Fig. 4: Introgressions among the Capsicum species.

a Phylogenetic structure and gene flow detected between the Baccatum and the Annuum clades. The red arrow line indicates the direction of gene flow. b Four-taxon topology ((P1,P2),P3,O) used in the ABBA-BABA model to detect the degree of introgression (fd) and proportion of introgression across the whole genome (PGI) between C. baccatum (var. baccatum and var. pendulum) and the subgroup of the Annuum clade including C. frutescens and C. chinense. c Degree of introgression (fd) from C. baccatum to C. chinense and C. frutescens across the pepper genome. The top five strongest introgression signals are indicated by black arrows. Dashed horizontal lines indicate the top 1% fd. d Nucleotide diversity (π) of the genome region at the end of chromosome 6 containing the strongest introgression signal. e Introgression from C. baccatum to C. chinense and C. frutescens at the end of chromosome 6. The dark red color represents alleles prevalent in C. baccatum accessions (allele frequency ≥ 0.8). f LD decay patterns of the introgressed region shown in (e). PUB, C. pubescens; BAB, C. baccatum var. baccatum; BAP, C. baccatum var. pendulum; FRU, C. frutescens; CHN, C. chinense; ANN, C. annuum var. annuum.