Cryptic lineages and potential introgression in a mixed-ploidy species (Phragmites australis) across temperate China

Polyploidization and hybridization are very common in natural plant species, and mixed-ploidy species provide a unique opportunity to study the effects of evolutionary history, local abundance, and ploidy level on the direction and extent of introgression between intraspecific lineages. First, we delimited two morphologically cryptic lineages of Phragmites australis Trin. ex Steud. in temperate China using 11 nuclear microsatellites and two chloroplast DNA fragments with 225 samples from China as well as 11 samples from Oceania and Europe. Our evidence supported that haplotype O and haplotype P were two relatively independent lineages with low and high ploidy levels, respectively; haplotype M might be ancient and could have undergone a complex evolutionary history. Then we examined the lineage divergence and compared the introgression patterns between two major lineages along geographical and abundance gradients with a large number of samples (n = 1067) collected from China. The sympatric coexistence of two lineages in north and northeast China implies an ongoing or potential introgression between them. Cline analysis showed that the level of genetic admixture were significantly correlated with longitude rather than latitude. Our results also suggested that ploidy level could deeply influence the introgression asymmetry, and the effect of the current local abundance on introgression might be covered by the past coexistence time driven by phylogeographic history. Our study draws a baseline for future research on the ecological and evolutionary consequences of migration and introgression of Chinese P. australis under global change.