Tree Thinking
In the age of genomics, groups of organisms can be compared by their DNA and evolutionary relationships can be proposed based on the
similarity of these sequences.
Define the following in your own words:
1. Phylogeny:
2. Homoplasy:
3. Cladogram:
4. Parsimony:
A molecular clock uses changes in DNA sequences to infer the time since two species diverged. To set, or calibrate, a molecular clock, we
need to calculate how much DNA sequences from a common but neutral genomic region have diverged over a known period of time. Below
are sequences from an imaginary gene for three closely related organisms. Most genes consist of several thousand nucleotides, but for
demonstration purposes, we are only going to use some of the bases.
Calculate the percentage sequence divergence between all three sequences. First examine the sequences in question and count the
differences between them. Divide the difference by the total number of nucleotides, and then multiply by 100 to convert to a percent.
Human
Chimp
Baboon
DNA Sequence of Cyt-b (Mitochondrial DNA)
ACTAGCAACGGATACCATAGGTATATCTAGGCTACATTGT
ACTAGAAACGGTTACCACAGGTATATCAAGGCAACATTGT
ACTGGATGCGGATGCCTCAGATTTATCAAGGCTACAATGT
Human
Chimp
Baboon
DNA Sequence of Cyt-b (Mitochondrial DNA) continued
TAGCTTACCGCTAGTACTGGTGACTCTAGAATGCCTAGTC
TACCTTACCGCTAGTACTGGTGACTCTCGAATGCCTTGTC
TACCATAGCGATACTTGTGGTGACTGTCGATTGCCTAGTG
5. Human and Chimp:
6. Chimp and Baboon:
7. Baboon and Human:
The major assumption of a molecular clock is that sequence divergence increases over time in a linear manner as species diverge. This
means that species that diverged 4 million years ago should have twice the sequence divergence as species that diverged 2 million years
ago. If one knows when two species diverged (by using the dates of fossils, geological events, etc.), one can use this information to
calibrate a molecular clock for that particular region of the genome. That clock can then be applied to other species and used to
determine when other species diverged.
8.
Calculate the ratio of the sequence divergence to the known age for each species pair below. What is the % divergence per million years for
this particular gene?
Species-Pair
Sequence Divergence
Known Age
Human-Chimp
9.8%
5.5 million
Human-Gorilla
12.0%
7.0 million
Chimp-Gorilla
12.8%
7.0 million
9. If the sequence divergence between chimpanzees and bonobos at this gene is 4.2%, calculate the estimated age of the divergence between
chimps and bonobos.
10. The sequence divergence between modern humans and Neanderthals (based on DNA obtained from fossils) is 1.2%. How long ago did
modern humans and Neanderthals share a common ancestor?
11. Suppose that other data showed that the Neanderthal fossil was .35-.4 million years old. What are other possible reasons for the discrepancy
between this age and the age obtained by the molecular clock method?
12. Construct a cladogram showing the relationship between humans, chimps, bonobos, and gorillas using this sequence data.
13. Now construct a phylogram showing the relationship between humans, chimps, bonobos, and gorillas using this sequence data. How is it
different from your cladogram?
14. Do you think the common ancestor to humans, chimps, bonobos and gorillas walked upright on two feet (biped)? Use parsimony to explain.
15. Do you think the common ancestor to humans, chimps, bonobos and gorillas had body covered with hair? Use parsimony to explain.
16. The amino acid sequence for cyt-c gene is given for several species at the end of this handout.
How many differences are there:

Between humans and rhesus monkeys?

Between humans and kangaroos?

Between ducks and chickens?

Between chickens and turkeys?

Between Neurospora and baker’s yeast?
17. What do the molecular data suggest about the relationship between a screwworm fly and a silkworm moth compared to the relationship
between a human and a rhesus monkey?
18. Explain how the pig-cow-sheep relationship is possible given that they are classified as different species.
19. Neurospora and Baker’s Yeast are both fungi and humans and monkeys are both primates. What can you say about the divergence time
between Neurospora and Baker’s Yeast compared to humans and monkeys?
AMINO ACID SEQUENCES IN CYTOCHROME-C PROTEINS FROM 20 DIFFERENT SPECIES
Amino Acid Number -----> 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5 6 7 8 9
Human ............
- - - - - - - - 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 H G L F G R K T G Q A P G Y S Y T A A
Rhesus 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 H G L F G R K T G Q A P G Y S Y T A A
Horse ...........
- - - - - - - - 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 H G L F G R K T G Q A P G F T Y T D A
Pig, cow, sheep...
- - - - - - - - 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 H G L F G R K T G Q A P G F S Y T D A
Dog..............
- - - - - - - - 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 H G L F G R K T G Q A P G F S Y T D A
Gray 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 H G L F G R K T G Q A V G F S Y T D A
Rabbit............
- - - - - - - - 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 H G L F G R K T G Q A V G F S Y T D A
Kangaroo..........
- - - - - - - - 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 N G I F G R K T G Q A P G F T Y T D A
Chicken, Turkey...
- - - - - - - - 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 H G L F G R K T G Q A E G F S Y T D A
Penguin...........
- - - - - - - - G D I E K G K K I F V Q K C S O C H T V E K G G K H K T G P N L H G I F G R K T G Q A E G F S Y T D A
Pekin duck........
- - - - - - - - G D V 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 H G L F G R K T G Q A E G F S Y T D A
Snapping turtle...
- - - - - - - - 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 N G L I G R K T G Q A E G F S Y T E A
Bullfrog..........
- - - - - - - - G D V E K G K K I F V Q K C A Q C H T C E K G G K H K V G P N L Y G L I G R K T G Q A A G F S Y T D A
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 W G L F G R K T G Q A E G Y S Y T D A
Screwworm fly.....
- - - - 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 H G L F G R K T G Q A A G F A Y T N A
Silkworm moth.....
- - - - G V P A G N A E N 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 H G F Y G R K T G Q A P G F S Y S N A
Wheat ............
A S F S E A P P G N P D A G A K I F K T K C A Q C H T V D A G A G H K Q G P N L H G L F G R Q S G T T A G Y S Y S A A
Fungus (Neurospora)
- - - - G F S A G D S K K G A N L F K T R C A E C H G E G G N L T Q K I G P A L H G L F G R K T G S V D G Y A Y T D A
Fungus(baker's yeast)
- - - 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 H G I F G R H S G Q A Q G Y S Y T D A
Fungus (Candida)
- - P A P F E 0 G S A K K G A T L F K T R C A E C H T I E A G G P H K V G P N L H G I F S R H S G Q A Q G Y S Y T D A
[CONTINUED FROM ABOVE]
Amino Acid Number
0
Human ............
N
Rhesus monkey.....
N
Horse ............
N
Pig, cow, sheep...
N
Dog...............
N
Gray whale........
N
Rabbit............
N
Kangaroo..........
N
Chicken, Turkey...
N
Penguin...........
N
Pekin duck........
N
Snapping turtle...
N
Bullfrog..........
N
Tuna..............
N
Screwworm fly.....
N
Silkworm moth.....
N
Wheat ............
N
Fungus 1 (Neurospora) N
Fungus 2 (bkrs yeast) N
Fungus 3 (Candida)
N
AMINO ACID SYMBOLS
A = Alanine
C = Cysteine
D = Aspartic acid
E = Glutamic acid
F = Phenylalanine
G = Glycine
1
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
I
K
2
N
N
N
N
N
N
N
N
N
N
N
N
N
S
A
A
N
Q
K
R
3
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
A
4
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
A
G
N
G
5
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
V
I
V
V
6
I
T
T
T
T
T
T
I
T
T
T
T
T
V
T
T
E
T
L
E
7
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
W
8
G
G
K
G
G
G
G
G
G
G
G
G
G
N
Q
G
E
D
D
A
9
E
E
E
E
E
E
E
E
E
E
E
E
E
N
D
D
E
E
E
E
0
D
D
E
E
E
E
D
D
D
D
D
E
D
D
D
D
N
N
N
P
1
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
N
T
2
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
M
M
3
M
M
M
M
M
M
M
M
M
M
M
M
M
M
F
F
Y
F
S
S
4
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
D
E
E
D
5
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
6
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
7
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
L
E
T
E
8
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
N
9
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
0
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
1
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
2
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
H
I
K
L
M
N
P
=
=
=
=
=
=
=
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Proline
3
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
4
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
P
5
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
6
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
T
7
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
8
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
M
9
I
I
I
I
I
I
I
I
I
I
I
I
I
I
I
V
V
A
A
A
0
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
F
1
V
V
A
A
A
A
A
A
A
A
A
A
A
A
A
A
P
G
G
G
2
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
G
3
I
I
I
I
I
I
I
I
I
I
I
I
I
I
L
L
L
L
L
L
4
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
5
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
6
K
K
K
K
T
K
K
K
K
K
K
K
K
K
P
A
P
D
E
A
7
E
E
T
G
G
G
D
G
S
S
S
A
G
G
N
N
Q
K
K
K
8
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
E
D
D
D
D
9
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
R
0
A
A
E
E
A
A
A
A
V
A
A
A
Q
Q
G
A
A
N
N
N
1
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
D
2
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
I
L
L
Q
R
S
T
V
W
Y
=
=
=
=
=
=
=
3
I
I
I
I
I
I
I
I
I
I
I
I
I
V
I
I
I
I
I
V
4
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
T
T
T
5
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
F
Y
Y
6
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
L
M
L
M
7
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
K
L
8
K
K
K
K
K
K
K
K
D
D
D
D
S
S
S
E
K
E
K
E
9
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
S
A
A
A
A
0
T
T
T
T
T
T
T
T
T
T
T
T
C
T
T
T
T
T
C
S
1
N
N
N
N
K
N
N
N
S
S
A
S
S
S
K
K
S
A
E
K
2
E
E
E
E
E
E
E
E
K
K
K
K
K
S
-
Glutamine
Arginine
Serine
Threonine
Valine
Tryptohpan
Tyrosine
Symbols in light blue or gray represent conserved amino acids (they show NO differences in any organism on the list), so you can ignore them.
(adapted from Strahler, Arthur, Science & Earth History, 1987, p. 348)