Fig. 4: Model of vertebrate genome evolution and reconstruction of proto-gnathostome chromosomes.

a Hypothetical scenario of an ancestral genome of three chromosomes that experiences two rounds of WGD (labelled 1R and 2R) and rearrangements. b Scatter plot of ohnologues created by the two WGD events. The hypothetical 2R genome is along each axis. Dots represent ohnologue pairs whose genome positions are indicated by the x- and y-axes. c Inversions result in extensive shuffling of gene order within a chromosome, scattering the dots over the entire chromosome. Red rectangles indicate regions that contain many ohnologue gene pairs between duplicated chromosomes. Yellow triangles represent intra-chromosome comparisons and are empty. d Inter-chromosomal rearrangements shuffle the genome further. The aim of our reconstruction analysis is to infer the post-2R genome structure (c) from modern genomes (d). e As expected, the actual ohnologue distribution in the human genome is similar to Panel d. Lines indicate chromosome boundaries, and human chromosomes 1–22, X and Y are ordered along the axes. f The human chromosomes were partitioned into 151 segments of conserved synteny based on comparison with other gnathostome genomes. g The segments were grouped into 10 clusters (red triangular regions) using the probabilistic macrosynteny model. Segments in individual clusters are expected to derive from a single pre-1R chromosome (no fusions), or alternatively derive from multiple pre-1R chromosomes if they involve fusions. h Optimal partitioning of each cluster of human segments into several paralogous subgroups (yellow triangles of low ohnologue density, representing 49 post-2R chromosomes). i Magnification of the diagonal part of h. Examples of fusion presence/absence similar to panel a are present, indicated by the chromosome cartoons above the plot shaded as per panel a. For example, the leftmost group of segments make up the Hox-bearing chromosomes and have not experienced fusion (blue chromosomes).