Michael J Stanhope

Faculty member

Department of Public and Ecosystem Health


Public and Ecosystem Health

Department of Public and Ecosystem Health
Cornell University College of Veterinary Medicine
Ithaca, NY 14853

Office: 607.253.3859
Email: mjs297@cornell.edu

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 comparative genomics, and population genomics within various groups of bacterial and viral pathogens. We are interested in the molecular evolutionary history, and specifics, of how pathogens 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 pathogens ranging from bacteria, to coronaviruses, to protozoans. 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 sharks, exploring such traits as their wound healing abilities, cancer protection, and electroreception. Dr. Stanhope joined Cornell PMDS in 2005 and has nearly 35 years of experience in molecular evolution research. Dr. Stanhope’s research has been funded continuously, since his arrival in 2005, from NIH, USDA, FDA and foundation 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


Below, a selection of publications; for a complete list see:

  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., 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. 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.
  35. 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.
  36. 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.
  37. 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.
  38. Zeng L., P. Xue, M.J. Stanhope, and R.A. Burne. 2013. A galactose-specific sugar: phosphotransferase permease is prevalent in the non-core genome of Streptococcus mutans. Mol. Oral Microbiol. 28:292-301.
  39. 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.
  40. Richards V.P., S.C. Choi, P.D. Pavinski Bitar, A.A. Gurjar, and M.J. Stanhope. 2013. Transcriptomic and genomic evidence for Streptococcus agalactiae adaptation to the bovine environment. BMC Genomics 14:920.
  41. Richards V.P., S.R. Palmer, P.D. Pavinski Bitar, X. Qin, G.M. Weinstock, S.K. Highlander C.D. Town, R.A. Burne, and M.J. Stanhope. 2014. Phylogenomics and the dynamic genome evolution of the genus Streptococcus. Genome Biol Evol. 6:741-53.
  42. Dogan, B, H. Suzuki, D. Herlekar, R.B. Sartor, B.J. Campbell, C.L. Roberts, K. Stewart, E.J. Scherl, Y. Araz, P. Pavinski Bitar, T. Lefébure, B. Chandler, Y.H. Schukken, M.J. Stanhope, and K.W. Simpson. 2014. Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation. Inflamm. Bowel Dis. 20:1919-32.
  43. Richards, V.P., T. Lefébure, P.D. Pavinski Bitar, B. Dogan, K.W. Simpson, Y.H. Schukken, and M.J. Stanhope. 2015. Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PLoS One 10:e0119799.
  44. Kaspar, J., S.-J. Ahn, S.R. Palmer, S.C. Choi, M.J. Stanhope, and R.A. Burne. 2015. A unique ORF within the comX gene of Streptococcus mutans regulates genetic competence and oxidative stress tolerance. Mol. Microbiol. 96:463-482. 
  45. Lutz, H.L., B.D. Patterson, J.C. Kerbis Peterhans, W.T. Stanley, P.W. Webala, T.P. Gnoske, S.J. Hackett, and M.J. Stanhope. 2016. Diverse sampling of East African haemosporidians reveals chiropteran origin of malaria parasites in primates and rodents. Mol Phylogenet Evol. 99:7-15.
  46. Lutz, H.L., N.J. Marra, F. Grewe, J.S. Carlson, V. Palinauskas, G. Valkiūnas, and M.J. Stanhope. 2016. Laser capture microdissection microscopy and genome sequencing of the avian malaria parasite, Plasmodium relictum. Parasitol Res. 115:4503-4510.
  47. Jacob, A.S., L.O. Andersen, P.D. Pavinski Bitar, V.P. Richards, S. Shah, M.J. Stanhope, C.R. Stensvold, and C.G. Clark. 2016. Blastocystis mitochondrial genomes appear to show multiple independent gains and losses of start and stop codons. Genome Biol Evol. 8:3340-3350.
  48. Marra, N.J., V.P. Richards, A. Early, S.M. Bogdanowicz, P.D. Pavinski Bitar, M.J. Stanhope, and M. Shivji. 2017. Comparative transcriptomics of elasmobranchs and teleosts highlight important processes in adaptive immunity and regional endothermy. BMC Genomics 18:87.
  49. Marra, N.J., M.J. Stanhope, N.K. Jue, M. Wang, Q. Sun, P. Pavinski Bitar, V.P. Richards, A. Komissarov, M. Rayko, S. Kliver, B.J. Stanhope, C. Winkler, S.J. O'Brien, A. Antunes, S. Jorgensen, and M.S. Shivji. 2019. White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. Proc. Natl. Acad. Sci. USA. 116:4446-4455.
  50. Richards, V.P., I.M. Velsko, T. Alam, R.N. Zadoks, S.D. Manning, P.D. Pavinski Bitar, H.B. Hasler, C. Crestani, G. Springer, B. Probert, C.D. Town, and M.J. Stanhope. 2019. Population gene introgression and high genome plasticity for the zoonotic pathogen Streptococcus agalactiae. Mol. Biol. Evol. 36:2572-2590.

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