Fig. 2: Summary of gene duplications mapped onto the Malus phylogeny.

a, The Malus phylogenetic tree with focal clusters of GD events. The left species-tree is a part of that in Supplementary Fig. 3d. Red squares to the right of the species name represent triploids, and blue ones represent tetraploids. GD counts of eight focal GD clusters (N1–N8) are placed below the corresponding branches in the species-tree. Red star indicates an ancient WGD event in the early evolution of the apple tribe. b, Illustrations of chromosomal collinearity (synteny) for gene pairs in four Malus representatives supporting the WGD event. Red and blue rectangles along a yellow line represent protein-coding genes with the transcriptional direction from 3′ to 5′ and 5′ to 3′, respectively. Red lines represent anchor genes with GD mapped at Malinae; purple lines represent anchor genes with GD mapped at the MRCA of Malus and Eriobotrya; blue lines represent anchor genes with GD mapped at Malus. Black lines represent anchor genes either mapped to a node without focal phylogenetic positions or which were not included into gene trees because the focal gene families require more shared species. c, An abbreviated version of the phylogenetic tree shown in a, with clades I–VII represented by individual branches. The red star marks the WGD event in a. The red number above each branch represents the GDs among those shown in a that correspond to syntenic anchor genes present in at least one genome from the species included in the relevant clade. The blue number below each branch represents the number of GDs matching the syntenic anchor genes in those syntenic block(s) that also include gene pairs mapped at Malinae and retained in the (AB)(AB) pattern. Detailed metadata of the number of GDs can be found in Supplementary Figs. 6–12. d, A model of introgression of genes from Gillenieae to the ancestor of Malinae and its descendant lineages. Purple and red branches of Malinae represent the possible subgenomes derived from Gillenieae and the other progenitor, respectively. Ma, millions of years ago.