Fig. 5
Genetic diversity of RegionA in the context of domestication. a–d RegionA harbors low genetic diversity and positive selection signals inside. Four indicators of sequence diversity and selection signals, nucleotide diversity (π), Watterson’s estimator (θW), Tajima’s D, and composite likelihood ratio (CLR) of modern inbreds were shown in a, b, c, and d, respectively. The 100 kb upstream and 500 kb downstream flanking regions were indicated by brown blocks. The two green vertical lines indicate RegionA, and indicators were calculated only based on presence line; for d, dashed horizontal lines indicate the cutoff of composite likelihood ratio. e Neighbor-joining tree of the HapMap lines in flanking regions of NOR (upstream 100 kb and downstream 500 kb). The bootstrap values on the tree are based on 1000 replicates and values more than 50 are displayed. Taxa in the tree are represented by different text colors: teosintes (yellow), landraces (red), and improved lines (blue). The tree tip points labeled by blue triangles indicate the RegionA-presence lines, while red circles indicate the absence lines