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Prediction of Driver Gene Matching in Lung cancer NOG/PDX Models Based on Artificial Intelligence

Engineering 2022年第8期8卷 102-114页

作者： Yayi He Haoyue Guo Li Diao Yu chen Junjie Zhu hiran c.fernando Diego Gonzalez Rivas Hui Qi chunlei Dai Xuzhen Tang Jun Zhu Jiawei Dai Kan He Dan chan Yang Yang School of Medicin5 Tongji UniversityShanghai 200092China Department of Medical Oncology Shanghai Pulmonary HospitalSchool of Medicin5Tongji UniversityShanghai 200433China Department of Automation School of Electronic Information and Electrical Engineerin7Shanghai Jiao Tong UniversityShanghai 200240China Spine center Orthopedic DepartmentShanghai Changzheng HospitalShanghai 200003China Department of Thoracic Surgery Shanghai Pulmonary HospitalSchool of Medicin5Tongji UniversityShanghai 200433China School of Materials Science and Engineerin7 Tongji UniversityShanghai 201804China Department of Thoracic Surgery Allegheny General HospitalPittsburg8PA 15212USA Department of Thoracic Surgery and Minimally Invasive Thoracic Surgery Unit(UcTMI) Coruna University HospitalCoruna 15006Spain Oncology and Immunology BU Research Service DivisionWuXi Appte3Shanghai 200131China SJTU–Yale Joint center for Biostatistics and Data Scienc5 Department of Bioinformatics and BiostatisticsSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China Division of Medical Oncology Department of Medicin5University of Colorado Anschutz Medical CampusAuror1CO 80045USA

Patient-derived tumor xenografts(PDXs)are a powerful tool for drug discovery and screening in ***,current studies have led to little understanding of genotype mismatches in PDXs,leading to massive economic ***,we established PDX models from 53 lung cancer patients with a genotype matching rate of 79.2%(42/53).Furthermore,17 clinicopathological features were examined and input in stepwise logistic regression(LR)models based on the lowest Akaike information criterion(AIc),least absolute shrinkage and selection operator(LASSO)-LR,support vector machine(SVM)recursive feature elimination(SVM-RFE),extreme gradient boosting(XGBoost),gradient boosting and categorical features(cat Boost),and the synthetic minority oversampling technique(SMOTE).Finally,the performance of all models was evaluated by the accuracy,area under the receiver operating characteristic curve(AUc),and F1 score in 100 testing *** multivariable LR models revealed that age,number of driver gene mutations,epidermal growth factor receptor(EGFR)gene mutations,type of prior chemotherapy,prior tyrosine kinase inhibitor(TKI)therapy,and the source of the sample were powerful ***,cat Boost(mean accuracy=0.960;mean AUc=0.939;mean F1 score=0.908)and the eight-feature SVM-RFE(mean accuracy=0.950;mean AUc=0.934;mean F1 score=0.903)showed the best performance among the ***,application of the SMOTE improved the predictive capability of most models,except cat *** on the SMOTE,the ensemble classifier of single models achieved the highest accuracy(mean=0.975),AUc(mean=0.949),and F1 score(mean=0.938).In conclusion,we established an optimal predictive model to screen lung cancer patients for non-obese diabetic(NOD)/Shi-scid,interleukin-2 receptor(IL-2R)γ^(null)(NOG)/PDX models and offer a general approach for building predictive models.

关键词： Machine learning Patient-derived tumor xenografts NOG mice

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Fibrin sealant for esophageal anastomosis:A phase II study

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World Journal of Gastrointestinal Oncology 2020年第6期12卷 651-662页

作者： Yao-Bin Lin Jian-Hua Fu Yan Huang Yi-Huai Hu Kong-Jia Luo Ke-Xi Wang AmosÉla Bella Dong-Rong Situ Ji-Yang chen Ting Lin Xavier B D’Journo Nuria M Novoa Alessandro Brunelli hiran c fernando Robert J cerfolio Mahmoud Ismail Hong Yang 无 Department of Thoracic Surgery State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Esophageal Cancer InstituteSun Yat-sen University Cancer CenterGuangzhou 510060Guangdong ProvinceChina Department of Thoracic Surgery Avicenne HospitalBobigny 93000France Department of Surgery and Specialties Faculty of Medicine and Biomedical SciencesUniversity of YaoundéIYaoundéCameroon Department of Surgery Royal Darwin HospitalNorthern Territory 0811Australia Department of Thoracic Surgery and Diseases of Esophagus Aix-Marseille UniversityHôpital NordMarseille 13915France Thoracic Surgery Service University Hospital of SalamancaSalamanca 37007Spain Department of Thoracic Surgery St James's University HospitalLeeds LS97TFUnited Kingdom Section of Thoracic Surgery Inova Fairfax Medical CenterInova Schar Cancer InstituteFalls ChurchVA 22042United States Department of cardiothoracic Surgery New York University Langone HealthNew YorkNY 10016United States Department of Thoracic Surgery Academic Hospital of the Charité–UniversitätsmedizinHumboldt University BerlinBerlin 10117Germany the AME Thoracic Surgery collaborative Group

BAcKGROUND Esophagectomy is a pivotal curative modality for localized esophageal or esophagogastric junction cancer(Ec or EJc).Postoperative anastomotic leakage(AL)remains *** use of fibrin sealant(FS)may improve the strength of esophageal anastomosis and reduce the incidence of *** To assess the efficacy and safety of applying FS to prevent AL in patients with Ec or *** In this single-arm,phase II trial(*** identifier:NcT03529266),we recruited patients aged 18-80 years with resectable Ec or EJc clinically staged as *** open or minimally invasive McKeown esophagectomy was performed with a circular stapled *** performing the anastomosis,2.5 mL of porcine FS was applied *** primary endpoint was the proportion of patients with AL within 3 *** From June 4,2018,to December 29,2018,57 patients were *** the data cutoff date(June 30,2019),three(5.3%)of the 57 patients had developed AL,including two(3.5%)with esophagogastric AL and one(1.8%)with gastric *** incidence of anastomotic stricture and other major postoperative complications was 1.8%and 17.5%,*** median time needed to resume oral feeding after operation was 8 d(Interquartile range:7.0-9.0 d).No adverse events related to FS were *** deaths occurred within 90 d after *** Perioperative sealing with porcine FS appears safe and may prevent AL after esophagectomy in patients with resectable Ec or *** phase III studies are warranted.

关键词： Esophageal cancer McKeown esophagectomy Fibrin sealant Anastomotic leakage Postoperative complications Prevention

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Divergence time calibrations for ancient lineages of Ascomycota classification based on a modern review of estimations

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Fungal Diversity 2019年第3期96卷 285-346页

作者： Milan c.Samarakoon Kevin D.Hyde Sinang Hongsanan Eric H.c.McKenzie hiran A.Ariyawansa Itthayakorn Promputtha Xiang-Yu Zeng Qing Tian Jian-Kui(Jack)Liu center for Informational Biology School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Shenzhen Key Laboratory of Microbial Genetic Engineering College of Life Sciences and OceanographyShenzhen UniversityShenzhenPeople’s Republic of China Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand Department of Plant Pathology and Microbiology College of Bio-Resources and AgricultureNational Taiwan UniversityNo.1Sec.4Roosevelt RoadTaipei 106TaiwanROC Environmental Science Research center Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand

Inaccurate taxonomic placement of fossils can lead to the accumulation of errors in molecular clock studies and their generated evolutionary *** are limited fossil data that can be used in divergence time ***,reliable morphological characterization and taxonomical identification of fossil fungi are extremely *** fossils of Dothideomycetes and Sordariomycetes are from the early cenozoic(66-23 Mya),with fewer from the late Mesozoic(174-145 Mya).However,it is hard to distinguish some fossil descriptions as photographs and illustrations are unclear;thus,the validity of using these fossils in calibrations of molecular clocks is *** study brings scattered paleobiological data on selected fossil Ascomycota,using descriptions,fossil images and illustrations,coupled with recent age estimations,and taxonomic and phylogenetic affinity of extant *** an integrated approach,this study summarizes a historical fossil outline with a reliable minimum age for 16 calibrating points *** of Aigialus,Anzia,Aspergillus,Asterina,calicium chlorosporum–***,capnodiales,chaenotheca,colletotrichum,Diaporthales,Meliola,Ophiocordyceps,Microthyriales,Microthyrium,Muyocopron,Pezizomycotina and Stigmatomyces.A scheme of Ascomycota ancient lineages is also provided in order to improve divergence time estimations.

关键词： Fossil fungi Morphological characterization Phylogeny Taxonomy Two new combinations

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Towards a natural classification and backbone tree for Lophiostomataceae,Floricolaceae,and Amorosiaceae ***.

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Fungal Diversity 2015年第5期74卷 199-266页

作者： Kasun M.Thambugala Kevin D.Hyde Kazuaki Tanaka Qing Tian Dhanushka N.Wanasinghe hiran A.Ariyawansa Subashini c.Jayasiri Saranyaphat Boonmee Erio camporesi Akira Hashimoto Kazuyuki Hirayama RenéK.Schumacher Itthayakorn Promputtha Zuo-Yi Liu Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyangGuizhou 550006People’s Republic of China center of Excellence in Fungal Research Chiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina Faculty of Agriculture and Life Sciences Hirosaki University3 Bunkyo-cho HirosakiAomori 036-8561Japan The United Graduate School of Agricultural Sciences Iwate University18-8 Ueda 3 chomeMorioka 020-8550Japan Apple Experiment Station Aomori Prefectural Agriculture and Forestry Research Center24 FukutamiBotandairaKuroishiAomori 036-0332Japan Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand A.M.B.Gruppo Micologico Forlivese BAntonio cicognani Via Roma 18ForlìItaly A.M.B.circolo Micologico BGiovanni carini C.P.314 BresciaItaly Hölderlinsraße 25 15517 Fürstenwalde/SpreeGermany

The genera Lophiostoma,Misturatosphaeria and several other allied taxa in Lophiostomataceae are *** of these taxa,including their history,morphology,and family placement,based on molecular phylogeny,are *** or representative specimens of Lophiostoma and Misturatosphaeria were examined and fresh specimens were obtained from Germany,Italy,Japan and Thailand.A multi-gene phylogenetic analysis of the lophiostomataceous genera Floricola,Lophiostoma,Misturatosphaeria and related taxa is *** genera including Lophiostoma,Lophiohelichrysum,Dimorphiopsis,Platystomum and Vaginatispora,plus eleven newly introduced genera Biappendiculispora,Alpestrisphaeria,capulatispora,coelodictyosporium,Guttulispora,Lophiopoacea,Neotrematosphaeria,Paucispora,Pseudolophiostoma,Pseudoplatystomum and Sigarispora are accepted in Lophiostomataceae based on morphology and *** caulium,Lophiostoma arundinis and Lophiostoma caudatum are accommodated in *** winteri and Lophiostoma fuckelii are placed in the genera Lophiopoacea and Vaginatispora *** curreya species and Misturatosphaeria claviformis are transferred to a new genus,*** other Misturatosphaeria species except Misturatosphaeria aurantiinotata and *** are separated in the new genera Asymmetrispora,Aurantiascoma,Magnibotryascoma,Pseudoaurantiascoma and Pseudomisturatosphaeria based on their morphological and phylogenetic *** new genus,Ramusculicola is introduced for a new collection from *** seven new genera are accommodated in a new family Floricolaceae,together with Floricola and *** massarina-like species clustered as a sister clade to Amorosia littoralis and are accommodated in a new genus Angustimassarina.A new family Amorosiaceae is proposed to accommodate the genera Amorosia and *** putatively named species Decaisnella formosa and Thyridaria macrostomoides form a s

关键词： Dothideomycetes Floricola Lophiostoma Misturatosphaeria Multi-gene phylogeny new species new genus Pleosporales taxonomy

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A molecular phylogenetic reappraisal of the Didymosphaeriaceae(=Montagnulaceae)

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Fungal Diversity 2014年第5期68卷 69-104页

作者： hiran A.Ariyawansa Kazuaki Tanaka Kasun M.Thambugala Rungtiwa Phookamsak Qing Tian Erio camporesi Sinang Hongsanan Jutamart Monkai Dhanushka N.Wanasinghe Ausanan Mapook Ekachai chukeatirote Ji-chuan Kang Jian-chu Xu Eric H.c.McKenzie E.B.Gareth Jones Kevin D.Hyde Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China World Agroforestry centre East Asia and CentralHeilongtanKunming 650201People’s Republic of China The Engineering and Research center for Southwest Bio-Pharmaceutical Resources of National Education Ministry of china Guizhou UniversityGuiyang 550025Guizhou ProvinceChina School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Faculty of Agriculture and Life Science Hirosaki University3 Bunkyo-choHirosakiAomori 036-8561Japan A.M.B.Gruppo Micologico Forlivese“Antonio cicognani” Via Roma 18ForlìItaly Manaaki Whenua Landcare Research Private Bag92170 AucklandNew Zealand Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia

The ascomycetous families,Didymosphaeriaceae and Montagnulaceae,have been treated in Pleosporales,Dothideomycetes,and both include saprobes,endophytes and pathogens associated with a wide variety of substrates *** was characterized by 1-septate ascospores and trabeculate pseudoparaphyses,mainly anastomosing above the asci,while species in Montagnulaceae had 1 to multi-septate ascospores and generally cellular *** recent treatments,Bimuria,Didymocrea,Kalmusia,Karstenula,Montagnula,Paraphaeosphaeria,Paraconiothyrium and Letendraea were placed in Montagnulaceae,while only Didymosphaeria has been placed in *** morphological and molecular data from recent collections have become available and thus the understanding of the families can be *** on analyses of concatenated internal transcribed spacer(ITS)with LSU,SSU andβ-tubulin gene sequences,the taxonomy of the genera classified in these families are *** phylogenetic analyses conclude that,the recently introduced Didymosphaeria rubi-ulmifolii with Paraconiothyrium brasi liense species complex,Alloconiothyrium,Bimuria,Deniquelata,Didymocrea,Kalmusia,Karstenula,Letendraea,Montagnula,Neokalmusia,Paraconiothyrium,Paraphaeosphaeria,Phaeodothis and Tremateia,forms a robust clade named here *** therefore synonymize Montagnulaceae under Didymosphaeriaceae which is the oldest name and has priority and provide a update account of the *** is represented by Didymosphaeria rubi-ulmifolii.A new genus,Neokalmusia,is introduced in the family to accommodate the bambusi colous taxa Kalmusia brevispora and *** introduction is based on molecular data coupled with *** new species,Paraconiothyrium magnoliae and the sexual morph of Paraconiothyrium fuckelii,is also *** and Barria are assigned to the family based on morphological similarity with ***(previously referre

关键词： Didymosphaeriaceae Montagnulaceae New species Phylogeny rDNA β-tubulin

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Revision of Phaeosphaeriaceae

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Fungal Diversity 2014年第5期68卷 159-238页

作者： Rungtiwa Phookamsak Jian-Kui Liu Eric H.c.McKenzie Dimuthu S.Manamgoda hiran Ariyawansa Kasun M.Thambugala Dong-Qin Dai Erio camporesi Ekachai chukeatirote Nalin N.Wijayawardene Ali H.Bahkali Peter E.Mortimer Jian-chu Xu Kevin D.Hyde Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China World Agroforestry centre East and Central AsiaKunming 650201YunnanPeople’s Republic of China School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand A.M.B.Gruppo Micologico Forlivese“Antonio cicognani” Via Roma 18ForlìItaly A.M.B.circolo Micologico“Giovanni carini” C.P.314BresciaItaly Societàper gli Studi Naturalistici della Romagna C.P.144BagnacavalloRAItaly college of Science Botany and Microbiology DepartmentKing Saud UniversityRiyadh 1145Saudi Arabia

Phaeosphaeriaceae is a large and important family in the order Pleosporales which includes economically important plant *** may also be endophytes or saprobes on plant hosts,especially on monocotyledons(e.g.,cannaceae,cyperaceae,Juncaceae,Poaceae);some species have also been reported on *** family previously accommodated 35 sexual and asexual genera and comprised more than 300 species with a range of morphological *** morphological characters of taxa in this family are often ambiguous and can be confused with other taxa in Leptosphaeriaceae and *** specimens of the type genera of Phaeosphaeriaceae were loaned from herbaria worldwide and were re-examined and *** collections were obtained from Italy and Thailand,characterized,examined,isolated into pure culture and used to obtain molecular *** asexual state was induced where possible on sterile bamboo pieces placed on water *** phylogenetic analyses of ITS,LSU,SSU,RPB2 and TEF1 sequence datasets were carried out using maximum likelihood,maximum parsimony and Bayesian *** analyses shows that 21 genera(Amarenomyces,Ampelomyces,chaetosphaeronema,Dematiopleospora,Entodesmium,Loratospora,Neosetophoma,Neostagonospora,Nodulosphaeria,Ophiobolus,Ophiosphaerella,Paraphoma,Parastagonospora,Phaeosphaeria,Phaeosphaeriopsis,Sclerostagonospora,Setomelanomma,Setophoma,Vrystaatia,Wojnowicia and Xenoseptoria)belong in Phaeosphaeriaceae,while seven genera(Amarenographium,Bricookea,Dothideopsella,Eudarluca,Phaeostagonospora,Scolecosporiella and Tiarospora)are included based on morphological *** is reinstated and Nodulosphaeria is confirmed in *** is distinguished from Sphaerellopsis based on its morphological characters and is typical of *** gene phylogenetic analys is indicates that Sphaerellopsis belongs to *** species form a clade within Phaeosphaeriacea

关键词： Asexualstate Didymosphaeriaceae Montagnulaceae Phaeosphaeria Phylogeny Pleosporales Taxonomy

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The families Distoseptisporaceae ***.,Kirschsteiniotheliaceae,Sporormiaceae and Torulaceae,with new species from freshwater in Yunnan Province,china

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Fungal Diversity 2016年第5期80卷 375-409页

作者： HongYan Su Kevin D.Hyde Sajeewa S.N.Maharachchikumbura hiran A.Ariyawansa ZongLong Luo Itthayakorn Promputtha Qing Tian chuanGen Lin QiuJu Shang Yongchang Zhao HongMei chai XiaoYing Liu Ali H.Bahkali Jayarama D.Bhat Eric H.c.McKenzie DeQun Zhou Faculty of Environmental Sciences&Engineering Kunming University of Science&TechnologyKunming 650500YunnanChina college of Agriculture and Biology Dali UniversityDaliYunnan 671003China center of Excellence in Fungal Research Mae Fah LuangUniversityChiang Rai 57100Thailand Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyangGuizhou 550006People’s Republic of China Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Departent of Biology Chiang Mai UniversityChiang MaiThailand Institute of Biotechnology and Germplasmic Resources Yunnan Academy of Agricultural SciencesKunming 650223People’s Republic of China college of Basic Medicine Dali UniversityDaliYunnan 671000China No.128/1-J Azad Housing SocietyCurcaP.OGoa Velha 403108India Department of Botany Goa UniversityGoa 403206India Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand

During a north–south latitudinal survey of aquatic fungi on submerged wood and herbaceous material in streams in the Asian region,we collected several hyphomycetous *** paper is part of a series where we provide illustrated accounts of these taxa and place them in a natural classification in the *** sequence based phylogenies in recent literature have shown that Dendryphion,Sporidesmium and Torula-like species are polyphyletic in the phylum Ascomycota and their taxonomyhas been problematic due to a lack of understanding of the importance of morphological characters used to delimit taxa,as well as the lack of ex-type or reference *** on multi-locus phylogenies together with morphology,we propose the novel family Distoseptisporaceae(Sordariomycetes)and three novel genera Neotorula(Pleosporales,Dothideomycetes),Distoseptispora(Sordariomycetes)and Pseudosporidesmium(Sordariomycetes).In addition,Dendryphion aquaticum,***,Distoseptispora fluminicola,***,Kirschsteiniothelia submersa,Neotorula aquatica,Sporidesmium aquaticum,*** and *** are introduced as new *** knawiae *** proposed to accommodate Sporidesmium knawiae in *** polyphyletic nature of Dendryphion,Sporidesmium and Torula-like species are partially resolved,but further sampling with fresh collections and molecular data of species are needed to obtain a natural classification.

关键词： Asexual fungi Dothideomycetes Freshwater fungi Hyphomycetes New species Phylogeny Sordariomycetes

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Integrative approaches for species delimitation in Ascomycota

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Fungal Diversity 2021年第4期109卷 155-179页

作者： Sajeewa S.N.Maharachchikumbura Yanpeng chen hiran A.Ariyawansa Kevin D.Hyde Danny Haelewaters Rekhani H.Perera Milan c.Samarakoon Dhanushka N.Wanasinghe Danilo E.Bustamante Jian-Kui Liu Daniel P.Lawrence Ratchadawan cheewangkoon Marc Stadler School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Entomology and Plant Pathology Department Faculty of AgricultureChiang Mai UniversityChiang MaiThailand Department of Plant Pathology and Microbiology College of Bio-Resources and AgricultureNational Taiwan UniversityTaipei City 10617Taiwan center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Research Group Mycology Department of BiologyGhent University9000 GhentBelgium Faculty of Science University of South Bohemia37005 Ceske BudejoviceCzech Republic center for Mountain Futures Kunming Institute of BotanyHonghe County 654400YunnanPeople’s Republic of China Instituto de Investigación Para el Desarrollo Sustentable de ceja de Selva(INDES-cES) Universidad Nacional Toribio Rodríguez de MendozaChachapoyasAmazonasPeru Department of civil and Environmental Engineering(FIcIAM) Universidad Nacional Toribio Rodríguez de MendozaChachapoyasAmazonasPeru Department of Plant Pathology University of CaliforniaDavisDavisCAUSA Helmholtz centre for Infection Research GmbH Department Microbial Drugs and German Centre for Infection Research(DZIF)Partner Site Hannover-Braunschweig38124 BraunschweigGermany Institute of Microbiology Technische Universität BraunschweigInhoffenstraße 738124 BraunschweigGermany

Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing *** high number of species that have yet to be described have generated extreme crisis to the ***,more than in any other era,effective ways to discover and delimitate species are *** paper reviews the historically fore-most approaches used to delimit species in Ascomycota,the most speciose phylum of *** include morphological,biological,and phylogenetic species *** argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and *** the rate of species discovery has increased because of the advancement of phylogenetic ***,traditional phylogenetic methods with few gene regions lack species-level resolution,and do not allow unambiguous *** detail the processes that affect gene tree heterogeneity,which acts as barriers to delimiting species boundaries in classical low-rank *** far,limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal *** addition to reviewing concepts and methodologies used to delimit species,we present a case *** applied differ-ent species delimitation methods to understand species boundaries in the plant pathogenic and cryptic genus Phyllosticta(Dothideomycetes,Botryosphaeriales).Several DNA-based methods over-split the taxa while in some methods several taxa fall into a single *** problems can be resolved by using multiple loci and coalescence-based ***,we discuss integrative approaches that are crucial for understanding species boundaries within Ascomycota and provide several examples for ideal and pragmatic approaches of species delimitation.

关键词： Ascomycetes Phylogenetics Species concept Systematics

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Special issue:The contributions of Erio camporesi

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Fungal Diversity 2020年第1期100卷 1-3页

作者： chayanard Phukhamsakda Nalin N.Wijayawardene hiran A.Ariyawansa Indunil c.Senanayake Wen-Jing Li Dhanushka N.Wanasinghe Rungtiwa Phookamsak Qing Tian Dinushani A.Daranagama Kasun M.Thambugala Saowaluck Tibpromma Anusha H.Ekanayaka Marc Stadler Kevin D.Hyde center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201YunnanPeople’s Republic of China Department of Plant Pathology and Microbiology College of Bio-Resources and AgricultureNational Taiwan UniversityTaipeiTaiwan Shenzhen Key Laboratory of Microbial Genetic Engineering College of Life Sciences and OceanographyShenzhen UniversityShenzhen 518060People’s Republic of China East and central Asia Regional Office World Agroforestry Centre(ICRAF)Kunming 650201YunnanPeople’s Republic of China centre for Mountain Futures(cMF) Kunming Institute of BotanyKunming 650201YunnanPeople’s Republic of China Mushroom Research Foundation 128 M.3 Ban Pa Deng T.Pa PaeA.Mae TaengChiang Mai 50150Thailand Industrial Science and Management(International Program) Faculty of Science and TechnologyThammasat University(Rangsit Center)Klong Luang 12121PathumthaniThailand Department of Biology Faculty of ScienceChiang Mai UniversityChiang Mai 50200Thailand Department of Microbial Drugs Helmholtz Centre for Infection Research and German Centre for Infection Research(DZIF)Partner Site Hannover/BraunschweigInhoffenstrasse 738124 BrunswickGermany center for Yunnan Plateau Biological Resources Protection and Utilization College of Biological Resource and Food EngineeringQujing Normal UniversityQujing 655011YunnanPeople’s Republic of China Department of Plant and Molecular Biology Faculty of ScienceUniversity of KelaniyaSri LankaKelaniyaSri Lanka

We are proud to publish a special issue of Fungal Diversity in honour of the contributions made by Erio camporesi,who has promoted mycological research as a prodigious amateur mycologist and collector of *** special issue includes Fungal Diversity notes 11,with many taxa named in Erio’s honour and a monograph of hyaline-spored coelomycetes,both incorporating many of Erio’s collections.

关键词： contributions include collection

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Epitypification and neotypification:guidelines with appropriate and inappropriate examples

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Fungal Diversity 2014年第6期69卷 57-91页

作者： hiran A.Ariyawansa David L.Hawksworth Kevin D.Hyde E.B.Gareth Jones Sajeewa S.N.Maharachchikumbura Dimuthu S.Manamgoda Kasun M.Thambugala Dhanushka Udayanga Erio camporesi Anupama Daranagama Ruvishika Jayawardena Jian-Kui Liu Eric H.c.McKenzie Rungtiwa Phookamsak Indunil c.Senanayake Roger G.Shivas Qing Tian Jian-chu Xu Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina World Agroforestry centre East and Central AsiaKunming 650201YunnanChina Institute of Excellence in Fungal Research School of ScienceMae Fah Luang UniversityChiang Rai 57100Thailand Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de MadridPlaza Ramón y CajalMadrid 28040Spain Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Mycology Section Royal Botanic GardensKewRichmond Surrey TW93DSUK Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia A.M.B.Gruppo Micologico Forlivese“Antonio cicognani” Via Roma18ForlìItaly Manaaki Whenua Landcare Research Private Bag 92170 AucklandNew Zealand Plant Pathology Herbarium Agri-Science Queensland40 Boggo RoadDutton ParkQld 4102Australia

review of phylogenetic studies carried out together with morphological ones shows that a major problem with most early studies is that they concentrated on techniques and used material or strains of fungi that in most cases were not carefully reference,and in a worrying number of cases wrongly *** classical species,particularly of microfungi,are not represented by adequate type material,or other authoritatively identified cultures or specimens,that can serve as DNA sources for phylogenetic study,or for developing robust identification *** classifications of fungi therefore suffer fromthe lack of reference strains in resultant phylogenetic *** some cases,epitypification and neotypification can solve this problem and these tools are increasingly used to resolve taxonomic confusion and stabilize the understanding of species,genera,families,or orders of *** manuscript discusses epitypification and neotypification,describes how to epitypify or neotypify species and examines the importance of this process.A set of guidelines for epitypification is *** where taxa have been epitypified are presented and the benefits and problems of epitypification are *** examples of epitypification,or to provide reference specimens,a new epitype is designated for Paraphaeosphaeria michotii and reference specimens are provided for Astrosphaeriella stellata,***,Phaeosphaeria elongata,Ophiobolus cirsii,and *** this way we demonstrate how to epitypify taxa and its importance,and also illustrate the value of proposing reference specimens if epitypification is not *** we provided guidelines for epitypification,the decision to epitypify or not lies with the author,who should have experience of the fungus *** responsibility is to be taken seriously,as once a later typification is made,it may not be possible to undo that,particularly in the case of epitypes,without using the lengthy and tedious f

关键词： Epitype Generic types Molecular data Nomenclature Systematics Taxonomy Typification

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