Fig 1

A) Shown is the assumed phylogeny of the eight species analyzed (see Methods). The TGD induces two mirrored gene trees, corresponding to the genes from the less fractionated parental genome (top) and the more fractionated parental genome (bottom, see Results for tests of the significance of the level of biased fractionation). Below the branches in each tree are POInT’s predicted number of gene losses along that branch for the parental genome in question. Above the branches in the upper tree are POInT’s branch length estimates, namely t (time) multiplied by the α parameter in Fig 2. Here αt corresponds to the overall estimated level of gene loss on that branch: a larger αt implies a greater number of losses relative to the total number of surviving ohnologs at the start of the branch. In the upper left are POInT’s parameter estimates (γ,ε_1,δ) for the WGD-bc^nbnf model (see Fig 2). B) An example region of the eight genomes, showing the blocks of DCS. For all species except zebrafish, truncated Ensembl gene identifiers are given; for zebrafish gene names are shown. The numbers above each column gives POInT’s confidence in the orthology relationship shown, relative to the 2⁸−1 (= 255) other possible orthology relationships. These other relationships entail swapping the two tracks of genes from one or more of the genomes between the top and the bottom panel: the confidence estimates indicate how much worse a fit is induced by assuming a different set of subgenome assignments. Genes are color-coded based on the pattern of ohnolog survival in the eight genomes. A pair of ohnologs expressed in the zebrafish retina are shown in magenta.