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The evolving species concepts used for yeasts:from phenotypes and genomes to speciation networks

Fungal Diversity 2021年第4期109卷 27-55页

作者： Teun Boekhout M.Catherine Aime Dominik Begerow Toni Gabaldón Joseph Heitman Martin Kemler Kantarawee Khayhan Marc-AndréLachance Edward J.Louis Sheng Sun Duong Vu Andrey Yurkov Westerdijk Fungal Biodiversity Institute UtrechtThe Netherlands Institute of Biodiversity and Ecosystem Dynamics(IBED) University of AmsterdamAmsterdamThe Netherlands Dept Botany and Plant Pathology College of AgriculturePurdue UniversityWest LafayetteIN 47907USA Evolution of Plants and Fungi Ruhr-University Bochum44801 BochumGermany Barcelona Supercomputing Centre(BSC-CNS) Jordi Girona2908034 BarcelonaSpain Institute for Research in Biomedicine(IRB Barcelona) The Barcelona Institute of Science and TechnologyBaldiri Reixac1008028 BarcelonaSpain Catalan Institution for Research and Advanced Studies(ICREA) BarcelonaSpain Department of Molecular Genetics and Microbiology Duke University Medical CenterDurhamNC 27710USA Department of Microbiology and Parasitology Faculty of Medical SciencesUniversity of PhayaoPhayao 56000Thailand Department of Biology University of Western OntarioLondonON N6A 5B7Canada Department of Genetics and Genome Biology Genetic Architecture of Complex TraitsUniversity of LeicesterLeicester LE17RHUK German Collection of Microorganisms and Cell Cultures Leibniz Institute DSMZBrunswickGermany

Here we review how evolving species concepts have been applied to understand yeast ***,a phenotypic species concept was utilized taking into consideration morphological aspects of colonies and cells,and growth *** the biological species concept was added,which applied data from mating *** measurements of DNA similarity between isolates were an early measure that became more broadly applied with the advent of sequencing technology,leading to a sequence-based species concept using comparisons of parts of the ribosomal *** present phylogenetic species concepts that employ sequence data of rDNA and other genes are universally applied in fungal taxonomy,including yeasts,because various studies revealed a relatively good correlation between the biological species concept and sequence *** application of genome information is becoming increasingly common,and we strongly recommend the use of complete,rather than draft genomes to improve our understanding of species and their genome and genetic *** genomes allow in-depth comparisons on the evolvability of genomes and,consequently,of the species to which they *** seems a relatively common phenomenon and has been observed in all major fungal lineages that contain *** that hybrids may greatly differ in their post-hybridization *** in-depth studies,initially using some model species or complexes may shift the traditional species concept as isolated clusters of genetically compatible isolates to a cohesive speciation network in which such clusters are interconnected by genetic processes,such as hybridization.

关键词： Fungi species concepts Comparative genomics Hybrids Nomenclature Taxonomy

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The art and science of species delimitation

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Current Zoology 2015年第5期61卷 846-853页

作者： Bruce RANNALA Department of Evolution and Ecology University of California Davis Davis CA 95616 USA

DNA-based approaches to systematics have changed dramatically during the last two decades with the rise of DNA barcoding methods and newer multi-locus methods for species delimitation. During the last half-decade, partly driven by the new sequencing technologies, the focus has shifted to multi-locus sequence data and the identification of species within the frame-work of the multi-species coalescent （MSC）. In this paper, I discuss model-based Bayesian methods for species delimitation that have been developed in recent years using the MSC. Several approximate methods for species delimitation （and their limitations） are also discussed. Explicit species delimitation models have the advantage of clarifying more precisely what is being delimited and what assumptions we are making in doing so. Moreover, the methods can be very powerful when applied to large multi-locus datasets and thus take full advantage of data generated using today＇s technologies [Current Zoology 61 （5）： 846-853,2015].

关键词： Bayesian species delimitation species concepts Multi-species coalescent

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species delimitation based on diagnosis and monophyly, and its importance for advancing mammalian taxonomy

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Zoological Research 2018年第5期39卷 301-308页

作者： Eliécer E.Gutiérrez Guilherme S.T.Garbino Pós-Graduacao em Biodiversidade Animal Departamento de Ecologia e Evolucao Centro de Ciências Naturais e Exatas Universidade Federal de Santa Maria Santa Maria RS 97105-900 Brazil Division of Mammals National Museum of Natural History Smithsonian Institution Washington DC 20013-7012 USA Pós-graduacao Departamento de Zoologia Instituto de Ciências Biológicas Universidade Federal de Minas Gerais Belo Horizonte Minas Gerais 31270-901 Brazil

A recently proposed taxonomic classification of extant ungulates sparked a series of publications that criticize the Phylogenetic species Concept （PSC） claiming it to be a particularly poor species *** opinions reiteratively stated that （1） the two fundamental elements of the ＂PSC＂,i.e.,monophyly and diagnosability,do not offer objective criteria as to where the line between species should be drawn;and （2） that extirpation of populations can lead to artificial diagnosability and spurious recognitions of *** sudden eruption of criticism against the PSC is *** attributed to the PSC are common to most approaches and concepts that modern systematists employ to establish species *** controversial taxonomic propositions that sparked criticism against the PSC are indeed highly problematic,not because of the species concept upon which they are based,but because no evidence （whatsoever） has become public to support a substantial portion of the proposed *** herein discuss these topics using examples from *** areas of biological research rest upon taxonomic accuracy （including conservation biology and biomedical research）;hence,it is necessary to clarify what are （and what are not）the real sources of taxonomic inaccuracy.

关键词： Alpha taxonomy Phylogenetic speciesConcept species concepts Taxonomic inertia Taxonomic inflation

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Defining a species in fungal plant pathology:beyond the species level

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Fungal Diversity 2021年第4期109卷 267-282页

作者： Ishara S.Manawasinghe Alan J.L.Phillips Jianping Xu Abhaya Balasuriya Kevin D.Hyde Łukasz Stępień Dulanjalee L.Harischandra Anuruddha Karunarathna Jiye Yan Janith Weerasinghe Mei Luo Zhangyong Dong Ratchadawan Cheewangkoon Innovative Institute for Plant Health Zhongkai University of Agriculture and EngineeringGuangzhou 510225People’s Republic of China Faculdade de Ciências Biosystems and Integrative Sciences Institute(BioISI)Universidade de LisboaCampo Grande1749-016 LisbonPortugal Department of Biology McMaster University1280 Main St.WestHamiltonON L8S 4K1Canada Department of Plant Science Faculty of AgricultureRajarata University of Sri LankaAnuradhapuraSri Lanka Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang RaiThailand Institute of Plant Genetics Polish Academy of SciencesPoznańPoland Institute of Plant and Environment Protection Beijing Academy of Agriculture and Forestry SciencesBeijing 100097China Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai University50200Chiang MaiThailand School of Chemistry and Physics Queensland University of Technology2George StreetBrisbaneQLD 4000Australia

In plant pathology,the correct naming of a species is essential for determining the causal agents of *** names not only serve the general purpose of concise communication,but also are critical for effective plant quarantine,prevent-ing the introduction of new pathogens into a *** phytopathogenic genera have multiple species and,in several genera,disagreements between the multiple prevailing species concept definitions result in numerous cryptic *** of these species were previously called by various names;forma speciales(specialised forms),subspecies,or ***,based on new molecular evidence they are being assigned into new *** frequent name changes and lack of consistent criteria to delineate cryptic species,species,subspecies,forms,and races create increasing confusion,often making communication among biologists ***,such ambiguous information can convey misleading evo-lutionary concepts and species *** aim of this paper is to review these concepts,clarify their use,and evaluate them by referring to existing *** specifically address the question,“Do plant pathogens require a different ranking system?”We conclude that it is necessary to identify phytopathogens to species level based on data from multiple ***,this identification must go beyond species level to clearly classify hitherto known subspecies,forms and *** addition,when naming phytopathogenic genera,plant pathologists should provide more information about geographic locations and host ranges as well as host specificities for individual species,cryptic species,forms or *** describing a new phytopathogen,we suggest that authors provide at least three representative strains together with pathogenicity test *** Koch’s postulates cannot be fulfilled,it is necessary to provide complementary data such as associated disease severity on the host ***,more sequenced collections of spec

关键词： Cryptic species Forms Fungal nomenclature New pathogen species concepts Subspecies Races

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Predicting global numbers of teleomorphic ascomycetes

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Fungal Diversity 2022年第3期114卷 237-278页

作者： Indunil C.Senanayake Dhandevi Pem Achala R.Rathnayaka Subodini N.Wijesinghe Saowaluck Tibpromma Dhanushka N.Wanasinghe Rungtiwa Phookamsak Nuwan D.Kularathnage Deecksha Gomdola Dulanjalee Harishchandra Lakmali S.Dissanayake Mei-mei Xiang Anusha H.Ekanayaka Eric H.C.McKenzie Kevin D.Hyde Hao-xing Zhang Ning Xie Guangdong Provincial Key Laboratory for Plant Epigenetics College of Life Science and OceanographyShenzhen UniversityNanhai AvenueNanshanShenzhen 3688GuangdongChina Innovative Institute for Plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Honghe Center for Mountain Futures Kunming Institute of BotanyChinese Academy of SciencesHonghe County 654400YunnanChina Centre for Mountain Futures(CMF) Kunming Institute of BotanyKunming 650201YunnanChina CIFOR-ICRAF China Program World Agroforestry(ICRAF)Kunming 650201YunnanChina Beijing Key Laboratory of Environment Friendly Management On Fruit Diseases and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China Engineering Research Center of the Utilization for Characteristic Bio-Pharmaceutical Resources in Southwest Ministry of EducationGuizhou UniversityGuiyang 550025GuizhouChina Manaaki Whenua-Landcare Research Auckland Mail CentrePrivate Bag 92170Auckland 1142New Zealand

Sexual reproduction is the basic way to form high genetic diversity and it is beneficial in evolution and speciation of *** global diversity of teleomorphic species in Ascomycota has not been *** paper estimates the species number for sexual ascomycetes based on five different estimation approaches,*** numbers of described fungi,by fungus:substrate ratio,by ecological distribution,by meta-DNA barcoding or culture-independent studies and by previous estimates of species in *** assumptions were made with the currently most accepted,“2.2–3.8 million”species estimate and results of previous studies concluding that 90%of the described ascomycetes reproduce *** Catalogue of Life,species Fungorum and published research were used for data *** average value of teleomorphic species in Ascomycota from all methods is 1.86 million,ranging from 1.37 to 2.56 ***,only around 83,000 teleomorphic species have been described in Ascomycota and deposited in data *** ratio between described teleomorphic ascomycetes to predicted teleomorphic ascomycetes is 1:***,where are the undiscovered teleomorphic ascomycetes?The undescribed species are no doubt to be found in biodiversity hot spots,poorly-studied areas and species *** poorly studied niches include extremophiles,lichenicolous fungi,human pathogens,marine fungi,and fungicolous *** species are present in unexamined collections in specimen repositories or incompletely described earlier *** issues,such as the use of separate names for teleomorph and anamorphs,synonyms,conspecific names,illegitimate and invalid names also affect the number of described *** introgression results in new species,while species numbers are reduced by extinctions.

关键词： Ascomycota Estimates Habitat diversity Molecular techniques species concepts

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What are fungal species and how to delineate them?

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Fungal Diversity 2021年第4期109卷 1-25页

作者： K.W.Thilini Chethana Ishara S.Manawasinghe V.G.Hurdeal Chitrabhanu S.Bhunjun M.A.Appadoo Eleni Gentekaki Olivier Raspé Itthayakorn Promputtha Kevin D.Hyde Innovative institute for plant health zhongkai university of agriculture and engineeringguangzhou 510225people’s republic of china center of excellence in fungal research mae fah luang universitychiang rai 57100thailand school of science mae fah luang universitychiang rai 57100thailand department of biology faculty of sciencechiang mai universitychiang mai 50200thailand

This is the opening paper in the special issue of Fungal Diversity,which collates the data on defining *** and recognizing species has long been a controversial *** Darwin’s proposed origin of species,over 30 species criteria have been brought forth and used to define species *** recent times,phylogenetic analyses based on multiple loci have been extensively used as a method to define species ***,only a few mycologists are aware that phylogenetic species criteria can mask discordances among fungal groups,leading to inaccurately defined species *** the current review,we discuss species recognition criteria,how and where these criteria can be applied along with their limitations and derived *** order to delimit fungal species,authors need to take into account not only the phylogenetic and phenotypic coherence,but also the timing of events that lead to fungal speciation and subsequent *** in the rate of phenotypic diversifications and convergent fungal evolution make it difficult to establish a universal species recognition *** best practice can only be defined in the context of each fungal *** this review,we provide a set of guidelines,encouraging an integrative taxonomic approach for species delimitation that can be used to define fungal species boundaries in the *** other papers in this special issue deal with fungal speciation in Ascomycota,Dothideomycetes,Basidiomycota,basal fungi,lichen-forming fungi,plant pathogenic fungi,and yeasts.

关键词： Allopatry Speciation species concepts species criteria species recognition Sympatry

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species from Darwin onward

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Integrative Zoology 2010年第3期5卷 187-197页

作者： Anouk BARBEROUSSE Sarah SAMADI Institute of History and Phylosophy of Sciences and Technics UMR 8590 National Center for Scientific ResearchUniversity Paris IENS Systematic Adaptation and EvolutionUMR 7138 CNRS-IRD-UMPC-MNHNFrance

Controversy regarding the species problem has been going on for many decades and no consensus has ever been reached about what a“species”really is and how best to define the *** Queiroz(1998)introduced a distinction between two aspects of this problem:on the one hand,the definition proper,and on the other,the criteria allowing biologists to recognize species in *** distinction is a first step on the way toward a solution of the *** the present paper,we show that de Queiroz’s distinction is made possible by the radical theoretical change introduced by *** emphasize that the species problem did not appear in the 20th century,but long before,and that Darwin addresses it indirectly in the Origin of *** might seem paradoxical to refer to Darwin’s views about species,because they are usually considered as ***,we propose that an analysis of these views in the context of Darwin’s own theory of evolution might reveal how a definition of the concept of species is made possible by being anchored to the very theory of *** this aim,we present a plausible reconstruction of Darwin’s implicit conception of species and show how this conception fits with the debates on species that took place in the 18th and 19th *** then turn to today’s biology and show what changes Darwin’s implicit conception of species has brought about relative to the species concept and species delimitation.

关键词： Buffon Darwin nomenclature species concepts taxonomy

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