Discussion
Paspalum vaginatum is a promising new genomic model system for the study of salt tolerance in cereals and other plant species. Our population genomic analyses, using new wild samples collected widely throughout the southern US, and without a bias toward turf-like (fine-textured) ecotypes, has allowed us to make several key insights into the genetic diversity, population structure and genomic composition of this species, with broader implications for mechanisms of salinity adaption in widespread species. Our findings include the following: 1) Clonal propagation occurs extensively in both P. vaginatumecotypes, as well as in the non-halophytic sister species P. distichum (Table 1; Table S1); 2) Clones of the coarse-textured ecotype are more widely distributed than the fine-textured ecotype, both geographically and with respect to the environment (Fig. 1; Fig. 2), suggesting a “general purpose genotype” adaptive strategy for the former and a “frozen niche” strategy for the latter; 3) The system is characterized by extensive ploidy variation, including diploids and allotriploids that vary in their subgenome composition (Table 1; Fig. S5, S6); and 4) Increasing number of P. vaginatum subgenomes within a genotype are associated with occurrence in more saline environments (Fig. 5), suggesting a direct effect of the halophytic species’ genome on salinity adaptation. Collectively these findings suggest that both clonal propagation and hybridization-associated ploidy variation play key roles in the ability of this species to grow widely across environments of varying salinity.