Caribbean Anoles & Interspecific Competition 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. For example, she used two-species enclosure experiments on two Caribbean islands to demonstrate increasing strength of interspecific competition as resource partitioning decreases: a central tenet for
competition theory. The
Anolis system thus provided an early example of an eco-evolutionary feedback, and with further development by
Jonathan Losos and others, has become an important example of
adaptive radiation.
Barnacles & Recruitment Limitation 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, (for example by
Pisaster seastars) and by competition, 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. 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. This in turn explained why field studies in the north had found interspecific interactions to be important, while her own field studies in the south had found larval recruitment to be most important for structuring intertidal populations. This deft synthesis helped to drive a paradigm shift in marine ecology which emphasized larval dispersal and recruitment dynamics over adult interactions and favored demographic models of populations open to larval recruits from distant localities, which dominated the field during the 1990s.
Criticism of sexual selection Around the time of her transition, Roughgarden began to shift her research focus to Darwin's theory of
sexual selection. In her 2004 book, ''Evolution's Rainbow'', Roughgarden analyzes how biology can influence human sexuality and gender identity and explores the substantial diversity of mating systems and sexuality throughout the animal kingdom, with an eye toward understanding human sexual categories like gay, lesbian, and trans. In this book, and other articles around the same time, she offered criticism of sexual selection theory by providing examples of species that depart from its predictions (such as homosexual behavior in bonobos, elephants and lizards) as well as highlighting contradictions between population genetic theory and sexual selection theory. She also provided the beginnings of an alternative theory to sexual selection called social selection, which she describes as being focused on natural selection based on differential offspring production, where sexual selection is focused on differential mating success. A 2006 article in the journal
Science with her student Erol Akçay, and Meeko Oishi, formally presented the theory of social selection in terms of game theory. Beyond the
Nash Competitive Equilibrium (NCE) imported to evolutionary biology by
John Maynard Smith as the
Evolutionary Stable Strategy, Roughgarden et al. discuss the
Nash Bargaining Solution (NBS), which exists as an alternative to the NCE that is reached through negotiation. When playing in developmental time (as opposed to evolutionary time), a game player that stands to lose individual fitness at an NCE relative to its competitor may establish a threat point by promising to play a sub-optimal strategy. Through negotiation, for example via a side payment, the players can arrive at an NBS through playing mixed strategies across repeated games which thereby maximizes the fitness of the cooperative "team" (which consists of both players) rather than to any one player. Roughgarden et al. provide several examples of what such cooperative game play would look like in nature, and then define the evolutionary theory of social selection as one which considers such cooperative team games in the developmental tier as the primitive state, with sexual conflict as the derived state. They argue that social selection theory is mutually exclusive with the evolutionary theory of sexual selection, which treats sexual conflict as the primitive state and sexual cooperation as derived. Following the
Science paper, forty scientists produced ten critical letters
Tim Clutton-Brock of Oxford University wrote a more detailed rebuttal in
Science in 2007, in which he concedes the point that males can engage in sexual selection on females, even in species where the operational sex ratio is biased towards males, stating: "Consequently, satisfactory explanations of the evolution of sex differences requires an understanding of the operation of sexual selection in females as well as males". Roughgarden continues to build a case against sexual selection theory and to present
social selection theory as an alternative. The book is titled as a response to the popular book,
The Selfish Gene, by
Richard Dawkins, which expounds what Roughgarden describes a "neo-Spencerian" view of nature "red in tooth and claw" in which competition and conflict dominate. In
The Genial Gene, after an initial section defining and attacking sexual selection, followed by a definition of social selection as one based on differences in offspring-production, rather than differences in mating success. A second section is focused on the genetic basis of social selection. 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. The second chapter explains the binary distribution of gamete types (sperm vs. egg) as a strategy to maximize gametic contact, rather than as a result of conflicting gametic strategies. A final chapter argues that hermaphroditism, rather than gonochorism, is the primitive state of sexuality. The third section takes a two-tier approach to developing social selection theory. A behavioral tier focuses on game theory and Nash Bargaining Solutions as outlined in her 2006 paper. Roughgarden's criticism of sexual selection has been rejected by the scientific community, and her papers on it have received few citations in scientific literature. In a 2019 interview, she stated that "Most biologists remain defensive of sexual selection theory". The group struggled to come to a consensus definition of sexual selection, but a subgroup offered a definition that for the first time explicitly differentiated fecundity selection for sexual selection
sensu stricto. 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
creationism and
intelligent design, but asserts her belief in
God's involvement in evolution. She was a speaker at the
Beyond Belief symposium in 2006.
Holobiont Evolution 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." 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. The close association between the microbiome and its host has led many to suggest that the holobiont may be an evolutionary unit of selection, in which the combination of the host's genes with those of its microbiome produce an extended genome, or hologenome. However, the hologenome concept has been criticized on the grounds that microbiomes are usually not vertically transmitted from parent to child, thereby violating what is commonly thought to be one of the key principles of natural selection: variation inherited in a Mendelian fashion. Together with other proponents of the holobiont concept, Roughgarden wrote a 2018 review of the topic They also cite the horizontal acquisition of DNA coding for
syncytin, a protein that allows formation of the
placenta, as a key step in the evolution of placental mammals, which also demonstrates adaptive evolution in the holobiont. In this review, that further fleshed out her model of holobiont evolution. The first showed that, when microbes colonize hosts following a
Poisson distribution, horizontal transmission can still lead to holobiont evolution when beneficial symbionts increase the success of their hosts and thus flood the microbial source pool (the converse case with parasitic microbes also holds true). She calls this phenomenon "collective inheritance" as opposed to lineal
Mendelian inheritance. The second paper adds a second microbial species to the model, as well as a "colonization parameter"
d, which partially determines the Poisson rate parameter. The
d parameter approximates the density of the symbiont strain around the host, or the host's selectivity for the symbiont species, depending on context. 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. She then reasons from this two-microbe model that the host is likely to use antibodies and "probodies" to modulate
d for each microbial species, in effect orchestrating things so that only microbes that provide some minimum amount of altruism toward their host are allowed to remain in symbiosis with the host. From the microbe's standpoint, those species that provide the minimum amount of altruism to clear the host's threshold will tend to outcompete those that provide more. This paper carefully demonstrates that this host-orchestrated species selection process is conceptually distinct from co-evolution or multi-level selection and can predict and explain the tight integration of hosts and their microbial symbionts found throughout the
eukaryotic tree of life. == Awards and honors ==