Fig. 1

Heatmap of pairwise genomic relationship coefficients among the 490 genotyped C. africana trees (a), principal component analysis of the three genotyped provenances (b) and density plot of the four additive realised relationship coefficients within the G-matrix (c). In plot (a), the heat scale represents the degree of pairwise relationship coefficients for all pairs of trees. It is based on the provided pedigree (A-matrix before pedigree correction) in the upper diagonal and the realized genomic relationship coefficients (G-matrix) in the lower diagonal. The three light blue triangles are placed diagonally along the lower diagonal, indicating moderate relatedness between individuals within a provenance in the serial order of P30 (the first triangle), P31 (the second triangle), and P34 (the third triangle) from left to right. The smaller green boxes along the diagonal represent the families within the provenances based on the A- and G-matrix, on the upper and lower sides of the diagonal, respectively. The G-matrix (lower diagonal) also shows pedigree errors in 15 individuals that appear to belong to different families, either within the same or different provenances. In plot (b), the first principal component (PC1) is plotted against the second principal component (PC2), and different colours represent different provenances: P30 in red, P31 in green, and P34 in blue. Plot (c) displays four peaks representing different levels of realised genetic relationships between individuals. The first peak (highest) shows the relationship between individuals from different provenances. The second peak represents the relationship between unrelated individuals among provenances and within provenances. The third peak represents the relationship between individuals from different families within the same provenance, and the fourth peak attached to the third peak represents the relationship within families