Phylogenetic or evolutionary trees are diagrams that are used throughout biology and studies ranging from conservation to epidemiology. They contain a great deal of information about the evolutionary relationships and diversification within and among different kinds of organisms. This video will address the following questions about phylogenetic trees. What are the parts?
How are they constructed? And finally, how are they interpreted? Although phylogenetic trees can be used for any taxonomic group, species will be used in this video for clarity. To begin with, phylogenetic trees can be drawn a number of different ways, whether sloped, with angled branches or even showing a slightly circular type of diagram, these phylogenies all show the same relationship among the species A through E because they have the same branching pattern.
You can even draw the phylogeny with a different angle of orientation and it still shows the same relationships among these species. Regardless of how the phylogeny is drawn, they are all made of the same parts. The ends are called the tips, the base is the root, the lines are branches or clades.
and the points where the branches diverge from one another are called nodes. The outgroup is a sister species that's used as a basis for comparison. The species that are the focus of the study are called the ingroup. Another important nuts-and-bolts kind of thing to know about phylogenetic trees is that you can rotate them around the nodes, but that doesn't change the relationship shown in them. For example, in all three of the trees shown here, The relationships among species A, B, and C are the same.
B and C are more closely related to one another than either is to species A because B and C share a more recent node with one another. Now let's compare the tree on the left with this tree showing a different relationship of branching patterns among A, B, and C. This tree shows a different relationship among the species because A and C share a more recent node with one another than either one does with B.
So while rotating around nodes doesn't matter, their sequence does. Let's now focus on interpreting trees in more detail. In the example shown here, we have four species, one shown by a square and then three circles. There is a time component to phylogenetic trees and in them the root indicates the past and the tips indicate the present. In this tree, The three circle species are joined at a node that indicates their most recent common ancestor, and the different branches represent lineages of organisms that gave rise to the species at the tips.
What this means is that at some point along these lineages, new characteristics arose and were passed on to all of the descendants in that lineage. So, as indicated by the traits of round, blue, and stripe in this tree, those traits arose due to some mutation and then became established in those lineages. Let's zoom in on the phylogeny to consider what that means.
Starting with the lineage, we have each branch, and it's composed of many different populations, which are indicated by these blue lines. Populations exist independently from one another, but they are genetically united by movement of individuals among them, a process called gene flow. Inside each of these populations are individuals who mate, reproduce, and pass their DNA from ancestors to descendants over time, as is indicated by these pedigrees. And so a lineage is actually a representation of many different populations composed of reproducing individuals over time.
Let's now consider what is represented by a node. Now I want you to think about what is being drawn here as a cross-section through the lineage just below the node with each population represented by a circle. Looking inside one of these populations, we can see the different individuals that compose it. Suppose a mutation arises in one of these individuals.
Let's also have this population with our new red mutation become isolated from the other populations of the species, so that there's no more gene flow between them. Either due to conferring some survival advantage or completely random processes, the red trait becomes more common and ultimately becomes the only trait found in this population. If other changes occur so that red individuals are reproductively isolated and can no longer mate with blue individuals when they come into contact with them, this results in genetic separation of the blue and red individuals, and lead to the evolution of a new species or speciation. So nodes represent reproductive isolation of lineages and ultimately speciation. These concepts about nodes and lineages are the basis of how modern biologists group species into larger groupings.
For example, grouping species B, C, and E into a genus that excludes D would be called a paraphiletic group because it is excluding one of the descendants of these four species'most recent common ancestor. Biologists prefer to include all of the descendants of a common ancestor in their groupings, so by including D in this genus, we now have what biologists call a monophiletic group. meaning that this genus now contains all of the descendants of the four species'most recent common ancestor.
This brings us to the question of how does one draw the correct phylogenetic tree for a group of species? Once again, let's return to our example with the circles and square. There are several possible arrangements of this N-group with the circles and the red square as the comparator outgroup species. Two are shown here.
Now, a phylogenetic tree is a graph... hypothesis of the relationship among species. So, as with any scientific hypothesis, we need to see which ones are rejected by our data and which ones do we fail to reject. In a simple phylogenetic study, our data are the traits that we collect from the different species. So, let's make a simple data matrix for these four species using the traits shape, color, and fill.
Let's further assume that the traits are independent of each other and each transition in character state represents a unique individual change in characteristics. In the tree on the left, we can place these traits on the tree showing how each trait changed or evolved once and there's no more than one trait change per branch. In the tree on the right, there are two changes on the first branch from red square to blue circle, a change in the fill pattern from solid to stripe, and a final change from blue stripe back to solid red. So the arrangement of species in the tree on the left required three trait changes.
while the tree on the right required five. Biologists would therefore consider the tree on the left to be the most likely pattern of relationship among these species given these data because it requires fewer trait changes, or it's more parsimonious than the tree on the right. For phylogenetic studies, researchers will often code the data numerically, which makes analysis easier. In this example, the ancestral traits are coded with a zero, and derived, or traits that have changed, are coded with a one. Let's now consider a slightly more complex tree.
In the phylogenetic tree shown here, species P through V form a single monophyletic clade. Members of this clade are unified by a shared ancestral trait called a plesiomorphy. Each clade, however, is defined by a unique derived trait called an apomorphy.
And as the lines in this diagram show, apomorphies are found throughout the tree, defining and characterizing each unique clade. In this phylogeny, P and Q share a recent common ancestor, and they both share a recent common ancestor with species R. Likewise, in the other clade, the other species show their own patterns of common ancestry among them. The lines being drawn on the right show how different groupings of these species are united by different shared common ancestors. The ability to read phylogenetic trees and interpret the information in them is called tree thinking.
So let's look at some examples and test your tree thinking skills. For the phylogeny shown here, who is species C more closely related to, species D or species F? The correct answer is that C is equally related to both.
If you said that C was more closely related to D because it is closer to it on the phylogeny, then you are likely reading across the tips, which is not a correct answer. way to read these types of diagrams. What matters are the nodes, and as this diagram shows, species C shares the same common ancestor with D and F, and is therefore equally related to both of them.
Now, let's look at another example. Who is C more closely related to, A or F? If you chose A, you may be reading across the tips again. Although C is closer to A in this phylogeny, It shares a more recent common ancestor with F and is therefore more closely related to that species.
You may have also chosen A because there are fewer nodes between C and A than there are between C and F. This is something called node counting and it is also an incorrect way to interpret a phylogeny. All that matters are the pattern of most recent common ancestors.
So, to interpret trees correctly, Don't read across the tips or use node counting to determine relationships. Let's look at one last example. This phylogeny shows the hypothesized relationships among five different clades of animals. Based on this tree, who would you say that fish are more closely related to, snails or humans?
The correct answer is humans because fish share a more recent common ancestor with the human clade. Here's another tree. Does it indicate a different relationship among these five species? The correct answer is no. Both trees show exactly the same relationships despite the node rotations.
To summarize, the ability to correctly apply tree thinking allows one to interpret and explain the information about the patterns of evolutionary relationships that are contained in phylogenetic tree diagrams. Biologists use these diagrams extensively to identify monophyletic groups using shared ancestral traits. that show unity and common ancestry among clades, and derived traits that help to differentiate and identify unique evolutionary traits and lineages.