I have a setting riff, one where life started on land instead of in the ocean. This meant for fantasy but I added a few ideas for Mutant Future as well. This idea can be used in settings with and without evolution.
In these fantasy settings, the very first creatures were those on land. When the gods were finished with them, instead of creating all new creatures for the sea (and the underdark), they used their initial creations as templates. That means sea life is derived from that on land. There are a few ways of using this.
The first is to take dinosaurs and other extinct creatures and place them in the oceans. They may walk the bottom or they could be actual marine creatures with or without gills. If they are animals with lungs, people will know of them because of the death toll to fishermen. Gilled dinosaurs may never surface, at least while they live. Instead they are a suprise for the PCs when they go hunting for sunken treasure.
The second is to use existing animals and plants, everything from fleas to elephants to monsters. The depth that vegetation can survive can be altered by the GM, thus allowing forests to grow down to the treeline. Everything below that should be considered a desert, if a rather wet one.
The third is to use Ages. Instead of an Age of Dinosaurs, there was an Age of Plants when the gods were working on normal and fantastic vegetation. And there could be Ages of Goblinoids, Fey, Giants, Dragons, Elementals (native), etc. They are made into aquatic species to populate the oceans.
The fourth is to use cultural mythologies. Norse, Greek, Seneca, Zulu, etc. This uses terrestrial monsters from those mythologies to populate the oceans.
And then there was the Age of Animals. This uses noble animals (ala The Noble Wild) or animals the civilized creature template in Rite Publishing's Book of Monster Templates. They were cast into the oceans or deep underground after humanoids were created.
In most cases the GM needs to apply a marine or amphibious template or otherwise adapt the creatures to life underwater or a template for life underground. In other cases, the creatures use their normal stats except they can not survive out of water for very long. In settings with evolution (or god who like tinkering with their creations), there could be families of former surface dwellers, some completely marine, some amphibious and possibly some (newly) terrestrial. They went into the oceans and came back out, altered by their ancestry.
Variations of this could be life started in the oceans (so the PCs are fish or seal people), life started underground (PCs are mole or cave cricket people), life started in space (got me, aberrations possibly?), or a more restricted version of life started on land (everything is derived from mountain goats and snow leopards or bison and wolves from the plains or even island dwellers).
As for Mutant Future, there are three sources of these kinds of creatures, both rather obvious. The Elder People probably created a lot of them just because they could. These creatures were well adapted to life in the oceans and the survivors' decendants have few drawbacks that would inhibit life underwater. Mutants are the opposite- they are usually very poorly adapted to life in the seas. The reasons they remain there are predation or a drawback that either removes or modifies their lungs so that they can not breathe air. Cyborgs with inherited implants (nanites that grow implants during development) are pretty much in the same boat as mutants. They can survive underwater but their bodies are not well adapted to living in such conditions. For both, it is going to take time for evolve better bodies. And, of course that means extinction for some and a lot of dead for the rest.
