Taxonomic status, phylogenetic affinities and genetic diversity of a presumed extinct genus, Paraisometrum W.T. Wang (gesneriaceae) from the karst regions of Southwest China

Abstract

Background: The karst regions in South China have an abundance of endemic plants that face high extinction risks. The Chinese Gesneriaceae endemic Paraisometrum mileense ( = Oreocharis mileensis), was presumed extinct for 100 years. After its re-discovery, the species has become one of five key plants selected by the Chinese forestry government to establish a new conservation category for plants with extremely small populations. For conservation purposes, we studied the phylogenetic and population genetic status of P. mileense at the three only known localities in Guangxi, Guizhou and Yunnan.

Methodology/principal findings: We collected 64 samples (52 species) of Oreocharis and 8 samples from three provinces of P. mileense and generated molecular phylogenies, and inferred that P. mileense represents a relatively isolated and derived taxonomic unit within Oreocharis. Phylogeographic results of 104 samples of 12 populations of P. mileense indicated that the populations in Yunnan have derived from those in Guangxi and Guizhou. Based on AFLP data, the populations were found to harbor low levels of genetic diversity (He = 0.118), with no apparent gradient across the species' range, a restricted gene flow and significant isolation-by-distance with limited genetic differentiation among the populations across the three provinces (FST = 0.207, P<0.001). The 10 populations in Yunnan were found to represent two distinct lineages residing at different altitudes and distances from villages.

Conclusion/significance: The low levels of genetic diversity found in P. mileense are perhaps a consequence of severe bottlenecks in the recent past. The distribution of the genetic diversity suggests that all populations are significant for conservation. Current in situ and ex situ measures are discussed. Further conservation actions are apparently needed to fully safeguard this conservation flagship species. Our work provides a model of an integrated study for the numerous endemic species in the karst regions with extremely small populations.

Figure 1. Map of localities of Paraisometrum mileense in Yunnan, Guangxi and Guizhou.

A. Pie charts for haplotypes (above) and nucleotypes (below) are given for the three main geographical distribution areas. B. Median-joining networks of chloroplast haplotypes based on trnLF and matK sequences (above) and of ITS nucleotypes (below) for P. mileense samples rooted on its closest relative Ancylostemon hekouensis.

Figure 2. Populations of Paraisometrum mileense in Yunnan.

A. Distribution of the ten populations analysed. B. Graphs of distance from village (left) and the average altitude (right) of populations 1–4 (light blue) and 5–10 (red).

Figure 3. Bayesian inference analysis placing Paraisometrum mileense in Oreocharis.

Tree based on combined ITS and trnLF sequence data with average branch lengths and posterior probabilities. Photo of P. mileense by Yu-Min Shui.

Figure 4. Results of the Bayesian inference STRUCTURE analysis on AFLP data of 12 Paraisometrum mileense populations.

A. Plot of K-clusters versus mean (±SD) likelihoods (L[K]). B. K plotted against the second order rate of change of the likelihoods (ΔK). C. STRUCTURE clustering results for K = 3 to 5 as suggested in B. Numbers refer to populations in Table 1. 1–10 = Yunnan, 11 = Guangxi, 12 = Guizhou.

Figure 5. Four genetic lineages exist in Paraisometrum mileense.

A. PCoA scatter plot based on AFLP data using the Jaccard distance on 12 populations of P. mileense. Axis 1(x) and 2(y). B. Unrooted NJ-tree based on Nei and Li’s restriction site distances. Bootstrap values only given for internal branches (1000 Neighbor-Joining replicates).