The Metagene is what creates and denotes a difference between human and Metahuman. This gene has been found by multiple aliens groups, which some of them feared the human potential. The aliens found that some human beings had a DNA difference which they named the meta-gene (also spelled "metagene"). Normally this gene was dormant in most humans, but sometimes in a persons life whether due to psychological, or physiological stress the gene would activate resulting in a entire genetic change causing the metahuman abilities.
In more recent years it has been seen that even certain people are born with the metagene active, even if neither parent had any "super-powers". A great example is to look at some of the new recruits in the JSA such as Cyclone and Wildcat II.
The aliens believe the activator of the gene was near the brain but they were not specific.
One of the alien races that saw the genetic potential for humans was the White Martians.
After discovering the possibility of a metagene in humans, the White Martians performed experiments on primitive humans. Unfortunately this changed the destiny of the human race because instead of the gene being developed over millennia so every human would eventually posses the gene only a percentage of humans would be able to develop the gene. The White Martians that caused this atrocity were banned to a prison very similar to the phantom zone. While this research was being developed though the White Martians invent a Meatvirus which was a process that allowed a metagene to be passed from person to person just be touching. This process is what gave the people who have called themselves Son of Vulcan their powers.
The phrase Metahuman generally applies to all people and aliens with super powers in the DC universe which makes the population of Metahumans a bit debatable if people want just Metagene Metahumans. According to Countdown to Infinite Crisis, there are roughly 1.3 million metahumans on Earth, however out of that number only .5% are considered dangerous or threats. Most Justice League members are generally considered Alpha threats and second string heroes are considered beta threats which are a little lower.
Due to the fact that the gene was supposed to be active for all humans, some humans felt that they should be able to create their own metahumans.
Lex Luthor was one of these type of people, he and his company created a toxic mutagen called the Exogene which was supposed to mimic the effects that the original metagene was able to produce. For a normal human to get their powers though they had to go through gene therapy at LexCorp. The first people to go through this process were part of Luthor's Everyman Project. As this process was not natural there was controversy, on top of the fact that a lot of the people who underwent the process became unstable. Luthor made sure when the process was devised that he would have a way to stop these people or control them, this caused a couple "accidental" deaths.
Not all Metahumans get there powers from the metagene, some humans have inherent ability to utilize magic. These particular humans seem to be part of a different branch in the evolutionary tree called ''Homo Magi". Now the "Homo Magi" can mate and breed with normal humans and have no distinct qualities other than magic use.
Other MetaHuman Origins
As almost all super hero and villains are classified as Metahumans listed below are other ways super powers were developed.
Atmosphere: Metahumans usually thrive in an oxygen/nitrogen rich atmosphere, although based on origin or powers some sustain themselves in other environments without a definable atmosphere.
Population: Population of this race but is estimated at 1.3 million.