Rarefaction I - how much is “enough”
1. Pour out Sample A onto grid paper (~evenly)
2. Start in grid “1” lower left and select the first five specimens.
3. Sort the specimens into discrete species using your characters.
4. Plot the number of species for first five specimens.
5. Repeat steps 2-4 working your way five specimens at a time through the first 30
specimens (6 rounds).
Questions:
For the first 30 specimens how many species have you found?
Based on what you have seen so far on your rarefaction curve,
do you expect to keep finding new species as you add data?
6. Repeat steps 2-4 for another 30 specimens (5 at a time).
Questions:
For the first 60 specimens how many species have you found?
Based on what you have seen so far on your rarefaction curve,
do you expect to keep finding new species as you add data?
For any given sample, write a description of how you would use a rarefaction cure to
determine whether you had observed the all (or majority) of the diversity present.
7. Go ahead an finish sampling and plotting the data (5 at time) just to be sure you did
not miss any species (6 species, 78 individuals)
Rarefaction II- Is it ever enough?
1. Carefully pour out Sample B onto large grid paper (~evenly)
2. Start in grid “1” lower left and select the first ten specimens.
3. Sort the specimens into discrete species using your characters.
4. Place the species on your large sorting paper beginning with
species #1. Just add species sequentially.
4. Plot the number of species for first ten specimens.
5. Repeat steps 2-4 working your way 10 specimens at a time through the first 100
specimens (10 rounds).
Questions:
For the first 100 specimens how many species have you found?
Based on what you have seen so far on your rarefaction curve,
do you expect to keep finding new species as you add data?
6. Repeat steps 2-4 for another 100 specimens (10 at a time).
Questions:
For the first 200 specimens how many species have you found?
Based on what you have seen so far on your rarefaction curve,
do you expect to keep finding new species as you add data?
6. Repeat steps 2-4 (10 at a time) until the your rarefaction curve begins to level off.
How many species did you find when the curve leveled?
How many individuals did you collect to reach this?
7. Note that the exhaustive count is 51 species, 311 individuals.
Comparing samples:
The two assemblages we have been working with have different properties.
Summarize them here:
Sample A
Sample B
Number of individuals
78
311
Number of species
6
51
One question we could ask is: “What would Sample B look like if we had only
collected 78 individuals (like Sample A)?
Rarefaction can answer this question! But the computational expectations are beyond
this course.
A simple way to compare is diversity index.
Simpson Coefficient = C / W * 100
emphasizes similarity (more sensitive to changes)
=
#of taxa in common * 100
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total # of taxa in smaller sample
Jacard Coefficient = C / (A + B – C)
emphasizes differences
=
# of taxa in common
–––––––––––––––––––––––––––––––––––––––
(# exclusive to A + # exclusive to B - # in common)
What the coefficients for our samples: C = 6, W = 6, A = 0, B = 45
Simpson Coeff. =
Jacard Coeff. =