You are making my point.
Yes, you may have a snake that dens in the same location. Ecological studies have shown us that by and large it is the females that establish den sites. So we have a denned female that you observe every year, is she breeding with the exact same male every year? And is that male her brother/father/son? No and no. The males of the species tend to be more travel prone because they move around a lot trying to find females to breed. So she is going to be seeing a new male each year.
Next question - Are all of the babies she produced every year also denning with her? No, because the carrying capacity of the area is really only sufficient to support a single adult animal. The babies may hang around for a part of the season because their prey specificity is not in competition with the female, but eventually they will have to move on because they cannot compete with her and each other. So they begin to travel outward to find their own territory/range/den.
Next question - What are the odds that the territory immediately next door is going to be openly available and not already inhabited by another adult, established animal? Probably pretty low. So the babies have to keep on moving until they find an open territory. Odds are that open territory is going to be rather distal from the mother’s denning site.
Even if the most immediately proximal territory is available however, revisit what I mentioned above about males being roamers. Males are not likely to be establishing any set den site, instead, they will essentially behave as a vagabond; traveling along looking for the best opportunity to eat and (once old enough) mate where and when they can but never actually settling down. By the time the males reach sexual maturity (1-2 seasons) they will have traveled some distance from their mother’s den site and (because snakes are not social pack animals) they will also be distanced from their siblings. You also have to account for the fact that the males reach sexual maturity faster than the females. So even if the male is proximal to one of his sisters when he reachs sexual maturity, he still will not be able to breed with her. And by the time she has reached sexual maturity and found a den site of her own, the male will have moved along in his own travels.
Add clutch attrition into the equation. High probability that only 1-2 animals in the clutch will even make it to sexual maturity
Can you honestly say that, even under this simplified accounting, when you combine all of these factors it is realistic that inbreeding is occurring at high levels in nature?
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Yes, there are many thousands of unrelated animals mating together in a small area. As a related analogy - if I stuck you and your sister together in a pitch black room with 1998 other strangers for a blind dance contest, what are the odds you would accidentally happen to pair up with her?
So again, low chance of inbreeding
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I work with Black Gaps so I know all the fun of locality alterna. But, you are conflating the captive population with no account of the ecological range. How much area makes up the entire range of the Black Gap locale? How many animals are inside of that locale? How likely is it that any two given random animals from within that locale are directly related to one another?
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Yes, to maintain the specific traits the line was selectively bred to have, you cannot outcross because of the potential to lose those traits. However, that does not mean those lines are perfectly fit and do not have issues unrelated to the specific traits they were bred for.