Over the past two decades, our understanding of Lauraceae, a large family of woody plants, has undergone significant advances in phylogeny, taxonomy, and biogeography. Molecular systematic studies have elucidated the basic relationships within the family with plastid phylogenomic analyses providing robust support for deep-level relationships between Lauraceae lineages, leading to the recognition of nine tribes: Hypodaphnideae, Cryptocaryeae, Cassytheae, Neocinnamomeae, Caryodaphnopsideae, Mezilaureae, Perseeae, Laureae, and Cinnamomeae, with Mezilaureae validated here. Nuclear genomes and comparative genomics studies have also clarified aspects of the family’s evolutionary history and metabolic diversity. Taxonomic studies have focused mainly on the most diverse regions, e.g., tropical Asia, tropical America, and Africa (Madagascar), with six new genera described and five reinstated since the last major overview of the family. The extensive fossil record suggests that Lauraceae diversified globally during the Late Cretaceous and Early Cenozoic. Biogeographic studies indicate that different lineages of the family are sorted into Gondwanan and Laurasian lineages, with patterns resulting from the disruption of boreotropical flora and multiple long-distance dispersal events. Phylogeographic studies, predominantly from East Asia, have shown patterns of in situ survival and demographic stability or expansion during the Quaternary. Nevertheless, many systematic relationships within the family remain unresolved and further research is needed into the complex biogeographic history and ecological roles of Lauraceae. A multifaceted approach integrating genomic studies, field work, morphological and ecological investigations is therefore needed to understand the evolution and diversity of this ecologically and economically significant plant family.

Comparative analyses in ecology and evolution often face the challenge of controlling for the effects of shared ancestry (phylogeny) from those of ecological or trait-based predictors on species traits. Phylogenetic Generalized Linear Models (PGLMs) address this issue by integrating phylogenetic relationships into statistical models. However, accurately partitioning explained variance among correlated predictors remains challenging. The phylolm.hp R package tackles this problem by extending the concept of “average shared variance” to PGLMs, enabling nuanced quantification of the relative importance of phylogeny and other predictors. The package calculates individual likelihood-based R² contributions of phylogeny and each predictor, accounting for both unique and shared explained variance. This approach overcomes limitations of traditional partial R² methods, which often fail to sum the total R² due to multicollinearity. We demonstrate the functionality of phylolm.hp through two case studies: one involving continuous trait data (maximum tree height in Californian species) and another focusing on binary trait data (species invasiveness in North American forests). The phylolm.hp package offers researchers a powerful tool to disentangle the contributions of phylogenetic and ecological predictors in comparative analyses.

The ecological and evolutionary mechanisms underlying montane biodiversity patterns remain unresolved. To understand which factors determined community assembly rules in mountains, biogeographic affinity that represents the biogeographic and evolutionary history of species should incorporate with current environments. We aim to address two following questions: 1) How does plant taxonomic and phylogenetic diversity with disparate biogeographic affinities vary along the subtropical elevational gradient? 2) How do biogeographic affinity and environmental drivers regulate the community assembly? We collected woody plant survey data of 32 forest plots in a subtropical mountain of Mt. Guanshan with typical transitional characteristics, including 250 woody plant species belonging to 56 families and 118 genera. We estimated the effects of biogeographic affinity, climate and soil properties on taxonomic and phylogenetic diversity of plant communities employing linear regression and structural equation models. We found that the richness of temperate-affiliated species increased with elevations, but the evenness decreased, while tropical-affiliated species had no significant patterns. Winter temperature directly or indirectly via biogeographic affinity shaped the assemblage of woody plant communities along elevations. Biogeographic affinity affected what kind of species could colonize higher elevations while local environment determined their fitness to adapt. These results suggest that biogeographic affinity and local environment jointly lead to the dominance of temperate-affiliated species at higher elevations and shape the diversity of woody plant communities along elevational gradients. Our findings highlight the legacy effect of biogeographic affinity on the composition and structure of subtropical montane forests.

Intraspecific genetic variance and gene flow can support the adaptive evolution of species challenged by climate shifts or novel environmental conditions. Less well understood is how genome organization and gene flow interact in closely related species during evolutionary divergence and differentiation. Here we conducted genomic footprint analyses to determine how three species of Pterocarya (P. stenoptera, P. hupehensis, and P. macroptera), which are sympatric but occupy different elevational niches, adapted to the heterogeneous environment of the Qinling-Daba Mountains, China. We identified candidate genes for environmental adaptation (i.e., PIEZO1, WRKY39, VDAC3, CBL1, and RAF), and also identified regions of gene introgression between P. hupehensis and P. macroptera that show lower genetic load and higher genetic diversity than the rest of their genomes. The same introgressed regions are notably situated in areas of minimal genetic divergence yet they are characterized by elevated recombination rates. We also identified candidate genes within these introgressed regions related to environmental adaptation (TPLC2, CYCH;1, LUH, bHLH112, GLX1, TLP-3, and ABC1). Our findings have thus clarified the important role of gene flow in ecological adaptation and revealed genomic signatures of past introgression. Together, these findings provide a stronger theoretical basis for understanding the ecological adaptation and conservation of Quaternary relict woody plants in East Asia.

Mimetic seeds attract birds to disperse seeds mainly by mimicking fleshy fruits or arillate seeds, however, they provide little nutritive reward for bird dispersers. The key characteristics of mimetic seeds are conspicuous seed color, hard seed coat, certain toxic secondary metabolites, and perhaps smooth waxy layer. In this review, we discuss the global distribution of mimetic seeds, the interaction of mimetic seeds with bird dispersers, and secondary metabolites that underlie key characteristics of mimetic seeds. Mimetic-seed species mainly occur in the tropics, with large numbers distributed along coastal areas. The interaction between mimetic-seed species and bird dispersers can be antagonistic, mutualistic, or both. These interactions are generally established by conspicuous visual cues and hard tactile cues from mimetic seeds. The formation and variation of key characteristics of mimetic seeds may contribute to the metabolism of several kind of secondary compounds. Here, we also discuss mimetic-seed dispersal in the context of an evolutionary game, and propose several aspects of mimetic-seed dispersal that remain unstudied. While this review is based on preliminary findings and does not account for other potential influencing factors such as climate, it is expected to contribute to an improved understanding of mimetic-seed dispersal.

The genus Salix is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of Salix is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 Salix accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of Salix, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved Salix into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of Salix into five subgenera: Salix, Urbaniana, Triandrae, Longifoliae and Vetrix. We observed a significant acceleration in the diversification rate within the Chamaetia-Vetrix clade, while Salix exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of Salix. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of Salix relationships.

The sugarcane subtribe Saccharinae (Andropogoneae, Poaceae) was established in 1846, but its delimitation has long been debated. Moreover, the relationships among the genera of Saccharinae remain unclear, and there is no consensus on whether Pseudosorghum, a small genus in tropical Asia with only two species, should be included. Here, we performed phylogenomic analyses using whole plastomes (69 of them newly sequenced) from 132 individuals, representing 65 species in 19 related genera. We also built trees with nuclear ribosomal DNA sequences. Our results justify the inclusion of Pseudosorghum, likely also the Eulalia Clade III, in Saccharinae. Furthermore, both morphological and molecular analyses support merging the two Pseudosorghum species. The backbone relationships of the Saccharinae phylogeny were highly supported with four polyphyletic clades of Miscanthus and the inclusion of Narenga and Tripidium rufipilum in Saccharum. Pseudosorghum is moderately supported as sister to the Miscanthus Clade I, while the remaining Tripidium species could be excluded from the subtribe. Saccharinae is estimated to have originated ~3.73 million years ago in East Asia, followed by intercontinental dispersals. Our study provides a comprehensive phylogenetic framework for future taxonomic revisions of this economically important subtribe.

Change of flower color can readily lead to a shift in pollinators, potentially causing pollinator mediated reproductive isolation or even speciation. Here, we examined the ecological and evolutionary consequences of flower color polymorphism in Roscoea cautleoides, an alpine ginger with sympatric distribution of purple- and yellow-flowered plants. Variations in pollinator visitation and specialization to the flower color contributed greatly to pre-zygotic reproductive isolation, with post-zygotic isolation also observed in reciprocal pollination. Yellow-flowered plants evolved independently from purple-flowered plants in two populations due to the absence of anthocyanins, as supported by metabolic, expression, and genetic analysis. Despite early genetic divergence between the two-flower-colored plants, highly differentiated genes were associated with reproduction and stress, while highly selective genes were enriched in stress. Our results suggest that parallel loss of anthocyanins leads to flower color polymorphism in different populations of R. cautleoides, with pollinator preference contributing to reproductive isolation and subsequent genetic differentiation, indicating the process of incipient speciation triggered by flower color changes with sympatric distribution.

Subtropical evergreen broad-leaved trees are usually vulnerable to freezing stress, while hexaploid wild Camellia oleifera shows strong freezing tolerance. As a valuable genetic resource of woody oil crop C. oleifera, wild C. oleifera can serve as a case for studying the molecular bases of adaptive evolution to freezing stress. Here, 47 wild C. oleifera from 11 natural distribution sites in China and 4 relative species of C. oleifera were selected for genome sequencing. “Min Temperature of Coldest Month” (BIO6) had the highest comprehensive contribution to wild C. oleifera distribution. The population genetic structure of wild C. oleifera could be divided into two groups: in cold winter (BIO6 ≤ 0 °C) and warm winter (BIO6 > 0 °C) areas. Wild C. oleifera in cold winter areas might have experienced stronger selection pressures and population bottlenecks with lower N_e than those in warm winter areas. 155 single-nucleotide polymorphisms (SNPs) were significantly correlated with the key bioclimatic variables (106 SNPs significantly correlated with BIO6). Twenty key SNPs and 15 key copy number variation regions (CNVRs) were found with genotype differentiation > 50% between the two groups of wild C. oleifera. Key SNPs in cis-regulatory elements might affect the expression of key genes associated with freezing tolerance, and they were also found within a CNVR suggesting interactions between them. Some key CNVRs in the exon regions were closely related to the differentially expressed genes under freezing stress. The findings suggest that rich SNPs and CNVRs in polyploid trees may contribute to the adaptive evolution to freezing stress.

The black wolfberry (Lycium ruthenicum; 2n = 2x = 24) is an important medicinal plant with ecological and economic value. Its fruits have numerous beneficial pharmacological activities, especially those of anthocyanins, polysaccharides, and alkaloids, and have high nutritional value. However, the lack of available genomic resources for this species has hindered research on its medicinal and evolutionary mechanisms. In this study, we developed the telomere-to-telomere (T2T) nearly gapless genome of L. ruthenicum (2.26 Gb) by integrating PacBio HiFi, Nanopore Ultra-Long, and Hi-C technologies. The assembled genome comprised 12 chromosomes with 37,149 protein-coding genes functionally annotated. Approximately 80% of the repetitive sequences were identified, of which long terminal repeats (LTRs) were the most abundant, accounting for 73.01%. The abundance of LTRs might be the main reason for the larger genome of this species compared to that of other Lycium species. The species-specific genes of L. ruthenicum were related to defense mechanisms, salt tolerance, drought resistance, and oxidative stress, further demonstrating their superior adaptability to arid environments. Based on the assembled genome and fruit transcriptome data, we further constructed an anthocyanin biosynthesis pathway and identified 19 candidate structural genes and seven transcription factors that regulate anthocyanin biosynthesis in the fruit developmental stage of L. ruthenicum, most of which were highly expressed at a later stage in fruit development. Furthermore, 154 potential disease resistance-related nucleotide-binding genes have been identified in the L. ruthenicum genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the L. ruthenicum genome enriched the number of genes involved in anthocyanin synthesis and resistance-related pathways. These results provide an important genetic basis for understanding genome evolution and biosynthesis of pharmacologically active components in the Lycium genus.

Integrative data from plastid and nuclear loci are increasingly utilized to resolve species boundaries and phylogenetic relationships within major angiosperm clades. Debregeasia (Urticaceae), an economically important genus, presents challenges in species delimitation due to its overlapping morphological traits and unstable taxonomic assignments. Here, we analyzed 14 morphological traits and generated 12 data matrices from the plastomes and nrDNA using genome skimming from the nine recognized morphospecies to clarify species boundaries and assess barcode performance in Debregeasia. We also used a universal set of 353 nuclear genes to explore reticulate evolution and biogeographic history of Debregeasia. Plastomes of Debregeasia exhibited the typical quadripartite structure with conserved gene content and marginal independent variations in the SC/IR boundary at inter- and intra-specific levels. Three Debregeasia species were non-monophyletic and could not be discerned by any barcode; however, ultra-barcodes identified the remaining six (67%), outperforming standard barcodes (56%). Our phylogenetic analyses placed Debregeasia wallichiana outside the genus and suggested six monophyletic clades in Debregeasia, although the placement between Debregeasia hekouensis and Debregeasia libera varied. There was extensive trait overlap in key morphologically diagnostic characters, with reticulation analysis showing potentially pervasive hybridization, likely influenced by speciation patterns and overlaps between species ranges. We inferred that Debregeasia crown diversification began at ca. 12.82 Ma (95% HPD: 11.54-14.63 Ma) in the mid-Miocene within Australia, followed by vicariance and later long-distance dispersal, mainly out of southern China. Our findings highlight the utility of genomic data with integrative lines of evidence to refine species delimitation and explore evolutionary relationships in complex plant lineages.

Studies on plant diversity are usually based on the total number of species in a community. However, few studies have examined species richness (SR) of different plant life forms in a community along large-scale environmental gradients. Particularly, the relative importance (RIV) of different plant life forms in a community and how they vary with environmental variables are still unclear. To fill these gaps, we determined plant diversity of ephemeral plants, annual herbs, perennial herbs, and woody plants from 187 sites across drylands in China. The SR patterns of herbaceous plants, especially perennial herbs, and their RIV in plant communities increased with increasing precipitation and soil nutrient content; however, the RIV of annual herbs was not altered along these gradients. The SR and RIV of ephemeral plants were affected mainly by precipitation seasonality. The SR of woody plants had a unimodal relationship with air temperature and exhibited the highest RIV and SR percentage in plant communities under the harshest environments. An obvious shift emerged in plant community composition, SR and their critical impact factors at 238.5 mm of mean annual precipitation (MAP). In mesic regions (> 238.5 mm), herbs were the dominant species, and the SR displayed a relatively slow decreasing rate with increasing aridity, which was mediated mainly by MAP and soil nutrients. In arid regions (< 238.5 mm), woody plants were the dominant species, and the SR displayed a relatively fast decreasing rate with increasing aridity, which was mediated mainly by climate variables, especially precipitation. Our findings highlight the importance of comparative life form studies in community structure and biodiversity, as their responses to gradients differed substantially on a large scale.

Understanding how and why assemblage dissimilarity changes along spatial gradient is a great challenge in ecology, because answers to these questions depend on the analytical types, dimensions, and components of beta diversity we concerned. To obtain a comprehensive understanding of assemblage dissimilarity and its implications for biodiversity conservation in the Himalayas, we explored the elevational patterns and determinants of beta diversity and its turnover and nestedness components of pairwise and multiple types and taxonomic and phylogenetic dimensions simultaneously. Patterns of beta diversity and their components of different types and dimensions were calculated based on 96 sampling quadrats along an 1800-5400 m elevational gradient. We examined whether and how these patterns differed from random expectations using null models. Furthermore, we used random forest methods to quantify the role of environmental variables representing climate, topography, and human disturbance in determining these patterns. We found that beta diversity and its turnover component, regardless of its types and dimensions, shown a hump-shaped elevational patterns. Both pairwise and multiple phylogenetic beta diversity were remarkably lower than their taxonomic counterpart. These patterns were significantly less than random expectation and were mostly associated with climate variables. In summary, our results suggested that assemblage dissimilarity of seed plants was mostly originate from the replacement of closely related species determined by climate-driven environmental filtering. Accordingly, conservation efforts should better cover elevations with different climate types to maximalize biodiversity conservation, rather than only focus on elevations with highest species richness. Our study demonstrated that comparisons of beta diversity of different types, dimensions, and components could be conductive to consensus on the origin and mechanism of assemblage dissimilarity.

The future distribution of invading species depends on the climate space available and certain life history traits that facilitate invasion. Here, to predict the spread potential of plant species introduced in North America north of Mexico (NAM), we compiled distribution and life history data (i.e., seed size, life form, and photosynthetic pathways) for 3021 exotic plant species introduced to NAM. We comparatively examined the species’ range size and climate space in both native and exotic regions and the role of key life history traits. We found that large climate space for most exotic plants is still available in NAM. The range sizes in global exotic regions could better predict the current range sizes in NAM than those in global native regions or global native plus exotic regions. C3 species had larger ranges on average than C4 and CAM plants, and herbaceous species consistently showed stronger relationships in range size between native and exotic regions than woody species, as was the case within the C3 species group. Seed size was negatively related to range size both in native regions and in NAM. However, seed size surprisingly showed a positive correlation with global exotic range size and no correlation with the current actual global (native plus exotic) range size. Our findings underline the importance of species’ native distribution and life history traits in predicting the spread of exotic species. Future studies should continue to identify potential climate space and use underappreciated species traits to better predict species invasions under changing climate.

The formation of pantropical intercontinental disjunction (PID) in plants has generally been attributed to vicariance, boreotropical migration, and long-distance dispersal. However, this pattern has primarily been examined in herbs, shrubs, and trees, and less commonly studied in interlayer plant taxa. Here we examined evolutionary processes that resulted in the PID of a pantropical woody liana, Uncaria (Rubiaceae). We first constructed a comprehensive phylogeny by employing 73 plastid protein-coding sequences from 29 accessions of Uncaria (including 16 newly sequenced) from different continents. We then inferred divergence time, history and ecological niche evolution of this genus. Our results showed that Uncaria consisted of four well-supported clades that belonged to two geographically distinct lineages: the Asia-Oceania lineage and the Afro-Neotropical lineage. Biogeographic reconstruction showed this genus likely originated in Asia during the early Miocene (ca. 19.03 Ma) and the Middle Miocene Climatic Optimum may have triggered the early diversification of Uncaria. Due to its recent origin and small seeds with long wings, wind or water-mediated long-distance dispersal may have contributed to the distribution of Uncaria in tropical Oceania (via stepping-stone dispersal) and tropical Africa and America (by transoceanic dispersal). Our findings also indicate that diversification of Uncaria was primarily driven by ecological niche divergence, particularly climatic factors. Our study emphasizes the dual role of climatic niche divergence and long-distance dispersal in shaping the PID of Uncaria, providing references for many other extant lineages with similar distributions.

Herbaceous plants are an essential component of forest diversity and driver of ecosystem processes. However, because the growth forms and life-history strategies of herbaceous plants differ from those of woody plants, it is unclear whether the mechanisms that drive patterns plant diversity and community structure in these two plant groups are the same. In this study, we determined whether herb and woody plant communities have similar patterns and drivers of alpha- and beta-diversity. We compared species richness, distribution, and abundance of herbs to woody seedlings in a 20-ha Donglingshan warm-temperate forest (Donglingshan FDP), China. We also determined whether variation in patterns of species richness and composition are better explained by environmental or spatial variables. Herbaceous plants accounted for 72% of all species (81 herbaceous, 31 woody) recorded. Alpha- and beta-diversity were higher in herbs than in woody seedlings. Although alpha-diversity of herbs and woody seedlings was not correlated across the site, the local-site contributions to beta-diversity for herbs and woody seedlings were negatively correlated. Habitat type explained slightly more variation in herb community composition than in woody seedling composition, with the highest diversity in the low-elevation slope. Environmental variables explained the variation in species richness and composition more in herbaceous plants than in woody seedlings. Our results indicate that different mechanisms drive variation in the herb and woody seedling communities, with herbs exhibiting greater environmental sensitivity and habitat dependence. These findings contribute to the better understanding of herbaceous plant diversity and composition in forest communities.

Biological collections are critical for the understanding of species distributions and for formulating biodiversity conservation strategies. However, biological collections are susceptible to various biases, including the “road-map effect”, meaning that the geography of biological collections can be influenced by road networks. Here, using species occurrence records derived from 921,233 plant specimens, we quantified the intensity of the “road-map effect” on floristic collections of China, and investigated its relationships with various environmental and socio-economic variables. Species occurrence records mainly distributed in major mountain ranges, while lowlands were underrepresented. The distance of species occurrence records to the nearest road decreased from 19.54 km in 1960s to 3.58 km in 2010s. These records showed significant clustering within 5 km and 10 km buffer zones of roads. The road density surrounding these records was significantly higher than that in random patterns. Collectively, our results confirmed a significant “road-map effect” in the floristic collections of China, and this effect has substantially intensified from the 1960s to the 2010s, even after controlling for the impact of road network expansion. Topographic, climatic and socio-economic variables that determine regional species diversity, vegetation cover and human impact on vegetation played crucial roles in predicting the intensity of the “road-map effect”. Our findings indicate that biological surveys have become increasingly dependent on road networks, a trend rarely reported in published studies. Future floristic surveys in China should prioritize the lowland areas that have experienced stronger human disturbances, as well as remote areas that may harbor more unique and rare species.

Rivers are crucial in the spread of invasive plants. Invasive plants alter their seed traits to adapt to environmental changes and promote invasion. Studying the trait changes in invasive plant seeds may improve the understanding of their propagation mechanisms along the river and provide appropriate control measures. In this study, seven Ambrosia trifida populations along the Liaohe River were used as study subjects. The results showed that the seven A. trifida populations were closely related and exhibited a certain gene exchange, but the absence of evidence of directed gene flow among populations did not confirm that rivers were the medium of seed dispersal of A. trifida. Along the Liaohe River, from top to bottom, the positive view area, length, width, perimeter, and thousand seed weight of A. trifida seeds showed an increasing trend. The total nitrogen and phosphorus contents in the river water of the A. trifida population in the lower reaches of the Liaohe River were higher than those at the other sites. Furthermore, along the river, from top to bottom, the available nitrogen, total nitrogen, total potassium, available potassium, and organic matter contents in the soil in which A. trifida populations grew showed significant increasing trends. River structure, water quality, and soil nutrients had direct and indirect effects on seed morphology. Soil total nitrogen, available potassium, and organic matter had significant positive effects on seed positive view area and perimeter, suggesting that the maternal effect played a critical role in shaping seed morphology. Our analysis showed that soil nutrients along the river may be the primary driver that governs changes in A. trifida seed traits.

The utilization of palynological data for plant diversity reconstructions offers notable advantages in addressing the discontinuity of plant fossils in the stratigraphic record. However, additional studies of modern processes are required to validate or refine the accuracy of diversity results obtained from palynological data. In this study, we used a modern pollen dataset of China to compare the accuracy of plant diversity reconstructions using five different palynological diversity indices (i.e., the pollen species number, Berger–Parker index, Simpson diversity index, Hill index, and Shannon–Wiener index) over a large spatial scale. We then identified climate factors that are most strongly correlated with these patterns of plant diversity. We found that the index that most accurately reflects plant diversity is the Shannon–Wiener index. Our analyses indicated that the most effective indices at reflecting plant diversity are the Shannon–Wiener index and Berger–Parker index. Numerical analysis revealed that palynological diversity (measured using the Shannon–Wiener index) was strongly correlated with climatic parameters, in particular average temperature in the coldest month and annual precipitation, suggesting these factors may be primary determinants of plant diversity distribution. We also found that a threshold value of the normalized Shannon–Wiener index (NH = 0.4) approximately aligns with the contour line specifying 400 mm annual precipitation, serving as a rudimentary indicator for assessing plant diversity in arid versus humid climates. This study suggests that pollen diversity indices have remarkable potential for quantitatively reconstructing paleoclimatic parameters.

Root anatomical traits play an important role in understanding the link between root physiological function and ecological process. To determine how plants change root anatomical traits to adapt to distinct environments, we measured four key root anatomical traits—stele diameter (SD), cortex thickness (CT), root diameter (RD), and the stele to root diameter ratio (SDRD)—of first-order roots of 82 species collected from different vegetation zones along a 2000 m altitudinal gradient on the northern slope of Taibai Mountain. Compared with other altitudes, plants located in temperate birch and fir forests had thinner SD, CT, RD, and SDRD. We found that elevational variation in root anatomical traits could largely be explained by phylogenetic taxonomy (clade). In addition, changes in SD were driven by soil bulk density, whereas variations in CT and RD were influenced by soil available nitrogen. When phylogenetic factors were removed from our analysis, allometric relationships between RD and root anatomical traits (SD and CT) were observed across different altitudes. Our study reveals the influence of phylogeny and environment on the elevational variation in root anatomical traits and further supports the allometric relationship between root anatomical traits (SD and CT) and RD. These findings enhance our understanding of the evolutionary and adaptive mechanisms of root anatomical structures, providing a basis for predicting how root anatomical traits respond to global changes.

The parasitic dodder (Cuscuta, Convolvulaceae) species have wide ranges of hosts. However, some plants, including the cultivated tomato (Solanum lycopersicum), have different degrees of resistance to Cuscuta. The cultivated tomato plants activate a strong hypersensitive response (HR) where Cuscuta haustoria penetrate stems of cultivated tomato, but the underlying mechanisms by which the cultivated tomato perceives Cuscuta and activates resistance remain unclear. In this study, we show that the phytohormones jasmonic acid (JA) and salicylic acid (SA) in cultivated tomato stems were highly induced by Cuscuta australis parasitization. Genetic analyses and experiments of supplementation of JA or SA indicated that the JA and SA pathway not only are both required for activation of HR against Cuscuta parasitization but also function in non-HR-based resistance. The Cuscuta Receptor 1 (CuRe1), which is a leucine-rich repeat receptor-like protein, and suppressor of BAK1-interacting receptor kinase (SOBIR1) and SOBIR1-like, two adaptor kinases, are also important for HR-based and non-HR-based resistance. Importantly, we found that the JA and SA pathway both transcriptionally regulate CuRe1. However, in the cure1 mutants, JA and SA levels were still normally induced by C. australis parasitization. We propose a linear model that an unknown receptor perceives Cuscuta parasitization and thus triggers accumulation of JA and SA, which in turn induce the transcription of CuRe1, and CuRe1 and SOBIR1/SOBIR1-like thereby activate HR-based and non-HR-based resistance to Cuscuta. This study underscores the important roles of hormone signaling and resistance (R) genes in host plant-parasitic plant interactions.

Species boundaries are dynamic and constantly challenged by gene flow. Understanding the strategies different lineages adopt to maintain ecological and genetic distinctiveness requires employing an integrative species concept that incorporates data from a variety of sources. In this study, we incorporated genetic, ecological, and environmental evidence to assess the extent of speciation or evolutionary divergence within a monophyletic yet dimorphic group (i.e., clade Leucolirion consisting of six species) within the genus Lilium. This clade consists of two lineages that exhibit unexpectedly distinct perianth appearances: whitish trumpet (funnel form, encompassing four species) and orange recurved (reflex form, including two species), respectively, which are separated by completely different pollination syndromes. Transcriptome-based nuclear and plastome datasets indicate that these two lineages are isolated, with only weak ancient gene flow between them. Within each lineage, several taxa with incomplete isolation have diverged, as indicated by weak genetic structure, strong gene flow, and conflicts between nuclear and chloroplast phylogenies, especially in the trumpet lineage. Although these taxa are not entirely independent, our evidence indicates that they are diverging, with recent gene flow disappearing and multiple isolation strategies emerging, such as differences in flowering time and niche specialization. Taken together, our findings suggest that species divergence and maintenance in Lilium are driven by a combination of adaptive and non-adaptive processes, highlighting the complex interplay of historical climate changes, ecological adaptation, and gene flow in shaping biodiversity within this genus.

The presence of heterozygous individuals in a population is crucial for maintaining genetic diversity, which can positively affect fitness and adaptability to environmental changes. While inbreeding generally reduces the proportion of heterozygous individuals in a population, polyploidy tends to increase the proportion. North American Populus tremuloides is one of the most widely distributed and ecologically important tree species in the Northern Hemisphere. However, genetic variation in Mexican populations of P. tremuloides, including the genetic signatures of their adaptation to a variety of environments, remains largely uncharacterized. The aim of this study was to analyze how inbreeding coefficient (F_IS) and ploidy are associated with clonal richness, population cover, climate and soil traits in 91 marginal to small, isolated populations of this tree species throughout its entire distribution in Mexico. Genetic variables were determined using 36,810 filtered SNPs derived from genome re-sequencing. We found that F_IS was approximately between 0 and -1, indicating an extreme heterozygosity excess. One key contributor to the observed extreme heterozygosity excess was asexual reproduction, although ploidy levels cannot explain this excess. Analysis of all neutral SNPs showed that asexual reproduction was positively correlated with observed heterozygosity (H_o) but negatively correlated with expected heterozygosity (H_e). Analysis of outlier SNPs also showed that asexual reproduction was positively correlated with H_o and negatively correlated with H_e, although this latter correlation was not significant. These findings support the presence of a Meselson effect.

The expansion of road networks in recent decades has drawn considerable attention due to its impact on biodiversity in high-altitude ecosystems. Here, we conducted a comprehensive field survey to investigate the effects of road disturbance on plant diversity in alpine grasslands on the Tibetan Plateau. Our results indicate that road disturbance caused no significant changes in species richness, Shannon-Wiener’s diversity, or Simpson’s diversity, and the alteration in species composition was limited. These findings demonstrate the robust resistance of alpine grassland plant diversity to road disturbance. Plant diversity exhibited more resistance to road disturbance in regions with more hostile environments, such as plateau sub-frigid regions and alpine steppes. Our study suggests that road construction in the Tibetan Plateau poses limited risk to plant biodiversity.

The island rule, a general pattern of dwarfism in large species to gigantism in small species on islands relative to mainland, is typically seen as a macroevolutionary phenomenon. However, whether the ecological processes associated with abiotic and biotic factors generate a pattern of plant size variation similar to the island rule remains unknown. We measured plant height for 29,623 individuals of 50 common woody plant species across 43 islands in the Zhoushan Archipelago (8500 years old and yet to undergo major evolutionary adaptation) and the adjacent mainlands in China. We found pronounced variations in plant height, similar to those of the island rule. Interestingly, islands with low resource availability, such as low soil organic matter content and low precipitation, had a high degree of dwarfism; islands experiencing high environmental stress, such as high soil pH, had a high degree of dwarfism; and islands experiencing less plant–plant competition had a high degree of gigantism. The magnitude of plant dwarfism was higher on small and remote islands than on larger and nearer islands. These results highlight the importance of ecological processes associated with abiotic and biotic conditions in shaping the island rule-like patterns of plant size variation. Since our studied archipelago is too young to undergo major evolution, ecological processes likely played a prominent role in generating the observed pattern, challenging the notion that the evolutionary process is the dominant factor underlying the island rule. Future studies on the island rule need to perform experiments to disentangle evolutionary from ecological mechanisms.

Pollination niches, which encompass the factors influencing pollen exchange among angiosperms, are fundamental to understanding reproductive success and the intricate eco-evolutionary dynamics of plants. In this study, we investigated pollination niche shift among four sympatric Eriosyce cacti with restricted distributions in the South American Mediterranean region. Utilizing a comprehensive approach—including pollination niche analysis, pollinator color perception studies, reproductive output assessments, molecular phylogenetics, gene flow analyses, and species distribution modeling—we revealed a significant pollination niche displacement in E. chilensis and its variety, E. chilensis var. albidiflora. These taxa transitioned from a hummingbird-pollinated system prevalent in the Eriosyce sect. Neoporteria, characteristic of their sister species E. litoralis, to a bee-pollination strategy akin to that of the co-occurring species E. mutabilis. This shift highlights a simultaneous convergence of E. chilensis toward E. mutabilis and divergence from E. litoralis in pollination strategies, providing adaptive advantages by reducing pollen limitation and enhancing seed production. The morphological and flowering phenological similarities between E. chilensis and E. mutabilis suggest the evolution of a shared advertising display, potentially indicative of floral mimicry, wherein both species benefit from attracting shared bee pollinators. Genomic analyses reveal distinct pollinator-driven selection pressures, with E. chilensis/E. albidiflora exhibiting traits that promote reproductive isolation from E. litoralis, supporting a scenario of rapid speciation occurring within the past half of million years in the absence of geographic barriers. These findings underscore the pivotal role of pollinator interactions in shaping angiosperm speciation and biodiversity, highlighting their dynamic influence on ecological and evolutionary processes.

The global rise in animal protein consumption has significantly amplified the demand for fodder. A comprehensive understanding of the diversity and characteristics of existing fodder resources is essential for balanced nutritional fodder production. This study investigates the diversity and composition of fodder plants and identifies key species for cattle in Zhaotong City, Yunnan, China, while documenting indigenous knowledge on their usage and selection criteria. Ethnobotanical surveys were conducted in 19 villages across seven townships with 140 informants. Data were collected through semi-structured interviews, free listing, and participatory observation, and analyzed using Relative Frequency Citation. A total of 125 taxa (including 106 wild and 19 cultivated) were reported. The most cited family is Poaceae (27 taxa, 21.43%), followed by Asteraceae (17 taxa, 13.49%), Fabaceae (14 taxa, 11.11%), Polygonaceae (9 taxa, 7.14%) and Lamiaceae (4 taxa, 3.17%). The whole plant (66.04%) and herbaceous plants (84.80%) were the most used parts and life forms. The most cited species were Zea mays, Brassica rapa, Solanum tuberosum, Eragrostis nigra, and Artemisia dubia. Usage of diverse fodder resources reflects local wisdom in managing resource availability and achieving balanced nutrition while coping with environmental and climatic risks. Preferences for certain taxonomic groups are due to their quality as premier fodder resources. To promote integrated crop-livestock farming, we suggest further research into highly preferred fodder species, focusing on nutritional assessment, digestibility, meat quality impacts, and potential as antibiotic alternatives. Establishing germplasm and gene banks for fodder resources is also recommended.

The primary mechanism driving plant species loss after nitrogen (N) addition has been often hypothesized to be asymmetric competition for light, resulting from increased aboveground biomass. However, it is largely unknown whether plants’ access to soil water at different depths would affect their responses, fate, and community composition under nitrogen addition. In a semiarid grassland exposed to 8-years of N addition, we measured plant aboveground biomass and diversity under four nitrogen addition rates (0, 4, 10, and 16 g m^-2 year^-1), and evaluated plant use of water across the soil profile using oxygen isotope. Aboveground biomass increased significantly, but diversity and shallow soil-water content decreased, with increasing rate of nitrogen addition. The water isotopic signature for both plant and soil water at the high N rate indicated that Leymus secalinus (a perennial grass) absorbed 7% more water from the subsurface soil layer (20-100 cm) compared to Elymus dahuricus (a perennial grass) and Artemisia annua (an annual forb). L. secalinus thus had a significantly larger biomass and was more abundant than the other two species at the high N rate but did not differ significantly from the other two species under ambient and the low N rate. Species that could use water from deeper soil layers became dominant when water in the shallow layers was insufficient to meet the demands of increased aboveground plant biomass. Our study highlights the importance of water across soil depths as key driver of plant growth and dominance in grasslands under N addition.

Co-flowering species may have evolved strategies to avoid or tolerate the adverse effects of heterospecific pollen deposition. However, the precondition for this evolutionary response is spatial-temporal stability, an aspect currently understudied. Here, we examined the spatial-temporal stability in conspecific and heterospecific pollen loads on stigmas across 19 co-flowering species in six sub-alpine meadow communities over four consecutive years. We found that, although conspecific and heterospecific pollen loads, as well as proportions of heterospecific pollen, differed significantly among species, with heterospecific pollen proportion ranging from 0.1% to 41.8%, variation in heterospecific pollen proportion among species was stable across different years and communities. The most important predictor of variation in both conspecific and heterospecific pollen loads, as well as heterospecific pollen proportions, was species identity; furthermore, this factor was independent of phylogenetic relationship. The proportion of heterospecific pollen varied less within species that had high proportions of heterospecific pollen. Furthermore, both the proportion of heterospecific pollen and its coefficient of variation were more strongly driven by heterospecific pollen than by conspecific pollen. Our study suggests that variation in stigmatic pollen load among co-flowering species is spatially and temporally consistent, a precondition for the tolerance-avoidance strategy. This study provides new insights into how different plant species respond to heterospecific pollen deposition.

Mating patterns in angiosperms are typically nonrandom, yet the mechanisms driving nonrandom mating remain unclear, especially regarding the effects of quantitative floral traits on plant mating success across male and female functions. In this study, we investigated how variation in spur length and flower number per plant influences mating patterns in Aquilegia rockii within a natural population. Using marker-based paternity analyses and manipulative experiments, we assessed the role of these traits in mating success across both sexual functions. We found significant variation in the mate composition between male and female function, with spur-length frequency positively associated with female outcrossing rate and mate number, but not with male outcrossing or mate number. Most mating events occurred within 10 m, and spur-length frequency positively correlated with mating distance. Regardless of selfing, there was evidence for assortative mating for spur length. Although spur length did not correlate with pollinator visitation, plants with mid-length spurs had higher seed set than those with shorter or longer spurs when autonomous selfing was excluded. Flowers number per plant was only associated with mating distance and female outcrossing rate. Our results suggest that spur length plays a key role in nonrandom mating by frequency-dependent mating, with implications for stabilizing selection and maintenance of genetic diversity. This study advances our understanding of floral diversity by dissecting the role of quantitative floral traits in plant mating through both female and male functions.

Nutrient acquisition through symbiotic ectomycorrhizal fungi is carbon (C) costly but fundamental for plant growth, community, and ecosystem functioning. Here, we examined the functions of roots and mycorrhiza with respect to nutrient uptake after artificially inducing C limitation-seven months after girdling of an ectomycorrhizal tree, Pinus taeda. Root physiological activity (measured as root nitrogen content and root exudation) declined after girdling and was accompanied with 110% and 340% increases in mycorrhizal colonization and extramatrical hyphal length, respectively. Fungi colonizing roots switched to a community characterized by higher C efficiency (lower C cost) of nutrient acquisition (CENA, the amount of nutrient acquisition per unit C cost) and lower network complexity, indicating a tradeoff between CENA and stability of the fungal community. Root transcriptome analysis suggested a shift in metabolic pathways from a tricarboxylic acid cycle decomposition of carbohydrate to lipid biosynthesis to maintain closer associations with mycorrhiza for nutrient cycling after the girdling. By integrating multi-level evidence, including root transcriptome, fungal composition, and network complexity data, we demonstrate an increased dependence on mycorrhiza for nutrient acquisition under the C limitation condition, which is likely due to a shift to fungal community with higher CENA at the cost of lower stability.

The karst forest in southwestern China is characterized by thin soil layers, numerous fissures and holes, resulting in low soil water availability and poor water retention, making it challenging for plant growth and survival. While the relationship between plant functional traits and tree growth performance has been extensively studied, the links between tree seasonal growth and drought-tolerant traits in tree species with different leaf habit remains poorly understood. This study evaluated the associations between four-year averaged rainy season stem diameter growth rate and 17 branch and leaf traits across evergreen and deciduous species in a tropical karst forest in southwest China. The cross-species variations in tree growth rates were related to plant hydraulic traits (e.g., vessel lumen diameter, xylem vessel density, stomatal density, and stomatal size) and leaf anatomical traits (e.g., total leaf thickness, lower/upper epidermis thickness, and spongy thickness). The growth of evergreen trees exhibited lower hydraulic efficiency but greater drought tolerance than deciduous tree, which enabled them to maintain higher persistence under low soil water availability and consequently a relatively longer growing season. In contrast, deciduous species showed no correlation between their functional traits and growth rate. The distinct water use strategies of evergreen and deciduous trees may offer a potential explanation for their co-existence in the tropical karst forests.

Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon (EASM) and subtropical evergreen broad-leaved forests (EBLFs). However, how the genomic insights of EBLFs' species correspond to environmental shifts induced by the EASM remains limited. In this study, we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of five closely related Engelhardia taxa and one Rhoiptelea species. Our findings revealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM. This genomic transition may have coincided with a significant expansion of the terpene synthase (TPS) gene family in E. fenzelii, driven by four distinct modes of gene duplication. This expansion enhances the biosynthesis of terpene volatiles, providing a defensive mechanism against potential herbivory in EASM affected environments. We also identified a shared whole-genome duplication (WGD) event across Engelhardia, along with substantial differences in transposable element (TE) composition and activity, which contributed to genome size variation between E. fenzelii and E. roxburghiana. In addition, demographic analyses revealed a continuous population decline over the past 10 million years, further exacerbated by recent human disturbance, underscoring the conservation urgency for these species. These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights (e.g., the intricate relationships between genomic variations, environmental changes, and adaptive responses driven by significant climatic events such as the EASM), but also provides valuable insights into the conservation significance of EBLFs.

Preserving genetic diversity is crucial for the long-term survival of wild plant species, yet many remain at risk of genetic erosion due to small population sizes and habitat fragmentation. Here, we present a comparative genomic study of the critically endangered Oreocharis esquirolii (Gesneriaceae) and its widespread congener O. maximowiczii. We assembled and annotated chromosome-level reference genomes for both species and generated whole-genome resequencing data from 28 O. esquirolii and 79 O. maximowiczii individuals. Our analyses reveal substantially lower genetic diversity and higher inbreeding in O. esquirolii, despite its overall reduced mutational burden. Notably, O. esquirolii exhibits an elevated proportion of strongly deleterious mutations relative to O. maximowiczii, suggesting that limited opportunities for purging have allowed these variants to accumulate. These contrasting genomic profiles likely reflect divergent demographic histories, with O. esquirolii having experienced severe bottlenecks and protracted population decline. Collectively, our findings highlight the critically endangered status of O. esquirolii, characterized by diminished genetic diversity, pronounced inbreeding, and reduced ability to eliminate deleterious alleles. This study provides valuable genomic resources for the Gesneriaceae family and underscores the urgent need for targeted conservation measures, including habitat protection and ex situ preservation efforts, to mitigate the extinction risk facing O. esquirolii and potentially other threatened congeners.

Local adaptation is critical for plant survivals and reproductions in the context of global environmental change. Heterogeneous environments impose various selection pressures that influence the fitness of organisms and leave genomic signatures during the process of adaptation to local environments. However, unveiling the genomic signatures of adaptation still poses a major challenge especially for perennials due to limited genomic resources. Here, we utilized Actinidia eriantha, a Chinese endemic liana, as a model case to detect drivers of local adaptation and adaptive signals through landscape genomics for 311 individuals collected from 25 populations. Our results demonstrated precipitation and solar radiation were two crucial factors influencing the patterns of genetic variations and driving adaptive processes. We further uncovered a set of genes involved in adaptation to heterogeneous environments. Among them, AeERF110 showed high genetic differentiation between populations and was confirmed to be involved in local adaptation via changes in allele frequency along with precipitation (Prec_03) and solar radiation (Srad_03) in native habitats separately, implying that adaptive loci frequently exhibited environmental and geographic signals. In addition, we assessed genetic offsets of populations under four future climate models and revealed that populations from middle and east clusters faced higher risks in adapting to future environments, which should address more attentions. Taken together, our study opens new perspectives for understanding the genetic underpinnings of local adaptation in plants to environmental changes in a more comprehensive fashion and offered the guides on applications in conservation efforts.

Invasive alien plant species (IAPS) pose severe threats to global biodiversity conservation. Effective management of IAPS requires mapping their distribution and identifying the environmental factors that drive their spread. The Gaoligong Mountains, a renowned biodiversity hotspot in southwestern China, currently face the dual challenges of IAPS invasion and climate change. However, we know little about the distribution patterns, key environmental drivers, and sensitivity of IAPS to future climate change in this region. In this study, we mapped IAPS richness distribution and identified invasion hotspots throughout the Gaoligong Mountains. In addition, we assessed the relative importance of environmental variables in shaping the spatial distribution of IAPS richness and projected potential shifts in IAPS richness under various climate change scenarios. We identified 161 IAPS, primarily concentrated in the low-elevation tropical and subtropical regions along river valleys, forming belt-like invasion hotspots. The key factors shaping IAPS richness included disturbance complexity, elevation, seasonal precipitation, and vegetation types. Notably, IAPS richness significantly declined with increasing elevation and latitude but increased with higher disturbance complexity. Moreover, IAPS were more prevalent in grasslands and shrublands than in forested areas. Ensemble modeling of future climate scenarios predicted that the distribution of IAPS richness would shift to progressively higher elevations. These findings provide valuable insights for managing IAPS in mountainous regions that play a crucial role in global biodiversity conservation.

Predicting whether alien species will invade a native community is a key challenge in invasion ecology. One factor that may help predict invasion success is phylogenetic relatedness. Darwin proposed that closely related species tend to share similar niches, although this relationship may be influenced by various ecological and evolutionary factors. To test this, we classified alien Asteraceae species in China into three categories based on their invasion status and the extent of ecological damage: introduced, naturalized, and invasive. We then compared the genetic relationships and niche overlap between alien and native Asteraceae species. We found that invasive Asteraceae species are more closely related to native Asteraceae species than are introduced and naturalized species. However, alien Asteraceae species (including introduced, naturalized, and invasive species) exhibited relatively low niche overlap with native Asteraceae species. These findings suggest that the main premise underlying Darwin's naturalization conundrum, namely, the universality of phylogenetic niche conservatism, may not hold true. Instead, our findings indicate that alien species are more likely to invade successfully when they are more closely related to native plants, exhibit less niche overlap, and maintain conservative niches during the invasion process. These findings provide new insights into the mechanisms of alien plant invasions, highlight the relationship between alien species invasions and native community vulnerability, and offer important insights into the development of effective biological invasion management strategies.

Tetracentron sinense is a 'living fossil' tree in East Asia. Understanding how this 'living fossil' responds to climate change and adapts to local environments is critical for its conservation. Here, we used re-sequenced genomes to clarify the evolutionary history and adaptive potential of T. sinense. We identified six divergent lineages in T. sinense: three lineages from southwestern China (Yunnan Province) and three lineages from the central subtropical region of China. Additionally, we detected hybridization events between some adjacent lineages. Demographic analysis revealed that over the past 10,000 years the effective population size (Ne) of three T. sinense lineages (i.e., NORTH, SWEST, and YNWEST) increased after their last bottleneck and then remained stable, whereas that of the remaining three lineages (i.e., YSEAST, YC, and EAST) declined steadily. The decline in effective population size in the Yunnan lineages aligned well with the decrease in genome-wide diversity and a significant increase in the frequency of runs of homozygosity. Deleterious variants and positively selected sites were involved in the evolution of different lineages. Further, genotype–environment association (GEA) analyses indicated adaptation to temperature- and precipitation-related factors. Genomic offset analyses found the most vulnerable populations, while SC and SC-yad were predicted to better handle extreme changes. Our findings provide insights into the evolutionary history and conservation of T. sinense and enhance our understanding of the evolution of living fossil species.

Managing invasive species requires identifying the factors that determine alien species invasion success. This study investigates how anthropogenic and biogeographical factors influence alien plant invasion in the Sanyang Wetlands, a human-dominated island system in Wenzhou City, China. Specifically, we analyzed whether human activities (e.g., habitat heterogeneity, proportion of road area, and cultivation) and island characteristics (e.g., island area, isolation) affect the diversity of native and invasive plant species similarly. We also assessed the applicability of the equilibrium theory of island biogeography to invasive plant species diversity and examined how these factors affect invasive plant species with different dispersal syndromes (anemochore, zoochore, and autochore). We found that both invasive and native species richness positively correlate with island area, habitat heterogeneity, and proportion of road area. However, although native species richness was negatively correlated with isolation, invasive species richness was not. The diversity and composition of invasive species with different dispersal syndromes were determined by different variables; for example, the composition and diversity of zoochores was increased by habitat heterogeneity, while anemochore species richness was increased by the proportion of road area, whereas anemochore species composition was influenced by distance to the nearest island. We conclude that habitat fragmentation differentially affects invasive and native plant diversity, aligning with the predictions of the equilibrium theory of island biogeography only for native species but not for invasive species. Our findings indicate that tailoring habitat attributes and regulating human activities could be effective strategies for mitigating the spread of invasive species in fragmented landscapes.

Species richness in any area results from the interplay of the processes of speciation, extinction, and dispersal. The relationships between species richness and climate should be considered as an outcome of the effects of climate on speciation, extinction, and dispersal. Diversification rate represents the balance of speciation and extinction rates over time. Here, I explore diversification rates in mosses across geographic and climatic gradients worldwide. Specifically, I investigate latitudinal patterns and climatic associations of the mean diversification rate of mosses at global, hemispheric, and smaller scales. I find that the mean diversification rate of mosses is positively correlated with species richness of mosses, increases with decreasing latitude and increasing mean annual temperature and annual precipitation, and is more strongly associated with mean annual temperature than with annual precipitation. These findings shed light on variation of species richness in mosses across the world. The negative relationship between species richness and latitude and the positive relationship between species richness and mean diversification rate in mosses suggest that higher moss species richness at lower latitudes might have resulted, at least to some degree, from higher moss diversification rates at lower latitudes.

Climate and grazing have a significant effect on vegetation structure and soil organic carbon (SOC) distribution, particularly in mountain ecosystems that are highly susceptible to climate change. However, we lack a systematic understanding of how vegetation structure reacts to long-term grazing disturbances, as well as the processes that influence SOC distribution. This study uses multiple sets of data spanning 20 years from a typical alpine grassland in the Qilian Mountains to investigate the effects of climate and grazing on various root-type grasses as well as the mechanisms that drive SOC distribution. We found that grazing increases the biomass of annual, biennial and perennial taproots while decreasing that of perennial rhizomes. We also found that various root-type grasses have different responses to climate and grazing. Multiple factors jointly control the variation of SOC content (SOCc), and the variation of SOC stock (SOCs) is mainly explained by the interaction between climate and grazing years. Climate and grazing can directly or indirectly affect SOCc through vegetation, and SOCs are mainly dominated by the direct effects of grazing years and grazing gradients. Grazing gradients and root-type grass biomass have a significant effect on SOC, with little effect from climate factors. Therefore, long-term grazing may affect the root-type grass and further affect SOC distribution through differences in nutrient acquisition ability and reproductive pathways. These findings provide important guidance for regulating soil carbon sequestration potential by varying the proportion of different root-type grass in the community via sowing, livestock configuration, or grazing time.

The conversion of forests to pastures is the most important human intervention that has shaped the natural landscape into the Anthropocene environment. The Qinghai-Tibet Plateau (QTP), which has both forest drought-lines and alpine treelines with specific ecotone structures, including isolated trees in treeless plant-covers that represent ever existed forest cover according to ‘Lonely Tooth Hypothesis’, offers an excellent model in which to examine the extent and timing of human activity on the conversion of forest to pasture. The objectives of this paper are to review (1) palaeo-environmental records of the Early Holocene that indicate when forests were first converted to ‘alpine meadows’, and (2) current records of the changing treeline ecotone in the region. ‘Alpine meadows’ of the QTP are part of the largest conversion of mountain forests into pastures worldwide. This change in forest cover is possibly a consequence of the agro-pastoral transition and the dawn of the Anthropocene on the QTP. To date, however, there is an interdisciplinary gap in knowledge of 5000 years between the palaeo-ecological and the archaeolocical and zoo-archaeological records. Rapid changes of the rural economy and the exodus from remote highland villages to down-country cities have diminished the age-old impacts of summer grazing and pasture management by fire; reforestation is obvious, but often seen exclusively as an effect of Anthropocene global warming. We believe that more interdisciplinary collaborations on the QTP are necessary to increase our understanding of the treelines of the Anthropocene in High Asia.

The Qinghai-Tibet Plateau (QTP) has three main grassland types: alpine meadow, alpine steppe, and alpine desert steppe. In this study, we asked how plant productivity and species diversity vary with altitude, longitude and latitude in alpine grasslands of the QTP. We then identified the environmental factors that drive these observed patterns of plant productivity and species diversity. We found that although plant productivity and species diversity varied greatly across large-scale longitudinal and latitudinal gradients, these changes were strongest across the longitudinal gradient. This finding indicates that moisture rather than temperature has the greatest impact on plant productivity and species diversity of the alpine grasslands in the QTP. We also found that besides soil and climate factors, partial pressure of carbon dioxide (pCO₂) also has significant effects on plant productivity, and barometric pressure and partial pressure of oxygen (pO₂) also have significant effects on species diversity. Furthermore, the relationship between the biomass of grassland-dominant species and species diversity was affected by the spatial scale at which these factors were studied. Our study provides new insights into the interconnections between plant productivity and species diversity and the major factors that influence alpine grasslands. It also provides a scientific basis for the maintenance of plant diversity and ecosystem functions in hypoxic (low-oxygen) regions.

Prunus spinulosa (2n = 4x = 32) is an evergreen species of significant medicinal usage and ecological value. However, the lacking of a high-quality genome of P. spinulosa has obstructed further exploration of its ecological study and phylogenetic relationship of Prunus. In this study, we present the first haplotype-resolved genome assembly of Prunus s.l. subgenus Laurocerasus, the tetraploid genome of P. spinulosa was phased into 32 pseudochromosomes with 4 haplotypes, the genome size of each haplotype ranged from 249.82 Mb to 259.69 Mb, and N50 fluctuated from 31.35 Mb to 33.25 Mb, the protein-coding genes vary from 21,272 to 22,668. Different evaluation methods showed that the P. spinulosa genome assembly has high quality of completeness, continuity and accuracy. Being the first complete genome of P. spinulosa, it provides a valuable genetic resource for the Prunus tetraploid species database and supports further functional genomic study of this species.