Fig. 3: Genetic diversity of African pigs.

a Effective population sizes over time for 18 medium-high depth pig samples as estimated by PSMC, assuming a mutation rate of µ = 1.49e⁻⁸ per site per generation and a generation time of six years^4,84. b Genome-wide heterozygosity measurements described as the proportion of heterozygous sites per bp across each individual genome. Medium-high depth (≥14×; n = 18; red triangles) and low-depth samples (n = 49; blue circles) are shown. Boxplots indicate median (centre line), 25th and 75th percentiles (box), and the highest and lowest values within the upper and lower quartiles ± 1.5* interquartile range, respectively (whiskers). c Estimated genome-wide runs of homozygosity (ROH) proportions for 18 medium-high depth individuals. Each bar represents a single individual, grouped by their population. Proportions of differing ROH length intervals are shown as subdivisions within bars. d Linkage disequilibrium decay for populations with five or more samples, described as mean r² values for SNP pairs 0–5 Mb apart (n = 5 for each population).