TABLE 4

The maximum-likelihood estimate for null allele frequencies (Ø), and frequency of introgessed alleles (u) for each of the loci at which apparent homozygotes for rare alleles was seen

LocusØ freq (pooled)u freqObserved vs. expected number of each genotypelog(L) (1 d.f.)
Ø Ø RR + ØRRSSS + ØS
Red0.2310.01519153410.02
TGLA3878.88153.133.801.20
Red0.3980.024326133440.12
DRB00326.47132.514.693.33
Red0.1950.00606159110.46
FCB0486.36158.641.610.40
Sika0.0570.0331014740.66
BOVIRBP0.260.394.7573.6
Sika0.1170.0389115720.02
HH0641.080.845.1971.90

Alleles are pooled into null (Ø), red (R), and sika (S). Missing data are assumed to be null homozygotes. The last column gives the difference in log likelihood by comparing the numbers of observed and expected numbers in each genotypic class (1 d.f.). For none of the five loci is there a significant deviation from the hypothesis that missing data represent null homozygotes (see also Appendix at http://helios.bto.ed.ac.uk/evolgen/).