Each population of squirrels evolved different adaptions for each side of the canyon and eventually became genetically different populations. This is an example of which stage of speciation?

Natural selection - the process whereby organisms better adapted to their environment tend to survive and produce more offspring. The theory of its action was first fully expounded by Charles Darwin and is now believed to be the main process that brings about evolution.

You posted it twice so here's the answer again but with a better explanation.

The populations become adapted to different environments and eventually become so different that they cannot interbreed to produce fertile offspring.