‘Dark Taxa’ and New Discoveries

The discovery of wide genetic variety in fungal species previously thought to belong to the same evolutionary lineages, termed “cryptic species' ', has prompted scientists to re-visit traditional scientific naming systems and call for more research into fungi taxonomy. But what is the best way to reconcile traditional scientific naming systems with new methods of species identification?

April 12, 2023

FFungi Staff


Betsy Middleton

FFungi Volunteer

We have been identifying, naming and using fungi for thousands of years, from the Neolithic people who gathered fungi to start fires, to current medical trials on fungal species which could help treat severe depression (Berihuete-Azorín et al., 2018; Sample, 2022). Modern identification techniques using DNA sequencing has given scientists new insights into fungal lineages which has led to a breakthrough in identification and species categorization, but it is not without its challenges. The discovery of wide genetic variety in fungal species previously thought to belong to the same evolutionary lineages, termed “cryptic species' ', has prompted scientists to re-visit traditional scientific naming systems and call for more research into fungi taxonomy. But what is the best way to reconcile traditional scientific naming systems with new methods of species identification?

The Traditional Scientific Naming System for Fungi

The official scientific names of living organisms play an important role in scientific practice and collaboration. The standard scientific naming system used for all living things was first developed by the famous Swedish botanist, Carl Linneaus. Each being is given a first name and a last name (usually in latin) that correspond to their genus (a group of organisms with a common ancestor) and their species. All animal, fungi and plant species are named using this same system. This means that scientists all over the world have a common language for discussing and understanding life and can quickly identify the evolutionary relationship between different specimens (Lerner, 1996). 

Traditionally, fungal species are identified by looking at their physical characteristics such as their colours, anatomy, or certain microscopic structures. These observations are used to describe the specimens and give them names. Similarities in the appearance of different specimens are taken as a sign of close evolutionary relationships. However, this can be particularly misleading in fungi, as many species have physical traits that vary a lot throughout their lifecycle, and often distantly related species can look very similar to each other. As a result, standard botanical systems for identifying, categorising and naming specimens has not always been easy to reconcile with fungal diversity (Money, 2013).

The DNA Barcoding Method

In recent years, the advance of molecular biology has enabled scientists to use DNA sequencing to identify specimens more accurately. This has led to a new identification process in which specific parts of a fungal specimen’s DNA are used to understand its evolutionary history and identify it in relation to other known species.

A DNA barcode is a short section of DNA which can be sequenced from a fungi sample. Once a specific region of DNA is sequenced from a sample of one species, it can be compared to the barcodes of other species to determine their evolutionary relationship, or it can be stored to be used as a reference for future samples. 

The wide use of DNA barcoding has led to a lot of change in the scientific names previously used for fungi as researchers have discovered mis-identified species and uncovered new evolutionary connections. The discovery of many “cryptic species” has revealed “unrecognised genetic diversity hidden in what was assumed to be a single lineage” (Yuhl et al., 2016). Following these discoveries, it is thought that known species with very large geographical distribution may actually represent much more diverse groups of cryptic species (Yahr et al, 2016). 

DNA barcoding technology is more accurate than previous identification practices, but has brought its own challenges for fungal taxonomy. 

Challenges of DNA Barcoding: ‘Dark Taxa’ and  Lack of Data

According to the rules of scientific practice, scientists must identify and preserve a physical specimen of a fungus in a fungarium, a biological collection of preserved fungi samples, before they can officially name it. However, with new DNA barcoding methods, many scientists have sequenced and identified single-cell or microscopic samples of fungi which cannot be tied to any identified physical specimens. These species are called “fungal dark taxa”, as they have been discovered and recorded in DNA sample records, but have no connection to a material sample and therefore remain unofficial species (Wallheimer, 2021). 

Furthermore, DNA barcoding relies on the existence of extensive reference databases, where scientists can compare new barcode sequences to sequences that have already been stored and identified with known, physical specimens. There are now far more DNA barcodes being found than there are references to compare them to. As a result, the number of unofficial species is growing rapidly without a similar expansion in the identification of collected specimens. 

Thus, scientists consider the integration of DNA sequence data with standardized and physical taxonomic systems for fungi as one of the main challenges facing mycology today (Yahl et al., 2016, p.2). To reap the full benefits of DNA barcoding methods, more scientists focused on mycology taxonomy are needed, to continue to collect and sequence specimens from underrepresented geographical regions, and to sequence the large archives of collected specimens currently held in herbariums and fungariums (Truong et al., 2017). This work will be critical for finding “a common approach linking sequences to an effective, scalable method of naming” (Yahr et al, 2016). 

The Importance of Traditional Naming Systems

New technologies and advanced understanding means that the scientific names and labels for fungi will likely continue to change, but other naming systems remain constant. Communities and cultures across the world have their own names for fungal species that hold particular importance to local populations.

Although traditional names vary across the world, the preservation of such naming systems is also important for the understanding and conservation of fungal species. Local naming and language systems are living records of important traditions and local knowledge of fungi species and their uses (Plotkin, 1994). Known traditional names are also important for communities to maintain a connection to local species and for motivating community-based and global conservation movements (Yahr et al, 2016, p. 5). As scientists delve into the complexities of fungi lineages and develop new systems of naming, it is important they maintain a connection between new understandings and established knowledge cultures to keep conservation groups and policy-makers engaged with the need to protect all fungi, regardless of what we call them! 


Berihuete-Azorín, M., Girbal, J., Piqué, R., Palomo, A., & Terradas, X. (2018). Punk’s not dead. Fungi for tinder at the Neolithic site of La Draga (NE Iberia). PLoS One, 13(4), e0195846.

Lerner, R. (1996, June). How Plants Are Named [Purdue University]. Yard and Garden News: Summer Gardening Stories. https://www.purdue.edu/hla/sites/yardandgarden/how-plants-are-named/#:~:text=Known%20as%20the%20%E2%80%9CInternational%20Code,is%20unique%20to%20each%20species.

Money, N. P. (2013). Against the naming of fungi. Fungal Biology, 117(7–8), 463–465. https://doi.org/10.1016/j.funbio.2013.05.007

Plotkin, M. J. (1994). Tales of a Shaman's Apprentice: An Ethnobotanist Searches for New Medicines in the Rain Forest. Penguin.

Sample, I. (2022, November 2). Magic mushrooms’ psilocybin can alleviate severe depression when used with therapy. The Guardian, Online. https://www.theguardian.com/science/2022/nov/02/magic-mushrooms-psilocybin-alleviate-severe-depression-alongside-therapy

Truong, C., Mujic, A. B., Healy, R., Kuhar, F., Furci, G., Torres, D., ... & Smith, M. E. (2017). How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity. New Phytologist, 214(3), 913-919.

Wallheimer, B. (2021, January 6). Naming rules tie hands of fungal researchers. Purdue scientist leads call for change. Purdue University. https://ag.purdue.edu/stories/naming-rules-tie-hands-of-fungal-researchers-purdue-scientist-leads-call-for-change/

Yahr, R., Schoch, C. L., & Dentinger, B. T. M. (2016). Scaling up discovery of hidden diversity in fungi: Impacts of barcoding approaches. Philosophical Transactions of the Royal Society B: Biological Sciences, 371(1702), 20150336. https://doi.org/10.1098/rstb.2015.0336