Fig. 4: Duplications, fusions and mixing in bony vertebrates.

a, Right: chromosomal descendants of CLGE (green) and CLGO (pink) are organized into five groups. Each chromosome is represented as in Fig. 2, with corresponding segments outlined by black dotted rectangles. The double-headed arrow indicates probable inversion that separated two CLG blocks. Within each group, segments with the CLGE and/or CLGO ancestry are orthologous among the chicken, gar and frog, and groups are paralogous to each other. Note that the frog chromosome XTR4 has distinct CLGE and CLGO segments with distinct ancestry (see Supplementary Note 6). Left: cladogram showing the most parsimonious evolutionary history leading to these vertebrate chromosomes, starting from CLGE and CLGO ancestors. This includes an early duplication (producing copies labelled 1 and 2), a fusion and subsequent mixing, and then a second duplication (producing copies labelled α and β). The CLGO-1β copy was not found, as indicated by a dashed pink rectangle. CLGE-1β was not found in chicken, as indicated by the dash. CLGO-1α was found split across XTR04 and XTR07, as indicated by the plus sign. b, Distribution of gene retention for the α and β segments listed in Fig. 3, with rug plot and kernel density estimator. The upper curves are for α–β pairs, whereas the orange curve is for α segments without β counterparts (presumed lost or possessing limited gene content and therefore undetected).