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

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Abstract

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.

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Acknowledgements

This work was funded by grants of the National Natural Science Foundation of China (NSFC 31210103919; 31600032; 31360015), Science and Technology Foundation of Guizhou Province (LH [2015]7061) and the Research of Featured Microbial Resources and Diversity Investigation in Southwest Karst area (Project No. 2014FY120100.). Jian-Kui Liu thanks Dr. Bang Feng (Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China) for his valuable help with phylogenetic analysis. Dr. Rui-Lin Zhao and Dr. H.A. Ariyawansa are thanked for their valuable suggestions. Dr. Hong Luo is thanked for commenting the manuscript. K.D. Hyde thanks the Chinese Academy of Sciences, Project Number 2013T2S0030, for the award of Visiting Professorship for Senior International Scientists at Kunming Institute of Botany. K.D. Hyde also extends his appreciation to the Thailand Research Fund (TRF) Grant (RSA5980068) and National Research Council of Thailand (NRCT) for Grants (60201000201; 592010200112). Alan JL Phillips acknowledges the support from Biosystems and Integrative Sciences Institute (BioISI, FCT/UID/Multi/04046/2013).

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Authors and Affiliations

  1. Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, People’s Republic of China

    Jian-Kui Liu & Qi Zhao

  2. Guizhou Institute of Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, People’s Republic of China

    Jian-Kui Liu

  3. Guizhou Key Laboratory of Agricultural Biotechnology, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, People’s Republic of China

    Jian-Kui Liu & Zuo-Yi Liu

  4. Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand

    Kevin D. Hyde

  5. Departmental of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius

    Rajesh Jeewon

  6. University of Lisbon, Faculty of Sciences, Biosystems and Integrative Sciences Institute, Campo Grande, 1749-016, Lisbon, Portugal

    Alan J. L. Phillips

  7. Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, PO Box 8, 123, Al Khoud, Oman

    Sajeewa S. N. Maharachchikumbura

  8. Department of Organismal Biology, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden

    Martin Ryberg

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Correspondence to Qi Zhao.

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Liu, JK., Hyde, K.D., Jeewon, R. et al. Ranking higher taxa using divergence times: a case study in Dothideomycetes. Fungal Diversity 84, 75–99 (2017). https://doi.org/10.1007/s13225-017-0385-1

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