BACKGROUND AND AIMS:The section Synstylae in the genus Rosa (Rosaceae) comprises 25-36 species and includes several major progenitors of modern rose cultivars. East Asian Synstylae species have recently diverged and are closely related, but their phylogenetic relationships remain unclear. In the present study, we employed conserved orthologue set (COS) markers and genome-wide nuclear orthologues to elucidate their phylogenetic relationships and unravel their complex evolutionary history. METHODS:Utilizing eight Rosaceae COS (RosCOS) markers, we analysed a total of 137 accessions representing 15 East Asian Synstylae taxa to establish a robust phylogenetic framework and reconstruct ancestral areas. Furthermore, we constructed the species tree for eight representative species and estimated their divergence times based on 1683 genome-wide orthologues. The species tree-gene tree coalescence time comparison, Patterson's D, f4-ratio and f-branch statistics were analysed to identify incomplete lineage sorting (ILS), genetic introgression and reticulation events using conserved orthologue data. KEY RESULTS:RosCOS markers and genome-wide orthologues effectively resolved a robust phylogeny of East Asian Rosa sect. Synstylae. Species divergence times estimated with genome-wide orthologues indicated that East Asian Synstylae species have recently diverged, with an estimated crown age of ~2 Mya. The rampant gene tree discordance indicated the possibility of ILS and/or genetic introgression. In the section Synstylae, deeper coalescence in the gene trees compared to the species tree suggested ILS as a source of gene tree discordance. Further, Patterson's D and f-branch statistics indicated that several lineages in the section were involved in genetic introgression. CONCLUSIONS:We have unravelled the complex evolutionary history of East Asian Rosa sect. Synstylae, including recent species divergences, ILS and genetic introgression. Coupled with the geographical and ecological complexity of East Asia, ILS and genetic introgression may have contributed to the rapid diversification of East Asian Synstylae species by permitting adaptation to diverse environments.

This study aims to compare Thalictrum (Ranunculaceae) plant species, tentatively identified as T. minus, from the Yambaru region of Okinawa Island, Japan, with closely related species using morphometric and molecular phylogenetic analyses. Morphological observations revealed that the unique plants from Okinawa Island had clavate filaments and thickened roots. These traits differed significantly from those of typical T. minus, which have filamentous filaments and slender roots. Molecular phylogenetic analyses revealed that the unique plant on Okinawa Island is sister to T. urbaini, endemic to Taiwan, and formed a separate clade from those containing T. minus. Based on current morphological comparisons and molecular phylogenetic analyses, the unique plant on Okinawa Island was concluded to be a previously undescribed species, newly named Thalictrum yambaruense. Furthermore, our molecular phylogenetic analyses of Thalictrum in Japan and Taiwan revealed that T. tuberiferum var. yakusimense, endemic to Yakushima Island, Japan, is phylogenetically distinct from T. tuberiferum var. tuberiferum. Therefore, we propose elevating the taxonomic status of T. tuberiferum var. yakusimense to the species level as T. yakusimense.

PREMISE:Plants in sympatric populations with congeners may have evolved tolerance to the negative effects of heterospecific pollen (HP) through selection on female or male reproductive traits. If so, then the degree of HP tolerance may vary depending on the co-existence history of the maternal and paternal plant source populations. Empirical evidence from species with a known history of contact is limited. METHODS:This study focused on sympatric and allopatric populations of the native Oxalis corniculata and its recently arrived congener O. dillenii in Japan. Specifically, we conducted heterospecific and conspecific crosses with O. corniculata and two sequential pollination treatments using conspecific (CP) followed by heterospecific (HP) pollen, with CP donors from sympatric or allopatric populations. RESULTS:Heterospecific crosses revealed lower seed production in O. corniculata than conspecific crosses, with sympatric populations showing a significantly greater reduction. Sequential pollination experiments reduced conspecific seed production, particularly when both the recipients and CP donor originated from sympatric populations. CONCLUSIONS:Our results suggest that individuals from sympatric populations may mitigate the negative effects of HP caused by hybrid seed formation. Furthermore, the variation in tolerance to the inhibition of conspecific fertilization by HP could be attributed to the recipient and CP donor origins. But the unexpectedly high susceptibility of sympatric populations to HP highlights the complex ecological and evolutionary factors that influence HP tolerance.

Recent developments in Unmanned Aerial Vehicles (UAVs) and Light Detection and Ranging (LiDAR) technology have enhanced the ability to capture precise three-dimensional forest information at a lower cost. This article reports four types of high-resolution digital datasets derived from UAV-LiDAR measurements and associated fieldwork. The dataset includes 5 cm resolution Digital Terrain Models (DTMs) and Canopy Height Models (CHMs), ortho-mosaic photos with sub-2.7 cm resolution, and 4328 tree crown polygons with information on 151 species, stem girth at breast height, and canopy height. Data were collected from 22 approximately 1-ha long-term monitoring plots across Japan, spanning major climate zones from subtropical to subarctic. These plots encompass evergreen conifer, broadleaf and conifer mixed, deciduous broadleaf, and evergreen broadleaf forests. UAV surveys were conducted from May 2022 to October 2023. Based on these data, we also report basic profiles of these natural forests: a median slope of 22.2 degrees (ranging from 2.5 degrees to 35.0 degrees across sites), median canopy height of 19.2 m (10.5-25.2 m), median maximum canopy height of 29.4 m (17.6-39.8 m), median gap ratios of 1.7% (0-10.7%) and 7.7% (0-28.9%) depending on gap definitions, and median crown area of 42.9 m2 (10.7-80.2 m2) for canopy trees. This dataset is the first publicly available collection of forest structure and individual tree crown information for Japanese natural forests. We hope this dataset will be useful for a wide range of studies and analyses, from site-specific case studies to global-scale meta-analyses. The metadata is available in MetaCat in JaLTER at .

In the Kyushu region of Japan, a novel species, Chrysosplenium brevifilamentum (Saxifragaceae), has been identified. The species was previously confused with either C. macrostemon var. macrostemon or C. macrostemon var. viridescens owing to its morphological similarities, including yellow anthers and overall appearance. However, C. brevifilamentum can be distinguished from the varieties of C. macrostemon by the oblong leaves of the scape with a cuneate base and flowers exhibiting a pronounced disk and abbreviated stamens. Additionally, Chrysosplenium brevifilamentum usually maintains greenish hued foliage during winter; C. macrostemon usually displays brownish coloration. Comprehensive molecular phylogenetic analyses, employing sequence variations in the ITS and ETS regions of the nuclear ribosomal DNA and six chloroplast DNA regions, corroborated the distinct phylogenetic position of C. brevifilamentum within Chrysosplenium Ser. Macrostemon in Japan. Like other species of Chrysosplenium Ser. Macrostemon, C. brevifilamentum is diploid, suggesting that polyploidization is not relevant to its origin. Chrysosplenium brevifilamentum is primarily restricted to calcareous areas in central Kyushu.

We re-examined the taxonomic status of a plant previously identified as Sedum formosanum subsp. formosanum from four islands in the Satsunan Islands, Japan. To clarify its taxonomic identity, we conducted morphological and phenological comparisons and performed molecular phylogenetic analyses based on nuclear internal transcribed spacer (ITS) and three chloroplast DNA regions using closely related species of Sedum in East Asia. Morphologically, the plants share traits with S. danjoense, S. formosanum subsp. formosanum, S. formosanum subsp. miyakojimense, S. plumbizincicola and S. tetractinum, but differ in key features such as their perennial life cycle, greenish to yellowish stem, presence of lateral branches, spatulate leaves with rounded apices, variation in sepal shape, yellow anthers, oblique fruits and autumnal flowering (October-December). Notably, the plants exhibit remarkable variation in floral merosity - in the number of petal, stamen, and pistils - a unique trait absent in other East Asian Sedum species. Phylogenetic analyses revealed inconsistency between the nuclear ITS tree and the chloroplast DNA tree: the nuclear ITS tree clustered the plants with S. danjoense, whereas the chloroplast DNA tree grouped them with S. formosanum subsp. miyakojimense. This finding suggests that the plants experienced chloroplast capture due to introgressive hybridization between the two species. Considering their distinct morphological, phenological and genetic features, we described these plants as a new species, Sedum diversiflorum.

BACKGROUND:The section Synstylae of the genus Rosa (Rosaceae) is predominantly distributed across the Eastern Asiatic Floristic Region and is characterized by increased species diversity and natural hybrids. These characteristics render species within this section exemplary for studying phenotypic variability and easy crossbreeding, which hold potential for advancements in the rose-breeding industry. However, genetic introgression and hybridization have posed challenges to our understanding of their phylogenetic relationships. Despite recurrent interspecific introgression, chloroplast DNA can still aid in phylogenetic inference within the section Synstylae due to its uniparental inheritance and high conservation. RESULTS:Phylogenetic inferences and haplotype network analysis identified seven distinct chloroplast haplotype groups within the East Asian Synstylae. Clear differentiation was observed between the chloroplast haplotypes of the Sino-Himalayan series Brunonianae and Sino-Japanese series Multiflorae lineages. The chloroplast haplotypes within each lineage aligned more closely with geographic gradients than with species boundaries. Consequently, various chloroplast haplotypes were shared among Sino-Japanese Synstylae species with broader distributions, whereas unique haplotypes were found in the species with restricted distribution ranges. Similarly, geographically specific haplotype groups were identified in the Japanese Archipelago, Taiwan, and Eastern China of the Sino-Japanese Subregion, respectively. CONCLUSIONS:The chloroplast genomes of Sino-Japanese Synstylae species may have diverged along geographic gradients, influenced by the geographical and ecological complexity of East Asia and the climate oscillations during the Pleistocene. The recurring cycles of fragmentation and rejoining in Sino-Japanese Synstylae populations have allowed founder effects and genetic drift to drive divergence and diversification of their chloroplast genomes along these geographic gradients. The substantial incongruence between the chloroplast and nuclear phylogenies evidenced the prevalent genetic introgression within the Sino-Japanese Synstylae lineage. Additionally, two putative hybrid speciation events highlighted the role of genetic introgression in species diversification of the East Asian Synstylae lineage. This study substantiates the value of chloroplast genomes in elucidating genetic introgression and the unique evolutionary history of recently diverged and closely related East Asian Synstylae species.

The clonal diversity of Nymphoides peltata in Japan was estimated using genome-wide SNPs. In total, 27 clones were detected by considering the genetic distances between clones. The number of clones was much smaller than the estimate of 61 from a previous study that used SSR (Short Sequence Repeats) markers. This may be because population have diminished due to environmental deterioration over the past decade, fewer samples were analyzed in this study, or there were technical problems with the SSR markers used in the previous study. The populations of N. peltata were genetically differentiated between the western and eastern regions of the Japanese archipelago. Artificial movements may have occurred in a few populations.

Unraveling species boundaries is pivotal for evolutionary biology and conservation endeavors. However, it proves challenging in instances where recent speciation is intertwined with complex demographic histories and natural selection processes. The Rhododendron keiskei complex, an evergreen rhododendron distributed in East Asia, consists of a widespread variety (R. keiskei var. keiskei) and a more restricted R. keiskei var. hypoglaucum. Intriguingly, the latter is exceptionally rare yet displays a disjunction that spans approximately 1100 km. This study aimed to elucidate the evolutionary backgrounds of the enigmatic disjunctions of R. keiskei var. hypoglaucum and to propose species delimitation within the species complex. An integrative approach, combining genomic data (MIG-seq and GBS-derived SNPs) with Scanning Electron Microscopy analysis of leaf microstructures was adopted in this study. Phylogenetic analyses revealed significant divergence among the studied rhododendrons. Genetic demographic analyses favored the population models that assumed non-monophyly of two disjunct populations of R. keiskei var. hypoglaucum indicating their independent origins. Recent gene flow between the widespread R. keiskei var. keiskei and "var. hypoglaucum" populations were limited due to geographic and habitat isolation factors, even in areas where their distributions overlap. Detailed morphological assessments detected distinctions between morphologically similar "var. hypoglaucum" populations based on leaf microstructures and flowering habits. Our study has shown that the apparent disjunctions of rare rhododendrons are more likely attributed to morphological convergence, possibly due to similar environmental selections in unrelated taxa. The finding highlights the importance of an integrative approach for resolving taxonomic challenges in plant species complexes.

Hydrangea sect. Macrophyllae comprises deciduous shrubs including two species with seven infraspecific taxa distributed throughout the Japanese Archipelago and adjacent areas. In this study, we revealed a phylogeny of Hydrangea sect. Macrophyllae by using a larger dataset of genome-wide SNPs than those employed in a previous study and by adding more comprehensive taxa/populations, which cover the entire distribution of the section. We then revised the taxonomic treatment of sect. Macrophyllae based on the higher-resolution phylogenetic trees obtained in this study. The phylogenetic trees estimated in this study showed five major clades, suggesting that H. serrata var. minamitanii and var. yesoensis should be treated as independent species from other H. serrata, that H. serrata var. australis and var. yakushimensis could be subclassified under the major clades and that var. angustata could be a synonym of var. serrata. The divergence time of these major clades was estimated to be in the Pleistocene.

Interspecific hybridization between the short (ca. 3.5 mm) corolla tube species, Isodon inflexus, and the long (ca. 12 mm) corolla tube species, Isodon longitubus, was examined using genetic and morphometric analyses. Bayesian clustering analysis using microsatellites revealed that plants in the contact zone consisted of two I. inflexus individuals, 32 I. longitubus individuals, and 13 hybrid individuals (F2-like and backcrosses to both I. inflexus and I. longitubus). Using the sequences of the psbA-trnH intergenic spacer in chloroplast DNA, three haplotypes were found among pure I. inflexus, while four haplotypes were found among pure I. longitubus. Most hybrid individuals had a haplotype found only in I. inflexus, suggesting that the initial F1 might have been formed by hybridization with I. inflexus as the maternal parent, and that in later hybrid formation, hybrids or I. inflexus tended to serve as the maternal parent. Although strong pre-mating isolation mechanisms contribute to preventing hybridization between the species, human habitat disturbance might have created the contact zone. Although mature hybrids in the contact zone contained equal proportions of backcrosses to both I. inflexus and I. longitubus, seedlings comprised more individuals originating from backcrosses to I. longitubus. The dominance of backcrosses to I. longitubus was probably caused by the quantitative difference between the parental species in the contact zone. In the contact zone, signs of contemporary hybridization in the nuclear genome might have been diluted by repeated backcrossing. The present study could illustrate the process of unidirectional introgression leading to chloroplast capture, a phenomenon frequently observed in Isodon species in Japan.

Paraphlomideae (Lamioideae, Lamiaceae) is a recently established tribe endemic to East and Southeast Asia. It comprises three herbaceous genera: Paraphlomis, Matsumurella, and Ajugoides. Phylogenetic relationships among these genera have not yet been satisfactorily resolved and the monophyly of Paraphlomis was challenged in previous molecular phylogenetic studies. In this study, we performed maximum likelihood and Bayesian inference analyses on complete plastomes and nuclear ribosomal internal and external transcribed spacer sequences to further resolve the generic relationships within Paraphlomideae. All phylogenetic analyses support the monophyly of Paraphlomideae. Contrary to traditional classifications, both Ajugoides and Matsumurella were deeply nested within Paraphlomis, indicating the need to expand Paraphlomis to include Ajugoides and Matsumurella. Hence, six new combinations and one replacement name are proposed. Morphologically, species of the newly defined Paraphlomis share a rhizomatous or stoloniferous habit, plants with simple hairs, nutlets with a truncate apex, and actinomorphic calyces. In addition, widespread incongruence between nuclear and plastid trees may have been caused by hybridization and incomplete lineage sorting after rapid diversification in the re-circumscribed Paraphlomis.

Although the monophyly of Phedimus has been strongly demonstrated, the species relationships among approximately 20 species of Phedimus have been difficult to determine because of the uniformity of their floral characteristics and extreme variation of their vegetative characters, often accompanied by high polyploid and aneuploid series and diverse habitats. In this study, we assembled 15 complete chloroplast genomes of Phedimus species from East Asia and generated a plastome-based backbone phylogeny of the subgenus Aizoon. As a proxy for nuclear phylogeny, we reconstructed the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) phylogeny independently. The 15 plastomes of subg. Aizoon were highly conserved in structure and organization; hence, the complete plastome phylogeny fully resolved the species relationships with strong support. We found that P. aizoon and P. kamtschaticus were polyphyletic and morphologically distinct or ambiguous species, and they most likely evolved from the two species complex. The crown age of subg. Aizoon was estimated to be 27 Ma, suggesting its origin to be in the late Oligocene; however, the major lineages were diversified during the Miocene. The two Korean endemics, P. takesimensis and P. zokuriensis, were inferred to have originated recently during the Pleistocene, whereas the other endemic, P. latiovalifolium, originated in the late Miocene. Several mutation hotspots and seven positively selected chloroplast genes were identified in the subg. Aizoon.

Differences in style length among closely related flowering plant species are recognized as a unilateral postmating-prezygotic barrier; species with longer styles prevent pollen fertilization by short-styled congeners. However, little is known about how style length variation within a species affects plant reproduction when exposed to heterospecific pollen. We investigated the relationship between style length in native Oxalis corniculata and hybrid seed formation resulting from interspecific pollination by alien O. dillenii using two O. corniculata populations with large style length variation. We found that the native O. corniculata individuals with longer styles produced hybrid seeds at a lower frequency. In con-trast, the effect of style length on seed production following intraspecific pollination conducted as a con-trol treatment was not statistically significant. These results suggest that longer styles of native species can hinder interspecific pollen fertilization owing to physical limitations and mitigate reproductive inter-ference from the alien congener by reducing the cost of ovule loss.

The genus Symplocarpus in basal Araceae includes both thermogenic and non/slightly thermogenic species that prefer cold environments. If floral thermogenesis of Symplocarpus contributes to cold adaptation, it would be expected that thermogenic species have a larger habitat than non/slightly thermogenic species during an ice age, leading to increased genetic diversity in the current population. To address this question, potential distribution in past environment predicted by ecological niche modeling (ENM), genetic diversity, and population structure of chloroplast and genome-wide single nucleotide polymorphisms were compared between thermogenic Symplocarpus renifolius and non/slightly thermogenic Symplocarpus nipponicus. ENM revealed that the distribution of S. nipponicus decreased, whereas that of S. renifolius expanded in the Last Glacial Maximum. Phylogeographic analyses have shown that the population structures of the two species were genetically segmented and that the genetic diversity of S. renifolius was higher than that of S. nipponicus. The phylogenetic relationship between chloroplast and nuclear DNA is topologically different in the two species, which may be due to the asymmetric gene flow ubiquitously observed in plants. The results of this study imply that floral thermogenesis of Symplocarpus contributes to expanding the distribution during an ice age, resulting in increased genetic diversity due to cold adaptation.

Aim Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Endemic plants on nearshore oceanic islands have received less attention. We investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands and examined the possibility of multiple colonizations onto the islands. Location Japanese mainland Honshu and the adjacent Izu Islands. Taxon Solidago virgaurea (Asteraceae). Methods Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands respectively; phylogeographical and population genetics analyses, including Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis and Discrete Phylogeographic Approach (DPA) to trace the history of colonization events onto the islands, were performed using plastid DNA and nuclear microsatellite DNA variations. Results Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island. Main conclusions The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.

We explored the genetic diversity and population genetic structure of an invasive alien species, the raccoon Procyon lotor, which was introduced into the Shikoku Island of Japan, using sequences of the mitochondrial control region and 10 polymorphic microsatellite loci. In 80 individuals examined, we detected two genetically divergent haplotypes, indicating that two maternal lineages had been introduced into Shikoku Island. Population clustering analysis suggested the nonexistence of genetic structure in the area. The relatedness network showed that the raccoon population in Shikoku Island consisted of closely related individuals. The genetic diversity of the Shikoku raccoon population was lower than that in the native range. These results and a prior report indicate that the Shikoku raccoon population is likely to have expanded from small numbers of founders originating from an initial invasive population. Raccoon captures outside Kagawa are decreasing, although past expansions into Tokushima and Ehime suggest that there are no geographical barriers among these areas. Therefore, action should be taken to prevent any re-expansion of the raccoon population in Kagawa. Intensive monitoring and the elimination of dispersers from Kagawa, as well as effort to eradicate potential source populations for expansion in Kagawa, are needed.

Anaphalis margaritacea var. yedoensis is a perennial herb adapted to the severe environment of pebbled river banks, where it is frequently found. In this study, we determined the complete chloroplast genome of A. margaritacea var. yedoensis and uncovered its phylogenetic relationships with other members of Gnaphalieae. The total chloroplast genome size of A. margaritaceae var. yedoensis is 153,231 bp, with a large single-copy region (LSC) of 84,981 bp, a small single-copy region (SSC) of 18,481 bp and a pair of inverted repeat (IR) regions of 24,885 bp. A total of 136 genes were annotated, including 39 tRNA genes, 8 rRNA genes, and 89 protein-coding genes. Phylogenetic analysis showed that A. margaritacea var. yedoensis and another Anaphalis species, A. sinica, do not form a monophyletic group, supporting previous phylogenetic studies using some specific regions of cpDNA that showed the genus Anaphalis is non-monophyletic.

Natural hybridization between the native species Rumex madaio endemic to Japan and the congeneric invasive species R. obtusifolius , which frequently co‐occurs with R. madaio , was examined by molecular identification. At low frequencies, interspecific hybrids between the two species were confirmed using restriction fragment length polymorphism analyses of the internal transcribed spacer region of ribosomal DNA. Whereas these two species can hybridize because their flowering periods overlapped to some extent, the extremely low fertility of R. madaio caused by unknown genetic factors seemed to prevent extensive hybridization between these species. Population genetic analyses based on single nucleotide polymorphisms showed that there was a distinct population genetic structure in R. madaio , suggesting that local populations should be treated separately for genetic conservation of the species.