Larger nuclei in the larval brain of Drosophila nasutoides often show underreplication, whereas metaphases provide a reliable DNA standard.

Specific nuclear regions are highly condensed as heterochromatin during the postembryonic life-span of dipterans. Somatic nuclei are usually endoreplicated to form polyploid sets of chromosomes or polytene elements, or even a mixture of both. Such genomic redundancy presents the possibility that condensation is superimposed by underreplication. From the very early stages, DNA in heterochromatin may be selectively excluded from endoreplication. The result is underrepresentation of heterochromatic sections (both DNA and heterochromatin associated proteins) relative to euchromatin in endoreplicated nuclei. Drosophila nasutoides possesses a novel karyotype in which chromosome 4 contains most or all of the heterochromatin DNA (62% of the genome). This characteristic makes it easy to follow the fate of chromosome 4 during genome multiplication. Larger cells were found adjacent to neuroblasts and ganglion mother cells in the larval brain. Heterochromatin DNA is underrepresented relative to euchromatin in some 60% of these larger nuclei, while DNA in euchromatin selectively undergoes up to five endoreplications. Underreplication begins in the very first endoreplication, more rarely during the second or the third. The resulting relative diminution of chromosome 4 corresponds with the quantity of nuclear DNA absent from other somatic tissues. Some brain nuclei are not underreplicated and carry out only three complete endoreplications at most. However, in a few nuclei heterochromatin DNA is amplified relative to euchromatin in the same cell. These results are based on data for mitotic metaphases from neuroblasts that were found to be reliable as an endogenous 4C DNA standard.