TABLE 1

Parameter estimates

GeneNo.
 lociaLengthbθ1θ2θAm1cm2ctuΣd(t × uΣ)/
 kbpeθ1 × uΣfθ2 × uΣfRgAhM1iM2i
per 914701.50.60.30.190.320.8711.16.5716.26.50.400.230.130.09
X00810 9973.60.30.50.0800.2516.14.0457.94.00.070.150.140
X009 6 6980.81.10.500.100.706.96.92 5.67.81.400.6500.05
Hsp82 319573.00.50.900.070.574.31.2513.12.20.170.2900.02
X010 1 8714.53.12.0004.7615.46 4.53.10.690.4500
2003 1 5225.41.71.0000.5711.09 5.41.70.330.1800
rh1 914432.41.70.30.3800.3410.62.5025.118.20.730.140.450
bcd 813711.20.60.5000.3211.32.6413.26.90.520.3800
2002 6 9155.50.60.3000.767.05.8138.74.30.110.0500
2001 4 6774.21.80.5000.314.42.0118.47.90.430.1100
300211 6600.90.40.50.025.000.0217.60.5316.46.60.410.580.010.94
4003 3 6195.53.81.00.3000.353.11.7516.911.60.690.180.820
Adh2034480.81.10.60.177.930.1628.61.3322.030.71.390.770.064.25
4002 1 8255.52.30.8001.4511.76 5.52.30.410.1500
Meanj 6.611773.21.40.70.080.960.823.120.550.310.120.38
Jointk14 3.01.60.70.060.140.620.540.230.090.11
mtDNAl 1182613.410171.80.200.822.2911.2513.41017.676.150.131.30414.65
  • a For individual genes, the number of “loci” is the number of apparently nonrecombining segments into which the data were divided to meet the four-gamete criterion for each segment.

  • b The average length of complete sequences.

  • c Migration rate estimates were identified as being at 0 when the highest observed value of the marginal posterior density was at the lower limit of resolution. The HKY model was used for the mtDNA.

  • d uΣ is the sum of the mutation rate scalars for the different segments.

  • e Divergence time in units of mutations per kilobase pairs of sequence (i.e., t/length).

  • f The product of θ estimates and the sum of the mutation rate scalars is an estimate of θ for the entire locus.

  • g The ratio of the estimates of population mutation rates, θ21, reflects the size of D. persimilis relative to that of D. pseudoobscura.

  • h The ratio of the estimates of population mutation rates, θA1, reflects the size of the ancestral species relative to that of D. pseudoobscura.

  • i Population migration rate estimates, M1 = 2N1m1 = m1 × θ1/2 and M2 = 2N2m2 = m2 × θ2/2.

  • j Mean parameter estimates for the 14 X-linked and autosomal loci.

  • k Results of fitting the model to all 14 loci. Those loci that showed evidence of recombination were represented only by the leftmost segment.

  • l Results for the mtDNA, including data from both ND4 and COI (Machado and Hey 2003).

  • Parameter estimates are obtained from the location of the peaks of the marginal posterior distributions. D. pseudoobscura was designated as species 1 and D. persimilis was designated as species 2. The average sample sizes were 16 sequences for D. pseudoobscura and 13 sequences for D. persimilis (Machado et al. 2002). Results are shown for each individual locus. For those loci that showed evidence of recombination, the data were divided into segments as described in the text. Also shown are the mean parameter estimates for the 14 X-linked and autosomal loci. The joint estimate is based on including the leftmost segment of each of the 14 loci in a single model. Results for the mtDNA sequences are shown separately, because of the unique history of this locus (Machado and Hey 2003).