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Integrative approaches for species delimitation in Ascomycota

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Abstract

Biodiversity loss from disturbances caused by human activities means that species are disappearing at an ever increasing rate. The high number of species that have yet to be described have generated extreme crisis to the taxonomist. Therefore, more than in any other era, effective ways to discover and delimitate species are needed. This paper reviews the historically foremost approaches used to delimit species in Ascomycota, the most speciose phylum of Fungi. These include morphological, biological, and phylogenetic species concepts. We argue that a single property to delineate species boundaries has various defects and each species concept comes with its own advantages and disadvantages. Recently the rate of species discovery has increased because of the advancement of phylogenetic approaches. However, traditional phylogenetic methods with few gene regions lack species-level resolution, and do not allow unambiguous conclusions. We detail the processes that affect gene tree heterogeneity, which acts as barriers to delimiting species boundaries in classical low-rank phylogenies. So far, limited insights were given to the DNA-based methodologies to establish well-supported boundaries among fungal species. In addition to reviewing concepts and methodologies used to delimit species, we present a case study. We applied different 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 species. These problems can be resolved by using multiple loci and coalescence-based methods. Further, 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.

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Acknowledgements

Danny Haelewaters is supported by the Research Foundation – Flanders (junior postdoctoral fellowship 1206620N). Dhanushka Wanasinghe thanks the CAS President’s International Fellowship Initiative (PIFI) for funding his postdoctoral research (number 2021FYB0005), the Postdoctoral Fund from Human Resources and Social Security Bureau of Yunnan Province.

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Authors and Affiliations

  1. School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 611731, People’s Republic of China

    Sajeewa S. N. Maharachchikumbura, Yanpeng Chen & Jian-Kui Liu

  2. Entomology and Plant Pathology Department, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand

    Sajeewa S. N. Maharachchikumbura & Ratchadawan Cheewangkoon

  3. Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei City, 10617, Taiwan

    Hiran A. Ariyawansa

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

    Kevin D. Hyde, Rekhani H. Perera & Milan C. Samarakoon

  5. Research Group Mycology, Department of Biology, Ghent University, 9000, Ghent, Belgium

    Danny Haelewaters

  6. Faculty of Science, University of South Bohemia, 370 05, Ceske Budejovice, Czech Republic

    Danny Haelewaters

  7. Center for Mountain Futures, Kunming Institute of Botany, Honghe County, 654400, Yunnan, People’s Republic of China

    Dhanushka N. Wanasinghe

  8. Instituto de Investigación Para el Desarrollo Sustentable de Ceja de Selva (INDES-CES), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru

    Danilo E. Bustamante

  9. Department of Civil and Environmental Engineering (FICIAM), Universidad Nacional Toribio Rodríguez de Mendoza, Chachapoyas, Amazonas, Peru

    Danilo E. Bustamante

  10. Department of Plant Pathology, University of California, Davis, Davis, CA, USA

    Daniel P. Lawrence

  11. Helmholtz Centre for Infection Research GmbH, Department Microbial Drugs and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, 38124, Braunschweig, Germany

    Marc Stadler

  12. Institute of Microbiology, Technische Universität Braunschweig, Inhoffenstraße 7, 38124, Braunschweig, Germany

    Marc Stadler

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  1. Sajeewa S. N. Maharachchikumbura
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  2. Yanpeng Chen
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Correspondence to Sajeewa S. N. Maharachchikumbura.

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Handling Editor: Chayanard Phukhamsakda.

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13225_2021_486_MOESM1_ESM.pdf

Supplementary file1 (PDF 721 kb) Supplementary Fig. 1. Color strips represent the species delimitation results from 5 methods, ABGD, bPTP, GMYC, mPTP, TCS based 5 single loci and combined sequences, respectively. Different symbols represent each complex. White means missing data. The number of defined species from different methods, number of reported species and percentages of recovered taxonomic species (Number of defined species/number of reported species * 100%) were displayed on the top.

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Maharachchikumbura, S.S.N., Chen, Y., Ariyawansa, H.A. et al. Integrative approaches for species delimitation in Ascomycota. Fungal Diversity 109, 155–179 (2021). https://doi.org/10.1007/s13225-021-00486-6

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