Files in this Data Supplement:

• Supplemental file 1 - Fig. S1. Maximum likelihood phylogenetic trees of each compartmentalized individual's sequence data.
  Fig. S2. Maximum likelihood phylogenetic tree of all sequence data associated with an individual who demonstrates inconsistent viral compartmentalization between blood and semen.
  Fig. 3. Maximum likelihood phylogenetic trees of each compartmentalized individual's sequence data.
  PowerPoint presentation, 155K.
• Supplemental file 2 - Fig. S4. Neighbor joining tree of sequence data from all individuals demonstrating viral compartmentalization between blood and semen.
  Fig. S5. Longitudinal diversity and divergence in individuals G, I, J, and K.
  PowerPoint presentation, 350K.
• Supplemental file 3 - Fig. S6. HIV-1 HXB2 gp120 structure with semen-specific signature residues highlighted.
  PowerPoint presentation, 105K.