Endemism of lineages lies at the core of understanding variation in community composition among geographic regions because it reflects how speciation, extinction, and dispersal have influenced current distributions. Here, we investigated geographic patterns and ecological drivers of taxonomic and phylogenetic endemism of angiosperm genera across the world. We identify centers of paleo-endemism and neo-endemism of angiosperm genera, and show that they are mostly located in the Southern Hemisphere in tropical and subtropical regions, particularly in Asia and Australia. Different categories of phylogenetic endemism centers can be differentiated using current climate conditions. Current climate, historical climate change, and geographic variables together explained ~80% of global variation in taxonomic and phylogenetic endemism, while 42-46%, 1%, and 15% were independently explained by these three types of variables, respectively. Thus our findings show that past climate change, current climate, and geography act together in shaping endemism, which are consistent with the findings of previous studies that higher temperature and topographic heterogeneity promote endemism. Our study showed that many centers of phylogenetic endemism of angiosperms, including regions in Amazonia, Venezuela, and west-central tropical Africa that have not previously been identified as biodiversity hotspots, are missed by taxon-based measures of endemism, indicating the importance of including evolutionary history in biodiversity assessment.

Sexual systems play important roles in angiosperm evolution and exhibit substantial variations among different floras. Thus, studying their evolution in a whole flora is crucial for understanding the formation and maintenance of plant biodiversity and predicting its responses to environmental change. In this study, we determined the patterns of plant sexual systems and their associations with geographic elements and various life-history traits in dry-hot valley region of southwestern China, an extremely vulnerable ecosystem. Of the 3166 angiosperm species recorded in this area, 74.5% were hermaphroditic, 13.5% were monoecious and 12% were dioecious, showing a high incidence of diclinous species. Diclinous species were strongly associated with tropical elements, whereas hermaphroditic species were strongly associated with temperate and cosmopolitan elements. We also found that hermaphroditism was strongly associated with showy floral displays, specialist entomophily, dry fruits and herbaceous plants. Dioecy was strongly associated with inconspicuous, pale-colored flowers, generalist entomophily, fleshy fruits, and woody plants, whereas monoecy was strongly associated with inconspicuous, pale-colored flowers, anemophily, dry fruits, and herbaceous plants. In addition, hermaphroditic species with generalist entomophily tended to flower in the dry season, whereas diclinous species with specialist entomophily tended to flower in the rainy season. However, independent of sexual systems, plants that produce dry fruits tended to flower in the rainy season and set fruits in the dry season, but the opposite pattern was found for fleshy fruit-producing plants. Our results suggest that in the dry-hot valleys, plant sexual systems are associated with geographic elements as well as various life-history traits that are sensitive to environmental change.

The identification and understanding of cryptic intraspecific evolutionary units (lineages) are crucial for planning effective conservation strategies aimed at preserving genetic diversity in endangered species. However, the factors driving the evolution and maintenance of these intraspecific lineages in most endangered species remain poorly understood. In this study, we conducted resequencing of 77 individuals from 22 natural populations of Davidia involucrata, a “living fossil” dove tree endemic to central and southwest China. Our analysis revealed the presence of three distinct local lineages within this endangered species, which emerged approximately 3.09 and 0.32 million years ago. These divergence events align well with the geographic and climatic oscillations that occurred across the distributional range. Additionally, we observed frequent hybridization events between the three lineages, resulting in the formation of hybrid populations in their adjacent as well as disjunct regions. These hybridizations likely arose from climate-driven population expansion and/or long-distance gene flow. Furthermore, we identified numerous environment-correlated gene variants across the total and many other genes that exhibited signals of positive evolution during the maintenance of two major local lineages. Our findings shed light on the highly dynamic evolution underlying the remarkably similar phenotype of this endangered species. Importantly, these results not only provide guidance for the development of conservation plans but also enhance our understanding of evolutionary past for this and other endangered species with similar histories.

Hybridization plays a significant role in biological evolution. However, it is not clear whether ecological contingency differentially influences likelihood of hybridization, particularly at ecological margins where parental species may exhibit reduced fitnesses. Moreover, it is unknown whether future ecosystem change will increase the prevalence of hybridization. Ficus heterostyla and F. squamosa are closely related species co-distributed from southern Thailand to southwest China where hybridization, yielding viable seeds, has been documented. As a robust test of ecological factors driving hybridization, we investigated spatial hybridization signatures based on nuclear microsatellites from extensive population sampling across a widespread contact range. Both species showed high population differentiation and strong patterns of isolation by distance. Admixture estimates exposed asymmetric interspecific gene flow. Signatures of hybridization increase significantly towards higher latitude zones, peaking at the northern climatic margins. Geographic variation in reproductive phenology combined with ecologically challenging marginal habitats may promote this phenomenon. Our work is a first systematic evaluation of such patterns in a comprehensive, latitudinally-based clinal context, and indicates that tendency to hybridize appears strongly influenced by environmental conditions. Moreover, that future climate change scenarios will likely alter and possibly augment cases of hybridization at ecosystem scales.

Understanding the evolutionary and ecological processes involved in population differentiation and speciation provides critical insights into biodiversity formation. In this study, we employed 29,865 single nucleotide polymorphisms (SNPs) and complete plastomes to examine genomic divergence and hybridization in Gentiana aristata, which is endemic to the Qinghai-Tibet Plateau (QTP) region. Genetic clustering revealed that G. aristata is characterized by geographic genetic structures with five clusters (West, East, Central, South and North). The West cluster has a specific morphological character (i.e., blue corolla) and higher values of F_ST compared to the remaining clusters, likely the result of the geological barrier formed by the Yangtze River. The West cluster diverged from the other clusters in the Early Pliocene; these remaining clusters diverged from one another in the Early Quaternary. Phylogenetic reconstructions based on SNPs and plastid data revealed substantial cyto-nuclear conflicts. Genetic clustering and D-statistics demonstrated rampant hybridization between the Central and North clusters, along the Bayankala Mountains, which form the geological barrier between the Central and North clusters. Species distribution modeling demonstrated the range of G. aristata expanded since the Last Interglacial period. Our findings provide genetic and morphological evidence of cryptic diversity in G. aristata, and identified rampant hybridization between genetic clusters along a geological barrier. These findings suggest that geological barriers and climatic fluctuations have an important role in triggering diversification as well as hybridization, indicating that cryptic diversity and hybridization are essential factors in biodiversity formation within the QTP region.

The East Asia (or Physospermopsis) clade was recognized in previous molecular phylogenetic investigations into the higher-level relationships of Apiaceae subfamily Apioideae. The composition of this clade, the phylogenetic relationships among its constituent taxa, and the placement of species previously determined to be problematic have yet to be resolved. Herein, nrDNA ITS sequences were obtained for 150 accessions of Apioideae, representing species whose distributions are in East Asia or genera having one or more species included within the East Asia clade. These data, along with published ITS sequences from other Apioideae (for 3678 accessions altogether), were subjected to maximum likelihood and Bayesian inference analyses. The results show that the East Asia clade contains representatives of 11 currently recognized genera: Hansenia, Hymenolaena, Keraymonia, Sinolimprichtia, Acronema, Hymenidium, Physospermopsis, Pimpinella, Sinocarum, Tongoloa, and Trachydium. However, the latter seven genera have members falling outside of the East Asia clade, including the generic types of all except Tongoloa. Within the clade, the species comprising these seven genera are widely intermingled, greatly increasing confusion among relationships than previously realized. The problematic species Physospermopsis cuneata is confirmed as falling within the East Asia clade, whereas P. rubrinervis allies with the generic type in tribe Pleurospermeae. Physospermopsis kingdon-wardii is confirmed as a member of the genus Physospermopsis, whereas the generic attributions of P. cuneata and Tongoloa stewardii remain unclear. Two species of Sinocarum (S. filicinum and S. wolffianum) are transferred into the genus Meeboldia. This is the most comprehensive molecular phylogenetic investigation of the East Asia clade to date, and while the results increase systematic understanding of the clade, they also highlight the need for further studies of one of the most taxonomically intractable groups in Apioideae.

Here, we infer the historical biogeography and evolutionary diversification of the genus Lilium. For this purpose, we used the complete plastomes of 64 currently accepted species in the genus Lilium (14 plastomes were newly sequenced) to recover the phylogenetic backbone of the genus and a time-calibrated phylogenetic framework to estimate biogeographical history scenarios and evolutionary diversification rates of Lilium. Our results suggest that ancient climatic changes and geological tectonic activities jointly shaped the distribution range and drove evolutionary radiation of Lilium, including the Middle Miocene Climate Optimum (MMCO), the late Miocene global cooling, as well as the successive uplift of the Qinghai-Tibet Plateau (QTP) and the strengthening of the monsoon climate in East Asia during the late Miocene and the Pliocene. This case study suggests that the unique geological and climatic events in the Neogene of East Asia, in particular the uplift of QTP and the enhancement of monsoonal climate, may have played an essential role in formation of uneven distribution of plant diversity in the Northern Hemisphere.

Chinese Assam tea (Camellia sinensis var. assamica) is an important tea crop with a long history of cultivation in Yunnan, China. Despite its potential value as a genetic resource, its genetic diversity and domestication/breeding history remain unclear. To address this issue, we genotyped 469 ancient tea plant trees representing 26 C. sinensis var. assamica populations, plus two of its wild relatives (six and three populations of C. taliensis and C. crassicolumna, respectively) using 16 nuclear microsatellite loci. Results showed that Chinese Assam tea has a relatively high, but comparatively lower gene diversity (H_S = 0.638) than the wild relative C. crassicolumna (H_S = 0.658). Clustering in STRUCTURE indicated that Chinese Assam tea and its two wild relatives formed distinct genetic groups, with considerable interspecific introgression. The Chinese Assam tea accessions clustered into three gene pools, corresponding well with their geographic distribution. However, NewHybrids analysis indicated that 68.48% of ancient Chinese Assam tea plants from Xishuangbanna were genetic intermediates between the Puer and Lincang gene pools. In addition, 10% of the ancient Chinese Assam tea individuals were found to be hybrids between Chinese Assam tea and C. taliensis. Our results suggest that Chinese Assam tea was domesticated separately in three gene pools (Puer, Lincang and Xishuangbanna) in the Mekong River valley and that the hybrids were subsequently selected during the domestication process. Although the domestication history of Chinese Assam tea in southwestern Yunnan remains complex, our results will help to identify valuable genetic resources that may be useful in future tea breeding programs.

Despite much research in the field of island biogeography, mechanisms regulating insular diversity remain elusive. Here, we aim to explore mechanisms underlying plant species-area relationships in two tropical archipelagoes in the South China Sea. We found positive plant species-area relationships for both coral and continental archipelagoes. However, our results showed that different mechanisms contributed to similar plant species-area relationships between the two archipelagoes. For coral islands, soil nutrients and spatial distance among communities played major roles in shaping plant community structure and species diversity. By contrast, the direct effect of island area, and to a lesser extent, soil nutrients determined plant species richness on continental islands. Intriguingly, increasing soil nutrients availability (N, P, K) had opposite effects on plant diversity between the two archipelagoes. In summary, the habitat quality effect and dispersal limitation are important for regulating plant diversity on coral islands, whereas the passive sampling effect, and to a lesser extent, the habitat quality effect are important for regulating plant diversity on continental islands. More generally, our findings indicate that island plant species-area relationships are outcomes of the interplay of both niche and neutral processes, but the driving mechanisms behind these relationships depends on the type of islands.

When benefiting other beneficiaries, cushion plants may reciprocally receive feedback effects. The feedback effects on different sex morphs, however, remains unclear. In this study, taking the gynodioecious Arenaria polytrichiodes as a model species, we aimed to assess the sex-specific facilitation intensity of cushion plant by measuring the beneficiary cover ratio, and to assess the potential costs in cushion reproductive functions by measuring the flower and fruit cover ratios. The total beneficiary cover ratio was similar between females and hermaphrodites. Females produced much less flowers but more fruits than hermaphrodites. These results suggested that females and hermaphrodites possess similar facilitation intensity, and female cushion A. polytrichoides may allocate more resources saved from pollen production to seed production, while hermaphrodites possibly allocate more resources to pollen production hence reducing seed production. The surface areas covered by beneficiaries produced less flowers and fruits than areas without beneficiaries. In addition, strong negative correlations between beneficiary cover and flower cover were detected for both females and hermaphrodites, but the correlation strength were similar for these two sex morphs. However, the correlation between beneficiary cover and fruit cover was only significantly negative for females, suggesting that beneficiary plants negatively affect fruit reproduction of females while have neutral effects on hermaphrodites. All the results suggest that to facilitate other beneficiaries can induce reproductive costs on cushion A. polytrichoides, with females possibly suffering greater cost than hermaphrodites. Such differentiation in reproductive costs between sex morphs, in long-term perspective, may imply sex imbalance in population dynamics.

Tall clonal grasses commonly display competitive advantages with nitrogen (N) enrichment. However, it is currently unknown whether the height is derived from the vegetative or reproductive module. Moreover, it is unclear whether the height of the vegetative or reproductive system regulates the probability of extinction and colonization, and determines species diversity. In this study, the impacts on clonal grasses were studied in a field experiment employing two frequencies (twice a year vs. monthly) crossing with nine N addition rates in a temperate grassland, China. We found that the N addition decreased species frequency and increased extinction probability, but did not change the species colonization probability. A low frequency of N addition decreased species frequency and colonization probability, but increased extinction probability. Moreover, we found that species reproductive height was the best index to predict the extinction probability of clonal grasses in N-enriched conditions. The low frequency of N addition may overestimate the negative effect from N deposition on clonal grass diversity, suggesting that a higher frequency of N addition is more suitable in assessing the ecological effects of N deposition. Overall, this study illustrates that reproductive height was associated with the clonal species extinction probability under N-enriched environment.

To determine the invasiveness of invasive plants, many studies have compared photosynthetic traits or strategies between invasive and native species. However, few studies have compared the photosynthetic dynamics between invasive and native species during light fluctuations. We compared photosynthetic induction, relaxation dynamics and leaf traits between the invasive species, Tithonia diversifolia and two native species, Clerodendrum bungei and Blumea balsamifera, in full-sun and shady habitats. The photosynthetic dynamics and leaf traits differed among species. T. diversifolia showed a slower induction speed and stomatal opening response but had higher average intrinsic water-use efficiency than the two native species in full-sun habitats. Thus, the slow induction response may be attributed to the longer stomatal length in T. diversifolia. Habitat had a significant effect on photosynthetic dynamics in T. diversifolia and B. balsamifera but not in C. bungei. In shady habitat, T. diversifolia had a faster photosynthetic induction response than in full-sun habitat, leading to a higher average stomatal conductance during photosynthetic induction in T. diversifolia than in the two native species. In contrast, B. balsamifera had a larger stomatal length and slower photosynthetic induction and relaxation response in shady habitat than in full-sun habitat, resulting in higher carbon gain during photosynthetic relaxation. Nevertheless, in both habitats, T. diversifolia had an overall higher carbon gain during light fluctuations than the two native species. Our results indicated that T. diversifolia can adopt more effective response strategies under fluctuating light environments to maximize carbon gain, which may contribute to its successful invasion.

Flower constancy describes the phenomenon that pollinators tend to successively visit flowers of a single species during foraging, reducing reproductive interference in natural communities. The extent of flower constancy is largely determined by the floral traits of co-flowering species. Both higher inter-specific and lower intraspecific differences of floral traits should contribute to a higher level of flower constancy. However, previous studies mainly focused on interspecific difference, and the intraspecific variation (consistency) of floral traits received much less attention. We hypothesise that selection may favour lower intraspecific floral trait variation in communities composed of multiple co-flowering congeners. We investigated the floral colour variation of three focal Pedicularis species that share pollinators in 19 communities composed of either single or multiple Pedicularis species. Colour was quantified using image-based colour analysis as perceived by pollinators. We found that most of the intrapopulation floral colour variation was below the colour discrimination threshold of bumblebees, implying strongly constrained by the visual selection by pollinators. Contrary to the hypothesis, there is no significant difference in intraspecific floral colour variation between different community contexts. It may be due to the relatively large interspecific floral colour differences of most co-flowering species. The influence of community context on intraspecific variation may be reflected in floral traits other than colours.