Native plant
Increasing agriculture and urban development is an increasing problem for Nelson's antelope squirrel. This species will not colonize cultivated land. Therefore, an increase in agriculture land is taking away their habitat and leaving them with no alternative. Grazing livestock further destroys what habitat may be left, and exotic plants are able to take over native grasses that the squirrel forages upon and relies on for shade and cover. Also, pesticide drift from nearby agricultural fields encroaches in on the existing squirrel habitat. Not only are these practices affecting the population of the Nelson's antelope squirrel, but they are also causing problems for other native animal and plant species in the San Joaquin Valley. Native plant species such as the kern mallow, San Joaquin woolly threads, California jewelflower, and Bakersfield cactus are all federally endangered plant species that are being outcompeted by invasive plant species. Many invasive plants grow in very dense patches. These dense patches are not adequate habitats for Nelson's antelope squirrel and many other San Joaquin Valley Species.