Phylogeny: Study with Video Lessons, Practice Problems & Examples

Taxonomy is the science of classifying organisms based on shared characteristics and evolutionary relationships. It includes hierarchical categories: domain, kingdom, phylum, class, order, family, genus, and species. Phylogeny studies evolutionary relationships, using traits like ancestral and derived characteristics. Homology indicates similarity due to shared ancestry, while analogy arises from convergent evolution. Cladistics classifies organisms into clades, with monophyletic groups containing an ancestor and all descendants, paraphyletic groups missing some descendants, and polyphyletic groups lacking a common ancestor. Understanding these concepts is crucial for studying biodiversity and evolutionary biology.

Reading a Phylogenetic Tree

I'm going to spend some time interpreting phylogenetic trees, and this is something we've done before. But in this section, you're going to be responsible for interpreting phylogenetic trees just as a skill on its own. And for whatever reason, some folks who are otherwise really good at biology get kind of tripped up reading phylogenetic trees. So we're going to start at a very basic level here and sort of build up on this as we go. So we'll start by just defining it here, a phylogenetic tree.

This is a branching diagram that shows these evolutionary relationships. And for me, actually breaking down the word helps me understand how I should interpret one of these trees. So phylogenetic comes from the Greek, philo. Philo means a tribe or a group, and genetic, it's not the science of genetics. It comes from the word genesis, which means origins.

So literally, what a phylogenetic tree is showing you is the origins of groups in this tree-like diagram. Right? So how do we find those groups? How do we find those groups and their origins? Well, we're going to say groups are made by finding common ancestors, and the common ancestors on a tree you can find by where lines connect on the tree.

So I just want to pause here for a second, because when you see a question about phylogenetic trees, the vast majority of questions, what you need to start doing is figuring out what organisms the question is about and then finding their common ancestors in the tree. Then once you find their common ancestors, you understand what groups are descended from those common ancestors, and that will lead you to the correct answer. Alright. So let's take a look at how this works out. To do this, I'm going to compare a phylogenetic tree to a family tree because we're going to say a phylogenetic tree can be read similarly to a family tree.

And a lot of folks who have trouble with phylogenetic trees can actually interpret these family tree relationships correctly. So here we have a family tree. Right? This is supposed to represent my family tree. That's supposed to be me second from the left there.

You also see my sister, my cousin, and my second cousin. A second cousin, someone that you share a great-grandparent with. And we're going to compare this to this phylogenetic tree. This phylogenetic tree shows a wolf, a fox, a bear, and a lion here. Now the thing you want to notice, right, the branching diagram here, how these individuals and how these animals are connected, it's the same in both trees.

So if we can interpret the family tree, we can interpret the phylogenetic tree. Alright. So when we start, we have some questions that should be really simple and obvious, but then we're going to get to some where we sort of flip it around and it tends to trip some people up. Alright. So for one of those really simple obvious questions, who am I most closely related to?

Well, obviously, it's my sister, but why? Because we share a common ancestor. Right? We are descended from my dad, and that puts us in a group together. Right?

We follow lines back, it reaches my dad. That's the group of my immediate family. But we can ask a similar question on this phylogenetic tree. Who is the fox most closely related to? Well, we follow its line back until it connects to another line that's there.

That represents a common ancestor. Who's descended from that common ancestor? Well, that means that both the fox and the wolf are part of that group. They're most closely related to each other. Alright.

Now just a quick obvious difference between a family tree and a phylogenetic tree that I want to note. My family tree, I just went back one generation. Right? Here, we're going back I actually don't know how much, maybe hundreds, maybe thousands, maybe millions of generations to find that common ancestor between a wolf and a fox. Right?

But it's still very real, you know, parent, grandparent, great grandparent, just, you know, a million times over or whatever until you find that common ancestor. Alright. Well, then after my sister, though, in this family tree, who am I next most closely related to? So the way we're going to do it, we're going to find the common ancestor. So we're going to follow my lines back until it connects with another line.

It connects here. That's my grandmother. Right? That's my grandmother. So who else comes out of that, that common ancestor, my grandmother?

Well, it's my dad, me, and my sister on one side, and on the other side, well, it'd be my aunt and my cousin. That puts us together in this sort of larger cousin group here. Right. But here's where it gets a little tricky. Right?

Obviously, I'm more closely related to my sister, and then I'm next most closely related to my cousin. Who is my cousin more closely related to? Me or my sister. Well and hopefully, that's pretty obvious. Right?

My cousin is most closely related to both of us or equally related to both of us because we're part of a family group. Right? It's my cousin's cousin to both of us. But it does trip people up when we look at the phylogenetic tree. So same question.

Who's the fox most closely related to after the wolf? Well, we're going to follow lines back. We get to this common ancestor descended from that common ancestor? Well, the bear. So the fox is most closely related to the wolf, and then next most closely related to the bear, because they're in this bigger group together.

But who's the bear more closely related to? Is the bear more closely related to the fox or the wolf? Well, hopefully, you see it's equally related to both of them. Right? From that common ancestor, on one side of that family is the bear.

On the other side is the wolf and the fox as a group. Alright. So we'll keep going here. I'll try this again. Right?

This second cousin, my second cousin, who is my second cousin most closely related to in my family tree? Well, to answer the question, I need to find the common ancestor. So I follow that line back from my second cousin until it connects with another line that's way back there at great grandmother Edith there. Right. So I can figure out, well, on one side of this tree, on one side comes my second cousin and I can fill in the people that she's descended from.

And what's on the other side? On the other side of this family, it's everyone in my cousin group. So my second cousin is equally related to me, my sister, and my cousin because she's second cousins with all of us. Right? Now, I can put all of us in a group together.

This is a big extended family. We see each other every 20 years at a family reunion or so. Right? Because we all share that common ancestor there. All right.

Now, I'm going to do the same question here with the lion. Who is the lion most closely related to on this tree? Sometimes people are tempted to say the bear, right, because they're right next to each other, and if you sort of try and connect their lines, there's fewer jigs and jogs you got to go through, but it's not how we do it. We find the common ancestor. So follow the line back from the lion.

Where does it connect with other lines? Here. Right. So there's that common ancestor. Now on one side from this common ancestor is the lineage that leads the lion.

What's on the other side? The other side is this group. Right? So the lion is equally related to everything in that group, because everything in that group shares this common ancestor here. It means the lion is most is equally related to the wolf, the fox, and the bear.

Now I can also, right, put them in this big group together. They are part of this big group. This is really all the carnivores because all of those organisms are descended from that common ancestor there at the top of that tree. All right. Hopefully, that all made sense.

Just remember, when you're trying to establish relationships, you do it by finding the common ancestor in the tree and then establishing what is the group that is defined by that common ancestor. If you can do that, you can answer the vast majority of this type of question. And if you ever get confused, just try to think of it like a family tree. Practice is a bunch more going forward, and I'll see you there.

Phylogeny Example 1

You want to evaluate the following statements as true or false based on the following phylogenetic tree. Alright. So we have this phylogenetic tree here. It shows us the relationship between all the different bears. Now before we start reading these, let's just remember what we said.

For most questions on phylogenetic trees, the first thing you want to do is figure out what the common ancestor is, and that will tell you something about the group that you are looking at. Alright. So now with that in mind, let's start reading our statements here. The first one says the tree shows that polar bears have undergone the most evolution. Take a look.

What do you think? Alright. The most evolution. That's just not something a phylogenetic tree can show you. What it shows you is how things are related by finding common ancestors.

This is a misconception sometimes people have because the polar bears are at the top of the tree, and if you sort of trace the line that leads to them, it goes through sort of the most splits in the tree. But again, that's just not something a phylogenetic tree shows you. The common ancestor of all these bears is back here. All of these bears are alive today, so they've all been evolving for the same amount of time. None are more evolved than any other.

So that means that this statement is false. Alright. Next, we have the sun bear is most closely related to the sloth bear. Take a look. What do you think?

Alright. Well, here's the sun bear. Here's the sloth bear. Let's find their common ancestor. I follow these lines back till they meet.

That common ancestor is right here. That means that they are a group and they're the only things in that group descended from that common ancestor, so, yeah, they are most closely related to each other. That statement is true. Alright. Next, we have the American black bear and the Asiatic black bear are most closely related to each other.

Take a look. What do you think? Well, here's that American black bear, here's that Asiatic black bear. Now, they're next to each other on the tree and they kind of look like each other in the drawings, their names are very similar, but where's their common ancestor? Let's follow the lines back.

Their common ancestor meets up way back here in the tree, bit pretty deep. That means that they're part of this big group that includes all these other bears. Right? And the American black bear, well, it actually meets up at a common ancestor here with the polar bear and the brown bear, so that puts them in a smaller group. That means that it's going to be more closely related to those bears.

The Asiatic black bear, it meets up at a common ancestor here. That puts it in a group with the sun bear and the sloth bear here. That means that it's in a group with those first, so it's more closely related to them. So that means that the American black bear and the Asiatic black bear are definitely not most closely related to each other. That's a false statement.

Alright. Next, we have the Andean bear and the panda bear are most closely related to each other. Take a look. What do you think? Alright.

Another common misconception here. Again, you see that they're next to each other, and as you sort of trace from one to the other, you kind of have to go through more fewer splits to get from one to the other, but that's not how you redefine a phylogenetic tree. Let's find the common ancestor. Common ancestor is here. Now, what is the group that's descended from that common ancestor?

All the bears. Right? Now on one side of this tree, you have the panda bear coming out. On the other side, you have this, line that leads to this common ancestor here, which is all the bears, including the Andean bear except for the panda bear. That means that that Andean bear is more closely related to all these other bears than it is to the panda bear, and the panda bear is equally related to everything on that side of the tree.

So this is a false statement. Next, we have the brown bear is equally related to the Asiatic black bear and the sloth bear. Alright. Take a look. What do you think?

Well, now if it's equally related to him, that means that the Asiatic black bear and the sloth bear are probably part of a group that share a common ancestor that's sort of on the other side of a split from the brown bear. Right? So here's our Asiatic black bear and our sloth bear. They share this common ancestor here. Right?

Now, what's the common ancestor that they share with the brown bear? Well, from this common ancestor, I go back to here, and that's that common ancestor. You trace the brown bear back to there. So that means that on one side of the tree, you have this, this lineage that leads to, well, this group of bears that the brown bear is part of. And then on the other side of this tree, you have both the Asiatic black bear and the sloth bear as part of that big group there or that small group of 3 bears rather.

So that means there, then yes, this is a true statement. The brown bear is equally related to the Asiatic black bear and the sloth bear, because both of those sort of come out of the other side of this tree from that common ancestor that we were talking about sort of right here, right here on the tree. Alright. Next we have, this tree shows that the ancestors of all bears were most similar to a panda bear. Take a look.

What do you think?

Based on the tree below, which of the organisms listed is most closely related to the tinamou?

• A. Rhea.
• B. Kiwi.
• C. Emu.
• D. Ostrich.

Answer: (C)

According to the phylogenetic tree below, which statement is correct?

• A. The rhea is most closely related to the tinamou.
• B. The rhea is equally related to both the cassowary and the kiwi.
• C. The ostrich and the rhea are most closely related to each other.
• D. The kiwi is more closely related to the rhea than it is to the cassowary. 

Answer: (B)

Based on the tree below, which of the birds listed is most distantly related to the tinamou?

• A. Cassowary.
• B. Kiwi.
• C. Rhea.
• D. Emu.

Answer: (C)

Parts of a Phylogenetic Tree

At this point, we should have a basic understanding of how to interpret relationships on a phylogenetic tree, but now we need to learn some vocabulary because phylogenetic trees use a specific set of vocabulary to describe them. And if you want to answer questions about phylogenetic trees, you need to know this vocabulary. So, to do this, we have this sort of example phylogenetic tree of these made-up beetles here and how they're all related to each other, and we're going to be looking at this tree and naming all the different parts. Let's go through it.

Now, probably the most obvious thing about a phylogenetic tree is the lines, right? So I'm going to highlight those now in orange. Those represent what we call the branches or a branch of a phylogenetic tree. So a branch is a line that represents a lineage. You could say a lineage or a population evolving over time.

So we have our taxa on our phylogenetic tree, all our different taxa here, and they're all going to be connected back to the base of the tree, the common ancestor of everything on this tree through these different branches. But of course, it's a branching tree, right? It's not just a bunch of sticks.

So, they all connect to each other, and where they connect, we're going to be highlighting here in red. Those are the nodes or the branch points in our tree. So, a node or a branch point represents the last common ancestor of multiple taxa on the tree. You have one population sort of evolving through time; it reaches a node, it splits into at least two new populations, and now you have two new branches going. That node was the last time that it was a single population.

Now, there's one line we haven't highlighted here, and that's the line all the way at the base of the tree. I'm going to highlight it now in blue. That's the root of the tree. So the root of the tree is going to be the common ancestor of all organisms on the tree. And just like the root of a real tree, the root of our phylogenetic tree is at the base of the tree, and all the branches come out of that root because all the taxa on our tree descended from that root.

I just want to be really clear: you actually don't need to draw a tree with a root. But in intro biology, probably all the trees that you are going to see will have a root, and all the trees that we're going to look at will have a root.

Now, we are going to highlight these two green beetles here. I want to highlight those right now. I'm going to call those two sister taxa. The reason I'm calling them sister taxa is that these organisms share an immediate common ancestor. As I trace their lineages back, they reach a common ancestor with each other before they reach a common ancestor with anything else. So they are very closely related in a group together just like I am very closely related to my sister because we share an immediate common ancestor.

Now, there's one node on this tree that looks different from all the others. I'm going to highlight it now. It's right here, this node in green, and that's because this is a node with more than two branches coming out of it. Now, this is called a polytomy. A polytomy is when you have more than two branches coming out of a node, and it could mean multiple things. It could mean that one day in the history of the Earth, there was a population, and it split into four, and since then, they've been independent populations evolving. That's certainly possible. But usually, when we draw a polytomy, what we're saying is some of these beetles are probably more closely related to each other. We just don't know which ones because we don't have enough data. Maybe the red beetles here.

Finally, we want to introduce this term clade or monophyletic group. To do that, we're going to circle the yellow and green beetles here that we've circled in yellow. This is a clade or a monophyletic group, and when we've been talking about groups descended from a common ancestor, that's a clade. So the term for such a group, when we're looking at a phylogenetic tree, is again clade or monophyletic group. We're going to define this as a group that includes a node and all taxa descended from that node.

The reason that knowing this word clade or monophyletic group is important is that when we do systematics or taxonomy, when we're naming organisms in science, we really usually want to base those groups on monophyletic groups or clades to make sure that all the organisms in the group that we're giving a scientific name are descended from a single common ancestor. We are going to look at clades and monophyletic groups separately coming up in a little while. But before then, we're just going to practice applying this vocabulary in examples and practice questions to come, and I'll see you there.

Phylogeny Example 2

Our example here says, using the tree below, answer the following. And so we have this phylogenetic tree here showing the relationships of these birds. Most of them are large flightless birds, so not quite all of them are large, not all of them are flightless. So let's just go see what it says here. First off, it says a, put a star on the node that represents the last common ancestor of the Tinamu and the emu.

Alright. So take a look at this phylogenetic tree. Here is the Tinamu. Here is the emu. Where is the node that represents the last common ancestor between those two organisms?

Alright. So remember, what I'm going to do is I'm going to follow these branches back until they meet. So from the emu, I'm going to follow back to here, and I can follow the Tinamu back and reach that same place. So this splitting point right there on the tree, that represents that node that is the last common ancestor of those two lineages. So, supposed to put a star on it.

Alright. There's my star. Okay. Next, we have circle the branch that leads to the ancestry of the kiwi and the cassowary. Alright.

So take a look. What branch leads to the kiwi and the cassowary? Alright. Well, here's the kiwi. Here's the cassowary.

So we're going to follow those branches back until they meet, which is at this node right here. But what it says to do is circle the branch that leads to the ancestor. So that node is the last common ancestor of the kiwi and the cassowary because when I follow those branches back, that's where they meet. So this is the branch that leads to that node. That's what we're talking about here.

So I'm going to circle that branch. That is that lineage that leads to that last common ancestor of the kiwi and the cassowary. Alright. C here says the cassowary is a sister taxon to which other organism? Alright.

Here's the cassowary. What do you think? Well, remember, sister taxon, that means two things. They are just most closely related to each other. So what's the cassowary most closely related to?

Well, as I follow the branch back to this node here, what else comes out of that node is the emu. So my answer for this one is going to be the emu. Alright. Next, we have put a box around the root of the tree. Take a look where you're going to put that box.

Alright. Well, remember the root of the tree, the root of the tree is the base of the tree that all the branches come out of. It's the common ancestor of everything on this tree. So the root of the tree, I'm going to put a box around right there. Alright?

That's the root of this tree. Now what does the root of the tree represent? Well, we just said it. It's the common ancestor of all taxa on the tree. Alright.

Next question, it says, does this tree contain a polytomy? Take a look. What do you think? So remember, a polytomy means many. So we're going to try and find a node where more than one branch comes out of.

Well, on this tree, every node, there are only 2 branches coming out of it. Right? So we can look real quick. Here's a node, 1, 2. That's not a polytomy.

Here's a node, 1, 2 branches coming out. Here's a node, 1, 2 branches coming out. Here's a node, 1, 2 branches coming out. And our final node here, 1, 2 branches coming out. So there are no polytomies here.

Right? If there was a polytomy, you'd see more than 2 branches, 3, 4, 5, whatever it is, coming out of a single node. Again, we don't see that. So finally, G says, if it does contain a polytomy, mark the polytomy with an asterisk. Well, there isn't one, so I guess we've done our job.

Alright. More practice after this. I'll see you there.

Based on the tree below, which statement is true?

i. Snow leopards and tigers are sister taxa.

ii. Lions, leopards, and jaguars represent a clade. 

iii. The node leading to lions, jaguars, and leopards is a polytomy.

• A. I & II. 
• B. I & III.
• C. II & III.
• D. I, II, & III.

Answer: (A)

Which node represents the most recent common ancestor of the rhea and the kiwi?

• A. A.
• B. B.
• C. C.
• D. D.
• E. E.

Answer: (B)

Which group represents a clade according to the tree below?

• A. Asiatic black bear & sun bear. 
• B. Asiatic black bear & American black bear. 
• C. Panda bear & Andean bear. 
• D. All the bears except the panda bear.

Answer: (D)

Different Ways to Draw a Phylogenetic Tree

One thing that can hang people up sometimes when interpreting phylogenetic trees is that we can take the same information, what we're going to call identical phylogenetic trees, and we can actually draw those trees in ways that look different from each other. So we want to go over this now so you don't get hung up by it, and you're interpreting trees the right way. Remember, what we want to do when we interpret trees is focus on the common ancestors. How do those branches connect at nodes? Alright.

So first off, we're going to look at identical trees here that just have different orientations. Orientation. Alright. Now this is one I'm sure you've seen before. We have this tree here.

We're going to be using the exact same tree for all of this. This tree shows a relationship going left to right here between the shark, the fish, the frog, the mouse, the lizard, the bird, and the crocodile. Alright. So I can take this tree and I can just copy and paste it, and I'll just turn it on its side. Identical tree.

Right? The relationships are the same. If I find the common ancestors, these taxa have the same common ancestors in both trees. I can do it again. I'll turn it upside down.

Again, identical trees. I haven't changed any of the branching patterns. All the branches meet at the same nodes, so don't get hung up if it's up and down, left to right, down and up, whatever it is. Right? Focus on the common ancestors.

These 3 trees show the exact same information. Alright. Now we can also just draw these identical trees with different shapes, and I'm sure that you've seen examples of this before, right? I kind of like to draw trees with these sort of square brackets, but you could just draw straight lines and end up with this sort of more V-shaped nodes. This is an identical tree.

It's the same information. If you follow the branches back, they meet at nodes in the same order. All these taxa have the same common ancestors in all these trees. Alright. I can take that same original tree again, and I can just kind of stretch it into a circle.

Right? Sometimes people draw trees in circles usually if they have a lot of taxa because you can fit a tree like that in a smaller space. But here I've just taken sort of those square bracket-like nodes, and I've just kind of bent them round. But if I follow the taxa back, right, if I follow the branches back from the taxa, they meet at the nodes in the same order. These taxa have the same ancestors in all these trees.

Alright. Now the one that it kind of hangs people up the most sometimes, though, is identical trees with rotation. Rotation on the nodes. So we're going to look at this tree here, and the thing that mixes people up is that sometimes they think that the order at the top of the tree matters, right? So the order here going left to right is shark, fish, frog, mouse, lizard, bird, crocodile.

That order is unimportant. Remember, what do we want to focus on is finding common ancestors and following the branches back to those nodes. Well, I can take this identical same tree here, and I'm just going to pick 1 node. Remember, anything that comes out of that node, I'm considering a group. So I can just sort of spin that group on 180.

Right? So I'm going to do that. I'm going to pick one node. I'm going to highlight it in red right there, and everything coming out of that node, I'm just turning around 180. Right.

If you follow the branches back, these things connect its nodes in the same order. If you find the common ancestors, all these taxa have the same common ancestors in both trees. Alright. I can do it again. Right?

I'll pick another node. I'm going to pick this one sort of near the bottom here. Remember, everything coming out of that node is a group, so I can just turn that group around. Right? And everything is still related in the same way.

All the nodes are connected by branches in the same order. Everything has the same common ancestor. Alright. Now this also sort of exposes another misconception that people sometimes have, right? On this tree on the left, you might see this and you just kind of say, like, whoa, it's kind of this straight shot evolution to the crocodile here, and everything else is just sort of branching off as it goes.

But the one on the right, right, to get to the crocodile, it's this kind of real windy route. Right? But there is no difference between these trees. It's the exact same information. So, do not get hung up by the order on the top of the tree or if it kind of looks like a straight shot towards something on the tree.

What's important is finding the common ancestors, and in these trees, all the common ancestors are the same. Alright. Like always, we are going to practice this more in examples and practice problems, so check it out.

Phylogeny Example 3

Our example says that the phylogenetic tree for living bear species is shown below. We see that in this blue box here. And then it says to the right, the same bears are listed in a different order. We want to draw a phylogenetic tree connecting the bears on the right so that the relationships are the same as the original tree. Alright.

So we see this phylogenetic tree here, and this is playing on this idea that the order of our taxa at the end of the tree, well, that doesn't matter. What matters is how they are connected to each other through our branches and nodes. So here we have these same bears in a different order. Alright. So to connect these, I'm just going to start by looking for sister taxa.

I want to know what things are definitely most closely related to each other, and then I'm going to start by connecting them. Alright. So looking at this tree, what do you see as sister taxa? Well, the polar bear and the brown bear, they're definitely most closely related to each other. They share an ancestor at this node.

They are descended from that ancestor, and nothing else is. That's also true for the sun bear and the sloth bear. They share an ancestor that nothing else is descended from. So those are 2 groups that are sister taxa on this tree. I can go ahead and connect them.

All right. I'm going to do that with a sort of V-style tree because I think that's just easier to draw when doing by hand. So I'm going to connect my brown bear and my polar bear. There we go. And I'm going to connect my sun bear and my sloth bear.

Alright. What can I connect next? Well, to connect to these, I want to find out well, what is the next most closely related to each one of these pairs? Right? So what I'm going to do is I'm going to follow my branches back.

So from the polar bear and the brown bear, I'm going to follow this branch back, and I have a common ancestor here. What else is descended from that common ancestor? The American black bear. So I can now connect the American black bear to my polar bear and my brown bear. So I'm going to draw back from my polar bear and my brown bear to another node, and I'm going to connect the American black bear to that node there.

Alright. Same thing. I can do that same thing with the sun bear and the sloth bear. Right? So I follow their branch back to this node here, that common ancestor.

What else comes out of that? Well, the Asiatic black bear. So how am I going to connect that? Well, I'm just going to draw a little branch back to another node, and I'm going to connect the Asiatic black bear. Alright.

What connects next? So what does each one of these groups connect to next? Well, I'm going to follow their branches back. What do you see? Well, as I've connected this group and this group here, so I can now follow those branches back, and they connect to each other at this common ancestor here.

So the next thing that these groups connect to is each other. So I can now go ahead and do that. So now I'm going to connect these together. Like that. Alright.

Now I just need to figure out how this Andean bear and the panda bear connect. So what connects next to this big group that I've made on my tree here? Well, I'm going to follow my branch back and follow my branch back to this common ancestor here. What else is descended from this common ancestor? The Andean bear.

So, coming out from so coming back from the branch here, we're going to draw a branch back from this node here, and connecting it to that new node is going to be that Andean bear. Alright. Finally, we have to connect the panda bear here. So how does the panda bear connect? Well, we have to draw another branch back from this common ancestor here, that last node that we drew to the root of the tree, the ancestor of everything on this tree, and the panda bear is going to come out of that.

So I'm going to start by drawing my branch back to a new node, and I'm going to connect the panda bear there. Alright. Now if I want, I can just put a little loop on my tree, and with that, we have recreated the tree. These two trees are identical. Right?

They might not look it, but they're identical. They show the exact same evolutionary relationships because all of the branches are connected at nodes in the same order. More practice after this. Give it a shot.

Based on the tree below, which tree shows the same evolutionary relationships?

• A.
• B.
• C.
• D.

Answer: (C)

Based on the tree below, which tree shows the same evolutionary relationships?

• A.
• B.
• C.
• D.

Answer: (C)

Which tree below shows the same evolutionary relationships?

• A.
• B.
• C.
• D.

Answer: (D)

Interpreting Branch Length

When looking at phylogenetic trees, you'll probably notice that the branch lengths on trees can sometimes be drawn very differently. Now, we want to talk about why that is here. I want to be clear, though. It's unlikely that you're going to get a lot of questions about branch length, but you are likely to see trees where branch length means different things, and you just want to be able to interpret those correctly. So we're going to start out here just by saying in different phylogenetic trees, branch length may mean different things.

And really, there are 3 options that it could mean, and we have them here. And for each of them, well, we have the same tree drawn where we have the same five taxa connected in the same way, just with different branch lengths indicating different things. So in our first tree here, well, branch length could just mean nothing. Right? And in that case, well, it's only the branching pattern that is important.

Right? How those branches connect at nodes. And that's what we have been practicing interpreting. And in fact, all of the trees that we have looked at so far, branch length has meant nothing. Right?

All we've been concerned about is how branches connect at nodes. So I want to be really clear. When you look at a phylogenetic tree, you should assume this. You should assume that branch length means nothing unless it is otherwise stated. Unless you are told it means something, assume it means nothing.

Alright. Now, when it does mean nothing, then you can often recognize it. Well, all the, taxa will usually be lined up nice and neat at the top, and quite often, the nodes will be nicely, evenly spaced, because, well, if branch length doesn't mean anything, you might as well just make your tree look pretty. Just to be clear though, even if your tree looks messy, it still might not mean anything. Alright.

So what could it mean though? Well, first off, it could refer to time. And in that case, the nodes are going to indicate when a split occurred in evolutionary history. Now, if branch length refers to time, this should be really obvious because there's a timeline. There's going to be a timeline there with dates.

All right. So we're going to say down here it will have a timeline and you can just know, you know, when did this evolutionary split occur? Well, you just go over and compare to the timeline. Now the other thing you'll notice here, not all of our taxa made it to the end of our timeline here, right? Taxon A.

Well, it ended short. So what happened there? Well, Taxon A went extinct. So a tree like this can show extinctions. All right.

Now, another thing that branch length could refer to is the amount of evolution. Now in an amount of evolution tree, the length of those branches represents DNA changes. Now a tree like this is usually pretty easy to recognize because the branch lengths are all different lengths, and that means that in the end, while your taxa are all sort of uneven at the top of the tree and they're all different lengths because the longer the branch, what they're telling you is that they have inferred that more mutations have happened along that branch. So we're going to say here that a longer branch equals more mutations. And the taxa, you can usually recognize it because those taxa are going to be all sort of uneven at the top of the tree.

Now I just want to be clear here, though. The amount of evolution tree shows you how many mutations have occurred in this section of DNA that they use to build their tree. But unless you know a lot about the DNA that they use to build that tree, the amount of mutations in it really probably doesn't tell you anything. You're usually still more interested in how those organisms are connected, how the branches connect at the nodes. Indeed, a tree like this is usually just about a way for people to show you something about their underlying data.

But again, unless you know a lot about that DNA, understanding that more mutations have happened in certain lineages really doesn't tell you anything informative. Alright. We'll look at different trees and more practice problems to come. I'll see you there.

In a tree that shows the amount of evolution, what does a shorter branch length indicate?

• A. Earlier branching events.
• B. Fewer genetic changes.
• C. Extinction events.
• D. Shorter time periods.

Answer: (B)

From the phylogenetic tree below, what can you infer from the branch lengths for the organisms Pakicetus, Rodhocetus, and Dorudon?

• A. They are more closely related to each other than to other organisms on the tree.
• B. They are extinct taxa.
• C. Those taxa experienced less genetic change than other branches on the tree.
• D. They represent the ancestors of modern whales and dolphins

Answer: (B)

Here’s what students ask on this topic:

What is the difference between taxonomy and phylogeny?

Taxonomy is the science of classifying organisms based on shared characteristics and hierarchical categories such as domain, kingdom, phylum, class, order, family, genus, and species. It focuses on naming and organizing organisms. Phylogeny, on the other hand, studies the evolutionary relationships between organisms. It uses traits like ancestral and derived characteristics to infer these relationships, often represented in phylogenetic trees. While taxonomy provides a structured way to name and categorize organisms, phylogeny aims to understand their evolutionary history and relatedness. Both fields are crucial for understanding biodiversity and the evolutionary processes that shape life on Earth.

How do you write the scientific name of an organism correctly?

The scientific name of an organism is written using binomial nomenclature, which includes the genus and species names. The genus name is always capitalized, while the species name is lowercase. When typed, both names should be italicized, e.g., Homo sapiens. When handwritten, they should be underlined, e.g., Homo sapiens. This format ensures consistency and clarity in scientific communication. For example, the scientific name for humans is Homo sapiens, and for domestic cats, it is Felis catus.

What is the significance of homology and analogy in phylogeny?

In phylogeny, homology refers to similarities between organisms due to shared ancestry. These homologous traits indicate evolutionary relationships and help construct phylogenetic trees. For example, the forelimbs of humans, dogs, birds, and whales are homologous, sharing a common tetrapod ancestor. Analogy, however, refers to similarities that arise from convergent evolution, not shared ancestry. These analogous traits result from similar environmental pressures leading to similar adaptations in unrelated organisms. An example is the wings of bats, birds, and pterosaurs, which evolved independently. Understanding homology and analogy is crucial for accurately interpreting evolutionary relationships.

What are monophyletic, paraphyletic, and polyphyletic groups?

In phylogenetics, a monophyletic group, or clade, includes an ancestor and all its descendants, representing a complete branch on the tree of life. A paraphyletic group includes an ancestor and some, but not all, of its descendants, leaving out certain lineages. A polyphyletic group consists of various organisms without including their common ancestor, often grouped based on similar traits rather than evolutionary history. Understanding these groupings helps in accurately classifying organisms and understanding their evolutionary relationships. For example, reptiles excluding birds form a paraphyletic group, while flying animals like bats and birds form a polyphyletic group.

What is a phylogenetic tree and how is it used?

A phylogenetic tree is a branching diagram that represents the inferred evolutionary relationships among various species based on their genetic, morphological, or other traits. Each branch point, or node, represents a common ancestor, and the branches represent the descendants. Phylogenetic trees are used to hypothesize the evolutionary pathways and relatedness of organisms. They are essential tools in evolutionary biology, helping scientists understand how species have evolved over time and how they are related. These trees are not set in stone and are continually refined as new data becomes available.