Thermal adaptation in GPI: Using the old-fashioned technique starch gel electrophoresis of native proteins, I have identified several species of invertebrates with allozyme clines associated with temperature for the enzyme glucose-6-phosphate isomerase (GPI). I will next sequence the coding regions of the Gpi genes in these species to see whether the amino acid differences between the warm-associated and cool-associated allozymes are similar across different species.
Morphological identification of bay mussels: Two species of bay mussels occur in the Salish Sea and elsewhere on the Pacific coast: Mytilus galloprovincialis, which was accidentally introduced from Europe, and the native Mytilus trossulus. These species are both commercially and ecologically important, but researchers generally have to use genetic characters (allozymes or DNA markers) to tell them apart, because the morphological differences in their shells are very subtle (McDonald et al. 1991). Researchers in the northwestern Pacific have described some shell characters that appear to be useful for telling M. galloprovincialis from M. galloprovincialis; I will collect local mussels from mixed populations, identify them using DNA markers, then see whether the species can be reliably identified using shell characters. This research is not conceptually exciting, but the results could be quite useful to both marine biologists and aquaculturists.
Undergraduate research and advising
I am not seeking a graduate student or post doc for my lab. I may have opportunities for Western undergraduates with a strong interest in evolutionary biology and a willingness to work independently. Undergrads interested in working in my lab should email me.
I was chair of the graduate admissions committe for the biology department at the University of Delaware for nearly 20 years, so I have read thousands of grad-school applications. I would be glad to share my expertise with Western biology majors; I can help you decide whether grad school is right for you, what you should be doing to improve your chances of getting into grad school, how to pick schools to apply to, and how to write a good personal statement for the grad school application. If you think you could use any of this advice, please email me.
These software programs analyze DNA and protein sequences for evidence of natural selection. I've provided both the source code (in Pascal) and compiled versions (Mac and Windows). They're all really old, so the compiled versions probably don't work.
DNA Slider: Tests heterogeneity in the polymorphism-to-divergence ratio among different regions of a gene, as a way of detecting selective sweeps or balancing selection (McDonald 1998).
SliderPrep: Prepares aligned DNA sequences for input into DNA Slider.
Asymmetry programs: AmbiguityRemover removes ambiguously aligned sites from protein sequence alignments, for input into AsymmetryCounter. AsymmetryCounter counts the number of amino acid subsitutions in each direction between pairs of protein sequences. AsymmetryScaler takes the results from AsymmetryCounter and summarizes substitutional asymmetry data in a single scale (McDonald 1999).
Handbook of Biological Statistics: A free, online textbook which surveys many of the statistical tests commonly used in analyzing biological data. The handbook includes instructions for performing the tests in SAS and also has downloadable spreadsheets to perform most of the tests. A print version of the handbook is available as a free pdf or a 304-page, spiral-bound book for $18. I will publish a new 4th edition in late 2020 or early 2021.
Myths of Human Genetics: A review of the literature on human traits that biology teachers often use to demonstrate genetics, such as tongue rolling, attached earlobes, and mid-digital hair. Almost all of these traits do not have a simple genetic basis, and teachers should stop using them. A print version is available as a free pdf or a 74-page, spiral-bound book for $10. I will publish a new 2nd edition in summer 2020.
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, and I would be glad to have further opportunities to promote evolution. To poke fun at 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.
Kumar, A.S., Park, E., Nedo, A., Alqarni, A., Ren, L., Hoban, K., Modla, S., McDonald, J.H., Kambhamettu, C., Dinesh-Kumar, S.P., and Caplan, J.L. 2018. Stromule extension along microtubules coordinated with actin-mediated anchoring guides perinuclear chloroplast movement during innate immunity. Elife 7: e23625.
Fisher, K.E., Mason, C.E., Flexner, J.L., Hough-Goldstein, J., and McDonald, J.H. 2017. Survivorship of Z-pheromone race European corn borer (Lepidoptera: Crambidae) on a range of host plants varying in defensive chemistry. Journal of Economic Entomology 110: 978-985.
Wenne, R., L. Bach, M. Zbawicka, J. Strand, and J.H. McDonald. 2016. A first report on coexistence and hybridization of Mytilus trossulus and M. edulis mussels in Greenland. Polar Biology 39: 343-355.
Bayha, K.M., M. H. Chang, C. L. Mariani, J. L. Richardson, D. L. Edwards, T. S. DeBoer, C. Moseley, E. Aksoy, M. B. Decker, P. M. Gaffney, G. R. Harbison, J. H. McDonald, and A. Caccone. 2015. Worldwide phylogeography of the invasive ctenophore Mnemiopsis leidyi (Ctenophora) based on nuclear and mitochondrial DNA data. Biological Invasions 17: 827-850.
McDonald, J.H. 2014. Handbook of Biological Statistics, 3rd ed. Baltimore: Sparky House Publishing.
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 gain and loss in protein evolution due to nearly neutral evolution. Mol. Biol. Evol. 23: 240-244.
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.
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.
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.
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.
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.
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.
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., 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.
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. 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. and M. Kreitman. 1991. Scientific correspondence. Nature 354: 116.
McDonald, J.H. and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
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.