Figure 3: Modelling European history with rarecoal.

(a) Rarecoal tracks the probabilities for the lineages of rare alleles (red) within a coalescent framework back in time, and approximates the distribution of non-derived alleles (dark blue) by its average. (b) By optimizing the likelihood of the data under the model, we can estimate population sizes and split times. Tested with simulated data, the estimates closely match the true values (in parentheses). (c) Applied to hundreds of European individuals, rarecoal estimates split times as indicated on the time axis and population sizes for each branch. (d) Same as c, but using samples from Kent instead of Cornwall as a proxy for the British population. The different tree topology between c and d reflects different population histories in Cornwall compared with Kent in the South of England.