Systematics lab assignment answers

You will need a Scantron in lab for this assignment. Use the long one with 50 questions per side. It doesn’t matter what color.

This page includes questions about using phylogenetic trees in systematics. You should work together with your lab partners to answer these questions during lab. There are two parts: a Scantron part and a blank paper part.

You should have already read the Phylogenetic Trees page; you may want to look at it again to help you answer some of the questions on this page.

The purpose of this exercise is to help you understand systematics concepts, which will be covered on lecture exams. The types of questions in this problem set won't be on the lab exam, but we will be using cladograms in lab.

Scantron questions

The correct answers are highlighted in orange.

Answer the following questions on your Scantron. You should work with your fellow students to come up with the right answers (or the wrong ones, if you prefer), but turn in your own individual Scantron with your name on it. Write “Systematics” in the subject area and include today’s date.

These questions are about the phylogenetic trees in the research article Updating the evolutionary history of Carnivora (Mammalia): a new species-level supertree complete with divergence time estimates.

Figure 2

You can look at figure 2 in the original article or in the Phylogenetic Trees page of this site.

1. Are seals more closely related to dogs or to giant pandas? In other words, did the giant panda share a common ancestor more recently with cats or with dogs?

  1. Seals are more closely related to dogs.
  2. Seals are more closely related to giant pandas.
  3. This question can't be answered from the cladogram.

2. Are red pandas more closely related to raccoons or to giant pandas?

  1. Red pandas are more closely related to raccoons.
  2. Red pandas are more closely related to giant pandas.
  3. This question can't be answered from the cladogram.

3. Are "pandas" (red pandas and giant pandas together, not including any other species) a monophyletic group?

  1. Yes.
  2. No.
  3. This question can't be answered from the cladogram.

4. Are horses more closely related to dogs or to rats?

  1. Horses are more closely related to dogs.
  2. Horses are more closely related to rats.
  3. This question can't be answered from the cladogram.

5. How long ago did the last common ancestor of humans and Norway rats live? (Round your answer to the nearest 5 mya or million years ago, and pick the closest answer.)

  1. 50 mya
  2. 60 mya
  3. 65 mya
  4. 80 mya
  5. 105 mya

6. How long ago did the last common ancestor of humans and dogs live? (Round your answer to the nearest 5 mya or million years ago, and pick the closest answer.)

  1. 50 mya
  2. 60 mya
  3. 65 mya
  4. 80 mya
  5. 105 mya

7. How long ago did the last common ancestor of cats and dogs live? (Round your answer to the nearest 5 mya or million years ago, and pick the closest answer.)

  1. 50 mya
  2. 60 mya
  3. 65 mya
  4. 80 mya
  5. 105 mya

8. How long ago did the last common ancestor of cats and horses live? (Round your answer to the nearest 5 mya or million years ago, and pick the closest answer.)

  1. 50 mya
  2. 60 mya
  3. 65 mya
  4. 90 mya
  5. 105 mya

Figure 3: Dog cladogram (family Canidae)

Here's a modifed version of figure 3:

Cladogram of the Canidae

Or you can see it in the original article. This tree shows only the dog family (Canidae), which was reduced to a single line in figure 2. In fact, there are a lot of dog species in the world. The next few questions are about the Canidae tree, and relate to phylogeny (evolutionary relationships) and taxonomy (classification and naming).

9. Are the animals commonly called "foxes" a monophyletic group?

  1. Yes.
  2. No.
  3. This question can't be answered from this phylogenetic tree.

10. Is the genus Canis a monophyletic group?

  1. Yes.
  2. No.
  3. This question can't be answered from this phylogenetic tree.

11. How long ago did the last common ancestor of coyotes and the gray wolf live?

  1. 2.5 million years ago.
  2. 10 mya.
  3. 16.5 mya.
  4. 255 mya.
  5. This question can't be answered from this phylogenetic tree.

12. How long ago did the last common ancestor of coyotes and the gray fox live?

  1. 2.5 million years ago.
  2. 10 mya.
  3. 16.5 mya.
  4. 255 mya.
  5. This question can't be answered from this phylogenetic tree.

13. According to the cladogram, the genus Urocyon (gray fox) was the first to split off from all the other members of the family Canidae. Are the researchers confident that this is true?

  1. Yes.
  2. No. The error bars, indicating uncertainty, are very large compared to the difference in timing of the splits. Since the 95% confidence intervals of the first few splits overlap, the researchers cannot be confident about the correct order of the first few splits. On the other hand, the analysis shows a high degree of confidence that the two species of Urocyon split from each other long after Urocyon split from the rest of the dog family.
  3. This question can't be answered from this phylogenetic tree.

Cat cladogram

Here's another figure from the same article:

Cladogram of the Felidae

14. According to the cladogram,  is the genus Panthera monophyletic?

  1. Yes.
  2. No.
  3. This question can't be answered from this phylogenetic tree.

15. According to the cladogram,  is the genus Lynx monophyletic?

  1. Yes.
  2. No.
  3. This question can't be answered from this phylogenetic tree.

16. According to the cladogram, is the genus Felis monophyletic? (What is Felis manul?)

  1. Yes.
  2. No. Felis manul should probably be moved to another genus.
  3. This question can't be answered from this phylogenetic tree.

17. How long ago did the last common ancestor of lions and domestic cats live?(Choose the closest answer, in mya: millions of years ago.)

  1. 5 mya.
  2. 9 mya.
  3. 15 mya.
  4. 16 mya.
  5. 24 mya.

That's it for the Scantron. Turn in your answers before you leave lab, and move on to the next part of this lab activity...

Blank paper

I'm calling it blank paper because that's what you start with; by the time you leave lab, you should turn in a paper with answers to the questions below. Work in a group for this part, and turn in one answer sheet for four or five people, with all your names at the top. The previous questions asked you to interpret cladograms from a research article; now I'm asking you to make cladograms of your own. Cladograms are often defined in terms of characteristics that are present on one branch but not on another, so that's what you should do next.

  1. One of the goals of modern systematics is that named taxa (orders, families, genera, species, etc.) should be monophyletic groups. As biologists learn more about biological diversity (especially through comparisons of DNA sequences), it sometimes becomes clear that some older taxonomic names don't apply to monophyletic groups. These names should be changed to apply to clades. For example, according to fig. 3, Cuon alpinus should be renamed Canis alpinus, because any clade that includes all the other Canis species must also include Cuon alpinus. Based on the cladograms on this page, give two other examples of species for which the genus name should be changed to accurately reflect clades, and suggest how the genus name should be changed.

Answer: I added this new question after you did the assignment. Don't worry, you weren't supposed to answer it! I'm including it here to show you something about taxonomy and phylogeny.

Fig. 3: Vulpes ferrilata should be renamed Dusicyon ferrilata. As mentioned in the example, Cuon alpinus should be renamed Canis alpinus.

Cat cladogram: Felis manul should be placed in a new genus with a new name. Uncia uncia should be renamed Panthera uncia.

On the other hand, experts could argue whether Caracal caracal and Profelis aurata should be placed in the same genus, but the current names do apply to clades.

In fact, some of these names have already been officially changed as a result of the research shown in these cladograms. Click on the links in this answer box to see the species with changed names.

The previous questions asked you to interpret cladograms from a research article; now I'm asking you to make cladograms of your own. Cladograms are often defined in terms of characteristics that are present on one branch but not on another, so that's what you should do next.

  1. Make a cladogram showing eight different species that you are familar with. Be as specific as you can -- "tree" is not a species, but "Douglas fir" is. No more than four can be animals, and no more than one from the order Carnivora. Don't look up the phylogeny -- instead, make up your own cladogram. For each node on the cladogram, define a characteristic that separates one branch from another. For example, if you had the cat family and the dog family, you could say "retractable claws" for the cats and "no retractable claws" for the dogs. Each branch should have a yes-or-no definition.
  2. Make a cladogram based on the table below. The column at left contains names of species. Don't look them up -- it's better if you don't know what they are! Characteristics such as "chloroplasts" fill the remaining columns; 1 means that the species has that characteristic, 0 means it doesn't. Use these characteristics to define the branches on your cladogram. For example, at one node, one branch is "chloroplasts" and the sister branch is "no chloroplasts." The order of the branches is up to you, but try to make the simplest possible cladogram.

Table showing characteristics for classifying some unknown organisms.

Hints: For the first question, you started with known species and then found differences that you could use to separate them into clades. For the second one, you can start with the defining characteristics and make a cladogram showing how they fit together. In principle, it should be easy; in practice it's challenging because not all similarites between species are homologies.

A characteristic that is shared by almost all the species probably  evolved early, so it should define one of the first branches of your cladogram. You don't necessarily need to know what the characteristics are to use them in your cladogram. Many of them are features that will be discussed in Bio 6A or 6B (I could tell you now, but that might spoil the fun). You don't necessarily need to use all the characteristics to make the branches on your cladogram.

You may find it very helpful to look at your lecture notes or at Campbell to help you answer these two questions; there's a figure in Campbell that shows exactly how to do this.

When you finish your Scantron questions and the two cladograms for the "blank paper" part, you're done! Make sure your all the group members' names are on the "blank paper" part with the cladograms and turn it in.

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