Survey a limited part and extrapolate from the results to get an estimate of the numbers, the key is in how you do the selection. 3000 years ago it is a little different you can look at the agricultural methods used and the size of the towns in the archaeology to estimate how large a population could be supported.
For wildlife (plants and animals), it’s often estimated based on samplings.
For example, a researcher looking to find numbers of plants in an area may lay out a line of 100 meters, and walk along that line, counting all the plants of type X that she sees. Then, she’d repeat that several more times to get an idea of the frequency of that particular plant in that habitat. The numbers would be estimated off of that.
For animals, techniques can include tagging and releasing, then recapturing animals later on, motion activated cameras, etc. In all those cases, the goal is to get an estimate of how common the animal is – there’s no way to get an exact number.
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