In the Beginning...
The Pikmin have been labeled as animal-plant hybrids. Though this as reasonable an explanation as any, I am under the impression that this is NOT true.
Consider, for example, the fact that both Pikmin and Candypop Buds show characteristics of dicotyledon plants. Also, the evolutionary bias that only animals may have limbs, though well-supported in our world, should have no relevance whatsoever to an alien world. For more info, see Planet of the Pikmin.
In all likelihood, the Pikmin is a mobile seed of the aforementioned candypop flowers, consisting of the epidermis, a semi-transparent but extremely mineral-absorptive layer, the dermis, a collection of food materials left for later use, and the endodermis, seat of the embryonic candypop flower.
It has already been observed that the Candypop flowers can readily transform a Pikmin into a seperate breed. This is simply a reconstruction of the DNA, easy enough to attain for a plant that naturally has to make its own seeds from its considerable foodstore. In fact, it is highly probable that the original Candypop flower fertilized the adults while still a Pikmin, as can be seen in the stalks of more mature specimens of the so-called animal-plant hybrids. It is the belief of this author that the original Pikmin, due to the nutrients in his dermis, was a drab brown. Upon fertilizing all possible Candypop Buds, it would bury itself and become one.
The Breeding Program
Though recent evidence states the planet of the Pikmin is a later-day Earth, this has not yet been confirmed. Therefore, the race that now enters the scene will be called the Breeders.
The Breeders saw potential in this strange quadrupedal seedling, and began to take matters into their own hands. Slowly but surely, over many generations, the Pikmin grew longer forelimbs, and the sense organs on their heads so-called were encouraged. Every now and then, there might (indeed, should) have been a relapse, but it was deleted from the strain. Then finally, the first of the Pikmin breeds came.
There were two of them. The Black Pikmin was a nutrient rich creature whose eyes were similar to those on the Red Pikmin, used commonly for menial labor (i.e., screwing in bolts). The White Pikmin had a caustic agent in the dermis, causing all harmful chemicals to find an impenetrable barrier, and poisoning those foolish enough to eat it. As an interesting side note, the Black Pikmin seed flower was white, though the adult flower was a strange wondrous black, while the white flower, seedling pink, matured into an ivory bud.
Coming of the Onions
Of course, the small Pikmin were practically useless except when used in large numbers. While the breeding conditions were favorable, they were not enough to make huge exports. Thus, the Onions, solar-powered bulbs now called Onions were formed. Capable of transferring all inserted organic material into a pre-programed genetic code. The flying feature was later added so that the Onion and its contents were protected from various household pests.
The New Generation
As the breeding company thrived and prospered, they continued their breeding program, and there came not two, but four new types of Pikmin.
From the side Black spawned the Splotched, a type with three specialized organs to harvest from the atmosphere nutrients, and the Indigos, a breed with a multi-layered net used to expel poisonous materials. From the pink-flowered seedlings came the Greygreens, one who managed some slight maintenance of their internal chemicals, and the Spiners, who grew deadly projections as an added arsenal in their already poisonous arsenal.
Onions That Never Were
While these new Pikmin were made known to the general public, they were not released, for various reasons.
The Spiner breed, obviously, was unsafe, but a lesser known fact is that an Onion emitting a Splotched would be instantly marred to an inoperational point. However, the Indigo breed probably was canceled due to aesthetic reasons (gurgling) and the Greygreens--well, they were just eerie. Clearly, the profit of these sales would be extremely low...
One Last Push
The Breeder company in question was most likely losing money, but they kept plugging on, and eventually came up with eight new successes. From the Splotched came the Yellow, able to neutralize electric flow with their semi-conductive ears, and the reds, who harvested nonflammable substances with their noses. From the Indigos came the Blues, who had gills, and the Skyblues, who could talk. From the Spiners came the Purples, whose eyelashes harvested strengthening nutrients, and the Oranges, whose fur increased their sensitivity tenfold. From the Greygreens came the Silvers, able to blend into any environment, and the Greens, capable of a sort of parasitical control, and therefore used as surgical tools.
The Breeders were not to know these would be the last Pikmin ever bred...
Onion Malfunctions
The Onions were all greatly modified in view of the above succeses, allowing the pointy tips of the petals which generated endorphins that influenced rebellion to be geneticly "cut" and resulting in a more docile breed. This, however completely did away with the creature's wanderlust and normal life-cycle, meaning that when a pikmin became a flower pikmin, it waited, then reverted to a leaf.
However, there were some pikmin born normally that exsisted.
Outskirts
In the various dumps of the breeders crawled multiple types of life, and it was to these dumps that the brown pikmin crawled. Eventually, they developed bipeduality, but by then, most had delveloped a symbiosis with the puffstool. It was then that their wanderlust began to grow.
Many strange creatures also trace their origins to mutations in the junk fields...