Extended Data Fig. 5: Timescale of vertebrate genome evolution.

a. Distributions of timings for speciation and duplication events derived from paralogon phylogenies, showing details of the distributions indicated in Fig. 3c. b. Scenario for genome duplication and speciation events during early vertebrate evolution. Filled black circles or ovals mark speciation events; horizontal rectangles indicate presumptive auto-tetraploidies; starbursts indicate allo-polyploidies arising from hybridization of distinct progenitors (for example, alpha–beta in gnathostomes). Timings are based on a. Note that although speciation times (for example, the split between gnathostome progenitors alpha and beta, divergence of lamprey and hagfish lineages) can be estimated from gene or paralogon trees, hybridization times (for example, 2R_JV, shown as green starburst) cannot be estimated from gene-tree analysis. Similarly, homoeologous recombination after auto-tetraploidization implies that the auto-tetraploidization event itself cannot be timed, but only the cessation of homoeologous recombination. Thus, the estimate of around 527 Ma for 1R_V (horizontal blue rectangle) represents the cessation of recombination after this presumptive auto-tetraploidy (open rectangle on vertebrate stem) with homologous recombination represented by blue shading. The absolute timing of 1R_V itself is unknown. (Auto-tetraploidy is suggested by the lack of differential gene loss between the two paralogous branches after 1R, as noted previously¹⁹.) The rough estimate of a 10-million-year interval between the alpha–beta split and 2R_JV allo-tetraploidy is based on analogy with recent vertebrate allo-tetraploidies in frogs and goldfish. Cyclostome hexaploidization 2R_CY is shown as a two-step process culminating in the hybridization of diploid and tetraploid stem cyclostomes (orange starburst). This scenario follows the recent model of hexaploidy in sturgeon in which auto-tetraploids and diploid species coexist and hybridize⁴⁸. In this scenario, the earliest divergences among cyclostome paralogues occurs around 511 Ma when the diploid and future tetraploid lineages split, which could be coincident with the early tetraploidization itself. Homoeologous recombination (shown as orange shading) is largely complete by around 493 Ma, defining a second peak in paralogue divergence (horizontal orange rectangle). Not shown is ongoing homoeologous recombination in CLGB which continues into the stem hagfish and lamprey lineages, as discussed further in the main text.