Figure 1. Definition of evolutionarily derived chromosome changes observed by molecular cytogenetic techniques. (a) Chromosome painting can show that two homologous chromosomes in two different species may give the same hybridization pattern. In analogy to definitions from somatic cell biology, we would define this as ‘conserved synteny’ in contrast to (b) ‘disrupted synteny’, when one chromosome is giving a different pattern. (c) To discriminate which of the two chromosomes shows the ‘conserved’ and ‘disrupted’ synteny, respectively, hybridization patterns are analysed in ‘outgroup’ species. (d) Chromosome breakage of an ancestral chromosome may produce two new syntenies, whereas fission may result in a new syntenic association. (e) Two species may have a conserved homologous segment on otherwise nonhomologous chromosomes. (f) Linkage of DNA fragments on an ancestral chromosome may be disrupted by an inversion. In this example the entire upper arm is inverted. The sequence of markers in the lower arm (A) is conserved, whereas linkage between the green and the red spot (B) is disrupted.

Figure 2. All different 21 acrocentric mouse chromosomes (19 autosomes and the X and Y sex chromosomes) were painted with chromosome-specific probes in different colours. (a) Metaphase and (b) chromosomes cut out and ordered into a karyogram. Different local mice populations may show various Robertsonian fusions that will form biarmed chromosomes stained in two different colours.

Figure 3. Evolution of chromosome numbers in bear species. Most extant bear species show a high chromosome number karyotype that obviously is simply derived by fission of chromosome arms from a supposed ancestral carnivore with 2n=42 chromosomes. But two bear species, the giant panda (Ailuropoda melanoleuca) and the spectacled bear (Tremarctos ornatus) show low chromosome numbers. Chromosome painting indicates that they independently evolved from a high chromosome bear karyotype by several different chromosome fusions.

Figure 4. Chromosome painting to the Indian muntjac (Muntiacus muntjak vaginalis). (a) Painting of muntjac chromosomes with probes derived from the same species. The arrow points to chromosome Y₁, which was painted with sheep probes specific for chromosomes 1, 4, 12, 10, 6 and 7 (b, c). Except for the sheep probe for chromosome 1, which also paints other segments in the muntjac genome (not shown), each probe paints only a single band in the entire muntjac karyotype (c), indicating the multiple fusion of chromosomes in an ancestral muntjac species.

Figure 5. Analysing intrachromosomal rearrangements (inversions) that have occurred during evolution. (a–c) Chromosome painting probes can be used that cover only part of a chromosome but span inversion breakpoints. Here, a chromosome painting probe derived from the African green monkey (Cercopithecus aethiops) (red box in (c)) was used to paint the human chromosome 3 homologue of the orangutan (a) and the chimpanzee (b). The pattern in the orangutan seems to differ from the African green monkey only by a fission, while the probe paints two segments in the chimpanzee. Gorilla and human chromosomes give the same pattern as those of the chimpanzee. A more detailed picture can be obtained when using smaller probes (d, e). Changes in the order of yeast artificial chromosome (YAC) clones can indicate intrachromosomal rearrangements. In (d), five YACs with human inserts are shown in different colours that were hybridized to the human chromosome 3 homologue of the orangutan. In the original work, 12 YACs were used that span the entire chromosome 3 (e). The numbers along the chromosome (1–12) indicate the mapping position of the 12 different YAC clones. The hybridization patterns indicate two overlapping inversions in which the human and African ape homologues differ from that of the orangutan (Bornean subspecies).