Chloroplast DNA phylogeography of the Chinese endemic alpine quillwort Isoetes hypsophila Hand.-Mazz. (Isoetaceae)

We examined chloroplast trnL intron sequence variation within Isoetes hypsophila, a Chinese endemic alpine quillwort species. Sequence data were obtained from 46 individuals in six populations throughout the natural distribution of the species. Sequences appeared to have neutral evolution (Tajima's criterion D = -1.66453, 0.1 > P > 0:05; Fu and Li's test D*= -1.92897, 0.1 > P > 0.05; F* = -2.17823, 0.1 > P > 0.05). Eleven haplotypes were identified in I. hypsophila. A relatively high level of haplotype diversity (h = 0.817) and a low level of nucleotide diversity (pi = 0.0045) were detected in I. hypsophila. Indirect estimates of gene flow based on cpDNA variation revealed significant genetic differentiation between the ZD1 population in Yunnan Province and the populations from Sichuan Province. High genetic differentiation between Yunnan and Sichuan populations was consistently indicated by both hierarchical analyses of molecular variance (AMOVA; G(ST) = 0.5011) and the structure of a neighbor-joining tree. From nested clade analysis, restricted gene flow with isolation by distance was inferred to be responsible for the current spatial genetic structure of I. hypsophila.