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We need to seriously assess our domestic pets... firstly the lack of genetic diversity has caused horrendous medical issues and often we have no choice but to put them down eventually.
We've got to a stage were breeds such as bulldog can't even mate with each other without human intervention because we have breed certain feature that we required or preferred. Quite strange.
Inbreeding is also a problem with humans too, to less of a degree.
I doubt that domestic pet have happier lives them wild ones... possibly less stressful tho.
I agree that historical or evolutionary precedent is no reason to either support or reject something. Unfortunately, everyone's life will have some impact on animals. We destroy their habitats when we build our homes, roads, shops, and factories that make the shit we buy. When we farm crops we displace or kill them to maximise yield. I'm not convinced that killing animals for food is fundamentally different from killing animals for any of the reasons above. We don't need to eat meat, but then we don't need to play golf or buy iphones (etc. etc.) either, both of which will have quite some impact on animals and their environment.
It's not unreasonable to argue that we shouldn't bring animals into the world just for the purposes of killing them later, but when we do so we make a tacit contract with the animal that we will provide it with a life that is as natural, comfortable and safe as possible and a quick stress-free death at the end of it. As a result many domesticated animals live much happier lives than their wild cousins.