TABLE 5

Analysis of linkage disequilibrium in red- and sika-like individuals for each site at which the phenotype was present

Number of introgressed alleles (observed vs. expected)G-statistic (P value)Randomization test P value
012345
Site (sika)
    1012.00
0.370.370.1573
    229610.240.480
28.836.410.720.6225
    3167000113.620.001
14.567.281.820.300.0380.00380.0086
    47511016.640.078
5.525.522.760.920.230.0460.2488
    5210.38
2.150.720.5386
Site (red)
    1012.00
0.370.370.1573
    230000112.840.003
1.151.430.900.370.120.0290.0249
    352111.800.632
4.133.221.250.320.6138
    41130.69
11.302.420.4047
    5420.76
4.301.430.3845
    636311.680.201
35.304.410.280.4327
    743411.260.275
42.365.290.330.5331
    812
12
    91010.09
10.040.910.7594
    102020.18
20.091.830.6649

The observed and expected numbers of individuals with 0–5 introgressed alleles. The G-statistic tests against the null hypothesis that introgressed alleles are in linkage equilibrium (approximated by a Poisson distribution). The associated p value is calculated using the asymptotic χ2-distribution. The last column gives the number of times the observed G value was exceeded in 1000 random permutations of the dataset. Significant deviations indicate introgressing alleles are in linkage disequilibrium, suggesting recent hybridization in that site.