Biology lab

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BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
Assignment 5
For this Individual assignment, you will be constructing two separate phylogenetic trees of
five plant species and an outgroup. The first tree will be constructed using morphological
characteristics only, and the second will use molecular phenotypes. Using the time in your lab
period, as a group you are encouraged to share screen the data tables and guiding questions
to facilitate group discussion. Although you may discuss this assignment with your group
members, you will be required to each submit your own work in your own words.
There are FIVE parts to this assignment. Parts 1 – 3 will be submitted to both Peerceptiv and
learn and parts 4 – 5 will be submitted to UMLearn only, in addition to parts 1 – 3
Part 1 – Construction of Morphological Phylogenetic Tree
Part 2 – Characteristic Additions on Molecular Phylogenetic Tree
Part 3 – Comparative Summary
Part 4 – Phylogeny Interpretation Questions *UMLearn Submission ONLY*
Part 5 – Review Reflection *UMLearn Submission ONLY*
To assist with Part 1 and Part 2 of your assignment, your group will first follow the steps in
Table 5.4 on the next page. Discussing these questions together will benefit in your
understanding of the construction of both the morphological tree and molecular tree.
BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
Table 5.4: Guiding questions to help with phylogenetic tree construction
Part 1 – Morphological Phylogenetic Tree Construction
Step 1
Are the species listed in a meaningful order? If not, reorganize them into a meaningful order.
Step 2
Identify which species is most similar to the pre-identified outgroup (least number of
morphological differences), where would it go on the tree?
Step 3
Identify which two species are likely to be most closely related (i.e., shared the most recent
common ancestor and have similar morphological characteristics). Where would those two
species go on the tree in Figure 5.14?
Step 4
If a trait is present (1) in the outgroup and absent (0) in the species, what does that mean?
Step 5
What information needs to go into the caption?
Part 2 – Molecular Phylogenetic Tree Construction
Step 1
Identify which nucleotide positions do not explain the molecular relationships shown in Figure 5.15
Step 2
Identify which nucleotide positions have only ONE change
How would each be placed on the tree (most parsimoniously, i.e., is one or multiple characteristic
tick marks needed?)
Step 3
Identify which nucleotide positions have TWO changes
How would each be placed on the tree (most parsimoniously, i.e., is one or multiple characteristic
tick marks needed?)
Step 4
Identify which nucleotide position have THREE changes
How would each be placed on the tree (most parsimoniously, i.e., is one or multiple characteristic
tick marks needed?)
Step 5
What information needs to go into the caption?
BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
Part 1 – Construction of Morphological Phylogenetic Tree
You will construct a phylogenetic tree of the five plant species provided using the following
morphological characteristic table (Table 5.5) and the outline of the morphological tree
(Figure 5.14), you will need to determine the placements of Species A – D. We have provided
the structure of the morphological phylogenetic tree. You will also place the characteristic tick
marks on the branches to explain the divergence of the plant species. Your morphological
phylogenetic tree diagram should also include a descriptive and unique caption.
Table 5.5: Six morphological characteristics for the outgroup and 4 plant species (A-D)
Figure 5.14: Phylogenetic tree structure based on the morphological characteristics
summarized in table 5.5.
Plant Spores
under
leaves
Height
<1.5 m
Feathery
leaf
margins
Smooth
Trunk
Multiple
Trunks
Fleshy
Species Fruit
Outgroup 1 1 0 0 1 1
Species A 0 0 1 0 0 0
Species B 0 0 0 0 1 0
Species C 0 1 1 1 1 1
Species D 0 0 1 0 0 0
BIOL 1030 – Lab Manual
© Scott & Debets Winter 2021
Part 2 – Characteristic Additions on Molecular Phylogenetic Tree
You will place molecular characteristic tick marks on the provided molecular phylogenetic tree
structure (Figure 5.15) using the molecular data for the five plant species (Table 5.6). The
molecular data is not responsible for any of the morphological divergences found in (Table
5.5). As such, the two trees will likely not have the same order of the terminal nodes (branch
tips). The molecular dataset is additional information that can be used to better understand
these plant species evolutionary relationships. Your molecular phylogenetic tree diagram
should also include a descriptive and unique caption.
Table 5.6: Molecular data (10 nucleotides) for the outgroup and 4 species (A – D).
Nucleotide Position
Plant
species 1 2 3 4 5 6 7 8 9 10
Outgroup A A C A C G G G T G
Species A A T C A C T G C T G
Species B T A C C C G G A T G
Species C T A C A T G G T A G
Species D T A C A C G G T A A
Figure 5.15: The evolutionary order of the 4 species (A – D) with the outgroup based on the
molecular data in Table 5.5.
BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
Part 3 – Comparative Summary
Provide a brief summary (max. 250 words) of the two phylogenetic trees that you have
generated. Be sure to compare similarities between the trees and differences between the
two trees. Highlight which characteristics (morphological and molecular) had the most
changes (i.e., you needed to place the most tick marks in order to explain the hypothesized
evolutionary relationships).
The summary you submit must be in your own words.
Part 4 – Molecular Phylogeny Interpretation Questions *Only for UMLearn Submission*
Include the answers to the following questions:
1. You find a new species that has the following nucleotide sequence. Which species in
your molecular phylogenetic tree is this newly discovered SPECIES E most likely to be
most closely related? Why?
2. Which nucleotide sequences are/are the most divergent (different) from the pre-identified
outgroup?
3. Which nucleotide sequence is/are the least divergent (different) from the pre-identified
outgroup?
Part 5 – Review Reflection*Only for UMLearn Submission*
Describe the most useful feedback you received and how you incorporated it into your final
version. If you did not take any suggestions from your reviewers describe why not.
Submitting Your Assignment
This assignment will be submitted to Peerceptiv, and UMLearn after the Peerceptiv process.
There are two additional parts that you will need to include in your summary for the UMLearn
submission ONLY. Review the rubric for what is being evaluated in each submission stage.
Perception
A. Submission – Submit your work to the Peerceptiv link located in the UMLearn Lab 4
content folder. Submissions MUST include both Part 1 – Morphological Phylogenetic Tree,
Part 2 – Molecular Phylogenetic Tree and Part 3 – the Comparative Summary as a single
Plant
species 1 2 3 4 5 6 7 8 9 10
Species E T T A G C T A C C G
BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
PDF (other formats tend to get lost in translation). Deductions due to conversion errors from
submitting other file types are NOT appealable.
Due 4 days plus 2 hours after your lab (i.e., 1:30 PM, 7:30 PM, or 11:59 PM).
B. Peer Review – You will be automatically assigned 3 documents from your peers. To
review. When you review, the most important thing to consider is the clarity of the two
phylogenetic trees and the clarity of the comparison.
Due 6 days plus 2 hours after your lab (i.e., 1:30 PM, 7:30 PM, or 11:59 PM).
C. Back Evaluations – These provide useful feedback on how well you provided
constructive feedback. Your back evaluations should not reflect whether you agree with the
ratings someone gave you, but their usefulness. If it made you reflect on your work or can
help you improve your work, it is a good comment.
Due 8 days plus 2 hours after your lab (i.e., 1:30 PM, 7:30 PM, or 11:59 PM).
learn
D. Submission – Take the feedback you get from your peers and improve upon your
document if necessary. In addition to your two phylogenetic trees and comparative summary
you have completed, you will also complete the two additional parts; Part 4 – Phylogenetic
Interpretation Questions and Part 5 – Reflective Statements for the UMLearn submission.
Due 8 days plus 2 hours after your lab (i.e., 1:30 PM, 7:30 PM, or 11:59 PM).
Assignment Evaluation
This lab is worth 4.5% of your BIOL 1030 final grade. Please read through the rubric entirely
and carefully so you can include all the components in your submissions.
Perception 50%
Writing Grade 70% of Peerceptiv Grade
Review Grade 10% of Peerceptiv Grade
Task Grade 20% of Peerceptiv Grade
UMLearn Submission 50%
Graded from the UMLearn Rubric provided below. You will include parts 1 – 5 for final
submission to UMLearn ONLY
BIOL 1030 – Lab Manual
© Scott & Debits Winter 2021
Rubric
Peerceptiv Rubric
Phylogenetic Tree – Part 1 and Part 2 ( /16 marks, 8 marks each)
Clarity
4 marks – The tree is easy to read and identify the relationships.
3 marks – The tree is easy to read and identify the relationships among most of the species.
2 marks – The tree identifies the relationships but is not easy to interpret.
1 mark – The tree identifies some of the clade relationships and is not easy to interpret.
0 marks – The tree doesn’t identify clades and is difficult to interpret.
Characteristics
2 marks – Enough characteristics are placed in the appropriate positions to describe the
evolutionary change of all species
1.5 marks – There is one characteristic missing to fully describe the evolutionary changes.
1 mark – There are two characteristics missing to fully describe the evolutionary changes.
0.5 mark – There are three characteristics missing to fully describe the evolutionary changes.
0 marks – The tree is missing characteristic and/or are placed in inappropriate places.
Descriptive
Caption
2 marks- The figure caption is numerically labeled; contains a short 1-2 sentence description of
figure contents that don’t contain excess detail; and the caption is placed underneath the
figure.
1.5 marks – The caption is present but missing one of the above criteria.
1 mark – The caption is present but missing two of the above criteria.
0.5 mark – The caption is present but missing three of the above criteria.
0 marks – The caption is not clearly identified, communicated or is missing.
Comparative Summary – Part 3 ( / 8 marks)
Clarity
2 marks – The summary is written clearly and in an appropriate length
1.5 marks – The summary is written clearly and contains unnecessary information
1 mark – The summary is not written clearly but is an appropriate length
0.5 mark – The summary is not written clearly and contains unnecessary information
0 marks – There is no summary of the phylogenetic tree
Comparison
Description
2 marks – The summary states the relationships between the species and is explained.
1.5 marks – The summary states some of the relationships and they are explained
1 mark – The summary states the relationships between all the species but not explained.
0.5 mark – The summary states some of the relationships but not explained
0 marks – The summary doesn’t explain or state the species relationships.
Continued on next page
BIOL 1030 – Lab Manual
© Scott & Debets Winter 2021
Accuracy
2 marks – The summary is clearly and accurately written based on the tree
1.5 marks – The summary is clearly written, but contains inaccuracies based on the tree
1 mark – The summary is a bit unclear but is accurately written based on the tree
0.5 mark – The summary is unclear and not accurately written
0 marks – There is no summary
Mechanics
2 marks – The summary is written clearly and contains no grammatical or spelling errors.
1.5 marks – The summary is written clearly, contains minor grammatical or spelling errors (< 2)
1 mark – The summary is written clearly and contains grammatical or spelling errors (3 – 5)
0.5 mark – The summary is written clearly and contains many grammatical or spelling errors (> 5)
0 marks – The summary is not written clearly for the reader to understand
UMLearn Rubric
Phylogenetic Tree – Part 1 and Part 2 ( /22 marks, 11 marks each)
*Uses same rubric as Peerceptiv plus this correctness criterion*
Correctness
3 marks – All the characteristics are appropriately placed
2 marks – Most of the characteristics are appropriately placed
1 mark – Most of the characteristics are inappropriately placed
0 marks – There are no characteristics placed on the tree.
Comparative Summary – Part 3 ( /8 marks)
*Uses same rubric as Peerceptiv*
Phylogenetic Interpretation Questions – Part 4 ( / 3 marks)
Correctness
3 marks – All three questions were correctly answered
2 marks – Two questions was correctly answered
1 mark – One question was correctly answers
0 marks – No questions were answered correctly/included
Review Reflection – Part 5 ( / 2 marks)
Reflective
Statement
2 marks – A reflective statement identifies the most useful feedback and describes how it was
incorporate or is justified why it was not
1 mark – A reflective statements outlines feedback that was useful but does not describe why or
how it was incorporated
0 marks – No reflective statement regarding the reviews received was included.
Copyright notice – This handout is the intellectual property of Kevin Scott and Cassandra
Debets ©2021 and is made available for private study only and must not be distributed in
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