Book 1 of a two part series, the Sequel is titled Crucible. From the back cover:
A human colony settles on a distant planet, a colony formed by jake Holman - a man trying to escape a dark past. ut as this diverse group of thousands comes to terms with their new lives on a new world, they make a startling discovery: primitive humanoid aliends. There are only a few isolated villages, and the evidence seems to indicate they aren't native to the planet. When a handful of human colonists finally learn the truth, they will face the toughest decision of their lives, a decision that could determine not just the fate of their new home, but the fate of all humanity.