The paper I wrote with Sergey Kryazhimskiy and John Wakeley (both at Harvard) came out this week in PLoS Genetics. In the paper we describe how genetic diversity is lost and recovered in HIV populations that evolve and become drug resistant. This was possible because of a dataset that was collected in the late 1990s. This dataset is unique because it has multiple sequences of the protease and reverse transcriptase regions at multiple time points for many patients. We found evidence for soft and hard sweeps.
Download the paper with the supplementary materials here: 2014PennKryWakeleyPGeneticsWSupplMat