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Honors 227
Ecology: Biodiversity and Ecosystems
Laboratories 9 and 10
Note: This is a two-part lab devoted to ecology and ecosystems. The first part investigates biodiversity and will be done the week of
29 October. The second part investigates productivity, nutrient cycling and energy flow in ecosystems and will be done the week of
05 November. Each lab is to be done in small groups and the report turned in the following week (turn in the Biodiversity analysis the
week of 05 November and the second exercise the week of 12 November). The report will require observations in the field and
analyses using Excel. The latter can be accessed using the Honors Computer Lab on the 3 rd Floor of Enterprise.
Introduction
The discipline of ecology is populated by an array of scientists from multiple scientific
fields. These include women and men from such diverse areas as aquatic biology (e.g.,
fish’ algae and water quality), terrestrial biology (e.g., plants and animals), atmospheric
chemistry (e.g., pollution chemistry), atmospheric physics (e.g., climate), remote sensing
(earth observing satellites), conservation biology, computer sciences and modeling,
natural resource economist, tourism, microbiology, and environmental policy (policy
wonks). The array of fields in ecology is required because most issues facing ecologists
require multiple perspectives in order to understand how systems work and how best to
manage them as a natural resource (e.g., timber lands) or as part of the global network of
ecosystems (sustainability).
The most basic functional unit of investigation and management in ecology is the
ecosystem, which consists of all the living/biotic components (plants, animals and
microbes) and the abiotic (nonliving) environment in which they live. Most ecosystems
are not explicitly defined in a geographical sense but rather are “units” on a landscape
that have similar assemblages of organisms and similar abiotic features. For example, in
the Northern Virginia area, hardwood forests are a distinct ecosystem being populated
mostly by oaks, hickories and tulip poplar trees; these ecological dominant species, plus
other plants (e.g., dogwood), animals (e.g., squirrels, dear) and microbes (e.g., soil
microbes and fungi), coupled with the abiotic components (soil, atmosphere and water)
collectively are the ecosystem. However, in the same area, you can have other distinctly
different ecosystems, including grasslands, streams, orchards, reservoirs, wetlands,
urban/suburban yards, and agriculture; each of these is a separate ecosystem with a
specific set of biotic and abiotic components.
While there are several cardinal features of all ecosystems, we will focus in these two
laboratories on only four: first lab - biodiversity; second lab - energy flow, element
cycling, and change.
The first - biodiversity - has surfaced as a major thrust in ecology over the last decade.
All ecosystems are comprised of organisms, and most commonly we define each
ecosystems by the species that are most common or ecologically dominant (e.g., oak and
hickory trees in a forest, grasses in a grassland, corn in a cornfield). Understanding the
host of organisms that thrive in an ecosystem is important because the diversity of these
organisms appears to play a role in the structure, function and long-term stability of the
ecosystem. Some ecosystems have a large number of species that make of the biotic
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component (e.g., oak-hickory forests or a tidal wetland may have 100+ species); in these
ecosystems the diversity is high. Conversely, others may have the same number of
individuals but the ecosystem is largely one species (e.g., corn field). Both of these are
functioning ecosystems (one natural and the other managed) but they differ significantly
because of their biotic component.
Ecologists have found that quantifying biodiversity within an ecosystem is important, and
they have devised two metrics to “capture” the (i) numerical diversity of the biological
community and (ii) the evenness with which the species are distributed. The first is
referred to as species richness and is the number of different species (not organisms).
The second is referred to as relative abundance and addresses the number of individuals
of each species and how evenly these numbers are distributed. In order to investigate the
biodiversity of an ecosystem, both of these metrics must be quantified.
The formula to calculate species richness is simple:
Species Richness
=
 (species)
Therefore, in a mixed deciduous forest (e.g., Shenandoah Mountains) species richness
commonly approaches several hundred different species of plants and animals.
The formula to quantify relative abundance is more complex:
Relative Abundance (D)
=
 (ni/N)2
Where ni is a measure of prominence of that species within the ecosystem, and N is the
total prominence value for all species summed over the whole ecosystem. As an
example, ni may be the number of individual organisms or the number of stems of a
specific plant species or the biomass of individual trees, etc. Biomass (dry weight of an
organisms in g) is one of the most useful metrics since it can be related to productivity.
The calculation of relative abundance is so important in the discipline of ecology that it is
given a name - the Simpson Index - and abbreviated as D. It is the sum of the squared
ratios for each species describing their ecological prominence. The value of D or the
Simpson Index ranges from 0 to 1.0. A mixed species prairie from the Midwest would
have a Simpson Index of 0.10 (and a very high species richness and a well
mixed/equitable number of individuals of each species), whereas a millet ecosystem
would have a Simpson Index of 0.9 (low species richness and all the organisms are
largely millet plus a few uninvited weeds). Thus, the more diverse ecosystems have
smaller Simpson Indices.
The second is the concept of energy flow, underpinned by the first and second law of
thermodynamics. The First Law of Thermodynamics states that energy can neither be
created nor destroyed but can be transformed from one form to another (e.g., chemical to
mechanical energy to run your car). The Second Law of Thermodynamics states that
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systems over time tend to dissipate energy as heat (increasing entropy). Both of these
Laws determine the flow of energy in ecosystems.
In a forest ecosystem, energy from the sun is captured in the leaves of the plant canopy
and converted from radiant energy into chemical energy in the process of
photosynthesis; organisms – plants - that accomplish this scheme are called autotrophs.
The radiant energy is in the visible spectrum of sunlight and pigments in the leaves
capture the energy and transfer it to chemical bonds linking carbon atoms together. The
bonds are complex molecules of 3-6 carbon atoms linked tighter covalently, and the
energy is stored in the bonds per se. This transfer of energy from one form to another is
consistent with the First Law of Thermodynamics.
The transfer of energy does not stop at the level of the leaves in the plant canopy.
Chemical energy is subsequently “utilized” by a host of organisms called consumers.
Herbivores consume plant matter directly (and transfer the chemical energy of the leaves
through metabolism in their body), carnivores consume other animals (and transfer the
stored energy in tissues), and saprovores decompose the dead plant and animal remains,
releasing the chemical energy stored in the remains. Thus, energy is transferred
throughout the ecosystem through various levels that are called “trophic levels”. On a
global scale, this transfer of energy occurs both in managed (agriculture and animal
husbandry) and unmanaged ecosystems, with the former created as the basis for human
civilization.
In the above trophic levels, the transfer of energy from one level to another (e.g.,
autotrophs to herbivores) is not without a cost. Some of the energy is “lost” in the
process of respiration, being re-radiated to the environment. In fact, this cost of energy
transfer is quite high, approaching 80-90% of the total energy flow. As a consequence,
for every 100 grams of carbon stored in chemical bonds in leaves in a plant canopy, only
a maximum of 20 grams is commonly transferred to herbivores and the rest is lost as
respiration. The same loss process occurs at every transition in the ecosystem, with only
a small part of the energy being transferred to the next trophic level. This fact is
consistent with the Second Law of Thermodynamics.
The third is the concept of element cycling and stands in contrast to the behavior of
energy, which flows through ecosystems according to the Laws of Thermodynamics.
Elements behave quite differently since elements tend to be re-cycled and re-used. For
example, for every 20 molecules of carbon in an ecosystem, there is ~1 molecule of
nitrogen. Nitrogen is a very very precious element in all ecosystems. In fact, most
ecosystems on the surface of the globe are limited in productivity because nitrogen is in
short supply (what do you fertilize your yard with in the spring and summer?).
Accordingly, most nitrogen molecules are preciously re-cycled in ecosystems. The same
is true of many elements, most notably phosphorous, calcium, sulfur, potassium, oxygen
and carbon. In fact, on the surface of the earth, all elements are re-cycled between the
four majors spheres in the following figure:
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Atmosphere
Biosphere
Hydrosphere
Geosphere
The last concept is the principle of change in ecosystems. While we tend to “lump”
ecosystems into categories (e.g., grasslands, oak-hickory forests), the reality is that all
ecosystems differ depending on the site specific biotic and abiotic components.
Moreover, all ecosystems are influenced by a number of external forcing functions that
push the ecosystem one way or another. The subsidies (e.g., fertilizers, pesticides) used
to maximize productivity of agricultural landscapes create a different type of ecosystem
from one that gets few or no subsidies. All ecosystems change over time and develop
from one stage to another. In some places on the globe, the ecosystems are very stable
over time as the ecological dominants exert their influence over thousands of years (e.g.,
redwood forests). For others dramatic change is an annual or decadal event that recalibrates the system (e.g., hurricane prone areas, fire prone areas in the western United
States). Disturbance/change is an expected and natural process in ecosystems, and all
ecosystems have intrinsic mechanisms for dealing with change.
In this laboratory you will investigate each of these features by collecting data from
multiple sites around the GMU campus. The materials you will need are only a few:
Excel Spreadsheet available off the web from the Honors Web Site
Pencil
Measuring stick that records in centimeters (cm; available in the lab)
It is best to work in groups of 2-4 (no more than four), with one individual recording data
and another measuring the sizes of the trees.
Four sites are identified on campus for investigation (see map). On each site, you need to
record the following information:
 number of different woody plant species (trees above 1 m tall; excluding
shrubs close to the ground);
 number of organisms per species (all stems as a separate organism);
 diameter (in cm) of each tree stem (do this as an approximate
measurement as related by your instructor).
The sites are defined as follows (a map will be distributed in lab):
Site No.
Name
1
Aquia Module
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2
3
4
Quadrangle
Enterprise
Nottoway
You can identify each tree species by three features: tree geometry (tree shape and size);
leave size/shape; and trunk characteristics (e.g., smooth bark, rough bark, bark color,
etc.). Do not be concerned as to what the species name is but be careful to “lump” all
individuals that are in the same species. Once you have determined how many different
species you have in each plot, simply call the Species A, B, C or D. If you know the
species, great, but that is not essential. And do not fret over mis-labeling one or several
trees since it will not affect the overall analysis.
To determine the number of individuals in each species, simply count each stem. For
each stem, record the diameter (in cm) at 1.0 m above the ground. This can be done
without measuring exactly from the ground level but be consistent in whatever plumb
line you select (chest or waist; but use the same metric height at all sites).
It is easiest to record the information on a separate sheet of paper and then transfer the
data to a spreadsheet for each site. A template spreadsheet is offered for each site,
although it needs to be modified depending on the number of species and individual trees
at each site (you need to know some basics of Excel). For each site, the spreadsheet
requires that you enter the following information for each individual species:
Stem diameter (cm) of each tree
The next steps can be handled using ‘macros’ in Excel and you can take the macros from
the Example Site Data spreadsheet that is appended. Biomass is estimated from the
tree’s diameter and is simply the following:
Diameter (cm) multiplied by the 400 (conversion factor), with the product being
biomass in g or
diameter (cm)
x
400
=
biomass (g)
Thus, create a separate column called “Plant Biomass (g)” on your spreadsheet as shown
in the example.
The next step (see example) is to provide Summary/Species data by entering the number
of stems (organisms) and a sum of the biomass (use a Macro; see the example
spreadsheet). Follow this sequence and complete the steps for all species in each site. At
the bottom of the page in the Summary Data for Site, fill in the corresponding data for
Species Richness (number of species), Sum No. Stems, and Sum Biomass.
The next step is to calculate the Simpson Index (D) for each species using a two-step
process. First (under Summary/Species) calculate the ni/N ratio for No. Stems and the
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ni/N ratio for Biomass. In the next column for each, simply square this number (ni/N)2.
Complete this column for each of the species in the plot.
The final step is to calculate the Simpson Index or D for the entire plot for both the No.
Stems and Biomass by summing () the individual values across all of the species. Enter
these two indices at the bottom of the site data as shown in the example spreadsheet.
These calculations can be handled individually with a calculator or via a series of macros,
and I recommend that you handle the process using the latter strategy.
When you have completed all four spreadsheets (one for each plot), you need to complete
an intermediate table of data as follows (in Excel) by taking the summary data (at the
bottom) from each spreadsheet:
Site No.
No. Species
No. Stems
Biomass (g)
_______
_________
________
____________
Simpson Index
No. Stems Biomass
________ ________
1
2
3
From this intermediate table, the following five graphs (as histograms) are requested
using Excel:
Graph No.
1
2
3
4
5
X Axis
Site No.
Site No.
Site No.
Site No.
Site No.
Y Axis
No. Species
No. Stems
Biomass
Simpson Index or D: No. Stems
Simpson Index or D: Biomass
For example, Graph 1 should be similar to the following (data are not from this study):
25
20
Number
of
1Species
15
10
5
0
No. 1
No. 2
No. 3
Site Number
No. 4
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To complete the laboratory, turn in the following materials:
Five Graphs
Intermediate Excel Table
Answers to the questions that follow
Enclosure
Template Spreadsheet
Spreadsheet for each site (N=4)
Map (handed out in lab)
Questions
1.
For each of the following metrics, list the hierarchy of the sites from high to low
(parenthetical data are the numbers off the spreadsheet for each site):
Example:
Nottoway > Quandrangle
(24)
(16)
> Enterprise >
(12)
Aquia
(7)
A. No. Species
B. No. Stems
C. Biomass
D. Simpson Index or D: No. Stems
E. Simpson Index or D: Biomass
Are there some general patterns that emerge irrespective of the rankings used?
Explain your answer.
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2. For the two Simpson Indices (D), are the rankings of the sites identical? Would
you expect the rankings to always be similar? Explain your answer.
3. If you were to order the sites from low to high degree of disturbance (disturbance
based on human intervention), how would you rank the sites? Explain your
answer.
4.
What is the ecological advantage to a site of having high species diversity?
5. Under what conditions might a low species diversity be expected and be
advantageous?
6. If you were to conduct the same study but over a larger transect - from the Artic
to the Tropics - and solely in natural landscapes (areas not disturbed or
maintained by human activity), how would you expect species diversity to
change from North to South (i.e., would the index increase or decrease).
Explain your answer.