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Crocodiles, and birds, and dinosaurs—oh my! While classifying organisms is nothing new, phylogeny— or, grouping organisms by their evolutionary relationships—is helping us see life in a whole new light. In this episode of Crash Course Biology, we’ll learn why this kingdom-phylum stuff is going out of style and why phylogenetic trees are in.

The Platypus & Phylogeny 0:00
Taxonomy 1:33
Systematics 2:44
Phylogeny & Genetics 4:32
Dr. Motoo Kimura 5:31
Phylogenetic Trees 6:56
The Complexities of Evolution 10:49
Review and Credits 12:43

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CC Kids:
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 name tags 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 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!