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Introduction to Phylogeny:
How to Interpret Cladograms

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Welcome to the online Cladogram Exercise 1 Web site. This online assignment will help you get more comfortable with cladograms. They are not as confusing as you probably thought they were. After completing the following steps, you will be on your way. Your feedback is valuable and encouraged.

Cladogram Terminology: Start with some basic definitions of terms such as node and branch.

Sister Taxa: Learn what a sister taxon is and why recognizing them will help you with all of the following steps.

Cladogram Styles: Examples of the same cladogram drawn in different styles and orientation.

Rotate at a Node: Are the two cladograms identical, merely rotated at nodes, or are they different topologies?

Polytomies: Are they "hard" or "soft" and how do they relate to strict consensus estimates?

ASSIGNMENT PRINTING INSTRUCTIONS (OPTIONAL)

To print out the lab for completion or for later reference:

1. If you want to conserve paper you can first reduce the scale after selecting Page Setup from the File menu.
2. Select Print from the File menu.
3. Saving the assignment to disk will not help because the resulting ASCII (text only) file will lack the tree graphics.
4. Printing this assignment will not automatically print other Web pages of on-line interactive help for provided sample questions. If you have limited time, first complete the sample questions and you can separately print the (correct) answer pages if you want.
5. E-mail to Prof. Eernisse (deernisse@fullerton.edu) if you find problems with these instructions or the links (remember to include your name and email address).

Each internal node is also at the base of a clade, which includes the common ancestral population (node) plus all its descendents. For example, the clade that includes both Taxon 2 and Taxon 3 is hypothesized, in this cladogram, to include their shared ancestor (actually, an interbreeding population of organisms) at internal node C and everything it gave rise to (in this case, Taxon 2 and Taxon 3). Likewise, the clade that includes all four terminal nodes and their most recently shared common ancestor originates at node A and includes all its descendents (i.e., everything to the right of node A).

Node A is termed the root of the cladogram because it is at the base of the cladogram. As in this case, the root is normally drawn with a dangling branch extending earlier (to the left in this case) of the root to indicate that this clade also is part of other more inclusive clades of living organisms, originating from even earlier ancestral populations. Eventually, this dangling connection would lead clear back to the ancestor of all of life. You can think about this cladogram as the hypothesis of what branching events happened since the moment in time when the ancestral population at node A first speciated, that is, split from one into two (in this case) species. Later in time, there were further splits, resulting in new clades that are hierarchically nested within the original clade. In particular, the clade arising from the ancestral population at node B originated later than the one arising from the original ancestral population at node A. The clade arising from the ancestral population at node B is hierarchically nested within the clade arising from node A. To use an example, mammals are nested hierarchically within the clade of all vertebrate animals. The common ancestor of all vertebrates lived before the common ancestor for all mammals. There are vertebrates that are not mammals, but all mammals are vertebrates. Mammals are a particular subgroup or part of the whole vertebrate clade.

There are four terminal nodes in this example. These include members of the ingroup: Taxon 1, Taxon 2, and Taxon 3, and a single outgroup taxon. The clade arising from node B includes all three ingroup taxa. The purpose of a cladogram is to express a particular hypothesis for the relative branching order of the ingroup taxa. This cladogram example suggests that Taxon 2 and Taxon 3 more recently shared a common ancestor than either does with Taxon 1. While this hypothesis implies that the ancestral population at node B lived before the ancestral population at node C, it does not stipulate how much earlier it lived. In other words, the cladogram is only a hypothesis of the relative order of branching; it does not indicate how much absolute time past between branching events.

You should be able to find a clade originating from each internal node in this particular cladogram example. A helpful way to think about which groupings of terminal nodes are clades, in a particular cladogram, is the snip rule. Whenever you "snip" a branch directly beneath an internal node, a clade falls off. The three such clades here are:
Taxon 2 + Taxon 3
Taxon 1 + (Taxon 2 + Taxon 3)
and Outgroup + (Taxon 1 + (Taxon 2 + Taxon 3)).
In contrast, a grouping of Taxon 1 and Taxon 2 without Taxon 3 is not a clade, according to this cladogram hypothesis, because there is no way to snip off the first two without Taxon 3 also falling off.

The use of parentheses above helped to more concisely indicate sister taxon associations within a clade. This reflects an accepted standard to specify a cladogram hypothesis with nested parentheses. Using this convention, the example cladogram can be unambiguously stated as:
(outgroup (Taxon 1 (Taxon 2, Taxon 3)))
Can you draw the following alternative cladogram hypotheses?:
(outgroup (Taxon 3 (Taxon 1, Taxon 2)))
(outgroup (Taxon 2 (Taxon 1, Taxon 3)))

Click here to open new window with above cladogram example.

NAME:

1. Taxa join at an internal node with their sister taxon, so the sister taxon of Taxon 3 is
Select an Answer a. Taxon 1 b. Taxon 2 c. Taxa 1 and 2 d. the outgroup taxon
 

2. The sister taxon of Taxon 1 is
Select an Answer a. the outgroup b. Taxon 2 c. Taxon 3 d. the clade (Taxon 2 and Taxon 3)

[Note: For this and following questions you should interpret "the clade (Taxon 2 + Taxon 3)" to include not just these terminal nodes but also the common ancestor of Taxon 2 and 3 and all its descendants; this follows from the definition of clade]

3. The sister taxon of Taxon 3 is
Select an Answer a. Taxon 1 b. Taxon 2 c. the clade (Taxon 1 and Taxon 2) d. the clade (Taxon 1 and Taxon 3)

4. The sister taxon of the outgroup is
Select an Answer a. Taxon 1 b. Taxon 1 and Taxon 2 c. the clade (Taxon 2 and Taxon 3) d. the ingroup

5. The most recent common ancestor of Taxon 1 and Taxon 3 is
Select an Answer a. the outgroup b. at node A c. at Node B d. at Node C

6. The most recent common ancestor of Taxon 2 and Taxon 3 is
  Select an Answer a. Taxon 1 b. at node A c. at Node B d. at Node C

7. The most recent common ancestor of the outgroup and the ingroup is
Select an Answer a. the dangling branch b. the root (Node A) c. at Node B d. Taxon 1

8. What clade (if any) is hierarchically nested within the ingroup?
Select an Answer a. the outgroup b. (Taxon 1 and Taxon 2) c. (Taxon 2 and Taxon 3) d. None of the above

9. How many total clades are depicted, not including terminal nodes?
Select an Answer a. one b. two c. three d. four

10. Which of these groupings of terminal nodes does not represent a clade, assuming their most recent common ancestor is included?
Select an Answer a. the ingroup b. (Taxon 1 and Taxon 2) c. (Taxon 2 and Taxon 3) d. (Taxon 1 and (Taxon 2 and Taxon 3))

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REARRANGED CLADOGRAMS: Answer True or False. Remember, internal nodes can be rotated and cladograms can be drawn in different styles with different branch lengths without altering the cladogram hypothesis of sister taxon relationships.

11.  Select an Answer a. true b. false Cladograms A and B below are equivalent, only they may be drawn differently.

12.  Select an Answer a. true b. false Cladograms C and D below are equivalent, only they may be drawn differently.

13.  Select an Answer a. true b. false Cladograms E and F below are equivalent, only they may be drawn differently.

14.  Select an Answer a. true b. false Cladograms G and H below are equivalent, only they may be drawn differently.

15.  Select an Answer a. true b. false Cladograms I and J below are equivalent, only they may be drawn differently.

16.  Select an Answer a. true b. false Cladograms K and L below are equivalent, only they may be drawn differently.

17.  Select an Answer a. true b. false   Cladograms M and N below are equivalent, only they may be drawn differently.

18.  Select an Answer a. true b. false   Cladograms O and P below are equivalent, only they may be drawn differently.

19.  Select an Answer a. true b. false   Cladograms Q and R below are equivalent, only they may be drawn differently.

20.  Select an Answer a. true b. false   Cladograms S and T below are equivalent, only they may be drawn differently.

Your LAST name:  

Instructor:  Eernisseother

21 (Not Graded). Please assess your present level of confidence in answering questions 1-20.

Select an Answer a. High: These questions are easy! b. Moderate: Most questions are easy but a few were challenging. c. Average: These questions were challenging but I think I understand the concepts. d. Low: Cladograms are still a bit of a mystery to me. e. No clue: I have no confidence I could answer similar questions on an exam.

Review each question and assess whether your preferred response appears in each window before you select the Submit button.  Only the FIRST set of responses you submit will count!

When you submit your responses, you will be taken to a summary showing how a cladogram is used to represent evolution.  Print or bookmark the next summary page so you can refer to it when needed.

NOTE: SORRY! THE SUBMIT BUTTON IS BROKEN. THE ANSWER KEY WILL BE POSTED BY THE DATE INDICATED ON THE COURSE SCHEDULE. TO MAKE IT EASIER TO COMPARE WITH THE KEY, ANSWER BY LETTER, NOT BY WHAT THE ANSWER SAYS.

Feedback on particular questions that confused you are welcome!
Email feedback to deernisse@fullerton.edu

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This website development began on August 27, 2000 and was last modified on February 22, 2005.

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