An earlier version of V.PhyloMaker has been broadly used to generate phylogenetic trees of vascular plants for botanical, biogeographical and ecological studies. Here, we update and enlarge this package, which is now called 'V.PhyloMaker2'. With V.PhyloMaker2, one can generate a phylogenetic tree for vascular plants based on one of three different botanical nomenclature systems. V.PhyloMaker2 can generate phylogenies for very large species lists (the largest species list that we tested included 365,198 species). V.PhyloMaker2 generates phylogenies at a fast speed. We provide an example (including a sample species list and an R script to run it) in this paper to show how to use V.PhyloMaker2 to generate phylogenetic trees.

Living gymnosperms comprise four major groups: cycads, Ginkgo, conifers, and gnetophytes. Relationships among/within these lineages have not been fully resolved. Next generation sequencing has made available a large number of sequences, including both plastomes and single-copy nuclear genes, for reconstruction of solid phylogenetic trees. Recent advances in gymnosperm phylogenomic studies have updated our knowledge of gymnosperm systematics. Here, we review major advances of gymnosperm phylogeny over the past 10 years and propose an updated classification of extant gymnosperms. This new classification includes three classes (Cycadopsida, Ginkgoopsida, and Pinopsida), five subclasses (Cycadidae, Ginkgoidae, Cupressidae, Pinidae, and Gnetidae), eight orders (Cycadales, Ginkgoales, Araucariales, Cupressales, Pinales, Ephedrales, Gnetales, and Welwitschiales), 13 families, and 86 genera. We also described six new tribes including Acmopyleae Y. Yang, Austrocedreae Y. Yang, Chamaecyparideae Y. Yang, Microcachrydeae Y. Yang, Papuacedreae Y. Yang, and Prumnopityeae Y. Yang, and made 27 new combinations in the genus Sabina.

Medicinal plants are the primary material basis for disease prevention and treatment in traditional Chinese medicine (TCM). The conservation and sustainable utilization of these medicinal plants is critical for the development of the TCM industry. However, wild medicinal plant resources have sharply declined in recent decades. To ameliorate the shortage of medicinal plant resources, it is essential to explore the development potential of the TCM industry in different geographical regions. For this purpose, we examined the spatial distribution of commonly used medicinal plants in China, the number of Chinese medicinal material markets, and the number of TCM decoction piece enterprises. Specifically, multispecies superimposition analysis and Thiessen polygons were used to reveal the optimal range for planting bulk medicinal plants and the ideal regions for building Chinese medicinal material markets, respectively. Furthermore, we quantitatively analyzed mismatches between the spatial distribution of commonly used medicinal plant richness, Chinese medicinal material markets, and TCM decoction piece enterprises. We found that?the areas suitable for growing commonly used medicinal plants in China were mainly distributed in Hengduan Mountain, Nanling Mountain, Wuling Mountain, and Daba Mountain areas. The Thiessen polygon network based on Chinese medicinal material market localities showed there are currently fewer markets in southwestern, northwestern, and northeastern China than in central and southern China. TCM decoction piece enterprises are concentrated in a few provinces, such as Hebei and Jiangxi. We found that the distribution of commonly used medicinal plants, Chinese medicinal material markets and TCM decoction piece enterprises are mismatched in Henan, Shaanxi, Hunan, Hubei, Zhejiang, Fujian, Chongqing, and Xizang. We recommend strengthening development of the TCM industry in Henan, Hunan, Zhejiang, Shaanxi, Hubei, Chongqing, Fujian, and Xizang; building more Chinese medicinal material markets in southwestern, northwestern, and northeastern China; and establishing medicinal plant nurseries in resource-rich provinces to better protect and domesticate local medicinal plants.

Biodiversity loss during the Anthropocene is a serious ecological challenge. Pollinators are important vectors that provide multiple essential ecosystem services but are declining rapidly in this changing world. However, several studies have argued that a high abundance of managed bee pollinators, such as honeybees (Apis mellifera), may be sufficient to provide pollination services for crop productivity, and sociological studies indicate that the majority of farmers worldwide do not recognize the contribution of wild pollinator diversity to agricultural yield. Here, we review the importance of pollinator diversity in natural and agricultural ecosystems that may be thwarted by the increase in abundance of managed pollinators such as honeybees. We also emphasize the additional roles diverse pollinator communities play in environmental safety, culture, and aesthetics. Research indicates that in natural ecosystems, pollinator diversity enhances pollination during environmental and climatic perturbations, thus alleviating pollen limitation. In agricultural ecosystems, pollinator diversity increases the quality and quantity of crop yield. Furthermore, studies indicate that many pollinator groups are useful in monitoring environmental pollution, aid in pest and disease control, and provide cultural and aesthetic value. During the uncertainties that may accompany rapid environmental changes in the Anthropocene, the conservation of pollinator diversity must expand beyond bee conservation. Similarly, the value of pollinator diversity maintenance extends beyond the provision of pollination services. Accordingly, conservation of pollinator diversity requires an interdisciplinary approach with contributions from environmentalists, taxonomists, and social scientists, including artists, who can shape opinions and behavior.

The genus Woodwardia, which together with the genera Anchistea and Lorinseria comprise the subfamily Woodwardioideae of Blechnaceae, has a disjunct distribution across Central and North America, Europe and the temperate to tropical areas of Asia. Fossil records of Woodwardia occur throughout the Paleogene and Neogene of North America, Europe and Asia. However, well-preserved fertile pinna fossils of this genus have not yet been reported in South China. In this paper, a new species, W.?changchangensis Naugolnykh et Song, sp. nov. is described from the middle Eocene of the Changchang Basin, Hainan Island, South China. Macromorphological and micromorphological features of the fertile pinna show a straight pinna rachis, alternate, subtriangular pinnules, acute pinnule apices, almost entire or slightly undulate pinnule margins, long-ovoid sori, stalked sporangia and spores with wing-like folds on the surface, which are characterised in detail. Overall, the present fossil is most similar to the extant species Woodwardia japonica, which mostly grows in warm and moist environments. The discovery of this new species from the Changchang Basin of Hainan Island indicates that this genus has been distributed in the low-latitude tropical regions of South China from as early as the middle Eocene. Based on this find, and previous studies of other ferns from the same site, we infer that the climate of the Palaeo-Hainan landscape during deposition of the Changchang Formation was warm and humid, similar to conditions prevailing today across this region.

Understanding how natural hybridization and polyploidizations originate in plants requires identifying potential diploid ancestors. However, cryptic plant species are widespread, particularly in Ceratopteris (Pteridaceae). Identifying Ceratopteris cryptic species with different polyploidy levels is a challenge because Ceratopteris spp. exhibit high degrees of phenotypic plasticity. Here, two new cryptic species of Ceratopteris, Ceratopteris chunii and Ceratopteris chingii, are described and illustrated. Phylogenetic analyses reveal that each of the new species form a well-supported clade. C.?chunii and C.?chingii are similar to Ceratopteris gaudichaudii var. vulgaris and C. pteridoides, respectively, but distinct from their relatives in the stipe, basal pinna of the sterile leaf or subelliptic shape of the fertile leaf, as well as the spore surface. In addition, chromosome studies indicate that C.?chunii and C.?chingii are both diploid. These findings will help us further understand the origin of Ceratopteris polyploids in Asia.

Though Berberis (Berberidaceae) is widely distributed across the Eurasian landmass it is most diverse in the Himalaya–Hengduan Mountain (HHM) region. There are more than 200 species in China where it is one of the most common mountain shrubs. The study on the taxonomy and evolution of Berberis in this region can thus provide an important insight into the origin and diversification of its flora. A prerequisite to this is mapping and describing the various species of Berberis in the region – a task that despite recent progress is by no means complete. It is clear that in China there may be a significant number of species still to be described and that even with published species much about their distribution remains to be discovered. As a contribution to the first of these tasks seven new species from the northern Hengduan Mountain of N. Sichuan and S. Qinghai: Berberis chinduensis, Berberis degexianensis, Berberis jiajinshanensis, Berberis jinwu, Berberis litangensis, Berberis longquensis and Berberis riparia, are described here. Differences in overall morphology and especially in floral structures with each other and with similar species of Berberis in the same region are presented. The report is the result of phylogenetic analyses based on plastome and partial nrDNA sequences of both the seven proposed new species and a significant number of similar species already published. Provisional conclusions as to the insights provides on the history of the genetic divergence are discussed.

Previous studies recognized three major lineages of the family Costaceae: a South American clade, an Asian clade and a Costus clade. However, the genus Hellenia within the Asian clade has been shown to be non-monophyletic and its morphology has not been studied carefully. Therefore, the complete plastid genomes of Hellenia species were obtained and the monophyly of Hellenia was tested through four different datasets in this study. Plastid phylogenomic analyses of Costaceae revealed that Hellenia is strongly supported as paraphyletic. Two major clades are recovered, namely the Hellenia s.s. subclade and the Parahellenia subclade. Phylogenetic analyses based on an enlarged taxon sampling of the Asian clade using a two chloroplast markers dataset (trnK intron and trnL-F spacer) confirmed the paraphyly of Hellenia. Meanwhile, morphological analyses suggested that members of the Parahellenia subclade differ from the remaining Hellenia species in many characters including inflorescences, bracts, stigma, axillary buds, floral tubes and labellum. According to the present molecular and morphological evidence, the latter subclade is recognized as a new genus, Parahellenia. Two new species are described, four new combinations are made, and identification keys are also provided.

The diverse members of the genus Daphne are prized for their fragrant flowers. Despite being promising ornamental plants in many countries, genetic information of Daphne is scarce. In this study, the plastomes of four species and one variety of Daphne were sequenced and analyzed. The plastomes were typical and contained a pair of inverted repeat (IR) regions that separated the large single-copy (LSC) region from the small single-copy (SSC) region. With a length ranging from 132,869 bp (D.?genkwa) to 174,773 bp (D. championii), 106 to 141 genes were predicted. Comparative plastome analysis of the newly sequenced plastomes with four publicly available Daphne plastomes identified an expansion of the IRs, sequence variations, and mutational hotspots. Phylogenetic analyses indicated that the genus Daphne in its current circumscription is polyphyletic. Daphne genkwa was nested within the genus Wikstroemia, while D.?championii was well resolved as sister to Edgeworthia. These findings concurred with results from our study that used nuclear ribosomal internal transcribed spacer sequence data. The conflicts on the molecular placement of D.?championii and D.?genkwa and the present taxonomic classification in Daphne suggest that a new intergeneric classification system of Daphneae warrants consideration.

The Qinghai-Tibet Plateau (QTP) is an important cushion plant hotspot. However, the distribution of cushion plants on the QTP is unknown, as are the factors that drive cushion plant distribution, limiting our understanding of the evolution of cushion species in the region. In this study, we assessed spatial patterns of total cushion plant diversity (including taxonomic and phylogenetic) over the entire QTP and compared patterns of diversity of cushion plants with different typologies (i.e., compact vs. loose). We also examined how these patterns were related to climatic features. Our results indicate that the southern QTP hosts the highest total cushion plant richness, especially in the south-central Hengduan Mountains subregion. The total number of cushion species declines from south to north and from southeast to northwest. Compact cushion plants exhibit similar patterns as the total cushion plant richness, whereas loose cushion plants show random distribution. Cushion plant phylogenetic diversity showed a similar pattern as that of the total cushion plant richness. In addition, cushion plant phylogenetic community structure was clustered in the eastern and southwestern QTP, whereas random or overdispersed in other areas. Climatic features represented by annual energy and water trends, seasonality and extreme environmental factors, had significant effects on cushion plant diversity patterns but limited effects on the phylogenetic community structure, suggesting that climatic features indeed promote the formation of cushion plants. Because cushion plants play vital roles in alpine ecosystems, our findings not only promote our understanding of the evolution and formation of alpine cushion plant diversity but also provide an indispensable foundation for future studies on cushion plant functions and thus alpine ecosystem sustainability in the entire QTP region.

Dove tree (Davidia involucrata), a tertiary vestige species, is well-adapted to cool conditions. Dormancy in D. involucrata seed lasts for an extremely long period of time, typically between 3 and 4 years, and this characteristic makes the species an excellent model for studying the mechanisms of seed dormancy. The molecular mechanisms governing germination control in D. involucrata are still unknown. Seed stratification have been reported to enhance germination in recalcitrant seeds. We performed a widely targeted metabolome profiling to identify metabolites and associated pathways in D. involucrata seeds from six different moist sand stratification durations (0-30 months) using the ultra-high-performance liquid chromatography-Q Exactive Orbitrap-Mass spectrometry. There was an increasing germination rate with prolonged stratification durations (12-30 months). Furthermore, we detected 10,008 metabolites in the stratified seeds. We also detected 48 differentially accumulated metabolites (DAMs) between all stratification periods in the seeds, with 10 highly conserved metabolites. Most of the differentially accumulated metabolites between unstratified and stratified seeds were enriched in purine metabolism, pyrimidine metabolism, flavone and flavonol biosynthesis, phenylpropanoid biosynthesis, and arginine biosynthesis pathways. Key phytohormones, abscisic acid, indole-3 acetic acid, and sinapic acid were differentially accumulated in the seeds and are predicted to regulate dormancy in D. involucrata. We have provided extensive metabolic information useful for future works on dove tree germination study.

Garlic (Allium sativum), an asexually propagated vegetable and medicinal crop, has abundant genetic variation. Genetic diversity evaluation based on molecular markers has apparent advantages since their genomic abundance, environment insensitivity, and non-tissue specific features. However, the limited number of available DNA markers, especially SSR markers, are insufficient to conduct related genetic diversity assessment studies in garlic. In this study, 4372 EST-SSR markers were newly developed, and 12 polymorphic markers together with other 17 garlic SSR markers were used to assess the genetic diversity and population structure of 127 garlic accessions. The averaged polymorphism information content (PIC) of these 29 SSR markers was 0.36, ranging from 0.22 to 0.49. Seventy-nine polymorphic loci were detected among these accessions, with an average of 3.48 polymorphic loci per SSR. Both the clustering analyses based on either the genotype data of SSR markers or the phenotypic data of morphological traits obtained genetic distance divided the 127 garlic accessions into three clusters. Moreover, the Mantel test showed that genetic distance had no significant correlations with geographic distance, and weak correlations were found between genetic distance and the phenotypic traits. AMOVA analysis showed that the main genetic variation of this garlic germplasm collection existed in the within-population or cluster. Results of this study will be of great value for the genetic/breeding studies in garlic and enhance the utilization of these garlic germplasms.

Delimiting species requires multiple sources of evidence. Here, we delimited two varieties of Halenia elliptica (Gentianaceae) using several lines of evidence, including morphological traits and mating system in a sympatric population, phylogenetic relationships based on nrITS and cpDNA (rpl16) data, and complete chloroplast genome sequences. Comparative analysis of 21 morphological traits clearly separates the two varieties of H.?elliptica. Examination of the flowering process and pollination treatments indicate that H.?elliptica var. grandiflora produces seeds via outcrossing, whereas H.?elliptica var. elliptica produces seeds via mixed mating. Furthermore, hand-pollinated hybridization of the two varieties produced no seeds. Observations of pollinators showed that when bees began a pollination bout on H.?elliptica var. grandiflora they preferred to continue pollinating this variety; however, when they began a pollination bout on H.?elliptica var. elliptica, they showed no preference for either variety. Phylogenetic analysis confirmed the monophyly of H.?elliptica, which was further divided into two monophyletic clades corresponding to the two varieties. A large number of variants from the chloroplast genomes reflected remarkable genetic dissimilarities between the two varieties of H.?elliptica. We recommend that the two varieties of H.?elliptica should be revised as two species (H.?elliptica and H. grandiflora). Our findings indicate that H.?elliptica varieties may have split into two separate species due to a shift in mating system, changes in flowering phenology and/or post-pollination reproductive isolation.

Litsea, a non-monophyletic group of the tribe Laureae (Lauraceae), plays important roles in the tropical and subtropical forests of Asia, Australia, Central and North America, and the islands of the Pacific. However, intergeneric relationships between Litsea and Laurus, Lindera, Parasassafras and Sinosassafras of the tribe Laureae remain unresolved. In this study, we present phylogenetic analyses of seven newly sequenced Litsea plastomes, together with 47 Laureae plastomes obtained from public databases, representing six genera of the Laureae. Our results highlight two highly supported monophyletic groups of Litsea taxa. One is composed of 16 Litsea taxa and two Lindera taxa. The 18 plastomes of these taxa were further compared for their gene structure, codon usage, contraction and expansion of inverted repeats, sequence repeats, divergence hotspots, and gene evolution. The complete plastome size of newly sequenced taxa varied between 152,377 bp (Litsea auriculata) and 154,117 bp (Litsea pierrei). Seven of the 16 Litsea plastomes have a pair of insertions in the IRa (trnL-trnH) and IRb (ycf2) regions. The 18 plastomes of Litsea and Lindera taxa exhibit similar gene features, codon usage, oligonucleotide repeats, and inverted repeat dynamics. The codons with the highest frequency among these taxa favored A/T endings and each of these plastomes had nine divergence hotspots, which are located in the same regions. We also identified six protein coding genes (accD, ndhJ, rbcL, rpoC2, ycf1 and ycf2) under positive selection in Litsea; these genes may play important roles in adaptation of Litsea species to various environments.

Larch forests are important for species diversity, as well as soil and water conservation in mountain regions. In this study, we determined large-scale patterns of species richness in larch forests and identified the factors that drive these patterns. We found that larch forest species richness was high in southern China and low in northern China, and that patterns of species richness along an elevational gradient depend on larch forest type. In addition, we found that patterns of species richness in larch forests are best explained by contemporary climatic factors. Specifically, mean annual temperature and annual potential evapotranspiration were the most important factors for species richness of tree and shrub layers, while mean temperature of the coldest quarter and anomaly of annual precipitation from the Last Glacial Maximum to the present were the most important for that of herb layer and the whole community. Community structural factors, especially stand density, are also associated with the species richness of larch forests. Our findings that species richness in China's larch forests is mainly affected by energy availability and cold conditions support the ambient energy hypothesis and the freezing tolerance hypothesis.

Elevation plays a crucial factor in the distribution of plants, as environmental conditions become increasingly harsh at higher elevations. Previous studies have mainly focused on the effects of large-scale elevational gradients on plants, with little attention on the impact of smaller-scale gradients. In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains. We found that the genetic structure (single, clonal, mosaic) of J. squamata shrubs is affected by differences in elevational gradients of only 150 m. Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower- or higher-elevation plots. Human activity can significantly affect genetic structure, as well as reproductive strategy and genetic diversity. Sub-populations at mid-elevations had the highest yield of seed cones, lower levels of asexual reproduction and higher levels of genetic diversity. This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations. Our findings provide new insights into the finer scale genetic structure of alpine shrubs, which may improve the conservation and management of shrublands, a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds. They are an excellent study system for examining whole-genome duplications (WGDs), or polyploidization, in spore-dispersed vascular plants. However, a lack of genome sequence data limits the reliable detection of very ancient WGDs, small-scale duplications (SSDs), and recent WGDs. Here, we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites (Ks) of the transcriptomes of 13 species of lycophytes to identify, locate, and date multiple WGDs in the lycophyte family Lycopodiaceae. Additionally, we examined the genus Phlegmariurus for signs of genetic discordance, which can provide valuable insight into the underlying causes of such conflict (e.g., hybridization, incomplete lineage sorting, or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae, with one occurring in the common ancestor of extant Phlegmariurus (Lycopodiaceae) approximately 22–23 million years ago (Mya) and the other occurring in the common ancestor of Lycopodiaceae around 206–214 Mya. Interestingly, we found significant genetic discordance in the genus Phlegmariurus, indicating that the genus has a complex evolutionary history. This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

Nervonic acid (NA) is a very-long-chain monounsaturated fatty acid with pharmaceutical and nutraceutical functions that plays an important role in treating several neurological disorders. One major source of NA is plant seed oil. Here we report fatty acid profiles of seeds and germplasm diversity of six plant species, including three woody plants with high amounts of NA-enriched seed oil, Malania oleifera, Macaranga adenantha, and M. indica. M. oleifera had the largest seed (average 7.40?g single seed), highest oil content (58.71%), and highest NA level (42.22%). The germplasm diversity of M. oleifera is associated with its habitat but not elevation. Seeds of M. adenantha contained higher NA levels (28.41%) than M.?indica (21.77%), but M.?indica contained a significantly higher oil content (29.22%) and seed yield. M.?adenantha germplasm varied among populations, with one population having seeds with high oil content (22.63%) and NA level (37.78%).Although M.?indica grow naturally at a range of elevations, no significant differences were detected between M.?indica populations. These results suggest that M. indica and M. oleifera have greater potential as a source of NA, which will contribute to constructing a germplasm resource nursery and establishing a selection and breeding program to improve the development of NA-enriched plants.

Orchid diversity provides a unique opportunity to further our understanding of biotic and abiotic factors linked to patterns of richness, endemism, and phylogenetic endemism in many regions. However, orchid diversity is consistently threatened by illegal trade and habitat transformation. Here, we identified areas critical for orchid conservation in the biogeographic province of Megamexico. For this purpose, we evaluated orchid endemism, phylogenetic diversity, and phylogenetic endemism within Megamexico and characterized orchid life forms. Our results indicate that the majority of the regions with the highest estimates of endemism and phylogenetic endemism are in southern Mexico and northern Central America, mostly located on the Pacific side of Megamexico. Among the most important orchid lineages, several belong to epiphytic lineages such as Pleurothallidinae, Laeliinae and Oncidiinae. We also found that species from diverse and distantly related lineages converge in montane forests where suitable substrates for epiphytes abound. Furthermore, the southernmost areas of phylogenetic diversity and endemism of Megamexico are in unprotected areas. Thus, we conclude that the most critical areas for orchid conservation in Megamexico are located in southern Mexico and northern Central America. We recommend that these areas should be given priority by the Mexican system of natural protected areas as complementary conservation areas.

The synthesis of evolutionary biology and community ecology aims to understand how genetic variation within one species can shape community properties and how the ecological properties of a community can drive the evolution of a species. A rarely explored aspect is whether the interaction of genetic variation and community properties depends on the species' ecological role. Here we investigated the interactions among environmental factors, species diversity, and the within-species genetic diversity of species with different ecological roles. Using high-throughput DNA sequencing, we genotyped a canopy-dominant tree species, Parashorea chinensis, and an understory-abundant species, Pittosporopsis kerrii, from fifteen plots in Xishuangbanna tropical seasonal rainforest and estimated their adaptive, neutral and total genetic diversity; we also surveyed species diversity and assayed key soil nutrients. Structural equation modelling revealed that soil nitrogen availability created an opposing effect in species diversity and adaptive genetic diversity of the canopy-dominant Pa. chinensis. The increased adaptive genetic diversity of Pa. chinensis led to greater species diversity by promoting co-existence. Increased species diversity reduced the adaptive genetic diversity of the dominant understory species, Pi. kerrii, which was promoted by the adaptive genetic diversity of the canopy-dominant Pa. chinensis. However, such relationships were absent when neutral genetic diversity or total genetic diversity were used in the model. Our results demonstrated the important ecological interaction between adaptive genetic diversity and species diversity, but the pattern of the interaction depends on the identity of the species. Our results highlight the significant ecological role of dominant species in competitive interactions and regulation of community structure.

Understanding the influence of environmental covariates on plant distribution is critical, especially for aquatic plant species. Climate change is likely to alter the distribution of aquatic species. However, knowledge of this change on the burden of aquatic macroorganisms is often fraught with difficulty. Ottelia, a model genus for studying the evolution of the aquatic family Hydrocharitaceae, is mainly distributed in slow-flowing creeks, rivers, or lakes throughout pantropical regions in the world. Due to recent rapid climate changes, natural Ottelia populations have declined significantly. By modeling the effects of climate change on the distribution of Ottelia species and assessing the degree of niche similarity, we sought to identify high suitability regions and help formulate conservation strategies. The models use known background points to determine how environmental covariates vary spatially and produce continental maps of the distribution of the Ottelia species in Africa. Additionally, we estimated the possible influences of the optimistic and extreme pessimistic representative concentration pathways scenarios RCP 4.5 and RCP 8.5 for the 2050s. Our results show that the distinct distribution patterns of studied Ottelia species were influenced by topography (elevation) and climate (e.g., mean temperature of driest quarter, annual precipitation, and precipitation of the driest month). While there is a lack of accord in defining the limiting factors for the distribution of Ottelia species, it is clear that water-temperature conditions have promising effects when kept within optimal ranges. We also note that climate change will impact Ottelia by accelerating fragmentation and habitat loss. The assessment of niche overlap revealed that Ottelia cylindrica and O. verdickii had slightly more similar niches than the other Ottelia species. The present findings identify the need to enhance conservation efforts to safeguard natural Ottelia populations and provide a theoretical basis for the distribution of various Ottelia species in Africa.

Wintergreen oil is a folk medicine widely used in foods, pesticides, cosmetics and drugs. In China, nine out of 47 species within Gaultheria (Ericaceae) are traditionally used as Chinese medicinal wintergreens; however, phylogenetic approaches currently used to discriminating these species remain unsatisfactory. In this study, we sequenced and characterized plastomes from nine Chinese wintergreen species and identified candidate DNA barcoding regions for Gaultheria. Each Gaultheria plastome contained 110 unique genes (76 protein-coding, 30 tRNA, and four rRNA genes). Duplication of trnfM, rps14, and rpl23 genes were detected, while all plastomes lacked ycf1 and ycf2 genes. Gaultheria plastomes shared substantially contracted SSC regions that contained only the ndhF gene. Moreover, plastomes of Gaultheria leucocarpa var. yunnanensis contained an inversion in the LSC region and an IR expansion to cover the ndhF gene. Multiple rearrangement events apparently occurred between the Gaultheria plastomes and those from several previously reported families in Ericales. Our phylogenetic reconstruction using 42 plastomes revealed well-supported relationships within all nine Gaultheria species. Additionally, seven mutational hotspot regions were identified as potential DNA barcodes for Chinese medicinal wintergreens. Our study is the first to generate complete plastomes and describe the structural variations of the complicated genus Gaultheria. In addition, our findings provide important resources for identification of Chinese medicinal wintergreens.

The survival rate of Castanopsis kawakamii from seed to seedling is relatively low, leading to difficulties in the regeneration of its natural forests. Forest gaps play a vital role in plant regeneration and biodiversity maintenance in forest ecosystems. Unfortunately, our understanding of the effects of gap size and within-gap position on the seed germination and radicle growth of C.kawakamii is still limited. In particular, our knowledge on the relationship between gap size and environmental factors and their influence on seed germination and radicle growth is incomplete. In the present study, we studied the influences of forest gaps and within-gap position on seed regeneration on the germination and radicle growth of an endangered species C.kawakamii in a subtropical natural forest in China. We selected three large gaps (LG, gap size above 200m²), three medium gaps (MG, gap size 50–100m²), three small gaps (SG, gap size 30–50m²), and non-gap (NG), and planted the seeds of C.kawakamii in five positions within each gap. The results showed that (1) the influence of forest gaps on seed germination rate was, from highest to lowest, medium gaps (51%), non-gap (47%), small gaps (40%) and large gaps (17%), and the seed germination rate was the highest in all positions in medium gaps, with the exception of the east position. (2) Radicle length in forest gaps was, from highest to lowest, medium gaps, small gaps, large gaps and non-gap, and it was the highest in the east, south, west and north positions of medium gaps. (3) Canopy openness (gap size) and air temperature were the main factors influencing seed germination and radicle growth of C.kawakamii. We concluded that medium-sized gaps were the most suitable for seed germination and radicle growth of C.kawakamii, and they promote the regeneration of this endangered species in the investigated natural forest.

Predicting species abundance is one of the most fundamental pursuits of ecology. Combining the information encoded in functional traits and metacommunities provides a new perspective to predict the abundance of species in communities. We applied a community assembly via trait selection model to predict quadrat-scale species abundances using functional trait variation on ontogenetic stages and metacommunity information for over 490 plant species in a subtropical forest and a lowland tropical forest in Yunnan, China. The relative importance of trait-based selection, mass effects, and stochasticity in shaping local species abundances is evaluated using different null models. We found both mass effects and trait selection contribute to local abundance patterns. Trait selection was detectable at all studied spatial scales (0.04-1 ha), with its strength stronger at larger scales and in the subtropical forest. In contrast, the importance of stochasticity decreased with spatial scale. A significant mass effect of the metacommunity was observed at small spatial scales. Our results indicate that tree community assembly is primarily driven by ontogenetic traits and metacommunity effects. Our findings also demonstrate that including ontogenetic trait variation into predictive frameworks allows ecologists to infer ecological mechanisms operating in community assembly at the individual level.

In the state Meghalaya, northeast India, >80% of the forest lands are owned by local communities and managed by traditional institutions. These forests are under severe threats due to a number of human disturbances. The present study was conducted to assess the plant diversity and identify the community forests for priority conservation in Khasi Hills of Meghalaya. Floristic explorations carried out in the 87 forests reveals the presence of 1300 plant species of which 400 are either rare, endemic or threatened. Of the different forest categories, reserve forests had the highest number of species (1190), followed by sacred forests (987 species) and village forests (786 species). Majority of the forests (56) had high-species richness, irreplaceability level (42 forests) and vulnerability level (54). In terms of area, 13.8% (1666.8?ha) fall under low risk while 1855?ha under high risk zone. High risk zone was mostly represented by village forests. An area of 7661.56?ha of community forests falls under high priority category and hence calls for immediate conservation actions. The conservation priority map generated in the present study will help to concentrate the protection strategy to the demarcated and adjoining areas and help conservationists and planners to evolve effective strategies for conservation of the community forests.

Recent paleobotanical investigations in Vietnam provide a good opportunity to improve our understanding of the biodiversity and paleoclimatic conditions in the geological past of Southeast Asia. Palms (Arecaceae) are a diverse family of typical thermophilous plants with a relatively low tolerance for freezing. In this study, we describe well-preserved fossil palm leaves from the Oligocene Dong Ho Formation of Hoanh Bo Basin, northern Vietnam. Characters of the fossil leaves, such as a fan-shaped costapalmate lamina, an unarmed petiole, a costa slightly enlarged at the base that then tapers distally into the blade, and well-preserved amphistomatic leaves with cuticles, suggest that they represent a new fossil species, which we herein designate Sabalites colaniae A. Song, T. Su, T. V. Do et Z.K. Zhou sp. nov. Together with other paleontological and palaeoclimatic evidence, we conclude that a warm climate prevailed in northern Vietnam and nearby areas during the Oligocene.

Walnuts are highly valued for their rich nutritional profile and wide medicinal applications. This demand has led to the intensification of breeding activities in major walnut production areas such as southwest China, in order to develop more superior cultivars. With the increasing number of cultivars, accurate identification becomes fundamental to selecting the right cultivar for grafting, industrial processing or development of new cultivars. To ensure proper identification of cultivars and understand the genetic structure of wild and cultivated material, we genotyped 362 cultivated and wild individuals of walnut trees from southwest China (with two additional populations from Xinjiang, plus three cultivars from Canada, France and Belgium) using 36 polymorphic microsatellite loci. We found relatively low indices of genetic diversity (H_O?=?0.570, H_E?=?0.404, N_A?=?2.345) as well as a high level of clonality (>85% of cultivars), indicating reliance on genetically narrow sources of parental material for breeding. Our STRUCTURE and PCoA analyses generally delineated the two species, though considerable levels of introgression were also evident. More significantly, we detected a distinct genetic group of cultivated Juglans sigillata, which mainly comprised individuals of the popular ‘Yangbidapao’ landrace. Finally, a core set of 18 SSR loci was selected, which was capable of identifying 32 cultivars. In a nutshell, our results call for more utilization of genetically disparate material, including wild walnut trees, as parental sources to breed for more cultivars. The data reported herein will significantly contribute towards the genetic improvement and conservation of the walnut germplasm in southwest China.

Recent sequencing efforts have broadly uncovered the evolutionary trajectory of plastid genomes (plastomes) of flowering plants in diverse habitats, yet our knowledge of the evolution of plastid posttranscriptional modifications is limited. In this study, we generated 11 complete plastomes and performed ultra-deep transcriptome sequencing to investigate the co-evolution of plastid RNA editing and genetic variation in Cymbidium, a genus with diverse trophic lifestyles. Genome size and gene content is reduced in terrestrial and green mycoheterotrophic orchids relative to their epiphytic relatives. This could be partly due to extensive losses and pseudogenization of ndh genes for the plastid NADH dehydrogenase-like complex, but independent pseudogenization of ndh genes has also occurred in the epiphyte C.?mannii, which was reported to use strong crassulacean acid metabolism photosynthesis. RNA editing sites are abundant but variable in number among Cymbidium plastomes. The nearly twofold variation in editing abundance is mainly due to extensive reduction of ancestral editing sites in ndh transcripts of terrestrial, mycoheterotrophic, and C.?mannii plastomes. The co-occurrence of editing reduction and pseudogenization in ndh genes suggests functional constraints on editing machinery may be relaxed, leading to nonrandom loss of ancestral edited sites via reduced editing efficiency. This study represents the first systematic examination of RNA editing evolution linked to plastid genome variation in a single genus. We also propose an explanation for how genomic and posttranscriptional variations might be affected by lifestyle-associated ecological adaptation strategies in Cymbidium.

Polyploids contribute substantially to plant evolution and biodiversity; however, the mechanisms by which they succeed are still unclear. According to the polyploid adaptation hypothesis, successful polyploids spread by repeated adaptive responses to new environments. Here, we tested this hypothesis using two tetraploid yellowcresses (Rorippa), the endemic Rorippa elata and the widespread Rorippa palustris, in the temperate biodiversity hotspot of the Hengduan Mountains. Speciation modes were resolved by phylogenetic modeling using 12 low-copy nuclear loci. Phylogeographical patterns were then examined using haplotypes phased from four plastid and ITS markers, coupled with historical niche reconstruction by ecological niche modeling. We inferred the time of hybrid origins for both species as the mid-Pleistocene, with shared glacial refugia within the southern Hengduan Mountains. Phylogeographic and ecological niche reconstruction indicated recurrent northward colonization by both species after speciation, possibly tracking denuded habitats created by glacial retreat during interglacial periods. Common garden experiment involving perennial R.elata conducted over two years revealed significant changes in fitness-related traits across source latitudes or altitudes, including latitudinal increases in survival rate and compactness of plant architecture, suggesting gradual adaptation during range expansion. These findings support the polyploid adaptation hypothesis and suggest that the spread of polyploids was aided by adaptive responses to environmental changes during the Pleistocene. Our results thus provide insight into the evolutionary success of polyploids in high-altitude environments.

Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi?>?0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies.

Assessing rangeland productivity is critical to reduce ecological degradation and promote sustainable livestock management. Here, we estimated biomass productivity and carrying capacity dynamics in the Borana rangeland of southern Ethiopia by using field-based data and remote sensing data (i.e., normalized difference vegetation index (NDVI)). Data was collected from both rainy and dry seasons when biomass production was high and low respectively. Results of linear regression showed that both biomass production (R²_adj?=?0.672) and NDVI value (R²_adj?=?0.471) were significantly decreased from 1990 to 2019. Field data and NDVI values for mean annual biomass showed a significant linear relationship. The model accuracy in the annual relationship between the observed and predicted biomass values was strong (R²_adj?=?0.986) but with high standard error, indicating that the observed biomass production in the rangeland area was not in good condition as compared with the predicted one. This study suggests that, using NDVI data and field-based data in combined way has high potential to estimate rangeland biomass and carrying capacity dynamics at extensively grazed arid and semi-arid rangelands. And to use for estimating stoking rates and predicting future management techniques for decision making.

Engelhardia, a genus of Juglandaceae (the walnut family), is endemic to tropical and subtropical Asia. The rich Cenozoic fossil records and distinctive morphological characters of the living plants have been used to explore the evolutionary history and geographic distribution of Juglandaceae. However, the taxonomy of this genus has been suffered from a lack of in-depth investigation and good specimens across its distribution ranges. Species delimitation of Engelhardia was defined with seven species in 2020, but detailed information on the circumscription of the species still remains poorly understood. In this study, two new species are described from Sulawesi and Borneo, Engelhardia anminiana and E.?borneensis. We also revised and reconstructed the phylogeny within Engelhardia using morphological, molecular (plastid and ribosomal), and distribution data. We sampled 787 individuals in 80 populations, and all the samples were genotyped using plastid regions, trnS-trnG, rps16, trnL-trnF, psbA-trnH, and rpl32-trnL; one ribosomal region, nuclear ribosomal internal transcribed spacer (nrITS). The all datasets were used to reconstruct the phylogenetic relationships. Then, the molecular analyses were combined for 738 sheets of specimens with 15 morphological characteristics to further explore the morphological clusters of Engelhardia. Cluster analysis using morphological data confirmed the delimitation of nine Engelhardia species. Also, phylogenetic analysis based on molecular data (i.e., plastid and ribosomal) supported the monophyly of Engelhardia and generated phylogenetic trees that included E.?fenzelii, E.?roxburghiana, E.?borneensis, E.?hainanensis, E.?anminiana, E.?serrata, E.?villosa, E.?apoensis and the varieties of E.?spicata (i.e., E.?spicata var. spicata, E.?spicata var. rigida, E.?spicata var. aceriflora, and E.?spicata var. colebrookeana). Our comprehensive taxonomic revision of Engelhardia will provide an insight into understanding the plant diversity in tropical and subtropical Asia.

Invasive species have profound negative impacts on native ranges. Unraveling the mechanisms employed by invasive plant species is crucial to controlling invasions. One important approach that invasive plants use to outcompete native plants is to disrupt mutualistic interactions between native roots and mycorrhizal fungi. However, it remains unclear how differences in the competitive ability of invasive plants affect native plant associations with mycorrhizae. Here, we examined how a native plant, Xanthium strumarium, responds to invasive plants that differed in competitive abilities (i.e., as represented by aboveground plant biomass) by measuring changes in root nitrogen concentration (root nutrient acquisition) and mycorrhizal colonization rate. We found that both root nitrogen concentration and mycorrhizal colonization rate in the native plant were reduced by invasive plants. The change in mycorrhizal colonization rate of the native plant was negatively correlated with both aboveground plant biomass of the invasive plants and the change in aboveground plant biomass of the native plant in monocultures relative to mixed plantings. In contrast, the change in root nitrogen concentration of the native plant was positively correlated with aboveground plant biomass of the invasive plants and the change in aboveground plant biomass of the native plant. When we compared the changes in mycorrhizal colonization rate and root nitrogen concentration in the native plant grown in monocultures with those of native plants grown with invasive plants, we observed a significant tradeoff. Our study shows that invasive plants can suppress native plants by reducing root nutrient acquisition rather than by disrupting symbiotic mycorrhizal associations, a novel finding likely attributable to a low dependence of the native plant on mycorrhizal fungi.

The processability and ultimate quality of coffee (Coffea?arabica) are determined by the composition of the matured fruits. The basis of genetic variation in coffee fruit quality could be explained by studying color formation during fruit maturation. Transcriptome profiling was conducted on matured fruits of four C.?arabica varieties (orange colored fruits (ORF); purple colored fruits (PF); red colored fruits (RF) and yellow colored fruits (YF)) to identify key color-regulating genes, biosynthesis pathways and transcription factors implicated in fruit color formation. A total of 39,938 genes were identified in the transcriptomes of the four C.?arabica varieties. In all, 2745, 781 and 1224 differentially expressed genes (DEGs) were detected in YF_vs_PF, YF_vs_RF and YF_vs_ORF, respectively, with 1732 DEGs conserved among the three pairwise groups. Functional annotation of the DEGs led to the detection of 28 and 82 key genes involved in the biosynthesis of carotenoids and anthocyanins, respectively. Key transcription factors bHLH, MYB, NAC, MADS, and WRKY implicated in fruit color regulation were detected. The high expression levels of gene-LOC113688784 (PSY), gene-LOC113730013 (β-CHY), gene-LOC113728842 (CCD7), gene-LOC113689681 (NCED) and gene-LOC113729473 (ABA2) in YF may have accounted for the yellow coloration. The differential expression of several anthocyanin and carotenoid-specific genes in the fruits substantially account for the purple (PF), red (RF), and orange (ORF) colorations. This study provides important insights into fruit color formation and variations in C.?arabica and will help to develop coffee varieties with specific color and quality traits.

A molecular cytogenetic investigation was conducted on plants of the allohexaploid species Elymus nutans with varying fertility on the Qinghai-Tibet Plateau. Molecular karyotyping revealed that chromosome variants were distributed unevenly among genomes and among different homologue chromosomes in each genome. The plants with varying fertility exhibited significantly higher numbers of chromosome variants than did the normal fertility samples, although both kinds of plants showed the same pattern of high-to-low polymorphism from the Y to St and H genomes. Heterozygosis and karyotype heterozygosity in the plants with varying fertility were 3- and 13-fold higher than those in normal samples, respectively. Significant negative correlations were found not only between seed setting rates and total genome heterozygosity but also between seed setting rates and heterozygosity of each genome in the plants of varying fertility. Chromosome pairing analysis was performed using genomic in situ hybridization in selected plants of different fertility levels. The pairing of chromosomes at meiotic metaphase I was mostly bivalent, although univalent, trivalent, quadrivalent, and other polyvalents also occurred; in addition, chromosome configuration forms and frequencies varied among the studied samples. ANOVA results showed that the average number of ring bivalents in the Y genome was significantly higher than those in the St and H genomes. Significant positive correlations between pollen grain fertility and ring bivalent number were found in the St and H genomes but not in the Y genome. Furthermore, chromosome configuration parameters (total bivalents, numbers of ring and rod bivalents) were found to be significantly correlated with heterozygosity and seed setting rates in the St and H genomes, respectively, but not in the Y genome. It was inferred that the seed setting rate and pollen grain fertility in E.?nutans are strongly influenced by the heterozygosity of each genome, but the Y genome differs from the St and H genomes due to chromosome pair alterations. The St and H genomes may contain more chromosome structural variations than the Y genome in E.?nutans.

For plant populations to persist, seedling recruitment is essential, requiring seed germination, seedling survival and growth. Drought and grazing potentially reduce seedling recruitment via increased mortality and reduced growth. We studied these seed–related processes for two species indigenous to the Pamir Mountains of Xinjiang in northwestern China: Saussurea glacialis and Plantago lessingii. Seeds collected from Taxkorgan, Xinjiang, had a viability rate of 15.8% for S.?glacialis but 100% for P.?lessingii. Of the viable seeds, the highest germination rates were 62.9% for S.?glacialis and 45.6% for P.?lessingii. In a greenhouse experiment, we imposed a series of stressful conditions, involving a combination of simulated grazing and drought events. These had the most severe impact on younger seedlings. Modelling showed that 89% of S.?glacialis mortality was due to early simulated grazing, whereas 80% of P.?lessingii mortality was due to early simulated drought. Physiological differences could contribute to their differing resilience. S.?glacialis may rely on water storage in leaves to survive drought events, but showed no shifts in biomass allocation that would improve grazing tolerance. P.?lessingii appears more reliant on its root system to survive grazing, but the root reserves of younger plants could be insufficient to grow deeper in response to drought. After applying all mortality factors, 17.7 seedlings/parent of P.?lessingii survived, while only <0.1 seedlings/parent of S.?glacialis survived, raising concerns for its capacity to persist in the Pamirs. Inherent genetic differences may underlie the two species’ contrasting grazing and drought responses. Thus, differing conservation strategies are required for their utilization and protection.

The genus Trigonotis comprises nearly 60 species mainly distributed in East and Southeast Asia. China has the largest number of Trigonotis species in the world, with a total of 44 species, of which 38 are endemic. Nutlet morphology is useful for the taxonomic delimitation of Trigonotis. However, there are still controversial circumscriptions of nutlet shape in some species. In previous studies, interspecies phylogenetic relationships were inferred using few DNA markers and very few taxa, which possibly led to erroneous or incomplete conclusions. In this study, the nutlet morphology of 39 Trigonotis taxa and the characteristics of 34 complete chloroplast genomes (29 taxa) were investigated and analyzed. Then, the phylogenetic relationships were discussed within this genus based on complete chloroplast genomes. To the best of our knowledge, this study is the first comprehensive analysis of nutlet morphology and complete chloroplast genome of Trigonotis. Based on nutlet morphology, Trigonotis can be divided into two groups: Group 1, hemispherical or oblique tetrahedron with carpopodiums, and Group 2, inverted tetrahedron without carpopodiums. The chloroplast genome of Trigonotis exhibited a typical quadripartite structure, including 84–86 protein-coding, 37 transfer RNA, and 8 ribosomal RNA genes, with a total length of 147,247–148,986 bp. Genes in the junctions were well conserved in Trigonotis, similar to those in other Boraginaceae s.str. species. Furthermore, Trigonotis chloroplast genomes showed relatively high diversity, with more conserved genic regions than intergenic regions; in addition, we detected 14 hot spots (Pi > 0.005) in non-coding regions. Phylogenetic analyses based on chloroplast genome data identified highly resolved relationships between Trigonotis species. Specifically, Trigonotis was divided into two clades with strong support: one clade included species with hemispherical or oblique tetrahedron nutlets with carpopodiums and bracts, whereas the other clade included species with inverted tetrahedron nutlets without carpopodiums or bracts. Our results may inform future taxonomic, phylogenetic, and evolutionary studies on Boraginaceae.

China covers a vast territory harbouring a large number of aquatic plants. Although there are many studies on the β-diversity of total, herbaceous or woody plants in China and elsewhere, few studies have focused on aquatic plants. Here, we analyse a comprehensive data set of 889 aquatic angiosperm species in China, and explore the geographic patterns and climatic correlates of total taxonomic and phylogenetic β-diversity as well as their turnover and nestedness components. Our results show that geographic patterns of taxonomic and phylogenetic β-diversity are highly congruent for aquatic angiosperms, and taxonomic β-diversity is consistently higher than phylogenetic β-diversity. The ratio between the nestedness component and total β-diversity is high in northwestern China and low in southeastern China. The geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms in China are obviously affected by geographic and climatic distances, respectively. In conclusion, the geographic patterns of taxonomic and phylogenetic β-diversity of aquatic angiosperms are consistent across China. Climatic and geographic distances jointly affect the geographic patterns of β-diversity of aquatic angiosperms. Overall, our work provides insight into understanding the large-scale patterns of aquatic angiosperm β-diversity, and is a critical addition to previous studies on the macroecological patterns of terrestrial organisms.

This study aims to identify medicinal plants traditionally used to treat diseases by local people living in Güce district, north-eastern Turkey. The study was carried out between 2018 and 2021 using a two-part semi-structured, open-ended questionnaire with 165 local people. Data were analysed using use-report, frequency of citation, and informant consensus factor. Informants identified 128 vascular medicinal plant taxa belonging to 54 families and 106 genera. The most common plant taxa belong to Rosaceae (16 taxa/12.5%), Asteraceae (12 taxa/9.4%), and Lamiaceae (9 taxa/7%) families. The most frequently used preparation method reported was decoction (39.8%); the most commonly utilized plant parts were leaves (40.3%). Statistical analysis reveals that women in Güce district (df?=?163, p?=?0.043?<?0.05) possess the most traditional knowledge. The highest frequency of citation (61) and use report (92) were recorded for Tilia rubra subsp. caucasica, and the highest informant consensus factors were cited for respiratory system disorders (0.86), digestive system disorders (0.73), and skin disorders (0.71). This study reported nine plant taxa as medicinal plants for the first time, and documented a total of 293 new therapeutic uses. However, the study indicates that the transfer of traditional knowledge to future generations is limited (F?=?3.355, p?=?0.020). Action should be taken as soon as possible to preserve existing traditional knowledge and to ensure its transfer to future generations.

Relationships between genome size and environmental variables suggest that DNA content might be adaptive and of evolutionary importance in plants. The genus Larrea provides an interesting system to test this hypothesis, since it shows both intra- and interspecific variation in genome size. Larrea has an amphitropical distribution in North and South American deserts, where it is most speciose. Larrea tridentata in North America shows a gradient of increasing autopolyploidy; while three of the four studied South American species are diploids, Larrea divaricata, Larrea nitida, Larrea ameghinoi, and the fourth is an allopolyploid, Larrea cuneifolia. We downloaded available focal species’ georeferenced records from seven data reservoirs. We used these records to extract biologically relevant environmental variables from WorldClim at 30 arcseconds scale, to have a broad characterization of the variable climatic conditions of both regions, and a climatic envelope for each species. We estimated relative DNA content index and relative monoploid genome values, by flow cytometry, of four most abundant Larrea species throughout their respective ranges. Then we winnow the bioclimatic dataset down to uncorrelated variables and sampled locales, to analyse the degree of association between both intra- and interspecific relative DNA content and climatic variables that are functionally relevant in arid environments using Pearson correlations, general linear and mixed effects models. Within the genus Larrea, relative DNA content increases with rising temperature and decreases with rising precipitation. At the intraspecific level, all four species show relative DNA content variation across climatic conditions. Larrea is a genus that shows genome size variation correlated with climate. Our results are also consistent with the hypothesis that extreme environmental pressures may have facilitated repeated whole genome duplication events in North America, while in South America, reticulate evolution, as allopolyploidization, and speciation might have been climate-dependent since the Oligocene.

Selaginella is the largest and most taxonomically complex genus in lycophytes. The fact that over 750 species are currently treated in a single genus makes Selaginellales/Selaginellaceae unique in pteridophytes. Here we assembled a dataset of six existing and newly sampled plastid and nuclear loci with a total of 684 accessions (74% increase of the earlier largest sampling) representing ca. 300 species to infer a new phylogeny. The evolution of 10 morphological characters is studied in the new phylogenetic context. Our major results include: (1) the nuclear and plastid phylogenies are congruent with each other and combined analysis well resolved and strongly supported the relationships of all but two major clades; (2) the Sinensis group is resolved as sister to S. subg. Pulviniella with strong support in two of the three analyses; (3) most morphological characters are highly homoplasious but some characters alone or combinations of characters well define the major clades in the family; and (4) an infrafamilial classification of Selaginellaceae is proposed and the currently defined Selaginella s.l. is split into seven subfamilies (corresponding to the current six subgenera + the Sinensis group) and 19 genera (the major diagnosable clades) with nine new species-poor genera. We support the conservation of Selaginella with a new type, S. flabellata, to minimize nomenclatural instability. We provide a key to subfamilies and genera, images illustrating their morphology, their morphological and geographical synopses, a list of constituent species, and necessary new combinations. This new classification will hopefully facilitate communication, promote further studies, and help conservation.

The cortex (i.e., absorptive tissue) and stele (transportive vascular tissue) are fundamental to the function of plant roots. Unraveling how these anatomical structures are assembled in absorptive roots is essential for our understanding of plant ecology, physiology, and plant responses to global environmental changes. In this review, we first compile a large data set on anatomical traits in absorptive roots, including cortex thickness and stele radius, across 698 observations and 512 species. Using this data set, we reveal a common root allometry in absorptive root structures, i.e., cortex thickness increases much faster than stele radius with increasing root diameter (hereafter, root allometry). Root allometry is further validated within and across plant growth forms (woody, grass, and liana species), mycorrhiza types (arbuscular mycorrhiza, ectomycorrhiza, and orchid mycorrhizas), phylogenetic gradients (from ferns to Orchidaceae), and environmental change scenarios (e.g., elevation of atmospheric CO₂ concentration and nitrogen fertilization). These findings indicate that root allometry is common in plants. Importantly, root allometry varies greatly across species. We then summarize recent research on the mechanisms of root allometry and potential issues regarding these mechanisms. We further discuss ecological and evolutionary implications of root allometry. Finally, we propose several important research directions that should be pursued regarding root allometry.

Prunus is an economically important genus widely distributed in the temperate Northern Hemisphere. Previous studies on the genus using a variety of loci yielded conflicting phylogenetic hypotheses. Here, we generated nuclear reduced representation sequencing data and plastid genomes for 36 Prunus individuals and two outgroups. Both nuclear and plastome data recovered a well-resolved phylogeny. The species were divided into three main clades corresponding to their inflorescence types, - the racemose group, the solitary-flower group and the corymbose group - with the latter two sister to one another. Prunus was inferred to have diversified initially in the Late Cretaceous around 67.32 million years ago. The diversification of the three major clades began between the Paleocene and Miocene, suggesting that paleoclimatic events were an important driving force for Prunus diversification. Ancestral state reconstructions revealed that the most recent common ancestor of Prunus had racemose inflorescences, and the solitary-flower and corymb inflorescence types were derived by reduction of flower number and suppression of the rachis, respectively. We also tested the hybrid origin hypothesis of the racemose group proposed in previous studies. Prunus has undergone extensive hybridization events, although it is difficult to identify conclusively specific instances of hybridization when using SNP data, especially deep in the phylogeny. Our study provides well-resolved nuclear and plastid phylogenies of Prunus, reveals substantial cytonuclear discord at shallow scales, and sheds new light on inflorescence evolution in this economically important lineage.

Three woody bamboo species collected in Hainan, China in 1940 have been described as Dinochloa based on vegetative specimens. However, the identity of these species has long been in doubt, largely because the vegetative phase in species of Dinochloa is morphologically similar to that in species of Melocalamus, a climbing or scrambling bamboo genus of the paleotropical woody bamboos (Poaceae: Bambusoideae) that consists of about 15 species and one variety. To determine the phylogenetic affinity of the three Dinochloa species from Hainan, we sampled almost all recognized Chinese species of Melocalamus and representative species of Dinochloa as well as other closely related genera, performed molecular phylogenetic analysis, and compared their morphology based on herbarium and fieldwork investigation. Our ddRAD data indicate that the three species from Hainan are closely related to Melocalamus, not Dinochloa. Morphological analysis showed that these three species have a climbing habit but do not grow spirally, their culm leaves have smooth bases, and there is a ring of powder and/or tomenta above and below the nodes. Taken together our findings indicate that the three species from Hainan originally published in Dinochloa should be transferred to Melocalamus, i.e., Melocalamus orenudus (McClure) D.Z. Li & J.X. Liu, Melocalamus puberulus (McClure) D.Z. Li & J.X. Liu, and Melocalamus utilis (McClure) D.Z. Li & J.X. Liu, respectively. This study concludes with an enumeration of Chinese species of Melocalamus, with a key to nine recognized species and one variety, and a lectotypification for M.compatiflorus.

Fargesia, the largest genus within the temperate bamboo tribe Arundinarieae, has more than 90 species mainly distributed in the mountains of Southwest China. The Fargesia bamboos are important components of the subalpine forest ecosystems that provide food and habitat for many endangered animals, including the giant panda. However, species-level identification of Fargesia is difficult. Moreover, the rapid radiation and slow molecular evolutionary rate of Fargesia pose a significant challenge to using DNA barcoding with standard plant barcodes (rbcL, matK, and ITS) in bamboos. With progress in the sequencing technologies, complete plastid genomes (plastomes) and nuclear ribosomal DNA (nrDNA) sequences have been proposed as organelle barcodes for species identification; however, these have not been tested in bamboos. We collected 196 individuals representing 62 species of Fargesia to comprehensively evaluate the discriminatory power of plastomes and nrDNA sequences compared to standard barcodes. Our analysis indicates that complete plastomes have substantially higher discriminatory power (28.6%) than standard barcodes (5.7%), whereas nrDNA sequences show a moderate improvement (65.4%) compared to ITS (47.2%). We also found that nuclear markers performed better than plastid markers, and ITS alone had higher discriminatory power than complete plastomes. The study also demonstrated that plastomes and nrDNA sequences can contribute to intrageneric phylogenetic resolution in Fargesia. However, neither of these sequences were able to discriminate all the sampled species, and therefore, more nuclear markers need to be identified.

The Hickeliinae (Poaceae: Bambusoideae) is an ecologically and economically significant subtribe of tropical bamboos restricted to Madagascar, Comoros, Reunion Island, and a small part of continental Africa (Tanzania). Because these bamboos rarely flower, field identification is challenging, and inferring the evolutionary history of Hickeliinae from herbarium specimens is even more so. Molecular phylogenetic work is critical to understanding this group of bamboos. Here, comparative analysis of 22 newly sequenced plastid genomes showed that members of all genera of Hickeliinae share evolutionarily conserved plastome structures. We also determined that Hickeliinae plastome sequences are informative for phylogenetic reconstructions. Phylogenetic analysis showed that all genera of Hickeliinae are monophyletic, except for Nastus, which is paraphyletic and forms two distant clades. The type species of Nastus (Clade II) is endemic to Reunion Island and is not closely related to other sampled species of Nastus endemic to Madagascar (Clade VI). Clade VI (Malagasy Nastus) is sister to the Sokinochloa + Hitchcockella clade (Clade V), and both clades have a clumping habit with short-necked pachymorph rhizomes. The monotypic Decaryochloa is remarkable in having the longest floret in Bambuseae and forms a distinct Clade IV. Clade III, which has the highest generic diversity, consists of Cathariostachys, Perrierbambus, Sirochloa, and Valiha, which are also morphologically diverse. This work provides significant resources for further genetic and phylogenomic studies of Hickeliinae, an understudied subtribe of bamboo.

Two new species of Polyalthiopsis (Annonaceae), P.nigra Y.H. Tan & Bin Yang from Guangxi and Yunnan Provinces and P.xui Y.H. Tan & Bin Yang from Yunnan Province, are described and illustrated. P.nigra is morphologically similar to P.chinensis in having narrowly elliptic-oblong, lemon to yellowish green petals, but differs by having obovoid monocarps, a higher number of leaf secondary veins, leaf blades usually widest above the middle, and a lower ratio of leaf blade length to width. P.xui is morphologically similar to P.floribunda in having axillary inflorescences, 1-3(-4) flowers, elliptic leaves, and elliptic-ovate petals, but differs in the numbers of carpels per flower and ovules per carpel. The molecular phylogenetic analysis using five plastid markers confirm that the two new species belong to the genus Polyalthiopsis and show clear interspecific divergences between P.nigra and P.xui and between them and other species in the genus. Detailed descriptions, colored photographs, and habitat and distribution data for the two new species are provided. In addition, the fruit morphology of P.chinensis is described for the first time, based on living collections. Geographical distributions and a diagnostic key for all Polyalthiopsis species are also presented.