Capture/recapture experiments can help. Say you capture 10 rhinos and spraypaint a dot on them. Release them, come back a year later and capture 10 rhinos again. Only 1 of them has spraypaint, which means that you capture 10% of the population, and the population is 100.
You can use that tool and some other fancy predictive modeling to track a population over time and be able to accurately estimate the population even when it gets very small.
There is never any way to know for sure, though.
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