Correction: Inference of past demography, dormancy and self-fertilization rates from whole genome sequence data

The mutation and recombination rates reported throughout the article are incorrect by a factor of 2. The captions of Figs 1–4, Table 2, and S1–S19 Figs are incorrect. Additionally, the Y axes of Figs 5 and 6 and S20 Fig are shifted by a factor of 2. The authors provide corrected versions here. The correct rates were used for the simulations (S2 Appendix) and as such this error does not affect the conclusions of the study.

There are several errors in the Simulation results subsection of the Results as listed below.

In the Convergence property in the absence of seed-banks and self-fertilization subheading, there are errors in the first sentence of the fourth paragraph. The correct sentence is: We now assume ρθ=rμ=5, with the mutation and recombination rate respectively set to 1.25 × 10⁻⁸ and 6.25 × 10⁻⁸ per generation per nucleotide.

In the Convergence property with dormancy (seed- or egg-banks) subheading of the Simulation results subsection of the Results, there is an error in the first sentence of the first paragraph. The correct sentence is: Using eSMC on sequences simulated under the “saw-tooth” scenario in the presence of seed-banks (mutation and recombination rates are set to 1.25 × 10⁻⁸ per generation per bp, (Fig 2), we obtain an accurate estimation of the demography (χ_t) and of the germination rates (β). There is also an error in the last sentence of the first paragraph. The correct sentence is: Therefore when the molecular mutation and recombination are set to 2.5 × 10⁻⁹ per generation per bp, better fits are obtained (S12 Fig).

In the Convergence property with dormancy (seed- or egg-banks) subheading, there are several errors in the second paragraph. The correct paragraph is: For simpler demographic scenarios (constant population size, bottleneck, expansion and decrease, see S13 Fig) and μ = r = 1.25 × 10⁻⁸ per generation per bp, the germination rate and the demographic histories estimated by eSMC are accurate for most of the demographic scenarios considered, except in the case of a bottleneck scenario (as expected from previous results). In presence of strong seed-banks (β = 0.2 or 0.1) there are biases in estimations of the far past. Once again, this tendency disappears when the molecular mutation and recombination rates per site are lowered so as not to violate the infinite site model (μ and r = 2.5 × 10⁻⁹ per generation per bp, see S14 Fig).

In the Convergence property with self-fertilization subheading, there is an error in the first sentence of the first paragraph. The correct sentence is: Under the “saw-tooth” scenario with different rates of self-fertilization σ, with mutation and recombination rates set to 1.25 × 10⁻⁸ per generation per bp (rμ=1), for four different self-fertilization rates σ = 0 (no self-fertilization), 0.5 (50% selfing), 0.8 (80% selfing) and 0.9 (90% selfing), we estimate the self-fertilization rate respectively at 0.19, 0.5, 0.77 and 0.87 (Fig 3). There are also errors in the fifth sentence of the first paragraph. The correct sentence is: When the mutation rate is set to 1.25 × 10⁻⁸ per generation per bp and the recombination rate to 6.25 × 10⁻⁸ per generation per nucleotide (rμ=5), the self-fertilization rate is overestimated for small values of σ (S15 Fig), but well estimated for higher values of σ.

In the Convergence property with both dormancy and self-fertilization subheading, there is an error in the first sentence of the first paragraph. The correct sentence is: Here we test different combinations of seed/egg-banks and self-fertilization rates that result in the same ratio ρθ=0.15, with rμ=1 (setting μ = r = 1.25 × 10⁻⁸ per generation per bp). There is also an error in the eleventh sentence of the first paragraph. The correct sentence is: We also test how recombination can influence the output of these models, notably by taking a higher recombination rate (8.335 × 10⁻⁸ per site per generation), more representative of the high recombination to mutation ratio observed in some species (notably D. pulex and A. thaliana [4, 45]).

There is a minor error in S2 Appendix. The command lines for S8, 10, and 11 Fig are incorrect. Please view the correct S2 Appendix below.

Supporting information

S2 Appendix [pdf]
Command lines.

S1 Fig [red]
Estimated demographic history in absence of selfing or seed banking using sequences of 10 Mb.

S2 Fig [red]
Estimated demographic history in absence of selfing or seed banking using sequences of 10 Mb when all method have same discretization of the population size as eSMC).

S3 Fig [red]
Estimated demographic history in absence of selfing or seed banking using sequences of 1 Mb.

S4 Fig [tif]
Estimated demographic history using eSMC in four simple demographic scenarios.

S5 Fig [tif]
Estimated demographic history using PSMC’ in four simple demographic scenarios.

S6 Fig [tif]
Estimated demographic history using MSMC in four simple demographic scenarios.

S7 Fig [tif]
Estimated demographic history using MSMC2 in four simple demographic scenarios.

S8 Fig [red]
Estimated demographic history under .

S9 Fig [red]
Estimated demographic history under .

S10 Fig [red]
Estimated demographic history under with initial value .

S11 Fig [red]
Estimated demographic history under with initial value .

S12 Fig [black]
Estimated demographic history with seed banking and μ = 2.5 × 10.

S13 Fig [red]
Estimated demographic history in four simple demographic scenarios with seed banking.

S14 Fig [red]
Estimated demographic history in four simple demographic scenarios with seed banking where = 2.5 × 10.

S15 Fig [black]
Estimated demographic history with selfing under .

S16 Fig [red]
Estimated demographic history in four simple demographic scenarios with selfing.

S17 Fig [b]
Possible selfing and seed banking value where .

S18 Fig [b]
Estimated demographic history with selfing and seed banking where .

S19 Fig [b]
Possible selfing and seed banking value where .

S20 Fig [blue]
Estimated demographic history of where selfing and seed banking is ignored.