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BIO47 Prelecture3 Instructions

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15 views2 pages

BIO47 Prelecture3 Instructions

Uploaded by

Alan Chau
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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BIO47 Pre-lecture Assignment 3

Part 1: Vannette et al. (2013) paper


BEFORE answering the questions below, download the Vannette et al. (2013) paper from
Canvas, and read the paper.

Please consider your responses thoughtfully, use your own words, and keep your answers
concise.

Q1. 10 pts
For both Figure 1 and Figure 2, list the question that the researchers asked and then concisely
describe the experiment that they performed to address this question. When describing the
experiment, be sure to identify:
–the independent variable that they manipulated or compared
–the dependent variable that they observed or measured
–the (negative) control that provided a baseline measurement in the absence of the experimental
treatment

Q2. 10 pts
Based on the results shown in Figures 1 and 2, do you think that the yeast, M. reukaufii, weakens
the mutualism between Diplacus (Mimulus) and its pollinators? Briefly explain your answer.

Q3. 10 pts
Based on the results shown in Figures 1 and 2, do you think that the bacterium, Gluconobacter
(now called Neokomagataea), weakens the mutualism between Diplacus (Mimulus) and its
pollinators? Briefly explain your answer.

Q4. 15 pts
List a question that you would like to answer based on the findings of Vannette and colleagues.
Then, concisely describe one experiment that you could perform to answer this question. Be
sure to provide sufficient detail for another researcher to actually do the experiment. Specifically,
be sure to specify:
1) your independent variable (what you will manipulate or compare),
– your control group (if you are proposing a manipulative experiment)
– # replicates
– when and where you will perform the experiment
2) your dependent variable (what you will measure or compare)
– how you will measure it

Part 2: R
Q5. 5 pts
Predict how the density of bacteria in Diplacus nectar would be affected if the flower were caged
or bagged, rather than exposed. Briefly explain your answer.

Q6. 5 pts
Use the data in JR_nectar_data_2012.csv to compare, by 1-Way ANOVA, the bacterial density of
Diplacus nectar as a function of flower treatment (exposed, caged, or bagged). Bacterial density
should be on a log scale.

1. Open RStudio by double clicking on the BIO47_Data.Rproj file inside the


BIO47_data_2023 folder.
2. When RStudio opens, navigate to the code folder within the BIO47_data_2023 folder and
open the Examples.R file.
3. Read all of the instructions in Part 3 carefully as you work through each line of the
example code. This code will guide you through how to conduct a 1-way ANOVA in R
using data that a previous BIO47 class collected on Diplacus flowers at Jasper Ridge in
2012.
4. Copy ALL text from Part 3 of Examples.R file into a new script file and save it as
W3PreLecture.R.
5. Modify the code that you copied into W3PreLab.R to answer your specific question. Note
that you will also need to copy line 164 from Part 2 of Examples.R into your W3PreLab.R
code in order to log-transform the bacterial density data.
6. NOTE: Since the histogram indicates that the data is not normally distributed and the
Bartlett test indicates that the data is not homoscedastic, an ANOVA would not be an
appropriate way to analyze this data. However, since we have not yet discussed
alternative approaches, please proceed with an ANOVA for the purpose of this
assignment only.
7. Conduct a Tukey HSD test to assay the statistical significance of any differences you
observe between the means of the different treatment groups.
8. Be sure to include axis labels, a title, and the Tukey test labels.
9. Insert a .pdf copy of your graph into your template.

Q7. 10 pts
Summarize your results and their statistical significance (the p-values you obtained from the
Tukey test). Based on your p-values, do your data support your hypothesis? Briefly, explain your
reasoning. Then, provide at least one possible biological explanation for the results you
obtained.

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