Beatriz Vicoso and Doris Bachtrog have a very interesting paper showing that the Drosophila 4th (dot) chromosome is homologous to the sex chromosome of more basally branching Diptera.  It seems that, early in Drosophilid evolution, Muller-A took over the role of the sex chromosome from Muller-F.  They also have an interesting discussion of how such takeovers could occur.