Chapter 3: Fungal Systematics

Welcome to Last Minute Lecture.

This free chapter overview is designed to help students review and understand key concepts.

These summaries supplement, not replace the original textbook and may not be redistributed or resold.

For complete coverage, always consult the official text.

Imagine a hidden kingdom right beneath our feet.

Sometimes even, you know, right within us.

It's true scope, it's ancient history.

We're really only just starting to get a handle on it.

Today we're embarking on a deep dive into the fascinating world of fungi.

We're gonna unravel some truly mind -bending stuff about how we classify them, how they evolved, and even the surprisingly complex rules for just giving them names.

It is an incredibly exciting time for mycology, the study of fungi.

For generations,

our picture of how fungi fit into, you know, the bigger tree of life was based on assumptions that, well, frankly, didn't quite hold up.

But new tools, new discoveries, they've completely rewritten the playbook and they're revealing a kingdom that's far more diverse

and way older than we ever really imagined.

Rewriting the rule book, I like that.

Our mission today, based on the material you shared from an introductory mycology chapter, is to unpack these complex ideas, walk you through the cutting edge science, and show you why understanding fungi is, well, probably more relevant to your world than you think.

So get ready to have your understanding of life on Earth maybe shift a little.

Let's get into it.

All right, so for the longest time, the way we tried to squeeze life into just a few big kingdoms,

it didn't quite work, did it?

Especially for fungi.

Turns out what we thought were fungi weren't always related in the way we assumed.

What happened there?

It's a really fundamental shift.

One of the biggest breakthroughs in fungal systematics, maybe in the last few decades, is realizing that many organisms we traditionally called fungi are actually polyphaletic.

Polyphaletic, okay, what does that mean in simple terms?

Think of it like drawing a family tree.

A polyphaletic group would be like grabbing a bunch of distant cousins from totally different branches and mistakenly labeling them all as siblings.

They just don't share one single recent common ancestor.

Wow, okay, so this isn't just tweaking a chart.

This means our whole biological map needed a serious redraw.

If the old idea of fungi was kind of a mishmash, how do we classify them now to really show their evolutionary story?

Right, so now we use what's called phylogenetic systematics.

The whole goal here is to create monophyletic groups.

Monophyletic.

Meaning each group contains a hypothetical ancestor and all of its descendants, no exceptions.

It's like building a true unmixed family tree.

Every branch shows its complete lineage, basically.

Gives us a much more accurate sort of hierarchical classification.

Gotcha.

So under this modern way of thinking, the true kingdom fungi is a solid monophyletic group.

It's basically made up of four main phyla.

Chytridiomycota, zygomycota, ascomycota, and basidiomycota.

When we talk about actual fungi today, these are the guys we're usually talking about.

Okay, the core four.

But you mentioned some organisms used to be called fungi, so where do they end up on this new map?

Yeah, that's where it gets really interesting.

Organisms like certain water molds, you might know Umicota, and some related groups, they were once lumped in with true fungi.

Why was that?

Mostly because they look similar in some ways, especially how they reproduce sexually, but now we know they're fundamentally different.

Their cell structures, their biochemistry, their genetics, even the structure of their little whip -like tails, the flagella, it's all distinct.

So different toolkits entirely.

Exactly.

These groups are now under a whole separate kingdom called Strominopola, and interestingly, this kingdom also includes certain types of algae.

Huh, and what about slime molds?

Everyone's heard of slime molds.

Right, the famous slime molds, groups like Myxomycota,

or Dictiosteliomycota.

Despite that common name, they're not closely related to true fungi at all, or even to each other, really.

No kidding.

Nope, they're now considered distinct protist phyla.

Fascinating organisms, for sure, but definitely not fungi.

So it really tidied up the family tree then, and speaking of family trees, what's one of the most maybe unexpected relationship scientists have found for the true kingdom fungi?

Is there a surprising relative kind of hiding in plain sight?

There absolutely is.

This is one of the really mind -blowing things.

The kingdom fungi and the kingdom animalia, that's us, they actually form a monophyletic group together.

Wait, fungi and animals, seriously?

Seriously, they're considered sister groups.

That means they share a more recent common ancestor with each other than either one does with, say, plants or algae.

Wow, wow.

Well, the connection is thought to be through a toanoflagellate -like ancestor.

Imagine a tiny, single -celled aquatic organism, kind of like a microscopic filter feeder with a little collar and a tail.

It's wild to think our deep history might link back to something like that.

That is wild.

Yeah, and despite these deep evolutionary separations now, mycologists often still study all these diverse fungus -like organisms together just because they share some similar looks or ways of feeding or roles in the environment.

Practical reasons sometimes.

Okay, it's a lot of reclassification.

So how do scientists actually figure all this out, these incredibly complex evolutionary relationships?

What kind of information are they actually using to draw these elaborate family trees?

They use what we call characters.

Basically,

any attribute of an organism you can observe or measure and compare.

Well, for instance, if you're looking at fungal spores, a character might be spore ornamentation, and the states of that character could be smooth or ornamented.

Mycologists gather just a huge array of these characters from stuff you can see with your eye right down to the molecular level.

So what are some of the different types of characters?

It sounds like it goes way beyond just what they look like.

Oh, absolutely.

Historically, yeah, we started with gross morphological features, just the shape of a mushroom, its color, size of the cap, you know.

By the late 1800s, that was the main way.

Basic observation.

Right.

Then with better microscopes, compound microscopes, we move to anatomical characters.

Looking inside, like how the fungal threads, the hyphae are arranged in tissues, or the specific structure of the cells that make spores like ocei or basidia.

Okay, getting smaller.

Exactly.

Then, starting around the 1960s, things got really detailed with ultra -structural features.

This came from electron microscopy.

Suddenly, you could see incredible detail inside the cells.

Like what?

Like the internal structure of mitochondria, the tiny layers in a cell wall, how flagella are put together, even how the nucleus divide.

It was like opening up a whole new world of information, finding crucial new characters you just couldn't see before.

Amazing.

And beyond just how they're built, what about what they're actually made of?

Does their chemistry tell us anything?

It sure does.

That's where biochemical characters come in.

Things like unique fungal pigments or specific enzymes they produce.

You can compare these using lab techniques like chromatography or electrophoresis.

And this helps show relationships.

Definitely.

These biochemical clues have been really key in showing, for example, those deep similarities between true fungi and animals we just talked about, and also the clear differences between fungi and those stromanopila guys.

We also look at physiological processes like, how does this specific fungus break down wood?

Or what's its exact relationship with a plant if it's a pathogen?

Right, how they function.

And then the big one these days, DNA.

Yes, molecular techniques.

Looking at nucleic acid sequences like DNA has just unleashed a flood of new characters.

A lot of studies focus on genes for ribosomal RNA, or RNA genes.

Why those genes specifically?

Well, partly because cells have lots of copies of them, which makes them easier to work with.

And also different parts of these genes evolve at different rates.

Some parts change slowly.

Good for looking at really ancient splits.

Other parts change faster.

Better for comparing closer relatives.

Yeah, so while one gene tree gives us a good hypothesis about how the organisms evolved, looking at more genes helps test and strengthen that picture.

And of course, the invention of PCR polymerase chain reaction was huge.

It let scientists work with tiny, tiny amounts of DNA.

Okay, so you gather all this incredible data morphology, biochemistry, genetics,

loads of it.

How do you actually build the trees?

How do you turn all that data into a map of relationships?

Is it like a mass computer puzzle?

It is kind of like a massive computational puzzle.

There are several powerful methods computers use.

One type is distance or phonetic methods.

They basically build a tree based on overall similarity.

If two organisms share more character states, the computer groups them closer together.

Simple idea, complex calculation.

Okay, similarity equals closeness.

Right.

Then there's maximum parsimony.

This works on the idea that the simplest explanation is usually the best.

So the computer tries to find the tree that requires the fewest evolutionary changes, the fewest character state shifts to explain the data we see.

The most efficient path.

Exactly.

And finally, there's maximum likelihood.

This one's a bit more complex statistically.

It asks,

given a specific model of how DNA sequences change over time, which tree makes the sequences we actually observe the most probable?

Probability -based.

And, you know, systematists are always debating which method is best.

But really, the development of better tools lets us test the robustness of the trees.

That means how consistently do we get the same basic tree shape even if we use different data or different methods?

If it keeps showing up, we get more confident it's reflecting reality.

This all leads to a really fundamental question in biology, one that could be surprisingly tricky.

How do we even define a species anyway, especially with fungi and all these new ways of looking at them?

That is a fantastic question.

And yeah, it's as debated as the tree building methods.

Traditionally, the main way was the morphological species concept.

Basically, if it looks the same, it's the same species.

Most fungi historically got defined this way.

Just based on appearance.

Pretty much.

Then there's the biological species concept.

This defines a species as a group that can actually or potentially interbreed and produce fertile offspring, but they can't successfully breed with other groups.

Reproductive isolation is key.

Okay, that makes sense for sexual organisms.

It works great for some sexually reproducing fungi, like certain mushrooms or molds, yeah.

Neurospora setophila, a classic lab fungus, was defined this way.

But what about all the fungi that only reproduce asexually, you can't apply it to them.

Right, huge limitation.

Exactly.

So more recently, especially with all this genetic data, the phylogenetic species concept has become really common.

It defines a species based on shared ancestry, essentially.

A distinct branch on that evolutionary tree we've been talking about.

Smallest group that shares a common ancestor.

Based on the tree itself.

Right.

This has been super helpful for groups that look really similar but are genetically distinct, like a lot of yeasts.

DNA studies are crucial there, but what's funny is, what one mycologist might call a species using one concept, another might not using a different one.

So disagreement happens.

Oh yeah, but despite these differences in definition,

in practice, researchers usually understand what the other person means.

There's a functional understanding.

It's amazing how we can piece together their present day family tree like this, but to really get their impact, we need to look back, like way back.

How far into Earth's past can we actually trace fungi?

And what can fossils tell us about their ancient roles?

Yeah, looking back is crucial.

And for a long time, the fungal fossil record was seen as kind of poor,

sparse.

But new evidence, new ways of looking, that's really changing.

But first, just think about this.

Estimates suggest there might be 1 .5 million species of fungi worldwide.

Wow.

And we currently know maybe 5 % of them?

Fewer than 70 ,000 describe species.

Only 5 %?

Yeah.

It makes fungi one of the least known major groups of organisms out there, maybe second only to tiny worms called nematodes.

So if we know so little about them now, imagine trying to find traces of them from millions of years ago.

Yeah, I can imagine.

They're soft, they decay fast.

It must be like looking for ghosts in ancient mud, right?

That's a good way to put it.

And yeah, they don't leave obvious calling cards.

For ages, many reports of fungal fossils just turned out to be wrong, like one thing thought to be an ancient bracket fungus turned out it was the dental plate from a lungfish.

Whoops.

Exactly.

But we're getting smarter.

We look for them where they likely lived, often preserved with or in ancient plants.

Look for their associates.

Right.

The earliest hints of eukaryotes, the group fungi belong to go back maybe 1 .8, 1 .9 billion years ago.

That's based on chemical traces, molecular fossils called strains left behind from their cell membranes.

Billion.

Incredible.

Isn't it?

Then jump way forward to the Ordovician period, maybe 485 million years ago.

We start seeing signs of early land life, tiny arthropods, bits of plants.

And alongside that, one credible report of a marine fungus that we don't know exactly what it was.

Okay, starting to emerge.

But it gets really exciting in the late Silurian around 420 million years ago.

From Gotland in Sweden, we have the first really good reports of terrestrial filamentous fungi.

What do they look like?

Amazingly well -preserved.

You can see the hyphae, those fungal threads.

You can see structures that look like simple spore -producing cells called phyleids and spores with multiple internal walls, multi -septate spores.

This find might push back the origin of the Ascomycota, a huge ungle group, much earlier than we thought.

Challenges some older ideas.

And then came the Devonian, when land plants really took off, were fungi right there with them.

Absolutely.

The Devonian, starting about 419 million years ago, was a boom time for land plants.

And right alongside them, we see more and more evidence of fungi.

The famous rhynie chert in Scotland, it's like a snapshot of an ancient ecosystem.

It's full of fungi.

What kinds?

We see diverse chytridiomycota, tiny flask -shaped things that were clearly parasites on ancient algae found in the same rocks, living right inside the plant cells.

Wow.

And what about beneficial fungi?

Critically, yes.

The rhynie chert also gives us the earliest evidence for the Glomalis indagonalis group, part of the Zygomycota.

And this group includes the vesicular arbuscular mycorrhizal fungi, or VAM fungi.

VAM fungi.

Those are the ones that team up with plant roots, right?

Exactly.

These fossils, maybe 350 to 460 million years old, show this incredibly early symbiosis.

Some scientists think these VAM fungi were absolutely essential for the very first plants to even colonize land.

They helped plants get nutrients from the primitive soils, literally helped them get a root hold.

So fungi might've paved the way for land plants.

It's a strong possibility.

Then, fast forward again to the Carboniferous, around 359 million years ago.

Huge forests, lots of insects, and boom, evidence for much higher fungal diversity.

More spores, different types of spores.

We even see structures like clamp connections, a telltale sign of basidiomyces, the group mushrooms belong to.

Clamp connections.

Yeah, they're like little bypass bridges on the hyphae.

Finding those tells us basidiomyces were likely breaking down wood almost as soon as plants evolved woody trunks.

Key players in nutrient cycling right from the start.

Okay, so they were decomposers early on.

What about later, like when dinosaurs were around?

By the Triassic, about 252 million years ago, the evidence is even clearer.

We find the first fossilized arbust gills, these intricate tree -like structures that VAM fungi form inside plant root cells for nutrient exchange.

And more clamped hyphae link to wood decay.

From then on through the age of dinosaurs and into more recent times, the fossil fungi look remarkably like the groups we see today.

It shows a really long stable history for many lineages.

So it sounds like fungi have been deeply tangled up with plants and maybe animals too for just an immense amount of time.

Decomposers, partners, parasites.

Precisely.

We know fungal parasites were bugging those ancient rhiny plants.

We know fungi, plants, and arthropods have been interacting in complex ways for hundreds of millions of years.

It really underscores their foundational role in land ecosystems throughout Earth's history.

And it's not just about identifying old species.

Fossil fungal spores called palinomorphs can also act as indicator fossils.

They can help scientists reconstruct ancient climates like suggesting it was wet and temperate in Northern Canada during the Eocene Epoch.

Or even help track major events like megafauna extinctions by looking at shifts in the types of fungi found in sediments.

Fascinating.

Using fungi as climate proxies.

Okay, so with all these discoveries, the constant reclassification, finding fossils,

it must be chaos trying to keep all the names straight.

How do mycologists manage it?

There must be like a rule book for naming things.

Oh, there absolutely is.

It's serious business.

All the naming activities fall under the International Code of Botanical Nomenclature.

Yeah, botanical code fungi have historically been studied by botanists, so they fall under those rules.

Why have a code?

It's essential for order.

Imagine if everyone just named things however they wanted.

The code promotes clarity, consistency, making sure a name means the same thing to scientists anywhere in the world.

Okay, so what are some of the key rules that keep things reasonably organized?

One really crucial rule is typification.

When someone describes a new species, they have to designate a holotype.

This is usually a specific preserved specimen, maybe dried, maybe in fluid, maybe a microscope slide.

A reference specimen.

Exactly.

That holotype is the definitive anchor for the species name.

It creates a clear chain.

The specimen defines the species name, which anchors the genus name it belongs to, and so on up the hierarchy.

And the rules are adapting now.

You can sometimes use illustrations, photos, maybe even DNA sequences as types in some cases.

Okay, so you need a physical anchor.

What else?

Another critical rule is priority.

Let's say two different mycologists working independently describe the exact same fungus, but give it different names.

The rule is the name that was published first has priority.

That's generally the name that gets accepted as the correct one.

First come, first served.

Basically, yeah.

But this can lead to issues.

Take the common button mushroom you buy in the store.

Most people know it as agaricus besporus, but technically someone described it earlier under the name agaricus brunessens.

So should we call it brunessens?

Well, strict adherence would say yes.

But the code has flexibility now.

There's a process called conservation, where a well -known, widely used name, like agaricus besporus, can be officially protected to avoid causing massive confusion, especially for economically important species.

Stability matters too.

Ah, okay, that makes sense.

That probably explains why you sometimes see names change or why there are names listed after the species name, sometimes in parentheses.

Exactly, that's the rule for citation of authorities.

The name of the person or people who first validly described the species is cited right after the name.

For example, puff ballast giganticus smith.

Smith described it.

Now, if later someone decides that species actually belongs in a different genus, say super puff ballast, the original author's name goes in parentheses, followed by the name of the person who made the transfer.

So it might become super puff ballast giganticus smith jones.

Ah, like a little history tag.

Precisely.

It tells you Smith originally named it, but Jones moved it to super puff ballast, like a scientific paper trail for the name.

If you see obsidia carimbifer, cone, sac and a trotter, cone first described it, then saccardo and trotter moved it to obsidia.

Got it.

Are there any quirks in the rules specifically for fungi, different from plants maybe?

Yeah, a couple of important ones.

First, lichens, those cool composite organisms, a fungus living with an alga or cyanobacterium.

They are named and classified based only on the fungal partner.

The fungus gets the official Latin name.

Interesting, the fungus defines the lichen taxonomically.

Right, second deals with pleomorphic fungi.

These are fungi that can produce different types of spores or structures at different stages of their life, often an asexual stage and a sexual stage, and they might look totally different.

And so they have multiple forms.

Exactly, the code actually allows mycologists to give different names to these different forms or morphs, usually one name for the asexual state, the anamorph, and one for the sexual state, the telomorph.

But the official name for the entire fungus, the holomorph, is always the name given to the sexual state if it's known.

That name has priority.

So even if the asexual form is found way more often, the sexual name is the real one for the whole organism.

Okay, so the sexual stage name trumps the others.

Yep, and finally, just a bit of trivia, the official starting date for naming fungi, set in 1981, is May 1st, 1753.

That's when Linnaeus published his big work, Species Plantarum, which is the starting point for plant names too.

These rules are complex, they evolve, and believe me, they lead to some pretty heated debates at botanical congresses.

People take naming seriously.

So yeah, we've covered a lot, this journey through fungal classification, seeing how tools like DNA are just revolutionizing our understanding, digging into that ancient fossil record, and even wading through the sometimes tricky rules for naming them.

It really feels like even with all these amazing advances, mycology is still, as the chapter put it, kind of poised at the threshold of exploration and discovery, doesn't it?

With potentially over a million species still unknown, new ways to analyze them, powerful computers, we're really just scratching the surface of the full fungal story.

It's like we found a massive hidden library, and we've only just started reading the titles on the spines.

That is a perfect analogy, yeah.

It means there are just countless discoveries still out there, waiting.

Discoveries that could give us exciting new insights into ecosystems, maybe new medicines, new tools for biotechnology, who knows?

Absolutely, from their really surprising evolutionary kinship with us animals,

to their absolutely critical role in shaping Earth's history, maybe even enabling life on land as we know it, and yeah, even the debates over what to call them, fungi are just so much more than meets the eye.

They really are.

We really hope this deep dive has given you some surprising facts, and maybe a clearer picture of this incredibly vital, often hidden kingdom.

Thank you for joining us on the deep dive.

Now that you know a bit more about this hidden kingdom, what new connections, what fungal roles might you start noticing in the world around you?