We are measuring how many animals existed at that time by how many exist today. For example God said choose 7 of every kind of bird. Obviously, today there are much more than 7 types of bird. After 4000 years those 7 types of bird have evolved into hundreds or is it thousands of types of bird?
Maybe there were just enough animals, birds etc sufficient to be the root of every future species evolving from the root of each kind of animal? For example zebras come from the horse root? Again I am no scientist, but it makes sense to me. It makes more sense to believe in God who created all things and if God created all things He is therefore fully capable of ensuring that the bible will be trustworthy for all generations