How do I place nodes on the same level in DOT?

Putting the rank = same; ... statements in braces, e.g.:

digraph G { 
  rankdir = TB;
  subgraph {
    A -> B
    A -> C
    C -> D
    X -> Y
    // note that rank is used in the subgraph
    {rank = same; A; X;}
    {rank = same; B; D; Y;}
  } /* closing subgraph */
}

… gives the desired result: