After Humboldt, Shannon continued to work as a wildlife biologist for Hoopa Valley Tribal Forestry, and then on to the US Forest Service Pacific Southwest Research Station.

For her thesis, Shannon examined the relationship between bear damage to trees and bird community composition and structure (especially cavity-nesters, such as woodpeckers) on the Hoopa Valley reservation. She surveyed stands historically clear-cut by the Bureau of Indian Affairs (BIA) and determined whether bears function as ecosystem engineers by killing trees and creating structural complexity in otherwise homogenous environments. Shannon's research helped reveal the cost of bear damage, in terms of lost timber value, and the benefit of bear damage in terms of enhanced habitat for species culturally significant to the Hupa.