Phylogenetic Trees

How do the changes in gene sequences allow us to reconstruct

the evolutionary relationships between related species?

Why?
The saying “Don’t 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

Millions of Years Ago
40 35 30 25 20 15 10 5 0

Raccoon

Red Panda

Common ancestor
of all modern
Raccoons, Pandas, Giant Panda
and Bears.
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?
Yo myd
b. Which two lines diverged 30 million years ago?
vacoon/redpanda & bear lives
c. List all modern descendants of the organism that was alive at the point indicated by the asterisk.
bears
spectated , gloth , sun , black, polar , & brown

Phylogenetic Trees 1
 2. According to Model 1, when did the Giant Panda line diverge from the line that led to
modern bears?
~ 17 wil years ago

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

4. In a complete sentence, describe what the branch points and lines in a phylogenetic
tree represent.
dncestor
The branch points represent a common
the diverging species from the
& the lives represent
common dncestor

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

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

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.
share
red by they
panda and panded
giant dncestor .
a common

2 POGIL™ Activities for AP* Biology

Model 2 – DNA Sample Comparison
Sample 4

GTTTCAGAACTTGGTGCTATC
Sample 3

CACTTTGGAAGTAGCAGGTTC
Sample 2

Sample 1 GAT
TCGGAA
CTTCGT
GGTTAC
CAGTTT GGACCTAACAGCTTC
GTGAAACCTTCATCGTCCAAG

DNA from organism A attached

to a nitrocellulose membrane.

8. How many bases are found in each of the DNA samples 1–4 as well as in the DNA
from organism A in Model 2?

2)

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

# 3

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

# I
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 3
 12. From your answer to Question 11, convert the number of noncomplementary pairs into a
per-centage of the total base-pairs. This is called the sequence divergence.
8 %
=
23
238 = .

13. Calculate the sequence divergence for the remaining two samples. Check your
calculations within your group.
#2 =

= = 57 %

#7 7%
=

E = 06 .

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

Most Homologous Sample Sequence Divergence

3 0%
I
23 .
8

2
57
Least Homologous Y 66 7.

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?
#3

16. With your group, describe how DNA sequence divergence can give scientists information
about relatedness.
DNA is the less
The more divergenta sequence ,
related

the organisms dre . Less DNA sequence divergences = more

closely related

17. Fill in the phylogenetic tree below with Samples 1 through 4 to summarize the relatedness
of the organisms that supplied the samples.
# 3

Common
Ancestor # /

# 2

#7

4 POGIL™ Activities for AP* Biology

Model 3 – Comparing the Cytochrome c Gene
Amino Acid

20
10

18
19

221
13

15
16
17

31
11
6
5
8
7
9
123

1
2
1
4

2
32
42
52
62
72
82
93
0
3
23
3
43
53
63
73
83
94
0
Position

4
Human * * * * * * * * G D V E K GKK I F I M K C SQCHT V EKGGKHK TG PNL
Tuna * * * * * * * * G D V O
A K G K KO
T F 00
V Q K C6 N G G K H K0
A Q C H T V E0
- VG PNL
Whale * * * * * * * * G D V E K GKK I V Q K CO
F00 AQCHT V EKGGKHK TG PNL -

R. Monkey * * * * * * * * G D E K G K K IV F I M K C SQCHT V EKGGKHK TG PNL

Chicken * * * * * * * * G DG
I E K GKK I F Do
V Q K C SQCHT V EKGGKHK TG PNL

Pig * * * * * * * * G D V E K G K K I F V Q K C0
00 AQCHT V EKGGKHK TG PNL
Yeast 000 00
* * * T EF KA G S A KK G A T L 000 08 F 000 08
K T R C E PHKO
LCHT V EKGGo VG PNL
Fly * * * * 00
GV 00
PA G D V E K G K K I V Q R CO
F 000 AQCHT V EO
A G G K H KO
VG PNL

Amino Acid

68
41
42
43

52
53

58

63

67

77
44

46
47
48
49

51

54
55
56
57

59
60
61
62

64
65
66

74
75
76
97

70
6
4
5

71
5
0

27
3
Position
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
I 000
8 G Q A O
g O K G
Tuna W G L F G R K T E G Y S Y T D A N K S V W N N D T L M E Y L E
Whale H G L F G R K T V G 8
G Q A 6 F S Y T D A N K N K G T W G E O
I G 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 IO
T W G E D T L M E Y L E
Y T O O
68
Chicken H G L F G R K T G Q A E G F S 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 O
D A N K N K G I O
T W G E 6E T L M E Y L E
Yeast H G I g F G R H S 00 Q G O
G Q A O Y S Y T O
D A N I K 00 K 000
N V L W g
D E 00dd
N N M S E Y L gT
Fly H G L F G R K T G Q A A8 G F A 00 Y T O
N A N KO
A K G 000 S
I T W Q D D T LF E Y L E

Amino Acid

111
112
100
101
102
103
104
105
106
107
108
109
110
81

91
78

88
7
78
98
0

8
28
38
48
58
68

99
0

9
29
39
49
59
69
79
89
9

Position
Human N P K K Y I P G T K M I F V G I K K K E E R A D L I A Y L K K A T N E
V A Y L KO S o
8 G E RG
Tuna N P K K Y I P G T K M I F A G I K K K G Q D LO S A T *
Whale N P K K Y I P G T K M I F A G I 6
K K K G E R A D L I A Y L K K A T N E
R. Monkey N P K K Y I P G T K M I F V G I K K K E E R A D L I A Y L K K A T N E
Chicken N P K K Y I P G T K M I F O
A G I K K KOS E R GV D L I A Y L KO
D A T 00
S K

⑧ G E R 8
K K K g
Pig N P K K Y I P G T K M I F A G I E D L I A Y L K K A T N E
OF G G 8 O 0 Ob
000
Yeast N P K K Y I P G T K M A L K K E K D R N D L I T Y L K K A O
C E *
Fly N P K K Y I P G T K M I F OA G O
L K K P N E ROG D L I A Y L K·
S A T 08
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?
G
b. What do the individual letters represent?
a mino acids

c. What do the asterisks represent?

acid
no amino

Phylogenetic Trees 5
 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 fund he both
a wave
↓
,

-& wickenie
.
b. pig and rhesus monkey or pig and chicken words

2
flies

undless
c
c. tuna and fly or tuna and chicken
ave
don
↑

monkeys
theest ends
mednins
are
numans
mamad's & mals
pigs
,

both man &

same mave
both which
and have S
structures (like fins &hands), Likelywicker
while fund are fish & US
have gills

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.
10
a. Tuna ____
21 e. Pig ____
18
b. Whale ____ f. Yeast ____
45

c. Rhesus monkey ____

I g. Fly ____
77

d. Chicken ____
13

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

b. Most distantly related to?

yeast

6 POGIL™ Activities for AP* Biology

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

yeast
fly
Hund

Chicken

numan is e
monte

23. How do your predictions about relatedness based on morphology, ecology, and lifestyle in
Ques-tion 19 compare to the relatedness information in the phylogenetic tree developed
from DNA data in Question 22?
to in
They are pretty similar my answer

question 19 .

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?
Tmey due from the same class bK the diverged
same commondncestor
from the

25. Compare the differences in amino acid sequences among the mammals with differences in
other animal classes. Is there a pattern?
related to exchother
The mammals are closer

is more relatedness
animal so there
thdh to other ,

in the some class .

26. Should scientists infer evolutionary relationships based on data from a single protein? Justify
your answer in complete sentences.
hundreds and thousands of
No by organisms have
only I will not
for proteins ,
so looking at

genes
accurate data -
provide

Phylogenetic Trees 7
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 Known Age of Common
Species-Pair
Divergence Ancestor (millions of years)
Human-Chimpanzee 9.8 5.5
Human-Gorilla 12 7.0
Chimpanzee-Gorilla 12.8 7.0
Human-Orangutan 16.65 11.0

20+ Sequence Divergence of Hominids

·
% Sequence Divergence

15
·
10 ·

0
0 2 4 6 8 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.

1901 . 245 % divergence (wil years

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.
4 : 2

- = 3 .
373 mil years

1 .
245

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.

8 =. 96 mil years
POGIL™ Activities for AP* Biology