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1. Freshwater fungal numbers.

Author

Calabon, Mark S., Hyde, Kevin D., Jones, E. B. Gareth, Luo, Zong-Long, Dong, Wei, Hurdeal, Vedprakash G., Gentekaki, Eleni, Rossi, Walter, Leonardi, Marco, Thiyagaraja, Vinodhini, Lestari, Anis S., Shen, Hong-Wei, Bao, Dan-Feng, Boonyuen, Nattawut, and Zeng, Ming

Abstract

A comprehensive account of fungal classification from freshwater habitats is outlined and discussed in the present review based on literature of biodiversity studies and recent morpho-phylogenetic analyses. A total of 3,870 freshwater fungal species are listed with additional details on the isolation source, habitat, geographical distribution, and molecular data. The Ascomycota (2,968 species, 1,018 genera) dominated the freshwater fungal taxa wherein Sordariomycetes (823 species, 298 genera) had the largest number, followed by Dothideomycetes (677 species, 229 genera), Eurotiomycetes (276 species, 49 genera), and Leotiomycetes (260 species, 83 genera). Other phyla included in the updated classification of freshwater fungi are: Chytridiomycota (333 species, 97 genera), Rozellomycota (221 species, 105 genera), Basidiomycota (218 species, 100 genera), Blastocladiomycota (47 species, 10 genera), Monoblepharomycota (29 species, 6 genera), Mucoromycota (19 species, 10 genera), Aphelidiomycota (15 species, 3 genera), Entomophthoromycota (6 species, 4 genera), Mortierellomycota (5 species, 3 genera), Olpidiomycota (4 species, 1 genus), Zoopagomycota (3 species, 2 genera), and Sanchytriomycota (2 species, 2 genera). The freshwater fungi belong to 1,361 genera, 386 families and 145 orders. The Pleosporales and Laboulbeniaceae are the largest freshwater fungal order and family comprised of 391 and 185 species, respectively. The most speciose genera are Chitonomyces (87, Laboulbeniomycetes), Verrucaria (50, Eurotiomycetes), Rhizophydium (52, Rhizophydiomycetes), Penicillium (47, Eurotiomycetes), and Candida (42, Saccharomycetes). [ABSTRACT FROM AUTHOR]

Published
2022
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2. Freshwater fungal numbers

Author

Mark S. Calabon, Kevin D. Hyde, E. B. Gareth Jones, Zong-Long Luo, Wei Dong, Vedprakash G. Hurdeal, Eleni Gentekaki, Walter Rossi, Marco Leonardi, Vinodhini Thiyagaraja, Anis S. Lestari, Hong-Wei Shen, Dan-Feng Bao, Nattawut Boonyuen, and Ming Zeng

Subjects
Molecular taxonomy, Fungal classification, Fungal taxonomy, Freshwater fungi, Higher fungi, Basal clades, Ecology, Ecology, Evolution, Behavior and Systematics
Published
2022
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3. Outline of Fungi and fungus-like taxa

Author

David L. Hawksworth, R. G. U. Jayalal, L. F. Zhang, G. A. da Silva, Samantha C. Karunarathna, Saowaluck Tibpromma, Kazuaki Tanaka, Saranyaphat Boonmee, I. V. Issi, Sajeewa S. N. Maharachchikumbura, Rajesh Jeewon, Oleg N. Shchepin, J. Ma, Fritz Oehl, P. B. Gannibal, Cristina Maria de Souza-Motta, Dhanushka N. Wanasinghe, Kunhiraman C. Rajeshkumar, A. A. Lateef, Ting-Chi Wen, L. K. T. Al-Ani, Kevin D. Hyde, Armin Mešić, Hans-Peter Grossart, Gabriela Heredia, Roshni Khare, Einar Timdal, Shubhi Avasthi, F. A. de Souza, Mounes Bakhshi, Richard A. Humber, Subhash Gaikwad, Dmitry V. Leontyev, Noha H. Youssef, Alexandre G. S. Silva-Filho, Sudhir Navathe, María Prieto, Marco Thines, Paul M. Kirk, Yuri Tokarev, Marc Stadler, P. O. Fiuza, André Aptroot, Damien Ertz, Monika C. Dayarathne, Julia Pawłowska, P. Liu, H. T. Lumbsch, Peter E. Mortimer, Elaine Malosso, Nalin N. Wijayawardene, Belle Damodara Shenoy, Huzefa A. Raja, Mikhail P. Zhurbenko, Somayeh Dolatabadi, Jos Houbraken, S. Mohammad, Zdenko Tkalčec, Andrei Tsurykau, Rampai Kodsueb, Mubashar Raza, Darbhe J. Bhat, Dsa Wijesundara, Jadson D. P. Bezerra, Javier Etayo, Walter P. Pfliegler, Leho Tedersoo, Jurga Motiejunaite, James D. Lawrey, Felipe Wartchow, Anusha H. Ekanayaka, Laura Selbmann, Sinang Hongsanan, Gothamie Weerakoon, Rafael F. Castañeda-Ruiz, Francis Q. Brearley, Enikő Horváth, R. L Zhao, B. O. Sharma, Y. Wang, Iván Sánchez-Castro, Martin Schnittler, Steven L. Stephenson, Y. Kang, Renate Radek, Eleni Gentekaki, Dagmar Triebel, F. R. Barbosa, Martina Réblová, Q. R. Li, Sayanh Somrithipol, Y. M. Li, D. K. A. Silva, L. Z. Tang, Hugo Madrid, Asha J. Dissanayake, Satinee Suetrong, Eric H. C. McKenzie, Mingkwan Doilom, E. S. Nassonova, J. C. Cavender, Neven Matočec, A. L. Firmino, R. K. Saxena, Olinto Liparini Pereira, J. Xu, V. Vázquez, M. Q. He, Xinlei Fan, Khadija Jobim, Martin Kukwa, Andrey Yurkov, R. F. Xu, K. Kolaríková, Lakmali S. Dissanayake, P. Alvarado, Rungtiwa Phookamsak, Dong-Qin Dai, Qing Tian, Ulrike Damm, D. W. Li, Pradeep K. Divakar, Jian-Kui Liu, Ajay Kumar Gautam, Viktor Papp, Peter M. Letcher, Pamela Rodriguez-Flakus, E. Kuhnert, F. Tian, I. Kusan, Makbule Erdoğdu, Alejandra Gabriela Becerra, B. T. Goto, Eric W.A. Boehm, K. Bensch, Sally C. Fryar, Yuri K. Novozhilov, Han Zhang, V. P. Hustad, André Luiz Cabral Monteiro de Azevedo Santiago, Danny Haelewaters, Gregorio Delgado, V. Dima, C. Y. Deng, Y. Z. Lu, Moslem Papizadeh, Ave Suija, Janusz Błaszkowski, Paul G. Mungai, Bryce Kendrick, Leonor Costa Maia, Gerhard Rambold, Adam Flakus, Alan J. L. Phillips, Josiane Santana Monteiro, Susumu Takamatsu, Ziraat Fakültesi, Makbule Erdoğdu / 0000-0001-8255-2041, Westerdijk Fungal Biodiversity Institute - Food and Indoor Mycology, Westerdijk Fungal Biodiversity Institute, Netherlands Institute for Neuroscience (NIN), Qujing Normal University, Abhilashi University, Jiwaji University, National Science and Technology Development Agency -NSTDA, University of Oslo, Universidade Federal da Paraíba, FRANCISCO ADRIANO DE SOUZA, CNPMS, Agroscope, Competence Div Plants & Plant Prod., Universidade Federal de Pernambuco, West Pomeranian University of Technology, Universidade Federal do Rio Grande do Norte, Universidade Federal de Mato Grosso, University of Ilorin, Kunming Institute of Botany, Mae Fah Luang University, ALVALAB, Shenzhen University, Hirosaki University, University of Electronic Science and Technology of China, Museu Paraense Emílio Goeldi, Leibnitz Institute of Freshwater Ecology and Inland Fisheries - IGB, University of Tartu, Helmholtz-Zentrum für Infektionsforschung GmbH, Institute of Microbiology Chinese Academy of Sciences, University of Mauritius, Russian Academy of Sciences, Universidad Rey Juan Carlos, University of Sri Lanka, K?r?ehir Ahi Evran University, Leibniz Institute, Ernst Moritz Arndt University Greifswald, Goethe University., USDA-ARS Emerging Pests and Pathogens Research, University of South Bohemia, National Fungal Culture Collection of India -NFCCI, State Key Laboratory of Mycology, Universidade Federal de Mato Grosso do Sul, Skovoroda Kharkiv National Pedagogical University, University Road, All-Russian Institute of Plant Protection, Universidade de Lisboa, University of Tuscia, University of Debrecen, Royal Botanic Gardens, Czech Academy of Sciences, University of North Carolina at Greensboro, Freie Universität Berlin, Szent István University, Eötvös Loránd University, Jiangxi Agricultural University, Flinders University, EMLab P&K Houston, Academy of Sciences, Chiang Mai University, Sabzevar University of New Technology, University of Warsaw, Pibulsongkram Rajabhat University, Universidad de Granada, Universidad Complutense de Madrid, CSIR-National Institute of Oceanography Regional Centre, Instituto de Investigaciones Fundamentales en AgriculturaTropical, BIOTEC, National Science and Technology Development Agency - NSTDA, Guizhou University, Valley Laboratory, Ru?er Boškovi? Institute, Pasteur Institute of Iran, Instituto de Ecolog? 'a A. C., Iranian Research Institute of Plant Protection, Oklahoma State University, Northwest Missouri State University, George Mason University, Universidade Federal de Uberlândia, The Natural History Museum, IES Zizur, Skorina Gomel State University, University of Málaga, Kenya Wildlife Service, Senckenberg Museum of Natural History Görlitz, Guizhou Medical University, Kunming University of Science and Technology, Universidad Nacional de Córdoba, Manchester Metropolitan University, Nature Research Centre, Agharkar Research Institute, National Institute of Fundamental Studies, Szafer Institute of Botany, Manaaki Whenua-Landcare Research, Jilin Agricultural University, Ohio University, Iranian Research Organization for Science and Technology -IROST, Guizhou Academy of Science, Universidade Federal de Viçosa, Beijing Forestry University, Leibniz University, Leibnitz Institute of Freshwater Ecology and Inland Fisheries -IGB, University of Baghdad, The University of Alabama, University of Arkansas, Botanic Garden Meise, The Field Museum, University of Gda?sk, Universidad Mayor, Mie University, Universität of Bayreuth, and Staatliche Naturwissenschaftliche Sammlungen Bayerns

Subjects
Plant Science, Blastocladiomycota, 030308 mycology & parasitology, purl.org/becyt/ford/1 [https], Glomeromycota, Genus, Neopereziida, Amblyosporida ord. nov, 0303 health sciences, Ascomycota, biology, ord. nov, Basal clades, Classification, FOUR NEW TAXA, GEN. NOV, CELLULAR SLIME-MOLDS, POLAR TUBE, SP.-NOV, Leotiomycetes, four new taxa, ascomycota, basal clades, basidiomycota, classification, emendation, microsporidia, Neopereziida ord. nov, Ovavesiculida ord. nov, Protosporangiaceae fam. nov, Redonographaceae stat nov, MOLECULAR PHYLOGENY, Four new taxa, BASAL CLADES, GENERIC NAMES, CLASSIFICATION, 03 medical and health sciences, Botany, MICROSPORIDIAN, NATURAL CLASSIFICATION, purl.org/becyt/ford/1.6 [https], Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Fungo, Entomophthoromycota, Phylum, Basidiomycota, Biology and Life Sciences, Emendation, 15. Life on land, biology.organism_classification, SUB-ANTARCTIC ISLANDS, Microsporidia, Polar tube, SP-NOV, Amblyosporidae, LEVEL PHYLOGENETIC CLASSIFICATION
Abstract

This article provides an outline of the classification of the kingdom Fungi (including fossil fungi. i.e. dispersed spores, mycelia, sporophores, mycorrhizas). We treat 19 phyla of fungi. These are Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. The placement of all fungal genera is provided at the class-, order- and family-level. The described number of species per genus is also given. Notes are provided of taxa for which recent changes or disagreements have been presented. Fungus-like taxa that were traditionally treated as fungi are also incorporated in this outline (i.e. Eumycetozoa, Dictyosteliomycetes, Ceratiomyxomycetes and Myxomycetes). Four new taxa are introduced: Amblyosporida ord. nov. Neopereziida ord. nov. and Ovavesiculida ord. nov. in Rozellomycota, and Protosporangiaceae fam. nov. in Dictyosteliomycetes. Two different classifications (in outline section and in discussion) are provided for Glomeromycota and Leotiomycetes based on recent studies. The phylogenetic reconstruction of a four-gene dataset (18S and 28S rRNA, RPB1, RPB2) of 433 taxa is presented, including all currently described orders of fungi., Nalin N. Wijayawardene thanks Mushroom Research Foundation and National Science Foundation of China (No. NSFC 31950410558) for financially supporting this project. Kevin D. Hyde acknowledges the Foreign Experts Bureau of Yunnan Province, Foreign Talents Program (2018; grant no. YNZ2018002), Thailand Research grants entitled Biodiversity, phylogeny and role of fungal endophytes on above parts of Rhizophora apiculata and Nypa fruticans (grant no: RSA5980068), the future of specialist fungi in a changing climate: baseline data for generalist and specialist fungi associated with ants, Rhododendron species and Dracaena species (grant no: DBG6080013), Impact of climate change on fungal diversity and biogeography in the Greater Mekong Subregion (grant no: RDG6130001). H.T. Lumbsch thanks support by the Grainger Bioinformatics Center. E. Malosso is grateful to CAPES for financial support (grant no. 88881.062172/2014-01). B.T. Goto, G.A. Silva and K. Jobim, L.C. Maia acknowledges CNPq (Brazilian Scientific Council, grants no. 465.420/2014-1, 307.129/2015-2 and 408011/2016-5) and CAPES for support. The study was partially supported by the National Science Centre, Poland, under Grants No. 2015/17/D/NZ8/00778 and 2017/25/B/NZ8/00473 to Julia Pawłowska. The research of Martin Kukwa received support from the National Science Centre (NCN) in Poland (project no 2015/17/B/NZ8/02441). Alan J.L. Phillips acknowledges the support from UID/MULTI/04046/2019 Research Unit grant from FCT, Portugal to BioISI. H. Zhang is financially supported by the National Natural Science Foundation of China (Project ID: NSF 31500017). S. Boonmee would like to thank the Thailand Research Fund (Project No. TRG6180001). Dong-Qin Dai and Li-Zhou Tang would like to thank the National Natural Science Foundation of China (No. NSFC 31760013, NSFC 31260087, NSFC 31460561), the Scientific Research Foundation of Yunnan Provincial Department of Education (2017ZZX186) and the Thousand Talents Plan, Youth Project of Yunnan Provinces for support. R. Phookamsak, M. Doilom, D. N. Wanasinghe, S.C. Karunarathna and J.C. Xu express sincere appreciations to Key Research Program of Frontier Sciences of the Chinese Academy of Sciences (grant no. QYZDY-SSW-SMC014) for research financial support. R. Phookamsak thanks the Yunnan Provincial Department of Human Resources and Social Security (grant no. Y836181261), Chiang Mai University and National Science Foundation of China (NSFC) project code 31850410489 for research financial support. S.C. Kaunarathna thanks CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (No. 2018PC0006) and the National Science Foundation of China (NSFC) for funding this work under the project code 31851110759. S. Tibpromma would like to thank the International Postdoctoral Exchange Fellowship Program (number Y9180822S1), CAS President’s International Fellowship Initiative (PIFI) (number 2020PC0009), China Postdoctoral Science Foundation and the Yunnan Human Resources, and Social Security Department Foundation for funding her postdoctoral research. Yuri S. Tokarev, Elena S. Nassonova and Irma V. Issi are indebtful to Yuliya Y. Sokolova (Institute of Cytology RAS, St. Petersbug, Russia) and Anastasia V. Simakova (Tomsk State University, Tomsk, Russia) for kind permission of reproduction of electron microscopy images of Metchnikovella incurvata and Crepidulospora beklemishevi, respectively. Yuri S. Tokarev and Irma V. Issi thank Russian Foundation of Basic Research, grant number 17-04-00871 (taxonomy of Rozellomycota). Elena S. Nassonova thank Russian Foundation of Basic Research, grant number 18-04-01359 (early evolution of Microsporidia, phylogeny of Metchnikovellida). Adam Flakus and Pamela Rodriguez-Flakus are greatly indebted to all staff of the Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, La Paz and the SERNAP (http://sernap.gob.bo), for their generous cooperation providing permits, assistance and facilities support for scientific studies. The research of AF and PRF were financially supported by the National Science Centre (NCN) in Poland (DEC-2013/11/D/NZ8/03274). Adam Flakus and Pamela Rodriguez-Flakus received additional support under statutory funds from the W. Szafer Institute of Botany, Polish Academy of Sciences, Krakow, Poland. The authors would like to thank Yunnan Innovation Platform for Development and Utilization of Symbiotic Fungi Resources for finance support. Li-Fang Zhang would like to thank grant-in-aid from Science and Technology Department of Yunnan Province (2018FD080) for finance support. Chun-Ying Deng thanks the Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China (2019HJ2096001006). Yingqian Kang would like to thank Guizhou Scientific Plan Project [(2019) 2873]; Excellent Youth Talent Training Project of Guizhou Province [(2017) 5639]; Guiyang Science and Technology Project [(2017) No. 5-19]; Talent Base Project of Guizhou Province, China [FCJD2018-22]; Research Fund of Education Bureau of Guizhou Province, China [(2018) 481]. D. N. Wanasinghe would like to thank the CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2019PC0008), the National Science Foundation of China and the Chinese Academy of Sciences for financial support under the following grants: 41761144055, 41771063 and Y4ZK111B01. Yuri K. Novozhilov and Oleg N. Shchepin acknowledge support from the Russian Foundation of Basic Research, project 18-04-01232 А. Ivana Kušan, Neven Matočec, Armin Mešić and Zdenko Tkalčec are grateful to Croatian Science Foundation for their financial support under the project grant HRZZ-IP-2018-01-1736 (ForFungiDNA). K. Tanaka would like to thank the Japan Society for the Promotion of Science (JSPS 19K06802)

Published
2020
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4. Outline of Fungi and fungus-like taxa

Author

Wijayawardene, N. N., Hyde, K. D., Al-Ani, L. K. T., Tedersoo, L., Haelewaters, D., Rajeshkumar, K. C., Zhao, R. L., Aptroot, A., Leontyev, D., V, Saxena, R. K., Tokarev, Y. S., Dai, D. Q., Letcher, P. M., Stephenson, S. L., Ertz, D., Lumbsch, H. T., Kukwa, M., Issi, I., V, Madrid, H., Phillips, A. J. L., Selbmann, L., Pfliegler, W. P., Horvath, E., Bensch, K., Kirk, P. M., Kolarikova, K., Raja, H. A., Radek, R., Papp, V, Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P. B., Triebel, D., Gautam, A. K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S. C., Delgado, G., Reblova, M., Doilom, M., Dolatabadi, S., Pawlowska, J. Z., Humber, R. A., Kodsueb, R., Sanchez-Castro, I, Goto, B. T., Silva, D. K. A., de Souza, F. A., Oehl, F. R., da Silva, G. A., Silva, I. R., Blaszkowski, J., Jobim, K., Maia, L. C., Barbosa, F. R., Fiuza, P. O., Divakar, P. K., Shenoy, B. D., Castaneda-Ruiz, R. F., Somrithipol, S., Lateef, A. A., Karunarathna, S. C., Tibpromma, S., Mortimer, P. E., Wanasinghe, D. N., Phookamsak, R., Xu, J., Wang, Y., Tian, F., Alvarado, P., Li, D. W., Kusan, I, Matocec, N., Mesic, A., Tkalcec, Z., Maharachchikumbura, S. S. N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V. P., Lawrey, J. D., Santiago, A. L. C. M. A., Bezerra, J. D. P., Souza-Motta, C. M., Firmino, A. L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A. J., Monteiro, J. S., Grossart, H. P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Vazquez, V., Mungai, P., Damm, U., Li, Q. R., Zhang, H., Boonmee, S., Lu, Y. Z., Becerra, A. G., Kendrick, B., Brearley, F. Q., Motiejunaite, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D. S. A., Tang, L. Z., He, M. Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M. P., McKenzie, E. H. C., Stadler, M., Bhat, D. J., Liu, J. K., Raza, M., Jeewon, R., Nassonova, E. S., Prieto, M., Jayalal, R. G. U., Erdogdu, M., Yurkov, A., Schnittler, M., Shchepin, O. N., Novozhilov, Y. K., Silva-Filho, A. G. S., Gentekaki, E., Liu, P., Cavender, J. C., Kang, Y., Mohammad, S., Zhang, L. F., Xu, R. F., Li, Y. M., Dayarathne, M. C., Ekanayaka, A. H., Wen, T. C., Deng, C. Y., Pereira, O. L., Navathe, S., Hawksworth, D. L., Fan, X. L., Dissanayake, L. S., Kuhnert, E., Thines, M., Wijayawardene, N. N., Hyde, K. D., Al-Ani, L. K. T., Tedersoo, L., Haelewaters, D., Rajeshkumar, K. C., Zhao, R. L., Aptroot, A., Leontyev, D., V, Saxena, R. K., Tokarev, Y. S., Dai, D. Q., Letcher, P. M., Stephenson, S. L., Ertz, D., Lumbsch, H. T., Kukwa, M., Issi, I., V, Madrid, H., Phillips, A. J. L., Selbmann, L., Pfliegler, W. P., Horvath, E., Bensch, K., Kirk, P. M., Kolarikova, K., Raja, H. A., Radek, R., Papp, V, Dima, B., Ma, J., Malosso, E., Takamatsu, S., Rambold, G., Gannibal, P. B., Triebel, D., Gautam, A. K., Avasthi, S., Suetrong, S., Timdal, E., Fryar, S. C., Delgado, G., Reblova, M., Doilom, M., Dolatabadi, S., Pawlowska, J. Z., Humber, R. A., Kodsueb, R., Sanchez-Castro, I, Goto, B. T., Silva, D. K. A., de Souza, F. A., Oehl, F. R., da Silva, G. A., Silva, I. R., Blaszkowski, J., Jobim, K., Maia, L. C., Barbosa, F. R., Fiuza, P. O., Divakar, P. K., Shenoy, B. D., Castaneda-Ruiz, R. F., Somrithipol, S., Lateef, A. A., Karunarathna, S. C., Tibpromma, S., Mortimer, P. E., Wanasinghe, D. N., Phookamsak, R., Xu, J., Wang, Y., Tian, F., Alvarado, P., Li, D. W., Kusan, I, Matocec, N., Mesic, A., Tkalcec, Z., Maharachchikumbura, S. S. N., Papizadeh, M., Heredia, G., Wartchow, F., Bakhshi, M., Boehm, E., Youssef, N., Hustad, V. P., Lawrey, J. D., Santiago, A. L. C. M. A., Bezerra, J. D. P., Souza-Motta, C. M., Firmino, A. L., Tian, Q., Houbraken, J., Hongsanan, S., Tanaka, K., Dissanayake, A. J., Monteiro, J. S., Grossart, H. P., Suija, A., Weerakoon, G., Etayo, J., Tsurykau, A., Vazquez, V., Mungai, P., Damm, U., Li, Q. R., Zhang, H., Boonmee, S., Lu, Y. Z., Becerra, A. G., Kendrick, B., Brearley, F. Q., Motiejunaite, J., Sharma, B., Khare, R., Gaikwad, S., Wijesundara, D. S. A., Tang, L. Z., He, M. Q., Flakus, A., Rodriguez-Flakus, P., Zhurbenko, M. P., McKenzie, E. H. C., Stadler, M., Bhat, D. J., Liu, J. K., Raza, M., Jeewon, R., Nassonova, E. S., Prieto, M., Jayalal, R. G. U., Erdogdu, M., Yurkov, A., Schnittler, M., Shchepin, O. N., Novozhilov, Y. K., Silva-Filho, A. G. S., Gentekaki, E., Liu, P., Cavender, J. C., Kang, Y., Mohammad, S., Zhang, L. F., Xu, R. F., Li, Y. M., Dayarathne, M. C., Ekanayaka, A. H., Wen, T. C., Deng, C. Y., Pereira, O. L., Navathe, S., Hawksworth, D. L., Fan, X. L., Dissanayake, L. S., Kuhnert, E., and Thines, M.

Published
2020

5. Efficiently resolving the basal clades of a phylogenetic tree using Bayesian and parsimony approaches: a case study using mitogenomic data from 100 higher teleost fishes

Author

Simmons, Mark P. and Miya, Masaki

Subjects
*OSTEICHTHYES, *PHYLOGENY, *MITOCHONDRIAL DNA, *BAYESIAN analysis
Abstract

Many phylogenetic analyses that include numerous terminals but few genes show high resolution and branch support for relatively recently diverged clades, but lack of resolution and/or support for “basal” clades of the tree. The various benefits of increased taxon and character sampling have been widely discussed in the literature, albeit primarily based on simulations rather than empirical data. In this study, we used a well-sampled gene-tree analysis (based on 100 mitochondrial genomes of higher teleost fishes) to test empirically the efficiency of different methods of data sampling and phylogenetic inference to “correctly” resolve the basal clades of a tree (based on congruence with the reference tree constructed using all 100 taxa and 7990 characters). By itself, increased character sampling was an inefficient method by which to decrease the likelihood of “incorrect” resolution (i.e., incongruence with the reference tree) for parsimony analyses. Although increased taxon sampling was a powerful approach to alleviate “incorrect” resolution for parsimony analyses, it had the general effect of increasing the number of, and support for, “incorrectly” resolved clades in the Bayesian analyses. For both the parsimony and Bayesian analyses, increased taxon sampling, by itself, was insufficient to help resolve the basal clades, making this sampling strategy ineffective for that purpose. For this empirical study, the most efficient of the six approaches considered to resolve the basal clades when adding nucleotides to a dataset that consists of a single gene sampled for a small, but representative, number of taxa, is to increase character sampling and analyze the characters using the Bayesian method. [Copyright &y& Elsevier]

Published
2004
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