John H. McDonald's home page

Office: 322 Wolf Hall
Lab: 026B Wolf Hall

Mailing address:
Dept. of Biological Sciences
University of Delaware
Newark, DE 19716

Phone: (302) 831-2007 (I don't check messages very often, so e-mail is better)
Fax: (302) 831-2281

E-mail: mcdonald@udel.edu

Education


B.S.: University of Washington, 1981 (Biological Oceanography)
M.S.: Oregon State University, 1984 (Biological Oceanography
Ph.D.: State University of New York at Stony Brook, 1990 (Ecology and Evolution)
Postdoctoral: Princeton University (1990-1991)
Postdoctoral: University of Chicago (1992)

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.

Prospective Students

I am not seeking a graduate student or post doc for my lab at this time. I may have opportunities for undergraduates with a strong interest in evolutionary biology and a willingness to work independently. Undergrads interested in working in my lab should apply using the undergraduate research interest form.

I will be glad to advise UD undergrads and others with an interest in evolutionary biology who are planning to apply to graduate schools.

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 et al. 1999, McDonald 2001). I am currently testing the consistency of these patterns by comparing seven mesophile-thermophile pairs whose genomes have been completely sequenced. As more genome data become available, I plan to extend this kind of analysis to eukaryotes.

Adaptation of mannose-6-phosphate isomerase to different habitats in the amphipod Platorchestia platensis: Several marine invertebrates exhibit small-scale geographic patterns of allele frequency differences in the gene for the enzyme mannose-6-phosphate isomerase (MPI). One of these species is the amphipod crustacean Platorchestia platensis, a "beach hopper" that lives in intertidal areas of bays, estuaries, and some exposed beaches of the eastern United States. Two allozyme alleles differ consistently in frequency between exposed beaches on Long Island Sound and beaches inside small bays on Long Island (McDonald 1987). I am currently surveying allozyme frequencies in Chesapeake Bay; preliminary evidence suggests that the geographic pattern is repeated there. I will follow up by isolating and sequencing the gene for MPI, so that several tests for selection can be applied, and I will conduct laboratory selection experiments to try to determine what environmental factor causes the selection.

Software

These software programs analyze DNA and protein sequences for evidence of natural selection. They and their Pascal source code are freely available, in both Macintosh and Windows versions.

Teaching

Courses

Resources

Public Outreach

I have given several public talks, have appeared on TV, and have been quoted in newspapers explaining the difference between the science of evolutionary biology and the pseudoscience of creationism. In response to creationist Michael Behe's claim that a mousetrap is a good analogy for an "irreducibly complex" biochemical system, I have drawn mousetraps in several stages of reduced complexity.

Publications

McDonald, J.H. 2006. Apparent trends of gain and loss in protein evolution due to nearly neutral evolution. Mol. Biol. Evol. 23: 240-244. [pdf]

Bayha, K.M., G.R. Harbison, J.H. McDonald, and P.M. Gaffney. 2004. Preliminary investigation on the molecular systematics of the invasive ctenophore Beroe ovata. In: Dumon, H.J., T.A. Shiganova, and U. Niermann (eds.) Aquatic invasions of the Black, Caspian and Mediterranean Seas. Kluwer Academica Publishers, Dordrecht.

Riginos, C., and J.H. McDonald. 2003. Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus. Mol. Biol. Evol. 20: 200-207. [pdf]

Verrelli, B.C., J.H. McDonald, G. Argyropoulos, G. Destrol-Bisol, A. Froment, A. Drousiotou, G. Lefranc, A.N. Helal, J. Loiselet, and S.A. Tishkoff. 2002. Evidence for balancing selection from nucleotide sequence analyses of human G6PD. Am. J. Hum. Genet. 71: 1112-1128. [pdf]

McDonald, J.H. 2001. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol. Biol. Evol. 18: 741-749. [pdf]

McDonald, J.H., A.M. Grasso and L.K. Rejto. 1999. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol. Biol. Evol. 16: 1785-1790. [pdf]

Edgcomb, V.P., J.H. McDonald, R. Devereux, and D.W. Smith. 1999. Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16s ribosomal DNA. Appl. Envt. Micro. 65: 1516 -1523. [pdf]

McDonald, J.H. 1998. Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 15: 377-384. [pdf]

Bradley, R.D., R.M. Adkins, R.L. Honeycutt, and J.H. McDonald. 1998. Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys. Mol. Biol. Evol. 15: 709-717. [pdf]

Miller, C., J. McDonald and D. Francis. 1996. Evolution of promoter sequences: elements of a canonical promoter for prespore genes of Dictyostelium. J. Mol. Evol. 43: 185-193. [pdf]

McDonald, J.H., B.C. Verrelli and L.B. Geyer. 1996. Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Mol. Biol. Evol. 13: 1114-1118. [pdf]

McDonald, J.H. 1996. Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol. Biol. Evol. 13: 253-260. [pdf]

McDonald, J.H. 1994. Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. pp. 88-100 in Non- neutral evolution: theories and molecular data, B. Golding, ed. New York: Chapman and Hall.

McDonald, J.H., R. Seed and R.K. Koehn. 1991. Allozymes and morphometric characters of three species of Mytilus in the Northern and Southern Hemispheres. Mar. Biol. 111: 323-333.

McDonald, J.H. and M. Kreitman. 1991. Scientific correspondence. Nature 354: 116. [pdf]

McDonald, J.H. and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654. [pdf]

McDonald, J.H. 1991. Contrasting amounts of geographic variation as evidence for direct selection: the Mpi and Pgm loci in eight crustacean species. Heredity 67:215-219.

McDonald, J.H., R. Seed and R.K. Koehn. 1991. Allozymes and morphometric characters of three species of Mytilus in the Northern and Southern Hemispheres. Mar. Biol. 111:323-333.

McDonald, J.H., R.K. Koehn, E.S. Balakirev, G.P. Manchenko, A.I. Pudovkin, S.O. Sergiyevsky and K.V. Krutovsky. 1990. On species identity of "the common mussel" inhabiting Asiatic coasts of the Pacific Ocean. Biologiya Morya 1990(1): 13-22. [in Russian]

McDonald, J.H. and J.F. Siebenaller. 1989. Similar geographic variation at the Lap locus in the mussels Mytilus trossulus and M. edulis. Evolution 43: 228-231.

McDonald, J.H. 1989. Selection component analysis of the Mpi locus in the amphipod Platorchestia platensis. Heredity 62: 243-249.

McDonald, J.H. and R.K. Koehn. 1988. The mussels Mytilus galloprovincialis and M. trossulus on the Pacific coast of North America. Mar. Biol. 99: 111-118.

McDonald, J.H. 1987. Repeated geographic variation at three enzyme loci in the amphipod Platorchestia platensis. Evolution 41: 438-441.

Rodhouse, P.G., J.H. McDonald, R.I.E. Newell and R.K. Koehn. 1986. Gamete production, somatic growth and multiple-locus enzyme heterozygosity in Mytilus edulis. Mar. Biol. 90: 209-214.

McDonald, J.H. 1985. Size-related and geographic variation at two enzyme loci in Megalorchestia californiana (Amphipoda: Talitridae). Heredity 54: 359-366.

Diehl, W.J., P.M. Gaffney, J.H. McDonald and R.K. Koehn. 1985. Relationship between weight-standardized oxygen consumption and multiple-locus heterozygosity in the mussel, Mytilus edulis. Proceedings of the 19th European Marine Biology Symposium, pp. 529-534.

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This page was last revised September 19, 2007. Its URL is http://udel.edu/~mcdonald/index.html