We have an old growth juniper on our property, and it has been taken over by squirrels. They have made their homes underneath the tree. I am afraid they will weaken the root structure, and the tree could fall over in a storm. What is the best and most humane way to get rid of the squirrels, and to fill in the holes where they have dug?
Old-growth juniper (>150 yrs old) provide important habitat elements (food, cover, thermal protection, etc.) for many species of wildlife, including several of the small mammals in the same community. It is likely that the squirrels and other animals are using opportunities that are already occurring in or around the tree as a consequence of its developmental/age stage, such as the cavities and tunneling opportunities.
I don't think the animals are damaging the tree such that the tree's survival is jeopardized and would advise no actions against the animals.
Juniper are very long-lived, resilient trees and it sounds as though yours is doing a great job as part of the ecosystem. This publication is quite old now but you might find the wildlife chapter (starts p. 37) and especially the small mammal section (table on p. 59) very interesting as there are likely many creatures (several nocturnal) using and enjoying the benefits of having a legacy tree available.