Fig. 2: History of genome duplications in vertebrates.
a, Probabilistic inference of polyploidization events in early vertebrate evolution on the basis of gene tree–species tree reconciliation (WHALE36; Extended Data Fig. 4, Supplementary Table 8 and Methods) supports an initial tetraploidization shared by all vertebrates (1RV), a jawed-vertebrate-specific tetraploidization (2RJV) and a cyclostome-specific polyploidization (2RCY). Supported polyploidization events (Bayes factors BFNull_vs_WGD < 10−3) are shown in colour (1RV, 2RJV and 2RCY) and non-supported ones in grey (2RV, hagfish-specific, lamprey-specific). The WHALE method cannot distinguish between tetraploidization and hexaploidization events. b, Paralogon-based polyploidization inference using molecular phylogenies reconstructed for each of the 17 informative CLGs (Supplementary Fig. 1). Successive polyploidization events during vertebrate evolution are shown as coloured polygons and the proportion of CLG trees displaying these duplication nodes is indicated below. c, Sample paralogon tree for CLGJ. As for gene trees, in paralogon trees some nodes correspond to speciation events (grey) and others to duplication events (coloured); both types of events can be dated using a molecular clock. Species and datasets used are listed in Supplementary Table 8, and dating was performed with PhyloBayes (Methods) using fossil calibrations reported in Supplementary Table 7. d, Molecular dating of the polyploidizations and speciation events in early vertebrate evolution. Divergence times are indicated for speciation (grey) and duplication nodes (coloured as in a) are indicated. In c,d, each node is labelled with the mean divergence time across CLGs. Ediac., Ediacaran; Cambr., Cambrian; Ord., Ordovician; Sil., Silurian; Devon., Devonian; Carbon., Carboniferous; Perm., Permian; Trias., Triassic.
