Does DNA barcoding create a "Brave New World" in mycology?

[AdamWargon]

NYT Mushroom article mentions iNat

teellbee

https://www.nytimes.com/2024/06/11/science/mushroom-hunters-dna.html?unlocked_article_code=1.zE0.KL0J.rBEUpiMMBWZc&smid=nytcore-ios-share&referringSource=articleShare

On 2024 Jun 11, under the NYT article shared by @teellbee, Debbie Viess from Oakland, California wrote this comment:

@Debbie Viess

I have been a serious mushroom hunter and mycologist here in California for more than 30 years. SOMA camp is probably our biggest California mushroom event, and it sends hundreds of people into the woods.

The best, most diverse place to hunt near SOMA camp, Salt Point State Park, is currently over-run with mushroom hunters, and paid mushroom forays, all year long, and it absolutely has had a deleterious effect on the environment.

DNA is being treated as the end all/be all in amateur field mycology right now, and fungal species database libraries are being developed, most of which merely contain a snippet of fungal DNA. Many of these species are so called cryptics of well known fungi. In other words, there is a bit of difference in their DNA from an already known species. But putting specifics onto fungi through DNA only is an iffy practise.

In fact, and as we first detailed at the original meeting of the Mycoflora project at Yale, we need carefully described collections, made by trained individuals, that look at and document the macro qualities while that mushroom is still fresh, and the micro qualities as well, after the fact. DNA can be sampled at any time thereafter. DNA sequencing is quick and relatively easy these days, and so is getting used almost exclusively. Sure, there is usually also photo documentation, but a photo is never enough.

Interest in mycology is increasing, and that’s a good thing. Now let’s examine how we go about creating a database for the ages.

[tiwane]

“Brave new world” can be interpreted in many ways - can you specify what you mean by it?

[AdamWargon]

Hi Tony!

@tiwane

“Brave new world” can be interpreted in many ways -— can you specify what you mean by it?

1: To answer your direct question, I actually looked up the definition of “Brave New World” before I posted this, just to make sure that I was using the term correctly:

“A world of radically transformed existence, especially one in which technological progress has both positive and negative results”

(The phrase is most often known from a book by Aldous Huxley, written nearly 100 years ago)

I think the quote by Debbie Viess speaks to the positive aspects of DNA barcoding (rapid ID of new species, increasing interest in mycology, etc.) as well as some of the negative aspects (issues with the “discovery” of new species, and issues with databases).

2: I think you might have a second, implied question in your question, which is, “Why did you create this post?”

I created this post in order to learn. I have zero experience with DNA barcoding, so I have no opinion on it. But many members of this forum DO have experience with it, and they also have strong opinions about the creation of new species, etc.

I am hoping to stimulate a discussion where I might learn something, and maybe someone else might learn, too!

[lothlin]

I basicallg 100% agree with Debbie. Sequencing is absolutely a useful tool but still, its just a tool, and all other steps need to be taken to describe species.

But I also don’t really know if anyone involved with sequencing would disagree with her.

EDIT: I want to add that while not all barcoding is going to be used for new descriptions, there are other purposes for it. For example, barcoding can be used to identify the true identities of old type specimans with less than clear descriptions (for example, see the recent sequencing of the Boletus subvelutipes type specimen.) Or, it can be used to figure out the real amount of macromorphological variation a species can have. Or how it looks as it ages. Or help delineate actual species ranges. etc etc. There’s multiple use cases, but to make use of those cases, there needs to be data to compare to, which means even a collection that may not be worthy of new description can still lend good data.

[jasonhernandez74]

@Debbie Viess

Many of these species are so-called cryptics of well-known fungi. In other words, there is a bit of difference in their DNA from an already known species.

This is the kind of skeptical language I would use. In another current thread, I recently used the term “genets” in referring to the mushroom splits between Europe and North America. I used that word advisedly, in the sense that it is used in discussing clonal plants (genets vs. ramets).

@lothlin

There are multiple use cases, but to make use of those cases, there needs to be data to compare to, which means even a collection that may not be worthy of a new description can still lend good data.

This makes more sense to me. I would add, though, that in addition to the macromorphological variation you referred to, there are species with considerable genetic variation. This is a tool used in conservation work – preventing inbreeding depression in an isolated population by bringing in genetically different individuals. We already recognize a fungal mycelial mat as the largest individual organism in the world:

The largest known organism of this species covers more than 3.4 square miles (8.8 km 2) in Oregon’s Malheur National Forest and is estimated to be 2,500 years old

Now, it would be interesting to compare the genetic makeup of this individual with that of other mycelial colonies of the same species. Will they be identical? If not, will they result in a revision of the genus, each genet a new taxon? To what extent has this kind of population-level genetic survey of fungi been conducted? This is the kind of study needed to tell us how genetically diverse a given species is, and I would be skeptical of splits that do not make comparisons with this kind of data.

[lothlin]

Would I expect it to have a 100% identical match if you did a full genome sequence of it and compared it to other full genome sequences of other Armillaria ostoyae specimans? Absolutely not because that’s not how genetics work.

Would I expect it to have an identical (or near identical) ITS barcode sequence to other Armilla ostoyae specimans? Yes. Because that’s how barcoding works.

I feel like I keep saying this, in every single thread this topic gets brought up - no one is splitting off a species simply because there’s a single BP difference in an ITS barcode. The temp codes we use in sequencing are merely useful for bioinformatics sorting and might end up leading to a new described species, but in most cases no new description is ever going to result for them. Will it sometimes? Sure. In most cases? Absolutely not.

[tiwane]

@AdamWargon

I think you might have a second, implied question in your question, which is, “Why did you create this post?”

Thanks. I think what I was getting at a bit more is to try and bring more specificity to the question, which you’ve done.

[regnierda]

Check out Kew’s 2023 State of the World’s Plants and Fungi, especially chapter 3 (“Finding out the fundamentals of fungi”). It kind of helped me to wrap my head around this same topic.

Key items from the chapter are:

• Over 90% of the world’s fungi have yet to be described.
• At the current rate that scientists are naming fungal species, it would take 750–1,000 years to fully describe the world’s fungi.
• Because conservation, we need to do that much, much faster than that.
• DNA sequencing is faster and so they propose taxonomists should be able to name and classify species of fungi based on DNA sequencing alone, so that we can describe them faster and thus effectively target conservation efforts to prevent as much species loss as possible.

I’m sold, even being a plant guy who loves that most plants can be distinguished via morphology. Given an option between “slow but more certain growth of the taxonomy that we don’t have to redo later, but centuries of conservation blind spots” and “fast growth of the taxonomy that maybe might need to be redone later, possibly (?), but we get a better idea of where conservation efforts need to be focused much, much sooner”, the latter seems like the better option to me.

Now, if a species description is its DNA “barcode”, that means I, a person without the ability to sequence DNA easily and with no real desire to in the near future, probably am not going to be able to ID many fungi any time soon – which I’ll admit, as a person who wants to know the identity and story of everything I see around me, is frustrating, but the fungi are more important than my need to identify them visually.

[apusaffinis]

+1. Someone in another thread linked that Sharkey 2021 paper, and a podcast discussing it. To not use this much more widely means to condemn the majority of species never being known.
Sharkey also proposes an iterative process - do barcoding first, do morphology on those that justify it.
Which seems pretty reasonable, and this is for Hymenoptera, which I assume are much less specious than Fungi.

An ignorant question - is horizontal gene transfer a big thing in Fungi? How do species descriptions work around that?

[lothlin]

Horizontal gene transfer is definitely a thing in fungi (it’s why you see Psilocybin producing fungi in genera that aren’t Psilocybe, AFAIK that’s due to horizontal gene transfer) but it’s definitely a subject that I need to look into more - I’m not sure how much it’s even been studied, TBH, outside of examples like the psilocybin gene.

‘barcoding-then-morphology’ on fungi that justify it is definitely the approach IMHO. There are so many interesting fungi that are clearly distinct and aren’t even that similar to anything in the database (like, 5%+ difference in the ITS sequence or more to anything in the database) when you barcode, there’s basically no need to even focus on things that are minor differences of a few bp that may only be justifiably a subspecies. IMHO

Though that doesn’t really apply to everything of course - reasonable variation in barcodes varies between groups

[AdamWargon]

@AdamWargon

Does DNA barcoding create a “Brave New World” in mycology?

@apusaffinis

Someone in another thread linked that Sharkey 2021 paper, and a podcast discussing it.

Thank you, @apusaffinis!

I listened to that podcast

(Michael Sharkey being interviewed by Art Woods and Cameron Ghalambor, on the Big Biology Podcast)

It was a great summary of all of the points that everyone mentioned in this thread!

Although I do feel like a Neanderthal now, with my cellphone taking PICTURES of organisms!

I also learned the phrase “dark taxon”:

"In mycology, a dark taxon or dark fungus is a taxon that does not appear to produce any observable morphological structure and that appears impossible to cultivate in laboratory conditions. Dark taxa are chiefly detected by DNA sequencing, and in particular environmental metabarcoding.

Dark taxa appear in every major fungal lineage, and they appear to make up a significant portion of extant fungal taxa. According to Wang et al. (2016) “the majority of the extant fungal diversity produces no distinguishing morphological structures that are visible or describable”, and according to Martin Ryberg, dark fungi “could well prove to be the dominant life style in the fungal kingdom”.

The naming of dark taxa is not supported by the ICN, as a type specimen requires direct observation."

[AdamWargon]

@AdamWargon

I feel like a Neanderthal now, with my cellphone taking PICTURES of organisms!

This is a concern about DATA. The primary purpose of iNaturalist is NOT data. It is ENGAGEMENT with nature!

And whether you’re:

• Walking around in nature with NO devices (just using your eyes, your ears, and your nose to be fully present)
• Taking photos of organisms with your cellphone or your DSLR
• Walking around with a DNA sequencer in your pocket, and ripping off insect legs so that you can sequence them

You are engaging with nature!

[jasonhernandez74]

@regnierda

they propose taxonomists should be able to name and classify species of fungi based on DNA sequencing alone, so that we can describe them faster and thus effectively target conservation efforts

One problem with that. As stated earlier,

@Debbie Viess

Many of these species are so-called cryptics of well-known fungi.

This means that effective conservation will require the ability to tell them apart. Otherwise, how will we know if we are dealing with a common, widespread, Least Concern species or its lookalike rare and threatened species? Who is going to provide the field ecologists and other conservation workers with portable barcoding apparatus?

[lothlin]

I think this specifically referring to environmental DNA (e-dna) barcoding; basically taking a soil or air sample and sequencing what pops out. If you look through genbank, you’ll see a lot of fungi sequences marked ‘uncultured fungus’; often when I follow these back to the attached paper, they’re papers less concerned with individual species ID and more concerned with, as an example, what type of pathogenic or mychorrhizal species may associate with a given type of plant. Or broad environmental sequences.

I still like having these in the system though, because it means if we do get a really novel sequence off of a mushroom, the e-dna can help confirm that it is a real unique sequence and not just weird contamination or an error in the sequencing process.

[regnierda]

That’s a very good question. Like with so much fungi-related, I think that’s something that needs to be figured out and may not end up conforming to all the rules we normally get to apply to plants and animals.

Even if we go about describing them slowly, if fungi prove to generally be difficult to distinguish without DNA (which it seems like it’s turning out that way, with many North American fungi previously thought to be the same as some described European species now being discovered with the help of DNA to be different), you still have to deal with this same question.

Being able to say “a rare species of fungi that most only really know from DNA has only ever been found in that forest over there” is probably better than saying “I have no idea what’s there” (which will likely often lead to the same result as saying “nothing special is there”).

How do you know the fungus is there in the first place? Fungi folk getting out there and sequencing everything and establishing distributions. You can’t effectively describe and monitor the thing’s distribution though if you don’t have a name to call it (or if it’s already ceased to exist).