Figure 3. Demographic inference using fastsimcoal2 and Stairway plot. a) Parameters inferred from coalescent simulations with fastsimcoal2 under the best-supported demographic model (MODEL A). For each parameter, we show its point estimate. Lower and upper 95% confidence intervals are found in Table S11. Model parameters include effective population sizes (NPOPM: H. maderiana from Porto Santo; NPOPH: H. insularum from Porto Santo; NPOPI: H. insularum from Madeira, Desertas and Bugio), the timing of divergence (TDIV1, TDIV2) in years, and new deme sizes (NPOPANC, N2). b) Historical Ne of the studied populations of H.insularum from Madeira, Desertas and Bugio, H.insularum from Porto Santo andH.maderiana from Porto Santo, inferred using Stairway plot 2. Panels show the median of effective population size (Ne) over time, estimated assuming a mutation rate of 6 × 10−9 and 1-year generation time.