Thompson's research interests encompass a wide range of organisms and topics in ecology and evolutionary biology. Working with students and several research collaborators he has investigated: habitat selection and movement ecology of bighorn sheep and cougar; the ecology and evolution of phenotypic plasticity and developmental integration in grasshoppers; molecular evolution; butterfly habitat selection and evolutionary ecology; recovery of alpine butterfly habitat following catastrophic fire; and scarab dune beetle ecology and evolution.

The research on butterflies, conducted with students and collaborators from federal agencies, is focused on understanding basic characteristics of the life-history, population biology, and larval myrmecophily of several endemic species in the Spring Mountains of southern Nevada. In alpine bristlecone pine environments, we have observed Mount Charleston blue butterfly oviposition (below) on three different species of legume cushion plants and quantified the influence of nectar plant availability and low tree cover on female selection of larval host plants. Portions of this research are described in the Federal Register (Endangered and threatened wildlife and plants; determination of endangered species status for Mount Charleston blue butterfly. Dept of Interior, Fish and Wildlife Service. June 30, 2015, Federal Register 80:37404-37430).

In other research, measuring the establishment of plants following the catastrophic Carpenter 1 fire, Thompson's team has found that the early stages of recovery are dominated by the plants essential for high quality habitat of the endangered Mount Charleston blue butterfly.  Using genetic markers and phylogeographic analyses, they have also studied phenological divergence, diapause plasticity, and gene flow in two cohorts of Spring Mountains dark blue butterflies whose larvae feed on the flowers of host plants that bloom at different times. This research establishes the importance of incorporating population eco-evolutionary dynamics into management and conservation plans.