I don't know, this happen in the anime:
Plus, I think there was something about returning the bones of pokemon killed for food to the sea so they can live again in DPPt. I can't remember exactly what it said, but I know something about that was there.
Edit: Found it:
"Sinnoh Folk Story 1"
Pick clean the bones of Pokémon
caught in the sea or stream.
Thank them for the meals they
provide, and pick their bones clean.
When the bones are as clean as can
be, set them free in the water from
which they came.
The Pokémon will return, fully
fleshed, and it begins anew.
How did I even remember this existed...?