Santa Ana College, Biology 212

Lab #21: Cabrillo Marine Aquarium Inner Beach Fish Biodiversity

Introduction:
In today’s lab, you will be introduced to the study of comparative diversity. In general, most habitats are filled
with a multitude of species of varying abundances. Without a way to measure such diversity, it would be
extremely difficult to compare one assemblage of organisms to another (e.g. comparing groups of organisms
from two or more locations). One way to make sense of such complexity is to use an index of biodiversity.
The most commonly used example is the Shannon Diversity Index (also known as the Shannon- Wiener
Diversity Index). This index takes into account (a) number of taxa to the lowest identifiable level and (b) the
contribution of each taxa’s abundance to the overall sample abundance. In a sense, it therefore gives you some
measure of the contribution of rare and common taxa to the overall biodiversity of the system.

Two Tasks For Today:

Long Beach Infauna

Your first assignment will be to work up a series of data that
were gathered as part of a monitoring effort in the Port of
Long Beach. This will be conducted in lab and will NOT be
turned in. The purpose is to get you familiar with the
procedure of calculating a diversity index for multiple
stations. These are real data that are part of the NPDES
compliance monitoring for the Long Beach Generation LLC
power plant. In order to ensure there are no negative impacts
to the benthic environment as a result of the power generating
station’s thermal outfall, samples are taken of the muddy
benthos at pre-determined stations each summer (see map). A
coring device known as a Van Veen grabber was used to
collect sediment from the sea bottom. This sediment was then
run through a series of screens, leaving behind the marine
invertebrates that live in the mud. The animals were then
sorted, identified, and tallied by species, and an analysis of
the species composition was then conducted. This process
was conducted for all six stations that appear in the map. The
outfall is located closest to Station B9. Station B3 is furthest
back in the harbor while Station B11 is closest to the harbor
entrance and the open ocean.

Download the MS Excel file “LBGS_infauna_2009.xls” and

open it. You will find all the species gathered during the 2009
survey at the six stations shown in the sampling map. Your
job will be to generate “summary statistics” for the list of
invertebrate species provided. Dr. Morris will provide a brief
tutorial for how to complete this in MS Excel. You must
calculate three summary statistics – (a) total number of
individuals per station, (b) total number of species per station,
and (c) Shannon Diversity Index (H’).
• The total number of individuals can simply be added
up using the formula [=sum(cell range)], where the
cell range includes all the cells to be added together.
Let’s say the numbers you wish to add are in cell C5 through C20 – pick a blank cell and write the
following formula in the quotes: “=sum(C5:C20)”.
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! To determine the number of species at each station, there are a few possible choices. The harder way
would be to simply count how many species are present. This method would be tedious, so you can
use another formula to figure it out for you. Basically, you will write a formula that counts the
number of cells that have actual numbers in them, effectively excluding cells with “0” in it. You will
use the COUNTIF command to tell excel to only count cells with numbers greater than zero, like this
[=countif(C5:C20,“>0”)] – this formula assumes the same range of data as in the above section. Be
! To calculate the Shannon Diversity Index (H’) for a given location, you must first determine the ratio
of each individual species relative to the abundance of all species counted in your sample from that
site. For example, if you sampled Area A and found 25 red beetles out of a total 250 individual
organisms, the ratio of red beetles to the total would be 25/250 = 0.1. You must then multiple this
number by the natural log of itself, like so: 0.1 x ln(0.1) = 0.23. After you have calculated this for all
species found at Area A, you must then add them all together to get the total Shannon Diversity for
Area A. The formula looks like this:
S
ni ni
H' = −∑ ln
i=1 N N
Don’t worry… I know this looks hard, but it’s actually easy once you get the hang of, which is why we will
go over this in class together. The formula has already been entered once into the diversity data worksheet.
You will need to copy it correctly into all the cells to build the diversity index. The actual formula in excel
looks like this: =IF((C5=0),0,(-(+C5/C$190)*(LN(C5/C$190)))) In this example, the formula points to two
€ count of a species and C$190 is the total count for the entire column. Note:
cells where C5 is the individual
At some point in the future (perhaps years from now), you may need to calculate similar summary statistics.
Therefore, I have also uploaded a file entitled “shannon_diversity_formula.xls” for you. It is basically a
truncated version of the Long Beach infauna file – it’s no different, just a little easier to see where everything
goes.

The portion of this assignment is to be completed in class and does NOT have to be turned in. You will want
to make sure you are comfortable with this data set in class since the portion below will require that you know
how to calculate Shannon Diversity (H’).

Cabrillo Marine Aquarium Inner Beach Survey Data

For this assignment, you will simulate the data that you
collected on the CMA inner beach survey field trip. The data
reduction you will be performing will be from the inner beach
survey that was completed in 2013. You must take these
hand-written sheets and enter them appropriately into MS
Excel and to provide the same summary statistics as before
for the three stations that were surveyed. The summary
statistics must include (a) abundance per station, (b) species
richness, and (c) Shannon Diversity (H’)

Generate an excel table (like in the previous section) that

compiles all the data from the 2013 Inner Beach Survey.
Rather than using the infauna file from above, you should
consider using the other MS Excel file I uploaded entitled
“shannon_diversity_formula.xls”. This is set up with one more column that is NOT included in the infauna
spreadsheet, “Common Name”. The reason it is excluded from the infauna spreadsheet is because the majority
of infauna invertebrates do not have common names, whereas the fish species you encountered all have
common names. Keep in mind, these are raw data sheets! They very likely have spelling errors, and it may be
difficult to read some of the numbers. Sometimes the common fish name is reported, and other times the
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species name is used. In fact, sometimes the name given is spelled wrong. In fact, some of the common names
written on the data sheets aren’t even the true common names! For example, you might see “Pacific staghorn
sculpin” written down, but there is no such fish! The correct common name is just “staghorn sculpin”. This is
the real world – your job will be to check the numbers you entered, make sure you are putting the proper
species names (with the genus names capitalized and species names in lower case, all italicized), and the
proper common names (where nothing is capitalized unless they are proper nouns like California or Pacific).
Note, when you are using a common name to look up a species name, make sure you are looking up the
correct species that is found in southern California (and not India for example). Invariable, each semester
students will incorrectly include a species name for an animal that is found somewhere else in the world
simply because it has the same common name. This will be marked wrong. Do NOT use Wikipedia as your
main search tool for species names. Wikipedia has no idea what fish you are referring to and will be perfectly
happy spitting back a WRONG species name for the common name you entered. If you are unsure, please use
a scientific source such as:

Miller, D.J. and R.N. Lea, 1972, Guide To The Coastal Marine Fishes of California, Fish Bulletin
157, 249p.

I have copies of this publication for you to borrow in lab, plus a PDF version is posted on Blackboard with
this assignment.

You will save this excel file and upload it with the following file name: “yourlastname_cmafish.xls”. You
will upload this file with the paper described below. You will be graded based on the accuracy of your
information.

THE ASSIGNMENT

In a separate MS Word document, complete a formal write up using the CMA data you completed above.
This write-up should NOT include the Long Beach infauna data. For this write-up will only use the CMA fish
data. You are required to include all parts of a scientific paper:
1. Title – Make sure you include a title that describes the thrust of your paper.
2. Abstract – You must include this after the title and before the introduction. This is the summary of
your entire paper. The easiest way to begin is to turn each of the following sections into one or two
sentences and then string them all together into a single paragraph. From here, you can edit the
paragraph to make it flow better. Generally there should be NO citations in the abstract (an exception
is if your paper was written specifically to give a counter argument to a previously published paper, in
which case you would cite that paper, but this is not common).
3. Introduction – This is one of the most challenging sections of your manuscript. In this section, you
are expected to set the stage for “why” you carried out your experiment or investigation. In the case
of this assignment, the purpose was to add to a long-term data set for the purpose of tracking any
trends in fish population dynamics as part of an environmental monitoring program with the Port of
Los Angeles. Therefore, you can think of this section as divided into three main parts: (a) What is
the motivation for why this project was designed in the first place – to address this, consider browsing
through the Port of Los Angeles 2006 PDF on the course website for this assignment. So, you would
start with what we know about how poor water quality conditions impact fish populations in general
(use some of the papers that are also listed). Then narrow it down to the Port of Los Angeles. What
are their water quality challenges, and what have they done to address this at Cabrillo Inner Beach?
All of this should appear in the Port of Los Angeles (2006) document. (b) Then you would discuss
how the benefits of improved water quality should be observable in the fish population in a disturbed
habitat. This would tie into part (a). (c) Finally, explain how the current study (your fish data) will
be useful in assessing long-term trends in environmental conditions in the Port of Los Angeles.
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4. Materials and Methods – In as much detail as you can, write precisely what you did during the CMA
Inner Beach field trip. Include the time, date and tide at the time you sampled. FYI – the seine net you
used is 20 m wide x 2 m high, and 1/8-inch mesh size (thought: what might this mean for the really
tiny organisms that we got in the net?). The distance that the net was towed was 45 m. Pretend that
the 2013 data you received were the actual data you collected during your survey. Include a general
map illustration showing the three stations where the samples were collected. The GPS locations of
the three locations are as follows: Station 1 (33° 42.736’ N, 118° 16.969’ W), Station 2 (33° 42.681’
N, 118° 16.967’ W), and Station 3 (33° 42.608’ N, 118° 16.880’ W). How were the fish divided and
tallied? What information was recorded on your data sheets? Don’t forget to tell your reader what
statistical approach you will be using in this analysis (e.g. Shannon Diversity).
5. Results – Using only the table you created, give a verbal summary of the data. You must include a
data summary table! This should NOT be the entire excel spreadsheet that you worked on. It should
be a boiled-down version (a concise summary). Which station had the highest diversity? Which had
the lowest? What species was most common? How many species contributed at least 1% of the
overall abundance? What sort of other results can you report? It is not necessary to include any
graphs, although you are welcome to do so if you think it helps. You may wish to include a summary
table that just shows the bottom portion of your spreadsheet (without the individual species and their
tallies).
6. Discussion – Discuss the data you gathered and the implications for comparing the three different
station locations. In what way do you think the data are meaningful? Is there information that you feel
would help the discussion – e.g. if you were to conduct this survey again, what data would you add
that would be illuminating? Consider addressing some of the points you raised in the introduction
section. You should consider citing papers in this section to corroborate your statements.
7. Literature Cited – Please be sure to include at least three primary literature citations for this
assignment. These should be written out in standard ADA citation formatting, as is customary in
scientific journals. Look at the way I listed the papers I provided as examples.

Save your document as an MS Word file and upload it with your completed MS Excel CMA fish file to
Blackboard before the due date.

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