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Species in lichen-forming fungi:balancing between conceptual and practical considerations,and between phenotype and phylogenomics

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Fungal diversity 2021年第4期109卷 99-154页

作者： Robert Lücking steven d.leavitt david L.Hawksworth Botanischer Garten Und Botanisches Museum Freie Universität BerlinKönigin-Luise-Str.6-814195 BerlinGermany department of Biology Brigham Young University4102 Life Science BuildingProvoUT 84602USA M.L.Bean Life Science Museum Brigham Young University1115 MLBMProvoUT 84602USA department of Life Sciences The Natural History MuseumLondon SW75BDUK Comparative Plant and Fungal Biology Royal Botanic GardensKewRichmond TW92ABSurreyUK

Lichens are symbiotic associations resulting from interactions among fungi(primary and secondary mycobionts),algae and/or cyanobacteria(primary and secondary photobionts),and specific elements of the bacterial microbiome associated with the lichen *** question of what is a species,both concerning the lichen as a whole and its main fungal component,the primary mycobiont,has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and *** this paper,we briefly revise the definition of lichens and the scientific and vernacular naming conventions,concluding that the scientific,Latinized name usually associated with lichens invariably refers to the primary mycobiont,whereas the vernacular name encompasses the entire *** the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture,this discrete variation does not warrant the application of different scientific names,but must follow the principle"one fungus=one name".Instead,broadly agreed informal designations should be used for such discrete morphologies,such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or *** taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same *** identify a number of current challenges and provide recommendations to address *** delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence,applying one or several of the following principles in what we call the LPR approach:lineage(L)coherence ***(phylogenetic component),phenotype(P)coherence ***(morphological component),and/or reproductive(R)compatibility ***(biological component).Species hypotheses can be e

关键词： Alpha taxonomy Beta taxonomy Biological species concept Cora Cryptic speciation Fungal farmers Gamma taxonomy Infraspecies Lichens as ecosystems Machine learning Morphological species concept One fungus=one name Photomorph Phylogenetic species concept Species pair concept Thamnolia

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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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Oligodendroglial heterogeneity in health,disease,and recovery:deeper insights into myelin dynamics

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Neural Regeneration Research 2025年第11期20卷 3179-3192页

作者： Pieter-Jan Serneels Julie d.de Schutter Lies de Groef Lieve Moons steven Bergmans KU Leuven Leuven Brain InstituteDepartment of BiologyAnimal Physiology and Neurobiology DivisionNeural Circuit Development&Regeneration Research GroupLeuvenBelgium KU Leuven Leuven Brain InstituteDepartment of BiologyAnimal Physiology and Neurobiology DivisionCellular Communication&Neurodegeneration Research GroupLeuvenBelgium

decades of research asserted that the oligodendroglial lineage comprises two cell types:oligodendrocyte precursor cells and ***,recent studies employing single-cell RNA sequencing techniques have uncovered novel cell states,prompting a revision of the existing *** forward,the oligodendroglial lineage should be delineated into five distinct cell states:oligodendrocyte precursor cells,committed oligodendrocyte precursor cells,newly formed oligodendrocytes,myelin-forming oligodendrocytes,and mature *** new classification system enables a deeper understanding of the oligodendroglia in both physiological and pathological *** this uniform terminology will facilitate comparison and integration of data across ***,including the consolidation of findings from various demyelinating models,is essential to better understand the pathogenesis of demyelinating ***,comparing injury models across species with varying regenerative capacities can provide insights that may lead to new therapeutic strategies to overcome remyelination ***,by standardizing terminology and synthesizing data from diverse studies across different animal models,we can enhance our understanding of myelin pathology in central nervous system disorders such as multiple sclerosis,Alzheimer's disease,and amyotrophic lateral sclerosis,all of which involve oligodendroglial and myelin dysfunction.

关键词： animal models demyelination fish mammals multiple sclerosis myelin neurodegeneration oligodendrocytes oligodendroglial lineage remyelination

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Hierarchical methodology to evaluate the quality of disparate axle load data sources for pavement design

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Journal of Traffic and Transportation Engineering(English Edition) 2022年第2期9卷 261-279页

作者： steven Wood Jonathan d.Regehr Transportation division City of WinnipegWinnipegMB R3B 1B9Canada department of Civil Engineering University of ManitobaMB R3T 5V6Canada

Axle load data are an essential input for pavement design,yet for most North American agencies,there is uncertainty about the quality of axle load data obtained from weigh-inmotion(WIM)systems,the applicability of these data for pavement design,and potential opportunities to integrate axle load data from disparate *** article presents a novel and practical methodology to evaluate the quality of axle load data from WIM systems and roadside weigh scales through a series of hierarchical analyses designed to test data *** applied using data from Manitoba,Canada,the methodology quantified the uncertainty of axle loads measured at the weigh scales and piezo-quartz WIM,concluding that both could be used for pavement design *** collected at piezo-polymer WIM sites exhibited poorer data validity;however,application of site-specific temperature correction factors significantly improved data validity at these *** article describes how other data quality dimensions,including spatial coverage,temporal coverage,and long-term data availability,could be considered when determining the suitability of disparate axle load data sources for pavement *** of the methodology enables a pragmatic evaluation of the quality and limitations of commonlyavailable axle load data,revealing uncertainties and data needs relevant for pavement design practice.

关键词： Road engineering Pavement design Axle load Weigh-in-motion data quality Truck traffic

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Current status of laparoscopy for the treatment of rectal cancer

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World Journal of Gastroenterology 2014年第41期20卷 15125-15134页

作者： Noam Shussman steven d Wexner department of Colorectal Surgery Cleveland Clinic Florida

Surgery for rectal cancer in complex and entails many *** the laparoscopic approach in general and specific to colon cancer has been long proven to have short term benefits and to be oncologically safe,it is still a debatable topic for rectal *** attempt to benefit rectal cancer patients with the known advantages of the laparoscopic approach while not compromising their oncologic outcome has led to the conduction of many studies during the past *** we describe our technique for laparoscopic proctectomy and assess the current literature dealing with short term outcomes,immediate oncologic measures(such as lymph node yield and specimen quality) and long term oncologic outcomes of laparoscopic rectal cancer *** also briefly evaluate the evolving issues of robotic assisted rectal cancer surgery and the current innovations and trends in the minimally invasive approach to rectal cancer surgery.

关键词： Laparoscopy Rectal cancer Minimally invasive surgery Oncological outcomes Short term benefits

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An investigation of roof runoff during rain events at the Royal Military College of Canada and potential discharge to Lake Ontario

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Journal of Environmental Sciences 2011年第7期23卷 1072-1078页

作者： david G. Kelly Ron d. Weir steven d. White Analytical Sciences Group & SLOWPOKE-2 Facility at RMC Department of Chemistry and Chemical Engineering Royal Military College of Canada 11 General Crerar Crescent

The Royal Military College of Canada, located on the north eastern shore of Lake Ontario, possesses an abundance of copper roofs and lacks surface water treatment prior to discharge into Lake Ontario. Rainwater, roof runoff and soil samples were collected and analyzed for copper and other parameters. Copper was consistently detected in runoff samples with average concentrations of 3200 ± 2100 μg/L. Multivariable linear regression analysis for a dependant copper runoff concentration yielded an adjusted R 2 value of 0.611, based on an independent variable model using minimum temperature, maximum temperature, total precipitation, and wind speed. Lake water samples taken in the vicinity of storm water outfalls draining areas with copper roofs ranged from 2.0 to 40 μg/L copper. Such data exceed the 2.0 μg/L Canadian Water Quality Guidelines for the Protection of Aquatic Life as outlined by the Canadian Council of Ministers of the Environment （CCME）. Analysis of raw, filtered and digested forms suggested that the majority of copper present in runoff and lake water samples was in a dissolved form. The majority of soils taken in this study displayed copper concentrations below the 63 μg/g CCME residential/parkland land use limits. These findings suggested that ion exchange processes between runoff water and soil do not occur to a sufficient extent to elevate copper levels in soil. It may therefore be concluded that the eventual fate of copper, which is not discharged via storm water outfalls, is lost to the water table and Lake Ontario through the sub-soil.

关键词： copper roof runoff Lake Ontario Canadian water quality guidelines for the protection of aquatic life

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New instability and mixing simulations using SPH and a novel mixing measure

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Journal of Hydrodynamics 2020年第4期32卷 684-698页

作者： Georgina Reece Benedict d.Rogers steven Lind Georgios Fourtakas department of Mechanical Aerospace and Civil EngineeringUniversityof ManchesterManchesterUK

This paper assesses the ability of smoothed particle hydrodynamics (SPH) to simulate mixing of two-phase flows and theirtransition to instabilities under different flow regimes. A new measure for quantification of the degree of mixing between phases in aLagrangian framework is also developed. The method is validated using the lid-driven cavity and two-phase Poiseuille flow cases. Thevelocity along the centre of the cavity is compared with results from the literature, whilst commercial volume-of-fluid codeSTAR-CCM+ provides a benchmark for the mixing and different mixing measures are considered. The velocity of two-phase Poiseuilleflow along the channel is compared to the analytical solution, and the appearance of interfacial instabilities with perturbation *** is the first time SPH has been used to investigate the onset and development of these instabilities. In particular, it is able to modelthe deforming shape of the interface, which is not given by analytical studies, while also offering improved predictions overconventional mesh-based computational fluid dynamics simulations.

关键词： Smoothed particle hydrodynamics(SPH) multi-phase mixing instability

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Plant photosystem Ⅱ assembly:TROL2 to the rescue

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Molecular Plant 2023年第11期16卷 1719-1721页

作者： Sujith Puthiyaveetil steven d.McKenzie department of Biochemistry and Center for Plant Biology Purdue UniversityWest LatayetteIN 47907USA

In one of the most consequential biochemical reactions on earth,a pigment-protein complex known as photosystem Ⅱ(PSⅡ)in photosynthesis extracts electrons,protons,and oxygen from water using energy from ***Ⅱ thereby sustains life on earth by harnessing the potential of two nearly inexhaustible raw materials:sunlight and *** plant PSllis a membrane-embedded *** monomer consists of around 28 unique protein subunits,157 chlorophylls,44 carotenoids,2 pheophytins,a heme,a non-heme iron,two quinones,and a Mn_(4)CaO_(5) cluster(Su et al.,2017;Cao et al.,2018).Within each monomeric complex,20 protein subunits constitute a core(Figure 1A).

关键词： Figure earth thereby

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