The mitotic metaphase chromosomes of Drosophila were first studied in 1907 by Stevens . The haploid chromosome number of D. melanogaster is 8, there being an acrocentric X chromosome, two metacentric autosomes (chromosomes 2 and 3) and a dot like 4th chromosome. In the male there is a J-shaped Y chromosome. In the family Drosophilidae as a whole the primitive chromosome number would appear to be n=6, with five long acrocentric chromosomes and a small dot like chromosome. Reduction in chromosome number has occurred many independent times by fusions of these elements.
Drosophila, like many other Diptera, possess polytene chromosomes in their larval tissues and ovarian nurse cells. Polytene nuclei are polyploid, they result from successive rounds of DNA replication without nuclear division. What distinguishes these polyploid nuclei is that the individual chromosome remain very tightly apposed to form very large polytene chromosomes, about 3 microns in diameter and hundreds of microns in length in their best developed form, in the salivary glands of third instar larvae.
Polytene chromosomes have a striking aperiodic pattern of strongly condensed bands and lightly condensed interbands. This pattern is constant within the species and detailed maps of these chromosomes were drawn in the 1930's and early 1940's, recognizing about 5000 bands. These have been very extensively used by geneticists to map chromosome mutations, to study gene function, since active genes may often be distinguished by a transient "puffing" of a band, and for evolutionary and population studies.
The reasons for their use in evolutionary and population studies are (a) that natural populations of D. melanogaster, and other species, are polymorphic for chromosome inversions; and (b) that closely related species of Drosophila often differ by fixed chromosome inversions. As Sturtevant realized in the mid-1930's these could be used for phylogenetic analyses. The best example of this is Hampton Carson's phylogeny over over 120 species of Hawaiian picture-winged species of drosophild based on their patterns of shared and unique chromosome inversions .
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