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Santa Ana College, Biology 212

Lab #21: Cabrillo Marine Aquarium Inner Beach Fish Biodiversity


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’).

per station, and (c) Shannon Diversity Index (H’). • The total number of individuals can simply
per station, and (c) Shannon Diversity Index (H’). • The total number of individuals can simply

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)”.

AKM, Lab Handout 21-1c.


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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:

H ' =


i =1




ln n i


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 cells where C5 is the individual count of a species and C$190 is the total count for the entire column. Note:

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’)

(b) species richness, and (c) Shannon Diversity (H’) Generate an excel table (like in the previous

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

Santa Ana College, Biology 212

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.


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.

Santa Ana College, Biology 212

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.