Figure 3

Inferred temporal process of gene loss after 3R-WGD in a teleost ancestor. (A) The estimated numbers of gene loss events in the teleost phylogeny was parsimoniously drawn from the presence or absence of loci belonging to the 116 orthologous gene groups. The branch lengths are proportional to the estimated divergence time among the lineages [33]. Gray bars indicate 95% confidence intervals for them. (B) Approximation of the number of gene loss events based on a neutral model of the loss-of-function of duplicated genes (αe^-2μt) [8, 65, 66]. Gray and black lines show the approximation from 3R-WGD and point c, and all data points, respectively. (C) Proposed phase transition during duplicate gene loss. All data points except the 3R-WGD were approximated by a linear equation. (D) Approximation of the number of gene loss events to the upper and lower extremes of the 95% confidence intervals of estimated occurrence time of the 3R-WGD [15, 17, 19] and divergence times of teleosts [33]. The approximations to the upper and lower extremes are shown by black and gray lines, respectively.