DNA Similarities and Phylogeny II
This is what you should have come up with...
Y
C
Y
C
B
R
F
A
0
4
2
10
6
6
0
4
10
6
6
0
10
6
6
0
10
10
0
2
B
R
F
A
0
Which species are the most similar? Why?
Now, let's construct a tree of similarity below, following the steps given. Try this on a piece of
paper as we go along; you'll do it for real later. This diagram will show all the data at once.
a) What species are the most similar? Put the letters at the top of the chart. Put a dot below them
opposite the number of nucleotide differences between them. Draw lines connecting the two
species to the dot. (Do this for each pair of very closely related species.) (Note: I did one pair for
you.)
b) What species is most similar to one pair from part a? Put its letter at the top and put a dot
below it opposite the number of nucleotide differences between it and either of the pair of
species from part a. Draw lines connecting the third species to the dot below the pair.
c) Repeat step b for each group of species, working from most similar to least similar.
Set the diagram up like this, with a scale of nucleotide differences down the side:
We'll plot two of the most similar, B & Y. They show a difference of 2 nucleotides. So, we
connect the lines at 2. After you plot these, the diagram should look like this:
Now let's add Y, which is the next closest (lowest number). C is different from Y by 4. It is also
4 from B, so this fits. It now looks like this:
F & A are also only separated by 2 so we need to connect them like B & Y:
Now we need to connect them to B, Y, and C. F is 6 from B, Y, and C. A is also 6 from each of
those three. This means they should all connect at 6. It should look like this then:
And lastly, we need to hook R to the rest. It is 10 from all of them. This means the
connection is back at 10:
To check your work, go back to the table. Check every number. They should all fit.
When you finish this process, you should have a diagram that gives the number of nucleotides
between any two species. If you want to know, say, how different the blue-throated garbler
(B)and the field twitterer (F) are, just follow the lines down from both of them till you come to
the spot where they join. Then look over to the side and see how many nucleotide differences
there are at that point --it will be 6, which is what was in the table. Note that the diagram also
resembles a phylogenetic tree. In fact, if the vertical axis were time, it would be a tree of
relationships, and the dots (connection points) would be common ancestors of groups.
DNA Similarities and Phylogeny II
Assignment:
What assumption is necessary for us to consider the vertical axis to be a measure of time?
Here are the data and bird names again:
CTAGC
Yellow-throated Garbler (Y)
CTGGC
California Garbler (C)
CTAGC
Blue-throated Garbler (B)
AGGCC
Red-footed Chump (R)
CTGGA
Field Twitterer (F)
CTGGA
Alzheimer's Twitterer (A)
AAGTA
AAGTA
AACTA
ATGGA
AAGGC
AAGGA
CTACT
CTTCT
CTACT
CGACT
CTAGT
CTAGG
TAGGA
TAAGG
TAAGA
ACAGA
TAAGA
TAAGA
Using your completed diagram, you can divide these birds into groups of close relatives. One
way would be to group them as garblers, twitterers, and chumps. Why is this a reasonable way to
group them?
How many nucleotides are different between the field twitterer and the yellow- throated garbler?
Between the Alzheimer's twitterer and the California garbler?
Why are these the same? Hint: They should only be the same if the molecular clock assumption
is correct.
Now you will do this for real on an assignment looking at primates!