How to Know When to Stop Sampling

One of the simplest questions an ecologist can ask about a place is how many species live there. The answer is important for basic researchers and managers alike, but can be deceptively hard to obtain. This exercise introduces the issues surrounding the estimation of species richness. You will learn to collect data in the field, obtain your own estimates of species richness, and evaluate the underlying assumptions and validity of these estimates.

Terms to Know:

Biodiversity is the population heterogeneity of a community, or the number of species in a given area. In addition to species diversity, it may also refer to genetic diversity and/or ecosystem diversity.

Species diversity is a combination of species richness and species evenness.

Species richness is the total number of species present in the community.

Species evenness refers to the relative abundance of individuals among the species present in a community.

Evenness contrasts with dominance (when individuals from one or a few species exists in high proportions, making up the majority of the community) and so evenness is maximized when all species have the same number of individuals.

How to Calculate:

Species Richness

Species richness (S) is a measure of the total number of species found in a sample. However, since the larger the sample, the more species we would expect to find, the number of species is divided by the square root of the number of individuals in the sample. This particular measure of species richness is known as D, the Menhinick index.

D=S/√N

where S equals the number of different species represented in your sample, and N equals the total number of individual organisms in your sample.

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Species Diversity

Species diversity differs from species richness in that it takes into account both the numbers of species present and evenness of species in relation to one another. As a measure of species diversity, we will calculate the Shannon index, H. Interestingly Shannon, a physicist, developed the index as a formula for measuring the entropy of matter in the universe. It turns out that the mathematical relationships hold true whether one is dealing with molecules in solution or species in an ecological community.

H = ∑(pi) |ln pi|

Where (p1) is the proportion of the total number of individuals in the population that are in species “1”. In other words, pi is the relative abundance of a species:

pi (relative abundance) = ni/N

where ni = number of individuals of species i and N = total number of individuals in all species.

H ranges from 0 for a community with a single species, to up to 7 for a very diverse community (though this is extremely rare).

Understanding the Difference Between Species Richness and Species Diversity

Consider the following data from samples of organisms obtained from two different biological communities, A and B.

Community A
Species # of individuals

A   59 B   12 C   11 D   10 E   5 F   3

Total 100

Community B

Species # of individuals

A   21 B   20 C   19 D   14 E   13 F   13  

Total 100

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Note that in both samples the same total number of individuals were obtained, and the same six species were found. The only difference seen between the two communities is in the distribution of the number of individuals among the six species.

If we calculate species richness for the two communities,

D = S/√N

where S equals the number of different species represented in your sample, and N equals the total number of individual organisms in the sample, we find that the resulting numbers are the same: D = 0.6, because both samples have the same number of species for the same number of total individuals. In other words, the species richness in the two communities is identical.

Now consider the species diversity of these two communities. In community A, one species, Species A, numerically dominates the other five species. In community B, the six species are more evenly represented. Because of this difference, community B would be considered to be more ‘diverse’ than community A despite both communities having the same total number of individuals and the same number of species. Thus, when measuring species diversity the relative abundance of each species must be taken into account.

In Table 1, species diversity is calculated for the two communities using the formula

H = ∑(pi) |ln pi|

Where (p1) is the relative abundance of species “1” in the community.

Table 1: Calculation of species diversity using the Shannon index, H

    Community A     

Species # of individ. (pi ) |ln pi| (pi) |ln pi|

A   59  .59 0.528   .311     B   12  .12 2.120   .254     C   11  .11 2.207   .243     D   10  .10 2.303   .230     E   5   .05 2.996   .150     F   3   .03 3.507   .105     Total   100 1.00        1.293        Community B     

Species # of individ. (pi ) |ln pi| (pi) |ln pi|

A   21  .21 1.561   .328     B   20  .20 1.609   .322     C   19  .19 1.661   .316     D   14  .14 1.966   .275     E   13  .13 2.040   .265     F   13  .13 2.040   .265     Total   100 1.00        1.771   

Question 1: What relative abundance would achieve the highest species diversity index?
ANSWER ON TOP HAT
In summary, the species diversity approach is generally a more reliable measure of biodiversity than species richness. While mathematically very easy to calculate, the limitations of the species richness concept can be seen when applying it to Communities A and B, where it fails to distinguish their quite different community structures.

Species Evenness (E)

Using species richness (S) and the Shannon-Wiener index (H), you can also compute a measure of evenness.

The formula is:

E = H/ln(S)

Evenness (E) is a measure of how similar the abundance of different species are. When there are similar proportions of all species then evenness is 1, but when the abundances are very dissimilar (some rare and some common species), then the value decreases.

How to Know When to Stop Sampling

A practical problem that arises when measuring species richness and species diversity is determining when you have done sufficient collecting to stop sampling, or in other words, to know when you’ve gotten just about all the species that matter. A good technique is to generate a cumulative species/sample (or cumulative species/area) curve, which plots the cumulative number of species collected (y-axis) vs. the number of samples collected (x-axis) as shown in Figure 1. This technique assumes that initially you will be collecting new species with each subsequent sample, but after a while you will be collecting the same species you have already collected in previous samples. Thus, you will get a curve that starts to flatten out. Once the curve levels off there is no need to sample further.

Relationship between number of species & number of samples

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12

10

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6

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0 1 2 3 4 5 6 7 8 9 10

Number of samples

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Figure 1: A species/sample curve generated by counting the number of new species accumulated as more and more samples are gathered from a sampling area.

2. ANSWER ON TOP HAT. Use all three indices described above (D, H & E) to determine which of the following three communities of 100 individuals is most diverse. Show your calculations.

• Community 1 contains 10 species with 91 individuals in the first species, and one individual in each of the remaining species.

• Community 2 also contains 10 species, but there are 10 individuals in each species.

• Community 3 only contains 5 species, with 20 individuals in each species.

Activity Procedure:

Prior to starting this assignment you MUST:
• Read the background material
• Complete the above two questions on Top Hat

• Prepare a data table that will assist you in the data collection process.

For this activity, you will be exploring the species diversity of something in your home, yard, or neighborhood. What constitutes a “species” in this activity will be different for each of you, depending on what materials you have available. You may be creative in your choice of “species” that comprise the two communities you compare but for simplicity, I offer the below two recommendations.

A) If you prefer to use something in your home, a “species” may be represented by the kinds of fruit and vegetables (or other foods) in your fridge, freezer, pantry or cupboards. You must be clear about how you define your species – that is, what makes a particular food a unique species so that you can be consistent in how you count them.

B) You may also choose to make observations of the vehicles driving down your street. Just like a species scientific name is made up of a genus and species, a vehicle name is comprised of make and model. However, for the sake of simplicity here, you should classify the vehicles you observe based on make (Dodge, Ford, Toyota, etc.) and vehicle type (i.e. whether it is a car, truck, SUV, minivan, or motorcycle). If you come across a vehicle that is somewhat ambiguous and you are not sure how to classify it, use your best judgement based on its morphology (size/shape, etc.).

The key for this activity is that you can observe your “species” in two different “habitats”, or locations, OR at two different time points to see how the two communities differ (or how the single community changed over time). For example, you might compare the “species” of food in your fridge vs. your freezer or in your fridge/freezer combined vs. your pantry/cupboard or better yet, exchange your dataset with a friend from class to compare your fridge “community” to theirs.
If you are observing vehicles driving down your street, you might compare the “species” you observe during the morning to those you observe in the afternoon. Alternatively, you might exchange data with a classmate to compare the species on your street to those that pass down theirs.

1) Determine what “species” data you will collect and how.

• If you plan to exchange data with a classmate, first reach out to that person and make a plan for how and when you will exchange data with one another.
• Determine how you will both identify/classify a “species”. In order to be comparable, this must be the same.
• For vehicles: A “species” will be based on the make of the automobile (e.g. Dodge, Honda, Chevy, etc.) and whether it is a “car”, “truck”, “SUV” or “minivan”. Be careful not to duplicate counts of the same car (i.e. if you counted a car that was parked and now see it driving down the street).
• For food: classification of a “species” will depend on what you have available. If you have lots of vegetables, you might treat each one as a unique species. If you don’t, perhaps “green vegetable” represents one species, “red vegetable” another, “grain product” another, “meat” another, and so on. Examine your available inventory then make the determination for what makes a unique species.
• If you are having difficulty classifying a “species”, you must make a decision based on the information you have available. No individuals are to be skipped.

2) Collect your data.
• Count the number of individuals of each species present in your community or communities. (How many green vegetables do you have? How many packages of meat or grains? Or how many carrots; tomatoes; potatoes? How many of each vehicle species – make and type – did you observe?)
• If you are exchanging data with a classmate, make sure all data is recorded in the same way.

3) Calculate the biodiversity of your two communities.

• Use the formulas provided in the background section above to calculate all three indices (D, H, & E) of diversity for both “communities” (i.e. your and your friend’s kitchen “habitat” or your street community in morning vs. in the afternoon).

• Remember that a well-designed data table can help this process immensely.
• You may do calculations by hand or use a spreadsheet.
• You must provide one example of each calculation in your submission.
• For the Shannon Index, you only need to show the calculations for one “species” to illustrate how you determined your answer.

4) Submit your results on Top Hat.

Individually summarize your analysis of the data into a clear, concise report. Make sure you include all of your findings and analysis and organize your summary as directed below.

Summary Outline:

1) Headings:

a. Introduction – Describe the purpose of the activity. Include biodiversity, species diversity and how they are measured.

b. Procedure – Describe how you defined your “species” and how your data was collected. The procedure should be clear and detailed enough so that someone who has never seen this assignment before would be able to go out and do the activity after having read your write-up.

c. Data Tables

d. Mathematical Analysis: Show the results of all of your indices as outlined in 3) above.

e. Conclusions: Include answers to the below questions.

• Which “community” is most diverse? You must support your conclusion with your experimental data and mathematical analysis.
• If both “communities” were similar in size, which one would you conclude has most likely experienced some sort of human disturbance? Explain. (In other words, how does human disturbance affect a community…. Does it usually encourage or discourage species diversity?)
• Did any species dominate in either “community”? If so, explain. What characteristics do you think make it successful?
• Were there opportunities for errors in your methods or conclusions? If so, explain in detail.