They would only have needed food and upkeep (Gen. 6:19-21) for the small number of species which under no circumstances slip into hibernation or estivation.
Kind of a big logical leap there is it not? From "some animals have the ability to hibernate or aestivate in response to no food" to "the small number of species which under no circumstances.....".
Where is the documentation that it is a small number? Many birds migrate instead of hibernating. There is little evidence of hibernation/aestivation in the tropics, food or no food. So far there is one documented case, a lemur in Madascar.
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I think hibernation is not a viable solution to the question of food supply/waste removal on the Ark until someone comes up with some evidence most animals can in fact hibernate. You would think it would have been mentioned in Genesis also. Kind of an important fact to leave out if you wanted your story to be believed. All that detail on the Ark construction and not one peep about hibernation to conserve food.