Fig. 4
Population analyses for resequenced individuals of Cinnamomum camphora. a A neighbour-joining phylogenetic tree and population structure plots (K = 2, 3, 4) of all accessions (n = 75) estimated based on high-quality SNPs. Two populations were divided according to the phylogenetic tree and assigned as Group 1 and Group 2. Individuals of C. camphora greater than 100 years old are marked by black triangles. b Principal component (PC) analysis plots of the first three components. The fraction of the variance explained is 13.39% for PC1, 12.96% for PC2, and 11.46% for PC3. Group 2 was divided into two subpopulations based on the PC analysis. c The FST distribution and density of the nucleotide diversity (π) ratio between Group 1 and Group 2-1. d The FST distribution and density of the π ratio between Group 1 and Group 2-2. The upper Manhattan plot represents the distribution of FST in each chromosome, and the lower line plot represents the distribution of the π ratio. The top 5% of FST values and π ratios are drawn as black dashed lines. Green and yellow heatmaps indicate the density of SNPs. The combination of extremal values of FST and the π ratio together defines ‘selective sweeps’ in this study. Genes with selective sweep signals in the top 10 enriched KEGG pathways are labeled