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

May 2018
IMA Fungus 9(1):167-175

DOI:10.5598/imafungus.2018.09.01.10

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CC BY-NC-ND 3.0

Authors:

Måns Svensson

Uppsala University

Roland Kirschner

National Taiwan University

Ibai Olariaga

King Juan Carlos University

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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 11th 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.

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Supporting Figure 1

Data

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Slavomir Adamcik · Teuvo Tapio Ahti · S A A Martyn Ainsworth · László Albert · Stefan Ekman

Supporting Figure 1

Data

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Juan Carlos Zamora · Måns Svensson · Roland Kirschner · Ibai Olariaga · Stefan Ekman

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Oct 1992
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Recent scientific and technological advances have improved and streamlined our ability to recognise and describe fungal species. Detailed comparative genomics studies have also expanded our understanding of species boundaries. Against this background, we explore the nature of fungal species and consider how this impacts our understanding of their genetics and evolution. The current body of evidence suggests that fungal species are unique evolutionary units that are separated from one another by boundaries that are "porous" under certain conditions ("semipermeable" in analogy to the differential permeability of membranes). Overall, the penetrability of these boundaries depends on the relatedness between donor and recipient species, the spatial proximity of related species to one another during their evolution, and the evolutionary potential associated with the breach of a boundary. Furthermore, the semipermeable nature of species boundaries fundamentally affects the population genetics of a species, with potentially profound effects on its overall evolution and biology. This also influences the methodologies used in taxonomy, because some species appear capable of maintaining their genetic isolation despite extensive penetrability of their boundaries. Most analytical procedures are also not able to distinguish the signals of species boundary permeability from those associated with incomplete lineage sorting or intraspecific diversity. Collectively, these issues greatly complicate how we study and name fungi. An awareness of the nature of species, their boundaries and the biological and genomic signatures of boundary breaches, will enhance our ability to identify them and, perhaps more importantly, to develop realistic strategies to manage and manipulate their growth and distribution.

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Article

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Two new species, Ripella decalvata and R. tribonemae (Amoebozoa, Vannellida), are described and the diversity of known strains assigned to the genus analyzed. Ripella spp. are closely similar to each other in the light microscopic characters and sequences of small-subunit (SSU) ribosomal RNA gene, but differences in the cell coat structure and cytochrome oxidase (COI) gene sequences are more prominent. SSU rRNA in R. platypodia CCAP1589/2, R. decalvata and R. tribonemae demonstrates an unusual pattern of intragenomic variation. Sequencing of multiple molecular clones of this gene produced numerous sequence variants in a number of specific sites. These sites were usually terminal parts of several variable helices in all studied strains. Analysis of all known Ripella strains shows that SSU rRNA sites differing between strains of different origin are mainly restricted to these areas of the gene. There are only two sites, which differ between strains, but not within genomes. This intragenomic variability of the SSU rRNA gene, seemingly characteristic of all Ripella spp., was never reported to be so extensive in Amoebozoa. The data obtained show another example of complex organization of rRNA gene cluster in protists and emphasize caution needed when interpreting the metagenomic data based on this marker.

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

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