Figure 1. (a) Vertebrate karyotype evolution. The left picture shows the phylogenetic tree of vertebrates. The right column displays the distribution of chromosome numbers in individual lineages. The data were obtained from the Animal Genome Size Database: http://www.genomesize.com. (b) A model of genome evolution involving the WGD events. (c) Paralogues shared in common between chromosomes S1 and S2 in (b) are represented by dot plots. (d) Dots enclosed in boxes represent paralogous blocks. (e) Similarly, dots show paralogues among S3, S4, S5 and S6. Reproduced with permission from Nakatani et al. (2007).

Figure 2. (a) Reconstruction of the ancestral genome before the 2R WGD. For simplicity, suppose that the ancestral chromosome had 10 genes. The 2R WGD produced ohnologues, represented by blue dots along the diagonal line in the triangular dot plot, in the duplicated chromosomes. (b) Chromosome breaks and inversions may have altered the order of ohnologues on the sister chromosomes. (c) In the course of early vertebrate genome evolution, the ancestral gene order was disrupted by numerous inversions, resulting in scattered ohnologue dots. (d) Eventually, CVL blocks were distributed across several human chromosomes through intensive interchromosomal rearrangements. Steps (a)–(d) illustrate a typical model of genome evolution involving the 2R WGD. In the next step, we handle real human genome data. (e) This is a real instance of the dot plot in (d). CVL blocks were ordered from the human chromosomes 1 to X and ohnologues shared among these CVL blocks were plotted. (f) This corresponds to the state in (c). The CVL blocks were reordered in such a way that paralogous CVL blocks were grouped so that each group represented one ancestral vertebrate chromosome. (g) This state corresponds to that in (b). The CVL blocks within individual vertebrate groups were further reordered to obtain ancestral gnathostome subgroups (namely, chromosomes), which were duplicated from a single ancestral vertebrate chromosome by the 2R WGD events. The partition of subgroups that optimizes the significance. (h) The vertebrate group A was decomposed into four gnathostome subgroups by statistical analysis, indicating that the ancestral chromosome underwent 2R WGD. Reproduced with permission from Nakatani et al. (2007).

Figure 3. Reconstruction of ancestral osteichthyan and amniote proto-chromosomes. The number of proto-chromosomes ranges from 10 to 13 depending on the choice of two alternative models that assume fissions or fusions between the two WGD events. The figure illustrates the scenario in which only fissions took place. The 10 reconstructed proto-chromosomes in the vertebrate ancestor shown at the top are assigned distinct colours, and their daughter chromosomes in the gnathostome ancestor are distinguished by the respective vertical bars. In the genomes of the osteichthyan, teleost and amniote ancestors, and human, chicken and medaka genomes, genomic regions are assigned colours and vertical bars that represent correspondences of individual regions to the proto-chromosomes in the gnathostome ancestor from which respective regions originated. In addition, for better understanding, each gnathostome proto-chromosome is assigned a unique identifier. These identifiers are used to emphasize the origins of extant and ancestral chromosomes. Unassigned blocks are shown in the rightmost chromosome labelled ‘Un’ in the osteichthyan and amniote ancestors. Reproduced with permission from Nakatani et al. (2007).

Figure 4. Scenario of vertebrate chromosome evolution. (a) For simplicity, we illustrate two proto-chromosomes duplicated by the first round of WGD. Subsequently, fission divided one of the duplicated chromosomes. (b) The second round of WGD doubled the proto-chromosomes. Blocks in chromosomes are labelled with their respective chromosome positions in the human genome. (c) After the second WGD, early vertebrates underwent slow changes in karyotype over a long evolutionary process. (d) In the ancestral mammalian lineage, intensive interchromosomal rearrangements occurred and the ancestral chromosomes were broken into smaller segments that were distributed across many human chromosomes. (e) In the ancient ray-finned fish lineage, intensive chromosome fusions merged the ancestral chromosomal segments into ancestral teleost chromosomes. (f) Another round of WGD in the ancestral teleost doubled the proto-chromosomes, and subsequently, a few global rearrangements shaped the present medaka genome. Reproduced with permission from Nakatani et al. (2007).

Figure 5. Teleost genome evolution. (a) The figure depicts a model of the distribution of ancestral chromosome segments in the human, zebrafish, medaka and Tetraodon genomes. Thirteen reconstructed ancestral chromosomes are represented by the coloured bars and the genomic regions originating in the ancestral chromosomes have the same colour coding. Major rearrangements are represented by arrows and lineage specific small-scale translocations by dotted arrows. The dotted box for the zebrafish indicates that most parts of the chromosome were lost through extensive translocations. (b) The basis of the logic of deducing the teleost genome evolution is shown by illustrating how ancestral chromosome b is inferred. (c) Dots represent synteny blocks between the medaka and Tetraodon chromosomes. Reproduced with permission from Kasahara et al. (2007).