Genome-wide evidence supports a hybrid origin and historical introgression in the critically endangered Atacama Desert shrub Strombocarpa burkartii (Muñoz)

Strombocarpa burkartii is a critically endangered shrub endemic to the Atacama Desert, Chile, currently restricted to a single known population. Its morphological intermediacy between S. tamarugo and S. strombulifera has long suggested a possible hybrid origin, yet this hypothesis has never been tested using genome-wide data. We generated whole-genome Illumina sequences for the three species and performed de novo nuclear genome assemblies. Genomic relationships were investigated using k-mer profiling (GenomeScope), whole-genome similarity analyses (Mash and Sourmash), simulated ddRAD datasets, and reference-based SNP calling against the Neltuma alba genome. GenomeScope estimated comparable haploid genome sizes for S. tamarugo (424.8 Mb) and S. burkartii (395.3 Mb), but revealed an exceptionally high heterozygosity in S. burkartii (6.99%), approximately fourteen times greater than in S. tamarugo (0.49%). Whole-genome and simulated ddRAD analyses consistently identified S. burkartii as genomically closest to S. tamarugo. Reference-based analyses identified 9,550,363 high-quality SNPs, including 1,545,697 diagnostic loci distinguishing S. tamarugo and S. strombulifera. Remarkably, S. burkartii was heterozygous for both parental alleles at 1,459,872 loci (94.45% of all diagnostic SNPs), whereas loci matching exclusively either parental species were comparatively rare. Multiple independent genomic approaches converge on the same conclusion, providing the strongest genome-wide evidence to date that S. burkartii originated through hybridization between S. tamarugo and S. strombulifera, followed by historical introgression. These findings clarify the evolutionary origin of one of the rarest desert legumes in South America and provide an important genomic framework for its taxonomy, conservation, and management.