Sequencing and population structure
A total of 78,198 possible SNPs were generated and filtered down to 13,534 independent SNPs, with 8,824 SNPs mapped to the 11Eucalyptus chromosomes. The number of SNPs per chromosome varied from 599 to 1,083, with a mean of 802 SNPs per chromosome. Of the remaining SNPs, 477 fell on unspecified scaffolds and 4,233 on regions that could not be aligned to the E. grandis genome (unknown location). Population differentiation was low (globalFST = 0.04) and similar to that identified in a previous RFLP analysis of variation (FST = 0.034; Wheeler et al., 2003) with population pairwiseFST values ranging from 0.011 to 0.18. The cross‐entropy analysis estimated that the optimal number of clusters (k ‐value) was 6 (Figure S1). SNMF analysis with six clusters revealed substantial admixture in populations. Five of the clusters could be geographically described (Figure 2, S2), one cluster was primarily located in the southern area, one in the central area and two in the northern area, where one cluster was dominant in populations along the coast. A fifth cluster occurred in the outlier population (JIL; blue colour), and the sixth cluster was present in four individuals (two individuals from BRA and BOO). The LES population displays mixed affinity, being similar to both southern (green) and northern (yellow and red) populations.