Extended Data Fig. 10. Schematics for estimating selection coefficients.

The time axis serves as an approximate reference of the relative sampling times for the empirical samples. Dashed vertical lines indicate the relative sampling time for each group of samples considered in the analysis, and the floating boxes with orange and blue dots represent pools of samples from a bi-allelic locus. Above and below the time axis are sketches that respectively correspond to the simulation scheme and the likelihood computations. The shaded red horizontal tree represents the population-continuity along approximate time (x-axis), with the Black Death pandemic occurring in the dark shaded period. The shortened branch with a skull at the end represents people who died of the disease. In each simulated replicate, ∆p and −∆p mark the respective changes of allele frequency during the pandemic in the mid-pandemic and post-pandemic sample pools. In the inference schematics, each horizontal straight line represents a sampling scheme from which a likelihood was computed. Lightning bolts labeled with s or −s represent the selection coefficients.