Fig. 3: Organization of bony vertebrate chromosomes after 2R.

The majority of CLGs have four copies in bony vertebrates; the remainder have three. Organizing these copies by chromosome fusion (solid rectangles joining cells) and gene retention (numbers in cells) shows that chicken, spotted gar and frog chromosomes can be sorted into ‘α–β’ pairs that share the same patterns of CLG fusion, and these pairs themselves form ‘1–2’ pairs. Bold dashed lines separating CLGA-2α and CLGB-1α from their fusions with other CLGs indicate either fusions in the α-lineage or fissions in β. Due to this ambiguity, the β pairings in these two rows are arbitrary. Similarly, the β copies for CLGG and CLGH are arbitrarily assigned to 2. In several cases (for example, CLGO) two distinct copies are found on the same chromosome of one species; these are indicated as a and b. Arrows imply that the entire source chromosome is orthologous to the target; double-headed arrows indicate reciprocal orthology; boxes indicate that segments of the chromosomes are orthologous; -- indicates undetected enrichment. The significance of associations between CLG and jawed vertebrate chromosomes was determined as described in Methods. Significance determined using 50-gene windows (P < 0.01) is indicated by an asterisk. Significance determined using 50-gene windows (P < 0.05), 100-gene windows (P < 0.01) and/or at the whole-chromosome level (P < 0.05) is determined by a plus sign. All P values were Bonferroni corrected.