Scientific Research plus a Little Secret Sauce

One of my favorite TV series was the original crime drama, LAW & ORDER. It had a dramatic musical introduction followed by a very consistent, 2-part story format. The first half was set around seeing the crime committed and the detectives working to identify and apprehend the suspect. The second half was about the prosecution of that suspect and the jury’s verdict. Despite the trial process being mostly well presented, the verdict sometimes left me with mixed feelings.

So, where am I going with this? Like LAW & ORDER, mushroom identification is also broken up into a 2-part format .The first part is Taxonomy, which is scientifically classifying a mushroom. The second part is Nomenclature, assigning an appropriate name to a mushroom. This two part format, most likely modeled after LAW & ORDER, makes perfect sense. Being an inquisitive kind of guy, I’ve been researching the methodology and subsequent criteria used to analyze mushroom species and then naming or renaming them when needed. During my working life, I dealt with many mathematically based classification programs designed to try and match unknown objects against already identified objects. The outcome from testing an unknown object was presented in percent of correlation to its closest match. Essentially, the likelihood of the unknown object being something you previously identified or being something totally new. The percent of correlation needed to call it a positive match to an already known object was totally dependent on the application. If correct identity was critical, a 99% or 100% correlation threshold may be required; otherwise, something less might be sufficient.

My naïveté led me to believe that all this mushroom species classification and reclassification was based on an equally well formulated, systematic, and consistent process. PT Barnum has been credited with originating the phrase “there is a sucker born every minute”. In my case, I thought it would be easy to just Google something like “DNA criteria used to classify fungal species”. My first attempt produced many results and the first scientific paper I read, Towards Genomic Criteria for Delineating Fungal Species, contained the following in its Abstract statement:“The discussion of fungal species delineation has yet to reach a consensus, despite the advancements in technology, which helped modernize traditional approaches. In particular, the phylogenetic species concept was one of the tools that has been used with considerable success across the fungal kingdom. The fast rise of fungal genomics provides an unprecedented opportunity to expand measuring the relatedness of fungal strains to the level of whole genomes. However, the use of genomic information in taxonomy has only just begun, and few methodological guidelines have been suggested so far.”

What’s important here is “yet to reach a consensus” and the last sentence stating that few guidelines have been suggested so far. OK, one might think that these researchers just haven’t gotten their “stuff” together while other researchers already have.  Therefore, I offer up the Abstract section from a different scientific paper; Fungal Species Concepts in the Genomics Era.

“The 140,000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and (or) molecular features. Incongruence’s are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic (randomly determined) process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology.”

Once again, as stated above, “a consensus has not been reached”. I have read similar scientific papers to the point of ad nauseam, yet I continued to hunt for that holy grail of papers just stating the standardized criteria used to categorize mushroom species. Whether it’s DNA sequencing, mating rituals, random mutation, spore shape, aroma, or whatever else is deemed important; just put together a standardized method we can all understand.

Out of frustration and computer screen eye fatigue I started emailing various mycologist with the following direct question. “After looking at countless scientific papers on DNA sequencing and subsequent renaming, I have not found a single one that specifies exactly what criteria was used to determine the percent of DNA difference necessary to split off and subsequently rename species from a genus. What is the percent of DNA difference between Hydnum olympicum and Hydnum subolympicum? Is it 98%, 95% or some other percent. From all the papers I have read, the one constant seems to be that there are no well-established criteria for determining what percent of fungal correlation needs to be or not be. I have emailed and spoken to mycologists and taxonomists who are also perplexed by this question. Yet, splitting up existing genera and renaming marches on. “

I started with Dr. Scott A. Redhead, the current chair of the Nomenclature Committee for Fungi. While he directed me toward a very interesting article on yeast to read, in his email he stated “You would think that there might be a simple answer, but there is not. Taxonomy is still part art and part science. Applying names, be they generic names or species names, should convey information and a taxonomist has to make a decision on whether the grouping of samples makes sense in some way. You mention generic changes, which is yet another somewhat subjective level. I admit that it has become such a fast moving science that it is confusing, even for those in the field.”

I also emailed mycologist Alan Rockefeller and received this response from him. “There is no exact number of differences that are needed to split a species, nor should there be. Species concepts should be based on a combination of macroscopic, microscopic, chemical, environmental and DNA differences. The more differences there are, the more likely that people will use a new name that is proposed. With less differences it is more likely that people will not use a new name. If you are making a bioinformatics pipeline that processes millions of sequences to see how many species are present, a reasonable cutoff would be 99% in the ITS (Internal Transcribed Spacer ) gene. That will lump some closely related species that are definitely different, and count twice some species that are the same but have variable ITS sequences, but would get the majority of them right.

Mr. Rockefeller also added this statement, “Maybe research papers have to gloss over this subject because they have to pretend to present solid findings, but few things in nature are simple, solid or clear-cut. Especially regarding evolution and taxonomy.”

Well, for all my Googling and reading scientific papers on this topic, the one thing that is clear-cut is everyone seems to agree that there are no currently agreed upon standards for naming or renaming mushrooms. This really doesn’t give me that warm fuzzy feeling as it hasn’t seemed to stop any of the naming and renaming currently going on. At least I can now stop trying to find something that apparently just can’t be found. Although, all this uncertainty did inspire me to write this little rap ditty.

I’d like to give a big thank you to both Dr. Scott A. Redhead and Alan Rockefeller for their expedient, well framed responses to my email. I understand that scientific advancements and consensus building takes time. According to Wikipedia, during the 4th century BC, Greek philosophers believed the Earth was the center of the universe. That concept was updated 20 centuries later during the 16th century by mathematician and astronomer Nicolaus Copernicus who theorized that the sun was actually the center of the universe. OK, so two wrongs don’t make a right but Nicolaus did move the bar a little closer to the truth. Eventually, a systematic classification method that uses DNA as well as other relevant data will be adopted. Hopefully, it won’t take 20 centuries to accomplish it.

That said, there is one more thing to ponder over. Who is this scientific system of mushroom classification being designed for? The amateur uses morphological characteristics to ID a mushroom while current naming criteria is focused on a more rigorous scientifically based approach. As exact species identification using visual means becomes increasingly complex due to more recent stringent naming conventions, the average mushroom enthusiast will be relegated to using more familiar colloquial names. This divergence in name usage will isolate the scientific process as being more of an esoteric endeavor by scientist and only for scientists with little value to the general public. Science will move in one direction while the rest of us will simply use our older mushroom ID books and stick with how we did it before “modern” methods added a new layer of complexity to cataloging species. Just something to think about.

In the meantime, get out into the woods and enjoy all the splendor nature has to offer us; and keep uploading those finds to iNaturalist.

Ron

P.S. The three mushrooms pictured above are from the CMS Macrofungi of Lane County Project and are among the nearly 1,000 specimens that have been DNA sequenced.