PDB files detailing the three dimensional structures of both gp120 (PDB ID: 2B4C, determined by X-ray diffraction, resolution of 3.3 Å , 338 amino acids, [55] ), and gp41 (PDB ID 1AIK, determined by X-ray diffraction, resolution of 2 Å , 70 amino acids, [56] ) were obtained from http://www.rcsb.org. It is important to point out that these structures are partial and that we therefore only analysed a fraction of the structural interactions involved in Env folding. We performed SCHEMA predictions of recombination induced fold disruptions using the set of natural HIV env recombinants (described above) essentially as described in Lefeuvre et al. ([8] ; See Protocol S1, Supplementary Analyses, for a description of the SCHEMA method). This involved: (1) computing protein fold disruption, or E, scores for each natural recombinant with identifiable parents; (2) based on every pair of parental sequences identified for the observed set of recombinants, simulating every possible recombinant that could have been produced with these parental sequence pairs that involved the exchange of the same number of non-synonymous polymorphisms as were exchanged during the actual recombination events; (3) calculating E scores for each of these simulated recombinants; and (4) using a permutation test to determine whether mean E scores calculated for the natural recombinants were significantly lower than mean E-scores for the same set of recombinants randomly drawn from the simulated recombinant datasets (Table S1 ). If fewer than 5% of simulated datasets had an average E score lower than that of the actual dataset (p,0.05) then this was taken to indicate that predicted fold disruptions incurred by real events were significantly less severe than if the observed distribution of breakpoints was uninfluenced by negative selection acting against recombinants with disrupted protein folding.