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John H. McDonald, Ph.D.
- BISC 413 - Advanced Genetics Laboratory
- BISC 495 - Evolution
- BISC 643 - Biological Data Analysis
- BISC 656 - Evolutionary Genetics
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.
- 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.
- Manthey, A.L., S.A. Lachke, P.G. FitzGerald, R.W. Mason, D.A. Scheiblin, J.H. McDonald, and M.K. Duncan. 2014. Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development. Mechanisms of Development 131: 86-110.
- McDonald, J.H., and K.W. Dunn. 2013. Statistical tests for measures of colocalization in biological microscopy. Journal of Microscopy 252: 295-302.
- McDonald, J.H. 2013. Geographic variation in Megalorchestia californiana allele frequencies may be caused by winter rather than summer temperatures. Marine Ecology Progress Series 488: 201-207.
- Hoffman, G., W.W. Le, A. Entezam, N. Otsuka, Z.-B. Tong, L. Nelson, J. Flaws, S. Jafar, J.H. McDonald, and K. Usdin. 2012. Ovarian abnormalities in a mouse model of Fragile X primary ovarian insufficiency. J. Histochem. Cytochem. 60: 439-456.
- McDonald, J.H. 2011. Myths of human genetics. Baltimore: Sparky House Publishing.
- Dunn, K.W., M.M. Kamocka, and J.H. McDonald. 2011. A practical guide to evaluating colocalization in biological microscopy. Am. J. Physiol.—Cell Physiol. 300: C723-C742.
- McDonald, J.H. 2010. Temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs. Genome Biol. Evol. 2: 267-276.
- McDonald, J.H. 2009. Handbook of Biological Statistics, 2nd ed. Baltimore: Sparky House Publishing.
- McDonald, J.H. 2008. Handbook of Biological Statistics. Baltimore: Sparky House Publishing.
- McDonald, J.H. 2006. Apparent trends of amino acid gain and loss in protein evolution due to nearly neutral variation. Mol. Biol. Evol. 23: 240–244.
- Bayha, K.M., G.R. Harbison, J.H. McDonald, and P.M. Gaffney, P.M. 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. Dordrecht: Kluwer Academica Publishers.
- 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.
- 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.
- McDonald, J.H. 2001. Patterns of temperature adaptation in proteins from the bacteria Deinococcus radiodurans and Thermus thermophilus. Mol. Biol. Evol. 18: 741–749.
- 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. Environ. Microbiol. 65: 1516–1523.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- McDonald, J.H. 1994. Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. pp. 88–100 in: Golding, B., ed. Non-neutral evolution: theories and molecular data. New York: Chapman and Hall.
- McDonald, J.H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652–654.
- 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.
Phone: (302) 831-2007
Fax: (302) 831-2281
Office: 322 Wolf Hall
Lab: 351B Wolf Hall
Department of Biological Sciences
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