DATA AVAILABILITY : The genomic data generated and analysed in this study are available online via the Dryad archives under accession https://doi. org/10.5061/dryad.h18931zj6.
SUPPLEMENTARY MATERIAL : FIG. S1. Population structure in relation to wild Eucalyptus grandis and other species in section Latoangulatae based on principal component analysis, discriminant analysis of principal components and sparse nonnegative matrix factorization. FIG. S2. Breeding Eucalyptus grandis population structure for all breeding samples, those excluding introgressed, and those excluding infused individuals in relation to the wild progenitor populations based on principal component analysis, sparse nonnegative matrix factorization and discriminant analysis of principal components analyses. FIG. S3. Population differentiation FST estimates among breeding Eucalyptus grandis, wild E. grandis and other species in section Latoangulatae. FIG. S4. Chloroplast (cp) haplotype network based on 24 cp single nucleotide polymorphisms. FIG. S5. Marker-specific Hardy–Weinberg equilibrium signed R values of wild vs breeding populations. FIG. S6. Genomic outliers and linkage disequilibrium plots per chromosome. FIG. S7. Breeding population linkage disequilibrium decay over genomic distance in kb. FIG. S8 Outlier detection by pcadapt scan.
TABLE S1. Ancestry assignment of chromosomal segments.
TABLE S2. Cluster assignment of samples using discriminant analysis of principal components to identify genetically infused breeding individuals. TABLE S3. Summary statistics of genetic diversity using hierfstat v.0.04-22. TABLE S4. Wilcoxon signed rank test P-values supporting the alternative hypothesis that the mean of the outliers was greater than the mean of the rest of the single nucleotide polymorphisms. TABLE S5. Gene Ontology enrichment analysis for genes in linkage disequilibrium with outlier single nucleotide polymorphisms (SNPs) before excluding organellar-targeting SNPs.
TABLE S6. Blastn against the organellar genomes.
TABLE S7. Marker statistics of single nucleotide polymorphisms with multigenome targets. Please note: Wiley Blackwell are not responsible for the content or functionality of any Supporting Information supplied by the authors. Any queries (other than missing material) should be directed to the New Phytologist Central Office.