The Himalayas represent a complex mountain system housing some of the world's richest floras along with a high level of endemism. Among them, Lysionotus (Gesneriaceae) stands out as a small genus (~34 species) that is unexpectedly distributed across southern to eastern Asia. Within this genus, the mountain forests of the south Pan-Himalaya region emerge as a hotspot of diversity, hosting most epiphytic and endemic Lysionotus species. To explore the origin, evolutionary history and development of the current distribution pattern of Lysionotus, we inferred a highly resolved phylogenetic framework using 649 nuclear genes sourced from transcriptomes for 27 species. We revealed three major clades within Lysionotus with strong support, corresponding to the genus's classification into three sections (sects. Didymocarpoides, Lysionotus, and Cyathocalyx) based on morphological characters. Molecular dating suggests that Lysionotus is likely to have originated in the karst regions of northern Vietnam to southwestern China during the middle Oligocene (28.18 Ma), and then migrated westward to the southern Himalaya regions during the Miocene. The speciation rates of Lysionotus were likely to be positively linked to changes in East Asian monsoons and past temperatures. Notably, epiphytic species of sect. Lysionotus began colonizing the tropical and subtropical forests of the Pan-Himalaya around the mid-Miocene Climatic Optimum, coinciding with the transition to long seed appendages. Our findings support that the formation and development of forests in the southern Himalaya, along with paleo-climate changes and morphological innovations, which probably facilitated the evolution and expansion of the spatial distribution of Lysionotus.

Understanding the Cenozoic vegetation history of what is now the Qinghai–Tibetan Plateau is crucial for elucidating the co-evolutionary dynamics between plateau development, its environment, and the organisms it hosts. In this study, we conduct a comprehensive analysis of phytoliths within the late Oligocene–Early Miocene lacustrine sedimentary section of the Lunpola Basin, central Qinghai–Tibetan Plateau. The diverse phytolith morphotype assemblages indicate that the vegetation of the central Tibetan region mainly comprised a mixed coniferous and broad-leaved forest. Grasses in the understory primarily consisted of Pooideae, distinguished by phytolith morphotypes such as rondel, crenate and Stipa-type bilobate forms. Combined with previous work, we infer that riparian vegetation of the central Tibetan region transitioned from a humid subtropical forest, dominated by broad-leaved woody plants during the middle Eocene, to a more seasonally arid open woodland containing abundant woody and herbaceous plants during the late Eocene, before developing into a cooler mixed coniferous and broad-leaved forest during the late Oligocene–Early Miocene. The growth of the central Tibetan region and retreat of the Tethys Ocean, together with the uplift of the Himalaya, contributed to this vegetation change. This study provides new evidence from the phytolith perspective for the evolutionary history of Qinghai–Tibetan Plateau vegetation being tied to plateau formation and regional climate change.

Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai–Tibet Plateau (QTP) and the mountainous region of southwestern China have long been regarded as biodiversity hotspots. However, despite considerable efforts, numerous plant species may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca. 58 perennial herb species, which have been used as an important traditional medicinal plant for centuries. Rampant exploitation has put some species at risk of extinction. Rhodiola has also been recognized as a promising model for investigating radiation speciation in the QTP. However, the phylogenetic relationships among major clades in the genus are still not well resolved, and the underlying causes of cytonuclear discordance briefly mentioned in previous studies remain unexplored. Through phylogenomic analyses utilizing data from both the nuclear genome and plastome of 42 species, we identified six major clades in Rhodiola and found extensive cytonuclear discordance, which was primarily attributed to hybridization and introgression occurring among clades or closely related species. In addition, the integration of morphological, phylogenomic, population genomic, and ecological evidence resulted in the identification and description of a new species of Rhodiola: R. renii sp. nov., and the reclassification of a previously Pseudosedum species merged into Rhodiola. Our results highlight the significant role of hybridization and introgression in the evolution of Rhodiola and probably other rapid-radiated groups in the QTP, and emphasize the need for increased species discovery efforts in biodiversity hotspots such as the QTP and its adjacent mountainous areas.

When and how disjunct distributions of biological taxa arose has long attracted interest in biogeography, yet the East Asian–Tethyan disjunction is understudied. Cupressus (Cupressaceae) shows this disjunction, with 10 species in East Asia and three in the Mediterranean region. Here we used target-capture sequencing and obtained 1991 single-copy nuclear genes, plus complete plastomes, to infer the evolutionary history of Cupressus. Our phylogenomic reconstruction resolved four well supported clades in Cupressus, but revealed significant phylogenetic conflicts, with inter-lineage gene flow, incomplete lineage sorting and gene tree estimation error all making important contributions. The Chengiana clade most likely originated by hybridization between the ancestors of the Himalayan–Hengduan Mountains and subtropical Asia clades, whereas orogenic and climatic changes may have facilitated gene flow within the Himalayan–Hengduan Mountains clade. Molecular dating suggested that the most recent common ancestor of Cupressus appeared in East Asia around the middle Eocene period and then became continuously distributed across Eurasia. The East Asian–Tethyan disjunction arose when the Mediterranean and Himalayan–Hengduan Mountains clades diverged, likely to have been driven by Eocene/Oligocene declines in global temperature, then reinforced by the ecogeographic barrier created by the uplift of the Qinghai–Tibet Plateau. Niche shifts in the common ancestor of the Mediterranean clade, and signatures of selection in genes for drought and salt tolerance, probably indicate adaptation of this clade to local conditions. Overall, our study suggested that in-depth phylogenomic analyses are powerful tools in deciphering the complex evolutionary history of the origin of East Asian–Tethyan disjunction of organisms, especially gymnosperms.

Large phylogenies derived from publicly available genetic sequences are becoming a popular and indispensable tool in addressing core questions in ecology and evolution, as well as in tackling challenging conservation issues. Optimizing taxonomic coverage and data quality is essential for improving the precision and reliability of phylogenetic reconstructions and evolutionary inferences. Here we present PyNCBIminer, a user-friendly software that automates the assembly of large DNA data sets from GenBank for phylogenetic reconstruction using the supermatrix method. PyNCBIminer uses the iterative BLAST procedure to retrieve genetic sequences accurately and efficiently from GenBank. The state-of-the-art strategies also serve to improve taxa coverage and the quality of target DNA markers. PyNCBIminer is designed to efficiently handle large data sets, but it is also suitable for medium and small data sets. It is open source and freely available at GitHub (https://github.com/Xiaoting-Xu/PyNCBIminer) and Gitee (https://gitee.com/xiaotingxu/PyNCBIminer). Its utility and performance are demonstrated through the assembly of phylogenetic data sets encompassing several genetic markers of varying sizes for the angiosperm order Dipsacales. PyNCBIminer holds an advantage over similar programs in that it performs the majority of computations on the NCBI server, eliminating the need for users to build and maintain large local databases and reducing the demands on their computers. In addition, it integrates other commonly used phylogenetic analysis software, providing users from various backgrounds with convenient options for retrieving and assembling GenBank sequence data, along with flexible features that allow for user-defined parameters and strategies.

Plants exhibiting different growth forms possess different capabilities in adapting to their respective environments, consequently displaying distinct geographical patterns of phylogenetic relatedness across a broad environmental gradient. Here, we compare the geographical patterns of phylogenetic relatedness between woody and herbaceous angiosperms in China, based on three phylogenetic relatedness metrics, namely, the standardized effect sizes of phylogenetic diversity (PD_ses), mean pairwise distance (MPD_ses), and mean nearest taxon distance (MNTD_ses). Additionally, we explore the effects of three categories of environmental variables (current climate, historical climate change, and environmental heterogeneity) on the geographical patterns of phylogenetic relatedness of both plant groups. Our results indicate that the geographical patterns of phylogenetic relatedness of herbaceous and woody plants are inconsistent, and the deviations of phylogenetic relatedness between woody and herbaceous angiosperms have geographical patterns and vary along environmental gradients. Our study found that environmental variables have a greater influence on the phylogenetic relatedness of herbaceous plants than on that of woody plants, emphasizing that environmental variables, especially current climatic variables, are the primary drivers of the deviations of phylogenetic relatedness between woody and herbaceous angiosperms. In summary, we illustrate the distinct differences in phylogenetic relatedness among plants of different growth forms, providing valuable insights into the driving factors of species coexistence at various spatial scales.

Quaternary climate fluctuations and complex mountain systems had a prominent impact on the genetic diversification and speciation of montane organisms. However, the genetic imprints of the interplay between past climate events and rugged relief on montane species remain largely unresolved. Here, we analyzed the phylogeny, population structure, divergence time, demographic simulations, and ecological niche modeling of the montane scorpionfly Cerapanorpa obtusa (Cheng) from 36 populations in the mountains of central China (MCC) using three mitochondrial and two nuclear genes to explore its evolutionary history. The results show that C. obtusa originated from the Minshan Mountains, and currently consists of six genetically fragmented lineages that diverged 1.25–0.52 Ma. Four minor lineages (S1−S4) are confined to the topographically rugged Minshan Mountains, and two major lineages (NW and NE) are widely distributed in the northern MCC with relatively homogeneous landscapes. The Minshan Mountains are likely interglacial microrefugia for C. obtusa, and as spatial buffers in response to past climate changes. These findings provide some evidence that the interplay between climate changes and rugged relief may play a significant role in shaping the distinct phylogeographical pattern of cold-adapted montane insects. These results would also seem to suggest the importance of topographically rugged mountain systems in the conservation of evolutionary diversity and endemic species.

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.

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. ciliate 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. ciliate were grouped into three distinct clusters. Approximately 29.82 Ma, T. rupestris diverged from its closely related species. Taihangia rupestris var. ciliate 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.

Adaptive radiation is usually triggered by great in situ or ex situ environmental changes. How an adaptive radiation occurs on lands and how species richness relates to morphodisparity have been a major focus of evolutionary biology. Petrocodon, diversified in the southeastern Qinghai–Tibet Plateau (QTP), represents an ideal model to address these questions. To elucidate the dynamics of adaptive radiation of Petrocodon, we took an integrative approach, including phylogenetic, dating, disparity versus diversity, pollination, and gene expression analyses. Petrocodon with six clades has experienced radiation following the QTP uplift. Multiple modes of floral morphodisparity versus species diversity occur in the radiation process that are directly linked to their colonizing new environments and diversification with geographic expansion. Pollination and gene expression analyses suggest that accelerated emergence of de novo mutations might be relevant to the multiplex floral disparity and pollinator shifts in Petrocodon. For the first time in plants, we report that decreased genetic constraints on floral architecture triggered by QTP uplift might have generated abundant floral morphological variants, which were further targeted by selection for ecological divergence. The multiple modes of floral disparity versus species diversity may be attributed to accelerated mutations in colonizing new environments and repeated modifications of the already evolved traits in subsequent diversification and geographic expansion in Petrocodon. Our findings shed novel light on the interplay of ecological, developmental and evolutionary dynamics of disparity versus diversity in relation to trajectory changes of floral architecture in responses to environmental disturbance in a terrestrial plant group.

Toona fargesii A. Chev., a versatile tree in the Toona genus of the Meliaceae family, is renowned for its exquisite timber and medicinal properties, offering promising benefits. Due to natural regeneration obstacles and long-term excessive exploitation, it has been threatened in China. Intriguingly, root sprouting, which may diminish the genetic diversity and hinder population development, dominates the reproductive pattern of T. fargesii in the wild. However, the lack of complete genome information has hampered basic studies on the regeneration, classification, evolution and conservation of this species. Here, we report the genome of T. fargesii, which was sequenced using the PacBio platform and assembled into a high-quality genome with a total size of 535.24 Mb. Of this, 97.93% of the assembled contigs were anchored onto 28 pseudochromosomes, achieving a chromosome-level genome. The long terminal repeat assembly index score was 21.34, and the consensus quality value was 39.90%, indicating the accuracy and completeness of the genome. Comparative genome analysis suggested that a recent whole genome duplication event occurred between 22.1 and 50.1 Mya in the Toona genus, with the divergence time between T. fargesii and its relative T. sinensis estimated at approximately ~16.7 Mya. Additionally, 13 TfARR genes, which play integral roles in root sprouting by mediating cytokinin signaling, underwent rapid gene expansion and showed significant enrichment in the plant hormone signal transduction pathway. Furthermore, transcriptomic analysis demonstrated that differentially expressed genes between root sprouts and nonroot sprouts were significantly enriched in the zeatin biosynthesis pathway, indicating that cytokinin regulation is involved in root sprouting development. Collectively, the findings provide valuable genomic resources for the Toona genus and genetic insights into the mechanisms of root sprouting in T. fargesii.

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.

Most species in the early divergent angiosperm family Annonaceae are apocarpous, with very diverse gynoecial morphologies. Although several Annonaceae genera with apocarpous flowers are known to possess an extragynoecial compitum (EGC) that enables intercarpellary pollen-tube growth to enhance fertilization success, the occurrence of EGC across the whole family remains obscure. Twenty Annonaceae species from all four subfamilies (Anaxagoreoideae, Ambavioideae, Annonoideae, and Malmeoideae) are examined here, with anatomical evidence revealing the occurrence of stigmatic exudate-mediated suprastylar EGC in all four subfamilies. Histological and ontogenetic studies furthermore indicate that trichomes in Cananga and Drepananthus form a confluent zone that connects adjacent stigmas, providing a structural premise for suprastylar EGC. Infrastylar EGC are reported in the Annonaceae for the first time in several genera, including Artabotrys, Annona, and Miliusa, associated with the opening on the ovary ventral groove and/or basal placentation. In addition to the sister genera Isolona and Monodora that are clearly syncarpous, flowers of the distantly related genus Cyathocalyx with a unicarpellate gynoecium have also been hypothesized to be syncarpous. Evidence of carpel vasculature and primordium development does not support that the solitary Cyathocalyx carpel is originated from carpel fusion, however, although the increased number of ovules renders it functionally similar to syncarpy. Gynoecial features, including the extensive occurrence of EGC and the increased number of ovules per carpel (consonant with reduction to a solitary carpel) in Cyathocalyx, may have evolved to overcome limitations associated with apocarpy and possibly contribute to the reproductive success and diversification of the family.

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.

The earliest ovules or seeds widely reported from the Late Devonian (Famennian) are crucial for understanding the evolution of seed plants. Cosmosperma, the first Devonian seed documented in China and East Asia, is characterized by cupules with multiple segments enclosing a single ovule and covered by prickles. Two new Cosmosperma species, Cosmosperma dicrana sp. nov. and Cosmosperma lepta sp. nov., are now identified from the Upper Devonian (Wutong Formation) of Zhejiang and Anhui provinces, China, respectively. C. dicrana exhibits dichotomized fertile branches terminating in pairs of cupulate ovules, with centrifugally extending cupule segments at their distal portions. C. lepta displays slender cupulate ovules on pinnate fertile branches. Both species possess prickles on their cupules. A comparison with coeval seed plant taxa reveals differences in fertile branch types and suggests different evolutionary levels. The potentially weak dispersal ability of Cosmosperma is suggested by the absence of specialized structures for wind or water transport. Prickles on Cosmosperma cupules do not suggest adaptations for epizoochory but facilitate entanglement and friction. The adaptations for short-distance dispersal can be advantageous in a disturbed and heterogeneous environment. The presence of Late Devonian seed plant taxa with dispersal-adapted traits hints at habitat divergence, with some possibly inhabiting uplands or areas away from the coast. The prickles may also be an adaptation for maintaining stability in small- to medium-sized plants of the Late Devonian coastal communities.

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.

Five new spider fossils of the family Macrothelidae (Araneae: Mygalomorphae) are described from mid-Cretaceous Kachin amber, Myanmar. A new genus Acanthomacrothele gen. nov. is established for three new species: Acanthomacrothele pauciverrucae sp. nov., Acanthomacrothele geminata sp. nov., and Acanthomacrothele longicaudata sp. nov. Both male and female specimens of A. pauciverrucae sp. nov. are described, representing a rare case of a fossil spider with both sexes known. We also describe an unidentified juvenile of Macrothelidae to document different developmental stages of Cretaceous species. To test the phylogenetic position of the new fossils, we undertook phylogenetic analyses using both topology-unconstrained and topology-constrained methods. Our analyses supported the placement of Acanthomacrothele gen. nov. in Macrothelidae, although its phylogenetic relationship to other genera of Macrothelidae differed among different analytical methods. The fossils documented here have elongated, widely spaced posterior lateral spinnerets, compact rectangular group of eyes on a tubercle, and more spines on male tibia of anterior legs than female, similar to extant macrothelids, suggesting that they probably have similar retreat construction behavior, habitat preference, and mating position to their living relatives.

Rich materials can provide more opportunities for exploring the mechanisms of speciation driven by sexual selection. Being the fastest-evolving arthropods to date, the sword-tailed crickets of Nudilla Gorochov, 1988 (= Laupala Otte, 1994) have rapidly diverged primarily due to the variability of their calling songs (sexual signals). In addition, they also exhibit morphological conservatism, with little variation between species. Similar circumstances can be seen in tree crickets (Oecanthinae), which have conservative morphology and a diverse range of song variations. Thus, we believe that tree crickets could serve as a model for research on sexual selection since they share a similar evolutionary history and mode of differentiation with Nudilla. However, due to the improper methods in analyzing the calling songs and nearly identical morphological features between taxa, there are many problems with the taxonomy of Oecanthinae in China. To solve these problems, we conducted an integrative taxonomic study of Chinese Oecanthinae based on comparative morphology, species delimitation, acoustical analysis, and phylogenetic analysis. This study recognized 12 Oecanthinae species in China, including four new species, and confirmed one new synonym and two misidentifications. Meanwhile, we confirmed the morphological stability of Oecanthinae, and revealed that variation in color, size, and morphology may be intraspecific polymorphism, which sometimes does not reflect the species relationships. The result indicates that the acoustic parameter freq.median can be used for efficient and accurate species delimitation in Oecanthinae. We speculate that incomplete species divergence leads to complexity in species relationships at the genetic level of Oecanthinae. The conservation of morphological characters, the interspecificity of songs and the complexity of species relationships suggest that sexual selection have played a role in the evolution of Oecanthinae. Our study resolves some systematic and taxonomic problems of Oecanthinae, clarifies the species relationships of Oecanthinae in China, and provides clues for expanding the cricket groups to be used in speciation studies.

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.

Several species in the genus Oxalis occupy Peruvian fog oases (Lomas) with a significant habitat-adapted 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.

Gene duplications have contributed to the innovation of morphological traits during plant evolution. An outstanding example is the role of CYCLOIDEA2 (CYC2) gene duplications in the formation of the complex structure of Asteraceae capitula. Previous studies have shown that Chrysanthemum lavandulifolium (Fischer ex Trautv.) Makino and a few other species of the Asteraceae harbor two copies of CYC2e. Here, we identified a lineage-specific CYC2e duplication event at the root of the phylogeny of the tribe Anthemideae by analyzing the evolutionary history of CYC2 genes across the Asteraceae. Although the gene expression patterns of CYC2e1 and CYC2e2 were similar in most of floral organs, CYC2e1 promoted ligule elongation by promoting cell expansion, whereas CYC2e2 showed a weak inhibiting effect on the ray-floret development, and overexpression of CYC2e2 resulted in the maldevelopment of stamens in disc florets. These results indicated differentiated functions of CYC2e1 and CYC2e2 in the capitulum development of the Anthemideae. Given the previous data that identified CYC2g and CYC2d as main regulators in ligule morphogenesis, we comparatively analyzed 10 Asteraceae genomic data, and identified tandem arrays of CYC2g, CYC2d, and CYC2e. We further investigated the regulatory relationships between CYC2g/CYC2d and CYC2e genes, and found that CYC2g can activate the expression of CYC2e1. The findings of this study elucidate the synergistic roles of CYC2 genes in regulating the formation of the Asteraceae capitula and enhance understanding of the mechanism of duplicated gene retention during plant evolution.

Aquilaria (Thymelaeaceae), a tropical and subtropical plant, is one of the main genera that can produce agarwood. Aquilaria sinensis and Aquilaria yunnanensis are native Chinese tree species, and A. sinensis is China's main agarwood source. Agarwood is a nontimber forest product with high economic and medicinal value. First-grade agarwood is sold as much as $100 000 per kilogram. There has been little research on the saprobic fungi associated with Aquilaria, with only 11 records having been reported. In the present study, 10 terrestrial saprobic fungi associated with A. sinensis and A. yunnanensis were collected in China. Based on morphological and phylogenetic studies, these 10 collections are introduced herein as one new genus (Aquilariomyces), nine new species – Aquilariomyces aquilariae, Corynespora aquilariae, Melomastia maomingensis, Nigrograna aquilariae, Parathyridariella aquilariae, Peroneutypa maomingensis, Phaeoseptum aquilariae, Pseudothyridariella aquilariae, and Triangularia aquilariae, and one known species (Camarographium clematidis). Descriptions, illustrations of morphological characteristics, photo plates, phylogenetic trees, and the results of a pairwise homoplasy index test (PHI) test results are provided.

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 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.

During the Cretaceous period, the lacewing superfamily Mantispoidea, with an assemblage of species possessing raptorial forelegs, have undergone a rapid species radiation, characterized by abundant species richness and high morphological plasticity. Nevertheless, the morphology and early evolution of the specialized predatory organ around the time of its origin in raptorial Mantispoidea have been poorly documented due to the rarity of fossil evidence, especially for the pre-Cretaceous fossils. Herein, a new genus and new species, that is Archarhachiberotha longitarsa Wang, Ren et Wang gen. et sp. nov., was described from the Middle Jurassic Jiulongshan Formation of northeastern China. This new genus was characterized by the remarkable raptorial forelegs, that is, typically elongated coxa, relatively less-swollen femur and rudimentary small femoral spines, and well-developed tarsi. Considering the peculiar morphological combination and antiquity of the new genus, it was assigned to be a stem-group lineage of Mantispoidea. Also, the detailed analyses of morphology and biological functions of raptorial forelegs were made to conclude that the new genus evolved into an unknown but primitive raptorial type that was distinctly different from the extant morphological features and raptorial mechanisms. In addition, the evolutionary tendency of raptorial Mantispoidea herein summarized highlights morphological diversity and disparity between fossil and extant representatives, and provides a rare case to explore the entire evolutionary history of a specialized structure in one lineage.

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.

Assessing sampling biases caused by nonrandom specimen collecting is crucial in systematics, biogeography, and conservation. Nevertheless, research on the collecting biases of vascular plants in China remains limited. Here, we investigated the collecting status of gymnosperms in China using 48 673 herbarium specimens representing 180 Chinese gymnosperm species. The spatial and temporal patterns, collector and determiner biases, and phylogenetic and taxon biases were studied to comprehend the collecting bias of gymnosperms in China during 1900–2021. Meanwhile, we assessed the inventory completeness of gymnosperms to identify collecting hotspots and coldspots. The results showed that gymnosperms predominantly inhabit mountainous areas in China. The historical collecting of gymnosperms in China can be divided into two distinct stages with four peaks of collecting activities. The distribution of collected or identified specimens per individual displays significant skewness, and the collecting of gymnosperms has the issues of overcollecting or undersampling. Inventory completeness remains deficient, and collecting intensity is weak in both northern China and the range of 22°–25° N in the southern region (i.e., central Yunnan, southern Guangxi, and eastern Guangdong). Additionally, observation of the spatial distribution reveals both hotspots and coldspots scattered across mountain regions, lacking clustering. This study revealed a highly polarized collecting pattern for gymnosperms in China. Consequently, we recommend optimizing collecting measures, targeted specimen collecting, and continuous dynamic monitoring of gymnosperms in future collecting efforts. These recommendations hold relevance not only for gymnosperms in China but also for other land plants worldwide.

A full understanding of local adaptation at the genomic level will help to elucidate its role in the differentiation between closely related species. This study focused on rice seed bugs sister species (Leptocorisa chinensis and Leptocorisa oratoria), which are native to East Asia and are notorious pests targeting growing rice spikelets. East Asia is a region where diverse geology and fluctuating climate are known to have profound impacts on organisms. In this study, single nucleotide polymorphisms (SNPs) from double-digest restriction site-associated DNA sequencing and geographic distribution information were used to investigate phylogeography and assess the environmental contribution to genetic variation. We found clear genetic differentiation between sister species, but a lack of genetic structure within species because of their long-distance dispersal ability. The demographic model involved a scenario in which divergence in isolation (~0.6 Ma) was followed by secondary contact (~7 kya). The initial divergence may have been caused by the intensification of the East Asian monsoon during the Pleistocene climate oscillation. The historical demography indicated that the effective population size (N_e) showed an evident increase from 9 to 7 kya, which may be related to rice domestication and extensive human cultivation during the Holocene. We also detected a significant correlation between genetic and environmental distance, and the niche difference occupied between them. Temperature-related variables were ranked as the main factors for the difference, and 410 selective SNPs involved in adaptation were identified. The Nanling Mountains in southern China serve as a geographical boundary between them and act as an ecological barrier belt that promotes local environmental adaptation. Our study demonstrates that historical climate change and local adaptation by climate-imposed selection shape the phylogeographical patterns of sister species.

Based on several earwigfly specimens with well-preserved mouthparts of Meropeidae from mid-Cretaceous Burmese amber, a detailed, initial analysis was conducted of the structure of Mesozoic meropeids. Compared to the singularly flattened mandible of modern meropeids, the new specimens reveal that Mesozoic representatives had two distinct types of mandibles: blade-shaped and scoop-shaped. Current fossil evidence indicates that during the Mesozoic Era, Meropeidae displayed sexual dimorphism that was reflected in the structure of their mandibles. This structural difference may indicate that about 99 million years ago, meropeids had a more complex diet than extant confamilial taxa. Phylogenetic results suggest that Torvimerope gen. nov., along with Burmomerope, two extinct genera, form a clade and that are the sister taxon to crown-group Meropeidae. The new material offers new possibilities for inferring the feeding habits and mating behavior of early Meropeidae.

Ecological interactions and evolutionary processes in areas of endemism remain little studied despite the fact that identifying the patterns of functional signatures in areas of endemism could reveal important information regarding community assembly and functioning. Here, we investigated whether areas of endemism of the orchids of Megamexico are hotspots of biotic interactions by comparing the orchid–pollinator interactions with those of adjacent areas. Patterns of functional signatures and phylogenetic signal were estimated, using pollination syndromes as a proxy for functional attributes. Phylogenetic signal was estimated by coding pollinator groups for every orchid recorded. Metrics of the interaction networks and the phylogenetic signal were compared with those obtained from adjacent areas. Our results indicate that areas of endemism show higher significant differences in the phylogenetic signal compared with adjacent areas. This can be explained by the many distantly related orchid lineages sharing attributes related to pollination. Network size and robustness differed statistically between the areas of endemism and the adjacent areas. The same configuration of modules in interaction networks was found in the areas of endemism; however, remarkably, the composition of species in large genera differed in these areas. Areas of endemism harbor more orchid lineages that closely interact with many groups of insects. The southerly areas of endemism in Chiapas and Central America are prominent, with the most significant phylogenetic signal and networks metrics. Results indicate that areas of endemism for the orchids of Megamexico represent hotspots of biotic interactions. Strategies for conservation must take this biotic interaction into account.

Eucalypt fossils were widely reported from the Cenozoic deposits across the Southern Hemisphere (Australia, New Zealand, and Argentina). However, no attached reproductive and vegetative fossil remains of this myrtaceous clade have been discovered till now. We report and describe for the first time a fossil eucalypt twig with attached foliage, flower buds, and mature flowers from the early Eocene (~55-52 Ma) sediments (Palana Formation) of Rajasthan, western India. As both vegetative and reproductive organs are in organic connection, they clearly represent the same species. In addition, here we also introduce fossil materials of isolated leaves, flower buds, inflorescence, and flowers recovered from the same stratigraphic level. Our Eocene fossils and extant members of the eucalypt clade are related morphologically by means of robust, thick petiolate lanceolate-shaped leaves with intramarginal secondary veins; operculate flower buds consisting of imbricate petals with discernable margins; solitary inflorescence with three flowers per umbellaster, epigynous and bisexual flowers. Based upon combined characteristics of leaf, flower, and bud morphology, these fossils conform to the Eucalypt clade and are recognized as a new fossil genus and species: Hindeucalyptus eocenicus Patel, R.F. Almeida, Ali et Khan gen. nov. et sp. nov. We also compare it with extant and extinct eucalypts using morphological phylogeny and character mapping analyses. In addition, we briefly discuss its phytogeographic and paleoclimatic implications regarding the distribution and habitat of fossil and modern eucalypts.