In the journal New Phytologist, the Dentinger Lab at the Natural History Museum of Utah has released a provocative new paper that details their work with the adored mushroom, Boletus edulis, most commonly known as the porcini to foodies throughout the world.
In the paper, Keaton Tremble and Bryn Dentinger, Ph.D., present a first-of-its-kind genetic survey of porcini mushrooms across the Northern Hemisphere. They discovered that these tasty fungi evolved in unexpected ways by analyzing the genetic codes of these samples from around the world, defying the beliefs of many who might have assumed that geographic isolation would be the main cause of species diversity.
In fact, despite not being geographically isolated from other genetic lineages, there are parts of the world where porcini maintain their genetic distinctiveness in local ecological niches.
The French word terroir, made famous by viticulturalists, immediately comes to mind. Terroir is the term used to define the regional elements, such as soil types, sunlight exposure, slope, microclimate, soil microorganisms, etc., that contribute to the distinctiveness of each vineyard’s wines. It honors the local ecology and how the plants, grapes, and ultimate product are affected by it.
The new research by Tremble and Dentinger provides mushroom hunters with enticing evidence to support their assertion that the porcinis in their private forest patch communicate the terroir in the same manner as the world’s top wines.
But this isn’t the point of the study. Since the invention of DNA sequencing, the majority of mycology genetic studies have concentrated on outlining the distinctive traits of fungi in a restricted geographic region. Dentinger and Tremble decided to try something new. They intended to better understand the global trends in how the genetic code was preserved or modified in porcini, rather than just comparing a group of mushrooms from Colorado to a group in California in order to declare them separate species.
“Our study is important because it goes beyond overly simplistic sampling method used in the past,” states Dentinger.
What they found is that porcini have evolved in different, but clearly recognizable ways across the globe. “In North America, there is a strong stratification of separate genetic populations in local areas, despite the fact that they aren’t reproductively isolated,” explains Tremble. “Yet in Europe, there is one lineage that dominates from Spain to Georgia to Scandanavia.”
Tremble and Dentinger have demonstrated that porcini actually exhibit several, divergent evolutionary strategies, contrary to the common belief of evolutionary biologists that a particular organism’s speciation process is governed by a single evolutionary strategy. In fact, this is the first genetic investigation of any kind to produce a result of this magnitude at the global level.
This paper shows that you don’t need isolation for genetic divergence. The force of ecological adaptation is so strong in Boletus edulis that even though you can disperse spores basically anywhere, there is strong selection to adapt to specific environments.
Keaton Tremble
Refutation of the conventional wisdom that isolation is the primary mechanism by which species establish their distinctiveness is a related and important result. As the Encyclopedia of Ecology (Second Edition 2019) proudly states: “all evolutionary biologists agree that geographic isolation is a common, if not the most common, the mechanism by which new species arise (Futuyma, 2013).”
More than identifying mushrooms
It’s an exciting time to be a mycologist. The classification of fungi has undergone a seismic change as a result of DNA sequencing technology, despite the fact that the fungal kingdom has hardly been studied or characterized. Humans have distinguished between edible and dangerous mushrooms based on how they appeared, or their phenotype, for millennia.
But phenotypes can be deceiving considering a brother and sister who have different hair colors, different nose shapes, etc. They are still more genetically similar to each other than to other people in the population. Thus, genetic similarities are considered the true marker of different species, bucking the trend of mushroom identification that stretches back to the beginning of humanity.
On top of this, let’s remember that mushrooms are just the reproductive structure of the main organism, called mycelium. Like icebergs, mycelia only show us the tip of themselves, while the massive fungal body lives underground, bound up with the roots of trees.
Boletus edulisspreads geographically thanks to the tiny spores released from the porcini mushrooms, borne on the wind, mammals, and even flies. Thus, biologists are tempted to believe that in whatever geographic area where spores can fly, a species will be defined by the genetic mixing within this geographic space.
Tremble and Dentinger’s study soundly refutes this assumption.
In North America, different genetic lineages exist side-by-side, and despite genetic evidence of intermixing, local ecological factors played a bigger role in maintaining the distinction of these lineages. “Utah happens to be one of the areas where two distinct lineages live,” notes Dentinger. What these lineages show is that the local ecology is a stronger factor in maintaining their genetic distinctiveness than genetic flow from other lineages.
“This paper shows that you don’t need isolation for genetic divergence,” Tremble asserts. “The force of ecological adaptation is so strong in Boletus edulis that even though you can disperse spores basically anywhere, there is strong selection to adapt to specific environments.”
The marvels of the dried porcini
The secret to their study resides deep in the heart of natural history museums: collections of mushrooms. Tremble is a Ph.D. candidate in the School of Biological Sciences, defending his thesis in spring 2023 to receive his degree in Evolutionary Biology. He made a fortuitous choice when working with Dentinger as his advisor as the Curator of Mycology at NHMU, Dentinger has established NHMU’s Genomics Lab to be able to analyze DNA quickly and efficiently.
More importantly for this study, Dentinger’s professional contacts at natural history museums around the world helped Tremble access the 160 samples that would have been near impossible to collect otherwise.
“You have to rely on opportunistic encounters in nature to collect a living sample,” Dentinger explains. “This is fundamentally different from working with plants, which are there in every season, and animals, which you can bait.”
Thus, it would have taken an incredible amount of logistics, timing, and luck to find, correctly identify, and ship 160 different samples across the Northern Hemisphere back to the lab at NHMU.
Instead, “our study was all possible thanks to fungaria,” Dentinger states, referring to the name for fungus collections in museums. They plumbed the depths of NHMU’s fungarium and reached out to collaborators around the globe.
“Without the accumulated field work by 80 different people, this would not have been possible,” Tremble notes. All of the samples were dried porcini mushrooms, stable and ready for Tremble to extract their DNA.
Since Boletus edulismycelia have a surprisingly long lifespan (estimated to be up to 45 years), they used samples only dating back to 1950 to make sure that the study kept to just a few generations.
Tremble used sophisticated software to run statistical analyses on these samples. He genotyped 792,923 SNPs (pronounced “snips,” short for single nucleotide polymorphisms), which are the individual ways in which the 160 porcini genomes differed from one another. In order to classify major lineages, he filtered out the SNPs that were only present in one sample (which would be considered just a “family unit” or individual variant) so that he could instead observe only major differences between genomes. In the end, Tremble identified 6 major lineages.
Feeding his data into mathematical models, Tremble uncovered a complex web of genomic mixing, where lineages remained distinct despite evidence that other lineages had mixed with them. Their modeling and geographical sample data showed that this ability to remain distinct was due to environmental adaptation, not physical isolation.
Lineages or species?
Tremble and Dentinger take a decidedly agnostic approach to the question of whether they should be identifying these 6 distinct lineages as “species.” They abstain from doing so in their paper because they want to focus on the genetic data and the larger questions related to strategies in evolutionary biology. Plus, that species discussion is one vexed conversation.
“There is no formal process for defining a species,” Tremble notes, “it’s an ongoing debate. We didn’t want to call them species or subspecies because it automatically implies that they are separately evolving groups, which they definitely aren’t.” They decided to call them lineages because this term is genetically resolvable, that is, lineages can be quantifiably distinguished from one another using statistical genetic approaches.
But that doesn’t mean they don’t want to tackle the taxonomy. “This is going to be a forthcoming article in a different journal,” Dentinger says.
The world of fungi never experienced the Victorian era explosion of identifying and naming species that happened with animals and plants. With only an estimated 5% of fungi diversity being identified, naming and taxonomy must happen, if only to help mycologists speak about their subject.
However the species-subspecies taxonomy for Boletus edulis shakes out, Dentinger assures us of one thing: “Terroir is more important than people thought.”
