TABLE 1

Comparison of five estimators of the recombination rate

MaxhapSequenceLDRholikeAverageComposite
kbρ/kbRMSEgRMSEgRMSEgRMSEgRMSEg
211.700.391.410.381.260.291.260.431.310.38
241.430.571.290.621.200.441.150.661.180.64
2160.680.600.600.700.660.590.600.740.610.70
10Embedded Image0.810.641.020.431.050.560.790.640.930.59
1010.580.860.570.800.470.900.500.890.450.91
1040.370.930.320.950.230.980.251.000.250.99
2510.360.730.330.710.310.850.280.820.270.86
  • MLEs of three different approximate-likelihood curves, the average of these three MLEs, and the MLE of a composite-log-likelihood curve calculated as a weighted average of the approximate log-likelihood curves are shown. Accuracy is measured by the root mean square (relative) error (RMSE) and by g, the proportion of estimates within a factor of 2 (for 2- and 10-kb data) or 1.5 (for 25-kb data). All simulations were under a neutral coalescent model with constant population size, random mating, and θ = 1/kb.