Prior to the Lineaus and the initiation of modern biology, medieval scholars believed in something called "The Great Chain of Being." This was a heirarchical structure of all living beings in the universe, real or unreal, descending from God at the top to rocks at the bottom ... all inclusive, the gentle reader must understand.
The balancing factor was perfection ... God, naturally, was the embodiment of absolute perfection. Man's existence at a high point in this chain did not result from man being a complex creature - it derived from Man's consciousness of God ... i.e., the knowledge of God made man more nearly perfect than anything else that was mundane - that is, of the earth. Rocks and stones, presumably, lacked any perfection whatsoever, being that they exhibited no degree of life and therefore no comprehension of God.
Higher than man came the various creatures of the christian pantheon: cherubs and seraphim and angels. Lower comes the various sorts of animals (with snakes, oysters and barnacles lower than cats, elephants or hawks), and below those the plants and so on.
I mention this to inspire the reader's imagination, in that there's possibility in a fantastical approach to the subject of biology that need not include listed by methods of reproduction and heat manufacture. Obviously, that's useful to a technical world - but what is specifically useful to a D&D world need not be so rigorous. The application of any biological principle to your world carries with it the potential to unify your world, in describing relationships between creatures and animals according to what works for YOU, and not necessarily what is needed for real life experimental applications.
Consider those animals mentioned by the Bible, for example: the sacrificial ram, the whale, the camel through the needle's eye or the scorpion ... animals with a thin biological association by the principles that science describes - but potentially a contingent of unified, blessed creatures within the D&D campaign. Whatever the animals may be, whatever they may stand for - their very presence in parts of your world may have significant reflections upon the cultures, the people's traditions, their moral reprehensiveness or even their fundamental importance to your world. Biologically, your world may - in Douglas Adams fashion - be controlled by groups of white mice in a manner which your players have yet to discover, yielding rich sources of plot hooks and social restructuring that has never occurred to you.
I don't mean to say that the animals are automatically in control of your world - I mean to say that your world's "biology" - as you choose to define it - is a MACHINE, one that you are free to disassemble and reorder in any way that suits your needs. Like geneticists restructuring frankenfood and interspecies crossbreeding, you are the creator. If you must get very weird, pegasi are bred from ordinary horses fed on extraordinary diets, or mutations occur from combinations of seismic activity and excessive local sexual activity ... who knows? Once you've defined the perameters, you need only sell those to the players and let them off the chain. Players will roll with whatever system you concoct ... they don't care.
I am only writing this because it may never have occurred to you to break the rules, biologically speaking, with regards to animal relationships. Perhaps goblins ride dire wolves not because wolves can be ridden by anything small, but because goblin tails emit endorphins which when stroked against dire wolf hides endorphins are released. Perhaps rocs satisfy their enormous appetites by eating rocks, being blessed with the sort of biology that one would normally associate with black puddings. Perhaps ships in your world move three times as fast as one would expect because a species of intelligent turtle - not knowing what they are - waft the ships along with the peculiar way in which said turtles worship the strange shapes upon the "sky." The rules are as endless as they are elaborate or imaginative. However it works out, the biology will be what you impose.
Consider all the possibilities you CAN impose.