1. Modern taxonomy is about identifying clades 

The branching diagram shown to the left is called a phylogenetic tree. Phylogeny is the study of evolutionary history and relationships among individuals or populations.

The species shown in this phylogenetic tree are among the most famous in biology. They’re Galapagos Finches, first identified by Charles Darwin in the early 1800s. The Galapagos are a group of volcanic islands in the Pacific Ocean,  about 1000 km (600 miles) west of Ecuador. It’s thought that a small population of birds from Ecuador colonized the islands, which then evolved into over a dozen species.

In a very compact format, phylogenetic trees accomplish two things.

• First, they tell the evolutionary history of a group of species. For example, a glance at the phylogenetic tree for the Galapagos Finches shows how one species (A) is the common ancestor of the entire group. A speciation event caused “A” to split into two major lineages or lines of descent. One lineage led to the Green Warbler finch. The other led to all the species that are descended from “B.”
• Second, phylogenetic trees show us the kind of nested, hierarchical groupings of species that we looked at in the previous tutorial.

Identifying groups with a common ancestor is one of the most essential moves in modern taxonomy. A clade is a group of organisms that includes a common ancestor and all of its descendants. A clade can be a group of species, a single species, or a population within a species.

Clades can be nested within clades. Knowing that, let’s do some analysis of this phylogenetic tree. Answer the question below.

To help you understand how clades work, I’ve redrawn the diagram below and added shading so that the clades are easier to identify.

The clade that’s descended from species “A” is numbered as clade “1.” Because “A” is the common ancestor of all of the species shown in the diagram, clade 1 consists of all of the six species shown on the right, plus their common ancestor on the far left.

For any clade that consists of more than one species, the common ancestors are located at nodes. The nodes are labeled “A” through “E.” Because nodes are where speciation events occur, they’re also called branch points.

A speciation event at node “A” created two clades, “2” and “3.” A second speciation event at node “B” produced two more clades (“4” and “5.”). Another speciation event at “C” produced clades “6” and “7.” Speciations at nodes “D” and “E” produced additional clades, each consisting of a single species.

A big part of taxonomy involves identifying the clades that an organism belongs to. For example, the large ground finch is a member of 5 clades

• Its own species (the large ground finch)
• Clade 7
• Clade 5
• Clade 3, and
• Clade 1

Note that some clades are very specific, consisting of just one species. Others are more general. In the preceding example, the large ground finch clade is the most specific: it contains just one species. Clade 7 is slightly more general: it contains two species. Clade 3 includes 5 species.

Let’s connect this to the hierarchical classification categories developed by Linnaeus. If biological classification is done correctly, then each taxon, within each category, should be a clade. That’s what we see in the example to the left.

All of the foxes within the genus Vulpes are a clade. That clade excludes other members of the dog family (the Canidae) such as wolves. Canidae is a clade that contains all members of the dog family (such as dogs, wolves, coyotes, and jackals) but excludes other carnivores (such as cats or bears). Similarly, the class Mammalia is a clade. All mammals, from kangaroos to whales, share a common ancestor. Other non-mammalian Chordates (such as fish or birds) are not part of the mammal clade.

Below, we’ll learn about how biologists identify clades. But before that, let’s consolidate what you read with flashcards and a quiz.

2. Phylogeny and Phylogenetic Trees Flashcards

3. Phylogeny and Phylogenetic Trees Quiz

4. Phylogenetic trees are built by identifying shared derived features

The phylogenetic tree below shows relationships among seven different vertebrate taxa and one non-vertebrate. Here are a few points to note before we deepen our analysis.

• A vertebrate is an animal with a backbone or a vertebral column. You’re a vertebrate. So are all mammals, fish, amphibians, reptiles, and birds.

  

• The tree includes one non-vertebrate species — the hagfish. Hagfish are closely related to vertebrates but lack a key vertebrate feature: a hinged jaw. In the context of this phylogenetic tree, that makes hagfish the outgroup. Including them in the tree helps us to better define the ingroup (the clade that we’re analyzing).

Note that you can scroll the text below the phylogenetic tree so that you can look at the tree as you read the text.

MISCONCEPTION ALERT: In a horizontally organized phylogenetic tree, like the one above, the vertical arrangement of the taxa says nothing about how closely related these taxa are. For example, a frog is no more closely related to a lizard than it is to a gorilla. That’s because the lineages in a phylogenetic tree can rotate around the nodes. A useful mental trick is to think of them as a mobile sculpture, with the root attached to the ceiling.

In other words, these two phylogenetic trees are equivalent.

Note that this is true regardless of the orientation. If the tree were oriented vertically, then the horizontal arrangement would be the one to ignore.

The basic idea is this: in a phylogenetic tree, you can’t identify the closeness of relationships between taxa by who’s next to whom. You can tell by moving back in time and finding the most recent common ancestor. Alligators and robins, for example, have a common ancestor at node “F.” Alligators and lizards have a common ancestor at “E.” Because the ancestor between robins and alligators is more recent than the common ancestor between alligators and lizards, you can conclude that alligators and robins are more closely related than alligators and lizards.

5. Flashcards: Using Traits to Trace Phylogeny

6. Challenge: Build a phylogenetic tree!

To understand how phylogenetic trees work, it helps to build one.

The table above is called a character table. In this context, a character is any quantifiable, inherited trait. A “1” means that the trait is present. “0” means that it’s absent.

When species share many characters, then they’re considered to be closely related. If they share very few characters, then they’re more distantly related. Take a look at the shark. Note that it shares the character of having a vertebral column with all of the other animals in the chart, but nothing else. That’s evidence that the shark can be classified as a more distant relation. Remember that, and use it in the exercise below.

Think of this as a puzzle. Don’t worry about getting the right answer right away. Use trial and error. The feedback will guide you to the solution.

One character listed in the table above might not be familiar to you. An amniotic egg is a complex egg found in birds, reptiles, and mammals (as opposed to the much simpler eggs found in fish and amphibians).

7. Evidence for Tracing Phylogeny

7a. Evidence from Morphology/Anatomy

In the phylogenetic trees that we’ve been discussing, the shared derived features for organizing the tree into clades have been based on morphology (the study of body structure). A slightly more specific term that’s almost identical to morphology is anatomy (the study of the structure of organisms). Different sources will use either term (or both).

In terms of phylogeny and classification, the important point is that using morphological or anatomical characteristics, you can look at a group of organisms and ask yourself questions like “Do they have fur? Do they have feathers?” Your answers would enable you to construct a phylogenetic tree.

Note that for one category of organisms — extinct species —  anatomical or morphological data is all we have. For example, should Archaeopteryx be classified as a bird or a dinosaur?

The answer is “both.” Birds are dinosaurs. If you’re interested in how that claim is supported by evidence, you can read about it in this article on BirdLife International’s website (the link opens in a new tab).

For living species, since about the 1940s, phylogenetic analysis has been based on molecular evidence. This evidence has focused on proteins and nucleic acids (DNA and RNA).

7b. Evidence from Proteins

In terms of phylogeny, the key thing to remember about proteins is that they’re composed of building blocks called amino acids. In the diagram at left, these amino acids are represented by three-letter abbreviations such as Asn, Gly, Phe, etc. During the process of protein synthesis, these amino acids are chained together in a genetically determined sequence.

A protein called cytochrome c has been widely used to determine evolutionary relationships. Why? Because cytochrome c is a key enzyme used by mitochondria during cellular respiration. As a result, every organism with mitochondria — that means millions of eukaryotic species — has this molecule. The fact that these species share mitochondria and cytochrome c is itself a shared derived feature, and it’s evidence that all eukaryotes make up a clade.

Cytochrome c is composed of 100 amino acids. In the table below, amino acids 60 through 66 within cytochrome c are compared for 9 species. In the table, the letters represent different amino acids (“K” represents lysine, “G” represents glycine, and so on).

Look at amino acid position 64. Every species on the table has the same amino acid at that position. It’s “L,” which represents leucine. At position 65, every organism except for the shark has the amino acid “M.”

By doing this type of analysis, you can count the amino acid differences within the cytochrome c protein among the members of any species. The result of one such analysis is shown below. Here’s how to read it. Find where the chicken and the moth intersect. The number 29 means that between chickens and moths, there are 29 amino acid differences in the cytochrome c sequence. Between chickens and penguins, there are three differences.

Complete the interactive reading below to see how the information in this table can be used to construct a phylogenetic tree.

7c. Evidence from DNA

The gold standard for analyzing phylogeny is DNA. To trace phylogeny, biologists find common DNA sequences and then identify mutations that have arisen in related lineages. Mutations within shared DNA sequences can be seen as shared derived features.

in the example above, the common ancestor, population A, and population B all form a clade with two branches.

The basic ideas behind phylogenetic analysis based on DNA are the same as we saw above for proteins.

1. In a given stretch of DNA, the more nucleotides that two species share, the more closely they’re related.
2. Similarities in DNA can be used as shared derived features for organizing species into clades.

The image below shows how DNA sequences were used to create a phylogenetic tree for 8 species.

Here’s some of the thinking involved in constructing the phylogenetic tree from this DNA evidence.

• The paired species (C and D, E and F, G and H, and A and B) were paired together because their sequences are the same. In other words, the shared sequence is a shared derived feature that puts each pair within the same clade.
• Species E, F, G, and H are organized into a clade because they share the nucleotide “T” at position 3. Again, the shared nucleotide is a shared derived feature.
• Species A and B share 3 nucleotide differences (at positions 2, 4, and 7). This makes their clade appear to be more distantly related to the clade that includes species C, D, E, F, G, and H.

The DNA of any species consists of millions or billions of nucleotides, so phylogenetic analysis of DNA usually involves huge amounts of data. The size of the data set is what makes DNA such valuable evidence for determining phylogeny. At the same time, that much data requires that most DNA-based phylogeny is done by computers. This type of evolutionary analysis is one of the topics studied in the emerging field of bioinformatics, which we briefly discussed in AP Bio Topic 6.8.

Using such analysis is enabling scientists to redraw the tree of life. For example, a 1999 analysis of DNA established that the land-living mammal that’s the closest relative of whales is the hippopotamus, as shown by the phylogenetic tree below.

7d. Phylogenies Using DNA Evidence

8. Is it a Cladogram or a Phylogenetic Tree?

Note that a distinction can be made between a cladogram and a phylogenetic tree.

Strictly speaking, a cladogram shows the branching pattern of evolution only, with no reference to time. A phylogenetic tree, by contrast, is usually scaled, with branch lengths being proportional to the amount of time between the events indicated on the tree.

Many sources, however, use the terms interchangeably.

9. Evidence for Tracing Phylogeny: Flashcards

10. What’s Next?

Proceed to Topic 7.9, Part 3: Clades, Taxonomy, and Molecular Clocks, the next tutorial in this AP Bio Unit 7 (Evolution)