Considerations and consequences of allowing DNA sequence data as types of fungal taxa

doi:10.5598/imafungus.2018.09.01.10

. 2018 Jun;9(1):167-175.

doi: 10.5598/imafungus.2018.09.01.10. Epub 2018 May 24.

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Juan Carlos Zamora¹, Måns Svensson¹, Roland Kirschner², Ibai Olariaga³, Svengunnar Ryman¹, Luis Alberto Parra⁴, József Geml⁵, Anna Rosling⁶, Slavomír Adamčík^{1

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6}, Teuvo Ahti^{1

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6}, Edgardo Albertó^{1

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6}, Reinhard Agerer^{1

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6}, Joe Ammirati^{1

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6}, Harry Andersson^{1

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6}, Claudio Angelini^{1

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6}, Vladimír Antonín^{1

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6}, Takayuki Aoki^{1

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6}, André Aptroot^{1

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6}, Matteo Carbone^{1

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6}, Rafael F Castañeda-Ruiz^{1

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6}, Philippe Clerc^{1

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6}, Karl Soop^{1

2

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6}, Viacheslav Spirin^{1

2

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6}, Toby Spribille^{1

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6}, Marc Stadler^{1

2

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6}, Joost Stalpers^{1

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6}, Soili Stenroos^{1

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6}, Ave Suija^{1

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6}, Stellan Sunhede^{1

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6}, Sten Svantesson^{1

2

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6}, Sigvard Svensson^{1

2

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6}, Tatyana Yu Svetasheva^{1

2

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6}, Krzysztof Świerkosz^{1

2

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6}, Heidi Tamm^{1

2

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6}, Hatira Taskin^{1

2

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6}, Adrien Taudière^{1

2

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6}, Jan-Olof Tedebrand^{1

2

3

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6}, Raúl Tena Lahoz^{1

2

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6}, Marina Temina^{1

2

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6}, Arne Thell^{1

2

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6}, Marco Thines^{1

2

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6}, Göran Thor^{1

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6}, Holger Thüs^{1

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6}, Leif Tibell^{1

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6}, Sanja Tibell^{1

2

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6}, Einar Timdal^{1

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6}, Zdenko Tkalčec^{1

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6}, Tor Tønsberg^{1

2

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6}, Gérard Trichies^{1

2

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6}, Dagmar Triebel^{1

2

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6}, Andrei Tsurykau^{1

2

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6}, Rodham E Tulloss^{1

2

3

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6}, Veera Tuovinen^{1

2

3

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6}, Miguel Ulloa Sosa^{1

2

3

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6}, Carlos Urcelay^{1

2

3

4

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6}, François Valade^{1

2

3

4

5

6}, Ricardo Valenzuela Garza^{1

2

3

4

5

6}, Pieter van den Boom^{1

2

3

4

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6}, Nicolas Van Vooren^{1

2

3

4

5

6}, Aida M Vasco-Palacios^{1

2

3

4

5

6}, Jukka Vauras^{1

2

3

4

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6}, Juan Manuel Velasco Santos^{1

2

3

4

5

6}, Else Vellinga^{1

2

3

4

5

6}, Annemieke Verbeken^{1

2

3

4

5

6}, Per Vetlesen^{1

2

3

4

5

6}, Alfredo Vizzini^{1

2

3

4

5

6}, Hermann Voglmayr^{1

2

3

4

5

6}, Sergey Volobuev^{1

2

3

4

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6}, Wolfgang von Brackel^{1

2

3

4

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6}, Elena Voronina^{1

2

3

4

5

6}, Grit Walther^{1

2

3

4

5

6}, Roy Watling^{1

2

3

4

5

6}, Evi Weber^{1

2

3

4

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6}, Mats Wedin^{1

2

3

4

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6}, Øyvind Weholt^{1

2

3

4

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6}, Martin Westberg^{1

2

3

4

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6}, Eugene Yurchenko^{1

2

3

4

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6}, Petr Zehnálek^{1

2

3

4

5

6}, Huang Zhang^{1

2

3

4

5

6}, Mikhail P Zhurbenko^{1

2

3

4

5

6}, Stefan Ekman¹

Affiliations

¹ Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.
² National Central University, Taoyuan City, Taiwan.
³ Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain.
⁴ Avenida Padre Claret 7, 5º G, 09400 Aranda de Duero, Burgos, Spain.
⁵ Naturalis Biodiversity Center, Vondellaan 55, 2332AA Leiden, The Netherlands.
⁶ Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.

PMID: 30018877
PMCID: PMC6048565
DOI: 10.5598/imafungus.2018.09.01.10

Considerations and consequences of allowing DNA sequence data as types of fungal taxa

Juan Carlos Zamora et al. IMA Fungus. 2018 Jun.

. 2018 Jun;9(1):167-175.

doi: 10.5598/imafungus.2018.09.01.10. Epub 2018 May 24.

Authors

Affiliations

¹ Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden.
² National Central University, Taoyuan City, Taiwan.
³ Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain.
⁴ Avenida Padre Claret 7, 5º G, 09400 Aranda de Duero, Burgos, Spain.
⁵ Naturalis Biodiversity Center, Vondellaan 55, 2332AA Leiden, The Netherlands.
⁶ Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden.

PMID: 30018877
PMCID: PMC6048565
DOI: 10.5598/imafungus.2018.09.01.10

Abstract

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11^th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Keywords: IMC11; nomenclature; speciation; taxonomy; typification; voucherless fungi.

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[1] Aas AB, Davey ML, Kauserud H. (2017) ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities. Molecular Ecology Resources 17: 730–741. - PubMed

[2] Aas AB, Davey ML, Kauserud H. (2017) ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities. Molecular Ecology Resources 17: 730–741. - PubMed

[3] Altermann S, Leavitt SD, Goward T, Nelsen MP, Lumbsch HT. (2014) How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS ONE 9: e97556. - PMC - PubMed

[4] Altermann S, Leavitt SD, Goward T, Nelsen MP, Lumbsch HT. (2014) How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS ONE 9: e97556. - PMC - PubMed

[5] Avise JC. (2000) Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.

[6] Avise JC. (2000) Phylogeography: the history and formation of species. Cambridge, MA: Harvard University Press.

[7] Avise JC, Ball RM. (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Survey of Evolutionary Biology 7: 45–67.

[8] Avise JC, Ball RM. (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Survey of Evolutionary Biology 7: 45–67.

[9] Badotti K, Silva de Oliveira F, Garcia CF, Martins Vaz AB, Camargos Fonseca PL, et al. (2017) Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiology 17: 42. - PMC - PubMed

[10] Badotti K, Silva de Oliveira F, Garcia CF, Martins Vaz AB, Camargos Fonseca PL, et al. (2017) Effectiveness of ITS and sub-regions as DNA barcode markers for the identification of Basidiomycota (Fungi). BMC Microbiology 17: 42. - PMC - PubMed

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Considerations and consequences of allowing DNA sequence data as types of fungal taxa

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Considerations and consequences of allowing DNA sequence data as types of fungal taxa

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