Chlorophyll and Zooplankton Data Analysis
Due Date: April 25th, 2013 at 1:30 p.m.
This exercise will familiarize you with the analysis of chlorophyll, bacterial, and net tow data.
After completing this exercise, you will be able to plot and interpret chlorophyll and density data
collected with a CTD, to plot and interpret bacterial abundance and correlate it to another
variable, to calculate zooplankton abundance per unit volume (m-3), to transform the abundance
data into biomass values (μg C m-3) using estimates of the carbon content of different organisms,
and to calculate diversity of organisms in a sample.
First, go to http://nvs.nanoos.org/CruisePrism and examine the PRISM station sites. PRISM is an
initiative through the UW and federal and state groups to understand the dynamics of Puget
Sound and its watersheds. They send out cruises periodically to set stations throughout the
Sound. We will be examining data from PRISM stations 4, 3, 5, 27, and 28 from October 2011.
(The data files are already in the Shared folder.) Think about how these stations are likely to
differ from each other. The paper by Primo et al. (2009) may help you interpret the zooplankton
data.
A. Plotting chlorophyll, density and salinity data
Using the .csv files collected from the five PRISM stations in Puget Sound in 2011, plot the
fluorescence (chlorophyll), potential density, and salinity profiles on separate graphs, with all of
the stations together in each graph. (So you will have 3 graphs, one for each variable, and each
graph will have five lines, one for each station.) The PRISM data files are .csv files. To import
.csv files:
How to import .csv files and plot depth profiles in Excel
Importing csv files
 Open a blank Excel spreadsheet.
 Go to “File/Open”. Choose “All Files” in the lower right hand corner.
 Double click on the .csv file to open it in the Text Import Wizard.
 Choose “Delimited.”
 Click “Next”. Choose “Comma” as the Delimiter; click “Next” then click “Finish”.
Making scatter plots
 On the Excel toolbar, click “insert”, select “Scatter with marks only”.
 When a blank chart box appears, right click and click on “Select data”
 Click “Edit” and select the appropriate X and Y series.
 To flip the axis, click on the y-axis, right click on the axis within the plot, select
‘Format Axis’ and check the box next to ‘Values in reverse order’ in the Axis Options
window. Click the Close button.
 Note: The resulting figure is NOT in L & O format.
B. Analyzing bacterial abundance
Plankton_data.xls contains chlorophyll and bacterial abundance data collected at 10 m depth
at all five PRISM stations. The data were collected at each station in two different weeks.
1. Create a scatterplot comparing the chlorophyll (x-axis) and bacterial abundance (y-axis).
The two weeks don’t need to be separate series; all the points should be in a single series.
2. Is this correlation significant?
a. First, calculate the regression. Click on the points in the scatterplot and click on
Chart  Add trendline. Choose “Linear,” and under Options, choose “Display
equation on chart.” This equation gives you the slope of the best-fit line as well as
the y-intercept value.
b. Next, calculate the coefficient of determination, or r2. This value gives you the
strength of the relationship between the x- and y-variable, and varies between 0
and 1. To do this in Excel, type =RSQ(y-data,x-data) where the y-data is the
bacterial abundance column and the x-data is the chlorophyll abundance column.
c. Next calculate the degrees of freedom, or d.f. For a regression analysis like this,
d.f. = n – 2, where n = the number of samples you took.
d. The null hypothesis assumes that the slope of the best-fit-line between these
variables (which you found in part a above) is equal to zero. To calculate how
much our data deviate from the null hypothesis, calculate the test statistic:
Test statistic = ts = (d.f. x r2) / (1 – r2)
e. To test the significance of the relationship, calculate the P-value. The P-value
gives you the probability of getting the observed result (the test statistic) if the
null hypothesis is true. Generally, in biology we say a result is significant if
P < 0.05. To calculate the P-value, type =FDIST(ts,1,d.f.).
C. Analyzing zooplankton net tow data
Plankton_data.xls contains zooplankton data collected at three of the PRISM stations (4, 5,
and 28).
1. Calculate the abundance of each species per m3. You should have an abundance
calculation for each species at each station (for each cell of the original count table).
Volume of water filtered = π x (radius of net)2 x distance towed
Abundance m-3 = total count per sample/m3 water filtered
2. Calculate the total biomass of each species (in µg C m-3) at each station using the table of
carbon values per individual of each species listed in the spreadsheet.
Biomass = Carbon ind-1 x abundance
3. Sum the species biomass values to find the total biomass of zooplankton at each station.
4. Determine species diversity at each station using two different methods: species richness
(r) and the Shannon-Weiner Index (H’).
Species Richness (r)
r = the number of species (or taxa) in a sample
Shannon-Weiner index (H’)
H’ = -Σ (Pi ln(Pi))
H’= index of species diversity, the Shannon-Weiner Index
Pi = proportion (percent) of total sample belonging to the ith species
ln= natural log (log base e = not the same as log!)
This index takes into account more than just the number of species (richness) in a sample,
but also how evenly distributed the species are (evenness) within the sample. The index
increases either by having more species richness, or by having greater species evenness.
Hint: -Σ (Pi ln(Pi)) = -(Pspecies1*ln(Pspecies1) + Pspecies2*ln(Pspecies2) + Pspecies3*ln(Pspecies3) + …)
Excel command for natural log: LN()
Written Assignment
Plot salinity, potential density, and fluorescence (chlorophyll) on separate graphs, with all of the
stations together in each graph. Present these in three panels in L&O style.
Plot the chlorophyll vs. bacterial abundance on a graph. Report the regression equation and the r2
value on the graph.
Present the total biomass, species richness, and the Shannon-Weiner Index for the three stations
in a table. Please make sure that you are following the L&O required style. To help me check
your calculations, please also submit your Excel spreadsheets, one for the depth profile data, one
for the bacterial abundance and statistics, and one for the zooplankton data. You can put multiple
worksheets in one Excel file.
The written assignment should be a roughly one-page description and interpretation of the data in
the figures and the table. The figures, figure captions, and table should be appended to the back
of the writing according to the L&O style guide. The first three paragraphs should summarize the
results. The last paragraph should be a discussion of the data. Paragraph one should be a
description of the vertical profiles of salinity, chlorophyll and density at the five stations.
Paragraph two should be a description of the relationship between bacterial abundance and
chlorophyll. Paragraph three should be a description of the zooplankton abundance and diversity
at the three stations. The last paragraph should be a discussion of your results. Questions to think
about: what is the relationship between chlorophyll and density? What is a possible explanation
for the relationship between bacterial abundance and chlorophyll? What is the explanation for
the changes in zooplankton distribution across the stations?
Submit your assignment via CollectIt by April 25th at 1:30pm. Please include both the written
assignment and your Excel spreadsheets.