Adaptation to extreme environments is an important problem in ecology and evolutionary biology. Serpentine soil, which has high concentrations of toxic heavy metals and low concentrations of essential plant nutrients, is an excellent model environment to study plant adaptations to harsh environments. The annual mustard, Caulanthus amplexicaulis var barbarae (CAB), which is serpentine tolerant, and its sister taxon, Caulanthus amplexicaulis var amplexicaulis (CAA), which is serpentine intolerant is a superb model to study genetic mechanisms underlying serpentine tolerance. Several approaches (QTL analysis, coding sequence evolution, RNAseq) are being used in our laboratory to identify candidate genes for serpentine tolerance in CAB. In this study, we are using the gene ancestry of CAB and CAA as an additional tool to prioritize candidate genes. To trace the ancestry of CAB and CAA, we are using ~30 species within the genera Caulanthus, Streptanthus, and related genera. Elucidation of the phylogenetic history of CAB and CAA is challenging due to at least one known episode of recent introgression. Here, we are determining the evolutionary history of CAB and CAA by comparing highly resolved phylogenies from both organellar (chloroplast and mitochondria) and nuclear genomes. Comparison of plastid genomes has led to identification of natural selection in this phylogenetic group. Results from chloroplast and mitochondrial phylogenies show that the maternal lineage of CAB and CAA clade is likely a serpentine-intolerant Caulanthus lineage. We are using gene-tree discordance between organellar and nuclear phylogenies to identify nuclear loci with paternal inheritance and explore the potential of using this information to prioritize candidate serpentine tolerance genes and test using synthetic biology and CRISPR/CAS9 mutagenesis approaches.