The advent of genomics has been a major boon to those interested in reconstructing the tree of life and has led to the new field of phylogenomics. Access to a greater proportion of the genome is allowing my lab to test the presumption that large amounts of molecular sequence data, properly analyzed and under adequate taxon sampling, can robustly resolve higher-level groupings across Arthropoda and, at a lower taxonomic level, across Lepidoptera. The caveat of properly analyzed is not a trivial one as rate and compositional heterogeneity, paralogous evolution, concerted evolution, evolution of indels, etc. confound the field's current working models of sequence evolution that are largely based on analysis of simple substitutions.

With these challenges in mind, my laboratory and our collaborators² have over the past dozen years developed methods to amplify about 60 single-copy, protein-encoding nuclear genes across taxonomic groups of interest. Direct sequencing of the amplicons provides the data sets for subsequent phylogenetic analysis. Genes targeted have few indels, and data sets within and across genes are chosen that evolve at overall rates suitable to the taxonomic question. For example, the slowly evolving protein sequences of EF-1 a are useful for resolving Paleozoic-age splits across arthropods, while synonymous nucleotide changes (mostly at third codon positions) in the same gene are useful within the mid- to late-Tertiary-age lepidopteran subfamily Heliothinae. All genes that we currently use in our phylogenetic studies are described here , along with sequences of PCR primers and methods for their optimal utilization.

The taxonomic focus of my laboratory is twofold. First, we and our collaborators are using sequence data to investigate deep-level relationships within the phylum Arthropoda (see also http://www.biology.duke.edu/cunningham/DeepArthropod.html), publishing studies that demonstrate, for example, the close affinity of insects and crustaceans to the exclusion of myriapods. We have also published separate studies of relationships across myriapods, hexapods, pancrustaceans, and tardigrades. Currently, we are building a data set that will sample 40 kb of nucleotide sequence for each of 75 diverse arthropods and their outgroups.

Through 2010, the second focus of my laboratory will be to resolve major groupings within Lepidoptera by sampling 250 diverse taxa and about 25 gene sequences that we have shown are suitable for lepidopteran phylogeny (see http://www.leptree.net/). In previous and ongoing smaller-scale studies, we have explored basal relationships across the non-ditrysian Microlepidoptera and across the macrolepidopteran superfamilies of Noctuoidea and Bombycoidea.

² Independent collaborators on current NSF-funded research projects include Drs. Michael Cummings (UMCP), Cliff Cunningham (Duke University), Don Davis (U.S. Museum of Natural History), Ian Kitching (The Natural History Museum, London), Jody Martin (Los Angeles Museum of Natural History), Richard Peigler (University of the Incarnate Word), Charles Mitter (UMCP), Jeffrey Shultz (UMCP), Jeff Thorne (North Carolina State University), and Susan Weller (University of Minnesota). Undergraduate and graduate students and postdoctoral fellows, past and present, are also acknowledged. See list of publications.