Identification of clonal replicates
The filtered GBS dataset was characterized by 127,282 SNPs in 218 accessions. Principal component analysis (PCA) and application of genetic similarity threshold criteria to identify clonal replicates (see Methods; Supporting Information, Fig. S1) revealed a large number of genotypically identical accessions (Supporting Information, Table S1). For the coarse-textured P. vaginatum ecotype, only 12 unique genotypes were detected among the 148 accessions, with just three widely-distributed genotypes accounting for >85% of the accessions. This indicates that extensive clonal propagation occurs in wild populations of this ecotype. Somewhat greater genotypic diversity was found in the fine-textured ecotype, but extensive clonality was still present; 24 unique genotypes were identified in 55 accessions. Four out of eight genotypes in the wild-collected fine-textured accessions were represented by multiple clonal replicates. For P. distichum , there were four unique genotypes in the collection of 15 accessions, two of which were unique to our wild collections. The final SNP dataset for all genotypically unique samples across both species, including wild-collected and USDA samples, totaled 40 genotypes (Table 1). Together these results suggest that clonal propagation occurs extensively in wild P. vaginatum and P. distichumpopulations.