arallel evolution is the evolution of similar or identicalfeatures independently in related lineages when subjected tosimilar selection pressures [1,2]. Parallel evolution has beenreported extensively both in natural isolates and in exper-imental populations of many microbes, most often viruses [2–4], but also bacteria [5], yeast [6], and protozoa [7]. Withviruses, similar amino acid replacements often occurred inimmune or antiviral escape variants. This is usually inter-preted as the fixation of a mutation with a beneficial effect.However, differences in founding genotypes may result indivergent evolutionary trajectories [5]. So, patterns ofadaptation to selective constraints may also be dependenton intraspecific polymorphisms. This is well documented forHIV resistance to antiretroviral agents, where pathways ofviral evolution towards drug resistance may proceed throughdistinct steps and at different rates among different HIVsubtypes [8,9]. The objective of this article is to assess the