Fig. 2
From: A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits
Genetic diversity and linkage disequilibrium for different walnut populations. a Circos plot for the genome-wide nucleotide diversity. Cycles from outside inwards: ①repeat density, ② gene density, the genome-wide distribution for θπ, θw, and Tajima’s D values are shown in cycles ③, ④, and ⑤, respectively. The line colors for each population are indicated inside of the circos plot. For estimation of the gene or repeat density of each 1 Mb window, the lengths of genes or repeats within the window were summed up and then divided by the window length. b Boxplot of genetic diversity. The θπ and θw values are indicated by dark blue and yellow, respectively. The P values are calculated based on pairwise t-test. c Distribution of Tajima’s D values. d Divergence of different walnut subpopulations estimated based on FST. The summary statistics are calculated based on 1 Mb window size with a step size of 1 Mb. e Linkage disequilibrium differences between J. sigillata and various J. regia subpopulations