The Anatolian languages thread had my little brain well addled*, and it led me to wonder what is known about the origin of African languages?  Apart from this wikipedia article: http://en.wikipedia.org/wiki/Languages_of_Africa.
(A brief google brought me to this Cambridge University site, which may or may not be familiar to some of you here. It’s new to me, anyway, so I thought I’d share the love).

*addled: cognate with Middle Dutch ael, first English citation meaning liquid dung. Not sure I like that comparison, accurate though some may think it is.

Seems a fairly broad question. “African languages” covers several unrelated languages family that would be discussed separately.

"Fairly broad” seems to be a gross understatement.  Each of the 4 major endogenous language families is probably as diverse as IE, and as unlike the others as IE is from the Sino-Tibetan family.  To make things worse, I don’t think any of the African languages outside of the Hamito-Semitic group ever developed writing systems of their own (I stand open to correction), which makes historical linguistics that much harder.

That’s not to criticize the question, just to say that I doubt much is known, or ever will be known unless approaches like the Atkinson paper’s can be validated and built upon. (Again, I welcome correction.)

(Interesting tidbit about “addled”, Eliza.)

Has there been any study comparing the vocabulary of IE with any of these African groups?  I almost hesitate to ask questions like this, for fear of invoking the scorn of those in the know.  (Note I say “almost").

The IE languages in Africa are imports, as you know (Afrikaans, Portuguese, English, etc.).  There are no cognate relationships (as opposed to borrowings) between IE and any of the many African language groups, as far as can be determined at this late date (though various linguists with slack standards of evidence and deep-rooted ambitions to link all the languages of earth into One Big Family will tell you otherwise).  The link with the greatest chance of having some truth to it is that between IE and Afroasiatic (or “Hamito-Semitic,” as it used to be called); there are suggestive similarities but nothing that proves a family relationship.

Note that in southern Africa, the Bantu language family which now dominates the region is also an import. Southern Africa was colonised by mainly iron-age Bantu speaking people in the first millennium AD, either displacing or assimilating the native stone-age peoples during the early 2nd millennium AD.

On the other hand, some individual Bantu _languages_ such as Zulu can be said to be native to southern Africa, as for that matter can one IE language, Afrikaans.

Zulu can be said to be native to southern Africa, as for that matter can one IE language, Afrikaans.

Afrikaans is a dialect of Dutch. Dutch speakers find it largely intelligible, especially in written form. It’s actually more difficult for an Afrikaans speaker to understand Dutch, as the main stem of the language family has undergone more change, but in morphology and lexical borrowings, than Afrikaans has in the last few hundred years.

To call Afrikaans a “native” African language, you would have to call Quebecois French a “native North American language” or Brazilian Portuguese a “native South American language.”

And those are defensible judgments.  It all depends how you want to define “native” and “language.”