TABLE 3

Results of coalescent simulations

TtyPuyPuxPsPyPc
M = 3.5, Ry = 0
0.100.250.0940.7360.1420.4780.021
0.100.2070.9070.1920.8540.100
0.010.4770.997*0.4031.000*0.372
0.200.250.0280.9030.0710.6200.006
0.100.0900.9850.1140.9290.047
0.010.3221.000*0.2610.995*0.250
0.300.250.0100.963*0.0570.6570.004
0.100.0530.995*0.0760.9380.025
0.010.2150.999*0.1620.981*0.150
Ry = 10
0.100.250.2220.3400.3700.2090.023
0.100.4310.5220.3720.5130.089
0.200.250.2090.3360.3520.2080.019
0.100.4330.5460.3840.5300.117
0.500.250.2190.3290.3840.2040.026
0.100.4110.5630.4040.5450.119
1.00.250.1940.3360.4020.2170.018
0.100.4090.5540.4010.5310.113
5.00.250.1970.3630.3640.2500.031
0.100.3690.6170.4160.5780.120
Ry = 100
0.10.250.3030.0950.6310.0580.008
0.100.4690.1100.5440.1170.022
5.00.250.2970.1470.6320.0900.013
0.100.3070.1890.6140.1520.022
M = 5, Ry = 10
0.10.250.1860.2990.3040.1790.012
0.100.4140.52910.3280.5130.075
5.00.250.1890.3670.3140.2260.018
0.100.2200.3760.3650.2600.091
Ry = 100
0.10.250.2910.0700.6160.0410.007
0.100.4610.0930.5180.0900.011
5.00.250.2680.1370.6320.0970.014
0.100.3680.1820.5720.1310.018

T is the time since the origin of the fusion (in units of the autosomal coalescent time); Ry is the rate at which a neo-Y allele moves to the neo-X chromosome, measured on the time-scale of the autosomal coalescent process (2Ne generations); ty is the coalescent time for genes on the neo-Y relative to the autosomal coalescent time; Puy is the fraction of runs that yielded a proportion of neo-Y variants unique to the neo-Y as small as or smaller than observed; Pux is the fraction of runs that yielded a fraction of neo-X variants unique to the neo-X as large as or larger than observed; Ps is the fraction of runs in which there were a proportion of singleton variants among the unique neo-Y variants as large as or larger than observed; Py is the fraction in which the ratio of the number of segregating sites on the neo-Y to the total for both chromosomes was as small or smaller than observed; Pc is the fraction of runs in which all of the criteria for Puy, Pux, Ps, and Py were met. Note that Puy, Pux, Ps, and Py were calculated only from runs where there was no premature coalescence (see materials and methods).

• * The probability of the observed value of the sample statistic is <0.05.