Extended Data Fig. 4: Monophyletic origin and diversification of five allotetraploid species.
a, The phylogeny of the polyploid species using 18,672 orthologous (37,344 homoeologous) genes and improved coalescence analysis. b, Geographic distribution and diversification of the five allotetraploid species G. hirsutum, G. barbadense, G. tomentosum, G. darwinii, and G. mustelium and their progenitor-like diploids, G. arboreum and G. raimondii. The world map was made using R scripts, and the distribution maps were redrawn based on published maps for Gd, Gt, and Gm30, Gh and Gb31, and diploid cultivated cottons32. c, Patterns of gene gain and loss using 4,369 single-copy orthologs (SCOs) (out of total 32,622), which are present in both diploids and in one or more allotetraploids. Numbers above and below each branch indicate number of gene gain (A-blue/D-red subgenome) or loss (A-green/D-purple subgenome), respectively.
