Department of Population Medicine & Diagnostic Sciences at the Cornell University College of Veterinary Medicine

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Michael J Stanhope

Professor

Department of Population Medicine and Diagnostic Sciences
College of Veterinary Medicine
Cornell University
Ithaca, New York 14853

607-253-3859, mjs297@cornell.edu

Education

Research and Professional Experience

Honors and Awards

Selected Publications

Research Interests

Current research activities of my laboratory center on the application of molecular evolutionary biology principles and techniques to issues of epidemiology and comparative genomics within various groups of bacterial pathogens. More specifically, we are interested in such things as the relative role of lateral gene transfer versus positive selection in the adaptation of various pathogens to their environment, both at the species and strain level. This work involves the acquisition of comparative genome sequence data using the latest genome sequencing technology, concomitant with evolutionary bioinformatic analysis of the resulting data. It also entails using the information arising from the evolutionary analyses to perform gene knockout and site specific mutagenesis experiments, in an attempt to assay the functional significance of genes under positive selection pressure. Another area of interest in my lab involves applying an evolutionary biology perspective to the development and spread of antibiotic resistance. This work involves a range of pathogen species and antibiotics and takes advantage of our extensive isolate collections.

Education

		Ph.D.	- 1989		Evolutionary Ecology and Molecular Population Genetics; Simon Fraser University
		B.Sc.	- 1980		Zoology and Environmental Biology, University of Calgary

Research and Professional Experience

		Sept 2005-Present			Professor, Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
		2002-Present			Adjunct Professor of Biology - Nova Southeastern University
		2001-2005			Head, Evolutionary Biology - Bioinformatic Sciences - GlaxoSmithKline
		1999-2001			Senior Investigator - Bioinformatics, SmithKline Beecham
		1998-2001			Reader (Assoc. Prof.) - Molecular Systematics - Queen's University of Belfast
		1993-1998			Lecturer (Assist. Prof) - Molecular Systematics - Queen's University of Belfast
		1989-1993			Research Associate (Prof. Morris Goodman), Wayne State University

Honors and Awards

		2003-2008			Honorary Professor - Queen's University of Belfast
		1988			National Science and Engineering Research Council Visiting Fellowship
		1983-86			Graduate Research Engineering and Technology Award. Science Council of British Columbia

Selected Publications

		1.			Stanhope, M.J., B.J. Leighton, and E.B. Hartwick. 1992. Polygenic control of habitat preference in an estuarine amphipod and its possible role in sympatric population subdivision. Heredity 69:279-288.
		2.			Stanhope, M.J., M. Connelly, and E.B. Hartwick. 1992. Evolution of a crustacean chemical communication channel: behavioural and ecological genetic evidence for a habitat modified, race specific pheromone. J. Chem. Ecol. 18:1871-1887.
		3.			Tagle, D.A., M.J. Stanhope, P. Benson, J.L. Slightom, and M. Goodman. 1992. The beta globin gene cluster of the prosimian primate Galago crassicaudatus: nucleotide sequence determination of the 41 kb cluster and comparative sequence analyses. Genomics 13:741-760.
		4.			Stanhope, M.J., J. Czelusniak, J.-S. Si, J. Nickerson, and M. Goodman. 1992. A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly. Mol. Phylogenet. Evol. 1:148-160.
		5.			Stanhope, M.J., D.A. Tagle, M.S. Shivji, M. Hattori, Y. Sakaki, J.L. Slightom, and M. Goodman. 1993. Multiple L1 progenitors in prosimian primates: phylogenetic evidence from ORF1 sequences. J. Mol. Evol. 37:179-189.
		6.			Stanhope, M.J., E.B. Hartwick, and D. Baillie. 1993. Molecular phylogeographic evidence for multiple shifts in habitat preference in the diversification of an amphipod species. Mol. Ecol. 2:99-112.
		7.			Stanhope, M.J., M.R. Smith, V.G. Waddell, C.A. Porter, M.S. Shivji, and M. Goodman. 1996. Mammalian evolution and the IRBP gene: convincing evidence for several superordinal clades. J. Mol. Evol. 43:83-92.
		8.			Tagliaro, C.H, M.P.C. Schneider, H. Schneider, I.C. Sampaio, and M.J. Stanhope. 1997. Marmoset phylogenetics, conservation perspectives, and evolution of the mtDNA control region. Mol. Biol. Evol. 14:674-684.
		9.			Springer, M.S., G.C. Cleven, O. Madsen, W.W. de Jong, V.G. Waddell, H.M. Amrine, and M.J. Stanhope. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388:61-64.
		10.			Springer, M.S., A. Burk, J. Kavanagh, V.G. Waddell, and M.J. Stanhope. 1997. The IRBP gene in therian mammals: Implications for higher level relationships and evidence for loss of function in the marsupial mole. Proc. Natl. Acad. Sci. 94:13754-13759.
		11.			Stanhope, M.J., O. Madsen, V.G. Waddell, G.C. Cleven, W.W. de Jong, and M.S. Springer. 1998. Highly congruent molecular support for a diverse superordinal clade of endemic African mammals. Mol. Phylogenet. Evol. 9:501-508.
		12.			Stanhope, M.J., V.G. Waddell, O. Madsen, W.W. de Jong, S.B. Hedges, G.C. Cleven, D. Kao, and M.S. Springer. 1998. Molecular evidence for multiple origins of Insectivora and for a new order of endemic African insectivore mammals. Proc. Natl. Acad. Sci USA 95: 9967-9972.
		13.			Gatesy, J., M.C. Milinkovitch, V.G. Waddell, and M.J. Stanhope. 1999. The stability of cladistic relationships between Cetacea and higher level artiodactyl taxa. Syst. Biol. 48:6-20.
		14.			Springer, M.S., H.M. Amrine, A. Burk, and M.J. Stanhope. 1999. Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition. Syst. Biol. 48:65-75.
		15.			Tan, I.H., D.G. Mann, H.J. Sluiman, G. Hansen, E. Leskinen, J. Blomster, C.A. Maggs, and M.J. Stanhope. 1999. Molecular phylogenetic evidence for a reversible morphogenetic switch controlling the gross morphology of two common genera of green seaweeds, Ulva and Enteromorpha. Mol. Biol. Evol. 16:1011-1018.
		16.			Teeling, E.C., M. Scally, D.J. Kao, M.L. Romagnoli, M.S. Springer, and M.J. Stanhope. 2000. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 403:188-192.
		17.			Waddell, V.G., M.C. Milinkovitch, M. B�rub�, and M.J. Stanhope. 2000. Molecular phylogenetic examination of the Delphinoidea trichotomy: Congruent evidence from three nuclear loci indicates that porpoises (Phocoenidae) share a more recent common ancestry with white whales (Monodontidae) than they do with true dolphins (Delphinidae). Mol. Phylogenet. Evol. 15:314-318.
		18.			Cassens, I., S. Vicario, V.G. Waddell, H. Balchowsky, D. Van Belle, W. Ding, C. Fan, P.C. Simoes-Lopes, R. Bastida, A. Meyer, M.J. Stanhope, and M.C. Milinkovitch. 2000. Independent adaptation to riverine habitats allowed survival of ancient cetacean lineages. Proc. Natl. Acad. Sci. USA 97:11343-11347.
		19.			Springer, M.S., R.W. DeBry, H.M. Amrine, C. Douady, O. Madsen, W.W. de Jong, and M.J. Stanhope. 2001. Mitochondrial versus nuclear gene sequences in deep level phylogeny reconstruction. Mol. Biol. Evol. 18:132-143
		20.			van Dijk, M.A.M, O. Madsen, F. Catzeflis, M.J. Stanhope, W.W. de Jong, and M. Pagel. 2001. Protein sequence signatures support the 'African clade' of mammals. Proc. Natl. Acad. Sci. USA 98:188-193.
		21.			Madsen, O., M. Scally, C.J. Douady, D.J. Kao, R.W. DeBry, R. Adkins, H.M. Amrine, M.J. Stanhope, W.W. de Jong, and M.S. Springer. 2001. Parallel adaptive radiations in two major clades of placental mammals. Nature 409:610-614.
		22.			McIvor, L.M., C.A. Maggs, J. Provan, and M.J. Stanhope. 2001. rbcL sequences reveal multiple cryptic introductions of the Japanese red alga Polysiphonia harveyi. Mol. Ecol. 10:911-919.
		23.			Chalker, A.F., H.W. Minehart, N.J. Hughes, K.K. Koretke, J.R. Brown, M.A. Lonetto, P.V. Warren, M.J. Stanhope, A. Lupas, and P.S. Hoffman. 2001. Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. J. Bacteriol. 183:1259-1268.
		24.			Delsuc, F., F.M. Catzeflis, M.J. Stanhope, and E.J.P. Douzery. 2001. The evolution of armadillos, anteaters, and sloths depicted by nuclear and mitochondrial phylogenies: implications for the enigmatic fossil Eurotamandua. Proc. Royal Soc. Lond. B. 268:1605-1615.
		25.			Springer, M.S., E.C. Teeling, O. Madsen, M.J. Stanhope, W.W. de Jong. 2001. Integrated fossil and molecular data reconstruct bat echolocation. Proc. Natl. Acad. Sci. USA 98:6241-6246.
		26.			Brown, J.R., C.J. Douady, M.J. Italia, W.E. Marshall, and M.J. Stanhope. 2001.Universal trees based on large combined protein sequence data sets. Nature Genetics 28:281-285.
		27.			Stanhope, M.J., A. Lupas, M.J. Italia, K.K. Koretke, V.C. Volker, and J.R. Brown. 2001. Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates. Nature 411:940-944.
		28.			Murphy, W.J., E. Eizirik, S.J. O'Brien, O. Madsen, M. Scally, C. Douady, M.J. Stanhope, W.W. de Jong, and M.S. Springer. 2001. Resolution of the early placental mammal radiation using a molecular supermatrix. Science 294:2348-2351.
		29.			Teeling, E.C., O. Madsen, R. van Den Bussche, W.W. de Jong, M.J. Stanhope, and M.S. Springer. 2002. Rhinolophoid diphyly, microbat paraphyly, and the convergent evolution of a key innovation in old world microbats. Proc. Natl. Acad. Sci. USA 99:1431-1436.
		30.			Shivji, M., S. Clarke, M. Pank, L. Natanson, N. Kohler, and M.J. Stanhope. 2002. Genetic identification of pelagic shark body parts for conservation and trade-monitoring. Conservation Biol. 16:1036-1047.
		31.			Douady, C.J., F. Catzeflis, D.J. Kao, M.S. Springer, and M.J. Stanhope. 2002. Molecular evidence for the monophyly of Tenrecidae (Mammalia) and the timing of the colonization of Madagascar by Malagassy tenrecs. Mol. Phylogenet. Evol. 22:357-363.
		32.			McIvor, L., C.A. Maggs, and M.J. Stanhope. 2002. RbcL sequences indicate a single evolutionary origin of multinucleate cells in the red algal tribe Callithamnieae. Mol. Phylogenet. Evol. 23:433-446.
		33.			Douady, C.J., P.I. Chatelier-Douady, O. Madsen, W.W. de Jong, F. Catzeflis, M.S. Springer and M.J. Stanhope. 2002. Molecular phylogenetic evidence confirming the Eulipotyphla concept and in support of hedgehogs as the sister group to shrews. Mol. Phylogenet. Evol. 25:200-209.
		34.			Douady, C.J., M. Dosay, M.S. Shivji, and M.J. Stanhope. 2003. Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks. Mol. Phylogenet. Evol. 26:215-221
		35.			Gentry, D.R., K.A. Ingraham, M.J. Stanhope, S. Rittenhouse, R.L. Jarvest, P.J. O'Hanlon, J.R. Brown, and D.J. Holmes. 2003. Variable sensitivity to bacterial methionyl-tRNA synthetase inhibitors reveals subpopulations of Streptococcus pneumoniae with two distinct methionyl tRNA synthetase genes. Antimicrob. Agents Chemother. 47:1784-9.
		36.			Douady, C.J., F. Catzeflis, J. Raman, M.S. Springer, and M.J. Stanhope. 2003. The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews). Proc. Natl. Acad. Sci. USA 100:8325-30.
		37.			Brown, J.R., D. Gentry, J. Becker, K. Ingraham, D.J. Holmes, and M.J. Stanhope. 2003. Horizontal transfer of drug-resistant aminoacyl-transfer-RNA synthetases of anthrax and Gram-positive pathogens. EMBO Rep. 4:692-8.
		38.			Chapman, D., D. Abercrombie, C.J. Douady, E. Pikitch, M.J. Stanhope and M. Shivji. 2003. A streamlined, bi-organelle, multiplex PCR approach to species identification: application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias. Conservation Genetics 4:415-425.
		39.			Douzery, E.J.P., F. Delsuc, M.J. Stanhope and D. Huchon. 2003. Local molecular clocks in three nuclear genes: Divergence ages of rodents and other mammals, and incompatibility between fossil calibrations. J. Mol. Evol.: S201-S213.
		40.			Stanhope, M.J., J.R. Brown and H. Amrine-Madsen. 2004. Evidence from the evolutionary analysis of nucleotide sequences for a recombinant history of SARS-CoV. Infect. Genet. Evol. 4:15-19.
		41.			Springer, M.S., M.J. Stanhope, O. Madsen, and W.W. de Jong. 2004. Molecules consolidate the placental mammal tree. TREE 19:430-438.
		42.			Stanhope, M.J., S.L. Walsh, J.A. Becker, M.J. Italia, K.A. Ingraham, M.N. Gwynn, T. Mathie, J.A. Poupard, L.A. Miller, J.R. Brown, and H. Amrine-Madsen. 2005. Molecular evolution perspectives on intraspecific lateral DNA transfer of topoisomerase and gyrase loci in Streptococcus pneumoniae, with implications for fluoroquinolone resistance development and spread. Antimicrob. Agents Chemother. 49:4315-26.
		43.			Nishihara H., Y. Satta, M. Nikaido, J.G. Thewissen, M.J. Stanhope, and N. Okada. 2005. A retroposon analysis of Afrotherian phylogeny. Mol. Biol. Evol. 22:1823-33.
		44.			Burk-Herrick, A., M. Scally, H. Amrine-Madsen, M.J. Stanhope, and M.S. Springer. 2006. Natural selection & mammalian BRCA1 sequences: elucidating functionally important sites relevant to breast cancer susceptibility in humans. Mammalian Genome 17:257-70.
		45.			Richards, V.P., J.D. Thomas, M.J. Stanhope, and M.S. Shivji. 2007. Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies. Mol. Ecol. 16:139-57.
		46.			Stanhope, M.J., S.L. Walsh, J.A. Becker, L.A. Miller, T. Lef�bure, P. Lang, P.D. Pavinski Bitar, and H. Amrine-Madsen. 2007. The relative frequency of intraspecific lateral gene transfer of penicillin binding proteins 1a, 2b and 2x, in amoxicillin resistant Streptococcus pneumoniae. Infect. Genet. Evol. 7:520-34.
		47.			Lef�bure T. and M.J. Stanhope. 2007. Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition. Genome Biol. 8:R71.
		48.			M.J. Stanhope, T. Lef�bure, S.L. Walsh, J.A. Becker, P. Lang, P.D. Pavinski-Bitar, L.A. Miller, M.J. Italia, and H. Amrine-Madsen. 2008. Positive selection in penicillin binding proteins 1a, 2b, and 2x from Streptococcus pneumoniae and its correlation with amoxicillin resistance development. Infect. Genet. Evol. 8:331-339.
		49.			Lang P., T. Lef�bure, W. Wang, R.N. Zadoks, Y. Schukken, and M.J. Stanhope. 2009. Gene content differences across strains of Streptococcus uberis identified using oligonucleotide microarray comparative genomic hybridization. Infect Genet Evol. 9: 179-188.
		50.			Lef�bure, T. and M.J. Stanhope. 2009. Pervasive, genome wide positive selection, leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 19:1224-32.
		51.			Lang P., T. Lef�bure, W. Wang, P. Pavinski Bitar, R.J. Meinersmann, K. Kaya, and M.J. Stanhope. 2010. Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts. Appl. Environ. Microbiol. 76:1913-25.
		52.			Lef�bure, T., P. Pavinski Bitar, H. Suzuki, and M.J. Stanhope. 2010. Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept. Genome Biol. Evol. (in press).

Last Update 4 August 2010