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The premise of the study Though phenological studies in montane forests are important, particularly in tropical Asia where primitive angiosperms are found, the phenology in these forests is still poorly understood. To characterize the phenological patterns and reveal the relationships between meteorological factors and phenology, we observed the leafing, flowering, and fruiting phenology in the tropical montane forests of Vietnam. Methods We observed the leafing, flowering, and fruiting phenology of 91 species every three months in five plots (elev. 1460–1920 m) in Bidoup-Nui Ba National Park, Vietnam, and analyzed how the number of species that were leafing, flowering, or fruiting varied in relation to precipitation, temperature, or daylength. Key results The leafing phenology showed a peak at the beginning of the wet season (April) and was significantly influenced by all of day length, precipitation, and temperature. The flowering phenology did not show any distinct peaks and was influenced by day length and precipitation. The fruiting phenology showed a low peak from the wet season (July) to the beginning of the dry season (December) and was not significantly influenced by any of the meteorological factors. Main conclusion The community-wide phenological patterns of leafing, flowering, and fruiting in the tropical montane forest of Bidoup-Nui Ba are unique among the tropical forests of East and Southeast Asia. In particular, our observation suggests that masting in tropical montane forests may be an ancestral state of both general flowering in tropical rainforests and masting found in temperate forests in East and Southeast Asia.

Climate warming is causing shifts in key life-history events, such as flowering time. To assess the impacts of climate warming on flowering phenology, it is crucial to understand the transcriptional changes of genes underlying the phenological shifts. Here, we comprehensively explore genes that contribute to the flowering phenology shifts under climate warming by monitoring the latitudinal gradient of seasonal expression dynamics of 293 flowering-time genes in a perennial herb,Arabidopsis halleri. Through transplant experiments conducted at northern, southern, and subtropical study sites in Japan, we have demonstrated that the flowering period was shortened with decreasing latitude and ultimately, the plants lost the opportunity to flower in subtropical climates. The key transcriptional changes underlying the shift in flowering phenology and the loss of flowering opportunity were the diminished expression of floral pathway integrator genes and genes in the gibberellin synthesis and aging pathways, all of which are suppressed by increased expression ofFLOWERING LOCUS C, a central repressor of flowering. These results suggest that the upper-temperature threshold beyond which plants cannot reproduce in response to warming is governed by a relatively small number of genes that suppress reproduction in the absence of winter cold.

It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and FST were computed. The estimates calculated from the data obtained by MIG-seq were compared to those obtained by Sanger sequencing of nine nuclear coding genes in D. cochinchinensis in our previous study. The nucleotide diversity at the MIG-seq loci was slightly higher than that at silent sites in the coding loci, whereas the FST values at the MIG-seq loci were generally lower than those at the coding loci, although the differences were not significant. Moreover, nucleotide diversities within populations of the two species were similar to each other, at approximately 0.005. Three and four population clusters were genetically recognized in D. cochinchinensis and D. nigrescens, respectively. Although the populations were differentiated from each other, the levels of differentiation among them, as measured by FST, were higher in D. cochinchinensis than in D. nigrescens. This indicates higher levels of gene flow between the populations in the latter species. We recommend using MIG-seq for quick surveys of genetic variation because it is cost-effective and results in smaller variance in the estimates of population genetic parameters.

Mallotus tokiae (Euphorbiaceae), a poorly known species, was described based upon a single fruiting specimen from Surat Thani Province, peninsular Thailand. We found this species with staminate and slightly mature pistillate flowers in Lampi Island, Myanmar. A new locality record, description of flowers, preliminary conservation assessment and DNA barcoding of this species are provided.

A new species, Gynochthodes honbaensis (Rubiaceae), from Hon Ba Nature Researve, Khanh Hoa Province, southern Vietnam, is described, with a key to the species of Gynochthodes in Vietnam. This species is phenotypically most similar to G. macrophylla distributed in Nicobar Islands, Thailand, and Peninsular Malaysia, but differs in having smaller leaves, and much longer and glabrous peduncles.

The new species of Clusiaceae, Calophyllum honbaense V.S. Dang, H. Toyama & Tagane, sp. nov., was discovered in the Hon Ba Nature Reserve of southern Vietnam and is here described and illustrated.

It is vital to measure the levels of genetic diversity and differentiation between populations in a species to understand the current genetic structure and evolution of the species. Here, MIG-seq (multiplexed inter-simple sequence repeat genotyping by sequencing) was employed to assess the genetic variation in two tropical leguminous tree species, Dalbergia cochinchinensis and D. nigrescens, in Cambodia and Thailand. Sequence data for 255-618 loci, each with an approximate length of 100 bp, were obtained, and the nucleotide diversity, Tajima's D and F

The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircum-scribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

A new species, Garcinia hopii H.Toyama & V.S.Dang is described from Bidoup Nui Ba National Park, southern Vietnam. This species is similar to Garcinia hendersoniana Whitmore but differs from that species in having larger leaves, clustered pistillate flowers, a greater number of sterile anthers and a larger stigma of young fruits. A description, preliminary conservation assessment, illustration, photographs and DNA barcodes of the new species are provided, as well as an updated key to Garcinia sect. Hebradendron in Indochina.

Two species of Araliaceae, Heteropanax thaiensis Tagane, Suddee & Rueangr., a new species from Phu Kradueng National Park, Loei Province, and Schefflera wrayi (King) R.Vig., from Khao Luang National Park, Nakhon Si Thammarat, formerly known only from Malaysia, are added to the flora of Thailand. Descriptions and illustrations, as well as DNA barcodes of rbcL and matK are provided based on our newly collected specimens.

Lasianthus honbaensis V.S. Dang, Tagane & H. Toyama sp. nova (Rubiaceae) is described and illustrated from Hon Ba Nature Reserve, Khanh Hoa Province, southern Vietnam. It resembles L. inodorus and L. inodorus subsp. pubescens in leaf morphology, but differs from them in having shorter stipules, calyx tubes and corolla, and orange fruits. It is also similar to L. latifolius and L. calycinus in deeply disected calyx lobes and orange fruits, but differs from them by having persistent bracts and shorter calyx tubes. A table comparing the new species with its closest allies is provided.

A new species of Hamamelidaceae, Eustigma honbaense H.Toyama, Tagane & V.S.Dang, sp. nov., is described from Hon Ba Nature Reserve, Vietnam. This species is similar to Eustigma oblongifolium Gardner & Champ., but differs from it in having entire leaves, longer infructescences, capsules with a longer apical part and seeds with a larger hilum. A description, preliminary conservation assessment, illustration and photographs of the new species are provided, as well as an updated key to the genus Eustigma.

Two new species, Machilus bokorensis Yahara & Tagane and Machilus brevipaniculata Yahara & Tagane (Lauraceae) are described from Bokor National Park, Cambodia with their illustrations and DNA barcodes of the two plastid regions of rbcL and matK and the nuclear region of ITS.

Some previous studies along an elevational gradient on a tropical mountain documented that plant species richness decreases with increasing elevation. However, most of studies did not attempt to standardize the amount of sampling effort. In this paper, we employed a standardized sampling effort to study tree species richness along an elevational gradient on Mt. Bokor, a table-shaped mountain in southwestern Cambodia, and examined relationships between tree species richness and environmental factors. We used two methods to record tree species richness: first, we recorded trees taller than 4 m in 20 uniform plots (5 × 100 m) placed at 266–1048-m elevation; and second, we collected specimens along an elevational gradient from 200 to 1048 m. For both datasets, we applied rarefaction and a Chao1 estimator to standardize the sampling efforts. A generalized linear model (GLM) was used to test the relationship of species richness with elevation. We recorded 308 tree species from 20 plots and 389 tree species from the general collections. Species richness observed in 20 plots had a weak but non-significant correlation with elevation. Species richness estimated by rarefaction or Chao1 from both data sets also showed no significant correlations with elevation. Unlike many previous studies, tree species richness was nearly constant along the elevational gradient of Mt. Bokor where temperature and precipitation are expected to vary. We suggest that the table-shaped landscape of Mt. Bokor, where elevational interval areas do not significantly change between 200 and 900 m, may be a determinant of this constant species richness.

Homalium glandulosum Tagane & V. H. Nguyen, from Vu Quang National Park in northern Vietnam, is newly described. This species is characterized by distinct glands, often stalked, at the base of the lamina and along the margin of the stipules and bracteoles. Illustrations, DNA barcodes of the two regions of rbcL and matK, and a key to the species of Homalium in Vietnam are also provided.

A new species, Glycosmis suberosa H.Toyama & Rueangr. is described from Khao Luang National Park, Nakhon Si Thammarat Province, Thailand. This species is distinguished from the other Glycosmis species by its characteristic corky branches.

A new species, Aporosa tetragona Tagane & V. S. Dang, sp. nov., is described and illustrated from Mt. Hon Ba located in the Khanh Hoa Province, South Vietnam. This species is characterized by tetragonal pistillate flowers and fruits, which are clearly distinguishable from the other previously known species of the genus. The morphology and phylogeny based on rbcL and matK of this species indicated that the new species belongs to section Appendiculatae Pax & K. Hoffm.

Lithocarpus vuquangensis Ngoc & Hung is described from Vu Quang National Park, North Central Vietnam. The morphological comparison and phylogenetic analysis based on rbcL, matK and ITS provided evidence that the new species was not assignable to any of the previously known taxa in Vietnam and its surrounding countries. The description, photographs, preliminary conservation status and DNA barcode sequences are also provided for the new species.

The taxonomy of Quercus langbianensis and its relatives in Vietnam and Cambodia have been revised based on evidence obtained from field observations, morphological comparison of herbarium specimens and molecular analyses using both classic and next generation DNA markers. Based on Bayesian inference using rbcL, matK and ITS regions and Neighbour-joining tree using genome-wide sequences amplified with multiplexed inter-simple sequence repeat (ISSR) primers (MIG-seq), the authors recognised ten species in the complex in Vietnam and Cambodia, three of which are newly described in this paper: Q. baolamensis sp. nov., Q. bidoupensis sp. nov. and Q. honbaensis sp. nov. These new species are all phenotypically similar to Q. langbianensis s. str. in having lanceolate to oblanceolate leaf shape, upper 4–5/6–serrated leaf margin, acute or acuminate leaf apex and bracts of cupule arranged in 5–9 rings but distinguished both morphologically and phylogenetically. In molecular phylogenetic reconstructions, Q. bidoupensis is not close to any other species. In the Bayesian tree, Q. honbaensis is sister to both Q. blaoensis and Q. camusiae that are found in the same locality but morphologically distinct and those three species are sister to Q. langbianensis s. str., while Quercus baolamensis is not sister to Q. langbianensis s. str. in both the Bayesian tree and MIG-seq tree. In addition, Q. cambodiensis and Q. baniensis previously reduced to Q. langbianensis s. lat. have been recognised as distinct species. Six species were in need of lectotypification and that is undertaken herein.

A new species, Goniothalamus flagellistylus Tagane & V. S. Dang, sp. nov. from Hon Ba Nature Reserve in Khanh Hoa Province, South Vietnam is described and illustrated. This species is most similar to Goniothalamus tortilipetalus M.R.Hend., but distinct in having 308–336 stamens (vs. ca. 170–260) and ca.120 carpels (vs. ca. 50–100) per flower, and Stigma and pseudostyles ca.8.5 mm (vs. 4–4.5 mm) long.

Lasianthus yaharae V.S. Dang, Tagane & H. Tran (Rubiaceae) is described and illustrated here based on material discovered in the Hon Ba Nature Reserve, southern Vietnam. It is most similar to L. dalatensis but differs in having fewer secondary veins in the leaves, a larger calyx and larger flowers (corolla tube and corolla lobes), and a different flower color at anthesis.

Dalbergia cochinchinensis Pierre ex Laness. (Fabaceae) is a commercially important tree in Southeast Asia. Although this species is under legal protections, illegal logging and disorderly developments have reduced its populations, and the conservation of this species is currently of much concern. In this study, we determined nucleotide sequences at six chloroplasts and ten nuclear loci in four populations of D. cochinchinensis in Cambodia, followed by population genetic analyses. The average silent nucleotide diversity over the nuclear loci, excluding one with an exceptionally high value, was 0.0057 in the entire population, and the mean F ST across the nuclear loci between each population pair was between 0.135 and 0.467. Thus, the nucleotide diversity in the studied populations was not low compared with that in other tree species, and the level of population differentiation was high. Neutrality test statistics indicated a recent reduction of population size and a subdivision of the population within this species. The divergence times and migration rates were estimated with a likelihood-based method assuming the isolation with migration model. Based on the results, the three populations split 68,000–138,000 years ago, possibly corresponding to the start of the last glacial period, and the level of gene flow among the populations was very low thereafter. Moreover, after the split, population sizes were reduced considerably. Notably, the nucleotide diversity in an insertion sequence in a noncoding region of nuclear C4H was much higher than the mean nucleotide diversity in silent sites across other nuclear genes, indicating that the region was affected by selection.

Hybrid zones formed from genetically and ecologically differentiated species provide an opportunity to examine how genetics and ecology interact to determine species boundaries. In this study, we examined a hybrid zone generated by invasion of shade-loving Viola eizanensis into habitat occupied by its close relative, V. chaerophylloides var. sieboldiana, which prefers more open areas. We used 339 AFLP loci to estimate genomic composition and generation of hybrids, and confirmed maternal inheritance through sequencing of the cpDNA atpI–atpH intergenic spacer region. Phenotypic variation was assessed using leaf thickness (leaf mass/area) and leaf dissection (leaf perimeter/area), which were diversified between species. Genetic analyses showed that the AFLP of hybrid individuals in having maternal origin from V. chaerophylloides var. sieboldiana were replaced by V. eizanensis in response to habitat. Significant correlations were observed between hybrid indices and the two leaf traits. These results suggest that genes of V. eizanensis that are adaptive to shaded habitats are fixed in the hybrids, and that the degree of leaf thickness and dissection is important in adaptation of the hybrids to their light environments.

A new species, Lasianthus bidoupensis V.S. Dang & Naiki (Rubiaceae) is described and illustrated from Bidoup Nui Ba National Park, Lam Dong Province, southern Vietnam. It resembles L. yaharae which was recently discovered from Mt. Hon Ba and L. dalatensis which is endemic to Dalat, southern Vietnam. However, L. bidoupensis differs from them by having larger leaves and bracts, longer petioles, stipules, calyx and corolla tubes, and deep-red mature fruits.

A new species, Popowia bachmaensis Ngoc, Tagane & Yahara, sp. nov. is described from Bach Ma National Park in Thua Thien Hue Province, Central Vietnam. This species is morphologically similar to Popowia pisocarpa (Blume) Endl. ex Walp., but can be readily distinguished from it by its lower stems, smaller leaves, shorter flowering pedicels, shorter carpels, longer sepals and inner petals. A detailed description, comprising illustrations, and supplemented with DNA barcodes of the two regions of rbcL and matK, are provided.

Five new species of Syzygium (Myrtaceae), S. honbaense, S. phamhoangii and S. yersinii from Khanh Hoa Province, Vietnam, S. phoukhaokhouayense from Phou Khao Khouay National Protected Area, Vientiane Province, Laos, and S. scabrum from Bung Khla, Phu Wua Wildlife Sanctuary, Buengkan Province, Thailand, are described and illustrated. Photographs, vernacular names and preliminary conservation assessments are provided for them.

Erythroxylum calyptratum, sp. nov. (Erythroxylaceae), from Mt. Fansipan, Hoang Lien National Park, Lao Cai Province, northern Vietnam, is newly described. The new species is characterized by thinly chartaceous leaves with 2–3 mm long petiole, 1–3 flowered inflorescences, downward facing white flowers, well-developed petal appendages (1/3–1/2 length of petals) and entirely free 3 styles. A description, illustrations, DNA barcodes of rbcL and matK and a key to the species of Erythroxylum in Indochina are provided.

Lecanorchis Blume (1856: 188) comprises about 30 species of mycoheterotrophic orchids (Seidenfaden 1978, Hashimoto 1990, Szlachetko & Mytnik 2000, Govaerts et al. 2017) characterized by having numerous, long, thick, horizontal roots produced from a short rhizome, presence of a calyculus (i.e. a cup-like structure located between the base of the perianth and apex of the ovary) and an elongate column with a pair of small wings on each side of the anther (Seidenfaden 1978, Hashimoto 1990). The genus is distributed across a wide area including China, Korea, India, Indonesia, Japan, Laos, Malaysia, New Guinea, Pacific islands, the Philippines, Taiwan, Thailand and Vietnam (Seidenfaden 1978, Hashimoto 1990, Pearce & Cribb 1999, Szlachetko & Mytnik 2000, Averyanov 2011, 2013).

Similar distribution ranges shared by closely related plant species may have been shaped through different migration histories if those species have differing habitat preference. To test this hypothesis, phylogeographical patterns and population genetic structures were compared between two sister Viola species: Viola eizanensis preferring woodland and V. chaerophylloides var. sieboldiana preferring grassland, both being native to the Japanese Archipelago. Amplified fragment length polymorphism (AFLP) was used for phylogenetic reconstruction, together with Bayesian ancestry analysis, AMOVA, analysis of genetic diversity statistics, and analysis of the relative contribution of each population to total diversity. The results indicated that V. eizanensis had two distinct lineages occurring in the western and eastern part of Japan, but such lineages are not distinct in V. chaerophylloides var. sieboldiana. Both species exhibited the low genetic diversity and high between-population differentiation typical of selfing plants. In V. chaerophylloides var. sieboldiana, one particular population made a significantly higher contribution to the total heterozygosity (H T), whereas in V. eizanensis, no population was identified as making a particularly higher contribution to H T. These findings suggest that V. eizanensis had been isolated in two large glacial refugia, whereas populations of V. chaerophylloides var. sieboldiana were restricted to a single small refuge. Different light requirements between these two closely related species probably caused these differing responses to climatic change during the last ice age.

Herein, Mussaenda recurvata, a new species from Hon Ba Nature Reserve, southern Vietnam, is described and illustrated. This species is morphologically similar to M. longipetala, distributed from southern China to northern Vietnam, in having recurved stipules and densely pilose and puberulent hairs throughout, but differs in its strongly recurved calyx lobes, a shorter corolla tube, and ovate corolla lobes. The species is morphologically heterostylous and it appears to be functionally dioecious. An updated key to Mussaenda species in Vietnam, Laos, and Cambodia is also provided.

A new species, Wikstroemia bokorensis (Thymelaeaceae), from Bokor National Park, Kampot Province, Cambodia, is described and illustrated. This species is morphologically most similar to W. nutans distributed in southern China and Vietnam, but differs in having pubescent branches and leaves, smaller anthers, a single disk scale, and glabrous ovary. DNA barcodes of ITS, rbcL, trnT-F, rps16, and rpl16 regions for the new species are also provided.

Selection of favorable alleles is sufficient to maintain species cohesion even with low levels of gene flow. Here, in the study of two sister species growing in contrasting restricted ecological areas, we assess whether their divergent traits have been subject to uniform selection among populations. Two different analyses were performed to evaluate the relative importance of selection and drift. First, we compared FST and PST indexes, analogous to QST, in eleven populations each of Viola eizanensis and V. chaerophylloides. PST was computed for two reproductive traits, two leaf traits and two allocation traits. Second, we compared the observed PST with the expected distribution of PST under neutrality generated by phylogeny-based simulation assuming the Brownian motion model for trait evolution. These analyses indicated that spring leaf mass per area and seed number per capsule were divergent between species and uniform among populations. We suggest that these candidate traits are associated with ecological speciation. We also show that uniform, not divergent, selection among populations is probably common in both species. This result suggests that uniform selection maintaining similarity of traits among populations is a more dominant force than divergent selection in species growing in restricted ecological areas.

Biodiversity loss is one of the most critical threats to global environments that has already transgressed planetary boundaries (Rockstrom et al. 2009). Indeed, nonlinear, often abrupt changes can drive unacceptable and irreversible deterioration. Rockstrom et al. (2009) claimed that earth’s system cannot sustain the current rate of biodiversity loss without significant erosion of resilience. To halt this biodiversity loss, global efforts to achieve “by 2010 a significant reduction of the current rate of biodiversity loss at the global, regional, and national level,” called the 2010 biodiversity targets, have been made since the agreement by the world’s governments in 2002. However, the latest data on the status and trends of biodiversity summarized in the third edition of Global Biodiversity Outlook (GBO-3) show that the target had not been met (Secretariat of the Convention on Biological Diversity 2010).

Ecological communities including tropical rainforest are rapidly changing under various disturbances caused by increasing human activities. Recently in Cambodia, illegal logging and clear-felling for agriculture have been increasing. Here, we study the effects of logging, mortality and recruitment of plot trees on phylogenetic community structure in 32 plots in Kampong Thom, Cambodia. Each plot was 0.25 ha; 28 plots were established in primary evergreen forests and four were established in secondary dry deciduous forests. Measurements were made in 1998, 2000, 2004 and 2010, and logging, recruitment and mortality of each tree were recorded. We estimated phylogeny using rbcL and matK gene sequences and quantified phylogenetic α and β diversity. Within communities, logging decreased phylogenetic diversity, and increased overall phylogenetic clustering and terminal phylogenetic evenness. Between communities, logging increased phylogenetic similarity between evergreen and deciduous plots. On the other hand, recruitment had opposite effects both within and between communities. The observed patterns can be explained by environmental homogenization under logging. Logging is biased to particular species and larger diameter at breast height, and forest patrol has been effective in decreasing logging.