Fig 1.

Maximum-likelihood trees of plasma and breast milk virus variants of AGMs 3 years after infection with an uncloned SIVsab virus stock. The trees show full-length SIV env sequences amplified by single-genome amplification from plasma (red squares) and milk (blue circles). There is evidence of compartmentalization between breast milk and plasma virus variants. The P values were generated by the Slatkin-Maddison test of compartmentalization. The scale bars represent 0.003 substitutions per site.