Worksheet

Creating Phylogenetic Trees

from DNA Sequences Student Handout

CREATING PHYLOGENETIC TREES FROM DNA SEQUENCES

INTRODUCTION
This worksheet complements the Click and Learn “Creating Phylogenetic Trees from DNA Sequences” developed
in conjunction with the 2011 Holiday Lectures on Science, “Bones, Stones, and Genes: The Origin of Modern
Human.”

PROCEDURE
Answer the following questions as you proceed through the activity slides.
1. Briefly explain how scientists draw relationships between organisms based on shared anatomical features.
on shared features and compare DNA and RNA between organisms

2. How are DNA sequences used to deduce evolutionary relationships?

they look at similarities and differences

3. What is one advantage of building phylogenetic trees using DNA comparisons rather than anatomical
features?
more adjective and not as unclear

4. Watch the video clip on slide 3 and then draw a simple tree illustrating the evolutionary relationships
between gorillas, chimpanzees, humans, and orangutans.
<br>
chimpanzees
gorillas
humans

orangutan

5. Watch the short video on slide 4. How has biotechnology affected the process of building phylogenetic trees
from DNA sequences?
Biotechnology has increased the amount of sequencing by 50,000-fold in the past ten years. This large database
is also very accessible, costing only a dollar.

Published December 2014

www.BioInteractive.org Revised February 2017
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 Worksheet
Creating Phylogenetic Trees
from DNA Sequences Student Handout

6. What do evolutionarily related organisms share?

common ancestor with an ancestral DNA sequence

7. What are two common types of mutations?

SNP's and Indel's

8. Watch the short animation on slide 6 and describe a SNP.

A SNP is a change of one DNA base pair to another.

9. Watch the short animation on slide 7 and describe an indel.

An Indel is a mutation in which one or more nucleotide pairs in a DNA strand is lost or gained

10. Explain the difference between distantly related and closely related organisms in terms of their DNA
sequences.
More distantly related species have had more time elapsed since they shared a common ancestor, which means
that they have had more time for mutations to occur and accumulate in their DNA. Closely related species have
not had as much time to accumulate mutations since their last common ancestor, so their DNA sequences are
much more similar.

11. What does it mean to compare “apples to apples” when referring to DNA sequences from different
organisms?
Comparing the sequences from different organisms is like comparing “apples to apples” because they are
homologous, meaning they are evolutionarily related. Comparing non-homologous sequences, however, is like
comparing apples to oranges.

12. Watch the short animation on slide 10 and explain what is meant by “aligning” DNA sequences.
Aligning” DNA sequences is maximizing the number of matches among all sequences being aligned by changing
the positions of the sequences relative to one another and/or by adding gaps

13. How is a SNP identified in an alignment?

A SNP in an alignment is a position where the letters in a column do not match.

14. How is an indel identified in an alignment?

An indel is an addition or removal of a pair of DNA bases so it would be a gap in an alignment (can be
represented by a dash)

Published December 2014

www.BioInteractive.org Revised February 2017
Page 2 of 5
 Worksheet
Creating Phylogenetic Trees
from DNA Sequences Student Handout

15. Look at the information on slide 15. From left to right, identify the base in each box as an indel or a SNP.
Write your answers in the spaces below.
Box 1 (left) indel Box 2 (center) SNP Box3 (right) indel
Now click on each box and check your answers to Question 15 above.
16. Watch the video clip on slide 17. How can you identify the two sequences that are most similar?
by looking at how many nucleotides differ between the two sequences. Then you find the best tree topology that
fits the data to indicate which sequences are more alike to one another.
17. Watch the video clip on slide 18 and describe the link between the length of the line and time.
With this data we can learn more about different species and see which one is more closely related to the other.

18. What is surprising about the placement of hippos on the phylogenetic tree?
the hippos are more closely related to the whale than they are to pigs because they are placed next to the whale
on the cladogram.

19. Define a branch point (also called a node) on a phylogenetic tree and describe what it represents.
the place where two branches split. It represents the most recent common ancestor of all the species on those
branches.

20. What is the root?

the single branch point from which all other branches originate.

21. What does the node closest to the root represent?

the most recent common ancestor for all organisms in the tree

22. Describe what an unrooted phylogenetic tree represents.

only relative relationships among compared organisms and they do not tell you where the common ancestor is
among a group of species

23. On slides 22 and 23, notice how phylogenetic trees can rotate around nodes and have different shapes.
Notice the relationships between the organisms do not change.
24. Using the information on slide 24, explain how DNA evidence supports the known biology of the seven cone
snails.
the shape of each snail reflects how it was placed on the cladogram. However, the DNA sequencing data
supports that classification as well.

Published December 2014

www.BioInteractive.org Revised February 2017
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 Worksheet
Creating Phylogenetic Trees
from DNA Sequences Student Handout

25. Write three conclusions drawn from the information provided in this Click and Learn.
a. DNA sequence comparison augments and sometimes clarifies anatomical comparison

b. Phylogenetic trees can be generated using DNA sequence alignments

c. With increased amounts of sequence data, we have more confidence than ever in the phylogenetic trees
that can be generated.

Published December 2014

www.BioInteractive.org Revised February 2017
Page 4 of 5
 Worksheet
Creating Phylogenetic Trees
from DNA Sequences Student Worksheet

EXTENSION ACTIVITY
Address the following concepts in essay form in the space provided below.

Phylogeny is the evolutionary history of a species:

a. The evolution of a species is dependent on changes in the genome of the species. Identify two mechanisms of
genetic change, and explain how each affects genetic variation.
DNA- duplication of genes,Gene "families," which then diverge by mutation; change in policy
b. Describe two types of evidence–other than the comparison of DNA sequences–that can be used to determine
the phylogeny of organisms. Discuss one strength of each type of evidence you described.

Fossil: Observe past organisms,Shows direct evidence of common ancestor, follow evolution
(changes over time) from common ancestor, and DNA sequence: Comparison of DNA
sequences in specific genes; molecular homologies,Similarities in sequences show common
ancestry

Published December 2014

www.BioInteractive.org Revised February 2017
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