Ranking higher taxa using divergence times: a case study in Dothideomycetes

文献类型： 外文期刊

第一作者： Liu, Jian-Kui

作者： Liu, Jian-Kui;Zhao, Qi;Liu, Jian-Kui;Liu, Jian-Kui;Liu, Zuo-Yi;Hyde, Kevin D.;Jeewon, Rajesh;Phillips, Alan J. L.;Maharachchikumbura, Sajeewa S. N.;Ryberg, Martin

作者机构：

关键词： BEAST;Clade age;Classification;Calibration;Family;Order;Phylogeny;Pleosporales

期刊名称：FUNGAL DIVERSITY （ 影响因子：20.372； 五年影响因子：16.344 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes with 55 families, to establish family divergence times. We have assembled a multi-gene data set (LSU, SSU, TEF1 and RPB2) from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: (i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and (ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesneriomycetales and these are treated as synonyms of Tubeufiales while Asterotexiales is treated as a synonym of Asterinales. In addition, we provide an updated phylogenetic assessment of Dothideomycetes previously published as the Families of Dothideomycetes in 2013 with a further ten orders and 35 families.

分类号： Q

  • 相关文献

[1]The evolution of Massarineae with Longipedicellataceae fam. nov.. Phukhamsakda, C.,Hongsanan, S.,Hyde, K. D.,Hongsanan, S.,Phukhamsakda, C.,Hongsanan, S.,Chomnunti, P.,Hyde, K. D.,Ryberg, M.,Phukhamsakda, C.,Chomnunti, P.,Ariyawansa, H. A.,Hyde, K. D.,Bahkali, A. H.,Hyde, K. D.. 2016

[2]The evolution of fungal epiphytes. Hongsanan, S.,Hyde, K. D.,Hongsanan, S.,Hyde, K. D.,Hongsanan, S.,Hyde, K. D.,Sanchez-Ramirez, S.,Sanchez-Ramirez, S.,Crous, P. W.,Ariyawansa, H. A.,Zhao, R. L.. 2016

[3]Freshwater ascomycetes: Lophiostoma vaginatispora comb. nov. (Dothideomycetes, Pleosporales, Lophiostomaceae) based on morphological and molecular data. Zhang, Huang,Hyde, Kevin D.,Hyde, Kevin D.,Zhao, Yong Chang,Mckenzie, Eric H. C.,Zhou, Dequn.

[4]Fungi from Asian Karst formations II. Two new species of Occultibambusa (Occultibambusaceae, Dothideomycetes) from karst landforms of China. Zhang, J. F.,Yang, W.,Zhang, J. F.,Liu, J. K.,Hyde, K. D.,Liu, Z. Y.,Zhang, J. F.,Hyde, K. D.,Liu, J. K.. 2017

[5]Periconia thailandica (Periconiaceae), a new species from Thailand. Liu, Ningguo,Liu, Jiankui,Liu, Zuoyi,Liu, Ningguo,Jumpathong, Juangjun,Hongsanan, Sinang,Yang, Jing,Bhat, D. Jayarama,Jumpathong, Juangjun. 2017

[6]Dendryphiella fasciculata sp nov and notes on other Dendryphiella species. Liu, N. G.,Liu, J. K.,Liu, Z. Y.,Liu, N. G.,Jumpathong, J.,Hongsanan, S.,Yang, J.,Lin, C. G.,Boonmee, S.,Hyde, K. D.,Bhat, D. J.,Jumpathong, J.. 2017

[7]Two novel species of Paradictyoarthrinium from decaying wood. Liu, Jian-Kui,Cheewangkoon, Ratchadawan,To-Anun, Chaiwat,Liu, Jian-Kui,Liu, Ning-Guo,Luo, Zong-Long,Liu, Ning-Guo. 2018

[8]Curvularia tsudae comb. nov et nom. nov., formerly Pseudocochliobolus australiensis, and a revised synonymy for Curvularia australiensis. Deng, Hui,Niu, Yong Chun,Tan, Yu Pei,Tan, Yu Pei,Shivas, Roger G..

[9]Microfungi on Tamarix. Thambugala, Kasun M.,Liu, Zuo-Yi,Thambugala, Kasun M.,Daranagama, Dinushani A.,Hyde, Kevin D.,Thambugala, Kasun M.,Daranagama, Dinushani A.,Eungwanichayapant, Prapassorn D.,Hyde, Kevin D.,Daranagama, Dinushani A.,Phillips, Alan J. L.,Bulgakov, Timur S.,Bhat, Darbhe J.,Bhat, Darbhe J.,Camporesi, Erio,Camporesi, Erio,Bahkali, Ali H..

[10]Families of Dothideomycetes. Hyde, Kevin D.,Mortimer, Peter E.,Xu, Jian-Chu,Hyde, Kevin D.,Mortimer, Peter E.,Xu, Jian-Chu,Hyde, Kevin D.,Liu, Jian-Kui,Ariyawansa, Hiran,Boonmee, Saranyaphat,Chomnunti, Putarak,Dai, Dong-Qin,Dissanayake, Asha,Doilom, Mingkhuan,Hongsanan, Singang,Jayawardena, Ruvishika,Monkai, Jutamart,Phookamsak, Rungtiwa,Senanayake, Indunil C.,Thambugala, Kasun M.,Wijayawardene, Nalin N.,Wikee, Saowanee,Chukeatirote, Ekachai,Li, Wen-Jing,Mapook, Ausana,Tian, Qing,Tibpromma, Saowaluck,Wanasinghe, Dhanushka N.,Yacharoen, Supalak,Hyde, Kevin D.,Liu, Jian-Kui,Ariyawansa, Hiran,Boonmee, Saranyaphat,Chomnunti, Putarak,Dai, Dong-Qin,Dissanayake, Asha,Doilom, Mingkhuan,Hongsanan, Singang,Jayawardena, Ruvishika,Monkai, Jutamart,Phookamsak, Rungtiwa,Senanayake, Indunil C.,Thambugala, Kasun M.,Wijayawardene, Nalin N.,Wikee, Saowanee,Bhat, D. Jayarama,Chukeatirote, Ekachai,Li, Wen-Jing,Mapook, Ausana,Tian, Qing,Tibpromma, Saowaluck,Wanasinghe, Dhanushka N.,Yacharoen, Supalak,Jones.

[11]Towards a natural classification of Astrosphaeriella-like species; introducing Astrosphaeriellaceae and Pseudoastrosphaeriellaceae fam. nov and Astrosphaeriellopsis, gen. nov.. Phookamsak, Rungtiwa,Dai, Dong-Qin,Mortimer, Peter E.,Xu, Jian-Chu,Hyde, Kevin D.,Phookamsak, Rungtiwa,Dai, Dong-Qin,Mortimer, Peter E.,Xu, Jian-Chu,Hyde, Kevin D.,Phookamsak, Rungtiwa,Norphanphoun, Chada,Dai, Dong-Qin,Luo, Zong-Long,Hyde, Kevin D.,Phookamsak, Rungtiwa,Norphanphoun, Chada,Dai, Dong-Qin,Luo, Zong-Long,Hyde, Kevin D.,Bhat, Darbhe J.,Bhat, Darbhe J.,Liu, Jian-Kui,Luo, Zong-Long,Su, Hong-Yan,Tanaka, Kazuaki,Bahkali, Ali H.,Hyde, Kevin D.,Xu, Jian-Chu.

[12]Ligninsphaeria jonesii gen. et. sp nov., a remarkable bamboo inhabiting ascomycete. Zhang, Jin-Feng,Zhang, Jin-Feng,Liu, Jian-Kui,Liu, Yong-Xiang,Liu, Zuo-Yi,Zhang, Jin-Feng,Hyde, Kevin D.,Zhang, Jin-Feng,Hyde, Kevin D.,Hyde, Kevin D.,Bahkali, Ali H..

[13]Ophiosimulans tanaceti gen. et sp nov (Phaeosphaeriaceae) on Tanacetum sp (Asteraceae) from Italy. Tibpromma, Saowaluck,Hyde, Kevin D.,Tibpromma, Saowaluck,Hyde, Kevin D.,Boonmee, Saranyaphat,Tibpromma, Saowaluck,Hyde, Kevin D.,Tibpromma, Saowaluck,Hyde, Kevin D.,Tibpromma, Saowaluck,Hyde, Kevin D.,Liu, Jian-Kui,Promputtha, Itthayakorn,Camporesi, Erio,Camporesi, Erio,Camporesi, Erio,Bhakali, Ali H.,Hyde, Kevin D..

[14]Proposal for a unified classification system and nomenclature of lagoviruses. Le Pendu, Jacques,Ruvoen-Clouet, Nathalie,Abrantes, Joana,Lopes, Ana Margarida,Almeida, Tereza,Celio, Alves Paulo,Marques, Sara,Monterroso, Pedro,Silverio, Diogo,Thompson, Gertrudes,Esteves, Pedro,Bertagnoli, Stephane,Guitton, Jean-Sebastien,Marchandeau, Stephane,Almeida, Tereza,Le Gall-Recule, Ghislaine,Alda, Fernando,Celio, Alves Paulo,Goncalves, David,Esteves, Pedro,Celio, Alves Paulo,Barcena, Juan,Blanco, Esther,Burmakina, Galina,Calvete, Carlos,Cavadini, Patrizia,Lavazza, Antonio,Cooke, Brian,Cooke, Brian,Dalton, Kevin,Parra, Francisco,Delibes Mateos, Miguel,Deptula, Wieslaw,Eden, John Sebastian,Eden, John Sebastian,Wang, Fang,Ferreira, Catarina C.,Ferreira, Catarina C.,Ferreira, Paula,Marques, Raquel M.,Ferreira, Paula,Marques, Raquel M.,Foronda, Pilar,Martin-Alonso, Aaron,Gavier-Widen, Dolores,Neimanis, Aleksija,Gavier-Widen, Dolores,Neimanis, Aleksija,Hall, Robin,Strive, Tanja,Hukowska-Szematowicz, Beata,Niedzwiedzka-Rystwej, Paulina,Kerr, Peter,Mah. 2017

[15]Towards a natural classification and backbone tree for Graphostromataceae, Hypoxylaceae, Lopadostomataceae and Xylariaceae. Daranagama, Dinushani A.,Liu, XingZhong,Daranagama, Dinushani A.,Hyde, Kevin D.,Thambugala, Kasun M.,Tian, Qing,Samarakoon, Milan C.,Jayasiri, Subashini C.,Tibpromma, Saowaluck,Thambugala, Kasun M.,Stadler, Marc,Sir, Esteban B.,Bhat, Jayarama D.,McKenzie, Eric H. C.. 2018

[16]The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts. Jayasiri, Subashini C.,Hyde, Kevin D.,Ariyawansa, Hiran A.,Abd-Elsalam, Kamel A.,Karunarathna, Samantha C.,Liu, Jian-Kui,Maharachchikumbura, Sajeewa S. N.,Boonmee, Saranyaphat,Dai, Dong Qin,Daranagama, Dinushani A.,Dissanayake, Asha J.,Ekanayaka, Anusha H.,Hongsanan, Sinang,Jayawardena, Ruvishika S.,Li, Wen-Jing,Perera, Rekhani H.,Phookamsak, R.,Thambugala, Kasun M.,Tian, Qing,Wijayawardene, Nalin N.,Hyde, Kevin D.,Karunarathna, Samantha C.,Dai, Dong Qin,Li, Wen-Jing,Tian, Qing,Zhao, Qi,Hyde, Kevin D.,Jones, E. B. Gareth,Bahkali, Ali H.,Ariyawansa, Hiran A.,Liu, Jian-Kui,Maharachchikumbura, Sajeewa S. N.,Thambugala, Kasun M.,Bhat, Jayarama,Bhat, Jayarama,Buyck, Bart,Cai, Lei,Daranagama, Dinushani A.,Zhao, Rui-Lin,Dai, Yu-Cheng,Abd-Elsalam, Kamel A.,Ertz, Damien,Raspe, Olivier,Ertz, Damien,Raspe, Olivier,Hidayat, Iman,Jeewon, Rajesh,Luangsa-ard, J. Jennifer,Lumbsch, H. Thorsten,McKenzie, Eric H. C.,Moncalvo, Jean-Marc,Moncalvo, Jean-Marc,Ghobad-Nejhad, Masoom.

[17]Identification, distribution pattern of IS231 elements in Bacillus thuringiensis and their phylogenetic analysis. Liu, JJ,Song, FP,Shu, CL,Qiu, JZ,Guan, X,Huang, DF,Zhang, J.

[18]Molecular characterization and expression analysis of the porcine caveolin-3 gene. Zhu, Zhengmao,Li, Yong,Mo, Delin,Li, Kui,Zhao, Shuhong.

[19]A semi-rational design strategy of directed evolution combined with chemical synthesis of DNA sequences. Xiong, Ai-Sheng,Peng, Ri-He,Zhuang, Jing,Liu, Jin-Ge,Gao, Feng,Xu, Fang,Cai, Bin,Yao, Quan-Hong.

[20]Proteomics analysis of major royal jelly protein changes under different storage conditions. Zhang, Zhao-hui,Pan, Ying-hong,Li, Jian-ke,Feng, Mao,Zhang, Lan.

作者其他论文 更多>>
  • Biocontrol performance and mass production potential of the larval endoparasitoid Campoletis chlorideae Uchida (Hymenoptera: Ichneumonidae) against the fall armyworm, Spodoptera frugiperda (J. E. Smith) (Lepidoptera: Noctuidae)

    作者：Zhang, Rui;Zhang, Wei;Zhao, Qi;Keyhani, Nemat O.;Lei, Xian-Fu;Liu, Chang-Hua;Al Dhafer, Hathal M.;Mohamed, Amr

    关键词：Spodoptera frugiperda; Field investigation; Campoletis chlorideae; Biological control; Mass production; Two-sex life table

  • Fungal diversity notes 1717-1817: taxonomic and phylogenetic contributions on genera and species of fungal taxa

    作者：Liu, Shi-Liang;Wang, Xue-Wei;Razaghi, Parisa;Raza, Mubashar;Cai, Lei;Jiang, Shuhua;Zhang, Chao;Zhou, Li-Wei;Wang, Xue-Wei;Li, Guo-Jie;Deng, Chun-Ying;Rossi, Walter;Leonardi, Marco;Liimatainen, Kare;Niskanen, Tuula;Kekki, Tapio;Smith, Matthew E.;Ammirati, Joe;Ammirati, Joe;Bojantchev, Dimitar;Abdel-Wahab, Mohamed A.;Zhang, Ming;Tian, Enjing;Bau, Tolgor;Lu, Yong-Zhong;Zhang, Jing-Yi;Ma, Jian;Zhang, Jing-Yi;Ma, Jian;Du, Tian-Ye;Peng, Xing-Can;Hyde, Kevin D.;Dutta, Arun Kumar;Acharya, Krishnendu;Saha, Rituparna;Tarafder, Entaj;Du, Tian-Ye;Du, Tian-Ye;Peng, Xing-Can;Hyde, Kevin D.;Xu, Jize;Kim, Ji Seon;Lim, Young Woon;Kim, Ji Seon;Lim, Young Woon;Gerlach, Alice;Zeng, Nian-Kai;Han, Yun-Xiao;Raza, Mubashar;Calabon, Mark S.;Jones, E. B. Gareth;Kumar, T. K. Arun;Krishnapriya, K.;Thomas, Anjitha;Kaliyaperumal, Malarvizhi;Kezo, Kezhocuyi;Gunaseelan, Sugantha;Singh, Sanjay Kumar;Singh, Paras Nath;Lagashetti, Ajay Chandrakant;Pawar, Kadambari Subhash;Rana, Shiwali;Zhang, Chao;Zhang, Huang;Qing, Yun;Peng, Xing-Can;Wen, Ting-Chi;Peng, Xing-Can;Wen, Ting-Chi;Ramirez, Natalia A.;Niveiro, Nicolas;Li, Mei-Xiang;Yang, Zhu L.;Wu, Gang;Li, Mei-Xiang;Yang, Zhu L.;Wu, Gang;Tennakoon, Danushka S.;Suwannarach, Nakarin;Kumla, Jaturong;Lumyong, Saisamorn;Tennakoon, Danushka S.;Suwannarach, Nakarin;Kumla, Jaturong;Lumyong, Saisamorn;Kuo, Chang-Hsin;da Silva, Tatiane M.;Bezerra, Jadson D. P.;Souza-Motta, Cristina M.;He, Gang;Ji, Xiao-Hong;Wannathes, Nopparat

    关键词：95 new taxa; Six new records; Ascomycota; Basidiomycota

  • Species diversity of fungal pathogens on cultivated mushrooms: a case study on morels (Morchella, Pezizales)

    作者：Yu, Feng-Ming;Li, Cui-Jin-Yi;Bao, Shu-Xin;Ba, Hong;Zhou, De-Qun;Hyde, Kevin D.;Zhao, Qi;Yu, Feng-Ming;Jayawardena, Ruvishika S.;Luangharn, Thatsanee;Li, Cui-Jin-Yi;Bao, Shu-Xin;Hyde, Kevin D.;Yu, Feng-Ming;Jayawardena, Ruvishika S.;Li, Cui-Jin-Yi;Bao, Shu-Xin;Hyde, Kevin D.;Zeng, Xiang-Yu;Zhou, De-Qun;Tang, Song-Ming;Hyde, Kevin D.

    关键词：3 new taxa; Cultivated mushrooms; Fungicolous fungi; Hypocreales; Species delimitation

  • Spatiotemporal variations of zooplankton community structure in the oyster (Crassostrea gigas)-macroalgae reef dual ecosystems adjacent to Luanhe River Estuary

    作者：Xu, Min;Zhang, Yi;Yang, Linlin;Xu, Min;Wang, Yun;Shen, Jiabin;Zhang, Yi;Yang, Linlin;Zhao, Qi;Wang, Shenzhi;Hou, Xiaolong;Zhang, Haipeng;Xu, Yufu;Xu, Kaida;Zhang, Yunling;Otaki, Takayoshi;Komatsu, Teruhisa

    关键词：

  • Current trends, limitations and future research in the fungi?

    作者：Hyde, Kevin D.;Gui, Heng;Hu, Yuwei;Mortimer, Peter E.;Wanasinghe, Dhanushka N.;Hyde, Kevin D.;Gui, Heng;Hu, Yuwei;Mortimer, Peter E.;Wanasinghe, Dhanushka N.;Hyde, Kevin D.;de Farias, Antonio R. Gomes;Gonkhom, Didsanutda;Jayawardena, Ruvishika S.;Khyaju, Sabin;Luangharn, Thatsanee;Phonemany, Monthien;Thongklang, Naritsada;Walker, Arttapon;Hyde, Kevin D.;Bahkali, Ali H.;Hyde, Kevin D.;Doilom, Mingkwan;Manawasinghe, Ishara S.;Senanayake, Indunil C.;Hyde, Kevin D.;Manawasinghe, Ishara S.;Baldrian, Petr;Kohout, Petr;Chen, Yanpeng;Chethana, K. W. Thilini;Maharachchikumbura, Sajeewa S. N.;Gonkhom, Didsanutda;Jayawardena, Ruvishika S.;Khyaju, Sabin;Phonemany, Monthien;Thongklang, Naritsada;Walker, Arttapon;De Hoog, Sybren;Goncalves, Micael F. M.;Hilario, Sandra;Goncalves, Micael F. M.;Gui, Heng;Hu, Yuwei;Mortimer, Peter E.;Wanasinghe, Dhanushka N.;Hilario, Sandra;Jayawardena, Ruvishika S.;Kirk, Paul M.;Maharachchikumbura, Sajeewa S. N.;Niego, Allen Grace T.;Sandargo, Birthe;Stadler, Marc;Surup, Frank;Sandargo, Birthe;Stadler, Marc;Surup, Frank;Senanayake, Indunil C.

    关键词：AMF; Biocircular economy; Biocontrol; Data repositories; Drug discovery; Ecology; Emerging diseases; Functional genomics; Fungal classification; HTS; Machine learning; Mycoremediation; Nanotechnology; Novel compounds; Phylogenomics; Plant pathology; Species numbers

  • A re-evaluation of Diaporthe: refining the boundaries of species and species complexes

    作者：Dissanayake, Asha J.;Zhu, Jin-Tao;Maharachchikumbura, Sajeewa S. N.;Liu, Jian-Kui;Chen, Ya-Ya;Hyde, Kevin D.;Hyde, Kevin D.;Hyde, Kevin D.;Hyde, Kevin D.

    关键词：Coalescence-based models; GCPSR; PTP/mPTP; Species/species-complexes; Species boundaries; Taxonomy

  • Identification of candidate genes for Fusarium head blight resistance from QTLs using RIL population in wheat

    作者：Zhang, Mingxia;Xu, Yongyu;Zhang, Mingxia;Wu, Qun;Han, Xu;Man, Junxia;Sun, Junsheng;Liang, Jinlong;Chen, Jingchuan;Zhao, Qi;Guo, Ying;An, Yanrong;Li, Sishen;Jia, Haiyan;Jiang, Peng

    关键词：Wheat; Fusarium head blight (FHB); Quantitative trait locus (QTL); Recombinant inbred line (RIL); Candidate gene

微信小程序