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Towards standardizing taxonomic ranks using divergence times-a case study for reconstruction of the Agaricus taxonomic system

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Fungal Diversity 2016年第3期78卷 239-292页

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li Jean-Marc Moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry UniversityBeijing 100083China Center of Excellence in Fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Natural History Royal Ontario MuseumTorontoON M5S 2C6Canada Department of Ecology and Evolutionary Biology University of TorontoTorontoON M5S 3B2Canada Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences132 Lanhei RoadKunming 650201China INRA-UR1264 Mycologie et Sécuritédes AlimentsCS 2003233882 Villenave d’Ornon cedexFrance Avda.Padre Claret n°7 5°G09400 Aranda de DueroBurgosSpain

The recognition of taxonomic ranks in the Linnean classification system is largely *** authors have proposed the use of divergence time as a universally standardized ***(Agaricaceae,Agaricales)is a mushroom genus that contains many species of high commercial *** studies using ITS sequence data discovered 11 new phylogenetic lineages within the genus,however their taxonomic ranks were uncertain due to the lack of criteria to define them within traditional *** this study,we analyzed ITS sequence data from 745 collections(nearly 600 being newly generated)including 86 from type specimens of previously recognized subgenera and *** monophyletic groups were recognized,but most basal relationships were *** hundred and fourteen representatives of the identified ITS clades were selected in order to produce a multi-gene phylogeny based on combined LSU,tef-1α,and rpb2 sequence *** times within the multi-gene phylogeny were estimated using BEAST *** on phylogenetic relationships and with respect to morphology,we propose a revised taxonomic system for Agaricus that considers divergence time as a standardized criterion for establishing taxonomic *** propose to segregate Agaricus into five subgenera and 20 *** Pseudochitonia is substantially emended;circumscription of the subgenera Agaricus and Flavoagaricus is restricted to taxa of sections Agaricus and Arvenses,respectively;and two new subgenera(Minores and Spissicaules)are *** Pseudochitonia,sections Bivelares,Brunneopicti,Chitonioides,Nigrobrunnescentes,Sanguinolenti and Xanthodermatei are maintained,but the latter two are reduced because we raise subsection Bohusia to sectional rank and a clade within section Xanthodermatei is formally introduced as section Hondenses;and sections Rubricosi,Crassispori,Flocculenti,and Amoeni are *** Laeticolores is placed in the subgenus Minores and sections Rarolen

关键词： Agaricaceae divergence times Multi-gene phylogenetics Systematics Taxonomy

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divergence times and the reconstruction of a standardized taxonomic system based on multigene sequences:case from the genus Agaricus

Divergence times and the reconstruction of a standardized ta...

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中国菌物学会2015年学术年会

作者： Rui-Lin Zhao Jun-Liang Zhou Jie Chen Simona Margaritescu Santiago Sánchez-Ramírez Kevin D Hyde Philippe Callac Luis A.Parra Guo-Jie Li Jean-Marc Moncalvo State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences Institute of Microbiology and Beijing Key Laboratory for Forest Pest Control Beijing Forestry University Institute of Excellence in Fungal Research Mae Fah Luang University School of Science Mae Fah Luang University Department of Natural History Royal Ontario Museum Department of Ecology and Evolutionary Biology University of Toronto Key Laboratory of Economic Plants and Biotechnology Kunming Institute of BotanyChinese Academy of Sciences INRA-UR1264 Mycologie et Sécurité des AlimentsCS 2003233882Villenave d'Ornon cedexFrance

the recognition of taxonomic ranks in current systematic and taxonomic research is lacking universally standardized criteria. Now molecular clock methods allow us to estimate divergence times based on multilocus sequences from extant and fossil agaric specimens. Agaricus（Agaricaceae, Agaricales） is a genus that contains many species of high commerial value. Recent research using ITS sequences discovered eleven new phylogenetic lineages. Proper taxonomic recognition and ranking of new lineages is essential to complete the natural systematics in this important group. In this study, we firstly conducted a preliminary ITS-only phylogenetic reconstruction using 745 ITS sequences（nearly 600 ITS sequences are new taxonomic contributions） including 59 from type specimens. Based on the preliminary ITS tree, 114 samples represented species from all twelve previously recognized Agaricus sections and seven of the eleven recently discovered clades were selected for producing LSU, tef-1α, and rpb2 sequences. Then the divergence time of the genus Agaricus and main clades within Agaricus were estamated using BEAST v1.8. Based on a phylogenetic consensus using a combination of multigene sequences genes（ITS, LSU, tef-1α and rpb2） and morphology, we propose a revised taxonomic system of Agaricus that considers the divergence time as a criterion for standardizing taxonomic rank, which can reflect evolutionary time while concomitantly redefining taxonomic groups based on phylogenetic relationships. The genus Agaricus was divided into five subgenera and 20 sections. Subgenera Minores and Spissicaules were created, subgenus Pseudochitonia was substantially emended, and circumscription of the subgenera Agaricus and Flavoagaricus was restricted to the members of sections Agaricus and Arvenses, respectively. Four new sections were created（Rubricosi, Crassispori, Flocculenti, and Amoeni）. Subsections Bohusia and Hondenses were raised to the sectional rank and placed into subgenus Pseudochiton

关键词： Agaricaceae divergence times multigene phylogenetics systematics taxonomy

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Phylogeny and divergence times of gymnosperms inferred from single-copy nuclear genes

Phylogeny and divergence times of gymnosperms inferred from ...

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生态文明建设中的植物学：现在与未来——中国植物学会第十五届会员代表大会暨八十周年学术年会

作者： Ying Lu Jin-Hua Ran Dong-Mei Guo Zu-Yu Yang Xiao-Quan Wang State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany Chinese Academy of Sciences

Phylogenetic reconstruction is fundamental to study evolutionary biology and historical biogeography. However, there was not a molecular phylogeny of gymnosperms represented by extensive sampling at the genus level, and most published phylogenies of this group were constructed based on cytoplasmic DNA markers and/or the multi-copy nuclear ribosomal DNA. In this study, we use LFY and NLY, two single-copy nuclear genes that originated from an ancient gene duplication in the ancestor of seed plants, to reconstruct the phylogeny and estimate divergence times of gymnosperms based on a complete sampling of extant genera. The results indicate that the combined LFY and NLY coding sequences can well resolve interfamilial relationships of gymnosperms and intergeneric relationships of most families. Moreover, the addition of intron sequences can greatly improve the resolution in Podocarpaceae but not in cycads, although cycads originated much

关键词： Molecular phylogeny divergence times Low copy nuclear genes LFY and NLY Gnetales Gymnosperms

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Origin and evolution of green plants in the light of key evolutionary events

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Journal of Integrative Plant Biology 2022年第2期64卷 516-535页

作者： Zhenhua Zhang Xiaoya Ma Yannan Liu Lingxiao Yang Xuan Shi Hao Wang Runjie Diao Bojian Zhong College of Life Sciences Nanjing Normal UniversityNanjing210023 China

Green plants(Viridiplantae)are ancient photosynthetic organisms that thrive both in aquatic and terrestrial ecosystems,greatly contributing to the changes in global climates and *** progress has been made toward understanding the origin and evolution of green plants,and plant biologists have arrived at the consensus that green plants first originated in marine deep-water environments and later colonized fresh water and dry *** origin of green plants,colonization of land by plants and rapid radiation of angiosperms are three key evolutionary events during the long history of green ***,the comprehensive understanding of evolutionary features and molecular innovations that enabled green plants to adapt to complex and changeable environments are still ***,we review current knowledge of phylogenetic relationships and divergence times of green plants,and discuss key morphological innovations and distinct drivers in the evolution of green ***,we highlight fundamental questions to advance our understanding of the phenotypic novelty,environmental adaptation,and domestication of green plants.

关键词： adaptation divergence times green plants key innovations phylogenetics terrestrialization

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Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogenfixing symbiosis in Fabaceae

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Molecular Plant 2021年第5期14卷 748-773页

作者： Yiyong Zhao Rong Zhang Kai-Wen Jiang Ji Qi Yi Hu Jing Guo Renbin Zhu Taikui Zhang Ashley N.Egan Ting-Shuang Yi Chien-Hsun Huang Hong Ma State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development Ministry of Education Key Laboratory of Biodiversity and Ecological EngineeringInstitute of Plant BiologyCenter of Evolutionary BiologySchool of Life SciencesFudan University2005 Songhu RoadShanghai 200433China Department of Biology The Huck Institutes of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPA 16802USA Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesLanhei RoadKunming 650201China Key Laboratory of Biodiversity Conservation in Southwest China State Forestry AdministrationSouthwest Forestry UniversityKunming 650224PR China Ningbo Botanical Garden Herbarium Ningbo 315201PR China Xishuangbanna Tropical Botanical Garden Chinese Academy of SciencesMenglunYunnan 666303PR China Department of Biology Utah Valley UniversityOremUT 84058USA

Fabaceae are the third largest angiosperm family,with 765 genera and~19500 *** are important both economically and ecologically,and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ***,resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive,precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in ***,we report a highly resolved phylogeny using>1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species,along with other datasets,for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 *** subfamilies are maximally supported as *** clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes,and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and *** clock estimation revealed an early radiation of subfamilies near the K/Pg boundary,marked by mass extinction,and subsequent divergence of most tribe-level clades within~15 million *** analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae,including those at the ancestors of Fabaceae and five of the subfamilies,and further analyses supported the Fabaceae ancestral *** evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switches)to rhizobial nodulation followed by multiple ***,these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.

关键词： Fabaceae Leguminosae nuclear phylogeny divergence times whole-genome duplication rhizobial nodulation

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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 *** major angiosperm clades comprise 64 orders,as recognized by the APGⅣ***,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 ***,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 *** phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome ***,there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were *** discuss ways to address these inconsistencies,which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of *** angiosperm phylogenies presented here provide a basic framework for further updates and *** 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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Phylogenomic Insights into Deep Phylogeny of Angiosperms Based on Broad Nuclear Gene Sampling

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Plant Communications 2020年第2期1卷 77-87页

作者： Lingxiao Yang Danyan Su Xin Chang Charles SPFoster Linhua Sun Chien-Hsun Huang Xiaofan Zhou Liping Zeng Hong Ma Bojian Zhong College of Life Sciences Nanjing Normal UniversityNanjingChina School of Life and Environmental Sciences University of SydneySydneyAustralia Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijingChina State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological EngineeringSchool of Life SciencesFudan UniversityShanghaiChina Guangdong Province Key Laboratory of Microbial Signals and Disease Control Integrative Microbiology Research CentreSouth China Agricultural UniversityGuangzhouChina Institute for Integrative Genome Biology and Department of Botany and Plant Sciences University of CaliforniaRiversideCAUSA Department of Biology Huck Institutes of the Life SciencesPennsylvania State UniversityUniversity ParkPAUSA

Angiosperms(flowering plants)are the most diverse and species-rich group of *** vast majority(99.95%)of angiosperms form a clade called Mesangiospermae,which is subdivided into five major groups:eudicots,monocots,magnoliids,Chloranthales,and *** relationships among these Mesangiospermae groups have been the subject of long *** this study,we assembled a phylogenomic dataset of 1594 genes from 151 angiosperm taxa,including representatives of all five lineages,to investigate the phylogeny of major angiosperm lineages under both coalescent-and concatenationbased *** dissected the phylogenetic signal and found that more than half of the genes lack phylogenetic information for the backbone of angiosperm *** further removed the genes with weak phylogenetic signal and showed that eudicots,Ceratophyllales,and Chloranthales form a clade,with magnoliids and monocots being the next successive sister *** frequencies of gene tree conflict are suggestive of incomplete lineage sorting along the backbone of the angiosperm *** analyses suggest that a fully bifurcating species tree may not be the best way to represent the early radiation of ***,we inferred that the crown-group angiosperms originated approximately between 255.1 and 222.2 million years ago,and Mesangiospermae diversified into the five extant groups in a short time span(27 million years)at the Early to Late Jurassic.

关键词： Mesangiospermae gene tree conflict phylogenomics phylogenetic signal divergence times

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An updated phylogeny of Sordariomycetes based on phylogenetic and molecular clock evidence

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Fungal Diversity 2017年第3期84卷 25-41页

作者： Sinang Hongsanan Sajeewa S.N.Maharachchikumbura Kevin D.Hyde Milan C.Samarakoon Rajesh Jeewon Qi Zhao Abdullah M.Al-Sadi Ali H.Bahkali Key Laboratory of Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fingal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityP.O.Box 34Al-Khod 123Oman Department of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia

The previous phylogenies of Sordariomycetes by ***,*** and ***,and *** and ***,were mainly based on morphology and thus were somewhat *** outlines by *** and ***,and Maharachchikumbura and co-authors,took into account phylogenetic ***,even these phylogenetic driven arrangements for Sordariomycetes,were somewhat subjective,as the arrangements in trees depended on many variables,such as number of taxa,different gene regions and methods used in the *** is needed is extra evidence to help standardize ranking in the *** of divergence times using molecular clock methods has been proposed for providing additional rational for higher ranking of ***,in Sordariomycetes,a divergence period(i.e.200–300 MYA)can be used as criteria to judge when a group of related taxa evolved and what rank they should be *** this paper,we provide an updated classification of accepted subclasses,orders of Sordariomycetes and use divergence times to provide additional evidence to stabilize ranking of taxa in the *** point out and discuss discrepancies where the phylogenetic tree conflicts with the molecular clock.

关键词： Class Classification divergence times Phylogenetics Ranking

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Muti-locus phylogeny and divergence time analyses of Russula from China

Muti-locus phylogeny and divergence time analyses of Russula...

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中国菌物学会2016年学术年会

作者： Guo Jie Li Hua An Wen Fu Cheng Lin Rui Lin Zhao State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of Sciences State Key Laboratory of Rice Biology Institute of BiotechnologyZhejiang University

The genus Russula is a group containing more than 760 species in the world,including many species of edible,medicinal and other economic *** of Russula form symbiotic association of mycorrhizae with roots of various species of shrubs and both coniferous and deciduous trees,playing an important role in *** genus is split into 11 subgenera in the current taxonomic systems of Russula,which are mainly based on morphological characteristics,such as pileus color,context taste,color of spore print,presence of dermatocystidia and primordial hyphae,and size of basidia and *** quite limited molecular phylogeny works are only based on ITS and LSU sequences analyses from several subgenera *** existence of huge number of species,highly variable phenotype and deficient phylogenetic study results Russula is becoming a difficult group in systematic *** this study,a comprehensive phylogenetic analyses based on ITS,n LSU,tef-1α,mt SSU,rpb1 and rpb2 sequences（all are newly generated from this research） derived from 256 Russula specimens in China which represent 161 species from all known 11 subgenera and 26 sections are *** clock dating analysis using BEAST v1.8.3 based on those 6 genes reveal the divergence times of Russula and related subgenera and *** divergence time is introduced as one of universal standardized criteria in taxa ranking as those of previous study in *** research shows the known subgenera Brevipes,Ingratula,Malodora,Russula and Tenellula are generally monophyletic groups,subgenera Coccinula,Compacta,Heterophyllidia,Incrustatula,Insidiosula and Polychromidia are obviously *** order to accommodation those new discoveries,a revised taxonomic system of Rususla is proposed,which composed of 5 new subgenera,sections Amethystina,Indolenta,Maculata,Rosea and Virdanta are raised into subgenera level,and along with 35 new ***,the revised taxonomic system of genus Russu

关键词： Russulaceae divergence times multigene phylogenetics systematics taxonomy

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Adding time-calibrated branch lengths to the Asteraceae supertree

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Journal of Systematics and Evolution 2010年第4期48卷 271-278页

作者： Rubén TORICES rea de Botánica Departamento de Ciencias AgroforestalesUniversidad de Valladolid

New inference techniques,such as supertrees,have improved the construction of large phylogenies,helping to reveal the tree of *** addition,these large phylogenies have enhanced the study of other evolutionary questions,such as whether traits have evolved in a neutral or adaptive way,or what factors have influenced ***,supertrees usually lack branch lengths,which are necessary for all these issues to be ***,divergence times within the largest family of flowering plants,namely the Asteraceae,are reviewed to estimate time-calibrated branch lengths in the supertree of this *** inconsistency between estimated dates of basal branching events and the earliest asteraceous fossil pollen record was *** addition,the impact of different methods of branch length assignment on the total number of transitions between states in the reconstruction of sexual system evolution in Asteraceae was *** least for this dataset,different branch length assignation approaches influenced maximum likelihood(ML)reconstructions only and not Bayesian ***,the selection of different branch length information is not arbitrary and should be carefully assessed,at least when ML approaches are being *** reviewed divergence times and the estimated time-calibrated branch lengths provide a useful tool for future phylogenetic comparative and macroevolutionary studies of Asteraceae.

关键词： Asteraceae character mapping divergence times sexual systems trait evolution

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