F Rosa Rubicondior: Creationism in Crisis - Evolution of Porcini Fungus

Thursday 7 March 2024

Creationism in Crisis - Evolution of Porcini Fungus

A tale of terroir: Porcinis evolved to the local environment – @theU
Structure of Fungi
This illustration is a little misleading because mycelia are often much larger than any of their mushrooms that appear on the surface of the soil or tree stumps. Fungi can grow up to a half a mile of the thread-like hyphae a day. In fact, the largest known organism on the planet is the Humongous Fungus (Armillaria ostoyae) in The Malheur National Forest, Oregon, measuring 2,385 acres (3.72 square miles) in area. It is estimated to be between 1900 and 8650 years old.
Photo credit: FoodPrint.org
The edible porcine fungus (Boletus edulis) also known as the boletus or penny bun is highly prized culinary delicacy throughout much of Europe. However, there is something strange about it evolution, especially in North America, according to a new report in the journal New Phytologist.

Creationists should note here that the scientists who produced the report see this 'problem' entirely within the Theory of Evolution by Natural Selection (TOE). The strangeness is not a problem for the theory but an example of how a fundamental principle of the theory - environmental selection - operates in North America.

The 'problem' is that while Boletus edulis exists in North America as a number of different varieties and genetically distinct populations, probably caused not so much by geographical isolation as environmental adaptation, albeit with regular ingress from surrounding populations, In Eurasia, a single genetic lineage dominates from Spain to Georgia to Scandinavia, so the interesting question is why does is the species genetically continuous in Eurasia but fragmented in North America; what is the difference between the two landmasses that causes this difference.

The Eurasian and North American populations are believed to have become separated during a period of climatic change and the onset of glaciation, 1.62–2.66 years ago. Attempts to segregate populations of Boletus edulis into distinct species based on phenotype have foundered on the genetic evidence, illustrating how small genetic differences can give large phenotypic differences and how a species in the process of speciating passes through a stage at which the diverging populations have not diverged sufficiently to qualify as new taxons because the practice of taxonomy tries to fit a continuous process into a series of distinct events.

The 'problem' is the subject of a free access paper in the journal New Phytologist by Keaton Tremble and Bryn T. M. Dentinger from Utah University, Utah, USA. together with J. I. Hoffman from Bielefeld University, Germany, and was described in a University of Utah press release:

The Dentinger Lab at the Natural History Museum of Utah has published a provocative new paper in the journal New Phytologist that describes their work with the much-beloved mushroom, Boletus edulis, better known by gastronomers worldwide as the porcini. In the paper, Keaton Tremble and Bryn Dentinger present a first-of-its-kind genetic survey of porcini mushrooms across the Northern Hemisphere. By evaluating the genetic code of these samples from across the globe, they learned that these delicious fungi evolved in surprising ways—contrary to the expectations of many who might think that geographic isolation would be the primary driver for species diversity. In fact, there are regions in the world where porcini maintain their genetic distinctiveness in local ecological niches, even if they are not isolated geographically from other genetic lineages.

The French word terroir, made famous by viticulturists, immediately comes to mind. Terroir describes all of the local factors such as soil types, amount of sunshine, degree of slope, microclimate, soil microorganisms, etc., that make each plot of land yield distinctive wines. It is a celebration of the local ecology and its impact on the vines, grapes and finished product. Tremble and Dentinger’s new study offers mushroom hunters tantalizing data to claim that the porcinis in their secret forest patch express the qualities of their terroir in the same way as the best wines in the world.

But this isn’t the point of the study. With the advent of genetic sequencing, most mycology genetic studies have focused on describing the unique characteristics of fungi in a small geographic area. Tremble and Dentinger wanted to do something different. Rather than just comparing a group of mushrooms from Colorado to a group in California in order to call them different species, they wanted to better understand the global trends in how the genetic code was preserved or changed in porcini. “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 Scandinavia.”

Evolutionary biologists typically believe that there is one evolutionary strategy that governs the speciation process for a particular organism, but Tremble and Dentinger have shown that porcini actually exhibit multiple, divergent strategies. In fact, this is the first genetic study of any organism to show such a result at a global scale.

A related, significant result is a refutation of the traditional notion that isolation is the main way that species develop their uniqueness. 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, mechanism by which new species arise (Futuyma, 2013).”

More than identifying mushrooms

It’s an exciting time to be a mycologist. Not only is the fungal kingdom barely explored and described, but DNA sequencing technology has introduced a seismic shift in how mycologists classify fungi. For millennia, humans have identified mushrooms that are good to eat from ones that are poisonous based on how they looked or their phenotype. But phenotypes can be deceiving – consider 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 a mycelium (see the illustration below, “The Basics of Fungi”). 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 edulis spreads 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 doctoral 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 edulis mycelia 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 six 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.”

So, find a mushroom hunter and get on his or her good side in order to find the porcini best adapted to your palate.
Technical detail and background to the research is given in the trio's free access paper in New Phytologist:
  • In the hyperdiverse fungi, the process of speciation is virtually unknown, including for the > 20 000 species of ectomycorrhizal mutualists. To understand this process, we investigated patterns of genome-wide differentiation in the ectomycorrhizal porcini mushroom, Boletus edulis, a globally distributed species complex with broad ecological amplitude.
  • By whole-genome sequencing 160 individuals from across the Northern Hemisphere, we genotyped 792 923 single nucleotide polymorphisms to characterize patterns of genome-wide differentiation and to identify the adaptive processes shaping global population structure.
  • We show that B. edulis exhibits contrasting patterns of genomic divergence between continents, with multiple lineages present across North America, while a single lineage dominates Europe. These geographical lineages are inferred to have diverged 1.62–2.66 million years ago, during a period of climatic upheaval and the onset of glaciation in the Pliocene–Pleistocene boundary. High levels of genomic differentiation were observed among lineages despite evidence of substantial and ongoing introgression. Genome scans, demographic inference, and ecological niche models suggest that genomic differentiation is maintained by environmental adaptation, not physical isolation.
  • Our study uncovers striking patterns of genome-wide differentiation on a global scale and emphasizes the importance of local adaptation and ecologically mediated divergence, rather than prezygotic barriers such as allopatry or genomic incompatibility, in fungal population differentiation.


Understanding the complex evolutionary pathways by which populations diverge and new species form has long been a goal of evolutionary biology (Fisher, 1930; Theodosius, 1982). Beyond gaining fundamental knowledge about the mechanisms that generate and maintain diversity, understanding the evolutionary history of genotypes and phenotypes allows us to predict how these characteristics will be impacted by environmental change. However, this understanding is challenging to achieve because the evolutionary processes that drive genetic divergence, such as demography, introgression, and adaptation, rarely act in isolation (Coyne et al., 2004). Moreover, the dynamic interaction of these processes can produce differing signatures of divergence depending on the geographic and temporal scale of the study (Bierne et al., 2013; Martin et al., 2013.1; Peñalba et al., 2019). To overcome the limitations of scale, and disentangle the complex evolutionary web weaved by the speciation process, research must be conducted within a global context.

Tractable systems that exhibit dynamic properties for which hypotheses can be generated and tested are essential to studying processes that give rise to genetic divergence in wild organisms. Species that are common, widely distributed geographically and ecologically, and highly variable are ideal targets for determining the genetic basis of divergence (Hoban et al., 2016). For example, systems such as the monkey flowers (Mimulus spp.) (Ferris et al., 2017; Puzey et al., 2017.1; Vallejo-Marín et al., 2021), black cottonwood (Populus trichocarpa) (Evans et al., 2014; Geraldes et al., 2014.1; McKown et al., 2014.2), and three-spine stickleback (Gasterosteus aculeatus) (Hohenlohe et al., 2010; Feulner et al., 2015; Marques et al., 2018) have been used to investigate how the complex interaction of demography, introgression, and local adaptation gives rise to genetic variation and population differentiation during speciation. However, none of these systems exhibit a truly global distribution or continuous ecological breadth, limiting our ability to investigate the interaction of evolutionary processes unconstrained by geography or ecology. Moreover, these examples give insight into processes in only a few plants and animals, limiting the generality of the observations. The third major eukaryotic lineage, Fungi, remains critically understudied (Coyne et al., 2004; Giraud et al., 2008; Gladieux et al., 2014.3) despite its ecological importance, enormous diversity, and more tractable genomes. The globally distributed prized edible ‘porcini’ mushroom, Boletus edulis, fulfills the need to study processes that both give rise to genome-wide divergence at a global scale and include organisms other than plants and animals.

Boletus edulis Bull. (‘porcini’) is a well-known ectomycorrhizal species complex that is found in nearly all temperate ecosystems across the northern hemisphere (Smith, 2005). Due to extensive phenotypic variation (Fig. 1), the taxonomy of B. edulis is a matter of some controversy with many alternative classifications (Arora, 2008.1; Dentinger et al., 2010.1; Arora & Frank, 2014.4). Current molecular evidence is equally ambiguous, indicating that this complex group may be in the early stages of speciation (Coyne et al., 2004; Beugelsdijk et al., 2008.2; Dentinger et al., 2010.1; Tremble et al., 2020). Taken together, the combination of morphological variation, enormous ecological amplitude, holarctic distribution, and small genome (c. 50 Mbp) makes B. edulis an ideal natural system to investigate the roles of demography, introgression, adaptation, and isolation in the speciation process at a global scale. Here, we utilize population genomics, ecological niche, and demographic modeling to investigate the primary forces driving lineage divergence within B. edulis and to identify loci under putative selection within a global and historical context.
Examples of phenotypic variation across the global distribution of Boletus edulis. Numerous attempts have been made to segregate groups of B. edulis into new species based on this phenotypic variation, yet these attempts have not been corroborated by genetic evidence.
Creationists wishing to maintain the childish delusion that the Theory of Evolution is about to be replaced in mainstream biology by their childish superstition involving magic and a supernatural magician creating things from nothing and making physics and chemistry do things they couldn't do on their own, might like to ignore how the scientists have no doubt at all that they are talking about an evolutionary process; the question is over the mechanism not the fact of evolution, with a side issue about whether evolution has progressed to the point that the different 'lineages' of B. Edulis between Eurasia and North America and within North America itself, have diverged enough to be regarded as distinct species.


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