Research Overview

We study the phylogeny and evolution of beetles (order Coleoptera) and other insects, the evolution and genomic basis of phytophagy, and interactions between beetles and plants on ecological and evolutionary time scales. Related interests include the evolution of insect genomes, and geographic patterns of insect (especially beetle) diversity and endemism. Most of our work is highly collaborative, involving students and other researchers worldwide (see collaborators). We use data from genomes, transcriptomes, morphological study of museum specimens, and field studies (host plant tissues and taxa, insect and host plant distributions, etc.). In recognition of the impacts of habitat loss and climate change on biodiversity, some projects also have conservation biological goals and implications.

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FOCAL AREAS OF STUDY

Reconstructing the Phylogeny & Evolution of Beetles (order Coleoptera)

We use phylogenomic data obtained via target enrichment (anchored hybrid enrichment, ultraconserved elements), genomic meta-characters, genomes and transcriptomes, and (to a lesser degree) traditional Sanger sequencing, to address longstanding questions about the phylogeny and evolution of beetles and other insects. For some groups, e.g., beetles in the superfamily Curculionoidea (weevils), we are also conducting large-scale studies of morphological characters. Recent papers have focused on the family Cerambycidae, the series Staphyliniformia (containing superfamilies Histeroidea, Hydrophiloidea, Scarabaeoidea, and Staphylinoidea), the superfamily Buprestoidea, and the order Coleoptera as a whole. These studies have uncovered a wealth of interesting phylogenetic and evolutionary patterns. For example, in the large clade comprised of rove beetles, scarab beetles, and allies (>100,000 species), we documented a high degree of evolutionary plasticity in microhabitat use, with leaf litter as the predominant source microhabitat for diversification – a pattern that is also observed in ants. Current studies, e.g., the 1KITE Beetle Subproject, and the Exemplar Beetle Genomes Project, will undoubtedly provide new and more substantial resolution of the beetle tree of life.

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Most current molecular phylogenetic and evolutionary studies in the McKenna lab are focused on major lineages within the beetle suborder Polyphaga, especially series Cucujiformia (>180,000 species), and within it, the informal clade Phytophaga (>120,000 species). Phytophaga typically feed on plants and are among the world’s most serious pests of agriculture and forestry. Examples include the Asian long horned beetle (Anoplophora glabripennis), the cotton boll weevil (Anthonomus grandis), the western corn root worm (Diabrotica virgifera virgifera), the citrus root weevil (Diaprepes abbreviatus), and the mountain pine beetle (Dendroctonus ponderosae). Many Phytophaga exhibit specialized interactions with endosymbiotic fungi and bacteria.

Most of our research is focused on the phylogeny and evolution of major lineages within Phytophaga, especially longhorned beetles (Cerambycidae and relatives), and weevils (superfamily Curculionoidea). For example, the 1,000 Curculionidae Phylogeny and Evolution Project (The 1K Weevils Project; funded by the U.S. National Science Foundation), is using phylogenomic and morphological data to reconstruct relationships and the evolution of host plant associations in Curculionoidea, with a particular focus on true weevils (family Curculionidae; >51,000 named species in >4,600 genera). Postdoctoral Fellows Dr. Dave Clarke, and Dr. Seunggwan Shin (University of Memphis), and Dr. Adriana Marvaldi (Argentina), Dr. Rolf Oberprieler (Australia), and Dr. Brian Farrell (Harvard MCZ) are close collaborators on this project. Other ongoing studies (see below) are providing new insights into the genomic basis of phytophagy in the Phytophaga and other groups of beetles.

Beetle Diversity, Endemism & Evolutionary Ecology

Tropical forests are home to most beetle species. However, timing and patterns of diversification in tropical lineages of beetles, including geographic variation in their host plant associations, degree of host specialization, and patterns of endemism, remain little known. Several projects in the McKenna Lab seek to gain insight into these patterns and to better understand human impacts on the ecology and diversity of beetles in the tropics. For example, Ph.D. candidate Cristian Beza is reconstructing the phylogeny of the bess beetle tribe Proculini (family Passalidae) in the Neotropics using DNA sequences and morphological data. Many of the species in this tribe occur only in island-like montane forests in Mesoamerica. He is also studying the distributions of Mesoamerican Proculini and their habitat requirements (“island biogeography in the continental tropics”) through extensive museum and field studies. This work will establish the geographic and temporal origins of the tribe and will provide a framework for forming and testing hypotheses relating to the temporal and geographic origins of the many locally-endemic montane-distributed species in the tribe. Dr. McKenna is studying cryptic speciation, endemism, and the evolution of host tissue and taxon specialization in Neotropical leaf beetles in the tribes Cephaloleiini and Arescini (Chrysomelidae: Cassidinae). This work builds on previously published studies by Dr. McKenna and colleagues.

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Several projects have a notable evolutionary-ecological focus. For example, we are studying phylogeny and evolution of the beetle family Cerambycidae and near relatives (longhorned beetles; ~30,000 described species) using both traditional molecular phylogenetic approaches focused on a few genes, and phylogenomic approaches that target hundreds to thousands of genes. Corresponding reconstructions of (1) the taxonomic distribution and evolution of volatile sex and aggregation pheromones used by longhorned beetles, and (2) longhorned beetle host plant associations, are also underway. The results of this research will have immediate application to developing targeted monitoring programs for longhorned beetle species at high risk of introduction via international commerce, and for trapping and control of native pest species. However, this research will also advance knowledge of the nature, ecology, and evolution of chemically mediated interactions in herbivorous insects, especially longhorned beetles. This research is funded in part by the U.S. Department of Agriculture.

Evolution of the Beetle Genome: The Exemplar Beetle Genomes Project

This Project Serves as an umbrella for the several genomes and transcriptomes that we are sequencing and assembling at the University of Memphis, or in collaboration with colleagues elsewhere. The project as a whole seeks to produce genomic resources that facilitate studies in beetle comparative genomics and evolution. However, each constituent project has its own goals.

Dr. McKenna is a collaborator on the 1,000 Insect Transcriptome Evolution (1KITE) Project and a contributor to the 1KITE beetle subproject (see: www.1kite.org/). He is part of the Insect 5000 Genomes (i5k) Pilot Project (www.arthropodgenomes.org/wiki/i5K), through which he is coordinating the Asian longhorned beetle genome project. He is also contributing to several other beetle genome projects through i5k, the University of Memphis Feinstone Center for Genomics, the 1K Weevils Project, and other collaborations. Genome sequencing and assembly in the McKenna Lab is supported in part by grants from the U.S. National Science Foundation, U.S. Department of Agriculture, the FedEx Institute of Technology and the University of Memphis College of Arts and Sciences. The following is a summary of two of these genome sequencing projects:

i5k ALB logoThe Asian longhorned beetle (Anoplophora glabripennis; ALB) genome project is a collaboration between the McKenna Lab and i5k, which is based at the Baylor College of Medicine Human Genome Sequencing Center. Genome sequencing, assembly, annotation and manual curation of the ALB genome are now complete, as are several summary papers, including the main ALB genome project summary paper (published in Genome Biology). A consortium of >70 collaborators was established in association with this project. Some of the genes and topics under study include: DNA methylation, genome structure, the RNAi pathway, CYP450’s, cuticle genes, germline genes, genes involved in diapause and stress tolerance, chemoperception, detoxification, and phytophagy and digestive physiology.

The McKenna Lab sequenced and assembled the genome of a primitive beetle (Priacma serrata: suborder Archostemata), which was analyzed along with the first genome for the enigmatic order Strepsiptera (twisted-wing parasites), and 11 other insect genomes, to resolve the phylogenetic placement of Strepsiptera (Niehuis et al. 2012; Current Biology). Based on analyses of data from more than 4,000 orthologous genes, and genomic meta-characters, Strepsiptera was established as the sister group of beetles. The P. serrata genome has also played an important role in developing anchored hybrid enrichment probes for beetles.

1KWeevilsLogo_08Dec2014We are using data from these projects to develop cutting-edge tools that enable phylogenomic studies of beetles. For example, with collaborators Alan Lemmon and Emily Moriarty-Lemmon (Florida State University) we have developed anchored hybrid enrichment probes for beetles. This work is supported in part by a grant from the U.S. National Science Foundation (The 1K Weevils Project), and a cooperative agreement with the U.S. Department of Agriculture.