Fig. 3: Limited lineage-specific rediploidization after vertebrate genome duplications.
a, Gene-tree topologies expected under the ancestral rediploidization (left) and lineage-specific rediploidization (right) models after the 1RV (Methods and Extended Data Fig. 6). In the ancestral rediploidization scenario, paralogous gene sequences diverge before the cyclostome–gnathostome split and thus group by duplicated gene copy. In the lineage-specific rediploidization scenario, paralogue sequences diverge independently in the stem gnathostome and cyclostome lineages, and thus genes are grouped by lineage. b, Number of significantly supported gene trees in favour of ancestral and lineage-specific rediploidization scenarios after 1RV, for each of 17 informative ancestral linkage groups (CLGs). c, Tree topologies expected under the ancestral and lineage-specific rediploidization models after 2RCY. The CLGB paralogon tree shows an ancestral rediploidization topology for 1RV copy 2, but lineage-specific rediploidization for 1RV copy 1, where two hagfish (chr. 4 and chr. 5) and two lamprey (chr. 10 and chr. 2) paralogons independently rediploidized. Myr, million years. d, Evolutionary history of vertebrate Hox gene clusters resolved by the CLGB paralogon phylogeny (see bottom of c).
