|Biology 325: Cladogram Exercise 3 – Indented Classification Skills
This exercise depends on the following article:
Angielczyk, K. D. 2009. Dimetrodon is not a dinosaur: Using tree thinking to understand the ancient relatives of mammals and their evolution. Evolution: Education and Outreach, available Online First at: http://www.springerlink.com/content/120878/
Also available for download under External Links at the Biol. 325 Blackboard site.
Consider Figure 2 from the above article:
This corresponds to the following unranked indented classification:
Notice how any two (or more) taxa indented under a higher grouping are at the same level of indentation if they are sister taxa. For example, Cat and Human are sister taxa under Clade 5. However, please note that Crocodile and Turtle are sister taxa under Clade 4. They are not sister taxa of cat and human, even though it might appear they are indented at the same level. Crocodile and turtle are nested within clade 4 and cat and human are nested within clade 5.
A. What is the sister taxon of Clade 4? ____________________________________________________
B. What is the sister taxon of Clade 2? ____________________________________________________
C. How does one construct a cladogram that exactly corresponds to the following unranked indented classification?
To complete this question, follow these steps exactly without turning the page over until you complete step 5:
1) Get out a blank page and a pencil with an eraser (recommended).
2) Put an asterisk after each terminal taxon, which are those taxa that don’t have anything indented immediately below them (i.e., in the very next line).
3) With your paper sideways (in landscape orientation), list the terminal taxa only in a single vertical column along the right margin of the bottom two thirds of your page.
4) Draw a line diagonally across the page from the upper left corner to the last-listed terminal taxon.
5) Connect up terminal taxa that are sister taxa. There can be more than two sister taxa that join at the same ancestral node, for example, in the case of ancestral taxon Gymnophiona (See “polytomy” note at end of exercise). Note that not all of the nodes connecting sister taxa will lie on the diagonal line. For example, if you drew the node connecting Anura and Caudata on the diagonal line then you drew the cladogram incorrectly. You should have started the cladogram as below:
6) Continue connnecting the terminal taxa and ancestral nodes together so that you are joining clades. Pay attention to which clades are sister taxa, according to the phylogenetic classification. Sister taxa are always at the same level of indentation. For example, Batrachia and Gymnophiona are sister taxa within the ancestral taxon, Amphibia (called "Lissamphibia" in many systems). (Note: It is OK to use the first three letters to abbreviate the taxon names.)
7) Finally, remember to leave a "dangling root" continuing beyond the most inclusive (deepest) node to indicate that these organisms are assumed to share a common history with other organisms outside this clade. A dangling root is simply the "tail" at the base of the lowest node of your cladogram, when you turn your paper so the names are on the top.
Question D: Comfortable? Try the following. On the next page are two competing classifications. Follow the above rules to draw each cladogram. Note that the hypothesized sister taxon relationships are mostly the same but differ in particular cases.
Craniate Classification 1:
Craniate Classification 2. Simplified from Philippe Janvier’s cladograms at http://tolweb.org/tree?group=Vertebrata&contgroup=Craniata
Question E: Next, provide the answers to the following study questions:
1. What is the sister taxon of lampreys in each classification?
2. What is the sister taxon of heterostracans in each classification?
3. Turn the cladogram of jawed fishes (clade Gnathostomata) below into an indented classification:
3 (cont.) Practice by writing the corresponding indented classification below, and then copy it to the paper you turn in.
Question F: (Note that some question similar in nature will be asked on the final exam.) Consider the following cladogram. The position of turtles is controversial but I have use the conventional placement based on morphology, not one of the more recent placements based on molecules.
The following sets of four taxa have been scrambled in order so ignore the order that they were listed. The exception is that the first, underlined, taxon is always the root branch, so is sister taxon to all the others. Draw a cladogram that matches the phylogeny and classification in the above tree but only includes the five taxa listed. To answer this question successfully, you need to consider the sister taxon relationships of only the taxa listed.
goldfish, human, frog, salamander, lizard
shark, lizard, lungfish, frog, goldfish
shark, lungfish, goldfish, human, salmon
human, lizard, bird, turtle, crocodile
crocodile, T. rex, Iguanodon, pterosaur, bird
Question G. Using the skills you have gained, turn either Fig. 4A (easier) or 4B (harder) from Angielczyk (2009) into an unranked indented classification.