Name__________________________________
Phylogenic Tree Activity
When considering evolution, one may envision an image of a tree that represents
the relationships of many organisms to one another and their ancestors. In the first part
of this activity, you are to propose a tree that represents your understanding of modern
organisms, compare it to your partner’s tree, and answer the questions before continuing.
In the second part of this activity, you will utilize an online program to compare a protein
that is found in each of those organisms to produce a tree and answer the questions.
Part I (10-15 minutes)
In your earliest days as a child, you have been comparing organisms and
categorizing them due to common and distinct characteristics. You also have gained
insights about similarities and differences between organisms through informal and
formal educational settings. With your partner, arrange the following organisms into a
tree diagram based on their shared characteristics.
Bull, Fish, Frog, Fruit Fly, Human, Moth, Mouse, Pig, Rat, Worm, and Yeast.
You must list the shared characteristics and your reasons for arranging the tree as you
did. For example, if three organisms are more closely similar to each other based on
anatomy than others in a group of seven, then you may draw a tree like the one below
(letters are used only for the example) on the second page of this handout.
A
B
C
D
E
F
G
X
Y
Z
X, Y, and Z represent branching points in the evolution of the life history of the
organisms A, B, C, D, E, F, and G.
Part I Tree
[Bull, Fish, Frog, Fruit Fly, Human, Moth, Mouse, Pig, Rat, Worm, and Yeast.]
Reasoning for the tree’s arrangement:
Part II (30-40 minutes)
There is a protein that is highly conserved (i.e. the same protein from different
organisms has a highly similar amino acid sequence) between a great assortment of
organisms. In fact, it is highly conserved between the organisms that you arranged into a
tree in the first part of this activity. The protein has many names, but the name we will
use is 8kD.
1. Why might a protein’s amino acid sequence be highly conserved?
2. Based on your tree from the first part of this activity, would you expect a tree
created by comparing the 8kD protein sequence to be similar or different from
it? Why?
The 8kD protein in question actually has two forms (two proteins that serve a
similar function with a slightly different amino acid sequence). Depending on the
organism, the first form is referred to as ‘LC8A’ or ‘1’ and the second form is referred to
as ‘LC8B’ or ‘2’. Read the excerpt from Wikipedia.org below about ‘phylogenetics’.
“In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth,
from genesis = birth) is the study of evolutionary relatedness among various groups of
organisms (e.g., species, populations). Also known as phylogenetic systematics,
phylogenetics treats a species as a group of lineage-connected individuals over time.
Phylogenetic taxonomy, which is an offshoot of, but not a logical consequence of,
phylogenetic systematics, constitutes a means of classifying groups of organisms
according to degree of evolutionary relatedness.
Phylogeny (or phylogenesis) is the origin and evolution of a set of organisms, usually a
set of species. A major task of systematics is to determine the ancestral relationships
among known species (both living and extinct). The most commonly used methods to
infer phylogenies include cladistics, phenetics, maximum likelihood, and MCMC-based
Bayesian inference. All methods depend upon an implicit or explicit mathematical model
describing the evolution of characters observed in the species included, and are usually
used for molecular phylogeny where the characters are aligned nucleotide or amino acid
sequences.”
Go to the following website: http://www.ebi.ac.uk/clustalw/ , and open the file named
“Tree Activity – LC8A”. Copy all of the type in the file and paste it into the box on the
bottom of the website that allows sequences to be pasted, alter the ‘Tree Type’ (an option
above the box) to ‘phylip’, click ‘Run’, and wait for the output. Once the output is
posted, scroll down to the bottom of the page and look at the Cladogram. Click on ‘Show
as Phylogram Tree’ and scroll down to the bottom of the page again. This diagram
should look similar to the tree you created originally.
Redraw the Phylogram Tree in the form that you used in the first part of this activity
(using the common names), so that you may compare the two easily.
LC8A Tree
3. Does your original tree (from Part I) match the tree created using a highly
conserved protein? How does it differ?
4. How might these trees be used to understand the history of life? What
additional information would be useful?
5. Would you expect LC8A and LC8B to be more similar to each other between
organisms, as opposed to within one organism? Why?
Again, go to the following website: http://www.ebi.ac.uk/clustalw/ , and open the file
named “Cytoplasmic Dynein 8kD”. Copy all of the type in the file and paste it into the
box on the bottom of the website that allows sequences to be pasted, alter the ‘Tree Type’
(an option above the box) to ‘phylip’, click ‘Run’, and wait for the output. Once the
output is posted, scroll down to the bottom of the page and look at the Cladogram. Click
on ‘Show as Phylogram Tree’ and scroll down to the bottom of the page again. This
diagram should look similar to the tree you created originally.
6. What additional information is included in this tree that is absent from the first
two you made?
7. What kind of tree would you expect if you used a different protein that was
also important for basic cellular processes?
8. What kind of tree would you expect if you used a protein that was not as
highly conserved?