Faculty

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Ronald W. Debry

Title: Associate Professor
Graduate Director
Office: 711I Rieveschl Hall
Tel: 513-556-9743
Email: ronald.debry@uc.edu

Education

  • PhD, Michigan State University, 1989 (Zoology).
  • M.S., University of Kansas, 1982 (Systematics and Ecology).
  • A.B., University of California, Berkeley, 1979 (Biology).

Research Information

Research Interests

I work at the intersection of phylogenetics, evolutionary biology, and molecular biology. I use DNA sequences to infer phylogenetic relationships. I also use phylogenies to help discover how gene sequences evolve. For example: What sort of regularities are there in the mutation process that generates molecular-level variation? What role does natural selection play, especially in places where traditionally we do not expect it to be very effective? An exciting new wrinkle in my lab is a project in which we directly alter the E. coli chromosome and measure the fitness effects of the changes.


Experimental Evolution in E. coli


Grad student: David Hauber
Undergrad (2007-08) Varun Pawar

E. coli is a great model system for experimental studies of evolutionary processes. In this project, we are introducing specific, targeted mutations to the wild-type E. coli chromosome. Then we take different strains (mutant and wild type) and measure their fitness differences by putting them in direct competition. Our basic question is "How do weakly selected loci interact with each other?" If we introduce multiple mutations, each of which is subject to very weak selection, is the end result simply equal to the individual selection coefficients added together, or are there non-linear (epistatic) interactions?


DNA-based Identification of Forensically Important Flies

Grad student (now postdoc!): Trevor Stamper
Postdoc: Alicia Timm

Sarcophagous flies are among the very earliest visitors at a corpse, and their goal there is to lay eggs (Calliphoridae, Muscidae) or deposit larvae (Sarcophagidae). If a body is discovered in the appropriate timeframe, the developmental stage of those larvae can be used to estimate the time of death. Such an inference requires that we know what species of fly the larvae represent, because developmental rates are species-specific. The larvae themselves are generally lacking in distinguishing morphological characteristics, so identification usually requires growing live larvae until they emerge as adults. The larvae do, however, carry the same DNA as an adult, so the field of forensic entomology is increasingly turning to DNA sequence data for species identification. Through funding from the National Institute of Justice, we are developing an extensive DNA sequence reference database, including nearly all species from the continental U.S. that have been reported as being associated with large carrion. Unknown larval sequences can be compared to the database in a phylogenetic analysis to provide species identification.


Molecular Systematics: Sarcophagidae and Calliphoridae (Diptera)


Grad student (now postdoc!): Trevor Stamper
Postdoc: Alicia Timm
Undergrad: Clifford Cookman
Major collaborator: Greg Dahlem, Northern Kentucky University

There are some 2500 species in the family Sarcophagidae, but the family is famous as the "flesh flies" because of the small percentage of species have larvae that feed on decaying (and, in a few cases, living) flesh. Along with the calliphorids, sarcophagids are the primary species used by death investigators to estimate the post-mortem interval (see the "Forensically Important Flies" project, above). Our current focus within the sarcophagids is on the New World representatives of the subfamily Sarcophaginae, and on the subgeneric structure with the large genus Sarcophaga. We are just beginning serious work on the Calliphoridae, but that is helped tremendously by the exstensive collection of North American specimens generated by the forensics project.


Molecular Systematics: Rodents


Major collaborator: Dorothee Huchon, Tel Aviv University

Research Support

  • (PI), Debry, Ronald, Resolving the Higher-Level Phylogeny of Rodential using Nuclear Genes and Short Interspersed Nuclear Elements, United States-Israel Binational Science Foundation. (2004407), $22,661.00. 10/01/2005 to 09/30/2007. Status: Active.
  • (PI), Debry, Ronald, DNA-based Identification of Forensically Important Diptera, National Institute of Justice. (2005-DA-BX-K102), $574,559.00. 03/01/2006 to 07/31/2011. Status: Closed.
  • (PI), Debry, Ronald, Molecular Systematics of Rodents, National Science Foundation. (DEB-0075306-NCE), $219,984.00. 09/01/2000 to 08/31/2004. Status: Closed.

Publications

Peer Reviewed Publications

  • Hauber, D. J., Grogan, D. W. and DeBry, R. W. (2016) Mutations to less-preferred synonymous codons in a highly expressed gene of Escherichia coli: fitness and epistatic interactions. PLoS ONE 11(1):e0146375. doi:10.1371/journal.pone.0146375
  • Wong, E. S., Dahlem, G. A., Stamper, T. I. and DeBry, R. W. (2015) Discordance between morphological species identification and mtDNA phylogeny in the flesh fly genus Ravinia (Diptera : Sarcophagidae). Invertebrate Systematics 29:1-11.
  • Kapoor, V., DeBry, R. Boccelli, D. and Wendell, D. (2014) Sequencing Human Mitochondrial Hypervariable Region II as a Molecular Fingerprint for Environmental Waters. Environmental Science & Technology. 48:10648-10655.
  • Stamper, T., G. A. Dahlem, C. Cookman, and R. W. DeBry. (2013) Phylogenetic relationships of flesh flies in the subfamily Sarcophaginae based on three mtDNA fragments (Diptera: Sarcophagidae). Systematic Entomology. 38:35-44
  • DeBry, R. W., Timm, A., Wong, E. S., Stamper, T., Cookman, C., Dahlem, G. A. (2013) DNA-Based Identification of Forensically Important Lucilia (Diptera: Calliphoridae) in the Continental United States. Journal of Forensic Sciences. 58:73-78.
  • White, C. P., DeBry, R. W.; Lytle, D. A. (2012) Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water. Applied and Environmental Microbiology  78: 6390-6394
  • DeBry, Ronald W, Timm, Alicia E, Dahlem, Gregory A, & Stamper, Trevor (2010). mtDNA-based identification of Lucilia cuprina (Wiedemann) and Lucilia sericata (Meigen) (Diptera: Calliphoridae) in the continental United States. Forensic Science International, 202(1-3), 102-9.
  • Stamper, Trevor, Davis, Paula, & DeBry, Ronald W (2009). The nocturnal ovipositing behavior of carrion flies in Cincinnati, Ohio. Journal of forensic sciences, 54(6), 1450-2.
  • Blanga-Kanfi, Shani, Miranda, Hector, Penn, Osnat, Pupko, Tal, DeBry, Ronald W, & Huchon, Dorothée (2009). Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC evolutionary biology, 9, 71.
  • Stamper, T. & DeBry, R. W. (2007). The nocturnal oviposition behavior of carrion flies in rural and urban environments: methodological problems and forensic implications. Canadian Society of Forensic Science Journal, 40, 173, 182.
  • Spears, T., DeBry, R. W., Abele, L. G., Chodyla, K. (2005). Peracarid monophyly and interordinal phylogeny inferred from nuclear small-subunit ribosomal DNA sequences (Crustacea : Malacostraca : Peracarida). Proceedings of the Biological Society of Washington, 118(1), 117, 157.
  • DeBry, R. W. (2005). The systematic component of phylogenetic error as a function of taxonomic sampling under parsimony. Systematic Biology, 54(3), 432, 440.
  • DeBry, R. W. (2003). Identifying conflicting signal in a multigene analysis reveals a highly resolved tree: The phylogeny of Rodentia (Mammalia). Systematic Biology, 52(5), 604, 617.
  • DeBry, R. W. (2001). Improving interpretation of the decay index for DNA sequence data. Systematic Biology, 50(5), 742, 752.
  • Springer, M. S., DeBry, R. W., Douady, C., Amrine, H. M., Madsen, O., de Jong, W. W., Stanhope, M. J. (2001). Mitochondrial versus nuclear gene sequences in deep-level mammalian phylogeny reconstruction. Molecular biology and evolution, 18(2), 132, 143.
  • DeBry, R. W., Sagel, R. M. (2001). Phylogeny of Rodentia (mammalia) inferred from the nuclear-encoded gene IRBP. Molecular phylogenetics and evolution, 19(2), 290, 301.
  • Madsen, O., Scally, M., Douady, C. J., Kao, D. J., DeBry, R. W., Adkins, R., Amrine, H. M., Stanhope, M. J., de Jong, W. W., Springer, M. S. (2001). Parallel adaptive radiations in two major clades of placental mammals. Nature, 409(6820), 610, 614.
  • DeBry, R. W., Seshadri, S. (2001). Nuclear intron sequences for phylogenetics of closely related mammals: An example using the phylogeny of Mus. Journal of mammalogy, 82(2), 280, 288.
  • DeBry, R. W., Olmstead, R. G. (2000). A simulation study of reduced tree-search effort in bootstrap resampling analysis. Systematic Biology, 49(1), 171, 179.
  • Debry, R. W. (1999). Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes. Systematic Biology, 48(2), 286, 299.
  • DeBry, R. W. (1998). Comparative analysis of evolution in a rodent histone H2a pseudogene. Journal of Molecular Evolution, 46(3), 355, 360.
  • DeBry, R. W., Seldin, M. F. (1996). Human/mouse homolgy relationships. Genomics, 33(3), 337, 351.
  • Wang, Z. F., Tisovec, R., Debry, R. W., Frey, M. R., Matera, A. G., Marzluff, W. F. (1996). Characterization of the 55-kb mouse histone gene cluster on chromosome 3. Genome research, 6(8), 702, 714.
  • Osborn, A., Gilkeson, G. S., Debry, R. W., Thompson, M. A., Rochelle, J. M., Seldin, M. F., Ruiz, P. (1995). Identification of Putative Qtls in Mrl-Lpr X B6-Lpr Crosses. Arthritis and Rheumatism, 38(9), 182, 182.
  • Debry, R. W., Abele, L. G. (1995). The Relationship between Parsimony and Maximum-Likelihood Analyses - 3 Scores and Confidence Estimates for 3 Real Data Sets. Molecular biology and evolution, 12(2), 291, 297.
  • Debry, R. W., Marzluff, W. F. (1994). Selection on Silent Sites in the Rodent H3 Histone Gene Family. Genetics, 138(1), 191, 202.
  • Debry, R. W., Abele, L. G., Weiss, S. H., Hill, M. D., Bouzas, M., Lorenzo, E., Graebnitz, F., Resnick, L. (1993). Dental Hiv Transmission. Nature, 361(6414), 691, 691.
  • Hill, M. D., Debry, R. W., Abele, L. G., Weiss, S. H., Bouzas, M., Lorenzo, E., Graebnitz, F., Resnick, L. (1993). A Phylogenetic Analysis of Possible Hiv Transmission through Invasive Dental Procedures. Journal of cellular biochemistry 48, 48.
  • Abele, L. G., Debry, R. W. (1992). Florida Dentist Case - Research Affiliation and Ethics. Science, 255(5047), 903, 903.
  • Debry, R. W. (1992). Biogeography of New-World Taiga-Dwelling Microtus (Mammalia, Arvicolidae) - a Hypothesis Test that Accounts for Phylogenetic Uncertainty. Evolution, 46(5), 1347, 1357.
  • Debry, R. W. (1992). The Consistency of several Phylogeny-Inference Methods Under Varying Evolutionary Rates. Molecular biology and evolution, 9(3), 537, 551.
  • Debry, R. W. (1989). Can Parsimony be used as a Test Statistic. American Zoologist, 29(4), A33, A33.
  • Zelditch, M. L., Debry, R. W., Straney, D. O. (1989). Triangulation-Measurement Schemes in the Multivariate-Analysis of Size and Shape. Journal of mammalogy, 70(3), 571, 579.
  • Williams, S. M., Debry, R. W., Feder, J. L. (1988). A Commentary on the use of Ribosomal Dna in Systematic Studies. Systematic zoology, 37(1), 60, 62.
  • Debry, R. W., Slade, N. A. (1985). Cladistic-Analysis of Restriction Endonuclease Cleavage Maps within a Maximum-Likelihood Framework. Systematic zoology, 34(1), 21, 34.
  • Junge, J. A., Hoffmann, R. S., Debry, R. W. (1983). Relationships within the Holarctic Sorex-Arcticus - Sorex-Tundrensis Species Complex. Acta Theriologica, 28(21-3), 339, 350.
  • Debry, R. W. (1981). A Probability Model for Cladistic-Analysis of Mitochondrial Restriction Enzyme Data. American Zoologist, 21(4), 991, 991.

Presentations & Lectures

Paper Presentations

  • DeBry, R. W., Hauber, D. Grogan, D. (06/29/2010). Measuring selection coefficients for single silent polymorphisms in E. coli. SSE/ASN/SSB Annual Meeting, Portland, OR.

Poster Presentations

  • Stamper, T., Timm, A., Dahlem, G., DeBry, R. W. (02-2010). A DNA database for species identifi cation of forensically important fl esh fl ies (Diptera: Sarcophagidae) in the continental United States American Academy of Forensic Sciences Annual Meeting, Seattle, WA.
  • Stamper, T., Timm, A., Dahlem, G., DeBry, R. W. (06-2010). A DNA database for species identifi cation of forensically important fl esh fl ies (Diptera: Sarcophagidae) in the continental United States North American Forensic Entomology Association Annual Meeting, Windsor, Ontario.
  • DeBry, R. W., A. E. Timm, T. Stamper, G. Dahlem, E. Wong (06/15/2010). A DNA database for species identification of forensically important carrion flies in the continental United States National Institute of Justice Conference, Arlington, VA.
  • Avanesyan, Alina, Trevor I. Stamper, Alicia Timm, Evan Wong, Gregory A. Dahlem, Ronald W. DeBry (12/14/2010). Phylogenetic relationships of the Sarcophagidae (Diptera), using three mitochondrial loci (COI, COII, and ND4) and one nuclear locus (PER) Entomological Society of America Annual Meeting, San Diego, CA.

Experience & Service

Service

  • Editor of Journal, Society of Systematic Biologists 01/01/2010 to 12/31/2010

Courses Taught

  • 15-BIOL-767 EVOLUTION
    Level: Graduate
    Term: 09W

  • 15-BIOL-131 GENETICS & SOCIETY
    Level: Undergraduate
    Term: 09S

  • 15-BIOL-767 EVOLUTION
    Level: Graduate
    Term: 10A

  • -BIOL-3077 DNA FORENSICS
    Level: Undergraduate
    Term: 13SS

  • Evolution
    Evolution
    Level: Graduate
    Term: 14FS

  • Evolution
    Evolution
    Level: Graduate
    Term: 13FS

  • -BIOL-3077 DNA FORENSICS
    Level: Undergraduate
    Term: 14SS