Supplementary Figure 9: PSMC analysis.
The historical effective population size (Ne) (y axes) was traced back in time (x axes) using the Pairwise Sequentially Markovian Coalescent (PSMC) model applied to four samples sequenced at ∼20× depth of coverage. PSMC reconstructs the variation of historical Ne values from patterns of heterozygosity along the chromosomes. (a) Analysis of the complete data set. Generation turnover time was specified to be 1 year and the mutation rate was estimated to be 0.53 × 10–8 mutations per base and generation, computed from divergence observed with the outgroup species A. cerana (confidence intervals computed from 125 bootstrap replicates). (b) Analysis of only transversions. Old coalescent events and historical population sizes were reconstructed with greater resolution when the genotype data were thinned to include only transversions, suggesting alternating patterns of population expansion and contraction that match the last two glaciation cycles (errors bars are computed as in a; the transversion mutation rate was estimated to be 0.15 × 10–8).
