Lab#3: Cladograms and Phylogenetic Analysis using BLAST, Part 2

More Practice with organizing Cladogram data and turning it into a tree


Let’s move on to another activity to see if we can get somewhere with making cladrograms. Here is a new set of data:making_tables_second_cladogram_activity

Take a few minutes and try to make the Venn diagrams. You will notice that the data is a lot neater than our first example, as in there is a clear progression of characteristics.


Did your resulting Venn diagram look like this?









Good! Now that we have an easier Venn diagram to work with, can you make the tree that goes with this? Give it a try before looking at the answer below – it is really important to struggle with learning a new skill before looking at the solutions. Once you have worked out a cladogram, you can look on the webpage where the question comes from – the cladogram is about halfway down the page:

Now, because we all know a bit about our ancestors and how animals fit into a larger cladogram, this particular cladogram looks way too simple to us, and almost wrong. However, it is the correct cladogram based on the given data, and that is what you might see on an AP exam.

Try another one  – it is on the same website as above, a little below the cladogram.

Any questions? Problems? Here are a few questions for you:
— What is the difference between a derived charateristic and an ancestral one? (Go back to Berkeley’s page about this to read again).
— What is the difference between homologous and analogous characteristics? (Berkeley’s evolution site has a nice explanation on this page).
— What is a clade? (related page on Berkeley’s evolution site).

More Practice with organizing Cladogram data and turning it into a tree

Let’s return back to our original data table and see what we’ve been missing. Download this document and have it accessible for reading/work: lemke_exploring_phylogenetic_reconstruction_canimacules

Instead of trying to copy everything into the webpage, I’m going to write up a walk through. Here goes:
Pages 1-2: a basic introduction and a cladogram covering most living vertebrates. Take a good look at this cladogram: did someone put this together with a simple table of data about shared derived characteristics? No, this is the work of multiple scientists using many tables of data and many characteristics to work out the Tree of Life. One of the things that can be difficult in learning how to write up cladograms is that these larger ones have so much data behind them, we think our simple ones need to look like them.
— In any case, what information can you glean from this cladogram? Do salamanders have a tetrapod limb with 5 digits? Scales covering their bodies? What else?
Pages 3-5: This part discusses why we classify living things, and the usefulness of this classification. And there are a few questions which I’ve copied here:
— Most mammals give birth to live young, but a small number of mammals (the Prototheria) lay eggs. Answer the following
set of questions, referring to Figure 1 if you need to, to make sure you are comfortable applying these concepts.
— Is egg-laying a derived or primitive feature among mammals? How do you know?
— Is the shared trait of egg-laying, by itself, an indication that egg-laying mammals are more closely related to each other than
either is to other mammals?

For the rest of the document, please see below.
— For what group of amniotes is live birth a shared derived characteristic?
— For what group of amniotes is shelled eggs a shared derived characteristic?

Pages 6-7:
Now the professors go through the construction of our original data table and offer up a different method of constructing the cladogram (finding the two organisms that share the most characteristics). Did you try and finish up the cladogram without looking at what they did?

Working with Caminalcules. Wait, what??

Pre-Lab Activity 1 (meaning we should go over the answer together in lab)

Back to this document: blast_lab_ap_lab_3_using_bioinformatics_to_invesitigate_evolutionary_relationships_-25672528

Pages 4-5: See the 4 aliens at the top of the page? Do the activity and make a cladogram. What are synapomorphies?

Now to take another tack; go to this website, and read through the section about cladograms:

He has some great information about cladograms that will make more sense now that you’ve been wrestling with making them.

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