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Dr. John Pepper, Assistant Professor

Positions and Education
Assistant Professor, Ecology and Evolutionary Biology, University of Arizona, 2002-present
Co-director, Complex Systems Summer School (Santa Fe Institute and Central European University), Budapest, Hungary, 2002
Postdoctoral Fellow, Santa Fe Institute. 1999 - 2002
Lecturer, University of Michigan. 1997 - 1999
Ph.D., Department of Biology, University of Michigan. 1996. Thesis title: "The behavioral ecology of the glossy black-cockatoo Calyptorhynchus lathami halmaturinus" Major advisor: Dr. Richard D. Alexander
B.A. in Biology, University of California at Santa Cruz. 1985. Highest Honors in Biology, College Honors, Honors on Senior Comprehensive Requirement
A.A. in Computer Science, Montgomery College, Maryland. 1983. Chancellor's Honor Award

Honors and Awards
Research Partnership Fellowship, University of Michigan 1993
Rackham Pre-doctoral Fellowship, University of Michigan, 1993 (declined) Walker Scholarship Award, University of Michigan Museum of Zoology, 1992
Hinsdale Scholarship Award, University of Michigan Museum of Zoology, 1991
T. C. Schneirla Award for Research in Comparative Psychology, 1991
Naturalist-Ecologist Training Program Fellowship, University of Michigan Biological Station, 1988
Regents Fellowship, University of Michigan, 1987

Research Interests
My research focuses on the dynamics of multilevel selection, or systems in which natural selection acts simultaneously at more than one level in a biological hierarchy. Any population evolves if variation in heritable traits affects the reproductive success of its members. This is equally true whether the population consists of organisms or any other reproducing entity. Life is hierarchically organized, and most reproducing entities contain collections of smaller reproducing entities. Examples include genes, chromosomes, organelles, cells, organisms, colonies, and mixed-species communities. As a result, selection can act simultaneously at more than one level of organization. Although each level of selection can be conceptualized as a separate process, they often interact in complex ways that can dramatically affect evolutionary outcomes.

Multilevel selection theory can be a useful tool for studying the evolution of any trait involving cooperation or conflict. Specific examples include problems in: intragenomic conflict, ontogeny, cancer, senescence, sexual reproduction, pathogen virulence, resource exploitation, interference competition, mutualism, social cooperation, and transitions in individuality. I typically study multilevel selection using agent-based computer models to generate the dynamics of interest, and the mathematical models to analyze and interpret those dynamics. In addition to refining multilevel selection theory, I am also working on applying it to several specific problems.

Read a profile of John Pepper in the Fall 2003 (Winter 2004) issue of Desert News & Views (pdf file)

PubMed list of publications for John Pepper
Selected Publications

  1. Mitteldorf, J.M., & Pepper, J.W. 2007. How can evolutionary theory accommodate recent empirical results on organismal senescence? Theory in Biosciences Published online 3/7/07:
    http://www.springerlink.com/content/x87g12n7276rm856/

  2. Pepper, J.W. 2007. Considering cooperation: Empiricism as a foundation for unifying the behavioral sciences. Behavioral and Brain Sciences 30(1):38-39.

  3. Pepper, J.W. 2007. Simple Models of Assortment through environmental feedback. Artificial Life, 13(1): 1-9.

  4. Merlo, L.M.F., Pepper, J.W., Reid, B.J., and Maley, C.C. 2006. Cancer as an evolutionary and ecological process.  Nature Reviews Cancer. 6: 924-935.

  5. G. A. Hoelzer, E. Smith, J. W. Pepper. 2006. On the logical relationship between natural selection and self-organization. Journal of Evolutionary Biology. 19(6):1785-1994

  6. Pepper, J.W. 2003. The evolution of evolvability in genetic linkage patterns. BioSystems.69:115-126.

  7. Jun, J., Pepper, J.W., Savage, V., Gillooly, J., & Brown, J.H. 2003. Allometric scaling of ant foraging trail networks. Evolutionary Ecology Research, 5: 297-303.
  8. Pepper, J.W. & Smuts, B.B. 2002. A mechanism for the evolution of altruism among non-kin: positive assortment through environmental feedback. American Naturalist 160: 205-212.

  9. Pepper, J.W. 2002. The evolution of evolvability in genetic linkage patterns. BioSystems (Special issue on Evolvability), vol 69/2-3 pp. 115 - 126 link Also available as SFI Working Paper 02-02-003.

  10. Mitani, J.C., Watts, D.P., Pepper, J.W., and Merriwether, D.A. 2002. Demographic and social constraints on male chimpanzee behaviour. Animal Behaviour, 63: 727-737.

  11. Pepper, J.W. and Hoelzer, G. 2001. Unveiling mechanisms of collective behavior. (Review of "Self-organization in Biological Systems", by Camazine et al.) Science 294: 1466-1467.

  12. Pepper, J.W. and Knudsen, T. 2001. Selection without multiple replicators? Behavioral and Brain Sciences 24(3):550-551.

  13. Pepper, J.W. and Smuts, B.B. 2001. Agent-based modeling of multilevel selection: the evolution of feeding restraint as a case study. Pp 57-68 in: W. C. Pitt, ed. Swarmfest 2000, Proceedings of the 4th Annual Swarm User Group Conference. Natural Resources and Environmental Issues, Volume XIII, S. J. and Jessie E. Quinney Natural Resources Research Library Logan, UT.

  14. Pepper, J.W. 2000. Relatedness in group-structured models of social evolution. Journal of Theoretical Biology 206(3):355-368.

  15. Pepper, J.W. and Smuts, B.B. 2000. The evolution of cooperation in an ecological context: an agent-based model. In: Dynamics in Human and Primate Societies: Agent-Based Modeling of Social and Spatial Processes. T. A. Kohler and G. J. Gumerman, eds. Pp. 45-76. Oxford: Oxford University Press.

  16. Pepper, J.W., Male, T. and Roberts, G. 2000. The foraging ecology of the South Australian glossy black-cockatoo, Calyptorhynchus lathami halmaturinus. Austral Ecology 25:16-24.

  17. Pepper, J.W., Mitani, J.C. and Watts, D.P. 1999. General gregariousness and specific social preferences among wild chimpanzees. International Journal of Primatology 20(5):613-632.

  18. Smolker, R.A. and Pepper, J.W. 1999. Whistle convergence among allied male bottlenose dolphins (Delphinidae, Tursiops sp.). Ethology 105:595-617.

  19. Heinrich, B. and Pepper, J.W. 1998. Influence of competitors on caching behavior in the common raven, Corvus corvax. Animal Behaviour 56:1083-1090.

  20. Pepper, J.W. 1997. A survey of the South Australian glossy black-cockatoo (Calyptorhynchus lathami halmaturinus) and its habitat. Wildlife Research 24:209-223.

  21. Arnett, A.E. and Pepper, J.W. 1997. Evidence of mate guarding in the Glossy Black-Cockatoo Calyptorhynchus lathami. Emu 97:177-180.

  22. Pepper, J. W. 1996. The behavioral ecology of the glossy black-cockatoo Calyptorhynchus lathami halmaturinus. Ph.D. thesis, The University of Michigan, Ann Arbor, MI.

  23. Smolker, R.A., Richards, A.F., Connor, R.C. and Pepper, J.W. 1992. Sex differences in patterns of association among Indian Ocean bottlenose dolphins. Behaviour 123(1-2):38-69.

  24. Pepper, J.W. 1992. A new food source for the Glossy Black Cockatoo. South Australian Ornithologist 31(6):144-145.

  25. Pepper, J.W., Braude, S.H., Lacey, E.A. and Sherman, P.W. 1990. Vocalizations of the naked mole-rat. In: The Biology of the Naked Mole-rat. P.W. Sherman, J.U.M. Jarvis, and R.D. Alexander, eds. Pp. 243-274. Princeton University Press: Princeton.

  26. Chamberlain, S.C., Pepper, J.W., Battelle, B.-A., Wyse, G.A. and Lewandowski, T.J. 1986. Immunoreactivity in Limulus. II. Studies of serotonin-like immunoreactivity, endogenous serotonin, and serotonin synthesis in the brain and lateral eye. Journal of Comparative Neurology 251:363-375.

  27. Battelle, B.A., Truckenmiller, M.E. and Pepper, J.W. 1983. Development of rat retinal neurons in monolayer culture: effect of elevating the concentration of K+ in the growth medium. Society for Neuroscience Abstracts, Vol. 9, Part 2, p. 1099.
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