Hopea hainanensisMerrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber,H.hainanensishas suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatenedHopeaspecies,H.hainanensisexhibited reduced overall genetic diversity and increased population differentiation (AMOVA:F_ST= 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assignedH.hainanensisindividuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances (r= 0.040,p= 0.418). The observed genetic structure suggests that long-distance gene flow occurred amongH.hainanensispopulations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered speciesH.hainanensisare proposed.

Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam. Twenty‐six microsatellite markers were developed based on next‐generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Twelve markers were found to be polymorphic in H. hainanensis. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Primer transferability was tested with Hopea chinensis Hand.‐Mazz. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine‐scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species.

Introduction: Hopea hainanensis Merrill & Chun is considered a keystone and indicator species in the tropical lowland rainforests of Hainan Island. Owing to its high-quality timber, H. hainanensis has been heavily exploited, leading to its classification as a first-class national protected plant in China and a plant species with extremely small populations (PSESPs).Methods: This study analyzed genome-wide single nucleotide polymorphisms obtained through restriction site-associated DNA sequencing from 78 adult trees across 10 H. hainanensis populations on Hainan Island.Results and discussion: The nucleotide diversity of the sampled populations ranged from 0.00096 to 0.00138, which is lower than that observed in several other PSESPs and endangered tree species. Bayesian unsupervised clustering, principal component analysis, and neighbor-joining tree reconstruction identified three to five genetic clusters in H. hainanensis, most of which were geographically widespread and shared by multiple populations. Demographic history analysis based on pooled samples indicated that the decline in the H. hainanensis population began approximately 20,000 years ago, starting from an ancestral population size of approximately 10,000 individuals. The reduction in population size accelerated approximately 4,000 years ago and has continued to the present, resulting in a severely reduced population on Hainan Island. Intensified genetic drift in small and isolated H. hainanensis populations may contribute to moderate differentiation between some of them, as revealed by pairwise F_st. In conclusion, our conservation genomic study confirms a severe population decline and an extremely low level of nucleotide variation in H. hainanensis on Hainan Island. These findings provide critical insights for the sustainable management and genetic restoration of H. hainanensis on Hainan Island.

Garcinia oblongifolia Champ. ex Benth is rich in bioactive molecules with immense remedial qualities and has pharmaceutical potentials. In this study, we reported the complete chloroplast genome (cpDNA) of G. oblongifolia, which is 156,577 bp in length, including a large single copy region (LSC) of 85,393 bp, a small single copy region (SSC) of 17,064 bp, and a pair of inverted repeats (IR) regions of 27,060 bp inserted between LSC and SSC. 129 genes are encoded, including 83 protein-encoding genes, 8 ribosomal RNA genes, and 36 transfer RNA genes. The overall GC content of the chloroplast genome is 36.2%, wherein the corresponding values in the LSC, SSC and IR regions are 33.6%, 30.3%, and 42.2%, respectively. Phylogenetic analysis showed that G. oblongifolia is sister to G. gummi-gutta with strong bootstrap support.

Hopea reticulata Tardieu is a critically endangered tree species distributed in limited regions in Thailand, Vietnam and Hainan Island of China. In this study, we reported the complete chloroplast genome sequence of H. reticulata assembled from pair-end reads generated by Illumina sequencing. The circular chloroplast genome is 151,407 bp in length and comprises a large single copy region of 84,352 bp, a small single copy region of 19,733 bp, and a pair of inverted repeats of 23,661 bp each. The complete genome encodes 129 functional genes, including 83 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The overall GC content of the chloroplast genome was 37.4%. Phylogenetic analysis showed that H. reticulata is sister to H. hainanensis with strong bootstrap support.

Habitat fragmentation can cause isolation and decline of a formerly continuously distributed population, which leads to loss of genetic variation and increased risk of extinction. Vatica mangachapoi Blanco is a dominant tree species growing in the lowland rainforests of Hainan Island, China. Remarkably, this species dominates a coastal forest in Shimei Bay, Wanning City of Hainan Province. Due to logging, expansion of farmland and villages, and construction of tourism facilities, the coastal V. mangachapoi-dominated forest has become fragmented, threatening its future. To evaluate the effects of habitat fragmentation on this unique coastal forest, two V. mangachapoi populations (SM and RY) along the coast and one population in the lowland rainforest near the coast were selected, and their genetic diversity was assessed based on 12 SSR markers. In addition, the genetic structure of the three populations and gene flow among them, and the fine-scale spatial genetic structure (FSGS) of the SM population were also studied. The results show that the three V. mangachapoi populations had comparable levels of genetic variation, and differentiation among them is negligible ($ {F}_{\mathrm{s}\mathrm{t}} $= 0.008 ~ 0.013). Model-based clustering, Principal co-ordinate analysis and the Neighbor-joining (NJ) methods consistently support a homogeneous genetic structure of the three populations, and strong gene flow was detected among them by MIGRATE analyses. Moreover, there is no significant FSGS in the SM population. A relatively short time since habitat fragmentation and gene flow mediated by seed dispersal might be the likely reasons for the high levels of genetic variation and an absence of genetic structure of the coastal V. mangachapoi populations. In conclusion, even though there are no significant effects of fragmentation on the coastal V. mangachapoi forest,strict protection is required to prevent further deforestation and fragmentation. Besides, saplings of V. mangachapoi should be planted in forest gaps to reconnect fragments of the coastal forest, which would be benefit for the long-term survival of the tropical coastal V. mangachapoi-dominated forest.