Lab#3: Cladograms and Phylogenetic Analysis using BLAST, Part 1

Start here: what is a Cladogram anyway? And how do you make one?

 

Learning about Cladograms:

1. Begin here on the Berkeley site with an introduction to phylogenies and cladograms (just read through the webpages for now):

http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_05
— What are examples of speciation events?

http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_06
http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_07

http://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_08
— What are characters?
— What are shared derived characters?

2. Now, let’s put some of this information into action. If I give you the following table, can you construct a cladogram from it? It is important to try this and struggle with it even if you think you haven’t learned enough about cladograms yet. Just give it a try and some time. Hint: don’t try to make a cladogram right away, think about organizing the information in the table in a visual or graphical way.

making_first_cladogram_activity_table

 

 

 

 

 

Okay, after you have wrestled with this for a while (and this isn’t an easy cladogram for beginners), try this: use a Venn diagram to organize the information. Work with this idea before reading further, I can’t stress enough that you need to wrestle with this before looking at someone else’s work. Some other ideas: can you arrange the data in the tables to show relationships? Which two animals share the most derived characters?

 

Here’s what I came up with:

Make a circle with “Human” and any traits that only humans have (in this case, none). But humans and porpoises are the only ones who share “nipples”, so make another circle outside humans with “porpoise” and “nipples”. Like this:

img_8189

 

 

 

 

 

 

 

 

 

Okay, so far, so good. So, is it just a matter of making circles? One of the counter intuitive things about Venn diagrams is that “Humans” have the characteristics of “live birth” and “nipples”, but if I had put “bipedal” in the “human” circle, porpoises would NOT have that characteristic. The “human” circle shares everything in the porpoise circle, but not vice versa. Continuing on – remember, I am working from the chart above:

img_8192

 

 

 

 

 

 

 

 

 

Do you notice any problems yet? How about now:

img_8194

 

 

 

 

 

 

 

 

 

 

And then when I try to fit in the last characteristic, I run into real problems:

img_8199

 

 

 

 

 

 

 

 

 

 

Okay, one last try to organize the information:

img_8202

 

 

 

 

 

 

 

 

 

 

 

 

Nope, that doesn’t really work either. And why? Well, one of the reasons is because evolution is not linear and orderly, traits disappear and reappear and it can be difficult to ascertain if a character has disappeared and reappeared, or if the organism isn’t in the sequence at all. Keep trying with this, we are going to come back to this cladogram. But it is time to move on to Part #2.

 

 

Leave a Comment