In the Cthulhu mythos, the origin of life on Earth was the result of the Elder Things' creations- the shoggoths. I was working on an ooze-ooze aggregate idea for Mutant Future and have come up with an idea on how shoggoths may have spawned other life. Aggregates are organisms that are made up of two or more species that are fusing into one. This is a real world concept- some cellular components, such as plant plastids, are an example of this.
I was working on a black pudding consuming a crystal ooze, an aquatic version of the grey ooze from the first or second edition of AD&D. The ooze becomes something like organs within the pudding, ones that can split and merge, thus allowing for multiple weak mutations or a few strong ones when the pudding needs them. When the whole splits, each daughter pudding takes some of the ooze with it. They go through evolution, adaptation and MF style mutation. Every time the pudding or ooze mutates, it has an impact upon the other. In this case, the pudding becomes marine, using the ooze as a gill of a sort. Other mutations that the ooze might gain to become more useful to the whole include chemical gland (tapping into the amazing number of raw materials in sea water), energy-retaining cell structure (the ooze becomes a second skin and produces a charge that zaps everything near the pudding) and drone (little oozlings that split from the whole and then merge with it again).
It is drone where things can get very interesting. Primary drones are little oozes. If they mutate themselves (i.e. separately from the pudding-ooze aggregate), they can become secondary drones- flesh and blood organisms with tissues and organs. A pudding could contain several kinds of secondary drones that act as organs as well as extra-ooze creatures that perform actions such as scouting and hunting. If a pudding/ooze was to die when several of its drones are outside it, those drones might survive and if they are of the same type, breed. They would be new species. Mutate them into various species using the ideas from Creatures of the Wastelands: Mutational Evolution, and one could get dozens or even thousands of new species all that exist because a black pudding was near some water and "ate" an ooze.
For those who want to try this out with non-oozes; fungi, worms or even tiny elementals could invade plants and animals, infest certain organs or tissues and, with something like the drone mutation, create entirely new species unlike anything else on the planet.
Shoggoths are massive oozes that were created to perform any task their creators wanted. If they needed to make drones, they could. The first plants could have been drones meant to collect local energy sources. The first animals could have been drones that escaped control, probably just before the shoggoths rebelled themselves. And, as there still are shoggoths on mythos Earth, that means they might still be spawning off new species...
While thinking about this, I also wonder can the living d20 creature types evolve into each other? I don't mean could a dog evolve into a rose, but rather a dog evolving into a creature that has all the plant traits. What would an ooze or a plant decended from dragons look and act like? I would actually expect this from settings like Epidemic's Oathbound, where magical evolution of characters and monsters is central. But I am not sure if it would be possible in other settings like the Realms and Iron Kingdoms.
One thing to keep in mind is that the results of a magical aggregate are usually not templated creatures, at least templates like elemental and fiendish. They may be spellpowered (Deluxe Book of Templates 3.5 from Silverthorne), but that is simply because of the supernatural powers the symbiont provides its host. Some unstatted examples:
A tapir with an earth elemental spirit symbiont was created when a jungle dwelling wizard opened a permanent gate to the plane of earth. Some minor spirits escaped and infested the local wildlife. The tapir makes all mineral (including metallic) substances it touches permanently transparent. This is not invisibility and someone wearing a suit of transparent armor is going to be visible.
A fire beetle with an air elemental symbiont weights just ounces and walks and climbs much faster. It can also control flames by providing or denying oxygen to an area. People and critters can suffocate in their sleep, never knowing of the danger they were in.
Some treants purposely take elemental spirits as symbionts. Those with water create oases (or keep drought at bay), those with fire make temperate lands in the far north, those with air tend to forests on solid clouds and those with earth defend their lands with the strength of stone (and move earth spells).
Rust monsters are an unusually common host for intelligent symbionts because of their inherent ability to destroy technology and protect themselves from the most common weapons. Earth elemental spirits are among the most common, though this is ironic as rust monsters are very unwelcome on the plane of earth. Usually the spirits provide the monster with more durability and possibly the ability to earthglide. The other elementals also use rust monster hosts, but that is to destroy metallic earth elementals and their food supply (how else do you think rust monsters get to another plane?). If the spirits hang around long enough, they start affecting the rust monster's offspring and provide the next generation with even more abilities.
Whales are so large they already have an abundant symbiont population. Magical parasites find them a difficult place to infest because of the existing complex ecology in and on the sea mammals. But that doesn't mean there aren't some that succeed. Whales have the advantage of more living space than terrestrial creatures- more surface area and depth. Deep sea creatures, such as worms and crustaceans, may find whales as the easiest way to have some effect on the surface world. Many use magic to influence weather or cause disasters such as flooding- a war on land walkers. But the whales may have an influence on the parasite's personalities and this can make all the difference in the aggregate's actions. Surface creatures, such as birds and sea snakes, may infest whales to allow them access to the depths and the abundant food down there. In both cases, whale survival is low but when they do reproduce, the results can be very different creatures from what we call whales.