SEARCH

SEARCH BY CITATION

Table S1. Summary of the data collected from the 22 population pairs from the Greater Mindanao and Negros--Panay Pleistocene Aggregate Island Complexes (PAICs).

Table S2. Estimates of the population mutation rate θ from different island populations of the same species used in the msBayes analyses and/or closely related species.

Table S3. Estimates of the population mutation rate θ for the island populations used in the msBayes analyses.

Table S4. Summaries of the posterior estimates from all msBayes analyses run with prior settings of τ ~ U(0, 20), θD ~ U(0.0001, 0.1), and θA ~ U(0.01, 0.05).

Table S5. Posterior estimates of msBayes from the empirical data under three different model priors, before and after the θA error in the source code was corrected.

Table S6. List of all data used in this study.

Figure S1. Plot of the mean and 95% highest posterior density of gene divergence times estimated for each of the 22 population pairs using a fixed rate of 2 × 10−8 substitutions per site per year in BEAST.

Figure S2. The estimated joint posterior densities of the dispersion index (Ω) and mean (E (τ)) of divergence time vector, τ, using (A and B) ABCLLR and (C and D) ABCGLM regression methods, and (A and C) the msBayes summary statistics and (B and D) partial least squares (PLS) components of the msBayes summary statistics.

Figure S3, S13, S14, S15, S16, S28, S29. Accuracy and precision of E(τ) estimates from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S4. Histograms of the true dispersion index of divergence times (Ω) from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S5. Histograms of the estimated posterior probability of one divergence event, p(ψ = 1 ∣ Bϵ(S*)), from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S6. Results of 1000 simulation replicates of no divergence between population pairs, using Sstats, ABCGLM, and 5 × 106 samples from the prior.

Figure S7-S8, S17-S20, S30-S31, S35-S36. Accuracy and precision of Ω estimates from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S9, S10, S21, S22, S23, S32, S37, S38. Histograms of the estimated number of divergence events Ψ from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S11, S12, S24, S25, S26, S27, S33, S34, S39, S40. Histograms of the estimated dispersion index of divergence times Ω from simulations where τ (in 4NC generations) for 22 population pairs is drawn from a series of uniform distributions, τ ~ U(0, τmax.

Figure S41. The relationship between the posterior and true probability of (A) Ψ = 1 and (B) Ω < 0.01 based on 100,000 simulations.

FilenameFormatSizeDescription
EVO_1840_sm_SuppMat.pdf8812KSupporting info item

Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.