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It's all about inflicting the maximum possible amount of psychological harm. Even animals dislike physical pain, but for a human rape is a violation on a deep, personal level. If you're looking for evidence of qualia, then the ability to feel 'degraded' is a good place to start.
Cold-war naval researchers used the same trick when they were researching dolphin sentience. Random beatings produced little usable data. Opiate withdrawal, forced prostitution, and mutilation/hobbling(fin removal, genital mutilation, partial blinding, etc.) produced a wealth of useful information, and such studies underpin much of our modern-day understanding of cetacean intelligence.