TABLE 2

Polymorphism statistics

LocusSpeciesSaEmbedded Image bEmbedded Image /bpγcDdDiv.e
Adhsim135.690.0082-0.820.0281
mau52.190.0031-1.340.0326
sec00.00.00.0279
asesim00.00.00.0252
mau52.400.00230.000.0267
sec00.00.00.0244
cisim10.370.0003-1.090.0504
mau10.440.0004-0.930.0504
sec00.00.00.0494
est6sim6937.640.0247149.00.190.0507
mau3615.770.010424.5-0.500.0503
sec00.00.00.0507
hbsim113.890.0155-1.89*0.0324
mau62.210.0084-1.120.0353
sec00.00.00.0328
In(2L)tsim3010.240.0154.30.520.0382
mau4416.190.024341.3-0.340.0407
sec2315.330.02390.0415
janussim3322.000.021523.9f0.0517
mau2919.330.019049.2f0.0494
sec0.0586
mt:ND5sim10.370.0013-1.090.0393
mau00.00.00.0505
sec10.390.0014-1.050.0510
persim5423.650.012744.3-0.590.0349
mau4821.020.011384.60.340.0402
sec41.750.0009-0.060.0391
Sxlsim82.580.010142.70.330.0362
mau41.470.0057-1.150.0353
sec10.310.00150.250.0572
wsim197.000.036112.2-0.150.0704
mau31.220.0066-1.89*0.0626
sec20.880.0042-1.130.0760
yp2sim31.310.0012-0.450.0258
mau41.750.0016-1.300.0285
sec10.440.0004-0.930.0280
zsim187.880.00806.0-0.070.0386
mau93.940.00400.030.0373
sec00.000.00.0387
Zwsim103.310.00269.31.330.0360
mau104.380.0033-1.160.0364
sec00.00.00.0411
  • For each gene, the top row shows values for D. simulans (sim), the second row shows values for D. mauritiana (mau), and the third row shows values for D. sechellia (sec). (—)Estimates cannot be obtained for small samples or for samples with few informative polymorphic sites.

  • a The number of polymorphic sites.

  • b An estimate of the population mutation rate 2Gu, where G is the effective number of gene copies and u is the mutation rate for the region (Watterson 1975). Also shown is the estimate of 2Gu/bp.

  • c An estimate of the population recombination rate, 2Gc, where c is the rate of crossing over per generation for the region (Hey and Wakeley 1997).

  • d Tajima’s statistic of equality between different estimates of 2Gu (Tajima 1989b). Negative values indicate an excess of low frequency polymorphisms. * indicates the value exceeds the expected 95% confidence interval.

  • e Average divergence, per base pair, between the sample sequences and a sequence from D. melanogaster.

  • f One outgroup sequence from D. melanogaster was included with the small janus samples to estimate γ.