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angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits

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Journal of Integrative Plant Biology 2024年第2期66卷 228-251页

作者： Yezi Xiang Taikui Zhang Yiyong Zhao Hongjin Dong Hongyi Chen Yi Hu Chien-Hsun Huang Jun Xiang Hong Ma State Key Laboratory of Genetic Engineering Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan UniversityShanghai 200438China Department of Biology Howard Hughes Medical InstituteDuke UniversityDurhamNC 27708USA Department of Biology the Eberly College of Scienceand the Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA 16802USA Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggang 438000China

Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types,yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families.Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny,with resolved relationships for orders and families with previously uncertain placements.Using this phylogeny as a framework,molecular dating supports a Triassic origin of the crown angiosperms,followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution.The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types,revealing a trend of parallel carpel fusions during early diversifications in eudicots,monocots,and magnoliids.Moreover,taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits;such associations of ovary,dry and fleshy fruits define several ovaryfruit"modules"each found in multiple families.One of the frequent modules has an ovary containing multiple ovules,capsules and berries,and another with an ovary having one or two ovules,achenes(or other single-seeded dry fruits)and drupes.This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types,such as capsule and berry,that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules(such as achenes and drupes).Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications,supporting a possible role of whole-genome duplications,in combination with climate changes and animal behaviors,in angiosperm fruit and ovary diversification.

关键词： angiosperm fruit evolution MADS-box molecular clock nuclear phylogeny ovary and fruit developmental genes

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Global patterns and ecological drivers of taxonomic and phylogenetic endemism in angiosperm genera

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Plant Diversity 2024年第2期46卷 149-157页

作者： Hong Qian Brent D.Mishler Jian Zhang Shenhua Qian Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA University and Jepson Herbaria Department of Integrative BiologyUniversity of CaliforniaBerkeleyCA 94720-2465USA Center for Global Change and Complex Ecosystems Zhejiang Tiantong Forest Ecosystem National Observation and Research StationSchool of Ecological and Environmental SciencesEast China Normal UniversityShanghai 200241China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment Ministry of EducationChongqing UniversityChongqing 400045China

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

关键词： angiosperm Current climate Endemism Historical climate change Topographic heterogeneity

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Geographic patterns of taxonomic and phylogenetic β-diversity of angiosperm genera in regional floras across the world

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Plant Diversity 2023年第5期45卷 491-500页

作者： Hong Qian Shenhua Qian Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment Ministry of EducationChongqing UniversityChongqing 400045China

Beta diversity(β-diversity)is the scalar between local(α)and regional(γ)diversity.Understanding geographic patterns ofβ-diversity is central to ecology,biogeography,and conservation biology.A full understanding of the origin and maintenance of geographic patterns ofβ-diversity requires exploring both taxonomic and phylogeneticβ-diversity,as well as their respective turnover and nestedness components,and exploring phylogenetic p-diversity at different evolutionary depths.In this study,we explore and map geographic patterns ofβ-diversity for angiosperm genera in regional floras across the world.We examine both taxonomic and phylogeneticβ-diversity and their constituent components,and both tip-weighted and basal-weighted phylogeneticβ-diversity,and relate them to latitude.On the one hand,our study found that the global distribution ofβ-diversity is highly heterogeneous.This is the case for both taxonomic and phylogeneticβ-diversity,and for both tip-weighted and basal-weighted phylogeneticβ-diversity.On the other hand,our study found that there are highly consistent geographic patterns among different metrics ofβ-diversity.In most cases,metrics ofβ-diversity are negatively associated with latitude,particularly in the Northern Hemisphere.Different metrics of taxonomicβ-diversity are strongly and positively correlated with their counterparts of phylogeneticβ-diversity.

关键词： angiosperm Beta diversity Flowering plant Latitudinal gradient Phylogenetic relatedness

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angiosperm phylogeny inferred from sequences of four mitochondrial genes

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Journal of Systematics and Evolution 2010年第6期48卷 391-425页

作者： Tory A.HENDRY Joseph W.BROWN Geordan T.HUDSON Department of Ecology and Evolutionary Biology University of Michigan

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes,atp1,matR,nad5,and rps3,from 380 species that represent 376 genera and 296 families of seed plants.It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB,matK,and rbcL,and nuclear 18S rDNA.The basalmost lineage consists of Amborella and Nymphaeales(including Hydatellaceae).Austrobaileyales follow this clade and are sister to the mesangiosperms,which include Chloranthaceae,Ceratophyllum,magnoliids,monocots,and eudicots.With the exception of Chloranthaceae being sister to Ceratophyllum,relationships among these five lineages are not well supported.In eudicots,Ranunculales,Sabiales,Proteales,Trochodendrales,Buxales,Gunnerales,Saxifragales,Vitales,Berberidopsidales,and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids.Within rosids,the COM(Celastrales-Oxalidales-Malpighiales) clade is sister to malvids(or rosid II),instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms.Santalales and Caryophyllales are members of an expanded asterid clade.This study shows that the mitochondrial genes are informative markers for resolving relationships among genera,families,or higher rank taxa across angiosperms.The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes,as found in this study,make them particularly useful for reconstructing ancient phylogenetic relationships.A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes,nuclear genes,and non-molecular data to reconstruct the underlying organismal phylogeny.

关键词： angiosperm homoplasy mitochondrial gene molecular evolutionary rate phylogeny rosids.

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Schmeissneria:An angiosperm from the Early Jurassic

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Journal of Systematics and Evolution 2010年第5期48卷 326-335页

作者： 1,2Xin WANG 1(Nanjing Institute of Geology and Palaeontology,Chinese Academy of Sciences,Nanjing 210008,China) 2(Fairylake Botanical Garden,Shenzhen 518004,China) (Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences Nanjing 210008 China) (Fairylake Botanical Garden Shenzhen 518004 China)

The origin of angiosperms has been a focus of intensive research for a long time.The so-called pre-Cretaceous angiosperms,including Schmeissneria,are usually clouded with doubt.To expel the cloud around the enigmatic Schmeissneria,the syntype and new materials of Schmeissneria collected previously in Germany and recently in China are studied.These materials include female inflorescences and infructescences.The latter are old materials but were under-studied previously.Light microscopy and scanning electron microscope observations indicate that the fruits in these infructescences have in situ seeds enclosed,and that the ovaries are closed be fore pollination.Thus the plants meet two strict criteria for angiosperms:angiospermy plus angio-ovuly.Placing Schmeissneria in angiosperms will extend the record of angiosperms up to the Early Jurassic,more compatible with many molecular dating conclusions on the age of angiosperms,and demanding a reassessment of the current doctrines on the origin of angiosperms.Although the phylogenetic relationship of Schmeissneria to other angiosperms apparently is still an open question,this study adds to research concerning the origin of angiosperms.

关键词： angiosperm earliest evolution flower fossil Germany Jurassic origin.

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A Novel angiosperm from the Early Cretaceous and Its Implications for Carpel-Deriving

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Acta Geologica Sinica(English Edition) 2018年第4期92卷 1293-1298页

作者： LIU Zhongjian WANG Xin Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture Fujian Agriculture and Forestry University Shenzhen Key Laboratory for Orchid Conservation and Utilization National Orchid Conservation Center of China and Orchid Conservation and Research Center of Shenzhen CAS Key Laboratory of Economic Stratigraphy and Palaeogeography Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment Chinese Academy of Sciences

The Yixian Formation （Lower Cretaceous） of China is famous for its fossils of early angiosperms, and these fossils have shed otherwise unavailable light on the evolution of angiosperms. The seeds in Archaefructus and Nothodichocarpum are inserted along the dorsal of the fruits while those in Sinocarpus are along the ventral of the fruits, suggesting different Bau-plans and pathways deriving the carpels in these plants of the Early Cretaceous. Adding further fossil evidence, here we report a novel fossil angiosperm, Neofructus lingyuanensis gen. et sp. nov, with its seeds inserted on both ventral and dorsal sides of the fruits documented through light microscopic and SEM observations, suggesting a novel way forming gynoecium in the Yixian Formation. These fossil angiosperms indicate that angiosperm gynoecia in the Yixian Formation （the Barremian to Aptian） are derived in obviously different ways, implying an evolutionary scenario for angiosperms quite different from formerly assumed.

关键词： angiosperm Neofructus gynoecium Yixian Formation Early Cretaceous Liaoning

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Relationship between clade age and temperature for angiosperm tree species in forest communities along an elevational gradient in tropical Asia

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Journal of Plant Ecology 2017年第4期10卷 618-625页

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

Aims The tropical conservatism hypothesis(TCH)links environmental tolerance,diversification,dispersal and evolutionary history in explaining why warm,wet tropical regions harbor more species than colder,drier regions.The TCH is considered as a dominant explanation for broad-scale patterns of species richness across the globe,such as the latitudinal diversity gradient.At its core,the TCH predicts a positive relationship between clade age and tempera-ture.Here,I test this prediction using a data set of angiosperm tree assemblages from Malesia.Methods I assembled an altitudinal gradient of 15 communities of angio-sperm trees.I calculated the mean family age(MFA)of tree species for each community.I used ordinary regression analysis and spatial autoregression analysis to determine the relationships of species richness and MFA with elevation,temperature and precipitation.I used correlation analysis to assess relationships between paired variables.Important Findings MFA is negatively correlated with tree species richness,and increases with elevation and decreases with temperature for the alti-tudinal gradient.MFA remains significantly increasing with decreas-ing temperature along the altitudinal gradient after accounting for spatial autocorrelation in a species-ordination space.The negative relationship between clade age and temperature along the altitudi-nal gradient in Malesia is contrary to the TCH.

关键词： angiosperm cold tolerance community assembly altitudinal diversity gradient environmental filtering mean family age phylogenetic niche conservatism

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A Dichocarpum-like angiosperm from the Early Cretaceous of China

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Acta Geologica Sinica(English Edition) 2017年第1期91卷 1-8页

作者： HAN Gang LIU Zhongjian WANG Xin Hainan Tropical Ocean University Sanya 572022 China Palaeontological Center Bohai University Jinzhou 121013 China Shenzhen Key Laboratory for Orchid Conservation and Utilization National Orchid Conservation Center of China and Orchid Conservation ＆ Research Center of Shenzhen Shenzhen 518114 China State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and Palaeontology CAS Nanjing 210008 China

The Yixian Formation（the Early Cretaceous） of China has yielded a diverse group of early angiosperms, revealing the charm of angiosperms from the formation is far from finishing. Here we report a fossil angiosperm, Nothodichocarpum gen. et sp. nov, with physically connected female parts, male parts, branches, and leaves with pinnate reticulate venation from the Yixian Formation of Liaoning, China. In addition to the previous reports, this report underscores the diversity of angiosperms in the Early Cretaceous Yixian Formation and earlier origin of angiosperms. The morphological variations in the reproductive parts in different stages allow us to infer the development of this early angiosperm. This fossil plant demonstrates a unique character assemblage that sheds new light on the origin and evolution of carpels.

关键词： angiosperm Nothodichocarpum Early Cretaceous Liaoning Yixian Formation

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Patterns of phylogenetic relatedness of non-native plants across the introduction-naturalization-invasion continuum in China

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Plant Diversity 2023年第2期45卷 169-176页

作者： Hong Qian CAS Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201China Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA

Human activities have caused the exchange of species among different parts of the world.When introduced species become naturalized and invasive,they may cause great negative impacts on the environment and human societies,and pose significant threats to biodiversity and ecosystem structure.Knowledge on phylogenetic relatedness between native and non-native species and among non-native species at different stages of species invasion may help for better understanding the drivers of species invasion.Here,I analyze a comprehensive data set including both native and non-native angiosperm species in China to determine phylogenetic relatedness of introduced species across a full invasion continuum(from introduction through naturalization to invasion).This study found that(1) introduced plants are a phylogenetically clustered subset of overall(i.***.native plus non-native) angiosperm flora,(2) naturalized plants are a phylogenetically clustered subset of introduced plants,and(3) invasive plants are a phylogenetically clustered subset of naturalized plants.These patterns hold regardless of spatial scales examined(i.***.national versus provincial scale) and whether basal-or tip-weighted metric of phylogenetic relatedness is considered.These findings are consistent with Darwin's preadaptation hypothesis.

关键词： angiosperm Community assembly Darwin's preadaptation hypothesis Exotic species Introduced species Phylogenetic dispersion

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Global patterns of taxonomic and phylogenetic diversity of flowering plants: Biodiversity hotspots and coldspots

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Plant Diversity 2023年第3期45卷 265-271页

作者： Hong Qian Jian Zhang Meichen Jiang Research and Collections Center Illinois State Museum1011 East Ash StreetSpringfieldIL 62703USA Center for Global Change and Complex Ecosystems Zhejiang Tiantong Forest Ecosystem National Observation and Research StationSchool of Ecological and Environmental SciencesEast China Normal UniversityShanghai 200241China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China

Species diversity of angiosperms(flowering plants) varies greatly among regions.Geographic patterns of variation in species diversity are shaped by the interplay of ecological and evolutionary processes.Here,using a comprehensive data set for regional angiosperm floras across the world,we show geographic patterns of taxonomic(species) diversity,phylogenetic diversity,phylogenetic dispersion,and phylogenetic deviation(i.e.,phylogenetic diversity after accounting for taxonomic diversity) across the world.Phylogenetic diversity is strongly and positively correlated with taxonomic diversity;as a result,geographic patterns of taxonomic and phylogenetic diversity across the world are highly similar.Areas with high taxonomic and phylogenetic diversity are located in tropical regions whereas areas with low taxonomic and phylogenetic diversity are located in temperate regions,particularly in Eurasia and North America,and in northern Africa.Similarly,phylogenetic dispersion is,in general,higher in tropical regions and lower in temperate regions.However,the geographic pattern of phylogenetic deviation differs substantially from those of taxonomic and phylogenetic diversity and phylogenetic dispersion.As a result,hotspots and coldspots of angiosperm diversity identified based on taxonomic and phylogenetic diversity and phylogenetic dispersion are incongruent with those identified based on phylogenetic deviations.Each of these metrics may be considered when selecting areas to be protected for their biodiversity.

关键词： angiosperm Biodiversity hotspot Phylogenetic diversity Phylogenetic structure Species richness

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