Relictithismia kimotsukiensis, a new genus and species of Thismiaceae from southern Japan with discussions on its phylogenetic relationship.

The family Thismiaceae, known as "fairy lanterns" for their urn- or bell-shaped flowers with basally fused tepals, consists of non-photosynthetic flowering monocots mainly in tropical regions, extending into subtropical and temperate areas. Here, we propose a new mycoheterotrophic genus, Relictithismia Suetsugu & Tagane (Thismiaceae), with its monotypic species Relictithismia kimotsukiensis Suetsugu, Yas.Nakam. & Tagane from Kimotsuki Mountains in the Osumi Peninsula, Kagoshima Prefecture, Kyushu Island, southern Japan. Relictithismia resembles Haplothismia Airy Shaw in having a cluster of tuberous roots, a feature previously observed only in this genus within the family Thismiaceae. However, it differs in having solitary flowers (vs. 2-6-flowered pseudo-raceme in Haplothismia), anther thecae largely separated (vs. connate), and the presence of an annulus (vs. absent). Additionally, Relictithismia differs from the geographically overlapping genus Thismia Griff. in its stamen structure and the position of the annulus. In Relictithismia, the stamens lack connectives, and its free filaments arise from the annulus located inside the perianth mouth, while in Thismia, the stamens typically have connate connectives, forming a staminal tube pendulous from the annulus located at the mouth of the floral tube. Our morphological and phylogenetic data indicated that R. kimotsukiensis holds an early-diverging position within the family, situated outside the Old World Thismia clade. This paper offers an extensive description and color photographs of R. kimotsukiensis, complemented by notes on its phylogenetic relationship and evolutionary history.

Molecular phylogeny and taxonomy of Hosta (Asparagaceae) on Shikoku Island, Japan, including five new species, one new subspecies, and two new status assignments.

Japan has 16 native species of the genus Hosta Tratt. (Asparagaceae). A recent study on Hosta based on field surveys and molecular phylogenetic analyses resulted in the discovery of six unknown taxa in Kochi Prefecture, Shikoku Island, southwestern Japan. We aimed to identify these unknown taxa. Therefore, we constructed a finely resolved phylogeny for 320 Hosta samples collected from the Honshu, Shikoku, and Kyushu Islands using multiplex inter-simple sequence repeat genotyping by sequencing (MIG-seq). Based on this phylogenetic analysis and related morphological observations, we describe five new species, H.longipedicellatasp. nov., H.minazukiflorasp. nov., H.polyneuronoidessp. nov., H.samukazemontanasp. nov., and H.takiminazukiflorasp. nov. and one new subspecies, H.takiminazukiflorasubsp.grandissubsp. nov. In addition, we propose two new status assignments, H.tardivasubsp.densinerviacomb. and stat. nov. and H.scabrinerviastat. nov. We also propose classifying H.kikutiivar.tosana as a species, H.tosana. Further studies that combine MIG-seq with careful morphological observations are needed for Hosta plants on all Japanese islands, which may result in the discovery of even more undescribed species.

Development of a system for the automated identification of herbarium specimens with high accuracy.

Herbarium specimens are dried plants mounted onto paper. They are used by a limited number of researchers, such as plant taxonomists, as a source of information on morphology and distribution. Recently, digitised herbarium specimens have begun to be used in comprehensive research to address broader issues. However, some specimens have been misidentified, and if used, there is a risk of drawing incorrect conclusions. In this study, we successfully developed a system for identifying taxon names with high accuracy using an image recognition system. We developed a system with an accuracy of 96.4% using 500,554 specimen images of 2171 plant taxa (2064 species, 9 subspecies, 88 varieties, and 10 forms in 192 families) that grow in Japan. We clarified where the artificial intelligence is looking to make decisions, and which taxa is being misidentified. As the system can be applied to digitalised images worldwide, it is useful for selecting and correcting misidentified herbarium specimens.

Molecular phylogeny and taxonomy of the Hydrangeaserrata complex (Hydrangeaceae) in western Japan, including a new subspecies of H.acuminata from Yakushima.

According to the contemporary classification of Hydrangea native to Japan, H.serrata is a polymorphic species including six varieties. We discovered a plant identified as H.serrata, but morphologically distinct from previously known varieties, in Yakushima island where approximately 50 endemic species are known. To determine the relationship of this plant with previously known varieties, we examined morphology and constructed a highly resolved phylogeny of H.serrata and its relatives using three chloroplast genomic regions, rbcL, trnL intron, psbA-trnH, and two nuclear genomic regions, ITS1 and ITS2, and Multiplex ISSR genotyping by sequencing (MIG-seq). Based on these morphological and phylogenetic observations, we describe Hydrangeaacuminatasubsp.yakushimensissubsp. nov. as a newly discovered lineage in Yakushima, Japan and propose Hydrangeaminamitanii stat. nov. and Hydrangeaacuminatasubsp.australisstat. nov. which were previously treated as varieties of H.serrata.

 Hydrangeamarunoi (Hydrangeaceae), a new species from Osumi Peninsula, southern Japan.

Hydrangeamarunoi Tagane & S. Fujii, from the Kimotsuki Mountains in the Ohsumi Peninsula, southern Japan, is described and illustrated. It is morphologically similar to H.alternifolia in having three-petaloid calyx lobes in marginal flowers, but is distinguished by the larger stamen number, and longer styles and seeds. Multiplex ISSR genotyping by sequencing (MIG-seq) demonstrated that the new species is monophyletic and closely related to H.amamiohsimensis and H.moellendorffii rather than H.alternifolia.

Validation of Hostaalata (Asparagaceae) as a new species and its phylogenetic affinity.

Molecular phylogenetic studies of Hostapulchella (Asparagaceae) and its relatives, which are native to Japan, have been conducted and resulted in a highly resolved phylogeny. Specifically, the relationship of H.pulchella to H.alata Hatusima, nom. nud. is investigated. These data include genome-wide SNPs obtained through conducting multiplexed ISSR genotyping by sequencing (MIG-seq). Based on these phylogenetic results, morphological observations, distribution, and differences in flowering periods of H.alata collections sympatric with H.pulchella, we find the two species closely related, but distinct. As such, we formally describe Hostaalata sp. nov. from the Oita Prefecture of Kyushu island, southwestern Japan.

Evaluating the genetic diversity in two tropical leguminous trees, Dalbergia cochinchinensis and D. nigrescens, in lowland forests in Cambodia and Thailand using MIG-seq.

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.

Morphological and molecular evidence reveals three new species of Lithocarpus (Fagaceae) from Bidoup-Nui Ba National Park, Vietnam.

Three new species, Lithocarpusbidoupensis Ngoc & Tagane, L.congtroiensis Ngoc & Yahara, and L.hongiaoensis Ngoc & Binh are described from Bidoup-Nui Ba National Park, Central Highland of Vietnam. Morphological analyses and Maximum likelihood tree based on genome-wide SNPs support the distinction of those species from the previously known taxa in the region. The three new species are considered to be endemic to the Bidoup-Nui Ba National Park and the preliminary conservation status for each species is evaluated as Critically Endangered.

A new subspecies of Stellariaalsine (Caryophyllaceae) from Yakushima, Japan.

An unknown taxon of Stellaria was discovered in Yakushima, a Japanese island known to harbor several endemic species. To determine the identity of this taxon, this study employed MIG-seq for the reconstruction of a finely resolved phylogenetic tree of the newly discovered taxon, along with some related species of Stellaria. The results showed that the newly discovered taxon is a relative of S.alsine. Based on this result, Stellariaalsinesubsp.nanasubsp. nov. was published.

Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea.

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.

Cryptocarya kaengkrachanensis, a new species of Lauraceae from Kaeng Krachan National Park, southwest Thailand.

A new species of Lauraceae, Cryptocarya kaengkrachanensis M.Z.Zhang, Yahara & Tagane, from Kaeng Krachan National Park, Phetchaburi Province, southwestern Thailand, is described and illustrated. This species is morphologically most similar to C. amygdalina in that its leaves are pinnately veined, leathery, and apparently glabrous (but microscopically hairy) abaxially, twigs are yellowish brown hairy, and fruits are 1.36 to 1.85 times longer than width. However, C. kaengkrachanensis is distinguished from C. amygdalina in having the leaves of ovate and elliptic (vs. oblong-lanceolate) with leaf aspect ratio (length:width) from 1.38 to 2.28 (vs. 2.46-3.43), and ovoid fruits (vs. ellipsoid) with stalk distinctly swollen (vs. not or only slightly swollen). In addition, phylogenetic trees constructed based on internal transcribed spacer sequences (ITS) and genome-wide SNPs using MIG-seq showed that C. kaengkrachanensis is not sister to C. amygdalina and is distinct from all the other Cryptocarya species hitherto recognized in Thailand. Analysis including other species demonstrates that C. floribunda should be a synonym of C. amygdalina, but we recognize C. scortechinii as a distinct species.

First molecular phylogenetic insights into the evolution of Eriocaulon (Eriocaulaceae, Poales).

Eriocaulon is a genus of c. 470 aquatic and wetland species of the monocot plant family Eriocaulaceae. It is widely distributed in Africa, Asia and America, with centres of species richness in the tropics. Most species of Eriocaulon grow in wetlands although some inhabit shallow rivers and streams with an apparent adaptive morphology of elongated submerged stems. In a previous molecular phylogenetic hypothesis, Eriocaulon was recovered as sister of the African endemic genus Mesanthemum. Several regional infrageneric classifications have been proposed for Eriocaulon. This study aims to critically assess the existing infrageneric classifications through phylogenetic reconstruction of infrageneric relationships, based on DNA sequence data of four chloroplast markers and one nuclear marker. There is little congruence between our molecular results and previous morphology-based infrageneric classifications. However, some similarities can be found, including Fyson's sect. Leucantherae and Zhang's sect. Apoda. Further phylogenetic studies, particularly focusing on less well sampled regions such as the Neotropics, will help provide a more global overview of the relationships in Eriocaulon and may enable suggesting the first global infrageneric classification.

A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences.

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. baolamensissp. nov., Q. bidoupensissp. nov. and Q. honbaensissp. nov. These new species are all phenotypically similar to Q. langbianensiss. 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. langbianensiss. str., while Quercus baolamensis is not sister to Q. langbianensiss. str. in both the Bayesian tree and MIG-seq tree. In addition, Q. cambodiensis and Q. baniensis previously reduced to Q. langbianensiss. lat. have been recognised as distinct species. Six species were in need of lectotypification and that is undertaken herein.

Lithocarpus vuquangensis (Fagaceae), a new species from Vu Quang National Park, Vietnam.

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.

A new species and two new records of Quercus (Fagaceae) from northern Vietnam.

A new species, Quercus xuanlienensis Binh, Ngoc & Bon, is described from Xuan Lien Nature Reserve, Vietnam. The new species is morphologically similar to Q. edithiae Skan, in having 8-11 pairs of secondary veins, bowl-shaped cupules and ellipsoid to cylindrical-ellipsoid and basally convex nuts. It differs in having serrulate leaf margins only at apical 1/5-1/7, almost entire margins of bracts on cupule and much longer nuts. The species is also similar to Q. fleuryi Hickel & A. Camus in having leaves glabrous on both surfaces with only an apically serrulate margin but differs in having shorter petioles, cupules enclosing 1/5 of the nut and much longer nuts. In addition, Q. disciformis Chun & Tsiang. and Q. bella Chun & Tsiang., previously known from China, are newly recorded from Ba Vi National Park, Vietnam.

Macrosolen bidoupensis (Loranthaceae), a new species from Bidoup Nui Ba National Park, southern Vietnam.

Macrosolen bidoupensis Tagane & V.S.Dang, sp. nov. (Loranthaceae) is newly described from Bidoup Nui Ba National Park in Lam Dong Province, southern Vietnam. The new species is characterized by small broadly elliptic to circular leaves, sessile to short petioles, slightly cordate to rounded leaf bases, 4-5 pairs of lateral veins and a basally green corolla tube. An illustration, a summary of DNA barcoding of the plastid genes rbcL and matK, and a key to the species of Macrosolen in Vietnam are provided.

Garcinia hopii (Clusiaceae), a new species from Bidoup Nui Ba National Park, southern Vietnam.

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.

Flora of Nam Kading National Protected Area I: a new species of yellow-flowered Strobilanthes (Acanthaceae), S. namkadingensis.

A new species of Acanthaceae, Strobilanthes namkadingensis Soulad. & Tagane from Nam Kading National Protected Area, Bolikhamxay Province, central Laos, is described and illustrated. It is characterized by long spicate inflorescences consisting of 6-32 flowers, yellow corolla, the absence of long white hairs on the bracts and 4-6 seeds per capsule. Three DNA barcode regions of the partial genes for the large sub-unit ribulose-1,5-bisphosphate carboxylase oxygenase (rbcL) and maturase K (matK) and internal transcribed spacers (ITS) are also provided.

Convergence, Consilience, and the Evolution of Temperate Deciduous Forests.

The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

Lithocarpus dahuoaiensis (Fagaceae), a new species from Lam Dong Province, Vietnam.

Lithocarpus dahuoaiensis Ngoc & L. V. Dung, a new species from the Central highland of Vietnam, is described and illustrated. The new species is morphologically similar to Lithocarpus macphailii (M. R. Hend.) Barnett or Lithocarpus encleisocarpus (Korth.) A. Camus in having completely entire leaf margin, solitary cupule, long stalks of fruits, deeply cup-shaped or turbinate cupules, with a number of horizontal filiform lines. The species differs in its nut enclosure ca. 1/2 - 2/3 of the nut, adaxially glabrous leaf blades, secondary veins 11-12 pairs and faintly to very faintly visible hairs on the outside of the cupule. A table showing the morphological comparison of Lithocarpus dahuoaiensis with Lithocarpus macphailii and Lithocarpus encleisocarpus is also provided.