John H. McDonald, Ph.D.


Research Interests

The overall theme of the research in my lab is detecting the effects of natural selection on nuclear genes. This includes detecting the effects of balancing selection and directional selection on variation within populations, variation among populations, and variation among species, and it includes a mix of empirical and theoretical work.

Current Projects

  • Statistical tests for adaptive evolution of proteins to different temperatures - When protein sequences from two species are compared, the neutral theory of molecular evolution predicts that the number of amino acid sites that differ in one direction should be equal to the number of sites that differ in the opposite direction. For example, the number of sites with serine in species A and alanine in species B should equal the number of sites with alanine in A and serine in B. Substitutional asymmetry, where one direction of difference is more common than the other, may indicate that natural selection favors one amino acid over the other in one of the species. I have compared protein sequences from high-temperature (thermophilic) prokaryotes and their cool-temperature (mesophilic) relatives and found a lot of evidence for asymmetrical patterns of substitution (McDonald 2010). As more genome data become available, I am extending this kind of analysis to eukaryotes.
  • Adaptation to winter temperatures in enzyme allele frequencies - In the 1970s and 1980s, the technique of allozyme electrophoresis revealed patterns of allele frequency in several species that were associated with latitude; this suggested that temperature was a common selective factor, but it was unclear whether it was summer or winter temperatures that were important. One example is the amphipod crustacean ("sand hopper") Megalorchestia californiana, which lives on sandy beaches on the Pacific coast of the United States. In 1983, I collected samples from Washington state to southern California, and I found that two enzymes (Gpi and Mpi) had alleles that were common in the southern populations but became less common towards the north. I have recently collected data that shows that allele frequencies for both enzymes are strongly correlated with winter temperatures, not summer temperatures. I will be surveying Gpi and Mpi allele frequencies in several species of peracarid crustacean on the Atlantic coast to see if they also show geographic patterns consistent with winter temperature as a selective factor. I will follow up by sequencing DNA to determine whether enzyme polymorphisms with similar geographic patterns have similar amino acid substitutions.

Selected Publications

Handbook of Biological Statistics cover

Associate Professor

Phone: (302) 831-2007

Fax: (302) 831-2281


Office: 322 Wolf Hall

Lab: 351B Wolf Hall

Department of Biological Sciences
Wolf Hall
University of Delaware
Newark, DE 19716


  • B.S. - University of Washington
  • M.S. - Oregon State University
  • Ph.D. - State University of New York at Stony Brook
  • Postdoctoral - Princeton University
  • Postdoctoral - University of Chicago