Most people have a theory on what exactly the Rathian and Rathalos subspecies are--why they happen. Now, I'm going to introduce my own theory.
First off, Rathalos. A normal, adult Rathalos is colored a deep and fiery shade of red, with his underbelly being white. This color is achieved from both genes and a diet of red things in its youth. In inhabited areas, this color remains until ancientness, which I will cover soon. However, in uninhabited areas, this color quickly goes to blue, depending on how close to the water they live and how strong they prove to be; only those who achieve mastery over several other Raths of either gender will turn this color, as it is brought on by hormones that are only released during fights and around water. Because of this, Rathalos in inhabited areas will not typically achieve this shade, unless they become the "Alpha male" of a pack.
Blue Rathalos get their color from a hormone that causes the pigments in the ends of their scales to turn blue, signaling to other Raths that this male is dominant, he is powerful, and shouldn't be tampered with. Be cautious! It was evolved presumably as both a camouflage from fish and predators that might fly above it over water, and a signal to avoid confrontation. Because of this brilliant color, however, they often become the goals of extreme hunts, so their number is considerably fewer than, say, the normal Red.
When a Rathalos is extremely aged, the pigments in its scales evaporate. This lost space is filled with airborne pollutants, minerals, and airborne dust within a few years, making it incredibly hard. After the process of re-filling the lost space is finished, the last growth to happen on the scales begins and they strengthen even harder; in addition, they gain a new enamel for the last time (the sixth) and it is quite transparent, due to the lack of pigmentation. This discoloration only happens in very, very old males who have fought their entire lives--and have lived through it.
Rathian start off a deep shade of forest green, a form of camouflage in the forests where it dwells that is caused primarily by genetics. Her underbelly is not even tinted green; it remains the same shade of dull white.
After Rathian go through several hatches of eggs, their hormones begin to change. As they grow stronger and older, they depend less and less upon camouflage and now need just a warning symbol to tell other Rathians and potential predators that they aren't to be messed with. This, like in the Azure Rathalos, only occurs when the animal has been in several battles, as well. Alpha females me achieve this color simply from the attention they get from males, the amount of eggs they hatch, and their adrenaline rushes from protecting the nest.
This, too, is caused by old age, but in a different way than the Silver Rathalos. Rather than a lack of color, it is a rebirth; in its old age, the Rathian converts old pigments to new colors and different functions, now to ward off predators from itself so that it can protect the nests of younger Rathians. Most of the pigment featured in these creatures is the result of Wyvern Stones and other impurities breaking down and becoming the only viable substances: poison or pigment.