Preparation:
• Completion of labs on biomass and importance values
• After completion of this lab you are should read the chapter by Keddy (2010) posted in MyCourses (this is required reading for the course)
The objectives of this lab are to:
• compare measures diversity and diversity amongst wetland types
• consider biotic and abiotic controls on diversity
Submit (hard copy, single sided with your name in the header):
1. One table for salt marsh and one for bog reporting diversity measures and environmental data (as per these instructions), for each plot within each wetland. Be sure each is formatted as per previous instructions with an informative table caption.
2. Two figures of species richness vs elevation, one for the salt marsh and one for the bog.
3. Two figures with dominance-diversity curves, one for the salt marsh and one for the bog.
Introduction
In this lab you will continue to consider importance values of species and relate this to diversity. Species richness, a count of the number of species present, is a simple and useful indicator of diversity. However, this simple count tells us nothing about the rarity of species or the eveness of species. Both types of information can be captured using more complex indices of diversity, such as the Shannon-Weaver (H) Index or Simpson’s Index. In this exercise you will apply all three indices to your field trip data. Since controls on diversity may include biotic and abiotic factors you will begin to explore the role of elevation in this lab.
I encourage you to help each other in these lab exercises, but each student is to perform these exercises individually –there are to be no jointly produced tables or graphs.
A. Species Richness
Species richness is a simple count which can be done by hand with your data, but with larger data sets would best be done with the “count” command in Excel.
Procedure
A.1. Start your summary tables
Prepare a summary table that includes the environmental data available so far and the four diversity indices you will be calculating in this lab. You have elevation for all the wetlands, plus pH for the bog and some salinities for the salt marsh. The first measure of diversity to calculate is species richness (use its abbreviation “S” as the title of that column), use cover data for the bog and biomass for the salt marsh. Later, you will calculate two other measures of diversity (using the same data), as well as eveness, which will be placed in the three columns to the right of S.
A2. Plot species richness vs. elevation for each plot in the salt marsh and bog.
On a single graph make a plot of species richness (on the vertical axis) vs. relative elevation (on the horizontal axis) for the bog and for the salt marsh. (I have made an attempt to adapt Keddy’s figure 9.9 on page 250 so that it also plots the independent and dependent variables on the proper axes – see the figure at the end of the lab instructions.)
A3. Reflection.
Can you explain the pattern in your data? (This may be one of the points you focus on in the final assignment.)
B. CALCULATE AND ADD SIMPSON’S INDEX (D) TO YOUR TABLES
Simpson’s Index (not to be confused with the Simpson’s similarity index) is derived from probability theory (Krebs, 1994) and asks the question “What is the probability that two specimens picked at random in a community of infinite size will be the same species?” Here is a simple example. If you went to the Canadian boreal forest and picked two trees at random, there is a high probability that they would be of the same species. In contrast, if you went into the tropical rain forest and picked two trees at random there would be a low probability that they would be the same species.
The formula for calculation of Simpson’s index is:
D = 1 - (pi )2
Where pi is the proportion of each species. (In our exercise for the bog use the proportion of total cover of each species in a plot; each species’ proportion of total plot biomass for the salt marsh.) The squared proportions are summed for all species in each plot and this sum is subtracted from 1.
Procedure
B.1 Within your Excel field data files for each wetland create a new worksheet for your diversity calculations. Copy the column headings from your existing tables and paste them into the worksheet you will be using for these calculations. The data cells should be blank. We will base the calculation of D on the same %s as above.
B.2. Calculate pi2, for each species in each plot. To do this click in the first empty cell and enter the formula. Type “=”; and select the function icon in the menu bar which brings up a dialog box offering a selection of functions, choose Math & Trig, POWER. This action should bring up two entry boxes. In the first box enter the cell which contains the value you wish to be squared (the corresponding value in the same tables you used for species richness, but you will change it to a proportion by typing /100 after the cell reference). (The /100 is required as data was multiplied by 100 to report % cover as whole numbers.) In the second entry box simply type the number 2 (to square a number is to raise it to the power 2). Signify that the formula is completed by pressing ENTER.
B.3. Fill down and fill right to perform this function for all species in all plots. Now go to the spreadsheet where you are building your summary diversity index table. Label the first blank column to the right of your table: D. In the cell of this column corresponding to the first plot enter the final part of the formula to calculate D: type “=” then “1-”; next select Insert, function, Math & Trig, SUM. In the entry box for number 1 enter the range of cells that correspond to proportional values for this plot (do this by typing or selecting the cells). You can ignore the entry box for number 2. The formula is complete, press ENTER. Now fill down to finish calculations.
C. SHANNON-WEAVER INDEX (H)
The Shannon-Weaver Index is calculated with the following formula.
H = – pi ln pi
Where pi is the proportion of the ith species (in this case, the proportion for each species in a plot) and ln is the natural logarithm. For each species in a plot you will multiply the proportion of cover or biomass by the natural log of the proportions and then sum all these products, and multiple by -1.
Procedure
C.1. Create another blank table, as you did for calculation of D (put it in this worksheet or another). Take care to label worksheets to keep them straight. We will base the calculation of H on the same data.
C.2. Calculate pi lnpi, for each species in each plot. To do this click in the first empty cell corresponding to the first species in the first plot to enter the formula. Type “=”; click in the appropriate cell of the table to enter it into your formula, type “/100)”, then type “*” and finally select Insert, function, Math & Trig, LN. In the entry box enter the same cell from the table divided by 100. (If you have “0” entries not that attempt to calculate the log of 0 will generate error message, #NUM! in some of the cells – you can ignore these.) The formula is complete, press ENTER. Fill down and fill right to perform this function for all table elements.
C.3. Label the first blank column to the right of your table: H. In the first cell enter the final part of the formula to calculate H: type “=” then “-1*”, and finally select Insert – function – Math & Trig – SUMIF. In the entry box for “range” enter the range of cells below the species names (do this by typing or selecting the cells). For Criteria enter <0; you can ignore Sum_range. The formula is complete, press ENTER. Now fill down to finish calculations. (In taking shortcuts we may have created error messages in some cells, noted by “NUM##”, which would prevent us from using the simple “sum” command.)
D. EVENESS (EQUITABILITY) (J)
The value of these indices is driven by the number of species (S) and the eveness with which individuals (or another measure of importance) are distributed among the species. Equitability can itself be quantified. For example one can calculate equitability (J) from the Shannon-Weaver Index:
J = – pi ln pi
lnS
Procedure
D.1. Calculate J for each plot in the column following your H values. Obviously, eveness has no meaning at sites that hold only a single species. Do not perform this calculation for single species plots and leave those table entries blank.
E. SUMMARY TABLE OF DIVERSITY MEASURES
Procedure
Because the entries for D and H contain formulas with referenced cells, we cannot simply copy and paste into a summary table. This is a time to take advantage of the paste special command. Complete the summary table following formatting instructions provided earlier.
F. Create dominance- diversity curves for the salt marsh and bog.
Procedure
F.1 For each wetland calculate the average importance value (IV) of each species and put these values in two rows beneath the lowermost plot in your importance value table. Then, sort this row by the average importance of the species (be sure that you do not lose relationships to formulas – you may need to utilize the “paste special – values” command). Directly below the average IV write the species’ rank, with the species with the highest rank as number one.
F.2 Now, make a graph for each wetland that plots species’ rank on the horizontal axis and average IV on the vertical axis. Organize the two graphs together on a single page, make sure that the vertical and horizontal axes are scaled the same, and include a title for each one.
F.3 Reflection
Compare your results to the dominance-diversity curves Keddy presents in figure 9.5 (p. 242) of your reading. This figure also is reprinted at the end of these instructions. Do your results support his statement that “the steeper the curve, the more a few species dominate the sample” (p. 240)?
REFERENCES
Krebs CJ (1994) Ecology: The Experimental Analysis of Distribution and Abundance, Fourth Edition. HarperCollins College Publishers, New York