Fig. 1: The Malus evolutionary landscape based on phylogenomics.

a, The fruit phenotypes of Malus species are highly diverse in size, color and shape. Size bars, 2 cm. Numbers on the photographs are the same as the numbers to the right of the species names in c. b, A Circos plot of the diploid ‘Golden Delicious’ apple genome assembly. Tracks from outer to inner (a to f) are chromosomes, gene density, repeat elements density, LTR/Copia, LTR/Gypsy and syntenic regions between chromosomes. c, A dated phylogenetic tree of Malus simplified from Supplementary Fig. 3. The tree branch length represents the estimated time (the median value) from divergence to the present. Species names are indicated in different colors to the right of terminal branches, with purple for Malus species and red for others in the apple tribe (Maleae). The Malus topology is a summarized phylogeny from phylogenetic analyses using three different gene sets (Supplementary Fig. 3). In Malus, seven clades are designated as I through VII and highlighted with different background colors. Numbers on the nodes represent the divergence times. Horizontal blue bars on each node indicate the 95% confidence intervals of the divergence time in millions of years. The numbers to the right of species are the same as those in a. Stratigraphic periods of Cretaceous (K), Paleogene (Pg), Neogene (Ng) and Quaternary (Q) are illustrated by colored boxes below the tree, based on the ages of their boundaries in the International Chronostratigraphic Chart Capella-Gutiérrez (version 2022/02). The orange curve in the graph below the tree indicates the changes in oxygen isotope records of δ¹⁸O (‰), reflecting the temperature changes as indicated by the right axis. The vertical yellow bar indicates the climatic changes during the origination and divergence of Malus. ADRG, apple domestication-related group. Ma, millions of years ago.