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Overview
Overview
Quantifying diversity is needed as the number and type of organisms and species differ across communities. This lab explores how data on diversity is collected and analyzed (graphically and numerically).
Background Reading
Background Reading
Objectives
Objectives
Students should be able to
Describe how species are separated by morphological characteristics
Create and interpret species accumulation curves
Calculate diversity metrics including richness, evenness, Simpson's Reciprocal Index, and Jaccard's Index
Use diversity indices to justify conservation decisions
Introduction
Introduction
Diversity is a central focus on ecology and evolutionary studies that considers the variation in species that are present in a a community. Studies of diversity can range from analysis of genetic diversity within a single species at a site to a common focus on taxonomic diversity, or the identity and relative abundance of species at a location. Diversity studies require data to be gathered from a site and then analyzed. We will consider this work by sampling simulated spider diversity from 5 forest sites.
Before data can be analyzed, efforts should be made to ensure a community has been adequately and fairly sampled. This requires a clear definition of what a study is trying to sample; most diversity studies focus on a single type or group of species due to practical constraints. To verify the adequacy of your sampling, we can create species accumulation curves ( also called Collector’s curve). A species accumulation curve indicates the number of novel species captured per sampling event or site by plotting the total number of species observed against the total number of samples or sites. For example, imagine if in your first survey of a community you observed 3 species A and 2 species B. In this case the number of species you encountered would be 2. Therefore, you will add your first data point at y = 2.
In the next location, you captured 0 species A, 1 species B, 1 species C. This time the only unique species in this group that you didn’t find in the previous site was species C, so you have only observed 3 total species. Therefore you add the next data point at y = 3.
In the third location, you found no new species. Therefore you data point for this site would be the same y-value as the site 2, y = 3 .
In the fourth location, new species D and E were found in addition to more specimens of species A and C. In this case you will need to increase the number of species by 2 in y-axis.
You will continue to grow the curve by adding data from your other stations. Hopefully you note that the end of the curve is reaching an asymptote (Fig.5-5); this is how you know that you are getting close to capturing all species present in your study area.
Once a site has been adequately sampled diversity metrics can be calculated. Common taxonomic measures of diversity include Species Richness and Species Evenness. Species richness, which is commonly abbreviated as S, is simply a number of species within an area, while species evenness refers to how evenly species are distributed in an area. Species evenness can also be numerically quantified in several ways. One way is to actually consider the opposite of evenness, or dominance. Simpson's Index considers dominance by summing the square of the relative proportion for each species in a community. The relative proportion for each species is simply the fraction of individuals in a community that are a given species.
Simpson's Index (D) = Σpi2
Σ means " sum of", so Σpi2 means sum of Pi2. Pi is the fractional abundance of the ith species in an area.
This sounds complicated, but consider what it implies. Relative proportion goes from 1 (when only one species is in a community) to zero as more species are evenly represented in a community; it's minimum is 1/S, which occurs when S species are represented equally in a community.
True species diversity metrics combine information on richness and evenness. This is essential for comparing different sites. There are many conventional methods to calculating species diversity. Here, we will use a standard index called Simpson Reciprocal Index, 1/D where it is a literally a reciprocal of Simpson Index D. Remember,
Simpson Index (D) = Σpi2
Σ means " sum of", so Σpi2 means sum of Pi2. Pi is the fractional abundance of the ith species in an area.
Simpson Reciprocal Index = 1/Simpson Index = 1/Σpi2
Since D goes from 1 (when a community has only one species) to 1/S (when a community has a equal number of S species), 1/D goes from 1 (when community has only one species) to S (when a community has an equal number of S species). Simpson Reciprocal Index takes into account both species richness and species evenness . The higher the reciprocal index value, the higher the diversity. Here are some examples of how the two aspects interplay to determine diversity.
Community 1
In this community we found 6 individuals of circle species and 4 individuals of triangle species. The proportion of each species is determined by dividing the number of individuals of each species by the total individual number from that site. For example, for circle species; 6 /10 = 0.6. The sum of Pi2 values is 0.52, and therefore the Simpson Reciprocal Index is 1.92 (calculated as 1/0.52).
Simpson Reciprocal Index = 1 / ((0.6)2 + (0.4)2) = 1/ΣPi2= 1/0.52 = 1.92
Community 2
In this community, again circle and triangle species were sampled, but the the abundance of the two species are now evenly distributed; proportion of circle species is 0.5, and the proportion of Triangle species is also 0.5. Now if you pay attention to the diversity calculated for site 2, the index is higher than the first location. This example shows that diversity increases with increasing evenness.
Simpson Reciprocal Index = 1 / ((0.5)2 + (0.5)2) = 1/Σ Pi2 = 1/0.5 = 2
Community 3
In the third community, we found two individuals of Circle, Triangle, Pentagon, Heart, and Square species. The similarity between the second and third sites were that both of them exhibited even distributions; site 2 {5:5}, site 3 {2:2:2:2:2}. However, the third site had a higher number of species than the second site (the third site exhibit 5 species in the group where the second site only contains two species). As a result, the third site has a Simpson Reciprocal Index of 5, which is higher than the second site’s index of 2. This example concludes that diversity increases with increasing species richness .
Simpson Reciprocal Index = 1 / ((0.2)2 + (0.2)2 + (0.2)2 + (0.2)2 + (0.2)2 )= 1/ΣPi2= 1/0.2 = 5
In summary, Simpson's reciprocal Diversity Index takes into account both species richness and evenness where the higher species richness and evenness result in a greater index value, hence greater diversity.
Community similarity:
Note that measures of specie richness and eveness (and thus diversity) do not consider species identity. For example, 2 sites with totally different species could both have a richness of 4 and a diversity of 2.98. Here we will measure how different communities are from one another using the Jaccard coefficient of community similarity. We will contrast community distinctiveness between all possible pairs of sites.
The Jaccard coefficient of community similarity:
CCJ = c/S
c is the number of species common to both locations, and S is the total number of species present in the two locations.
For example, two sites A and B both contains two species, but one of which is common between two sites. Therefore;
c = 1 (number of common species: Square species)
S = 3 (total the total number of species present in the two communities)
CCJ = c/S = 1/3 = 0.33
This index ranges from 0 (when no species are found in common between communities) to 1 (when all species are found in both communities).
You will need to calculate this index to compare each pair of sites separately. For example, comparing Site A with Site B, Site A with Site C, Site A with Site D, etc… for however number of sites we sampled as all of our sampling sites together.
Methods
Methods
For this lab exercise we will utilize materials produced by the American Museum of Natural History's Network of Conservation Educators and Practitioners. The lab focuses on applying the concepts discussed above to spider biodiversity.
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