The DNA Dilemma: Should Sequences Replace Specimens in Fungal Taxonomy?

A quiet revolution challenges centuries of scientific tradition as mycologists debate whether DNA sequences alone should serve as official references for naming new fungal species.

Taxonomy Mycology DNA Sequencing

Introduction

In the hidden world of fungi, a quiet revolution is underway—one that challenges centuries of scientific tradition. Of the estimated 3 million fungal species on Earth, only about 140,000 have been formally described 1 . The remainder represents biology's "dark matter," detected through DNA sequencing but often without physical specimens 1 . This revelation has sparked a fierce debate among mycologists: should DNA sequences alone be allowed to serve as the official reference for naming new fungal species, replacing the physical specimens that have anchored taxonomy for generations?

Fungal Species Discovery
The DNA Revolution

Environmental DNA techniques have revealed a hidden world of fungal diversity, with sequences representing entirely new lineages with no known physical specimens.

This isn't merely an academic dispute. The outcome could reshape how we catalog Earth's biodiversity, affecting everything from disease control to conservation efforts. As one group of scientists argues, "When DNA sequence data corresponding to a new taxon have been detected, but no physical specimen has been found to serve as the type, the type may be composed of DNA sequence data deposited in a public repository" 1 . Others counter that this fundamental change would "cause nomenclatural instability and unnecessary work for future researchers" 1 . The debate represents a pivotal moment where traditional methods collide with technological advancement, forcing scientists to reconsider the very meaning of biological classification.

The Bedrock of Traditional Taxonomy

For centuries, biological nomenclature has operated on a simple principle: each species name must be permanently linked to a physical reference specimen called the "nomenclatural type" 1 . These preserved specimens—whether pressed plants, pinned insects, or dried fungi—reside in museum and herbarium collections where researchers can re-examine them indefinitely.

Physical Reference

Type specimens provide a tangible, permanent reference that can be re-examined as scientific methods advance.

Nomenclatural Stability

The physical anchor prevents confusion that might occur if names could float freely between different species concepts.

Limitations

Many fungi resist straightforward classification, with some species known only from environmental DNA.

The type provides "the face — the desiccated, flattened face to be sure, but still the face — that is attached to the name of a species" 1 .

The Case for DNA-Based Nomenclature

Proponents of sequence-based typification point to the staggering diversity of fungi being overlooked by traditional methods. Between 2.2 and 3.8 million fungal species are predicted to exist, meaning we've documented less than 5% of the total diversity 7 . Environmental DNA techniques have begun revealing this hidden world, detecting sequences that represent entirely new lineages with no known physical specimens.

Primary Fungal DNA Barcodes
Key Genetic Markers
  • ITS Primary
  • TEF-1α For Fusarium & Trichoderma
  • rRNA subunits For mycorrhizal & rust fungi

Advocates for change argue that refusing to name these DNA-based discoveries creates a scientific limbo where significant components of ecosystems remain invisible to formal science. They propose modest amendments to the International Code of Nomenclature for algae, fungi, and plants (ICNafp) that would allow DNA sequences to serve as types when physical specimens cannot be obtained 1 . Recommendations suggest that such taxa should be described with reference to phylogenetic analyses and ideally represented by multiple sequences from independent studies 1 .

The Scientific Concerns About Sequence-Only Types

Despite the appeal of naming the unknown, many scientists urge caution, pointing to fundamental biological and practical problems with DNA-only types.

The Gene-Species Discordance Problem

A central issue lies in the complex relationship between gene histories and species histories. The process of allele distribution among taxa means that "alleles may not consistently and uniquely represent the species within which they are contained" 1 . Several genetic processes create discordance between gene trees and species trees:

Genetic Discordance Factors
  • Ancestral polymorphisms: When species diverge, they initially share genetic variations
  • Incomplete lineage sorting: Random loss of ancestral alleles over time
  • Horizontal gene transfer: Movement of genetic material between unrelated organisms
  • Hybridization: Interspecies breeding that combines genomes
Challenges with Sequence-Only Types

Practical and Philosophical Objections

Irreproducible Science

Future researchers cannot extract new types of data from a DNA sequence in the way they can from a physical specimen 1 .

Typification on Artifacts

Sequences could be named that later prove to be technical artifacts rather than biological entities 1 .

Nomenclatural Instability

A potential flood of poorly-supported names could complicate rather than clarify fungal taxonomy 1 .

Changing the Type Concept

The fundamental meaning of a nomenclatural type would shift from a physical object to data itself 1 .

A Middle Ground: Integrated Approaches and Alternative Systems

Many scientists propose compromise solutions that acknowledge the importance of DNA data while preserving scientific rigor.

Integrative Taxonomy

Combines genealogical, phenotypic, and reproductive information for species delimitation 7 .

Polyphasic Approach
Alternative Naming

Formulas for naming putative taxa without formal taxonomic status, requiring no modification of the International Code of Nomenclature 1 .

Enhanced Databases

Better documentation and linkage to physical vouchers when possible, with improved curation of sequence labels 7 .

Database Enhancement Strategies

  • Documenting intraspecific and intragenomic variation
  • Expanding sequence repositories
  • Improving curation of sequence labels
  • Linking sequences to digital voucher information

The Road Ahead: Technological Solutions and Community Consensus

The debate over DNA types reflects broader tensions in how science adapts to technological change. Similar controversies accompanied the adoption of "one fungus = one name" principles when DNA evidence revealed that many sexual and asexual forms represented the same species 2 . The mycological community ultimately embraced this change, suggesting that consensus on DNA types might also be possible with careful deliberation.

Timeline of Key Developments
Traditional Taxonomy Era

Centuries of using physical specimens as nomenclatural types

DNA Sequencing Revolution

Revealed vast "dark matter" of fungal diversity undetectable by traditional methods

Proposals for DNA as Types

Suggested amendments to ICNafp to allow DNA sequences as types

Current Debate

Twice rejected by nomenclature committees but pressure continues to build

Future Solutions

Whole-genome approaches and tiered evidence systems may provide resolution

Real-World Impact
Clinical Settings
Precise identification affects treatment decisions
Agriculture
Accurate names enable effective quarantine measures
Conservation
Proper species delimitation essential for protecting biodiversity

Conclusion: The Future of Fungal Names

The debate over DNA sequence types represents more than an esoteric taxonomic dispute—it's about how we know and name the living world. As we detect ever more life through environmental DNA, we face fundamental questions about what constitutes sufficient evidence to declare a species' existence.

The current proposal to allow DNA sequences as types has been rejected twice—first by the Nomenclature Committee for Fungi and subsequently by the International Botanical Congress 1 . Yet the pressure to name the unknown continues to build as sequencing technologies reveal ever-greater diversity.

Potential Path Forward
  • Tiered levels of evidence with different naming protocols
  • More sophisticated systems accommodating both specimens and sequences
  • Portable sequencers linking environmental sequences to physical specimens
Certain Outcome

Our understanding of fungal diversity stands at a threshold. How we decide to name what we cannot yet hold may shape mycology for generations to come, determining whether we illuminate or obscure the vast, hidden world of fungi that sustains our planet's ecosystems.

References