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ANYWAY... the consequences of inbreeding are fairly simple. The short version is that it can tank the offspring's Fertility or Immunity stats.
CAN. Doesn't mean it will though.
But there is Hard Inbreeding (that the game warns you about) and Soft Inbreeding (which it doesn't).
See... normally if two animals breed, the Size and Longevity stats tend to be an average of their parents, though they can extend one level above or below that, particularly if the parents both have the same stat level. For instance, if the mother has Size in the 90s and 100 Longevity while the father has 100 size and 90 Longevity... they could produce a child with 100 Size and 100 Longevity... or 90 Size and 90 Longevity... or any other combination in that range.
HOWEVER... Fertility and Immunity are different. You can, in theory, get Mother and Father both with 0 Immunity to breed and pop out a kid with 100 Immunity. You could hypothetically do the same with Fertility except 0 Fertility basically puts a stop to breeding, so that is a no-go. The point is that the range of Fertility and Immunity values for offspring isn't immediately obvious just by looking at the parents.
... Anyway...
When the game tells you two animals are Inbreeding... i.e. "hard inbreeding"... that means that the effective range for their Fertility and Immunity has no lower cap. It can be anywhere between the parent range and 0. A Brother and Sister with 100 Fertility might pop out a kid with 100 Fertility.... or one with 50 Fertility.... or one with 0 Fertility. Same for Immunity.
But what the game does NOT tell you is that because it is influenced by the hidden genetics, there is also Soft Inbreeding. Like if you put two Cousins in a pen together, the game will not warn you that they're Inbreeding, since it doesn't keep track of multiple generations of the family. BUT their Fertility / Immunity ranges will often still extend quite far into the negative, and they can still produce offspring with utterly crappy Fertility (albeit at a lower probability rate than Hard Inbreeding). Okay... and crappy Immunity, but that doesn't matter at all.
SHORT VERSION: Inbreeding can produce sterile animals. That is bad. Try to avoid it.
Still... on the whole inbreeding isn't too bad.
Hear me out here!
I mean yeah, it can produce completely dud offspring with crapped out Immunity and Fertility, but assuming they're not completely infertile, you can actually just let them continue inbreeding and get back to 100% of both within a single generation if you're lucky.
Thinking about my usual approach, I'm constantly trying to get 4x100 animals. But the number of generations when I have to swap the males with ones bought online that have unpredictable effects on the stats, sometimes I figure I might be better off just letting the animals inbreed after all, then trimming off the crap results and keeping the good ones.