Integrative Biology Journals

25 May 2025, Volume 47 Issue 03
    

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  • Lang Li (李朗), Bing Liu (刘冰), Yu Song (宋钰), Hong-Hu Meng (孟宏虎), Xiu-Qin Ci (慈秀芹), John G. Conran, Rogier P.J. de Kok, Pedro Luís Rodrigues de Moraes, Jun-Wei Ye (叶俊伟), Yun-Hong Tan (谭运洪), Zhi-Fang Liu (刘志芳), Marlien van der Merwe, Henk van der Werff, Yong Yang (杨永), Jens G. Rohwer, Jie Li (李捷)
    Plant Diversity. 2025, 47(03): 341-364. https://doi.org/10.1016/j.pld.2025.04.001
    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.
  • Articles
  • Fangdong Geng (耿方东), Miaoqing Liu (刘苗青), Luzhen Wang (王璐珍), Xuedong Zhang (张雪栋), Jiayu Ma (马佳雨), Hang Ye (叶航), Keith Woeste, Peng Zhao (赵鹏)
    Plant Diversity. 2025, 47(03): 365-381. https://doi.org/10.1016/j.pld.2025.04.002
    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.
  • Kai Chen, Yan-Chun Liu, Yue Huang, Xu-Kun Wu, Hai-Ying Ma, Hua Peng, De-Zhu Li, Peng-Fei Ma
    Plant Diversity. 2025, 47(03): 382-393. https://doi.org/10.1016/j.pld.2025.03.002
    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.
  • Ziwei Chen, Dongsheng Zhao, Siqi Deng, Yu Zhu, Ke Wang, Shunsheng Wang, Du Zheng
    Plant Diversity. 2025, 47(03): 394-402. https://doi.org/10.1016/j.pld.2024.09.006
    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.
  • Jingyang He, Wenjing Yang, Qinghui You, Qiwu Hu, Mingyang Cong, Chao Tian, Keping Ma
    Plant Diversity. 2025, 47(03): 403-414. https://doi.org/10.1016/j.pld.2025.02.001
    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.
  • Javier Hernández-Velasco, José Ciro Hernández-Díaz, Sergio Leonel Simental-Rodríguez, Juan P. Jaramillo-Correa, David S. Gernandt, José Jesús Vargas-Hernández, Ilga Porth, Roos Goessen, M. Socorro González-Elizondo, Matthias Fladung, Cuauhtémoc Sáenz-Romero, José Guadalupe Martínez-Ávalos, Artemio Carrillo-Parra, Eduardo Mendoza-Maya, Arnulfo Blanco-García, Christian Wehenkel
    Plant Diversity. 2025, 47(03): 415-428. https://doi.org/10.1016/j.pld.2024.12.006
    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 (FIS) 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 FIS 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 (Ho) but negatively correlated with expected heterozygosity (He). Analysis of outlier SNPs also showed that asexual reproduction was positively correlated with Ho and negatively correlated with He, although this latter correlation was not significant. These findings support the presence of a Meselson effect.
  • Zhi-Li Zhou (周知里), Tial C. Ling, Jian-Li Zhao (赵建立), Xin-Zhi Wang (王欣之), Lin-Lin Wang (王林林), Li Li (李莉), Wen-Jing Wang (王雯婧), Dong-Rui Jia (贾东瑞), Zhi-Kun Wu (吴之坤), Xu-Dong Sun (孙旭东), Yong-Ping Yang (杨永平), Yuan-Wen Duan (段元文)
    Plant Diversity. 2025, 47(03): 429-439. https://doi.org/10.1016/j.pld.2025.03.004
    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.
  • Pablo C. Guerrero, Jaime Martínez-Harms, Mary T.K. Arroyo, Deren Eaton, Beatriz M. Meriño, Antonio Varas-Myrik, Heidy M. Villalobos-Barrantes, Gastón O. Carvallo
    Plant Diversity. 2025, 47(03): 440-453. https://doi.org/10.1016/j.pld.2025.03.001
    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.
  • Yu-Mei Yan, Ze-Xin Fan, Pei-Li Fu, Zhi-Yong Zhang
    Plant Diversity. 2025, 47(03): 454-465. https://doi.org/10.1016/j.pld.2024.08.001
    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.
  • Jing Chen, Jingjing Cao, Binglin Guo, Meixu Han, Zhipei Feng, Jinqi Tang, Xiaohan Mo, Junjian Wang, Qingpei Yang, Yuxin Pei, Yakov Kuzyakov, Junxiang Ding, Naoki Makita, Xitian Yang, Haiyang Zhang, Yong Zhao, Deliang Kong
    Plant Diversity. 2025, 47(03): 466-478. https://doi.org/10.1016/j.pld.2025.02.004
    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.
  • Fu-Qiang Huang, Josep Peñuelas, Jordi Sardans, Scott L. Collins, Kai-Liang Yu, Man-Qiong Liu, Jiu-Ying Pei, Wen-Bin Ke, Jian-Sheng Ye
    Plant Diversity. 2025, 47(03): 479-488. https://doi.org/10.1016/j.pld.2025.02.006
    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.
  • Tao Zhang, Qiang Fang
    Plant Diversity. 2025, 47(03): 489-498. https://doi.org/10.1016/j.pld.2024.12.003
    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.
  • Yufeng Xu, Chenyang Xue, Xuezhi Wang, Lin Meng, Ying Gao, Mengyang Yu, Lin Geng, Meini Shao, Bo Qu
    Plant Diversity. 2025, 47(03): 499-510. https://doi.org/10.1016/j.pld.2024.10.005
    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.
  • Jianxiang Yang (杨建翔), Guojing Shen (申国境), Jianqiang Wu (吴建强)
    Plant Diversity. 2025, 47(03): 511-521. https://doi.org/10.1016/j.pld.2025.03.003
    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.
  • Case Report
  • Xiaoyan Hu, Jinyu Zhang, Bo Wang
    Plant Diversity. 2025, 47(03): 522-525. https://doi.org/10.1016/j.pld.2025.02.002
  • Corrigendum
  • Zhen Yang, Lisong Liang, Weibo Xiang, Lujun Wang, Qinghua Ma, Zhaoshan Wang
    Plant Diversity. 2025, 47(03): 526-527. https://doi.org/10.1016/j.pld.2025.02.007