True and inferred selection parameters and times for a case in which sequence data partially describes the selected alleles within a system.

We here simulated the evolution of populations of viruses, each comprised of genotypes containing 24 polymorphic alleles (numbered 1 to 24 for convenience; genotype positions are also provided). The columns showing the true model parameters describe, for each of the 20 simulated systems, which loci were modelled as being under selection (seven loci were chosen at random in each case, the remainder being neutral), the time at which selection for the variant at each locus began, and the magnitude of selection acting on this variant. The columns showing inferences show the loci at which selection was inferred to act, and for each of these loci the time at which selection was inferred to begin, and the magnitude of selection inferred to act upon the variant allele. Inferences were conducted using a partial set of data restricted to a description of changes in the system occurring between loci 441 and 759 in the genotype making it impossible to infer selection acting at loci outside of this window.
(XLSX)