Money and public support are the two biggest factors. Just about any animal could be protected and allowed to breed naturally with an unlimited amount of funding, but for the most part no one is going to spend billions of dollars buying and protecting a massive reserve to keep the animals safe. Because of that, these programs need to use their much smaller budgets to keep the animals safe on public lands.
The US red wolf recovery program is a perfect example of how this can fail. There’s a huge network of zoos and wildlife centers breeding them in captivity to ensure they don’t go extinct. Yet, none of that matters if there’s nowhere to *put* the wolves. The only wild population known is in South Carolina after being reintroduced there in the 70’s, and the local government has made it repeatedly clear since that they no longer want the wolves around. They do everything they can to hinder additional reintroductions, while simultaneously looking the other way as local landowners illegally kill them.
Without somewhere for the wolves to live in the wild, there’s only so much a breeding program can do.
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