Molecular Biology and Primate Phylogenetics
Introduction
Studying the nucleotide sequences of DNA, and/or the amino acid sequences of proteins, gives
scientists one of a growing number of ways to analyze relationships and infer ancestry for life on earth.
The work of molecular biologists has been important in further clarifying and refining our
understanding of not only family trees (phylogenies) for all life on earth, but also the possible rate of
mutation, selection, and speciation.
Among the first proteins to yield its amino acid sequence was hemoglobin, and it remains today one of
the most investigated of all proteins. The basic unit of hemoglobin consists of an iron-containing
porphyrin (heme) that can reversibly bind oxygen attached to a globin polypeptide chain that is usually
no less than 140 amino acids long. In vertebrates, hemoglobins are usually the primary protein of red
blood cells, making them relatively easy to isolate and purify in large quantities. (Strickberger, M. W.
Evolution. Jones and Barlett Publishers, 1990)
Purpose
To examine the amino acid sequence differences for a specific protein (beta hemoglobin) in several
primate species, and from this infer ancestral relationships.
Procedure Part A: Table 1 lists the comparison of the 146 amino acid beta chain of the hemoglobin
molecule in 7 selected primate species. Notice that the amino acid position numbers may not be
continuous. This is because those that are the same for ALL seven species have been left off the chart
to save space. Count the number of amino acid differences between each of the possible pairs of
organisms using the data below and then enter it in Table #2. Draw a diagonal line from the upper left
to lower right of the grid and then cross out all of the squares in the upper right side of the table. No
need to duplicate your work.
Procedure Part B
The data that you have gathered and entered in Table 2 represents the amount of time (in amino acid
substitutions) since one organism has diverged from a common ancestor with another organism. A
fewer number of amino acid differences between any two creatures implies that the two organisms
share a relatively recent common ancestor, whereas a large number of amino acid differences implies
the two organisms share a relatively distant common ancestor. Scientists can take this information to
construct a phylogenetic tree that shows the branching patterns of descent. Using the data from Table
2, enter the appropriate letter (A, B, C, D, E, F, or G) in each of the appropriate spaces above the
phylogenetic tree in Graph 1. The vertical line to the left of the tree represents time which will be used
later.
Discussion
1. The following are the list of primates analyzed: lemur, gorilla, human, chimpanzee, gibbon, rhesus
monkey, squirrel monkey. Assign a letter to each primate based on an analysis of the animal and the
phylogenetic tree.
2. Which two species share the most recent common ancestor? Why?
3. What is the reason for the differences in amino acid sequences among the different primates? In
other words, how did they arise?
4. If chimps and humans are about 99% identical and horses and zebras are 96% identical in their
amino acid sequences for hemoglobin, which pair do you think shares a more recent common
ancestor? Explain your answer.
5. Upon examining the DNA sequences for hemoglobin between chimp and human and horse and
zebra, the data indicates that horse and zebra show 99% homology and human and chimp show 97%
homology. Who is more closely related?
6. What might explain the difference in sequence homology for the protein data and DNA data in
question 4 and 5? Explain your answer. Hint: use the codon sheet. Which data do you think is more
reliable?
7. By examining evidence from fossils, and molecular and anatomical comparisons, evolutionary
biologists have inferred that lemurs and humans share a common ancestor at about 43 million years
ago. What appears to be the rate of mutation for beta hemoglobin (1 amino acid/#million years)
Table 1: Amino Acid Sequences of parts of Hemoglobin for Various Primate Species
amino
acid
position
1
2
4
5
6
8
9
10
12
13
21
22
33
50
52
56
69
73
76
80
87
104
111
112
113
114
115
116
120
121
122
123
125
126
130
amino acid
species A
val
his
thr
pro
glu
lys
ser
ala
thr
ala
asp
glu
val
thr
asp
gly
gly
asp
ala
asn
thr
arg
val
cys
val
leu
ala
his
lys
glu
phe
thr
pro
val
tyr
species B
val
his
thr
pro
glu
lys
ser
ala
thr
ala
asp
glu
val
thr
asp
gly
gly
asp
ala
asn
thr
arg
val
cys
val
leu
ala
his
lys
glu
phe
thr
pro
val
tyr
species C
val
his
thr
pro
glu
lys
ser
ala
thr
ala
asp
glu
val
thr
asp
gly
gly
asp
ala
asn
thr
leu
val
cys
val
leu
ala
his
lys
glu
phe
thr
pro
val
tyr
species D
val
his
thr
pro
glu
lys
ser
ala
thr
ala
asp
glu
val
thr
asp
gly
gly
asp
ala
asp
lys
arg
val
cys
val
leu
ala
his
lys
glu
phe
thr
gln
val
tyr
species E
val
his
thr
pro
glu
lys
asn
ala
thr
thr
asp
glu
leu
ser
asp
gly
gly
asp
asn
asn
gln
lys
val
cys
val
leu
ala
his
lys
glu
phe
thr
gln
val
tyr
species F
val
his
thr
gly
asp
lys
ala
ala
ala
ala
glu
asp
val
thr
asp
asn
gly
asp
thr
asn
gln
arg
val
cys
val
leu
ala
his
lys
glu
phe
thr
gln
leu
tyr
species G
thr
leu
ser
ala
glu
asp
ala
his
thr
ser
glu
lys
val
ser
ser
ser
ser
glu
his
asn
gln
lys
ser
ala
glu
ser
glu
leu
his
asp
lys
ser
ala
val
phe
Table 2: A comparison of the number of amino acid differences between seven primate species.
A
A
B
C
D
E
F
G
B
C
D
E
F
G
Graph #1: Evolutionary tree for seven primate species based on a comparison of amino acid
dissimilarities of beta hemoglobin