Aphra

This name is pretty much synonymous with Aphra Behn (I don't know of any other famous Aphras), so I don't see anyone using this name who doesn't like Restoration literature and / or drama.

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That said, Aphra Behn was an admirable woman (though Victorian women condemned her for embracing the "licentious mores" of her time). She was perhaps the first woman in recorded history to make her living entirely off of her writing - writing which often challenged the status quo of her time (particularly gender roles / dynamics; e.g. when the men take liberties Florinda near the end of "The Rover," it was supposed to shock the audience).

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If a little girl were named Aphra today, I would guarantee she would be the only one in her class.

I do not have any clue about the origin of the name but I do know there was a Aphra Behn in England some centuries ago. She is the first professional female author we know of. Here are some links with the information we have on her:
http://feminism.eserver.org/memoir-of-aphra-behn.txt

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This one is particularly interesting as it offers some variants of the name, which might help to trace the etymology.
http://en.wikipedia.org/wiki/Aphra_Behn

Aphra Behn (1640-1689) was one of the first English women to earn a living through her writing.