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Using a temporal phylogenetic method to harmonize familyand genus-level classification in the largest clade of lichen-forming fungi

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Fungal Diversity 2017年第3期84卷 101-117页

作者： pradeep k.divakar Ana Crespo Ekaphan kraichak Steven D.Leavitt Garima Singh Imke Schmitt H.Thorsten Lumbsch Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain Department of Botany Faculty of ScienceKasetsart UniversityBangkokThailand Department of Biology and M.L.Bean Life Science Museum Brigham Young University4102 Life Science BuildingProvoUT 84602USA Department of Biological Sciences Institute of EcologyEvolution and DiversityGoethe Universitat and Senckenberg Biodiversity and Climate Research Centre(BiK-F)Frankfurt am MainGermany Science&Education The Field MuseumChicagoILUSA

Although classification at supra-specific ranks is inherently arbitrary,comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among *** circumscriptions of the hyper-diverse lichen-forming fungal family Parmeliaceae and widely different generic circumscriptions among authors have been *** this study,we use a recently developed temporal approach that uses timecalibrated chronograms to identify temporal bands for specific ranks in Parmeliaceae and allied groups with the overarching goal of establishing a consistent,stable classification.A data set of 330 species,representing 73 genera in the family and 52 species of related families was used to address the circumscription of Parmeliaceae and its genera following the proposed temporal *** on the results of this study,we propose a revised,temporal-based classification for Parmeliaceae,including all clades that share a common ancestor 102.13–112.88 Ma for families and a time window of 29.45–32.55 Ma for *** of the currently accepted genera in Parmeliaceae were supported in their current *** subfamilies are accepted within Parmeliaceae:Protoparmelioideae divakar et ***.,including Protoparmelia and the resurrected genus Maronina,and Parmelioideae,including the bulk of genera in the *** new genus Austromelanelixia divakar et *** proposed to accommodate a clade of southern Hemisphere species previously included in *** and tentatively Dolichousnea are resurrected as genera separate from *** following genera are reduced to synonymy:Allocetraria,Cetrariella,Usnocetraria,and Vulpicida with Cetraria;Arctocetraria,Cetreliopsis,Flavocetraria,kaernefeltia,Masonhalea,Tuckermanella,and Tuckermannopsis with Nephromopsis;and the lichenicolous genera Nesolechia and Raesaenenia with the lichen-forming genera Punctelia and Protousnea,respectively.A total of 47 new combinations and

关键词： Ascomycota Gypsoplacaceae Lecanorales Lichenized fungi Parmeliaceae Phylogeny Protoparmelia Taxonomy Taxonomicranks

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Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi

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Fungal Diversity 2018年第5期92卷 31-41页

作者： David Pizarro pradeep k.divakar Felix Grewe Steven D.Leavitt Jen-Pan Huang Francesco Dal Grande Imke Schmitt Mats Wedin Ana Crespo H.Thorsten Lumbsch Departamento de Farmacologı́a Farmacognosia y BotánicaFacultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain Science&Education The Field Museum1400 S.Lake Shore DriveChicagoILUSA Department of Biology and M.L.Bean Life Science Museum Brigham Young UniversityLife Science Building 4102ProvoUT 84602USA Senckenberg Biodiversity and Climate Research Centre(SBik-F) Senckenberganlage 2560325 Frankfurt am MainGermany Institute of Ecology Evolution and DiversityGoethe UniversityFrankfurt am MainMax-von-Laue-Str.960438 Frankfurt am MainGermany Department of Botany Swedish Museum of Natural HistoryPO Box 5000710405 StockholmSweden

Phylogenomic datasets continue to enhance our understanding of evolutionary relationships in many lineages of ***,genome-scale data have not been widely implemented in reconstructing relationships in lichenized *** we generate a data set comprised of 2556 single-copy protein-coding genes to reconstruct previously unresolved rela-tionships in the most diverse family of lichen-forming fungi,*** sampling included 51 taxa,mainly from the subfamily Parmelioideae,and represented six of the seven previously identified major clades within the *** results provided strong support for the monophyly of each of these major clades and most backbone relationships in the topology were recovered with high nodal support based on concatenated dataset and species tree *** alectorioid clade was strongly supported as sister-group to all remaining clades,which were divided into two major *** the first major clade the anzioid and usneoid clades formed a strongly supported sister-group relationship with the cetrarioid?hypogymnioid *** sister-group relationship of Evernia with the cetrarioid clade was also strongly supported,whereas that between the anzioid and usneoid clades needs further *** the second major clade Oropogon and Platismatia were sister to the parmelioid group,while the position of Omphalora was not fully *** study demonstrates the power of genome-scale data sets to resolve long-standing,ambiguous phylogenetic rela-tionships of lichen-forming ***,the topology inferred in this study will provide a valuable framework for better understanding diversification in the most diverse lineage of lichen-forming fungi,Parmeliaceae.

关键词： Fungi Lecanorales Lichenized fungi Parmeliaceae Parmelioideae Phylogeny Systematics

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Towards a revised generic classification of lecanoroid lichens(Lecanoraceae,Ascomycota)based on molecular,morphological and chemical evidence

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Fungal Diversity 2016年第3期78卷 293-304页

作者： Xin Zhao Steven D.Leavitt Zun Tian Zhao Lu Lu Zhang Ulf Arup Martin Grube Sergio Pérez-Ortega Christian Printzen LucynaŚliwa Ekaphan kraichak pradeep k.divakar Ana Crespo H.Thorsten Lumbsch College of Life Sciences Shandong Normal UniversityJinan 250014People’s Republic of China Science&Education The Field MuseumChicagoILUSA Biological Museum Lund UniversityBox 117SE-22100 LundSweden Institute of Plant Sciences Karl-Franzens-University GrazHolteigasse 68010 GrazAustria Departamento Biogeoquímica y Ecología Microbiana Museo Nacional de Ciencias NaturalesMadridSpain Present address:Real Jardín Botánico Plaza de Murillo 228014 MadridSpain Department of Botany and Molecular Evolution Senckenberg Research Institute and Natural History Museum FrankfurtSenckenberganlage 25D-60325 Frankfurt am MainGermany Laboratory of Lichenology W.Szafer Institute of BotanyPolish Academy of SciencesLubicz 4631–512 KrakówPoland Department of Botany Faculty of ScienceKasetsart University10900 BangkokThailand Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain

Abstract The phylogenetic relationship of lecanoroid lichens is studied using two data sets:1)a 2-locus data set including 251 OTUs representing 150 species,and 2)a 6-locus data set with 82 OTUs representing 53 *** genus Lecanora as currently circumscribed is shown to be highly polyphyletic and several genera,including Adelolecia,Arctopeltis,Bryonora,Carbonea,Frutidella,Lecidella,Miriquidica,Palicella,Protoparmeliopsis,Pyrrhospora,and Rhizoplaca are nested within Lecanora sensu lato.A core group of Lecanora is supported as monophyletic and includes species of the ***,***,and *** groups,and a core group of the *** *** monophyletic clades that are well supported in our analyses and well characterized by phenotypical characters are accepted here:1)Myriolecis to accommodate the Lecanora dispersa group and Arctopeltis;2)Protoparmeliopsis for the *** group;and 3)Rhizoplaca is emended to include three placodioid taxa previously classified in Lecanora(***,***),whereas *** and *** are excluded from *** latter is transferred into *** is strongly supported as a monophyletic *** studies indicate the presence of additional clades of species currently placed in Lecanora sensu lato that warrant taxonomic recognition but additional data will be necessary before the circumscription of these entities is fully understood.37 new combinations are proposed into the genera Myriolecis(30),Protoparmeliopsis(2),and Rhizoplaca(5).

关键词： Arctopeltis Classification Generic concept Lecanora Lichenized fungi Myriolecis Rhizoplaca Protoparmeliopsis Rhizoplaca Taxonomy

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Discovering hidden patterns:Association rules for cardiovascular diseases in type 2 diabetes mellitus

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World Journal of Methodology 2024年第2期14卷 97-106页

作者： pradeep kumar Dabla kamal Upreti Dharmsheel Shrivastav Vimal Mehta divakar Singh Department of Biochemistry Govind Ballabh Pant Institute of Postgraduate Medical Education and ResearchDelhi 110002India Department of Computer Science CHRISTGhaziabad 201003India Department of Cardiology Govind Ballabh Pant Institute of Postgraduate Medical Education and ResearchDelhi 110002India Barkatullah University Institute of Technology Barkatullah UniversityBhopal 462026India

BACkGROUND It is increasingly common to find patients affected by a combination of type 2 diabetes mellitus(T2DM)and coronary artery disease(CAD),and studies are able to correlate their relationships with available biological and clinical *** aim of the current study was to apply association rule mining(ARM)to discover whether there are consistent patterns of clinical features relevant to these *** leverages clinical and laboratory data to the meaningful patterns for diabetic CAD by harnessing the power help of data-driven algorithms to optimise the decision-making in patient *** To reinforce the evidence of the T2DM-CAD interplay and demonstrate the ability of ARM to provide new insights into multivariate pattern *** This cross-sectional study was conducted at the Department of Biochemistry in a specialized tertiary care centre in Delhi,involving a total of 300 consented subjects categorized into three groups:CAD with diabetes,CAD without diabetes,and healthy controls,with 100 subjects in each *** participants were enrolled from the Cardiology IPD&OPD for the sample *** study employed ARM technique to extract the meaningful patterns and relationships from the clinical data with its original *** The clinical dataset comprised 35 attributes from enrolled *** analysis produced rules with a maximum branching factor of 4 and a rule length of 5,necessitating a 1%probability increase for *** patterns emerged,highlighting strong links between health indicators and diabetes likelihood,particularly elevated HbA1C and random blood sugar *** ARM technique identified individuals with a random blood sugar level>175 and HbA1C>6.6 are likely in the“CAD-with-diabetes”group,offering valuable insights into health indicators and influencing factors on disease *** The application of this method holds promise for healthcare practitioners to offer valuable insights for enhanc

关键词： Coronary artery disease Type 2 diabetes mellitus Coronary angiography Association rule mining Artificial intelligence

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