Supplementary table. 1.- Total number of polymorphic sites in this study

Polymorphic sites

/ N / Si / Se / S
Madagascar / 60 / 56 / 98 / 154
Mayotte / 59 / 60 / 87 / 147
Tanzania / 56 / 54 / 74 / 128
Kenya / 55 / 72 / 48 / 120
Reunion / 60 / 68 / 42 / 110
Zimbabwe / 55 / 66 / 25 / 91
Cameroon / 48 / 56 / 27 / 83
Europe / 57 / 55 / 22 / 77
Antilles / 57 / 32 / 27 / 59

N: total number of sequences over four loci; Si: number of internal polymorphis sites; Se: number of external polymorphic sites (singletons); S: total number of polymorphic sites.


Supplementary table 2.- Neutrality tests at four X-linked loci in nine populations of D. simulans

Population

/ D / Fs / H-test / CV

Sex-lethal

Madagascar

/ -1.58** / -8.80 / 1.000 / 0.323*

Mayotte

/ -1.13 / -6.68 / 0.990 / 0.351

Tanzania

/ -1.01 / -7.23 / 0.981 / 0.460

Kenya

/ -0.35 / 1.94* / 0.890 / 0.496

Reunion

/ 0.60 / 1.10 / 0.895 / 0.533

Zimbabwe

/ -0.34 / -0.09 / 0.924 / 0.391

Cameroon

/ 0.34 / 2.30* / 0.864 / 0.575

Europe

/ 0.49 / 3.60** / 0.800* / 0.702**

Antilles

/ 2.20** / 9.05** / 0.629** / 0.870**
vermilion
Madagascar / -1.44** / -7.66 / 1.000 / 0.267**
Mayotte / -0.92 / -4.08 / 0.990 / 0.273+
Tanzania / -1.06 / -4.10 / 1.000 / 0.298
Kenya / -0.80 / -3.72 / 0.987 / 0.351
Reunion / -0.38 / 0.10 / 0.914 / 0.609*
Zimbabwe / -0.41 / 0.72 / 0.911 / 0.424
Cameroon / -0.74 / -1.96 / 0.970 / 0.530
Europe / 0.05 / 3.50** / 0.727** / 0.689**
Antilles / -0.79 / 2.45* / 0.667** / 0.805**


(Supplementary table 2, continued)

sevenless
Madagascar / -0.88 / -8.35 / 1.000 / 0.309*
Mayotte / -0.84 / -3.07 / 0.978 / 0.382
Tanzania / -1.04 / -8.01 / 1.000 / 0.319
Kenya / -0.81 / -1.36 / 0.956 / 0.296*
Reunion / -0.48 / 0.69 / 0.848* / 0.500
Zimbabwe / 0.88 / 2.67** / 0.857 / 0.524
Cameroon / -0.22 / 2.76** / 0.576** / 0.976**
Europe / 1.79** / 7.79** / 0.648** / 0.760**
Antilles / -2.15** / 3.42** / 0.133** / 2.604**
runt
Madagascar / -1.54** / -8.87 / 1.000 / 0.346
Mayotte / -1.42** / -9.86 / 1.000 / 0.536
Tanzania / -0.73 / -2.14 / 0.952 / 0.407
Kenya / -0.04 / -0.57 / 0.934 / 0.454
Reunion / -0.99 / 0.82 / 0.895 / 0.619
Zimbabwe / 0.42 / 0.24 / 0.914 / 0.436
Cameroon / -0.50 / 4.73** / 0.439** / 1.172**
Europe / 1.30* / 4.30** / 0.810 / 0.586
Antilles / -0.84 / 4.32** / 0.448** / 1.189**

D: Tajima’s (1989) D statistics; Fs: Fu’s (1997) Fs statistics; H: Depaulis and Veuille (1998) H-haplotype test; CV: Mousset, Derome and Veuille (2004) CV-test; *: p < 0.05; **: p < 0.01.