The devs have put out that the gene pool is an average over the habitat for a species, and more specifically a bell curve. For any non-statistics majors, this means that over the whole of a group, most will fall in the average category (in our case an average fitness for the animals), a small amount will be lower than average, and the other small amount will be above average.
So to put this to the test, I went out and tried to take a species in a specific habitat, and harvest all low fitness animals and see how the numbers at different fitness levels were present. I ended up harvesting 27 animals with fitness ranging from 10% to 49.9%. I counted them in bins of 5 % fitness, so 10 to 14.9%, and then 15 to 19.9% and so on. The numbers in each bin did look like a bell curve as shown by the solid bars in the below bar graph. If we assume that it is indeed a bell curve, then the high fitness half of the graph would probably look something like the cross hatched bars in the graph.
In section 5.4 on Herd Management, I did a good bit of testing on the topic. When I was managing that group of herds, I did not notice much impact on the caribou in the grassland or mountain habitats. So I am thinking that management and any impact that you make on a gene pool in one habitat, does not significantly impact others.
One take away from this topic is that even without herd management, there are more than likely some quality animals on a map, you just don’t know where or how old they are.