It used to be thought that alligators’ jaws had a stronger bite, which was necessary for preying on turtles. Recent biomechanical studies found no correlation, though.
You wouldn’t think it, but alligators and crocodiles are only very distantly related. Their last common ancestor lived about 80 million years ago, during the late Cretaceous. To put that in perspective, the last common ancestor between humans and elephants lived around 60-70 million years ago. Modern crocodiles and alligators have converged on the same basic body plan and lifestyle because it’s so successful, but they’ve been evolving independently for an extraordinarily long time. It’s possible the differences in jaw shape are not reflective of significant differences in evolutionary pressures (or at least, not anymore) unlike, say, the famous Darwin finches.
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