There are villages_nether.dat and villages_end.dat files in the map data, positioned at .minecraft/Map Name/data. The name suggests they are for storing information about villages in the Nether and the End, although they actually (as far as I know) don’t generate in either dimension, only in the Overworld, for which the villages.dat file is used.

Note: I’m currently playing the demo version since I haven’t bought the premium license.