The statement that is most likely is:
The proportion of short-tailed squirrels may have decreased due to decreased food availability.
This is because the long-tailed squirrels are better adapted for life in trees, which suggests that they might be more successful at obtaining resources (such as food) in that environment, leading to their increased proportion in the population over time. If food availability decreased, it could disproportionately affect short-tailed squirrels, causing their numbers to decline relative to long-tailed squirrels.