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The skull cubone wears is not the biological skull of his mother.
It is the skull of a Kangaskhan.
Cubone/Marowak's main weapon is the boomerang, a tool used by Aboriginees to hunt kangaroos in real life.
So Marowaks hunt Kangaskhan, and wear their skulls like headdresses.
When a Marowak dies, the skull is passed down to the Cubone as an heirloom.