Research Overview
Genomics and Phylogenomics
Animal genes consist of DNA, and together with other genetic elements constitute a genome. According to evolutionary theory, all animals are descended from a common ancestor. Their evolutionary relationships can be described through a precise branching pattern (sometimes called the "tree of life") in which the connections of the branches identify who is most closely related to whom through descent, and the branch lengths represent some measure of evolutionary distance. Analyzing the DNA in genomes of various living animals provides one means of reconstructing the "tree of life." The availability of a well-supported tree is an essential step in reconstructing the evolution of life in all its complexity.
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Research Description
Research Area: Genome Sciences
Research Specialty: Arthropod and lepidopteran phylogenomics
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...
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Additional Info
*Secondary Appointment: Affiliate Professor, Department of Entomology, University of Maryland College Park (UMCP).
*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.
SERVICE
Professor Regier supervises the DNA Sequencing Facility at the Center.
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Representative Publications
Regier, J.C., Shultz, J.W., Zwick, A., Hussey, A., Ball, B., Wetzer, R., Martin, J.W., and Cunningham, C.W. 2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463: 1079-1083.
Regier, J.C., Zwick, A., Cummings, M., Kawahara, A.Y., Cho, S., Weller, S., Roe, A., Baixeras-Almela, J.,, Brown, J.W., Parr, C., Davis, D.R., Epstein, M., Hallwachs, W., Hausmann, A., Janzen, D.H., Kitching, I.J., Solis, M.A., Yen, S.-H., Bazinet, A., and Mitter, C. 2009. On reconstructing the hyper-diverse radiation of advanced moths and butterflies (Lepidoptera: Ditrysia): Initial evidence from 123 species, 55 families and 5 protein-coding nuclear genes. BMC Evolutionary Biology 9: 280.
Regier, J.C., Shultz, J.W., Ganley, A.R.D., Hussey, A., Shi, D., Ball, B., Stajich, J.E., Cummings, M.P., Martin, J.W., and Cunningham, C.W. 2008. Resolving arthropod phylogeny: Exploring phylogenetic signal within 41 kb of protein-coding nuclear gene sequence. Systematic Biology 57: 920-938.
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