Bryophytes, a monophyletic group comprising three major lineages, diversified soon after the terrestrialization of land plants. However, their internal phylogenetic relationships remain controversial. In this study, we reconstructed the ordinal and familial phylogeny of bryophytes using the largest plastid data set to date, including 549 taxa that represent almost all known orders and two-thirds of families. The strongly supported phylogenetic inference enabled us to propose in mosses seven newly segregated families, that is, Baldwiniellaceae, Calyptrochaetaceae, Ctenidiaceae, Herpetineuraceae, Isodrepaniaceae, Pseudotaxiphyllaceae, and Rozeaceae, and one reduced family, that is, Climaciaceae. We also transferred the liverwort family Calyculariaceae from Fossombroniales to Pelliales. Recent advancements in molecular phylogeny have revolutionized bryophyte classification, tending to be more fragmental. Hence, we further propose a revised familial classification system for bryophytes that includes 45 orders and 142 families in mosses, 23 orders and 85 families in liverworts, and five orders and five families in hornworts.

Hainan Island has the most extensive and well-preserved tropical forests in China. With rapid economic development of Hainan, biodiversity is increasingly at risk. Determining the spatial patterns of plant diversity in Hainan and explaining the drivers behind plant diversity are important considerations in assessing and maximizing the effectiveness of national parks, such as the newly designated Hainan Rainforest National Park. We assessed phylogenetic diversity patterns, and species richness using 106,252 georeferenced specimen records and a molecular phylogeny of 3,792 native plant species. Based on phylogenetic range-weighted turnover metrics, we divided Hainan flora into four major floristic units. The Grade of Membership model was used to further verify the four units, and to understand their boundaries and the internal structure of each floristic unit. Finally, the best combination model was used to explore the driving mechanisms underlying the division. Our results reveal that central Hainan is the most important hotspot for plant endemism and diversity, followed by the southern area. Environmental energy is the main factor determining the spatial patterns of native plant diversity on the island, and accessibility has the greatest impact on native plant diversity among social factors. We explore patterns of spatial phylogenetics and biogeography to identify potential priorities for management and conservation drivers of plant diversity patterns across Hainan, to provide the basis for the effective protection of native plant diversity and the improvement of national parks of Hainan Island.

Dietary specialization stands as a major factor in the study of adaptive evolution and the field of conservation biology among animals. Although bats show unparalleled dietary diversification among mammals, specialized carnivory remains relatively rare within this group. Consequently, our comprehension of the genetic and conservation aspects associated with this specific dietary niche in bats has largely remained uncharted. To investigate molecular adaptations and conservation genetics in carnivorous bats, we produced a new draft genome assembly for the carnivorous bat Vampyrum spectrum. Furthermore, we utilized this genome alongside another distantly related carnivorous bat Megaderma lyra, to conduct genome-wide comparative analyses with other bat species. Our findings unveil that genes linked to lipid metabolism exhibit signatures of positive selection and convergent molecular adaptation in the two divergent lineages of carnivorous bats. Intriguingly, we have uncovered that the evolution of dietary specialization in carnivorous bats is accompanied by molecular adaptations acting on genes in the peroxisome proliferator-activated receptors pathways, which are crucial in regulating plasma lipid metabolism and sustaining lipid homeostasis. Additionally, our genomic analyses also reveal low genetic diversity in both carnivorous bat species. This pattern is attributed to their continuously declining population sizes and low levels of heterozygosity, signaling their vulnerability and emphasizing the pressing need for conservation efforts. These genomic discoveries advance our understanding of genetic underpinnings of carnivory in bats and underscore substantial conservation concerns associated with carnivorous bat species.

Many examples of phenotypic modifications resulting from high-elevation adaptation have been documented, however, the underlying processes responsible for these modifications and whether the continuity of the adaptation process remain elusive, particularly in plants. The alpine plants distributed along wide elevational gradients provide an ideal system to address this question. Here, we collected transcriptomes from multiple tissues of three species with different elevations (~1500, ~2500, and ~3600 m in the Hengduan Mountains, Southwest China) in two genera Fargesia and Yushania of alpine bamboos, respectively, and conducted evolutionary and expressional analyses. Results showed that high-elevation adaptation emerged earlier in the evolutionary history of both genera and evolved continuously as the elevation increased. Moreover, convergence of genetic changes was observed in the two genera, with amounts of candidate genes responsible for high-elevation adaptation identified under positive selection. Overall, our study provides an empirical example and valuable genetic resource for further investigation of high-elevation adaptation in plants and sheds new light on how plants adapting to high-elevation environments in a biodiversity hotspot.

Pseudo-nitzschia is a group of widely distributed planktonic diatoms. Some species produce the neurotoxin domoic acid. Herein, two new Pseudo-nitzschia species were described from Chinese coastal waters and the South China Sea after combining morphological and molecular data, together with biogeographical traits. Pseudo-nitzschia punctionis sp. nov. was similar to Pseudo-nitzschia bipertita morphologically, but differed in poroid structure, which was undivided in P. punctionis but divided in two sectors in P. bipertita. This difference corresponded to the presence of two hemicompensatory base changes (HCBCs) in the secondary structure of internal transcribed spacer 2. Pseudo-nitzschia polymorpha sp. nov. was sister to Pseudo-nitzschia limii phylogenetically, but distinct by the various shapes of perforations on the valve and copula, which was supported by four HCBCs. In a metabarcoding analysis, multiple new ribotypes were identified within the two new species, and intraspecific genetic divergences were analyzed. Metabarcoding data revealed that P. punctionis had a broader temperature range (12.9–30.5°C) than P. polymorpha (22.3–30.5°C). Within the two new species, different traits were found among the amplicon sequence variants regarding temperature and biogeography, representing different microevolutionary directions under environmental selection. The two new species had different biogeographical traits when compared to their closely related species. Domoic acid was detected in strains of P. punctionis at a concentration of 13.5–17.7 fg/cell, but the toxin was not found in strains of P. polymorpha. A combination of characters based on laboratory strains and field metabarcoding data provided more data for delimiting Pseudo-nitzschia species and gave new insights into their diversity and biogeography.

Rosa-associated fungi are rich in species and diverse in function, with many potential new taxa. However, only a few publications have reported Rosa-associated endophytic fungi using a combination of molecular systematics and morphology. Rosa roxburghii is an economically important source of medicine and food. We reported earlier the diversity and antimicrobial activities of the fungal endophytes of this plant, but further confirmation is needed for possible new taxa. In this study, we describe 10 novel species and two new host records isolated from healthy tissues of R. roxburghii while identifying three new combinations, all belonging to the Sordariomycetes. The new species described herein include Chaetomium rosifloricola, Chaetomium rosiradicicola, Chrysofolia fructicola, Coniella cili, Hypoxylon florendophyticum, Hypoxylon rosicaulendophyticum, Ilyonectria radicigena, Neopestalotiopsis caulicola, Neopestalotiopsis fructicola, and Seimatosporium endophyticum. Monochaetia bulbophylli, Neopestalotiopsis anacardii, and Neopestalotiopsis termitarii were introduced as new combinations, while Coniella quercicola and Hypoxylon pulicicidum were described as new host records on R. roxburghii. All the taxa have been described, illustrated, and phylogenetically analyzed, in addition to the lifestyles of each genus. Altogether, the results of this study have important implications for identifying novel endophytic fungi and developing potential applications of these fungi in the future.

Both hybridization and intraspecific morphological variation across environmental gradients complicate species delineation. We aimed to discern both possibilities that may blur species boundaries in the Carpinus viminea-Carpinus laxiflora-Carpinus londoniana species complex. We conducted statistical analyses on 535 specimens encompassing the entire distribution of this species complex to identify phenotypic clusters. Additionally, we analyzed genetic divergence and probable hybridization between clusters using 76 individuals from 37 populations. Based on phenotypic and genetic clusters, we tentatively recognized four species: C. viminea, C. fargesii, C. laxiflora, and C. londoniana. Except for rare overlapping distributions between C. fargesii and C. londoniana, the redefined four species are mostly allopatric to each another based on their distributions. The morphological delimitation, species boundary and distribution of each species differ distinctly from past taxonomic treatments. For example, specimens previously identified under C. viminea, in fact, belong to three different species. Hybrids between C. fargesii and C. londoniana exhibit morphological traits similar to C. viminea, thereby contributing to difficulties in determining species boundaries and outlining species distributions. These findings suggest that local selection and geographical isolation may together have promoted both phenotypic and genetic divergences within this species complex. However, interspecific hybridization blurs species boundaries by producing hybrids with phenotypic similarity in addition to intraspecific variation. This study emphasizes the importance of statistical analyses of population-level morphological and genetic variations across major distributional ranges for an integrative delimitation of species boundaries and the identification of hybridization and hybrids.

The Crepidinae are the largest subtribe of the Cichorieae (Asteraceae). Debate remains over the circumscription and phylogeny of this subtribe, mainly due to its complex morphology and the poor phylogenetic signal provided by traditional Sanger sequencing markers. In this study, a well-resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, was obtained for the first time using nuclear data with a phylogenomics approach (Hyb-Seq). Using this phylogeny along with other evidence, we propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae. We also describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles.

Panax (Araliaceae) is a small genus containing several well known medicinally important species. It has a disjunct distribution between Eastern Asia and Eastern North America, with most species from eastern Asia, especially the Himalayan-Hengduan Mountains (HHM). This study used the genomic target enrichment method to obtain 358 nuclear ortholog loci and complete plastome sequences from 59 accessions representing all 18 species of the genus. Divergence time estimation and biogeographic analyses suggest that Panax was probably widely distributed from North America to Asia during the middle Eocene. During the late Eocene to Oligocene Panax may have experienced extensive extinctions during global climate cooling. It survived and diverged early in the mountains of Southwest China and tropical Indochina, where some taxa migrated northwestward to the HHM, eastward to central and eastern China, and then onward toward Japan and North America. Gene flow is identified as the main contributor to phylogenetic discordance (33.46%) within Panax. We hypothesize that the common ancestors of the medicinally important P. ginseng + P. japonicus + P. quinquefolius clade had experienced allopolyploidization, which increased adaptability to cooler and drier environments. During the middle to late Miocene, several dispersals occurred from the region of the HHM to contiguous areas, suggesting that HHM acted as a refugium and also served as a secondary diversification center for Panax. Our findings highlight that the interplay of orographic uplift and climatic changes in the HHM greatly contributed to the species diversity of Panax.

Elucidating how plant species respond to variable light conditions is essential to understanding the ecological adaptation to heterogeneous environments. Plant performance and gene regulatory network underpinning the adaptation have been well documented in heliophytic species. However, it remains largely unclear how the sciophytic plants respond to distinct light conditions. We measured phenotypic and transcriptomic features of four sciophytic (Fatsia japonica, Metapanax delavayi, Heptapleurum arboricola, and Heptapleurum delavayi) and one heliophytic woody species (Tetrapanax papyrifer) of the Araliaceae family under distinct light conditions. Our phenotypic comparisons demonstrate that the four sciophytic species maintain similar photosynthesis efficiency between high light and low light conditions. However, a significantly decreased photosynthesis rate was observed under the low light conditions of the heliophytic species compared with the high light conditions. In addition, our leaf anatomical analyses revealed that, while all five species showed different anatomical structures under distinct light conditions, the sciophytic species possessed a lower degree of phenotypic plasticity relative to the heliophytic species. Further comparisons of the transcriptome profiling showed that differentially expressed genes identified in the five species were functionally related to photosynthesis, secondary metabolites, and other basic metabolisms. In particular, differential regulation of the photosynthesis-related and photomorphogenesis-related genes were potentially correlated with the phenotypic responses to the distinct light conditions of the five species. Our study provides evolutionary and ecological perspectives on how the heliophytic and sciophytic woody species respond to shade and sunlight environments.

The genus Didymocarpus Wall. is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high-density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (external transcribed spacer [ETS], internal transcribed spacer [ITS], 18S, 26S) and five chloroplast DNAs (atpB-rbcL, rpl16, rps16, trnH-psbA, and trnL-F). The results indicated that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitated the range of the Didymocarpus sensu stricto (s. str.) with two-section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, in that it is found only in Southeast China. In addition, we proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera.

In the Mountains of Southwest China (MSC), accelerated diversification triggered by mountain uplift and monsoon intensification in the Miocene is widely revealed, but less is known about the stage after the Pliocene. Thus, the tempo‐spatial evolution of the endemism of Gaoligong Shan (GLGS), a young and isolated mountain with the highest biodiversity in the MSC, was determined. Temporal patterns were inferred by the stem ages of the endemic species and spatial patterns were inferred through ancestral area reconstructions and the distributions of the sister taxa. Temporally, the calibrated origin times of 114 phylogenetically well resolved endemic species (75 plants, 33 animals and six fungi) ranged from the early Miocene to the Holecene. Spatially, 82 centric origin species (mean = 3.08 Ma) were significantly younger than 32 eccentric origin species (6.84 Ma). Eccentric origins accumulated smoothly while centric origins burst after the late Pliocene, especially after the Pleistocene (n = 52). In centric origins, most of the sister taxa showed sympatric (n = 47) or allopatric (n = 23) distributions in the GLGS. The eccentric origins were mainly dispersed from the southern lower latitude region (n = 20). Principle component analysis indicated that niche conservatism exerted greater contribution to the speciation of the endemic species. Uplift of the GLGS and monsoon intensification during the late Pliocene accelerated the formation of its endemism. The “Species pump” effect of the Pleistocene climatic fluctuations is further revealed. Speciation triggered by geological isolation by mountain and river barriers through niche conservatism exceeds adaptive evolution.

Rubisco is assembled from large subunits (encoded by chloroplast gene rbcL) and small subunits (encoded by the nuclear rbcS multigene family), which are involved in the processes of carbon dioxide fixation in the Calvin cycle of photosynthesis. Although Rubisco has been studied in many plants, the evolutionary divergences among the different rbcS genes are still largely unknown. Here, using a rice closely related wild species, Oryza punctata Kotschy ex Steud, we investigated the differential properties of the rbcS genes in the species. We identified five rbcS genes (OprbcS1 through OprbcS5), OprbcS1 showed a different evolutionary pattern from the remaining four genes in terms of chromosome location, gene structure, and sequence homology. Phylogenetic analysis revealed that plant rbcS1 and other non-rbcS1 genes originated from a common ancient duplication event that occurred at least in seed plants ancestor. RbcS1 was then retained in a few plant lineages, including Oryza, whereas non-rbcS1 was mainly amplified in angiosperms. OprbcS1, OprbcS2–OprbcS4, and OprbcS5 were prominently expressed in stems and seeds, young leaves, and mature leaves, respectively. The yeast two-hybrid assay detected a significant decrease in the interaction between OprbcS1 and OprbcL compared to the other four pairs of proteins (OprbcS2–OprbcS5 and OprbcL). We propose that OprbcS1 might be assigned a divergent function that was predominantly specific to nonphotosynthetic organs, whereas OprbcS2–OprbcS5, having different affinity in the assembly process of Rubisco, might be subfunctionalized in photosynthetic organs. This study not only deepens our understanding of the fine assembly of Rubisco, but also sheds some light on future de novo domestication of wild rice.

Among the lineages of the tree of life, land plants exhibit a remarkably high genomic disparity because of their distinct evolutionary trajectories in the phylogenetic history of their major lineages. The macroevolutionary pattern of genomic evolution has been mainly investigated to obtain insights into well-studied lineages such as angiosperms, but little attention has been given to many important lineages such as bryophytes. This study was designed to resolve this gap by comparing the genomic evolution trajectories of mosses and liverworts. Thus, a data set comprising chromosome number and genome size was compiled, including previously published and newly generated data that were used to trace the phylogenetic history of these two parameters among mosses and liverworts via ancestral state reconstruction and phylogenetic comparative analyses. Contrasting patterns of chromosome number and genome size evolutions were detected between the two sister lineages. Mosses accumulated high chromosome number disparity via repeated whole-genome duplications and descending dysploidy but maintained a small genome size. By contrast, the chromosome number of liverworts was highly conserved, and heterogeneous trends in genome size evolution were identified among major lineages. These contrasting patterns may be partly explained by the difference in genomic dynamics: Active dynamics enables genome downsizing and reorganization in mosses, whereas genome stability leads to the accumulation of large genomes in liverworts. The results of this study confirmed the distinct trends of genomic evolution in bryophytes.

The genus Xylaria comprises a diverse group of fungi with a global distribution and significant ecological importance, known for being a source of bioactive secondary metabolites with antibacterial, antioxidative, anticarcinogenic, and additional properties. In this study, we present a comprehensive taxonomic revision of the species of Xylaria found in some parts of southern China, characterized by an extensive multilocus phylogeny analysis based on internal transcribed spacer (ITS), TUB2 (β-tubulin), and DNA-directed RNA polymerase II subunit 2 (rpb2) gene regions. Morphological examination and detailed comparative analyses of the collected specimens were conducted to determine the distinctiveness of each species. The multilocus phylogeny approach allowed us to infer evolutionary relationships and assess species boundaries accurately, leading to the identification of 40 novel Xylaria species hitherto unknown to science. The newly described species are: X. baoshanensis, X. bawanglingensis, X. botryoidalis, X. dadugangensis, X. doupengshanensis, X. fanglanii, X. glaucae, X. guizhouensis, X. japonica, X. jinghongensis, X. jinshanensis, X. kuankuoshuiensis, X. liboensis, X. negundinis, X. orbiculati, X. ovata, X. pseudoanisopleura, X. pseudocubensis, X. pseudobambusicola, X. pseudoglobosa, X. pseudohemisphaerica, X. pseudohypoxylon, X. puerensis, X. qianensis, X. qiongzhouensis, X. rhombostroma, X. serratifoliae, X. shishangensis, X. shuqunii, X. shuangjiangensis, X. sinensis, X. tongrenensis, X. umbellata, X. xishuiensis, X. yaorenshanensis, X. yinggelingensis, X. yumingii, X. yunnanensis, X. zangmui, and X. zonghuangii. The study's findings shed light on the distinctiveness of the newly described species, supported by both morphological distinctions and phylogenetic relationships with their close relatives. This taxonomic revision significantly contributes to our understanding the diversity of Xylaria in China and enriches the knowledge of fungal biodiversity worldwide.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitatadapted and endemic diversity. Acknowledging this aspect, the genus Oxalis is a conceivable group for evolutionary and biogeographic hypothesis testing; however, molecular resources for the genus still need improvement. We conducted a genome skimming approach to assemble new plastomes from 18 accessions (six species) of Oxalis collected in Lomas locations in Peru. These complete plastomes of Oxalis species (several reported for the first time) present a highly conserved composition. Our phylogenetic results were congruent with previous section‐based backbone phylogenies of Oxalis; however, a closer look at the phylogeny of sect. Carnosae revealed nonmonophyletic arrangements involving Oxalis megalorrhiza and Oxalis bulbocastanum individuals. We also propose a set of three hypervariable plastid regions as potential molecular markers. Likewise, an array of primers for nuclear simple sequence repeat markers based on the most widely distributed species, O. megalorrhiza, were listed and evaluated for their transferability to the other species under examination. These new genomic resources represent a significant development for future population, phylogenetic, and biogeographic studies in Oxalis.

Tongoloa is a herbaceous genus of East Asia Clade (Apiaceae) distributed in the alpine regions. The use of DNA fragments has not provided a well-resolved evolutionary history. For this research, we primarily collected samples from the type localities of Tongoloa and closely related taxa in the Hengduan Mountains. The chloroplast (cp) genomes and nuclear ribosomal (nr) DNA repeats of 27 taxa were assembled using genome skimming sequencing reads. We analyzed the characteristics of the Tongoloa cp genome, and found a remarkable expansion of the Inverted Repeats. Three genes (ndhC, ndhJ, and petG) related to photosynthesis appear to have undergone significant selective pressure. Through high-resolution phylogenetic analysis, the cpDNA provided compelling evidence supporting the inclusion of Sinolimprichtia as an early taxon within Tongoloa. However, the nrDNA suggested that Tongoloa and Sinolimprichtia belong to distinct branches. Morphological analysis showed that Tongoloa has broadly oval fruits with a cordate base, whereas the fruits of Sinolimprichtia are long-obovate with an obtuse base. The specific fruit morphology of Sinolimprichtia was found to be nested within Tongoloa in the cpDNA phylogenetic tree. Ancient introgression and chloroplast capture provide the most plausible explanation for the significant conflict between the nrDNA and cpDNA phylogenies. Our study highlights the potential impact of the complex evolutionary history of Tongoloa on the challenges encountered in previous taxonomic treatments.

Rhododendron is a significant plant genus, with over 600 identified species in China. The subgenus Hymenanthes holds the largest number of Rhododendron germplasms and showcases strong environmental adaptability. However, there remains a lack of understanding regarding Rhododendron's evolution and environmental adaptations. Rhododendron bailiense Y.P.Ma, C.Q.Zhang & D.F.Chamb., an exceedingly rare species, thrives in the alkaline karst landforms of Guizhou, southwest China, different from the typical growing environment of other Rhododendron species. In this study, we present a chromosome-level genome assembly of R. bailiense, revealing a genome size of 923.3 Mb, a contig N50 of 24.5 Mb, and a total of 47 567 predicted genes. An evolutionary analysis indicated that R. bailiense diverged from its ancestors prior to the other subgenus Hymenanthes rhododendrons, with the expanded and contracted genes being notably enriched in “stress response” and “growth,” respectively. Rhododendron bailiense is predominantly found on limestone soil in the mountains of Guizhou, with only two wild populations known. The genome of R. bailiense contained a high copy number of ankyrin repeat (ANK) and Ca²⁺-ATPase (CAP) genes, primarily involved in Ca²⁺ transport, shedding light on how R. bailiense copes with karst high-calcium stress. In contrast, the structures of the ANKs displayed unique characteristics, while the CAPs showed conservatism. The R. bailiense genome provides new insights into the adaptation and evolutionary history of Rhododendron plants in karst environments, potentially offering valuable information for adaptive breeding and ecological enhancement in such challenging settings.

The soil-nitrogen condition, which differs greatly between paddy fields (mainly in the form of ammonium, NH₄⁺) and dry fields (mainly in the form of nitrate, NO₃^-), is a main environmental factor that drives the adaptive differentiation between upland and lowland rice ecotypes. However, the adaptive differentiation in terms of the nitrogen use efficiency (NUE) between upland and lowland rice has not been well addressed. In this study, we evaluated NUE-related traits among rice landraces as well as the genetic differentiation between NUE- associated genes and quantitative trait loci (QTLs). The japonica upland and lowland rice ecotypes showed large differences in their NUE-related traits such as the absorption ability for NH₄⁺ and NO₃^-. The indica upland and lowland rice exhibited similar performances when cultivated in solutions containing NH₄⁺ or NO₃^- or when planted in paddy or dry fields. However, the indica upland rice possessed a greater ability to absorb NO₃^-. We identified 76 QTLs for 25 measured traits using genome-wide association analysis. The highly differentiated NUE- associated genes or QTLs between ecotypes were rarely shared by japonica and indica subspecies, indicating an independent genetic basis for their soil-nitrogen adaptations. We suggested four genes in three QTLs as the candidates contributing to rice NUE during the ecotypic differentiation. In summary, the soil-nitrogen condition drives the adaptive differentiation of NUE between upland and lowland rice independently within the japonica and indica subspecies. These findings can strengthen our understanding of rice adaptation to divergent soil-nitrogen conditions and have implications for the improvement of NUE.

Understanding plant diversity and the phylogenetic divergences in the Northern Hemisphere is essential for in-depth evolutionary studies and conservation efforts. Maianthemum is an ideal example to explore plant diversification processes in the Northern Hemisphere, with more than 35 species widely distributed in forests in North to Central America, Europe and eastern Asia. Yet the phylogenetic relationships within Maianthemum remain elusive. In this study, we reconstructed a well-supported phylogenetic framework of Maianthemum and explored possible gene introgressions and reticulate evolution using nuclear and chloroplast genomes based on the target enrichment Hyb-Seq approach. Both nuclear and chloroplast phylogenetic results supported three clusters corresponding to their biogeographic distribution of the New World, the Himalayan-Hengduan Mountains, and the north temperate zone, respectively. The genus was inferred to be most likely originated in North America with migrations into Central America and eastern Asia in the late Miocene. Our results suggested that both incomplete lineage sorting and hybridizations/introgressions along with geographic isolation have contributed to the rapid divergence of Maianthemum in eastern Asia, which may represent a complex model for the evolutionary radiation of plants in eastern Asia and even the Northern Hemisphere.

Coccoidea (Hemiptera, Sternorrhyncha) are widely distributed and agriculturally significant insects known for their distinctive morphology and biological traits. The Coccoidea are often called scales or mealybugs because many species have a shell‐like covering resembling a scale or are covered with mealy wax. Knowledge of scale insects beyond the female adult stage is limited, partly because other life stages are less conspicuous, shorter‐lived, and less impactful on host plants. This complicates accurate classification, further compounded by limited molecular phylogenetic studies. This study presents the first phylogenetic analyses combining genome and transcriptome sequence data. We sequenced five whole genomes and one transcriptome from Pseudococcidae and integrated these new genome‐scale data with existing genome and transcriptome sequences to perform phylogenomic analysis of scale insects. The analysis yielded robustly supported relationships within Coccoidea, resolving several high‐level relationships. The current genome‐scale data support the monophyly of Monophlebidae, Pseudococcidae, Kerriidae, and Diaspididae, while not supporting the monophyly of Coccidae and Eriococcidae. Bayesian inferences using site‐heterogeneous models corroborated Pseudococcidae as the sister group of all other neococcoid families. Within Pseudococcidae, two subfamilies, Phenacoccinae and Pseudococcinae, were supported. At the tribe level, Phenacoccini was found to be monophyletic, whereas Planococcini, Trabutinini, and Pseudococcini were not.

The uplift of the Qinghai-Tibet Plateau shaped the landforms and influenced Asia's climate system and ecosystem. Vegetations on the Plateau are the first to be affected by the uplift history of the Qinghai-Tibet Plateau and related ecological impacts. However, original research on vegetation in the central Qinghai-Tibet Plateau remains limited. Here, we reconstructed the vegetation in the Lunpola Basin, central Qinghai-Tibet Plateau from 24.3 to 16 Ma based on pollen data from the Dingqinghu Formation. Pollen assemblages reveal a temperate mixed deciduous broad-leaved and coniferous forest around the Lunpola paleolake during the latest Oligocene to the Early Miocene. An obvious vegetation vertical zone existed near the Lunpola Basin. Dark coniferous forests grew in the highlands, thermophilous shrubs stayed in the lowlands. This work provides new and original data on plant composition and vegetation in the central Qinghai-Tibet Plateau and enhances our understanding of the ecological impacts of the Qinghai-Tibet Plateau uplift.

Members of the genus Juglans (walnuts, family Juglandaceae) are typical Tertiary relict tree species. They are widely distributed in China and are well known for their edible nuts and high‐quality wood. The genetic structure and historical gene flow patterns of Chinese Juglans still need to be resolved. Here, we collected samples from a total of 2242 trees from 142 populations of three walnut species (Juglans regia L., Juglans sigillata Dode, and Juglans mandshurica Maxim.) and a hybrid taxon Juglans × hopeiensis. These samples were distributed throughout China. We analyzed population genetic structure, interspecific relationships, lineage differentiation, and speciation using 21 EST‐SSR genetic markers. All populations of J. regia and J. sigillata clustered into one lineage, corresponding to the Juglans sect. Dioscaryon, and all J. mandshurica and Juglans × hopeiensis populations (section Cardiocaryon) clustered into a second lineage. For J. mandshurica, there was an obvious north-south genetic cline. Interestingly, except for seven populations of the hybrid Juglans × hopeiensis, there was almost no gene flow between the populations of section Juglans/Dioscaryon and section Cardiocaryon. A DIYABC analysis showed that J. regia and J. mandshurica differentiated during the Oligocene. Juglans sigillata originated during the Pliocene to the Pleistocene. Subsequently, during the Middle Pleistocene, J. regia and J. mandshurica hybridized within a narrow zone to produce Juglans × hopeiensis. These results demonstrate the impact of repeated turbulent climate changes in the Quaternary on the evolutionary history of Tertiary relict plants.

Despite the importance of gamete production this topic has rarely been investigated in angiosperms using comparative approaches. Here, we investigated pollen and ovule numbers per flower in 73 species and 99 populations of Primula comprising both distylous and homostylous reproductive systems. We investigated whether phylogenetic relationships influenced associations between variation in gamete production, floral traits and elevation, and whether the evolutionary breakdown of distyly to homostyly resulted in parallel changes to gamete production. We used a Bayesian approach facilitated by the MCMCglmm method to model pollen and ovule traits across species and determined whether they exhibited phylogenetic signals. We detected significant positive correlations between pollen number and elevation in both the long‐styled and short‐styled morphs (L‐morph and S‐morph, respectively), whereas ovule number was not influenced by elevation. Pollen production was significantly higher in the L‐morph than in the S‐morph, but there was no significant difference between morphs in ovule number. Pollen volume exhibited a positive correlation with the style length of compatible morphs. The transition from distyly to homostyly was associated with significant decreases in pollen production but not ovule number. Our findings demonstrate the importance of elevation on pollen production, perhaps because of selection to improve pollen‐transfer efficiency in uncertain pollinator environments. In contrast, ovule number variation appears to be more constrained by phylogenetic relationships. Our comparative analyses of a well defined angiosperm lineage highlight the complex interactions between intrinsic and extrinsic factors influencing gamete production in plants and emphasize the importance of considering pollen and ovule data separately.

The family Primulaceae s.l. is estimated to comprise approximately 60 genera and 2600 species worldwide. Although extensive research has been conducted on the family Primulaceae and its subfamily boundaries, there is a lack of systematic studies utilizing complete plastid genome data, leading to uncertainties in the phylogenetic positions of certain key taxa, such as Stimpsonia. In this study, plastid genomic data were collected from 67 accessions representing four subfamilies and 28 genera within the Primulaceae family. Phylogenetic trees were constructed using coalescent and concatenated approaches to elucidate the evolutionary history of the family. By employing a comprehensive dataset of 67 plastid genomes from all four subfamilies, a robust phylogenetic framework for the family was established. Contentious relationships were identified at the early stages of divergence in Primula and among Cyclamen and its relatives, probably due to rapid diversification. Our plastid genomic data support the idea that Stimpsonia is sister to the remainder of the subfamily Primuloideae, in contrast with its placement in Myrsinoideae based on nuclear data. A cytonuclear discordance in the phylogenetic position was also detected in Aegiceras corniculatum. The divergence time estimates from this study align with previous findings, indicating significant diversification events during the Eocene and Oligocene epochs. These timeframes coincide with major geological and climatic changes, which were likely to have influenced the distribution and diversification of Primulaceae. These results underscore the complex evolutionary history of the Primulaceae family and lay the groundwork for future research aimed at unraveling the intricate evolutionary dynamics within this family.

Pan-Himalaya, including Himalaya and its neighboring areas, hosts a rich and unique flora that is crucial for understanding the evolutionary history of mountainous biodiversity. Phylogenetic regionalization can provide novel insights into biodiversity distribution patterns and their formation mechanisms. In this study, based on comprehensive species distribution data and a species-level phylogenetic tree, we propose a phylogenetic regionalization scheme of the Pan-Himalayan vascular flora comprising 15 zones, which can be grouped into five floristic subregions and three floristic regions (i.e., the West Himalayan [WH], the Southeast Himalayan [SEH], and the Northeast Himalayan [NEH] regions). Our results reveal that the SEH and NEH regions are closely clustered, which are then grouped with the WH region. The floras of these three regions exhibit distinct evolutionary histories and phylogenetic structures. The WH region presents a phylogenetically clustered flora with Euro-Mediterranean affinities and the highest evolutionary uniqueness. The NEH region has the highest species richness and phylogenetic diversity, with most of its areas, especially at higher elevations, displaying phylogenetic clustering. In contrast, the SEH region exhibits a phylogenetically overdispersed flora, characterized by harboring species-rich families with tropical, temperate, and alpine distributions, as well as relict plant lineages. This study provides valuable insights into the evolutionary history of the Pan-Himalayan flora and informs the development of effective conservation strategies.

Taihangia rupestris Yu & Li, an early spring flowering plant of the Rosaceae family, is classified as a second-level protected species in China. Endemic to the cliff faces of the Taihang Mountains in central China, this rare species requires a comprehensive understanding and conservation approach. In this study, we analyzed population-level genetic variations in both chloroplast and nuclear genomes. Taihangia rupestris var. ciliata exhibited higher genetic diversity than T. rupestris var. rupestris in both genome types. All individuals of T. rupestris var. rupestris formed a single cluster, while individuals of T. rupestris var. ciliata were grouped into three distinct clusters. Approximately 29.82 Ma, T. rupestris diverged from its closely related species. Taihangia rupestris var. ciliata appeared first, followed by the differentiation of T. rupestris var. rupestris, which adapted to the climate of the southern Taihang Mountains, around 3.55 Ma. Additionally, our study identified several chloroplast genes potentially involved in variety adaptive differentiation. These findings enhance our understanding of environmental adaptation and differentiation in the two T. rupestris varieties, providing valuable genetic insights for the conservation and utilization of this species.

Evolutionary theory suggests the hypothesis that among genetically isolated populations, phenotypic variation should be smaller in populations with smaller ratios of nonsynonymous to synonymous substitutions (dN/dS) because smaller dN/dS ratios occur under greater purification selections. Two distinct lineages (JPN₁ and JPN₂) of panarctic Daphnia cf. pulex sensu Hebert (1995), invaded independently into Japan from North America, provide an excellent opportunity to test this hypothesis because the earlier invader JPN₁ has a lower dN/dS ratio than JPN₂. Therefore, we examined phenotypic variations in fitness-related traits, including digestive, life-history, and morphological traits, among several genotypes within these two lineages. We found that phenotypic variations were smaller within the JPN₁ lineage than within the JPN₂ lineage. Furthermore, within-lineage variation of the phenotypic plasticity to changing food levels was smaller in the JPN₁ lineage than in the JPN₂ lineage. These results support the hypothesis that the JPN₁ lineage has been more efficiently subjected to negative selection. However, the magnitude of the phenotypic plasticity of these traits was, on average, at the same level between the JPN₁ and JPN₂ lineages and its direction differed among genotypes of these lineages, suggesting that the JPN₂ genotypes might have exploited niches that were different from those of the JPN₁ genotypes.

For clades originating in warm climates, the tropical niche conservatism hypothesis predicts that current biological assemblages in colder or drier climates are expected to have lower phylogenetic diversity, and species in colder or drier climates are expected to be more closely related to each other (i.e., higher phylogenetic clustering). Liverworts are one of the oldest clades of extant land plants. They originated about 500 Ma during a warm (“greenhouse”) period and experienced multiple major cycles of warm and cold periods. Here, I test the tropical niche conservatism hypothesis using liverwort assemblages distributed along an elevational gradient crossing about 5000 m of elevation in the central Himalaya. I found that, in general, phylogenetic diversity and dispersion decrease with increasing elevation and thus with decreasing temperature, which is consistent with the tropical niche conservatism hypothesis. Phylogenetic diversity decreases with elevation monotonically, but phylogenetic dispersion decreases with elevation in a triphasic (zig-zag) pattern, which is generally consistent with the triphasic pattern found in angiosperms and polypod ferns along the same elevational gradient. Temperature-related variables explained approximately the same amount of the variation in phylogenetic diversity and dispersion as did precipitation-related variables, although mean annual temperature explained 9%−15% more variation than did annual precipitation. Climate extreme variables explained approximately the same amount of variation in phylogenetic diversity and dispersion as did climate seasonality variables.

Speciation events often occur with adaptive radiation. The factors that promote these adaptive radiating species diversity patterns have intrigued biologists for more than a century. In the present study, we used the adaptive radiated genus Ligustrum to evaluate the relative contributions of the environment, species interactions, phylogenetic diversity, and diversification rates in generating extant species diversity patterns. Using complete chloroplast genome data, we reconstructed the highly supported and dated backbone phylogenetic relationships of Ligustrum. Biogeographic results indicated that Ligustrum originated in Southwest China during the Oligocene and spread to suitable areas that were warm and humid via 18 dispersal events. For the overlapping ranges of species pairs, a smaller phylogenetic distance was detected in high species overlap than in low species overlap, which is consistent with no significant difference in niche among the different species. We found that the phylogenetic diversity and interspecies competition induced by insignificant niche divergence shaped the global pattern of Ligustrum diversity.

The loss of biodiversity is one of the most serious environmental issues in the Anthropocene. Understanding the extinction risk of species is essential for preemptive conservation measures, but is hampered by gaps in geographical and evolutionary knowledge, especially in areas/regions that are highly diverse in species. Combined with a 21 109-taxon angiosperm mega-phylogeny and comprehensive species distribution database, we evaluated the characteristics of angiosperm extinction risk at the Sino-Himalaya and the Tibetan Plateau (SHTP). Overall, our results show that there is a strong interaction between evolutionary and environmental factors on extinction risk, and both contribute spatially to threat processing in the SHTP. The extinction risk of angiosperms in this region is spatially and phylogenetically clustered; the clades with low species richness are significantly more vulnerable to extinction than species-rich ones; the regions with the highest extinction risk are concentrated in the mountainous areas of southwest China. Integrated with the existing Red List, we further delineated more than 3000 potentially threatened species and proposed practical conservation priorities for four types of species in the SHTP. The extinction risk of angiosperms showed both phylogenetically and spatially aggregate characteristics, serving as an important reference for predicting extinction trends and the formulation of targeted conservation strategies.