Phylogeny: How We're All Related: Crash Course Biology #17

Summary

This Crash Course Biology episode introduces phylogeny, the study of branching evolutionary histories, using the platypus as an example of evolutionary oddities. Host Dr. Sammy explains how taxonomy and systematics help biologists categorize organisms based on shared traits and evolutionary relationships. The episode covers homologous and analogous traits, Motoo Kimura's neutral theory, and phylogenetic trees. These trees illustrate species' common ancestors and help us understand life's interconnectedness. It also highlights how evolution isn't a linear process but a complex web of traits and relationships constantly evolving.

Takeaways

• 🦆 The platypus, discovered in 1799, looked so strange to biologist George Shaw that he initially thought it was a hoax due to its duck-like beak.
• 🧬 Phylogeny is the study of evolutionary relationships, helping us understand how species like the platypus evolved and relate to other organisms.
• 🦸‍♂️ Taxonomy categorizes organisms based on traits, but it can be subjective, while systematics uses more objective data, including genetic information, to classify species.
• 🐴 Homologous traits, such as similar bone structures in horses, bats, and humans, indicate a shared evolutionary ancestry.
• 🧠 Analogous traits, like the thumb-like structures of humans and pandas, may appear similar but evolved independently from different ancestors.
• ⏳ The molecular clock hypothesis suggests that genetic changes occur at a relatively constant rate, helping scientists estimate how long ago species diverged.
• 🎲 Motoo Kimura's neutral theory proposed that many genetic changes are due to random chance rather than natural selection, reshaping our understanding of evolution.
• 🌳 Phylogenetic trees visually represent evolutionary relationships, showing how species like birds and crocodiles are closely related despite their differences.
• 🐻 In phylogenetic trees, nodes represent common ancestors, while clades include all descendants of those ancestors, such as different species of bears.
• 🔄 Evolution is not a straight ladder; it's a network of branching, rejoining, and gene flow, making life’s evolutionary history complex and interconnected.

Q & A

What did George Shaw initially think when he saw the platypus for the first time?

George Shaw thought the platypus looked like a deceptive creation, as if a duckbill had been sewn onto the body of a furry animal.

What are some unique features of the platypus that make it unusual among mammals?

The platypus lays eggs, sweats milk through its skin, and is venomous, which are rare traits among mammals.

What is phylogeny, and how does it help us understand species like the platypus?

Phylogeny is the study of evolutionary branching histories, helping us understand the ancestors and evolutionary relationships of species like the platypus.

How does Linnaean taxonomy differ from systematics in classifying organisms?

Linnaean taxonomy classifies organisms based on observable traits and organizes them into nested groups, whereas systematics classifies them based on evolutionary history (phylogeny) and genetic data.

What are homologous traits, and how do they help in understanding evolutionary relationships?

Homologous traits are features shared between species due to common ancestry. These traits help biologists trace evolutionary relationships, such as the similar bone structure in human arms, horse legs, and bat wings.

What is an analogous trait, and how is it different from a homologous trait?

An analogous trait is a feature that looks similar between species but evolved independently, like the 'thumb' of pandas and human thumbs, which are functionally similar but evolved from different structures.

What is Motoo Kimura’s 'neutral theory,' and how did it challenge Darwin's ideas?

Kimura's neutral theory suggests that most genetic changes are neutral and occur due to random chance, not natural selection. This challenged Darwin's idea that evolution was primarily driven by survival of the fittest.

What are phylogenetic trees, and what do they represent?

Phylogenetic trees are diagrams that represent hypotheses about the evolutionary relationships between species, showing how they diverged from common ancestors and how closely related they are.

How are polar bears and brown bears related according to a phylogenetic tree?

Polar bears and brown bears are sister taxa, meaning they are closely related and share a recent common ancestor, represented by a node on a phylogenetic tree.

What is gene flow, and how does it complicate the idea of distinct evolutionary branches?

Gene flow refers to the exchange of genes between populations, including different species, which blurs the lines between distinct evolutionary branches. For example, polar bears and brown bears can interbreed, producing hybrids like the 'pizzly' or 'grolar' bear.

Outlines

00:00

🦆 The Fascinating Platypus and Evolutionary Phylogeny

In 1799, biologist George Shaw studied the platypus, initially mistaking it for a fake due to its strange features. The platypus, however, is real and even weirder than Shaw thought—laying eggs, sweating milk, and being venomous. As a unique mammal, it diverged from other mammals during the dinosaur era. The study of evolutionary branching, called phylogeny, helps us understand the lineage of organisms like the platypus. Understanding phylogeny also allows scientists to categorize and explore the evolutionary history of life on Earth. The segment introduces Dr. Sammy, the presenter of Crash Course Biology, and begins to dive into the science of taxonomy.

05:04

🧬 Systematics: A More Objective View of Evolution

This paragraph discusses how Linnaean taxonomy classifies organisms based on observable traits but can miss deeper evolutionary connections. Systematics, on the other hand, categorizes species based on their evolutionary history (phylogeny), providing a more objective analysis. Through anatomical and genetic comparisons, scientists identify homologous traits—features shared due to common ancestry—and distinguish them from analogous traits, which evolved independently. This leads to a better understanding of relationships among species, such as horses, bats, and humans sharing a common arm bone structure, unlike birds and dragonflies whose wings evolved separately.

10:05

🎲 Kimura’s Neutral Theory and Evolution by Chance

In 1968, Dr. Motoo Kimura proposed the neutral theory of evolution, arguing that most genetic changes occur by random chance rather than natural selection. This controversial idea challenged Charles Darwin’s theory of survival of the fittest, but it has since become an important concept in evolutionary biology. Kimura showed that many genetic changes have no impact on an organism's survival, shaping our modern understanding of evolution. Phylogenetic trees help visualize these relationships, revealing surprising connections, such as birds and crocodiles being closely related despite their differences.

🐻 Reading Phylogenetic Trees: Bears, Clades, and Evolutionary Hypotheses

Phylogenetic trees are tools used to visualize evolutionary relationships. By examining a tree of eight bear species, we see how closely related brown bears and polar bears are. These species share a common ancestor represented by a node on the tree. Phylogenetic trees help identify clades, or groups of organisms that share a common ancestor, allowing scientists to trace evolutionary lineages. The concept of clades extends to other species, showing how giant pandas, although unique, are part of the larger Ursidae bear family. Phylogenetic trees highlight the complexity of these connections.

🌊 The Complexity of Evolution: Interbreeding and Gene Flow

Phylogenetic trees illustrate how species evolve, but these branches are not always as distinct as they seem. Some species, like polar bears and brown bears, can interbreed, producing hybrids like the ‘Pizzly’ or ‘Grolar bear.’ This gene flow shows that evolutionary relationships are not always straightforward, as species can reconnect and exchange genes. The metaphor of evolutionary history as a network of streams rather than a simple tree reflects the intricate nature of life’s evolutionary processes. Phylogeny provides a framework to understand these complexities and trace the deep connections between species.

Keywords

💡Platypus

The platypus is a unique and strange animal that puzzled early biologists like George Shaw. It has distinct features such as a duck-like beak, lays eggs, sweats milk, and is venomous. The platypus is one of two living members of an ancient mammalian lineage, making it an example of evolutionary divergence, a key theme in the video.

💡Phylogeny

Phylogeny is the study of evolutionary relationships and branching histories of organisms. It helps biologists understand the ancestry and connections between species, such as how the platypus split from other mammals. In the video, phylogeny is used to explore how species like birds and crocodiles share a common ancestor and how species are connected on the 'tree of life.'

💡Taxonomy

Taxonomy is the system used to classify and label organisms based on shared traits. Historically, this classification followed the Linnaean system, which organized species into categories such as genus and family. The video highlights how taxonomy has limitations, especially when relying only on physical traits, and contrasts it with systematics, which uses evolutionary data.

💡Systematics

Systematics is the science of classifying organisms based on their evolutionary history or phylogeny, rather than just observable traits. The video contrasts systematics with traditional taxonomy, showing how DNA and anatomical comparisons lead to a more accurate understanding of species relationships. For example, systematics helps clarify why birds and crocodiles are more closely related than birds and lizards.

💡Homologous traits

Homologous traits are features shared by species due to common ancestry. In the video, examples include the similar bone structures in the limbs of horses, bats, and humans, showing how these traits stem from a shared evolutionary blueprint. The concept helps explain how evolutionary relationships are identified.

💡Analogous traits

Analogous traits refer to features that appear similar but evolved independently in different species. An example from the video is the panda’s thumb, which evolved separately from the human thumb but performs a similar function. These traits illustrate how evolution can solve similar problems in different ways, without shared ancestry.

💡Neutral theory

Neutral theory, proposed by Motoo Kimura, suggests that most genetic changes in organisms are due to random chance rather than natural selection. This was a departure from Darwin’s idea of 'survival of the fittest.' The video explains how neutral theory revolutionized evolutionary biology by emphasizing the role of chance in genetic evolution.

💡Phylogenetic tree

A phylogenetic tree is a visual representation of evolutionary relationships between species, illustrating how they have diverged from common ancestors. In the video, the bear family tree shows how polar bears and brown bears are sister taxa, meaning they share a recent common ancestor. Phylogenetic trees are key tools in understanding the branching of life’s evolutionary history.

💡Clade

A clade is a group of organisms that includes a common ancestor and all its descendants. In the video, bears are grouped into clades based on their evolutionary history. For example, giant pandas form their own distinct branch, but still belong to the broader bear clade. Clades help organize and visualize evolutionary relationships.

💡Gene flow

Gene flow refers to the transfer of genetic material between populations or species. In the video, it’s used to explain how closely related species, like polar bears and brown bears, can still interbreed and produce hybrids. Gene flow complicates the idea of evolutionary branches being entirely distinct, suggesting that species are more interconnected than we might think.

Highlights

In 1799, biologist George Shaw received a strange animal skin that resembled a duck's bill sewn onto a quadruped's head, which turned out to be the platypus.

The platypus is a real and unique mammal that lays eggs, sweats milk, is venomous, and diverged from other mammals when dinosaurs still roamed.

Phylogeny is the study of branching evolutionary histories, helping us understand the relationships and features of species like the platypus.

Taxonomy is the system of naming and categorizing organisms based on observable traits, but it can be subjective and miss less visible markers of relationship.

Systematics categorizes organisms based on their phylogeny, providing a more objective understanding of species relationships.

Homologous traits are common features due to shared ancestry, like the bone structure in human arms, horse legs, and bat wings.

Analogous traits look similar but evolved independently, such as the 'thumbs' of giant pandas and humans.

Genetic similarities are used to construct phylogenies, based on the hypothesis of a roughly regular molecular clock.

Dr. Motoo Kimura proposed the 'neutral theory' suggesting that most genetic changes are random and neutral, not driven by natural selection.

Phylogenetic trees, popularized by Charles Darwin, represent hypotheses about organisms' ancestry and relationships.

Birds and crocodiles share many traits because they are each other's closest living kin, as shown on a phylogenetic tree.

Phylogenetic trees can be used to trace the evolution of features like feathers, which first appeared on dinosaur-bird ancestors.

Evolution is not a ladder from primitive to advanced; instead, it's a network of life forms with many different ways of surviving.

Phylogenetic trees are regularly updated as scientists make new connections, reflecting the dynamic nature of evolutionary understanding.

Gene flow and interbreeding can blur the distinctions between species, as seen with grizzly-polar hybrids.

Life's evolutionary history is like a network of streams, with species growing apart and sometimes finding their way back together.

Phylogenetic studies help us understand the deep interconnectedness of all life on Earth and trace connections between living things.

Transcripts

In 1799, a strange animal skin landed in the hands of biologist George Shaw.

Studying its features, Shaw noticed

“The perfect resemblance of the beak of a Duck engrafted on the head of a quadruped.

So accurate is the similitude, that, at first view, it naturally excites the idea of some

deceptive preparation by artificial means.”

So, basically: “This thing seriously looks like a duckbill sewn onto some fur.”

That animal, the platypus, is very much real.

And even weirder than Shaw realized: platypuses lay eggs,

they sweat milk through their skin, and they’re venomous to boot.

They’re also mammals like us, but...

they're a different kind of mammal, one that split off from the rest

back when the dinosaurs were still around.

Today, they are one of only two living members of that weird, wonderful lineage.

We call the study of branching evolutionary histories, like these, phylogeny.

Understanding it helps us paint a picture of our pal the platypus,

like who their ancestors were, and why they look so distinguished today.

And beyond that, phylogeny helps us understand all kinds of lineages

to make sense of life’s big, whopping family.

Hi, I’m Dr. Sammy, your friendly neighborhood entomologist,

and this is Crash Course Biology.

[Yawns]

I’m sorry…I didn’t get enough theme music last night.

[THEME MUSIC]

Life’s extended family is full of second cousins you’ve never met

and great-uncles twice-removed.

Nobody’s wearing name tags.

And there’s no auntie with an encyclopedic memory

to tell us how we’re related.

But we humans make and share knowledge about the world

by naming and categorizing stuff,

whether that’s movie genres, art styles, or types of burritos.

We slap nametags on life’s diversity through taxonomy,

systems of labeling and categorizing organisms.

For over 250 years, biologists have largely used the Linnaean system of classification.

It files living things into groups, called taxa, based on observable traits they share.

The sortings are basically a bunch of nested boxes:

species goes in genus, genus in family, family in order, and so on.

But these taxonomic boxes are kind of subjective. 

Boxes like genus or family, for example, can be very broad or very specific,

depending on when in history they were coined.

I mean, there is literally one family for ants.

More than 12,000 species but just one family!

Who’s idea was that?

And because Linnaean taxonomy often relies on physical traits to sort organisms,

it can miss other, less visible markers of relationship between species.

Enter systematics — the science of categorizing  organisms based on their phylogeny,

that fancy word for evolutionary history.

Unlike Linnaean taxonomy, which rested on how we humans historically named things,

systematics works to uncover more objective  data about how species are related.

Biologists construct phylogenies by comparing  the anatomy and DNA of different organisms.

For example, sometimes organisms have common features because of shared ancestry,

called homologous traits.

Homologous comes from the Greek "homologos" which means “consistent,”

and with homologous traits, you see a consistency in the evolutionary blueprint.

Like, if a horse, a bat, and you walked into an X-ray machine

–and no, this is not the setup for a terrible joke—

you’d find the same basic bone structure

in your arm, the horse’s front legs, and the bat’s wing.

Different arrangement; same hand-me-downs from a common ancestor. 

But if you put a bird and a dragonfly in there,

you’d see that their wings aren’t made from the same stuff.

They have totally different evolutionary origins

and so wings between those organisms are not homologous structures.

But it’s not always that simple to determine how organisms are related.

Giant pandas also share their basic arm bone structure with us, 

plus a thumb-like appendage.

So you might look at a panda’s paw and think, “Boom, samesies, we’re close relatives.”

And while our thumbs do perform similar jobs, like firmly grasping snacks, 

our jointed thumb consists of several bones.

A panda’s “thumb” is actually a single wrist bone that evolved into a lengthened hook.

So these are analogous traits: they look similar, but evolved independently.

It’s also why pandas can’t play video games.

So, in addition to comparing physical similarities,

biologists will use genetic similarities to construct phylogenies.

This is based on the hypothesis that life runs on a roughly regular molecular clock:

meaning DNA and protein sequences have evolved at a relatively constant rate over time.

So theoretically, the more genetically different two species are,

the more time has passed since their most recent common ancestor.

Some models assume that the rate of change varies across time and organisms,

but averages out to a fairly steady rhythm. 

Other models assume that the rate has evolved in step with other traits,

like the rate at which an organism metabolizes its food.

But either way, the point is, we can compare apples and oranges

…genetically, anyway.

Now, some genetic differences arise from natural selection

because they’re traits that lend an advantage or disadvantage as an organism evolves.

But others? They’ve arisen due to sheer, random chance.

Let’s pay a visit to the Theater of Life.

Even as a kid, Japanese biologist and geneticist Dr. Motoo Kimura

wasn’t afraid of thinking differently.

He was outspoken, brimming with questions

—even when they rubbed his teachers the wrong way.

So it’s no surprise that Kimura went on to ask a really big question in 1968.

What if evolution isn’t entirely about survival of the fittest

—but also survival of the lucky?

Complex math led Kimura to suspect most  genetic changes are random and neutral—

they don’t impact whether the organism does better or worse in their environment.

He called this idea “neutral theory,”

and argued that sheer chance had a bigger effect on evolution than natural selection.

This was very different from what Charles Darwin had proposed—

and how most biologists thought evolution worked.

So it didn’t go over well at first.

But Kimura defended the idea with dogged determination.

And by challenging one of Darwin’s basic ideas,

Kimura refined our understanding of evolution

—he showed us random chance does play a role

—a role so big that it’s now typically assumed to be the reason for a genetic change, 

unless we have strong evidence for selection.

He even won the Darwin Medal for his efforts

—the first Asian biologist to receive the esteemed award.

And one of his most vocal critics presented it to him with a smile.

Because even when biologists don’t agree on everything,

we often delight in the discussion and in growing our knowledge of life.

Biologists today still debate Kimura’s ideas

and apply them to inform their understanding of the phylogenies of different species.

And these are often visualized  with phylogenetic trees.

These nifty diagrams were created way back in the middle of the 1800s,

and popularized by Charles Darwin.

They represent hypotheses about organisms’ ancestry,

including how groups have diverged, or grown apart,

and who’s most closely related to whom.

Like, you might not expect a tiny canary and  a toothy crocodile to have much in common.

But there are lots of traits that connect them.

For starters, birds and crocs both have a four-chambered heart.

They also both build nests, keep their eggs warm, and sing.

I mean, to be fair, a crocodile’s song is more like a yell.

But just like canaries, it uses its voice to croon to lovers and tell competitors: “back off”.

And none of this is a coincidence.

It’s because birds and crocs are each other’s closest living kin.

And you can see this relationship illustrated on a phylogenetic tree.

Evolutionarily speaking, crocs are closer to birds 

than they are to other reptiles  like lizards or snakes.

And whatever traits birds and crocodiles share, it’s likely that their most recent common ancestor

—and other descendants of it— had those traits, too.

Including dinosaurs.

Now, we’re probably not going to find fossilized dinosaur hearts

—or vocal recordings—to confirm this.

But we do have fossils of nest-building, egg-protecting, feathered dinos,

and a pretty strong hypothesis.

So, let’s learn to read one of these puppies.

Take the phylogeny of the eight species of bear.

Each line, or branch,  represents a distinct lineage.

Polar bears sit at the tip of this branch, and brown bears at the tip of this one.

Their branches connect at  this little joint, or node, 

representing their most recent shared ancestor.

Think of that node as an ancient population of bears

that were neither polar, nor brown bear, but the latest ancestor of both species.

We don’t necessarily know exactly who  they were or what they looked like,

so they’re not pictured here; just represented by this little node.

Brown bears and polar bears are what’s considered sister taxa,

that is – two descendants of a shared ancestor.

And if we imagine slicing off their little chunk of the tree,

we can think of them as a clade:

a group including the ancestor and all of its descendants.

Zoom out, and we can group organisms in broader clades.

Like, snipping at this node groups brown bears and polar bears

with four other bears and their more distant common ancestor.

And if we go back in time even further, we find a more distant ancestor,

and we add spectacled bears to the mix—new clade alert!

And still deeper in the past, giant pandas split away from the other bears,

forming a weird little branch all their own. 

But they’re still within that big bear clade by the name of Ursidae,

because they descended from the same bearish ancestor as the others.

Giant pandas and red pandas, you might notice,

go by a similar common name and sit near each other on our tree.

But they’re not each other’s closest genetic relatives.

The clue is the node nearest the red panda branch, shared with raccoons.

That’s the most recent ancestor that red pandas share with another species.

Phylogenetic trees like this one can be drawn vertically, horizontally, or even diagonally.

Like, this tree shows evolutionary relationships among fish, frogs, lizards, mice, and humans,

who all have a common ancestor way-back-when.

But we humans share an ancestor with mice more recently than with fish.

So, you’ve got more to talk about with the rodents at the pet store than the goldfish.

And that makes some sense.

But it might come as a surprise that water-loving frogs

are more closely related to people than they are to fish.

And that’s because frogs and fishes’ most recent shared ancestor

lived longer ago than the shared ancestor of humans and frogs.

And beyond telling us how organisms are related, 

phylogeny can also help us answer cool questions like “where did feathers come from.”

We’ve seen traces of feather-like appendages on dinosaurs from the Cretaceous period.

And scientists believe the first feathers capable of sustaining flight

developed on a dinosaur-bird ancestor  a little further along the evolutionary tree.

But there’s no hierarchy here, no ladder from primitive to advanced,

no matter how far back in time we go.

It’s more like, the deeper we look back at the phylogenetic tree of the bears,

the more unbear-like their ancestors were.

Or maybe it’s that bears became less bacteria-like?

No judgment from me either way, because there’s no top dog…er, bear…in evolution.

Just many different ways  of accomplishing survival.

So, phylogenetic trees represent hypotheses  about how those ways of living evolved,

and they are regularly updated when scientists make new connections.

Meanwhile, life as always, is more complicated than we can ever truly capture.

For example, these branches aren’t as distinct as they seem.

Some closely related branches can still interbreed.

Like, those polar bears and brown bears that we met earlier?

They’ve been known to mate in the wild,

producing grizzly-polar hybrids called “Pizzly” or “Grolar bears.” 

Pretty good hunters, but not strong swimmers.

We see similar evidence that many organisms change on a population level

as a result of moving around and breeding with other populations — what’s called gene flow.

So, it’s not enough to think of life’s branches as only splitting off from common ancestors.

Because the distinctions between branches are fuzzier than that.

Branches can link back up again.

Genes can also flow between species.

So while we often do think of life’s evolutionary history sort of like a tree…

it’s also like a network of streams.

Winding and meandering as species grow apart

but sometimes find their way back together again.

Constructing the phylogenies of different  species helps us make sense of Earth’s

big, ongoing, extended family, with all of its weird and wonderful offshoots.

It helps us trace connections between living things, 

comparing what they share and how they differ.

And it helps us understand how all life evolved  and visualize how deeply interconnected we are.

In our next episode, we’ll scope out a great view of the tree of life

when we talk about biological diversity.

I’ll see you then! Peace!

This series was produced in collaboration with HHMI BioInteractive.

If you’re an educator, visit BioInteractive.org/crashcourse

for classroom resources and professional development

related to the topics covered in this course.

[as Patti the Platypus] Thanks for watching this episode of Crash Course Biology,

which was filmed at our studio in Indianapolis, Indiana,

and was made with the help of all these nice people.

And if you want to help keep Crash Course free for everyone, forever,

you can join our community on Patreon. Bye!