She has engaged in theory and observation of coevolution and competition in Anolis lizards of the Caribbean, and recruitment limitation in the rocky intertidal zones of California and Oregon.
She founded and directed the Earth Systems Program at Stanford and has received awards for service to undergraduate education.
Roughgarden's early work in the 1970s and 80s helped to develop the Anolis lizards of the Caribbean as an important model system for evolution and ecology.
After setting up a lab at the Hopkins Marine Station, Roughgarden sought to extend her approach of combining theoretical with field research by studying intertidal acorn barnacles (Balanus and Chthamalus spp).
Earlier work by Joseph Connell, Bob Paine and others had suggested that the characteristic zonation of rocky intertidal communities was predominantly structured by predation,[5] (for example by Pisaster seastars) and by competition,[6][7] wherein dominant Balanus species displaced Chthamalus species to the high intertidal zones.
Together with her student, Steve Gaines, Roughgarden showed that these interspecific interactions were most important in intertidal localities and communities with a high density of barnacles, such as those Connell and others had studied in Scotland.
[6][8] At Hopkins in Central California, however, barnacle density was lower, and the amount of free space was best explained by periodic pulses of larval recruitment.
Following the Science paper, forty scientists produced ten critical letters[17][18] stating that the article was misleading, that it contained misunderstandings and misrepresentations, that sexual selection accounted for all the data presented and subsumed Roughgarden's theoretical analysis, and that sexual selection explained data that her theory could not.
[17][18] Troy Day stated that "many people felt that this was completely shoddy science and poor scholarship, all motivated by a personal agenda".
The first chapter addresses how sexual reproduction evolved in the first place, and makes the case for Roughgarden's Portfolio hypothesis, which emphasizes that sexual reproduction creates genetic diversity through recombination, as opposed to the more commonly favored Muller's ratchet, which emphasizes that sex removes deleterious mutations through recombination.
[15] In 2013, Roughgarden funded a Catalysis meeting at the National Evolutionary Synthesis Center with the goal of debating and reviewing "the status of sexual selection studies and to indicate challenges and future directions".
[26] 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.
[28] As professor emerita, Dr. Roughgarden turned her attention to the emerging concept of the holobiont, which she defined as "an animal or plant host together with all the microbes living on or in it, exosymbionts and endosymbionts, respectively.
[29]" The concept, which originated in 1943, has had increasing recognition with the rise of second and third-generation DNA sequencing methods that allow the microbial communities (i.e. the microbiome) of a host to be examined.
However, the hologenome concept has been criticized on the grounds that microbiomes are usually not vertically transmitted from parent to child,[33] thereby violating what is commonly thought to be one of the key principles of natural selection: variation inherited in a Mendelian fashion.
They considered the tight integration of physiological, developmental, reproductive and even immunological components between host and microbial symbionts to provide a foundation for this concept.
Because microbial colonization of the host follows a Poisson distribution, there is no Hardy-Weinberg analog, and directional selection tends to be more diffuse than expectated under vertical transmission.