Phylogenetic Trees

How do the changes in gene sequences allow us to reconstruct

Why?
The saying Dont judge a book by its cover. could be applied to the topic of evolution. For example,
humans share 75% of their DNA with chickens. Biologists point to this as evidence that humans and
chickens once shared a common ancestor. The advent of DNA technology has given scientists the tools
with which to examine how closely related certain species are. DNA analysis allows scientists to construct
phylogenetic trees whose branches link together the relatedness of different organisms.

Model 1 Phylogenetic Trees

35

Millions of Years Ago

Raccoon
Red Panda

Common ancestor
of all modern
Raccoons, Pandas,
and Bears.

Giant Panda
Spectacled Bear

Sloth Bear
Sun Bear
Black Bear
Polar Bear
Brown Bear

1. Refer to Model 1.
a. How long ago did the common ancestor of all the organisms on this phylogenetic tree exist?
b. Which two lines diverged 30 million years ago?
c. List all modern descendants of the organism that was alive at the point indicated by the asterisk.

Phylogenetic Trees

2. According to Model 1, when did the Giant Panda line diverge from the line that led to modern
bears?

3. According to Model 1, what animal shares the most recent common ancestor with the Brown
Bear?

4. In a complete sentence, describe what the branch points and lines in a phylogenetic tree
represent.

5. Which of the two branches from the common ancestor in Model 1 has the most living
descendants?

6. According to the phylogenetic tree in Model 1, the Red Panda is most closely related to which
animal?

7. Which are more closely related, the Giant Panda and the Red Panda or the Giant Panda and the
Polar Bear? Justify your answer using grammatically correct sentences.

POGIL Activities for AP* Biology

Model 2 DNA Sample Comparison

G TT TC A GA AC T TGGTG CT A TC
Sample 3

C A C T T T G G A A G T A G C A GG T T C
Sample 2

Sample 1

G AT TCG
G

A ACTTC
G

TG GT T A
C

C AG T T T GG A C C T A A C A GC T T C
G TG A A A CC T TC A TCG T C C A A G

DNA from organism A attached

9. Using your knowledge of base-pairing, which DNA sample in Model 2 will be 100% complementary to organism A?

10. Which other DNA sample in Model 2 is likely to pair with one of the strands from organism A?

11. How many of the total number of base pairs in the sample you chose in Question 10 are
noncomplementary between the strands?

Phylogenetic Trees

12. From your answer to Question 11, convert the number of noncomplementary pairs into a percentage of the total base-pairs. This is called the sequence divergence.

13. Calculate the sequence divergence for the remaining two samples. Check your calculations
within your group.

14. Use the calculations from the previous questions to fill in the table below.
Most Homologous

Sample

Sequence Divergence

0%

Least Homologous
15. Based on your previous knowledge of DNA, which sample from Model 2 is from an organism
that is most closely related to Organism A?

16. With your group, describe how DNA sequence divergence can give scientists information about
relatedness.

17. Fill in the phylogenetic tree below with Samples 1 through 4 to summarize the relatedness of the
organisms that supplied the samples.

Common
Ancestor

POGIL Activities for AP* Biology

Amino Acid
Position

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40

Model 3 Comparing the Cytochrome c Gene

* * * * * * * * G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L

Tuna

* * * * * * * * G D V A K G K K T F V Q K C A Q C H T V E N G G K H K V G P N L

Whale

* * * * * * * G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L

R. Monkey * * * * * * * * G D V E K G K K I F I M K C S Q C H T V E K G G K H K T G P N L

* * T E F K A G S A K K G A T L F K T R C E L C H T V E K G G P H K V G P N L

77

76

75

74

73

72

71

70

69

68

67

66

65

64

63

62

61

60

59

58

57

56

55

54

53

52

51

50

49

48

47

46

* * * * G V P A G D V E K G K K I F V Q R C A Q C H T V E A G G K H K V G P N L

45

Amino Acid
Position

44

Fly

* * * * * * * G D I E K G K K I F V Q K C S Q C H T V E K G G K H K T G P N L

* * * * * * * * G D V E K G K K I F V Q K C A Q C H T V E K G G K H K T G P N L

43

Yeast

42

Pig

41

Chicken

Human

H G L F G R K T G Q A P G Y S Y T A A N K N K G I

I W G E D T L M E Y L E

Tuna

W G L F G R K T G Q A E G Y S Y T D A N K S K G I

V W N N D T L M E Y L E

S Y T D A N K N K G I

T W G E E T L M E Y L E

R. Monkey H G L F G R K T G Q A P G Y S Y T A A N K N K G I

Whale

H G L F G R K T G Q A V G F

T W G E D T L M E Y L E

Chicken

H G L F G R K T G Q A E G F

S Y T D A N K N K G I

T W G E D T L M E Y L E

Pig

H G L F G R K T G Q A P G F

S Y T D A N K N K G I

T W G E E T L M E Y L E

K K N V L W D E N N M S E Y L T

Human

N P K K Y

P G T K M I

F V G

K K K E E R A D L

Tuna

N P K K Y

P G T K M I

F A G

K K K G E R Q D L V A Y L K

Whale

N P K K Y

P G T K M I

F A G

K K K G E R A D L

R. Monkey N P K K Y

112

111

110

109

108

107

106

105

104

103

101

100

99

98

97

96

95

94

93

92

91

90

89

88

87

86

85

84

83

82

81

T W Q D D T L F E Y L E

102

F G R H S G Q A Q G Y S Y T D A N I

H G L F G R K T G Q A A G F A Y T N A N K A K G I

80

Amino Acid
Position

H G I

79

Fly

78

Yeast

A Y L K K A T N E
S

A T

A Y L K K A T N E

P G T K M I

F V G

K K K E E R A D L

A Y L K K A T N E

Chicken

N P K K Y

P G T K M I

F A G

K K K S

E R V D L

A Y L K D A T

Pig

N P K K Y

P G T K M I

F A G

K K K G E R E D L

A Y L K K A T N E

Yeast

N P K K Y

P G T K M A F G G L K K E K D R N D L

T Y L K K A C E

Fly

N P K K Y

P G T K M I

A Y L K

F A G L K K P N E R G D L

S K

A T K

*No amino acid at this position

18. Cytochrome c is a protein used in cellular respiration in many species. Refer to Model 3 to
answer the following questions about cytochrome c.
a. How many different species are represented in the cytochrome c amino acid sequences?
b. What do the individual letters represent?
c. What do the asterisks represent?

Phylogenetic Trees

19. Circle the pairing of organisms from Model 3 that you predict would have the most divergence
in their DNA. Support your choices with a group discussion about morphology (observable
characteristics and structure), ecology, and lifestyles of the animals.
a. whale and human

or

whale and tuna

b. pig and rhesus monkey

or

pig and chicken

c. tuna and fly

or

tuna and chicken

Read This!
Cytochrome c is a protein that is shared by many organisms due to its vital role in cellular respiration. Over
time (billions of years) mutations have occurred in the cytochrome c gene that do not affect the function
of the cytochrome c protein. These mutations are called neutral mutations. By looking at these mutations
scientists can predict when the organisms diverged from a common ancestor and from each other.
20. Refer to Model 3. Write down the number of differences between the amino acid sequence of
cytochrome c in a human and each of the following organisms.
a. Tuna

____

e. Pig

____

b. Whale

____

f. Yeast

____

c. Rhesus monkey

____

g. Fly

____

d. Chicken

____

21. Based on the differences in amino acid sequences, to which organism from the list are humans
a. Most closely related to?

b. Most distantly related to?

POGIL Activities for AP* Biology

22. Enter the names of the seven organisms in Model 3 into the tree below, to illustrate a phylogenetic relationship between these organisms and humans, as suggested by the cytochrome c data.

23. How do your predictions about relatedness based on morphology, ecology, and lifestyle in Question 19 compare to the relatedness information in the phylogenetic tree developed from DNA
data in Question 22?

24. Circle all of the mammals in the phylogenetic tree in Question 22. How does the tree illustrate
the fact that those animals are all members of the same class?

25. Compare the differences in amino acid sequences among the mammals with differences in other
animal classes. Is there a pattern?

26. Should scientists infer evolutionary relationships based on data from a single protein? Justify your
answer in complete sentences.

Phylogenetic Trees

Extension Questions
Read This!
Scientists have found that neutral mutations like those found in cytochrome c occur at a fairly steady rate
throughout evolutionary history. For this reason, neutral mutations are used to measure the time that has
passed since two species have diverged through evolution. The rate of mutation must be calibrated with
samples where the actual time of species divergence is known from fossil records. In other words, scientists
have developed a molecular clock that can be used to estimate the divergence time between organisms.
27. Plot the percentage sequence divergence on the y-axis and the known age of common ancestor on
the x-axis for the following species pairs.
Percentage Sequence
Divergence

Known Age of Common

Human-Chimpanzee

9.8

5.5

Human-Gorilla

12

7.0

Chimpanzee-Gorilla

12.8

7.0

Human-Orangutan

16.65

11.0

Species-Pair

% Sequence Divergence

20+

Sequence Divergence of Hominids

15
10
5
0

10

12

Known age of common ancestor (millions of years)

28. Draw the trend line for the points you have plotted. Using the trend line, calculate the slope of
the line that describes the relationship between sequence divergence and known age. Give a value
as % divergence/million years. This is the calibration value for this molecular clock.

29. At the same gene the sequence divergence between chimpanzees and bonobos is 4.2%. Using the
calibrated molecular clock estimate the time at which these species diverged.

30. The sequence divergence between humans and Neanderthals at the same gene is 1.2%. Using the
calibrated molecular clock, estimate the time these species diverged.

POGIL Activities for AP* Biology