The genetic consequences of adaptation to changing environments can be deciphered using landscape genomics, which may help predict species’ responses to global climate change. Towards this, we used genome-wide SNP marker analysis to determine population structure and patterns of genetic differentiation in terms of neutral and adaptive genetic variation in the natural range of Eucalyptus grandis, a widely cultivated subtropical and temperate species, serving as genomic reference for the genus. We analysed introgression patterns at subchromosomal resolution using a modified ancestry mapping approach and identified provenances with extensive interspecific introgression, suggesting early hybrid speciation in response to increased aridity. Furthermore, we describe potentially adaptive genetic variation as explained by environment-associated SNP markers, which also led to the discovery of a large structural variant. Finally, we show that genes linked to these markers are enriched for biotic and abiotic stress responses.

Seed collected from 193 wild-growing Eucalyptus grandis trees were germinated and leaves were collected for DNA isolation and SNP genotyping using the EUChip60K SNP chip. Genotyping was done by the genomics service provider, GeneSeek, in Lincoln, NE. A total of 596 individuals were genotyped. Genotype calls were optimised by reclustering the SNPs according to published standards (see Silva-Junior et al., 2015. A flexible multi-species genome-wide 60K SNP chip developed from pooled resequencing of 240 Eucalyptus tree genomes across 12 species). Furthermore, technical replicates and SNPs with no unique map position on the E. grandis reference genome v.2 were removed.

This data resource is a .csv file with 596 individuals in rows and metadata, environmental data and SNPs (for 57,567 markers) in columns. Metadata columns include source loacation/provenance ("Location"), family ID ("FAMILY_ID"), provenance ID ("PROV_ID"), "Subpopulation", "Region", and whether or not a sample was included in the balanced sample set where no family is represented by more than two half-siblings ("Balanced_sample_set_n362").

Missing data is encoded as "NA".