Table 5

The estimation of divergence time, migration rates, past population sizes and present population sizes in model 3 when the mutation rate or the recombination rate varies across the genome regions

Parameter (true value)

Varying mutation rate (θ = 4Neμ)

Varying recombination rate (ρ = 4Ner)

E[θ] = 5/3

E[θ] = 5

E[θ] = 5 × 3

E[ρ] = 40/2

E[ρ] = 40

E[ρ] = 40 × 2


T (0.1)

Mean

0.0700

0.1070

0.1168

0.0662

0.1154

0.1489

95% CI

[0.0252, 0.1383]

[0.0656, 0.1759]

[0.0726, 0.1864]

[0.0274, 0.1259]

[0.0626, 0.1883]

[0.1018, 0.2054]

m12 (2.0)

Mean

3.1771

2.4135

4.9080

1.5306

2.5406

2.6228

95% CI

[0.4462, 4.8543]

[0.4741, 4.6774]

[4.5929, 4.9939]

[0.0379, 4.2540]

[0.5208, 4.6828]

[1.0433, 4.6559]

m21 (1.0)

Mean

0.7207

0.9144

0.0476

4.6749

0.9631

0.1092

95% CI

[0.0465, 3.4811]

[0.1033, 3.0788]

[0.0000, 0.2378]

[2.8810, 4.9834]

[0.1032, 3.1232]

[0.0190, 0.3659]

N1' (2,000)

Mean

1,268

2,349

9,014

1,820

2,474

4,779

95% CI

[499, 2,460]

[1195, 4,227]

[7,253, 9,884]

[796, 3,402]

[1,186, 4,390]

[2,738, 6,790]

N2' (5,000)

Mean

1,777

4,777

9,338

3,562

4,888

4,104

95% CI

[770, 3,361]

[3,344, 6,235]

[7,878, 9,971]

[2,301, 4,836]

[3,324, 6,276]

[2,620, 5,496]

N1 (100,000)

Mean

164,116

116,700

75,603

44,265

115,277

192,358

95% CI

[94,583, 198,448]

[47,239, 191,310]

[40,493, 133,925]

[13,558, 159,882]

[44,780, 191,187]

[177,723, 199,615]

N2 (150,000)

Mean

183,527

154,968

24,650

45,778

151,010

196,899

95% CI

[14,273, 199,210]

[102,065, 195,442]

[12,964, 75,434]

[16,968, 140,253]

[98,170, 195,246]

[190,142, 199,659]


For each "observed" dataset, we randomly draw a mutation rate or a recombination rate for each genome region from a normal distribution with parameter (E[θ], 0.2) or (E[ρ], 1). The ABC procedure uses fixed values for the mutation and the recombination rates, θ = 5 and ρ = 40. The means and 95% CIs are averaged over 50 replicate "observed" datasets. Compare with Table 4 which shows the ABC estimates when the "observed" data are generated from a model with fixed values for the mutation and the recombination rates

Li and Jakobsson BMC Genetics 2012 13:22   doi:10.1186/1471-2156-13-22

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