Genetic structure of the threatened Dipterocarpus costatus populations in lowland tropical rainforests of southern Vietnam.

Dipterocarpus costatus is an endangered species restricted to the lowland forests of southern Vietnam. Habitat loss and over-exploitation of D. costatus wood are the major threats to this species. We investigated the level of genetic variability within and among populations of D. costatus in order to provide guidelines for the conservation, management, and restoration of this species to the Forest Protection Department, Vietnam. Nine microsatellite markers were used to analyze 114 samples from four populations representing the natural range of D. costatus in southeast Vietnam. We indicated the low allelic diversity (NA = 2.3) and low genetic diversities with an average observed and expected heterozygosity of 0.130 and 0.151, respectively, in the lowland forests of southeast Vietnam. The low genetic diversity might be a consequence of inbreeding within the small and isolated populations of D. costatus owing to its habitat loss and over-exploitation. All populations deviated from Hardy-Weinberg equilibrium showing reduced heterozygosity. Alleles were lost from the populations by genetic drift. Genetic differentiation among populations was high (average pairwise FST = 0.405), indicating low gene flow (<1) and isolated populations due to its destructed habitat and large geographical distances (P < 0.05) among populations. Heterozygosity excess tests (except of Bu Gia Map only under infinite allele model) were negative. The high genetic variation (62.7%) was found within populations. The STRUCTURE and neighbor joining tree results suggest strong differentiation among D. costatus populations, with the three genetic clusters, Phu Quoc, Tan Phu and Bu Gia Map, and Lo Go-Xa Mat due to habitat fragmentation and isolation. The threatened status of D. costatus was related to a lack of genetic diversity, with all its populations isolated in small forest patches. We recommend the establishment of an ex situ conservation site for D. costatus with a new big population comprising all genetic groups in order to enhance its survival under different environmental stresses.

Application of DNA barcoding markers to the identification of Hopea species.

Hopea chinensis (synonym: H. hongayensis) (Dipterocarpaceae) is a threatened species found so far in only two locations: Quang Ninh (Vietnam) and Guangxi (China). The species shares many morphological characteristics with H. mollissima and the two species are often confused. To overcome this problem of identification and to investigate the genetic relationships of Hopea species with other Dipterocarp species, we sequenced three candidate DNA barcodes for the chloroplast markers rbcL, trnH-psbA, and matK. These markers were used separately and in different combinations to determine whether they could establish an accurate and effective identification system for H. chinensis in Quang Ninh (Vietnam). Our analyses indicated that two of the candidate DNA barcodes, matK and rbcL, performed best. We also generated a neighbor-joining phylogenetic tree and confirmed the presence of four Hopea species (H. odorata, H. hainanensis, H. mollissima, and H. chinensis) in nature reserves and natural parks of Vietnam. These species showed a close relationship with an average genetic distance of 0.0045; both matK and rbcL separated all species, but their use in combination gave higher bootstrap values. The matK region was found to provide the most reliable barcode for the identification of the most closely related Dipterocarp species. Our study provides a means to identify rare Hopea species non-ambiguously and to support the protection of this decreasing natural genetic resource.

Genetic variation in and spatial structure of natural populations of Dipterocarpus alatus (Dipterocarpaceae) determined using single sequence repeat markers.

Dipterocarpus alatus (Dipterocarpaceae) is widely distributed in lowland forests in central and southern Vietnam, Cambodia, Laos, Myanmar, Philippines, Thailand, and India. Due to over-exploitation and habitat destruction, the species is now threatened. The genetic variation within and among populations of D. alatus was investigated on the basis of 9 microsatellite (single sequence repeat, SSR) loci. In all, 268 sampled trees from 10 populations in central and southern Vietnam were analyzed in this study. The SSR data showed a high genetic variability within populations with an average of HO = 0.209 and HE = 0.239. Genetic differentiation among populations was high (FST = 0.266), indicating limited gene flow (Nm = 0.69). Analysis of molecular variance showed that most genetic variation was within populations (74.96%). This study highlights the importance of conserving the genetic resources of D. alatus species.