[1] Gaut's research focuses on the evolution of genetic variation in populations and its impact on adaptation, speciation, and the maintenance of biodiversity, as well as the evolution of transposable elements and their role in shaping genetic architecture and epigenetic state in plants.
[4] Gaut's early work provided several fundamental ideas about the genetic effects of domestication on crop plants; with postdoctoral scholar Adam Eyre-Walker, he used coalescent theory-based models to establish the occurrence of genetic bottlenecks during the domestication of maize,[7] a phenomenon which is now thought to influence the diversity and genome content of many agriculturally important species.
[11] Together with John Doebley, Gaut provided the first DNA sequence-based estimates for the time of polyploidization event in a plant[12][13] and he has contributed to basic methods used in evolutionary studies, such as the codon model of evolution.
[21] His lab also identified loci which may confer resistance to the agriculturally destructive bacterium Xylella fastidiosa.
[22][23][24] Gaut has used experimental evolution of E. coli to characterize the extent of epistasis and antagonistic pleiotropy in the evolutionary process.