Nested clade analysis of Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle DNA sequences

Dunnia sinensis, a monotypic genus of the Rubiaceae endemic to the southeast mainland China, is an endangered species due to habitat destruction over the past decades. Information on levels and apportionment of genetic variation across populations and geographical regions is fundamental to conservation. In the present study, we used organelle DNA variation and nested phylogeographic analyses to test the isolation-by-distance model in this species with wind-mediated seed-dispersal and to distinguish ongoing gene flow from historical processes. As expected, low levels of genetic variation were detected at the ribosomal ITS region of mtDNA (theta = 0.0019 +/- 0.0002) and the atpB-rbcL intergenic spacer of cpDNA (theta = 0.0022 +/- 0.0009) in the rare species. Six and seven haplotypes of mt- and cpDNA were identified from 125 individuals, respectively, according to the reconstructed neighbor-joining trees. Both data sets suggested consistent phylogenies that recovered two differentiated lineages corresponding to western (Yangchun) and eastern (four others populations) portions of the range. Hierarchical analyses of the molecular variance (AMOVA) of mt- and cpDNA indicated that molecular variance was attributable to the difference between regions (Phi(ct) = 0. 911 and 0.771 for mt- and cpDNA, respectively) in D. sinensis. Based on geographic distributions of haplotypes in the haplotype networks, significant genetic differentiation between the two geographic regions, which can be seen as evolutionarily conservation units, was associated with historical fragmentation. In contrast, limited gene flow with occasional long-range dispersal shaped the apportionment of organelle DNA alleles among populations of the eastern region, within which two incompletely isolated phylogeographic groups can be recognized as conservation units for management.