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Global multifaceted biodiversity patterns,centers,and conservation needs in angiosperms

Science China(Life Sciences) 2024年第4期67卷 817-828页

作者： Ao Luo Yaoqi Li Nawal Shrestha Xiaoting Xu Xiangyan Su Yichao Li Tong Lyu Kilara Waris Zhiyao Tang Xiaojuan Liu Luxiang Lin Yongsheng Chen Kuiling Zu Wenqi Song Shijia Peng Niklaus E.Zimmermann Loïc Pellissier Zhiheng Wang Institute of Ecology and Key Laboratory for Earth Surface Processes of the Ministry of Education College of Urban and Environmental SciencesPeking UniversityBeijing 100871China Department of Health and Environmental Sciences Xi’an Jiaotong-Liverpool UniversitySuzhou 215123China State Key Laboratory of Grassland Agro-Ecosystems College of EcologyLanzhou UniversityLanzhou 730000China Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China Land Consolidation and Rehabilitation Center Ministry of Natural ResourcesBeijing 100035China State Key Laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing 100093China CAS Key Laboratory of Tropical Forest Ecology Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesKunming 650201China Swiss Federal Research Institute WSL Birmensdorf 8903Switzerland Department of Environmental Systems Science ETH ZürichZürich 8092Switzerland

The Convention on Biological Diversity seeks to conserve at least 30%of global land and water areas by 2030,which is a challenge but also an opportunity to better preserve biodiversity,including flowering plants(angiosperms).Herein,we compiled a large database on distributions of over 300,000 angiosperm species and the key functional traits of 67,024 species.Using this database,we constructed biodiversity-environment models to predict global patterns of taxonomic,phylogenetic,and functional diversity in terrestrial angiosperms and provide a comprehensive mapping of the three diversity facets.We further evaluated the current protection status of the biodiversity centers of these diversity facets.Our results showed that geographical patterns of the three facets of plant diversity exhibited substantial spatial mismatches and nonoverlapping conservation priorities.Idiosyncratic centers of functional diversity,particularly of herbaceous species,were primarily distributed in temperate regions and under weaker protection compared with other biodiversity centers of taxonomic and phylogenetic facets.Our global assessment of multifaceted biodiversity patterns and centers highlights the insufficiency and unbalanced conservation among the three diversity facets and the two growth forms(woody vs.herbaceous),thus providing directions for guiding the future conservation of global plant diversity.

关键词： angiosperms species richness phylogenetic diversity functional diversity plant traits woody species herbaceous species

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Nuclear phylogenomics of angiosperms and insights into their relationships and evolution

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Journal of Integrative Plant Biology 2024年第3期66卷 546-578页

作者： Guojin Zhang Hong Ma College of Life Sciences Hunan Normal UniversityChangsha 410081China Department of Biology 510 Mueller LaboratoryHuck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA

angiosperms(flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the “abominable mystery,”hence contributing to the heightened interest in angiosperm evolution. angiosperms display wide ranges of morphological, physiological,and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences,dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families,and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella,Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families.Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore,we discuss the implications of nuclear phylogenomic analyses on ancestral

关键词： angiosperms evolution flowering plants nuclear gene phylogenomics phylogeny

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Evolutionary history shapes variation of wood density of tree species across the world

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Plant Diversity 2024年第3期46卷 283-293页

作者： Fangbing Li Hong Qian Jordi Sardans Dzhamal Y.Amishev Zixuan Wang Changyue Zhang Tonggui Wu Xiaoniu Xu Xiao Tao Xingzhao Huang Anhui Province Key Laboratory of Forest Resources and Silviculture Anhui Agricultural UniversityHefei 230036China State Key Laboratory of Subtropical Silviculture Zhejiang A&F UniversityHangzhou 311300China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA CREAF Cerdanyola del VallesBarcelona 08193Spain Global Ecology Unit CREAF-CSIC-UAB CSICBellaterraBarcelona 08193Spain Key Laboratory of Ecosystem Carbon Source and Sink China Meteorological Administration(ECSS-CMA)School of Applied MeteorologyNanjing University of Information Science&Technology219 Ningliu RoadNanjing 210044China Department of Natural Resources Management Lakehead UniversityThunder BayOntario P7B 5E1Canada School of Forestry&Landscape of Architecture Anhui Agricultural UniversityHefei 230036China Research Institute of Subtropical Forestry Chinese Academy of ForestryHangzhou 311400China

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density,but this has largely not been tested.Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide,we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species.We assessed phylogenetic signal in different taxonomic(e.g.,angiosperms and gymnosperms)and ecological(e.g.,tropical,temperate,and boreal)groups of tree species,explored the biogeographical and phylogenetic patterns of wood density,and quantified the relative importance of current environmental factors(e.g.,climatic and soil variables)and evolutionary history(i.e.,phylogenetic relatedness among species and lineages)in driving global wood density variation.We found that wood density displayed a significant phylogenetic signal.Wood density differed among different biomes and climatic zones,with higher mean values of wood density in relatively drier regions(highest in subtropical desert).Our study revealed that at a global scale,for angiosperms and gymnosperms combined,phylogeny and species(representing the variance explained by taxonomy and not direct explained by long-term evolution process)explained 84.3%and 7.7%of total wood density variation,respectively,whereas current environment explained 2.7%of total wood density variation when phylogeny and species were taken into account.When angiosperms and gymnosperms were considered separately,the three proportions of explained variation are,respectively,84.2%,7.5%and 6.7%for angiosperms,and 45.7%,21.3%and 18.6%for gymnosperms.Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

关键词： Wood density Phylogeny angiosperms Gymnosperms Climate factors Biophysical parameters

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A novel protein domain is important for photosystem Ⅱ complex assembly and photoautotrophic growth in angiosperms

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Molecular Plant 2023年第2期16卷 374-392页

作者： Wei Li Jiangfan Guo Xue Han Xiaowen Da Kai Wang Hongfei Zhao Shi-Tang Huange Bosheng Li Hang He Ruirui Jiang Shichen Zhou Peng Yan Tao Chen Yi He Jiming Xu Yu Liu Yunrong Wu Huixia Shou Zhongchang Wu Chuanzao Mao Xiaorong Mo State Key Laboratory of Plant Environmental Resilience College of Life ScienceZhejang UniversityHangzhou 310058PR China College of Life Science Shaanxi Normal UniversityXi'anShaanxi Province 710062PR China School of Advanced Agricultural Sciences and School of Life Sciences State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijing 100871China Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangShandong 261000China College of Urban Construction Zhejiang Shuren UniversityHangzhou 310015PR China School of Life Sciences Peking UniversityBeijing 100871PR China State Key Laboratory of Subtropical Silviculture Zhejiang A&F UniversityLin'anHangzhou 311300PR China

Photosystem Ⅱ(PSⅡ)is a multi-subunit protein complex of the photosynthetic electron transport chain that is vital to photosynthesis.Although the structure,composition,and function of PSⅡ have been extensively studied,its biogenesis mechanism remains less understood.Thylakoid rhodanese-like(TROL)provides an anchor for leaf-type ferredoxin:NADP^(+)oxidoreductase.Here,we report the chacterizaton of a second type of TROL protein,TROL2,encoded by seed plant genomes whose function has not previously been reported.We show that TROL2 is a PSⅡ assembly cofactor with essential roles in the establishment of photoautotrophy.TROL2 contains a 45-amino-acid domain,termed the chlorotic lethal seedling(CLS)domain,that is both necessary and sufficient for TROL2 function in PSⅡ assembly and photoautotrophic growth.Phylogenetic analyses suggest that TROL2 may have arisen from ancestral TROL1 via gene duplication before the emergence of seed plants and acquired the CLS domain via evolution of the sequence encoding its N-terminal portion.We further reveal that TROL2(or CLS)forms an assembly cofactor complex with the intrinsic thylakoid membrane protein LOW PSⅡ ACCUMULATION2 and interacts with small PSⅡ subunits to facilitate PSⅡ complex assembly.Collectively,our study not only shows that TROL2(CLS)is essential for photoautotrophy in angiosperms but also reveals its mechanistic role in PSⅡ complex assembly,shedding light on the molecular and evolutionary mechanisms of photosynthetic complex assemblyin angiosperms.

关键词： PSⅡassembly TROL2 assembly factors angiosperms evolution

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Integrating Early Cretaceous fossils into the phylogeny of living angiosperms:Magnoliidae and eudicots

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Journal of Systematics and Evolution 2010年第1期48卷 1-35页

作者： James A.DOYLE Peter K.ENDRESS Department of Evolution and Ecology University of California DavisCA 95616 USA Institute of Systematic Botany University of Zurich 8008 ZurichSwitzerland

Over the past 25 years, discoveries of Early Cretaceous fossil flowers, often associated with pollen and sometimes with vegetative parts, have revolutionized our understanding of the morphology and diversity of early angiosperms.However, few of these fossils have been integrated into the increasingly robust phylogeny of living angiosperms based primarily on molecular data.To remedy this situation, we have used a morphological dataset for living basal angiosperms(including basal eudicots and monocots) to assess the most parsimonious positions of early angiosperm fossils on cladograms of Recent plants, using constraint trees that represent the current range of hypotheses on higher-level relationships, and concentrating on Magnoliidae(the clade including Magnoliales, Laurales, Canellales, and Piperales) and eudicots.In magnoliids, our results confirm proposed relationships of Archaeanthus(latest Albian?) to Magnoliaceae, Endressinia(late Aptian) to Magnoliales(the clade comprising Degeneria, Galbulimima, Eupomatia, and Annonaceae), and Walkeripollis pollen tetrads(late Barremian?) to Winteraceae, but they indicate that Mauldinia(early Cenomanian) was sister to both Lauraceae and Hernandiaceae rather than to Lauraceae alone.Among middle Albian to early Cenomanian eudicots, we confirm relationships of Nelumbites to Nelumbo, platanoid inflorescences and Sapindopsis to Platanaceae, and Spanomera to Buxaceae.With the possible exception of Archaeanthus, these fossils are apparently not crown group members of living families but rather stem relatives of one or more families.

关键词： angiosperms Cretaceous eudicots flowers Magnoliidae paleobotany phylogeny pollen.

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Genome-scale angiosperm phylogenies based on nuclear,plastome,and mitochondrial datasets

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Journal of Integrative Plant Biology 2023年第6期65卷 1479-1489页

作者： Hongyin Hu Pengchuan Sun Yongzhi Yang Jianxiang Ma Jianquan Liu State Key Laboratory of Grassland Agro-Ecosystems College of EcologyLanzhou UniversityLanzhou 730000China Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengdu 610065China

angiosperms dominate the Earth’s ecosystems and provide most of the basic necessities for human life.The major angiosperm clades comprise 64 orders,as recognized by the APGⅣclassification.However,the phylogenetic relationships of angiosperms remain unclear,as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized,from targeted genes to transcriptomes.Here,we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear,plastid,and mitochondrial genomes of the same species with compatible datasets.The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type.However,there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined.We discuss ways to address these inconsistencies,which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life.The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons.These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.

关键词： angiosperms divergence times genomic phylogenomics

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Intercontinental comparison of phylogenetic relatedness in introduced plants at the transition from naturalization to invasion:A case study on the floras of South Africa and China

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Plant Diversity 2023年第4期45卷 363-368页

作者： Hong Qian Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA

Invasive species may pose significant threats to biodiversity and ecosystem structure and functioning.The number of introduced species that have become invasive is substantial and is rapidly increasing.Identifying potentially invasive species and preventing their expansion are of critical importance in invasion ecology.Phylogenetic relatedness between invasive and native species has been used in predicting invasion success.Previous studies on the phylogenetic relatedness of plants at the transition from naturalization to invasion have shown mixed results,which may be because different methods were used in different studies.Here,I use the same method to analyze two comprehensive data sets from South Africa and China,using two phylogenetic metrics reflecting deep and shallow evolutionary histories,to address the question whether the probability of becoming invasive is higher for naturalized species distantly related to the native flora.My study suggests that the probability of becoming invasive is higher for naturalized species closely related to the native flora.The finding of my study is consistent with Darwin's preadaptation hypothesis.

关键词： angiosperms Exotic species Introduced species Invasive species Naturalized species Phylogenetic relatedness

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Phylogenomics and the flowering plant tree of life

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Journal of Integrative Plant Biology 2023年第2期65卷 299-323页

作者： Cen Guo Yang Luo Lian-Ming Gao Ting-Shuang Yi Hong-Tao Li Jun-Bo Yang De-Zhu Li Germplasm Bank of Wild Species Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botanythe Chinese Academy of SciencesKunming 650201China Lijiang Forest Diversity National Observation and Research Station Kunming Institute of BotanyChinese Academy of SciencesLijiang 674100China Kunming College of Life Science University of Chinese Academy of SciencesKunming 650201China

The advances accelerated by next-generation sequencing and long-read sequencing technologies continue to provide an impetus for plant phylogenetic study.In the past decade,a large number of phylogenetic studies adopting hundreds to thousands of genes across a wealth of clades have emerged and ushered plant phylogenetics and evolution into a new era.In the meantime,a roadmap for researchers when making decisions across different approaches for their phylogenomic research design is imminent.This review focuses on the utility of genomic data(from organelle genomes,to both reduced representation sequencing and whole-genome sequencing) in phylogenetic and evolutionary investigations,describes the baseline methodology of experimental and analytical procedures,and summarizes recent progress in flowering plant phylogenomics at the ordinal,familial,tribal,and lower levels.We also discuss the challenges,such as the adverse impact on orthology inference and phylogenetic reconstruction raised from systematic errors,and underlying biological factors,such as whole-genome duplication,hybridization/introgression,and incomplete lineage sorting,together suggesting that a bifurcating tree may not be the best model for the tree of life.Finally,we discuss promising avenues for future plant phylogenomic studies.

关键词： angiosperms hybridization incomplete lineage sorting orthology inference phylogenetic conflicts reduced representation sequencing whole-genome sequencing whole-genome duplication

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A Biased, Misleading Review on Early angiosperms

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Natural Science 2017年第12期9卷 399-405页

作者： Xin Wang CAS Key Laboratory of Economic Stratigraphy and Palaeogeography Nanjing Institute of Geology and Palaeontology Nanjing China

A recently published review by Herendeen?et al.?is misleading, self-centered, self-praising, and self-conflicting. They excluded the famous early angiosperm?Archaefructus?from their list of exemplar angiosperms, which contained only fossil plants they published themselves, leaving the impression that they were only authoritative on the origin and early history of angiosperms. Their 57-year-old “No angiosperms Until the Cretaceous” conception does not reflect the truth about the origin and early history of angiosperms. Reinforcing such vapidly repeated statement does not help resolving any problem in science but leads to no solution for the origin of angiosperms. The authors tried to establish a criterion identifying a fossil angiosperm but their own exemplar angiosperm?Monetianthus?overturns their own criterion. Apparently, such a review does not positively contribute much to science.

关键词： Age angiosperms Flowers Review Fossil Origin Jurassic

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Statistical analysis on adaptive evolution of SQUA genes in angiosperms

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Progress in Natural Science:Materials International 2005年第1期 94-97页

作者： CHEN Yongyan 1,2, ZHONG Yang 3*, TIAN Bo 1, YANG Ji 4 and LI Dezhu 1*(1. Laboratory of Plant Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China 2. College of Bioengineering, Dalian University, Dalian 116622, China 3. Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, School of Life Science, Fudan University, Shanghai 200433, China 4. College of Life Sciences, Peking University, Beijing 100871, China)

SQUAMOSA (SQUA) subfamily includes important perianth identity genes of MADS-box gene family. SQUA genes of Dendrocalamus latiflorus were sequenced, and phylogenetic form on SQUA genes in angiosperms was analyzed. Relative rate and adaptive evolution after SQUA gene duplication in recent common ancestor of monocots and eudicots were analyzed using the methods of relative rate test, statistic on synonymous and non-synonymous coden substitution sites and likelihood rate test. The results show that both of relative rate and synonymous and non-synonymous coden substitution in eudicot clade are significantly higher than those in monocot clade, and the value of d N/d S uncovered possible positive selective pressure in eudicot clade.

关键词： angiosperms Dendrocalamus latiflorus SQUA gene relative rate test likelihood rate test adaptive evolution.

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