Fig. 3: Analyses of introgression history in Malus.

a, A summary of the sisterhood of (A, B) in gene trees of the Malus orthogroup, where A represents the gene from any focal polyploid and is supported (BS ≥50) as sister to B, which represents the gene(s) from a potential progenitor of the polyploid. At the top is a phylogeny of the Malus clades I to VII, derived from the species tree in Fig. 1c. Also in the phylogeny, the dotted line represents the MRCA of clades I to IV, with the numbers below this dotted line for genes from the MRCA of clades I to IV as the potential progenitor. For each of four triploids in the column on the left, up to three numbers are shown below the clade(s) with sisterhood, as support for those clades being potential progenitors. For each of six tetraploids in the left column, up to four numbers are shown below the clade(s) with sisterhood. The number in parenthesis represents the number of gene sisterhoods that have at least two genes from the focal polyploid. The metadata of the sisterhood for each polyploid can be found in Supplementary Figs. 13–22. b, An evolutionary model of the polyploids and their possible progenitors. The phylogeny with diploid species (with branches of solid lines) is derived from the Malus phylogeny; different colors of the lines correspond to different genome types (A–E genomes; their respective clades in Fig. 1c are shown to the right in parenthesis) represented by closely related diploids, as supported by the tree in Supplementary Fig. 23. Dashed lines correspond to the phylogenetic positions of proposed subgenomes of polyploids. Sister groups of the subgenomes represent their possible progenitors (see support values and phylogeny in Supplementary Fig. 23). The red and blue squares on the right indicate triploids and tetraploids, respectively.