Sometimes the population is so small that you end up with indbred offspring.
This happened with cheetahs: their population numbers underwent a sudden drop in the past, introducing what is known as a genetic bottleneck. Since so much of the population died, there is less genetic variation in the species, leading to an increased chance for harmful mutations appearing in offspring.
This is made worse by human activity (hunting, habitat loss), which further reduces the genetic variance of cheetah populations.
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