In Drosophila, the availability of polytene chromosome maps and of set
s of probes covering most regions of the chromosomes allows a direct c
omparison of the organization of the genome in different species. In t
his work, we report the localization, in Drosophila virilis, D. montan
a, and D. novamexicana of >100 bacteriophage P1 clones containing simi
lar to 65 kilobase inserts of genomic DNA from D. virilis. Each clone
hybridizes with a single euchromatic site in either chromosome 1 or ch
romosome 3 in D. virilis. From these data, it is possible to estimate
the minimum number of inversions required to transform the map positio
ns of the probes in one species into the map positions of the same pro
bes in a related species. The data indicate that, in the D. virilis sp
ecies group, the X chromosome has up to four times the number of inver
sions as are observed in chromosome 3. The first photographic polytene
chromosome maps for D. montana and D. novamexicana are also presented
.