With the global biodiversity loss, it is crucial to protect the threatened species. While endemic species not only are important components of regional biodiversity, also the ecological niche of one has significant implication for ecosystem. The low genetic diversity of the endemic species is highly vulnerable to extinction. However, conservation of threatened or endemic species is relatively weak. It is urgent to formulate appropriate protection strategies. In this paper, based on chloroplast DNA sequencing, the 3,133 base pairs (bp) of combining 5 chloroplast genes (ycf13125-ycf14381, ycf11205-ycf12402, psbA-trnH, trnD-psbM and trnL-trnF) were analyzed from 6 populations of M. adenophora, a vulnerable and endemic tree growing in forests or at forest edges in China, detecting only 5 haplotypes with 4 polymorphic sites (0.13%). The total haplotype diversity (Hd) and nucleotide diversity (π) was 0.234 and 0.0001, respectively. It is shown that the extremely low genetic diversity in the species and thus 49 individuals shared common haplotype H1. The results of haplotype network, haplotype geographical distribution analysis and neutrality tests supported that populations had experienced recent expansion. The low genetic diversity values found in the present study raise considerable concern about the conservation status of M. adenophora and highlight the need to further protect genetic diversity to strengthen their resilience against further decline.

The Yunnan-Guizhou Plateau (YGP) is characterized by the distinctive isolated habitat of limestone Karst Islands and features the Wumeng Mountains (Mts), which divide the YGP into the two Plateaus of Yunnan and Guizhou. This study aims to assess the effects of past geographic and environmental isolation and climate fluctuation on the flora distribution in the YGP. To this effect, we analyzed the phylogeographical pattern and genetic structure for Myrica nana, a vulnerable species endemic to the YGP, based on chloroplast and nuclear ribosomal DNA sequence. The results suggest that the genetic and haplotype network structures are divided into at least two groups—cpDNA haplotype H2 (or nrDNA haplotypes h1, h2, and the native haplotype) mainly distributed to the east of the Wumeng Mts, and cpDNA haplotype H1 and haplotypes H3–H10 (or nrDNA haplotype h3) distributed to the west of the Wumeng Mts. A deep genetic split was noted within the two groups to reach 25 steps, especially for the cpDNA fragment variation. The east–west divergence reveals the existence of a natural geographical isolation boundary in the form of the Wumeng Mts, which divides the YGP into the Yunnan and Guizhou Plateaus. Therefore, there existed at least two glacial refugia during the Quaternary glacial period, along with a genetic diversity center, and at least two large geographic protection units for the vulnerable species of M. nana, distributed throughout the eastern and western sides of the Wumeng Mts. This study not only clarifies that the phylogeographical pattern and genetic structure for M. nana can be attributed to geographic and environmental isolation and climate fluctuation, but it also proposes an effective strategy to protect vulnerable species and the important wild flora of the YGP.