So I can't help you with the history here, but I'd just like to give you a warning if you're ever traveling in the Balkans: in Bulgaria, nodding indicates 'no' while shaking one's head is a 'yes'. I've heard that the same gesture-reversal is also present in Macedonia and parts of Greece & Albania.

There's a really interesting story that's been told to me many times - but mostly by my girlfriend, her relatives, and others in Northern Bulgaria, so I can't vouch for it as a unified 'national myth'. What I've been told is that this reversal dates back to the Ottoman occupation of the Balkans - the story goes that a group Bashi-bazouk had captured a number of Orthodox Bulgarians, and with swords held at their throats demanded that they convert to Islam. These heroic Bulgarians shook their heads violently up and down, killing themselves on the Ottoman swords and signifying 'no' in their refusal to renounce Orthodoxy. Since that time, Bulgarians have nodded to indicate 'no' and shook their heads to mean 'yes'.

Of course, this is undoubtedly a sort of 'folk genealogy' of the gesture reversal in Bulgaria, but I think it's worth posting here as a particular cultural explanation. It's fascinating how, in this story, a mere gestural difference is located within a larger narrative of historico-culturo-religious difference at the heart of Bulgarian national identity.

That being said, I can't claim that this story is universal to all of Bulgaria, and I would be curious to see other popular explanations around the Balkans (I'm especially interested in hearing those that might be given in Albania, which doesn't possess the same sort of national mythology founded on heroic cultural/religious resistance to Ottoman occupation).

Non-verbal communication specialist here. As pointed out (in the modern era) head nodding does not always mean yes. In Albania, Bulgaria, Greece, and Macedonia a single nod means no.

Generally speaking, a nod is a submissive gesture. Protect the neck, lower the head. It's a type of bow. "Go do this!", followed by a bow would mean something like, "Yes, I will do that".

As for head shaking, it might be a universal gesture. Some monkeys, bonnet macaques, baboons, and gorillas similarly "turn their faces sideward" in aversion Altmann 1967. It's also been observed in children born deaf and blind (though I can't remember a source right now).

A popular theory about head shaking is that we learn it as babies, turning the head away from the nipple when we don't want to feed.

There are very few, if any universal gestures. If you're interested, you could have a look at the work of Dr. Paul Eckman (whose work the TV series "Lie To Me" was based on.

In India and other South-East Asian countries the conventions of nodding for 'yes' and shaking your head for 'no' is inverted to mean the opposite.

Anecdotally this can get very confusing when conversing with elderly people from those communities.

From a historical/literature stand point there is a reference in the Mahabharata in which Arjuna shakes his head to signify acceptance of Krishna's words at the end of the tale. The composition date of the Mahabharata is hard to pinpoint but the latest editing is commonly said to be around the 8th century.