The size and shape of the posterior lobe of the male genital arch differs d
ramatically between Drosophila simulans and D. mauritiana. This difference
can be quantified with a morphometric descriptor (PCI) based on elliptical
Fourier and principal components analyses. The genetic basis of the intersp
ecific difference in PC1 was investigated by the application of quantitativ
e trait locus (QTL) mapping procedures to segregating backcross populations
. The parental difference (35 environmental standard deviations) and the he
ritability, of PC1 in backcross populations (>90%) are both very large. The
use of multiple interval mapping gives evidence for 19 different QTL. The
greatest additive effect estimate accounts for 11.4% of the parental differ
ence bur could represent multiple closely linked QTL. Dominance parameter e
stimates vary among loci from essentially Ilo dominance to complete dominan
ce, and mauritiana alleles tend to be dominant over simulans alleles. Epist
asis appears to be relatively unimportant as a source of variation. All but
one of the additive effect estimates have the same sign, which means that
one species has nearly all plus alleles and the other nearly all minus alle
les. This result is unexpected under many evolutionary scenarios and sugges
ts a history of strong directional selection acting on the posterior lobe.