Correlations with ocean salinity
To investigate the potential roles of ploidy and subgenome composition in adaptation to salt tolerance, we compared the surface salinity of the ocean nearest to the collection location of each P. vaginatumsample. Salinity levels did not differ significantly between the locations of diploid and triploid individuals (P = 0.5328, Fig. 5); thus, ploidy variation alone does not obviously contribute to adaptive variation in salinity tolerance. In contrast, a linear model that incorporated both the number of P. vaginatum subgenomes (one vs. two, independent of ploidy) and the number of the unidentified subgenomes (zero, one, or two) revealed that having two P. vaginatum subgenomes was strongly associated with higher local ocean salinity (P = 7.6e-11 ), while having an additional copy of the unknown genome was weakly associated with decreased salinity (P = 0.033, Fig. 5). This finding suggests that the relative proportion of subgenomes from the halophytic species has a detectable effect on salinity adaptation. It should be noted, however, that we could not entirely remove the effect of ploidy from this analysis because after accounting for the number of P. vaginatum subgenomes, a change in the copy number of the other subgenome necessarily changes ploidy as well (2:0 to 2:1 and 1:1 to 1:2).