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Understanding and building phylogenetic trees

Constructing a phylogenetic tree involves hypothesizing evolutionary relationships among species based on observable traits and genetic evidence. By practicing parsimony, we aim for the simplest explanation. This graphical representation helps determine relatedness and common ancestors, allowing us to understand the evolutionary history of different species. Created by Sal Khan.

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Video transcript

- [Voiceover] When we look at all of the living diversity around us, then a natural question is, well, how related are the difference species to each other? And if you put that into an evolutionary context, relatedness should be tied to how recent did two species share a common ancestor. And what we're going to try to do in this video is construct a tree for showing how different species evolved from common ancestors, and we're gonna do it based on some of these observable traits that we see. But this is going to be a huge oversimplification. I'm only doing it with five species and five very simple traits. As we'll see, or as we'll talk about in future videos, this can be done in a much more complex way, and that's what biologists would do. They would look at much more than five traits, and they would look at molecular evidence, molecular evidence in terms of protein differences, in terms of DNA differences, to really start to build out what we call a phylogenetic tree. So let me write this down. That's what we're going to create. Phylogenetic, genetic, tree. Phylo comes from the Greek for group or kind or tribe, and then genetic comes, you know, related to the word "genesis." How do these things come about? How do the different groups or tribes, or in this case, how do the different species come about? Well, when you're trying to make one of these trees, it's important to realize that this is a hypothesis, but you're, like always, trying to come up with the simplest hypothesis that can explain the observations that you actually see. And when we look at these, at least the species that we have listed here, it looks like there's one that is more different than all the other ones. The lamprey here does not have any of these five traits that we are observing. So this, we would call the out group. The lamprey is the outgroup. And a lot of times when you need to construct a phylogenetic tree, they might provide you something, with something that is clearly an outgroup. Here it doesn't have any of these observable traits. And sometimes, if we're looking at genetic differences, it might have the largest number of genetic differences relative to everything else. And so it makes sense, the simplest hypothesis is its common ancestor is most distant into the past with everything else. And so let me start to draw this tree. So I'm going to put deep into the past, so deep into the past, there is a branching out point where you have the common ancestor of the lamprey and everything else we see here. So eventually, you have that common ancestor, and there's many, many species along the way, and eventually, we get, we get a lamprey in present time. In present time. And so the next thing to think about is, alright, well how did everything else end up branching? Well, what's common about everything else that maybe wasn't common about the lamprey? Well, one common thing is we see that everything else, at least that we have listed here, have jaws. And so it's reasonable to say, alright, we have this common ancestor, between the lamprey and everything else at this branching point right over here, and then it branched off into multiple species, and one of those species must have evolved jaws. So let me put jaws right over here. So jaws right over there. And jaws, that's called, jaws are considered a derived trait. This ancestral species at this root did not have jaws, we're assuming, but at some point, they evolved, and they stuck around because they proved to be favorable in certain environments. Or it could have even been things like genetic drift, who knows, but I'm guessing that it was favorable in certain environments. So let's see, let's see if we can classify everyone else. So now, out of the four, so we've, let's actually cross out the lamprey just for simplification since we've already classified that character. Now of everyone else, we've already thought about everyone's got jaws, so now let's go to the next most common trait. So, and actually, let me cross out the jaws too, just for, keep things simple. So we can do that a little bit cleaner. So I'm gonna cross out the jaws. And now, let's see, the next most common trait are the lungs, but not every species that we have left has lungs. The sea bass does not have lungs. It does not breathe air the way that animals that live outside of the water breathe air. And so the next point of divergence must be between the sea bass and everything that we have left over. So let me draw that. So, now once again, I said, "must be." This is a hypothesis. I think it's a reasonable hypothesis. So let me draw that. So this is the sea, sea bass. And there's a common ancestor between the sea bass and everything else, and the antelope, the bald eagle, and the alligator. And at some point, that common ancestor diverged into multiple species, and one of those child species must have evolved lungs. So lungs must have evolved at some point, but we're assuming that that wasn't on this lineage for the sea bass. And once again, I'm just trying to find the simplest explanation. There might have been some situation where maybe lungs evolved and then went away at some point. You reverted to an ancestral form. But we like to go with the simplest explanation. This is a property that biologists will also often call parsimony, and actually, let me write this down. Parsimony, which in everyday language, means cheap. When someone tells you that you're parsimonious, it's a nice sounding word, but it means that you are cheap. But parsimony, in this context, say hey, we're trying to be cheap with complexity. We're trying to be as simple as possible in our explanation of what's going on. But anyway, let's go back to what we were doing. So we've already put into consideration, we have already talked about the sea bass here, and we have already talked about lungs. Alright, so what do we have left? So we have to talk about the antelope, the bald eagle, the alligator, and gizzards and fur. Alright, it looks like the bald eagle and alligator have a gizzard. The antelope has fur, oh and actually, we haven't talked about the bald eagle and feathers as yet, either. Alright, so it is possible. So let's make the next thing between, well, we could do it this way. And once again, I'm trying to do this in real time, something that seems, so let's make a branch here. And let's say that that is the branch for, now let's say that's the branch for the bald eagle. Say, "B. Eagle." That's the branch for the bald eagle, and let's see if I can construct one that will explain the differences between the bald eagle, the antelope, and the alligator. Well, the bald eagle and the alligator have something in common. They have a gizzard in common. So let me make a branching point. Make them a little bit closer than the bald eagle is to the antelope. So let me do that. So let me put the alligator there, and then I'm gonna talk about when we get these derived traits. So that is the alligator. And obviously, I could have written the alligator on this side and the bald eagle on that side, or I could've rotated, I could rotate at any one of these branching points. And then what we would have left is the antelope. Now let's see if I can account for all of these derived traits. Antelope. Alright. So we have the common ancestor of the sea bass, the bald eagle, the alligator, and antelope right over here. We have a branching point. At some point, the lungs, we're hypothesizing evolved in this branch. And then this branch, well let's say that this branch, this is the common ancestor between the antelope, alligator, and bald eagle. And a common ancestor of the bald eagle and alligator, they have to get the gizzard. So let's put the gizzard down right over here. This is where the gizzard, this is our hypothesis. Doing the same color as, so that's the gizzard. Gizzard right over there. And so everything that descended from that ancestor that had the gizzard, well, they're going to have gizzards. That's what we're assuming, but once again, that can be lost. This is a hypothesis. And so we have accounted for the gizzard. Let me, let me cross that out. So we have accounted for the gizzard. And so let's see, we have to account for the feathers, and the bald eagle is the only one that has feathers. So let me put that here. So at some point, you have a common ancestor of an alligator and a bald eagle. It branches off into multiple species, one of which gets a feather or gets feathers. And once again, you know, that could have branched off into many, many things, 'cause we know that the bald eagle isn't the only species with feathers. But the bald eagle, for sure, is a species that has feathers. And let's see, so we've accounted for the feathers now. Feathers. And now, we just have to account for the fur, the fur of the antelope. And so, we don't know where this could have happened. We might wanna look for more evidence to come up with a good hypothesis. But some place along this right branch, we could put, we could put the fur. And so there you have it. This is actually a reasonable phylogenetic tree. I practiced the practice of parsimony to come up with the simplest explanation, but there are more complicated explanations. And we don't know, some of those more complicated explanations could very well be true. But from this, we have a very quick and easy graphical representation of how related different species could be and where they share common ancestors. So bald eagle and an alligator, based on this phylogenetic tree, we would say are more related than a bald eagle is to an antelope. They have a more, the bald eagle and the alligator, have a more common common ancestor, or more recent common ancestor right there than both of their common ancestors with the antelope, and that would make them more related. And if we were doing this for real, we would wanna look at genetic evidence and look at the various proteins and say, okay, does that back this up? Are the bald eagle and alligator's DNA, do they have more in common with each other than they do with the DNA, say, of an antelope? And many, for especially once you get complex, there could be many different explanations, and we just wanna get more and more and more evidence to keep refining our phylogenetic trees.