Fig. 4: Box-and-whisker plot distributions of mutation burden in domesticated and wild soybean populations and demographic history of soybean.
From: The patterns of deleterious mutations during the domestication of soybean
Each box represents the median and interquartile range (IQR). The whiskers represent the range of 1.5 times IQR and the open circles beyond the whiskers are outlier values. a Total mutation burden in individual domesticated (Glycine max, landrace cultivars = 332 and improved lines = 86) and wild (Glycine soja, n = 345) soybean accessions. b Mutation burden among landrace, improved, and wild soybean accessions in domestication sweep regions. c Mutation burden in wild, landrace, and improved soybean accessions between domestication-selective sweeps and control regions (rest of the genome). Vertical axis shows number of deleterious alleles per 100-kb CDS length. In panels a–c, the subgroups in each of plots are significantly different between one another with P < 2.2e−16 in two-sided t-tests or Tukey multiple comparison tests except deleterious burdens between landrace and improved soybean accessions with P = 0.0003 (a) and with P = 0.97 (b) and deleterious burdens with P = 5.4e−13 for deleterious burden in wild soybean accessions (c). Source data are provided as a Source Data file. d PSMC-inferred demographic history of domesticated (blue lines) and wild (red lines) soybean. Each line represents the change in the past effective population size through time inferred for a pair of genomes. Both the x and y axis are log10 scaled.
