The stage during which separation of the paired homologous chromosomes begins is

The separation of the paired homologous chromosomes begins in the diplotene stage. In this phase, the dissolution of the synaptonemal complex begins. The recombined homologous chromosomes separate from each other except at the sites of crossovers.

Zygotene is the second stage of prophase I of meiosis. It is associated with the formation, of synapsis.

Pachytene during which crossing over occurs between non-sister chromatids of the homologous chromosomes.

Diakinesis is the final stage of meiotic prophase-I. This is marked by terminalization of chiasmata.