Department of Biological Sciences: Leading the way to Prominence

John H. McDonald, Ph.D.

Associate Professor

McDonald

Phone: (302) 831-2007
Fax: (302) 831-2281
Email: mcdonald@udel.edu
Web: Dr. McDonald's Homepage
Office: 322 Wolf Hall
Lab: 026B Wolf Hall

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

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Education

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

Teaching

BISC 413 - Advanced Genetics Laboratory
BISC 495 - Evolution
BISC 643 - Biological Data Analysis
BISC 656 - Evolutionary Genetics

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 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. 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.
Adaptation to global warming 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. One example is the amphipod crustacean ("sand hopper") Megalorchestia californianus, 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 had alleles that were common in the southern populations but became less common towards the north. Allele frequencies were strongly correlated with the average January temperatures near the sample locations. Since that time, the climate in that area has warmed by over one degree Celsius. This spring, I will sample from the same locations and see whether the southern-associated alleles have increased in frequency in the last 25 years in response to global warming.

Selected Publications

McDonald JH. Handbook of Biological Statistics. Baltimore: Sparky House Publishing; 2008.
McDonald JH. Apparent trends of amino Acid gain and loss in protein evolution due to nearly neutral variation. Mol Biol Evol. 2006;23(2):240–244.
Bayha KM, Harbison GR, McDonald JH, Gaffney PM. Preliminary investigation on the molecular systematics of the invasive ctenophore Beroe ovata. In: Dumon HJ, Shiganova TA, Niermann U, eds. Aquatic invasions of the Black, Caspian and Mediterranean Seas. Dordrecht: Kluwer Academica Publishers; 2004.
Riginos C, McDonald JH. Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus. Mol Biol Evol. 2003;20(2):200–207.
Verrelli BC, McDonald JH, Argyropoulos G, et al. Evidence for balancing selection from nucleotide sequence analyses of human G6PD. Am J Hum Genet. 2002;71(5):1112–1128.
McDonald JH. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol Biol Evol. 2001;18(5):741–749.
Edgcomb VP, McDonald JH, Devereux R, Smith DW. Estimation of bacterial cell numbers in humic acid-rich salt marsh sediments with probes directed to 16S ribosomal DNA. Appl Environ Microbiol. 1999;65(4):1516–1523.
McDonald JH, Grasso AM, Rejto LK. Patterns of temperature adaptation in proteins from Methanococcus and Bacillus. Mol Biol Evol. 1999;16(12):1785–1790.
Bradley RD, Adkins RM, Honeycutt RL, McDonald JH. Nucleotide polymorphism at the alcohol dehydrogenase locus of pocket gophers, genus Geomys. Mol Biol Evol. 1998;15(6):709–717.
McDonald JH. Improved tests for heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol Biol Evol. 1998;15(4):377–384.
McDonald JH. Detecting non-neutral heterogeneity across a region of DNA sequence in the ratio of polymorphism to divergence. Mol Biol Evol. 1996;13(1):253–260.
McDonald JH, Verrelli BC, Geyer LB. Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Mol Biol Evol. 1996;13(8):1114–1118.
Miller C, McDonald J, Francis D. Evolution of promoter sequences: elements of a canonical promoter for prespore genes of Dictyostelium. J Mol Evol. 1996;43(3):185–193.
McDonald JH. Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. In: Golding B, ed. Non-neutral evolution: theories and molecular data. New York: Chapman and Hall; 1994:88–100.
McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991;351(6328):652–654.
Mcdonald JH, Seed R, Koehn RK. Allozymes and morphometric characters of three species of Mytilus in the Northern and Southern Hemispheres. Mar Biol. 1991;111(3):323–333.