Nuclear and chloroplast phylogeny of P. australislineages
Given that the native North American population diverged early from other populations (C. Wang, Liu, Yin, Eller, Brix, Wang, Salojärvi, et al., 2021), we rooted the nuclear phylogeny on the USnat lineage. The lineages then diverged in the following order: Med, EU, AU and CN, with AU clustering closely with CN (Fig. 1a ). In contrast, the unrooted chloroplast phylogenetic tree grouped the CN lineage with other lineages (Fig. 1b ), while the AU lineage formed its own distinct clade. Discrepancies between the nuclear and chloroplast phylogenies were observed for some individuals, where they clustered with the CN lineage in the nuclear phylogenetic tree but grouped with the AU lineage in the chloroplast phylogenetic tree. These include the populations labeled as CN_brackish, Heze, and Panjin. These mismatches suggest substantial gene flow between the two lineages, indicating ancient hybridization events. In contrast, the Australian populations, including both brackish water and freshwater ecotypes, all clustered within the same genetic group, suggesting that the octoploid AU lineage possesses genes conferring salinity tolerance (Fig. 1a,b ).