Fig. 2: Population differentiation and history of Capsicum species.
a Fixation index (FST) between different pepper populations. For each comparison, all FST values generated from 100 permutations were lower than the empirical FST value. b Total size of highly differentiated genome regions (top 1% FST) among the five domesticated Capsicum species. c Number of genes within the highly differentiated regions. d UpSet plot of common and unique genes within the differentiated regions among the five domesticated Capsicum species. e History of the effective population size of different pepper groups. f Linkage disequilibrium (LD) decay pattern of different pepper groups. g Boxplots of nucleotide diversity (π) for different pepper groups. For each box plot, the lower and upper bounds of the box indicate the first and third quartiles, respectively, and the center line indicates the median. The numbers of windows (n) for PUB, CHA, BAB, BAP, GLA, ANN, FRU and CHN are 28,893, 28,672, 28,736, 29,061, 29,007, 29,141, 29,242, 29,189, respectively. Note, π values could be overestimated due to the sub-sampling using GenoCore. PUB, C. pubescens; CHA, C. chacoense; BAB, C. baccatum var. baccatum; BAP, C. baccatum var. pendulum; FRU, C. frutescens; CHN, C. chinense; GLA, C. annuum var. glabriusculum; ANN, C. annuum var. annuum. Detailed gene information is provided in Supplementary Data 5.
