While the movie doesn't give a straight answer, there are three possible conclusions that the movie supports:
1) Predatory Evolution - It seems strange that there would be a species that went well over its 'circle of life' balance in which it consumed all available species within the known area of the movie. It did show the elephant grave yard of what appeared to be the indigenous lifeforms that were the alien elephants (called whales), and that none existed in the area anymore. Such mass consumption doesn't seem natural as evolution tends to bring things back into check in the predator/prey ratio. Since they were at the point of eating one another (and would have to do so in the 'sunlight' phase) you would think they would have exterminated itself unless the species has adopted both sides of the predator/prey ratio. I don't think a species can realistically survive being its own food source for a sustainable length of time, as it would eventually eat itself out of existance. There might be another food source that the movie doesn't cover.
2) Extraterrestials - They're from somewhere else, planted or crashed onto the desert planet. I wouldn't guess crash, with the large drawback of the bioraptors being so photosensitive that it would destroy them. It could be that they are a bioweapon planet on the planet, but their photosensitivty seems to make them a rather lopsided weapon, only useful on 'dark' planets or area without any strong light source.
3) Horribly Mutated - The species might have once been something else, but due to something like nuclear radiation or strange experimentation, have altered into the bioraptor. This is a little more plausible, as it is a native creature that didn't have a chance to strip the planet bare until the more recent past. The survivors of the movie assume that the bioraptors consumed everything on the planet, but there is nothing saying that industrial dump/nuclear testing/bioengineering didn't have a hand in it as well. Think Godzilla. Horrible, horrible Godzilla. The bioraptors could indeed be a bioweapon, but more of a testing phase, a species seeing if they can tailor a weapon to a specific condition. It could have been that they wanted something wiped out that was once subterrainian, but because of the dark phase of the planet, they come out every 22 years for buffet a la terra. Because of this, the bioraptors could indeed be the cause of the mass extinction event, or be a result of it from outside influences.