A natural disaster.
Step-by-step explanation:
A natural disaster would most likely have occurred to have the population of squirrels completely diverge from each other in order for them to become two separate species.
If a tornado, flood, earthquake, or another type of a natural disaster were to happen, it may have caused drastic damage to the ecosystem and environment of the squirrels. This would most likely cause the squirrels to split up, or diverge from each other and go to separate places in search of a new home.
Over time, these squirrels will reproduce with their own group. Each new group of squirrels, as they are both in different environments now, will have different adaptations from each other. This will eventually make it so they will never be able to reproduce with each other again if they were to meet, as they are now completely different species of squirrel.