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Michael J Stanhope

Faculty member

Department of Population Medicine and Diagnostic Sciences



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

Office: 607.253.3859

Research Interest

The research activities of the Stanhope laboratory are primarily concerned with the application of molecular evolutionary biology principles and techniques to issues of epidemiology, comparative genomics, and population genomics within various groups of bacterial pathogens. We are interested in the molecular evolutionary history, and specifics, of how bacteria are adapted to different hosts, and in identifying genes associated with various disease phenotypes in both animals and humans. This work involves NGS comparative genomic and transcriptomic data acquired from a number of different groups of pathogenic bacteria, with particular emphasis on Streptococcus and Campylobacter. Additional interests of the laboratory include the pan-genome dynamics of bacterial speciation and the application of an evolutionary biology approach to understanding the development and spread of antibiotic resistance. Recently we have taken a foray into eukaryotic genomics and are studying comparative genomics of the gastrointestinal protozoan Blastocystis, as well as avian malaria. Finally, we are also interested in various aspects of shark biology, such as the evolution of endothermy and alternative reproductive life histories, which we are exploring through comparative transcriptomics. Dr. Stanhope joined Cornell PMDS in 2005 and has nearly 30 years of experience in molecular evolution research. Dr. Stanhope’s research has been funded continuously, since his arrival in 2005, from NIH and USDA sources.


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

Biography/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


  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: behavioral and ecological genetic evidence for a habitat modified, race specific pheromone. J. Chem. Ecol. 18:1871-1887.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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 Biology 16:1036-1047.
  23. 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.
  24. 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.
  25. 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 100:8325-8330.
  26. 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. 4:692-698.
  27. 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.
  28. Springer, M.S., M.J. Stanhope, O. Madsen, and Jong. 2004. Molecules consolidate the placental mammal tree. TREE 19:430-443
  29. 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. 49:4315-4326.
  30. 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 17:257-270.
  31. Stanhope, M.J., S.L. Walsh, J.A. Becker, L.A. Miller, T. Lefébure, 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. 7:520-534.
  32. Lefébure 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
  33. Stanhope, M.J., T. Lefébure, 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.
  34. Lang P., T. Lefébure, 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.
  35. Lefébure, T. and M.J. Stanhope. 2009. Pervasive, genome wide positive selection, leading to functional divergence in the bacterial genus Campylobacter. Genome Res. 19:1224-1232.
  36. Lang P., T. Lefébure, 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. 76:1913-1925.
  37. Lefébure, 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. 2: 646-655.
  38. Suzuki H, T. Lefébure, M.J. Hubisz, P. Pavinski Bitar, P. Lang, A. Siepel, and M.J. Stanhope. 2011. Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution. Genome Biol. Evol. 3:168-185.
  39. Richards, V.P., P. Lang, P.D. Pavinski Bitar, T., Y.H. Schukken, R.N. Zadoks, and M.J. Stanhope. 2011. Comparative genomics and the role of lateral gene transfer in the evolution of bovine adapted Streptococcus agalactiae. Infect. Genet. Evol. 11:1263-1275.
  40. Suzuki, H., T. Lefébure, P.D. Pavinski Bitar, and M.J. Stanhope. 2012. Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. BMC Genomics 13:38.
  41. Suzuki H. and M.J. Stanhope. 2012. Functional bias of positively selected genes in Streptococcus genomes. Infect. Genet. Evol. 12:274-277.
  42. Lefébure, T., V.P. Richards, P. Lang, P.D. Pavinski-Bitar, and M.J. Stanhope. 2012. Gene repertoire evolution of Streptococcus pyogenes inferred from phylogenomic analysis with Streptococcus canis and Streptococcus dysgalactiae. PLoS One 7:e37607.
  43. Burne, R.A., L. Zeng, S.-J. Ahn, S. Palmer, Y. Liu, T. Lefébure, M.J. Stanhope and M. Nascimento. 2012. Progress dissecting the oral microbiome in caries and health. Advances Dental Res. 24:77-80.
  44. Choi. S.C., M.D. Rasmussen, M.J. Hubisz, I. Gronau, M.J. Stanhope, and A. Siepel. 2012. Replacing and additive horizontal gene transfer in Streptococcus. Mol. Biol. Evol. 29:3309-3320.
  45. Richards V.P., R.N. Zadoks, P.D. Pavinski Bitar, T. Lefébure, P. Lang, B. Werner, L. Tikofsky, P. Moroni and M.J. Stanhope. 2012. Genome characterization and population genetic structure of the zoonotic pathogen, Streptococcus canis. BMC Microbiol. 12:293.
  46. Cornejo O.E., T. Lefébure, P.D. Pavinski Bitar, P. Lang, V.P. Richards, K. Eilertson, T. Do, D. Beighton, L. Zeng, S.J. Ahn, R.A. Burne, A. Siepel, C.D. Bustamante, M.J. Stanhope. 2013. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol. Biol. Evol. 30:881-893.
  47. Richards V.P., T. Lefébure, P.D. Pavinski Bitar, M.J. Stanhope. 2013. Comparative characterization of the virulence gene clusters (lipooligosacharide [LOS] and capsular polysaccharide [CPS]) for Campylobacter coli, Campylobacter jejuni subsp. jejuni and related Campylobacter species. Infect. Genet. Evol. 14:200-213.
  48. Zeng L., S.C. Choi, C.G. Danko, A. Siepel, M.J. Stanhope, and R.A. Burne. 2013. Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PLoS One 8:e60465.
  49. Kim J.N., M.J. Stanhope, and R.A. Burne. 2013. Core-gene-encoded peptide regulating virulence-associated traits in Streptococcus mutans. J Bacteriol. 195:2912-2920.
  50. Palmer S.R., J.H. Miller, J. Abranches, L. Zeng, T. Lefébure, V.P. Richards, J.A. Lemos, M.J. Stanhope and R.A. Burne. 2013. Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLoS One. 8:e61358

Awards and Honors

  • 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

Professional/Academic Affiliations

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