Board Thread:Naruto Discussions/@comment-3279282-20140413164418/@comment-28861328-20140413174910

To all of that: we don't know.

Well, all except for the first part. Kaguya's chakra came from the Shinju, so the Sage was the first person to have chakra in his DNA. Therefore, his sons and their descendants would have chakra in their DNA. For the rest of the world, after the Sage gave them chakra, my assumption would be that chakra evolved along with their genetic mutations from that generation on.

Put simply, Kishi told us so. There is no other real explanation for any of what you just asked at this point.