Were they native species?
My impression was that Arrakis was turned into Dune fairly recently, geologically/paleontologically speaking.
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No, they weren't a native species. Leto Atreides II remembers via his Other Memory that long ago Arrakis used to be a wet planet, but after the sandtrout were introduced to the environment, they dried it up as part of their life-cycle.
"The sandtrout ... was introduced here from some other place. This was a wet planet then. They proliferated beyond the capability of existing ecosystems to deal with them. Sandtrout encysted the available free water, made this a desert planet ... and they did it to survive. In a planet sufficiently dry, they could move to their sandworm phase"
Children of Dune
There was evidence on Arrakis of this change, dried up lakebeds and such.