Fig 1.
Estimated demographic history with no selfing or seed banking.
Estimated demographic history using four simulated sequences of 30 Mb under a saw-tooth scenario with 10 replicates. Mutation and recombination rates (respectively μ and r) are set to 1.25 × 10−8 per generation per bp. Therefore . The simulated demographic history is represented in black. a) Demographic history estimated by eSMC (red). b) Demographic history estimated by MSMC (purple). c) Demographic history estimated by MSMC2 (blue). d) Demographic history estimated by PSMC’ (orange).
Fig 2.
Estimated demographic history with seed banking.
Estimated demographic history using four simulated sequences of 10 Mb and ten replicates under a saw-tooth demographic scenario (black). The mutation and recombination rates are set to 1.25 × 10−8 per generation per bp. Therefore . We simulate under four different germination rates β = 1 (red), 0.5 (blue), 0.2 (green) and 0.1 (purple), hence we respectively have
, 0.5, 0.2 and 0.1. The demographic history is estimated using a) eSMC, b) MSMC, c) MSMC2 and d) PSMC’. β* represents the estimated germination rate by eSMC.
Fig 3.
Estimated demographic history with selfing.
Estimated demographic history using four simulated sequences of 10 Mb and ten replicates under a saw-tooth demographic scenario (black). The mutation and recombination rates are set to 1.25 × 10−8 per generation per bp, and simulations were run for four different self-fertilization rates (σ = 0 (red), 0.5 (blue), 0.8 (green) and 0.9 (purple)), and as , this gives
, 0.6667, 0.333 and 0.182 respectively. The demographic history is estimated using a) eSMC, b) MSMC, c) MSMC2 and d) PSMC’. σ* represents the self-fertilization rate estimated by eSMC.
Fig 4.
Estimated demographic history with selfing and seed banking.
Demographic history estimated by eSMC for ten replicates using four simulated sequences of 10 Mb under a saw-tooth demographic scenario and four different combinations of germination (β) and self-fertilization (σ) rates but resulting in the same . Mutation and recombination rates are set to 1.25 × 10−8 per generation per bp, giving
. The four combinations are: a) σ = 0.4 and β = 0.25, b) σ = 0.75 and β = 0.6, c) σ = 0.85 and β = 1 and d) σ = 0 and β = 0.15. Hence, for each scenario
. For each combination of β and σ, eSMC was launched with five different prior settings: ignoring seed-banks and self-fertilization (red), accounting for seed-banks and self-fertilization but without setting priors (blue), accounting for seed-banks and self-fertilization with a prior set only for the self-fertilization rate (green), only for the germination rate (orange) or for both (purple). σ* and β* respectively represent the estimated self-fertilization and germination rate.
Fig 5.
Estimated demographic history of Arabidopsis thalinana.
Demographic history of two European (Sweden (S, blue) and German (G, green)) populations of A. thaliana estimated using eSMC: a) accounting only for selfing (σ is a variable and β = 1) and b) accounting simultaneously for selfing and seed-banking (σ bounded between 0.5 and 0.99 and β bounded between 0.5 and 1). Mutation rate is set to 7 × 10−9 per generation per bp and recombination respectively set for chromosome 1 to 5 to 3.4 × 10−8, 3.6 × 10−8, 3.5 × 10−8, 3.8 × 10−8, 3.6 × 10−8) per generation per bp. σ* and β* respectively represent the estimated self-fertilization and germination rates.
Fig 6.
Estimated demographic history of Daphnia pulex.
Demographic history estimated by eSMC on six individuals of D. pulex accounting for egg-banks (β is a variable and σ = 0). Different assumptions concerning the number of parthenogenetic cycles before the production of the dormant egg are made: Five cycles (pink), two cycles (red) and no parthenogenesis (dark red). A subset of demographic history estimated by PSMC’ are plotted in orange. Mutation and recombination rates are respectively set to 4.33 × 10−9 and per generation per bp, where np is the number of reproductive cycles per year, parthenogenetic and sexual.
Table 2.
Calculation times of eSMC on simulated data under the “saw-tooth” demographic scenario with mutation and recombination rate set to 1.25 × 10−8 per generation per bp.
Results are in minutes given the sequence length and the number of haplotypes.