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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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 chromosomelevel 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.

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.

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.

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.

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.

The small subfamily Linnaeoideae of Caprifoliaceae exhibits a disjunct distribution in Eurasia and North America, including Mexico, with most taxa occurring in eastern Asia or Mexico and the monospecific Linnaea Gronov. ex L. having a circumboreal to north temperate distribution. We sampled 17 of the 20 species representing all Linnaeoideae genera and used nuclear (target enrichment) and complete plastome sequence data to reconstruct the phylogeny. Our results show strong topological conflicts between nuclear and plastid data, especially concerning Dipelta Maxim. and Diabelia Landrein, supporting hybridization events complicating the deep diversification. Nuclear data were used for divergence time estimation and ancestral area reconstruction. The divergence time between the Mexican Vesalea M. Martens & Galeotti and the Linnaea clade was dated to 39.5 Ma, with a 95% highest posterior density of 28.2 Ma (mid-Oligocene) to 45.2 Ma (mid-Eocene). Reconstructed ancestral areas support a widespread common ancestor of Linnaea plus Vesalea in Mexico and at least another area (eastern Asia, North America, or Europe). The biogeographic analysis, including fossils, supports the ancestral range of Linnaeoideae to be widespread in central and western China + Europe + Mexico, or eastern and northern Asia + central and western China + Mexico, or central and western China + North America + Mexico. The North Atlantic and/or the Bering land bridges may be important in the widespread distribution across continents in the Northern Hemisphere. Our study highlights the importance of utilizing fossils in biogeographic inferences andusing data from different genomes while reconstructing deep and shallow phylogenies of organisms.

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.

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.

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.

As an important halophyte in the Yellow River Delta, the Amaranthaceae C₃ Suaeda salsa (L.) Pall. has attracted much attention for the “red carpet” landscape, and could be simply divided into red and green phenotypes according to the betacyanin content in the fleshy leaves. However, S. salsa has not been sequenced yet, which limited people's understanding of this species at the molecular level. We constructed a high-quality chromosome-scale reference genome by combining high-throughput sequencing, PacBio single molecule real-time sequencing, and Hi-C sequencing techniques with a genome size of 445.10 Mb and contigs N50 of 2.94 Mb. Through the annotation of the S. salsa genome, 298.76 Mb of the repetitive sequences and 23 965 protein-coding genes were identified, of which the proportion of long terminal repeats type in the repetitive sequences was the most abundant, about 50.74% of the S. salsa genome. Comparative genomics indicated that S. salsa underwent a whole-genome duplication event about 146.15 million years ago (Ma), and the estimated divergence time between S. salsa and Suaeda aralocaspica was about 16.9 Ma. A total of four betacyanins including betanidin, celosianin II, amaranthin and 6′-O-malonyl-celosianin II were identified and purified in both phenotypes, while two significantly up-regulated betacyanins (celosianin II and amaranthin) may be the main reason for the red color in red phenotype. In addition, we also performed transcriptomics and metabolomics in both phenotypes to explore the molecular mechanisms of pigment synthesis, and a series of structural genes and transcription factors concerning with betacyanin production were selected in S. salsa.

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.

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.