Yet all

The subordinate clause in bold is a participle clause, which means:

although all (these languages) share certain basic elements.

Are you saying that it's basically:

There are about five to six thousand different languages around the world, all sharing certain basic elements.

and it's out of the scope of the with-phrase?

Your comma before yet is correct, but I don't believe you need a comma before with. Everything in the sentence up to yet is all one thought. Also, the 'the' after with is unnecessary.

Here's a revision:

There are about five to six thousand different languages around the world with separate vocabularies and grammar, yet all share

Sorry Maku. The original didn't have 'the' you've pointed out. It was my mistake.

So, don't you think even without 'yet' in the original as:

There are about five to six thousand different languages around the world with separate vocabularies and grammars, all sharing certain basic elements.

would it still sound natural and make sense?

Using yet is perfectly fine, Taka. An alternative to my previous post would be to use but in the place of yet:

There are about five to six thousand different languages around the world with separate vocabularies and grammar, but all share certain basic elements.

Also, the word grammar is never used with an 's' trailing.

My question is purely grammatical. How come the conjunctive 'yet', which is the same as 'but', can accompany a noun modified with the present participle 'sharing', not an absolute sentence?

(What do you mean by 's' trailing, by the way?)

I'm not sure exactly what you mean, but the word 'share' in the sentence does not modify anything before the conjunction. The part of the sentence before the coordinating conjunction (yet/but) is a completely separate thought from the part after the coordinating conjunction. 'Share' in this sentence is referring to certain basic elements.

Also, the word gra

MakuAlso, the word grammar is never modified when used in a plural form, so it never ends with an s.

AH! That is a typo. I just hurriedly wrote it. Sorry again.

OK, my question is this. When we have the coordinating conjunction, why don't we have a complete sentence (i.e. subject+verb) here? After the coordinating conjunction, we just have 'noun+-ing

Coordinating conjunctions are not limited to simply helping combine two separate sentences. They can also help add a separate phrase or clause to the sentence, so the subject-verb agreement doesn't apply. In this case, we have an independent clause being added to the sentence using the coordinating conjunction.

If so, this sentence would sound as natural as the one in question?

The sons are lazy workers, but/yet their father working so hard every day.