29 September 2025, Volume 47 Issue 05

    

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  Evaluating the relative importance of phylogeny and predictors in phylogenetic generalized linear models using the phylolm.hp R package

  Jiangshan Lai (赖江山), Yan He (何雁), Mi Hou (侯蜜, Aiying Zhang (张爱英), Gang Wang (王刚), Lingfeng Mao (毛岭峰)

  Plant Diversity. 2025, 47(05): 709-717. https://doi.org/10.1016/j.pld.2025.06.003

  Abstract ( 17) Download PDF ( 18 ) HTML   Knowledge map   Save

  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.
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  Genome analyses provide insights into Engelhardia's adaptation to East Asia summer monsoon

  Min Li, Jing-Jing Wu, Ren-Ping Su, Ou-Yan Fang, Xiang Cai, Pei-Han Huang, Xiao-Yang Gao, Xin-Xing Fu, Xiao-Hui Ma, Lin-Yue H, Yi-Gang Song, Guo-Xiong Hu, Shi-Shun Zhou, Yun-Hong Tan, Yves Van de Peer, Jie Li, Sheng-Dan Wu, Hong-Hu Meng

  Plant Diversity. 2025, 47(05): 718-732. https://doi.org/10.1016/j.pld.2025.07.003

  Abstract ( 8) Download PDF ( 3 ) HTML   Knowledge map   Save

  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.
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  Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit

  Quan Jiang, Yufang Shen, Lianhai Wu, Zhengwang Jiang, Xiaohong Yao

  Plant Diversity. 2025, 47(05): 733-745. https://doi.org/10.1016/j.pld.2025.02.003

  Abstract ( 9) Download PDF ( 1 ) HTML   Knowledge map   Save

  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.
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  Genomic and population genomic analyses reveal contrasting diversity and demographic histories in a critically endangered and a widespread Oreocharis species

  Nana Peng (彭娜娜), Lihua Yang (杨丽华), Xizuo Shi (史习佐), Hanghui Kong (孔航辉), Ming Kang (康明)

  Plant Diversity. 2025, 47(05): 746-758. https://doi.org/10.1016/j.pld.2025.06.006

  Abstract ( 8) Download PDF ( 4 ) HTML   Knowledge map   Save

  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.
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  Genomic insights into the evolutionary history and conservation of the living fossil Tetracentron sinense

  Zhao-Yang Jing (景昭阳), Ren-Gang Zhang (张仁纲), Yang Liu (刘阳), Ke-Guang Cheng (程可光), De-Tuan Liu (刘德团), Heng Shu (舒恒), Jiali Kong (孔佳莉), Zhong-Hua Liu (刘忠华), Yong-Peng Ma (马永鹏), Ping-Li Liu (刘平丽)

  Plant Diversity. 2025, 47(05): 759-771. https://doi.org/10.1016/j.pld.2025.05.008

  Abstract ( 7) Download PDF ( 2 ) HTML   Knowledge map   Save

  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.
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  Climatic niche divergence and long-distance dispersal contributed to the pantropical intercontinental disjunctions of a liana lineage (Uncaria, Rubiaceae)

  Xian-Han Huang (黄先寒), Jing-Yi Peng (彭敬宜), Nan Lin (林楠), Jian Liu (刘健), Jun-Tong Chen (陈俊通), Qun Liu (刘群), Xin-Jian Zhang (张信坚), Quan-Sheng Fu (付全升), Peng-Rui Luo (罗芃睿), Zhi-Yu Wang (王治宇), Shiou Yih Lee, Qiang Zhou (周强), Hang Sun (孙航), Tao Deng (邓涛)

  Plant Diversity. 2025, 47(05): 772-783. https://doi.org/10.1016/j.pld.2025.05.001

  Abstract ( 9) Download PDF ( 6 ) HTML   Knowledge map   Save

  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.
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  Biogeographic affinity partly shapes woody plant diversity along an elevational gradient in subtropical forests

  Zhaochen Zhang (张昭臣), Fang Wang (王芳), Xiaoran Wang (王潇然), Mufan Sun (孙慕梵), Pu Zheng (郑普), Jingchao Zhao (赵静超), Junhong Chen (陈俊红), Min Guan (关敏), Pengcheng Liu (刘鹏程), Xiaofan Shang (商晓凡), Yaoshun Lu (卢尧舜), Qingpei Yang (杨清培), Qingni Song (宋庆妮), Lin Chen (陈琳), Quying Zhong (钟曲颖), Jian Zhang (张健)

  Plant Diversity. 2025, 47(05): 784-792. https://doi.org/10.1016/j.pld.2025.06.004

  Abstract ( 10) Download PDF ( 3 ) HTML   Knowledge map   Save

  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.
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  Grazing management can achieve the reconfiguration of vegetation to combat climate impacts and promote soil carbon sequestration

  Yu-Wen Zhang, Ze-Chen Peng, Sheng-Hua Chang, Zhao-Feng Wang, Lan Li, Duo-Cai Li, Yu-Feng An, Fu-Jiang Hou, Ji-Zhou Ren

  Plant Diversity. 2025, 47(05): 793-803. https://doi.org/10.1016/j.pld.2024.09.002

  Abstract ( 5) Download PDF ( 1 ) HTML   Knowledge map   Save

  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.
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  Phylogenetically close alien Asteraceae species with minimal niche overlap are more likely to invade

  Xing-Jiang Song, Gang Liu, Xin-Di Li, Yu Chen, Jia Wang, Chun-Ling Zhang, Xin-Ping Ye, Zhi-Hong Zhu

  Plant Diversity. 2025, 47(05): 804-813. https://doi.org/10.1016/j.pld.2025.02.005

  Abstract ( 8) Download PDF ( 1 ) HTML   Knowledge map   Save

  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.
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  Environmental drivers and future distribution of invasive alien plant species in the Gaoligong Mountains, southwestern China

  Yu Xiao (肖俞), Xuecan Wu (吴学灿), Hexiang Duan (段禾祥), Zhengtao Ren (任正涛), Zhicheng Jiang (姜志诚), Tingfa Dong (董廷发), Yuran Li (李宇然), Jinming Hu (胡金明), Yupeng Geng (耿宇鹏)

  Plant Diversity. 2025, 47(05): 814-823. https://doi.org/10.1016/j.pld.2025.05.002

  Abstract ( 9) Download PDF ( 2 ) HTML   Knowledge map   Save

  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.
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  Habitat fragmentation differentially affects invasive and native plant diversity in a human-dominated wetland island system

  Jinliang Liu, Mengyuan Chen, Lu Wang, Tengteng Liu, Xinjie Jin, Fei-Hai Yu, Yonghua Zhang

  Plant Diversity. 2025, 47(05): 824-832. https://doi.org/10.1016/j.pld.2024.09.003

  Abstract ( 4) Download PDF ( 1 ) HTML   Knowledge map   Save

  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.
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  Diversification rates in large-scale moss assemblages along latitudinal and climatic gradients across the world

  Hong Qian

  Plant Diversity. 2025, 47(05): 833-838. https://doi.org/10.1016/j.pld.2025.07.002

  Abstract ( 6) Download PDF ( 1 ) HTML   Knowledge map   Save

  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.
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  Genomic analyses provide insights into the genetic basis of quality traits in Amomum tsaoko

  Yingmin Zhang (张颖敏), Congwei Yang (杨从卫), Jiahong Dong (董家红), Jinyu Zhang (张金渝), Ticao Zhang (张体操), Guodong Li (李国栋)

  Plant Diversity. 2025, 47(05): 839-842. https://doi.org/10.1016/j.pld.2025.07.006

  Abstract ( 6) Download PDF ( 1 ) HTML   Knowledge map   Save
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  Chromosome-level genome assembly of Myristica yunnanensis sheds light on genomic limitations underlying its critically endangered status in China

  Yongting Zhang, Zihe Li, Xue Liu, Peng Zeng, Chuan Peng, Botong Zhou, Yingmei Peng, Wenbo Zhu, Jian Huang, Jing Cai

  Plant Diversity. 2025, 47(05): 843-847. https://doi.org/10.1016/j.pld.2025.08.004

  Abstract ( 6) Download PDF ( 2 ) HTML   Knowledge map   Save