Plant Diversity最新文献

{"title":"Genomic signatures of local adaptation to precipitation and solar radiation in kiwifruit.","authors":"Quan Jiang, Yufang Shen, Lianhai Wu, Zhengwang Jiang, Xiaohong Yao","doi":"10.1016/j.pld.2025.02.003","DOIUrl":"10.1016/j.pld.2025.02.003","url":null,"abstract":"<p><p>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 <i>Actinidia eriantha</i>, 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, <i>AeERF110</i> 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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 5","pages":"733-745"},"PeriodicalIF":6.3,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12496532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145239239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impacts of road networks on the geography of floristic collections in China.","authors":"Jingyang He, Wenjing Yang, Qinghui You, Qiwu Hu, Mingyang Cong, Chao Tian, Keping Ma","doi":"10.1016/j.pld.2025.02.001","DOIUrl":"10.1016/j.pld.2025.02.001","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 3","pages":"403-414"},"PeriodicalIF":4.6,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267140","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seed size distributions of fleshy-fruited species are more right-skewed compared to that of dry-fruited species.","authors":"Xiaoyan Hu, Jinyu Zhang, Bo Wang","doi":"10.1016/j.pld.2025.02.002","DOIUrl":"10.1016/j.pld.2025.02.002","url":null,"abstract":"<p><p>•We compiled the first dataset on skewness of seed size distribution.•The dataset encompasses 103 species, belonging to 72 genus and 33 families.•Skewness varied among species, ranging from -1.4 to 4.84.•Fleshy-fruited species was more right skewness in seed size than dry-fruited species.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 3","pages":"522-525"},"PeriodicalIF":4.6,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146852/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effective palynological diversity indices for reconstructing angiosperm diversity in China.","authors":"Yuxuan Jiang, Fuli Wu, Xiaomin Fang, Haitao Wang, Yulong Xie, Cuirong Yu","doi":"10.1016/j.pld.2025.01.004","DOIUrl":"10.1016/j.pld.2025.01.004","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"244-254"},"PeriodicalIF":4.6,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative nectar spur length governs nonrandom mating in a bee-pollinated <i>Aquilegia</i> species.","authors":"Mingliu Yang, Zhi-Qiang Zhang","doi":"10.1016/j.pld.2025.01.005","DOIUrl":"10.1016/j.pld.2025.01.005","url":null,"abstract":"<p><p>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 <i>Aquilegia</i> <i>rockii</i> 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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"323-336"},"PeriodicalIF":4.6,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Environmental drivers of herbaceous plant diversity in the understory community of a warm-temperate forest.","authors":"Tingting Deng, Qingqing Du, Yan Zhu, Simon A Queenborough","doi":"10.1016/j.pld.2025.01.003","DOIUrl":"10.1016/j.pld.2025.01.003","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"282-290"},"PeriodicalIF":4.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The chromosome-scale genome of black wolfberry (<i>Lycium ruthenicum</i>) provides useful genomic resources for identifying genes related to anthocyanin biosynthesis and disease resistance.","authors":"Gulbar Yisilam, Enting Zheng, Chuanning Li, Zhiyong Zhang, Ying Su, Zhenzhou Chu, Pan Li, Xinmin Tian","doi":"10.1016/j.pld.2025.01.001","DOIUrl":"10.1016/j.pld.2025.01.001","url":null,"abstract":"<p><p>The black wolfberry (<i>L</i> <i>ycium</i> <i>ruthenicum</i>; 2<i>n</i> = 2<i>x</i> = 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 <i>L. ruthenicum</i> (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 <i>Lycium</i> species. The species-specific genes of <i>L. ruthenicum</i> 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 <i>L. ruthenicum</i>, 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 <i>L. ruthenicum</i> genome. The whole-genome and proximal, dispersed, and tandem duplication genes in the <i>L. ruthenicum</i> 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 <i>Lycium</i> genus.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"201-213"},"PeriodicalIF":4.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome compaction underlies the molecular adaptation of bay cedar (<i>Suriana maritima</i>) to the extreme habitat on the tropical coral islands.","authors":"Miaomiao Shi, Ping Liang, Zhonglai Luo, Yu Zhang, Shiran Gu, Xiangping Wang, Xin Qian, Shuguang Jian, Kuaifei Xia, Shijin Li, Zhongtao Zhao, Tieyao Tu, Dianxiang Zhang","doi":"10.1016/j.pld.2025.01.002","DOIUrl":"10.1016/j.pld.2025.01.002","url":null,"abstract":"<p><p>•The assembled genome of Bay cedar is 292.8 Mb, representing a small genome size within Fabales.•The compact genome was likely caused by remarkable reduction of long terminal repeat retrotransposons and gene losses.•The genes related to cold tolerance and pest/pathogen resistance were largely lost.•Expanded, positively selected, or retained genes after WGD may drive Bay cedar's adaptation to tropical coral islands.•Differentially expressed genes under salt and drought stresses were particularly identified in the abscisic acid pathway.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"337-340"},"PeriodicalIF":4.6,"publicationDate":"2025-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Causes of heterozygosity excess: The case of Mexican populations of <i>Populus tremuloides</i>.","authors":"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","doi":"10.1016/j.pld.2024.12.006","DOIUrl":"10.1016/j.pld.2024.12.006","url":null,"abstract":"<p><p>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 <i>Populus tremuloides</i> is one of the most widely distributed and ecologically important tree species in the Northern Hemisphere. However, genetic variation in Mexican populations of <i>P. tremuloides</i>, 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 (<i>F</i> _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 <i>F</i> _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 (<i>H</i> _o) but negatively correlated with expected heterozygosity (<i>H</i> _e). Analysis of outlier SNPs also showed that asexual reproduction was positively correlated with <i>H</i> _o and negatively correlated with <i>H</i> _e, although this latter correlation was not significant. These findings support the presence of a Meselson effect.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 3","pages":"415-428"},"PeriodicalIF":4.6,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12146867/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multi-disciplinary evidence illuminates the speciation history of a monophyletic yet dimorphic lily group.","authors":"Yu Feng, Chaochao Yan, Wen-Qin Tu, Yu-Mei Yuan, Jing-Bo Wang, Xiao-Juan Chen, Chang-Qiu Liu, Yundong Gao","doi":"10.1016/j.pld.2024.12.005","DOIUrl":"10.1016/j.pld.2024.12.005","url":null,"abstract":"<p><p>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 <i>Lilium</i>. 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 <i>Lilium</i> 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.</p>","PeriodicalId":20224,"journal":{"name":"Plant Diversity","volume":"47 2","pages":"189-200"},"PeriodicalIF":4.6,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11963083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}