Gene differences between the sex ratio and standard gene arrangements of the X chromosome and linkage disequilibrium between loci in the standard gene arrangement of the X chromosome in Drosophila pseudoobscura

The Standard and Sex Ratio gene arrangements of the X chromosome of D. pseudobscura differ from each other in allele frequencies at the four X chromosome loci, esterase 5, adult acid phosphatase 6, phosphoglucomutase 1 and octanol dehydrogenase 3. The Standard arrangement which is the common arrangement in all populations is polymorphic at these loci in varying degrees, the geographically less widespread Sex Ratio arrangement has little polymorphism and is genically predominantly E 5 (1.04) AP 6^- Pgm1(1.0) ODH 3(1.10). The Sex Ratio arrangement from different populations is alike at all of the four loci, the Standard arrangement shows some gene frequency differences among populations. The Standard and Sex Ratio arrangements differ from each other by three inversions which suggests that the two arrangements are 'old'. Gene differences between these two chromosome arrangements can be explained due to differential natural selection of alleles in the Standard and Sex Ratio arrangements. The order and percentage of recombination among these four loci in the Standard arrangement are: E 5-.294-AP 6-.335-Pgm 1-.024-ODH 3. The Standard X chromosomes from four different wild populations were analyzed for evidence of linkage disequilibrium between pairs of loci at these four loci. No evidence of linkage disequilibrium between pairs of loci was obtained. However, when linkages involving simultaneously three loci, E 5, AP 6 and Pgm 1 are considered, then significant departure from linkage equilibrium is observed.