Roughgarden received a Bachelor of Science in biology and a Bachelor of Arts in Philosophy from University of Rochester in 1968 and a Ph.D. in biology from Harvard University in 1971. As of 8/2011, she is the author of 8 books and over 178 articles. In 1998, Roughgarden transitioned from male to female.
Roughgarden has taught at Stanford University since 1972. She founded and directed the Earth Systems Program at Stanford and has received awards for service to undergraduate education. In 2011 she retired from Stanford and moved to Hawaii, where she became an adjunct faculty member at the Hawaiʻi Institute of Marine Biology.
In addition to a textbook on ecological and evolutionary theory in 1979, Roughgarden has carried out ecological field studies with Caribbean lizards and with barnacles and their larvae along the California coast. In 2004 Roughgarden published a challenge to sexual selection titled Evolution's Rainbow: a critique of Darwin's sexual selection theory based on instances in which animals do not follow traditional sex roles where the male attempts to impress the female, and the female chooses her mate. It also contains a literature survey on unexpected sexual behavior in many species of animals.
An article published by her lab on these ideas received criticism in the pages of the journal Science. Forty scientists produced ten critical letters, some of which were vitriolic. However, Roughgarden, quoted as being "not altogether surprised" by the volume of dissent, argued that her team had replied to most of the criticisms.
In The Genial Gene (2009) the case against sexual-selection theory is continued and social-selection theory presented as an alternative. It lists 26 phenomena not explained by current sexual-selection theory that are better explained by social selection. According to Roughgarden, sexual selection theory derives from a view of natural behavior predicated on the selfish-gene concept, competition and deception, whereas the social-selection theory derives from teamwork, honesty, and genetic equality.
Roughgarden has written on the relationship between Christianity and science. Her book Evolution and Christian Faith: Reflections of an Evolutionary Biologist presents scripture passages that emphasize her belief that the Bible does not conflict with evolutionary biology and relates Christianity and evolution by asserting that all life is interconnected, as members of a faith community are connected. Roughgarden opposes the theories of creationism and intelligent design, but asserts her belief in God's involvement in evolution. She attended and was a speaker at the Beyond Belief symposium in November 2006.
Selected bibliography 
- Roughgarden, J. The Genial Gene: Deconstructing Darwinian Selfishness. Hardcover ed. University of California Press, 2009 ISBN 978-0-520-25826-6
- Roughgarden, J. Evolution and Christian Faith: Reflections of an Evolutionary Biologist. Hardcover ed. Washington, D.C.: Island Press, 2006. ISBN 1-59726-098-3
- Roughgarden, J. Evolution's Rainbow: Diversity, Gender and Sexuality in Nature and People. Paperback ed. Los Angeles: Univ. of California Press, 2004. ISBN 0-520-24073-1
- Roughgarden, J. Primer of Ecological Theory. 1st ed. Prentice Hall, 1997.
- Roughgarden, J. Anolis Lizards of the Caribbean: Ecology, Evolution and Plate Tectonics. Hardcover ed. Oxford Univ. Press, 1995.
- Roughgarden, J, May, R. M., and Levin, S. A. (eds.). Perspectives in Ecological Theory. Oxford Univ. Press, 1995.
- Ehrlich, P. R., and Roughgarden, J. Science of Ecology. Hardcover ed. Prentice Hall, 1987.
- Roughgarden, J. Theory of Population Genetics and Evolutionary Ecology: an Introduction. 1st ed. Prentice Hall, 1979.
- Stonewall Book Award, 2005
- American Academy of Arts and Sciences, Fellow 1993
- Guggenheim Foundation, Fellow 1985
- Jonah Lehrer. "The Effeminate Sheep". Seed (June/July 2006). Reprinted in Richard Preston, ed. (2007). The Best American Science and Nature Writing. New York: Houghton Mifflin. ISBN 978-0-618-72231-0.
- "Sexual selection alternative slammed". Retrieved 2007-05-15.
- "First Congregational Church of Berkeley: Event Details". Retrieved 2006-09-19.
- Roughgarden, Joan. Evolution and Christian Faith: Reflections of an Evolutionary Biologist. Washington D.C.: Island Press, 2006.
- Joan Roughgarden profile – Stanford Univ.
- Joan Roughgarden 50-min interv. – Web Radio (Gender Talk)
- Seed Magazine article on sexual selection theory
- Video (with mp3 available) of conversation with Roughgarden and Robert Wright on Bloggingheads.tv