Laboratory Worksheet.

General Biology 2
Science, Technology, Engineering, and Mathematics

Lab Activity 6
Constructing a Phylogenetic Tree 60 to 90 minutes

Let’s Review
In this unit, you have learned about the evolutionary basis of phylogenetic relationships
between organisms or groups. Recall that organisms are classified based on their
taxonomic hierarchical organization, with the domain being the highest level, followed
by kingdom, phylum, class, order, family, genus, and species. Scientists aim to make
these classifications indicative of evolutionary relationships.

However, the best way of inferring evolutionary relatedness is by looking at similarities

and differences in the morphology and genetic data of organisms. A phylogenetic tree is
a diagram that shows these relationships and is usually based on molecular data.

A sample phylogenetic tree

Objectives
At the end of this laboratory activity, the students should be able to do the following:
● Compare DNA sequences based on their similarities and differences.
● Construct a phylogenetic tree based on sample sequences.

Lab Activity 6. Constructing a Phylogenetic Tree 1

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Materials
● DNA sequences, given in the procedures below
● scratch paper

Procedure
1. You are given the following DNA sequences for a specific gene in 3 different
organisms. The sequences are as follows:
○ Organism C: ACT ATT ATG CCC
○ Organism D: ACT ATT ATG AAA
○ Organism E: ACT ATT ATC CCC
2. You are sure that Organism A gave rise to Organism B and another organism.
However, you are not sure what this other organism is. You also know that this
unknown organism gave rise to two more organisms.
3. To find out, align the triplets of letters found in the sequences above. Compare the
similarities between the triplets in the same positions to find the degree of similarity
between them. For example:
ACT ATT ATC CCC
ACT ATT ATG AAA
(triplets in boldface indicate similarity, ACT, and ATT are similar
between the two organisms because they are in the same
position)
50% similarity between these organisms.

Reminder
Make sure that you compare the sequences based on three letters each to
symbolize the triplet code of DNA.

4. Find all the permutations for alignments between Organisms C, D, and E and write
the alignments and percentages down in Table 6.1.
5. After writing down the alignments, construct a phylogenetic tree based on the
degrees of similarity that you have gathered in Table 6.1.. Take note that you are

Lab Activity 6. Constructing a Phylogenetic Tree 2

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

sure that Organism A gave rise to Organism B and an unknown organism,

which in turn gave rise to two more organisms so keep this in mind when
constructing your phylogenetic tree.
6. Create your phylogenetic tree in Figure 6.1.
○ You may do so by filling out the missing boxes.
○ Take note that Organisms A and B have already been filled in.
○ In addition, write the percentage of similarity in the lines between the letters.
7. Justify the placement of the organisms in Table 6.2.
8. Answer the guide questions afterward.

Data and Results

Table 6.1. Degrees of similarity

Organisms
Alignment Similarity
to be compared

Organisms C and D

Organisms D and E

Organisms C and E

Figure 6.1. Phylogenetic Tree

Lab Activity 6. Constructing a Phylogenetic Tree 3

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Table 6.2. Justifications

Justification

Placement of Organism C

Placement of Organism D

Placement of Organism E

Guide Questions
Answer the following questions.
1. What is the triplet code of DNA?

2. How do the percentages indicate the degree of similarity and relatedness?

3. What is the basis for the similarities based on the percentages?

Lab Activity 6. Constructing a Phylogenetic Tree 4

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

4. What is a real-world application of this activity?

Conclusion

Bibliography
Russell, Peter J. Biology: The Dynamic Science. Student Ed. Belmont, CA:
Thomson/Brooks/Cole, 2008.

Starr, Cecie, Ralph Taggart, Christine A. Evers, and Lisa Starr. Biology: the Unity and Diversity
of Life. Boston, MA: Cengage, 2019.

Lab Activity 6. Constructing a Phylogenetic Tree 5

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Lab Activity 6
Constructing a Phylogenetic Tree

Data and Results

Table 6.1. Degrees of similarity

Organisms
Alignment Similarity
to be compared

ACT ATT ATG CCC

Organisms C and D 75%
ACT ATT ATG AAA

ACT ATT ATG AAA

Organisms D and E 50%
ACT ATT ATC CCC

ACT ATT ATG CCC

Organisms C and E 75%
ACT ATT ATC CCC

Figure 6.1. Phylogenetic Tree

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Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Table 6.2. Justifications

Justification

Organism C is placed in this position because it may be the

Placement of Organism C
likely ancestor of D and E based on similarities.

Placement of Organism D Based on similarities, Organism D may be descended from C.

Placement of Organism E Based on similarities, Organism E may be descended from C.

Answer Key

Guide Questions:
1. What is the triplet code of DNA?

The triplet code refers to the codons, wherein every three base pairs codes for an
amino acid.

2. How do the percentages indicate the degree of similarity and relatedness?

The percentages show the similarity between the sequences of the organisms,
with higher numbers indicating more similarity. This may indicate relatedness.

3. What is the basis for the similarities based on the percentages?

The similarities based on the percentages have their basis in phylogenetic

inheritance since ancestors may pass on their characteristics and genetic data to
descendants.

4. What is a real-world application of this activity?

A good example of an application of this activity is that it can be used to

determine the relatedness between organisms.

Lab Activity 6. Constructing a Phylogenetic Tree 7

Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Process Skills Rubric

Please rate your students from 0 to 5 where 0 is “not observed.” Not all descriptors are
necessary for the process skills to be scored.

Category 0 1 2 3 4 5

Critical Thinking

Analysis Evaluates or ranks Evaluates or ranks Effectively evaluates

Analyzing relevant information information with or ranks information
info to form an incorrectly in terms some errors in terms in terms of the
argument or reach a of the usefulness of the usefulness usefulness
conclusion supported (importance) in (importance) in (importance) in
with evidence supporting the supporting the supporting the
conclusion conclusion. conclusion

Synthesis Minimally Partially synthesizes Effectively

Synthesizing relevant synthesizes and and examines synthesizes and
info to form an examines different different types of examines different
argument or reach a types of information information to create types of information
conclusion supported to create a new a new understanding to create a new
with evidence understanding of of the project understanding of the
the project outcome outcome project outcome

Argument Constructs weak Constructs Constructs effective

Forming an argument arguments: makes arguments: makes arguments: makes
to reach a conclusion claims and provides claims and provides claims and provides
supported with minimal or incomplete but complete and
evidence irrelevant evidence relevant evidence to relevant evidence to
to support them support them support them

Critique Provides a weak Provides some Provides a

Evaluating relevant analysis to minimally analysis to minimally compelling analysis
info to form an compare or critique compare or critique to minimally compare
argument or reach a results or arguments results or arguments or critique results or
conclusion supported arguments
with evidence

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Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Information Processing

Evaluating Minimally evaluates, Partially evaluates Effectively evaluates

Evaluating or simply recognizes, information for information for
information information for relevance or relevance or
relevance or importance to the task importance to the
importance to the task
task

Interpreting Inaccurately Interprets information Correctly interprets

Interpreting interprets with some errors information
information information

Transforming Minimally Partially manipulates Effectively

Transforming or manipulates or or transforms manipulates or
manipulating transforms information from one transforms
information information from form to another information from one
one form to another form to another

Oral Communication

Speaking Expresses Expresses partly Expresses complete

Exchanging incomplete thoughts complete thoughts thoughts about
information through about concepts with about concepts with concepts with
speaking irrelevant or somewhat relevant relevant and
ineffective language and effective effective language
language

Listening Minimally listens to Partially listens to Effectively listens to

Exchanging group members as group members as all group members as
information through they explain their they explain their they explain their
listening ideas with frequent ideas with some ideas with minimal
interruption interruption interruption

Nonverbal Cues Minimally shows Partially shows Clearly shows

Exchanging exchange through exchange through exchange through
information through nonverbal cues nonverbal cues nonverbal cues
nonverbal behaviors (turning toward each (turning toward each (turning toward each
other, nodding, other, nodding, other, nodding,
gesturing) when gesturing) when gesturing) when
others speak others speak others speak

Response Minimally promotes Partially promotes Effectively promotes

Understanding exchange of exchange of exchange of
exchange of information by information by information by
information responding to others’ responding to others’ responding to others’
ideas, explaining, and ideas, explaining, and ideas, explaining, and
checking for checking for checking for
understanding understanding understanding

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Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Management

Planning Inadequately plans Partially plans a Effectively plans a

Planning one’s own a course of action by course of action by course of action by
and others’ efforts to describing or describing or referring describing or
accomplish a goal referring to a few of to a few of the steps referring to a few of
the steps required to required to the steps required to
accomplish the goal accomplish the goal accomplish the goal

Organizing Minimally organizes Partially organizes Effectively organizes

Organizing one’s own tasks, time, and tasks, time, and tasks, time, and
and others’ efforts to resources with resources with respect resources with
accomplish a goal respect to the goal to the goal respect to the goal

Directing Minimally directs Sometimes directs Routinely directs

Directing one’s own tasks to group tasks to group tasks to group
and others’ efforts to members members members
accomplish a goal

Coordinating Ineffectively Sometimes Effectively

Coordinating one’s coordinates a coordinates a coordinates a
own and others’ collective interaction collective interaction collective interaction
efforts to accomplish among few group among some group among all group
a goal members, including members, including members, including
monitoring monitoring monitoring
performance, to performance, to performance, to
accomplish the goal accomplish the goal accomplish the goal

Problem-Solving

Analysis Minimally analyzes Partially analyzes the Effectively analyzes

Identifying a strategy the problem and problem and identifies the problem and
that goes beyond identifies a few some pieces of key identifies all key
routine action to find pieces of key information and information and
a solution to a information and variables needed to variables needed to
situation or question variables needed to solve it solve it
solve it

Strategy Arrives at a strategy Arrives at a strategy Arrives at a strategy

Planning a strategy that is not that is functional but that is functional
that goes beyond functional not optimal and optimal
routine action to find
a solution to a
situation or question

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Laboratory Worksheet.
General Biology 2
Science, Technology, Engineering, and Mathematics

Execution Has serious flaws in Has minor flaws in Implements the

Executing a strategy implementing the implementing the strategy effectively
that goes beyond strategy strategy
routine action to find
a solution to a
situation or question

Solution Addresses a few Addresses most parts Addresses all parts of

Finding a solution to parts of the problem of the problem and the problem and
a situation or and/or reaches a reaches a reasonable reaches a reasonable
question conclusion that is conclusion conclusion
not reasonable

Teamwork

Interaction Engages in Engages in sporadic Engages in

Interacting with infrequent interactions or continuous
others interactions or communication with interactions or
communication with all group members communication with
group members group members

Contribution Considers the Considers the Considers the

Building on one contributions, contributions, contributions,
another’s individual strengths, and skills strengths, and skills of strengths, and skills of
strengths and skills of few group most group members all group members
members

Progress Makes little progress Makes moderate Makes steady

Making progress toward a common progress toward a progress toward a
toward a goal goal, rarely on track common goal, mostly common goal,
on track completely on track

Cohesiveness Minimally unites Partially unites and Effectively unites and

Working toward a and functions as a functions as a functions as a
common goal cohesive unit cohesive unit cohesive unit

Adapted from Gil Reynders, Erica Suh, Renée S. Cole, and Rebecca L. Sansom, "Developing
Student Process Skills in a General Chemistry Laboratory," Journal of Chemical Education 96,
no. 10 (2019): 2109-2119, https://doi.org/10.1021/acs.jchemed.9b00441. Copyright 2019 by
the American Chemical Society.

Lab Activity 6. Constructing a Phylogenetic Tree 11