In interphase cells, as noted previously, chromosome territories can be visualized with chromosome-specific fluorescently labeled hybridization probes (see Figure 8-33), but the detailed structure of individual chromosomes cannot be observed, even with the aid of electron microscopy. During mitosis and meiosis, however, the chromosomes condense and become visible in the light microscope. Therefore, almost all cytogenetic work (i.e., studies of chromosome morphology) has been done with condensed metaphase chromosomes obtained from dividing cells—either somatic cells in mitosis or dividing gametes during meiosis.

The condensation of metaphase chromosomes probably results from several orders of folding of 30-nm chromatin fibers (see Figure 8-36). At the time of mitosis, cells have already progressed through the S phase of the cell cycle and have replicated their DNA. Consequently, the chromosomes that become visible during metaphase are duplicated structures. Each metaphase chromosome consists of two sister chromatids, which are linked at a constricted region, the centromere (see Figure 8-35).

The number, sizes, and shapes of the metaphase chromosomes constitute the karyotype, which is distinctive for each species. In most organisms, all somatic cells have the same karyotype. However, species that appear quite similar can have very different karyotypes, indicating that similar genetic potential can be organized on chromosomes in very different ways. For example, two species of small deer—the Indian muntjac and Reeves muntjac—contain about the same total amount of genomic DNA. In one species, however, this DNA is organized into 22 pairs of homologous autosomes and two physically separate sex chromosomes. In contrast, the other species contains the smallest number of chromosomes of any mammal, only three pairs of autosomes; one sex chromosome is physically separate, but the other is joined to the end of one autosome.