastructure in the United States. This research will provide training opportunities for undergraduate students, graduate students, and post-doctoral researchers in sophisticated methods of DNA sequencing, bioinformatics, computer programming, and phylogenetic analysis. The data generated will be made publically available through Genbank, TreeBase, Dryad, and the Encyclopedia of Life webpages. Protocols developed as part of the project will be made widely available to others researchers interested in applying these methods. Finally, in collaboration with the Paleontological Research Institute, the project will lead to the development of a 600 square foot traveling public exhibit on the biodiversity, evolutionary history, and importance of our most important agricultural pollinators (the bees).

Maximum likelihood estimate of relationships among bees based on a supermatrix approach. Our matrix consists of 20 genes, with over 17,000 aligned nucleotide sites, for over 1,300 bee and apoid wasp species, representing over two-thirds of the described bee genera.

The following genes were included in the analysis: abdominal A (abdA), arginine kinase (ak), mitotic checkpoint control protein (bub3), calcium/calmodulin-dependent protein kinase II (cad), carbamoylphosphate synthetase/aspartate transarbamylase/dihydroorotase (camkii), deoxyribonucleoside kinase (dnk), ecdysone receptor B1 (ecrb-1), elongation factor 1a f1 and f2 copies (ef1af1, ef1af2), feminizer (fem), glycerol kinase (gk), sodium potassium adenosine triphosphate (nak), odorant receptor 2 (or2), phosphoenolpyruvate carboxykinase (pepck), long wavelength rhodopsin (rho), RNA polymerase II (polII), ultraspiracle (ultra), vasa, white, and wingless (wg). (From Hedtke et al. 2013)

Gallery

Related Files

NSF Aculeata project summary 2017 (PDF)