James D. Fry

Associate Professor

Contact Information:

University of Rochester
Department of Biology

River Campus Box 270211
Rochester, New York 14627-0211

Hutchison 318 (office)
Hutchison 314 (lab)

(585) 275-7835 (office)
(585) 275-8834 (lab)

Research Overview


Elucidating the genetic basis of adaptation is one of the primary goals of evolutionary biology. I am using adaptation to dietary ethanol in Drosophila melanogaster, the common fruit fly, as a model system for studying the genetics of adaptation. Ethanol occurs naturally in the decaying fruits in which D. melanogaster breed, and natural populations in temperate regions have evolved high ethanol tolerance relative to ancestral tropical populations (and most other organisms!). By taking advantage of the many genetic resources available for D. melanogaster, my laboratory is identifying the genetic changes underlying the temperate-tropical difference (e.g., Fry et al. 2008).

Other research interests, which I pursue mainly through theory and analysis of publicly available data, include the role of ecological divergence in speciation (e.g., Fry 2009) and the maintenance of genetic variation in life-history traits (e.g., Fry 2010).

melanogaster

For one approach to identifying genes involved in ethanol tolerance, we measured gene expression in replicate D. melanogaster populations that had been maintained on either ethanol-supplemented or normal medium for more than 300 generations (Yampolsky et al. 2012). From each population, RNA was isolated from newly hatched larvae that had been previously exposed, as embryos, to either plain water or an ethanol solution. As shown above, the ethanol pre-treatment dramatically increases ability of larvae to survive on ethanol-supplemented medium (Fry 2001). Using Affymetrix microarrays (see figure below), we identified ca. 100 genes that consistently differed in expression between ethanol-adapted and non-adapted populations, regardless of whether larvae came from ethanol- or water-treated embryos. Based on sequence and genetic mapping data, several of these genes are promising candidates for contributing to the temperate-tropical difference in ethanol tolerance. We are currently conducting experiments using mutants and other approaches to verify their roles in ethanol tolerance.

Expression

Selected Publications

  • Yampolsky, L., G. Glazko and J. D. Fry. 2012. Evolution of gene expression and expression plasticity in long-term experimental populations of Drosophila melanogaster maintained under constant and variable ethanol stress. Molecular Ecology, 21: 4287–4299. [link]
  • Chakraborty, M., and J. D. Fry. 2011. Drosophila lacking a homologue of mammalian ALDH2 have multiple fitness defects. Chemico-Biological Interactions 191: 296-302. [link]
  • Fry, J.D. 2010. The genomic location of sexually antagonistic variation: some cautionary comments. Evolution 64-5: 1510-1516. [pdf]
  • Fry, J.D. 2009. Laboratory experiments on speciation. Pages 631-656 in T. Garland and M. Rose, eds., Experimental Evolution: Methods and Applications. University of Califronia Press, Berkeley. [pdf]
  • Fry, J.D., D. Donlon and M. Saweikis. 2008. A world-wide polymorphism in Aldehyde dehydrogenase in Drosophila melanogaster: evidence for selection mediated by dietary ethanol. Evolution 62:66-75. [pdf]
  • Fry, J.D. and M. Saweikis. 2006. Aldehyde dehydrogenase is essential for both adult and larval ethanol resistance in Drosophila melanogaster. Genet. Res. 87:87-92. [pdf]
  • Phadnis, N. and J.D. Fry. 2005. Widespread correlations between dominance and homozygous effects of mutations: implications for theories of dominance. Genetics 171:385-392. [pdf]
  • Fry, J.D. 2004. On the rate and linearity of viability declines in Drosophila mutation-accumulation experiments: genomic mutation rates and synergistic epistasis revisited. Genetics 166:797-806. [pdf]
  • Fry, J. D. 2004. Estimation of genetic variances and covariances by Restricted Maximum Likelihood using PROC MIXED. Pages 11-34 in A. Saxton, ed., Genetic Analysis of Complex Traits with SAS. SAS Institute, Cary, NC. [programs]
  • Fry, J.D. 2003. Detecting ecological trade-offs using selection experiments. Ecology 84:1672-1678. [pdf]
  • Fry, J.D. 2003. Multilocus models of sympatric speciation: Bush vs. Rice vs. Felsenstein. Evolution 57:1735-1746. [pdf]
  • Fry, J.D. 2001. Direct and correlated responses to selection for larval ethanol tolerance in Drosophila melanogaster. Evol. Biol. 14:296-309. [pdf]