Download Multivariate Analysis of Woody Species in the

Multivariate Analysis of Woody Species in the
Duke Forest
Mid-Piedmont Region:
Durham, North Carolina
Brian Wang
December 5, 2005
Biology 112-001
Introduction
The vegetative structure of a community is determined by the combination of three
interacting factors: species composition, environmental influences, and historical past.
Through the analysis of these three components, the varying patterns and processes that
affect the composition of a plant community can be looked at in more detail. Different
environmental variables can be examined separately and in groups, in order to determine
if they drive noticeable patterns in the plant community (Jacobs, 2004). Also, it is
important to achieve a more thorough knowledge of plant communities because it allows
ecologists to predict their future patterns of growth and changing diversity.
The goal of this study was to analyze and classify the vegetative, woody species
community of the Duke Forest. The vegetation community of this particular area was
examined through indirect gradient analysis or ordination. In this approach to vegetation
analysis, the different community types of the area were identified in terms of the
vegetation, and the underlying influences of the environmental factors were applied the
various sectors of the community. In the first part of the study, an ordination was applied
to both the species data and environmental data of Duke Forest. This allowed particular
objects of interest such as species, samples, plots, and soil characteristics to be grouped
together according to their similarities. In the second phase of this investigation, the
various groups of the vegetation data were identified and were grouped to the ordination
analysis. The final part of the study defined and classified the groups of the study using
the method of indicator species analysis.
Methods
The initial part of the vegetative analysis of the Duke Forest dealt with the simple
grouping of the species, samples, plots, quadrants, and soil data from the area. First, a
step-down ordination was applied to the data to identify the best number of axes to use
for the focal run. In this step, a NMS ordination was run on the species data, and the
stress and instability were calculated. The measure of distance for the ordination was
Sorensen (Bray-Curtis). The dimension for which the stress levels off was found to be
three. This numerical dimension was then used for the focal NMS ordination of the data.
Next, the woody species data was opened for both the main and second matrix of the
ordination. This ordination was then graphed, with the species data overlaid as a biplot.
Then another ordination was conducted, with the species data as the main matrix and the
environmental factors of the Duke Forest as the second matrix. This ordination was also
graphed, with the environmental variable overlaid as the biplot.
The second component of the analysis identified the different groups of the previous
ordination data based on species composition. First, a cluster analysis was used to group
the main and second matrix of species data. This was followed by another cluster analysis
of the main matrix species data and second matrix of environmental variables. With the
application of the cluster analysis, grouping levels were added to both data files in order
for them to be used as second matrixes to display ordination with the groups in the biplot.
The cluster dendrogram was formed from this data analysis to identify the groups and
their corresponding plots. Next, the groups were qualitatively examined in biplots using
the focal ordination results from the first phase of the study. The species data was used as
the main matrix, with the species and groups data from the first phase being used as the
second matrix. With this data being collectively graphed, the ordination results form the
first phase are displayed along with the color coding of the various plots, allowing the
various species of each group to be identified.
In the final section of the data analysis, the groups of the study were defined and
classified using the indicator species analysis. To determine the correct number of
groupings to use, the indicator species analysis was applied to the four different species
and group data sets. Then the p-value data for each group was imported into an excel data
file, in which the p-values were organized in ascending value, their average p-values
were calculated, and the number of indicators (below 0.05) for each group were recorded.
The 3rd grouping level found to be the best level of grouping because it was identified to
have the lowest average p-value and the highest number of indicators. Finally, using this
specific level of grouping, the abundance, frequency, and indicator values was found for
each group.
Results/Data
The first part of the vegetative analysis produced graphs of the species and the
environmental variables. In figures 1 and 2, the 2:1 axis format shows that the location
and distribution of Liquidambar styraciflua, Carpinus carolininiana, and Ulmus alata are
heavily influenced by the concentrations of soil Mg-A and Ca-A, with these species being
distributed in a close proximity to these soil nutrients. Also, these three species seem to
be slightly affected by the soil PH and Mn concentration, with them being closely located
to these factors as well. From these same graphs it can also be interpreted that the
location and distribution of the Acer rubrum and Quercus pinus is influenced by the soil
concentration of aluminum, while the species Oxydendrum arboretum is related to the
elevation of the environment and white oak is affected by the location of water sources.
The graphs of the species and environmental variables, figures 3 and 4, in the 3:1
axis format show that the location and distribution of Fagus grandifolia, Juniperus
virginiana, Liriodendron tulipifera, and Quercus stellata are slightly influenced by the
amount of Ca-A and Mn in the soil, as well as the soil PH, with their distribution being
further away from these variables. However, the two tree species Acer rubrum and
Quercus pinus seem to be more impacted by the soil concentration of Al, with a close
proximity to this nutrient in the area.
Figure 1
Figure 2
Figure 3
Figure 4
In second analysis section, the different various groups of the vegetation data were
identified and were grouped to the ordination analysis. The dendrogram, in figure 5,
illustrates the groups by color coding and ordering the plot numbers by group.
Figure 5
ENVLONG:wk2
Distance (Objective Function)
1.6E-02
5.1E+00
100
75
1E+01
1.5E+01
2E+01
25
0
Information Remaining (%)
00001
PSP37
00018
00021
00574
00004
00008
00014
00002
00005
00007
00509
00520
00016
00024
00023
00033
00010
00031
00020
00042
00019
00069
00517
PSP36
00555
00581
00598
00589
00571
00579
00009
00012
00011
00015
00017
00022
00067
00618
00513
00514
00620
00537
00619
00501
00504
00524
00502
PSP88
PSP86
00508
PSP87
00617
PSP35
PSP34
00081
00606
00590
00510
00596
00512
00511
00607
00621
00608
00609
00003
00612
00616
00611
00614
00615
00622
00624
00575
00593
00582
00013
00029
PSP44
PSP61
00503
00507
00025
00026
00583
00584
00585
00032
00505
00506
00625
PSP10
00027
00587
00518
00588
00602
00515
PSP43
00028
00516
00030
00610
00613
00623
50
Group6
1 3 12 36 37 87
When the ordination results from the first section were combined with the color coding of
this section, ordination graphs were created that showed the different color coded groups
along with their corresponding environmental variables. In figures 6, 7, and 8, the graphs
of these groups are displayed in the various axis combinations.
Figure 6
TLwk1
Group6
1
3
12
36
37
87
LIST
Axis 2
CACR
ULAL
ACRU
QUPR
OXAR
QUAL
Axis 1
Figure 7
TLwk1
Group6
1
3
12
36
37
87
QUST
Axis 3
JUVI
QUPR
ACRU
LITU
FAGR
Axis 1
Figure 8
TLwk1
Group6
1
3
12
36
37
87
QUST
Axis 3
JUVI
QUAL
ULAL
LIST
OXAR
CACR
LITU
FAGR
Axis 2
The red group (group 1) is comprised of woody trees species whose distribution and
location seem to be greatly influenced by the environmental variable of H2O and slightly
influenced by the habitat elevation, with these trees distributions increasing in their
vicinity. This particular group seems to be composed of the species Quercus alba,
Oxydendrum arboretum, Quercus stellata, and Juniperus virginiana. The green group
(group 3) is made up of species that seem to be affected by the concentrations of
magnesium and calcium in the soil. From the different ordination graphs it looks as if this
group is dominated by the species Liquidambar styraciflua. The species of the turquoise
group (group 12) is influenced by the pH of the soil and also by the soil concentration of
Mn. The species of this group are Carpinus caroliniana and Ulmus alata. The pink group
(group 36) is composed of species whose distribution is shaped by the soil concentration
of Aluminum. The species of this group seem to be Acer rubrum and Quercus pinus. The
blue group (group 37) is made up of species that are affected by the soil PH and soil
concentration of calcium. The final group, group 87 (yellow) is comprised of species that
seem to not be directly affected by any of the corresponding environmental variables in
this vegetation analysis. However, this group might be influenced by a particular
combination of variables.
In the third part of the vegetative analysis an excel worksheet, figure 9, was created using
the indicator species analysis to determine the abundance, frequency, and indicator values
for each woody tree species in the Duke Forest.
Figure 9
Species
ACNE
ACRU
ACSA
AMAR
BENI
CACR
CACA
CACO
CAGL
CAOL
CAOV
CAPA
CATO
CECA
CEOC
COFL
CRMA
CRUN
CRAT
DIVI
FAGR
FRAX
ILAM
ILDE
ILOP
JUNI
JUVI
LIST
LITU
MATR
MORU
NYSY
OSVI
OXAR
PITA
PIEC
PIVI
PLOC
PRAM
PRSE
QUAL
QUCO
QUFA
QUMA
QUMI
QUNI
QUPH
QUPR
QURU
Abundance
0
45
0
15
0
0
0
0
24
14
0
100
27
0
0
10
0
88
0
58
0
0
88
0
35
0
3
2
14
0
15
21
3
47
25
66
33
0
0
18
23
86
19
94
0
0
0
99
9
Frequency
3
96
16
6
4
31
1
6
62
35
48
7
66
23
8
89
4
4
3
27
34
53
6
11
16
6
53
53
59
3
41
88
26
71
27
27
26
3
1
44
78
25
21
11
5
2
9
37
55
IV
3
32
8
2
4
21
1
6
22
15
22
6
23
12
5
30
3
3
3
11
19
25
3
7
8
6
28
25
22
3
18
29
12
26
12
10
9
3
1
16
30
14
8
6
4
1
6
33
21
p-value
0.158
0.095
0.073
0.626
0.058
0.001
0.733
0.019
0.235
0.02
0.193
0.009
0.155
0.202
0.142
0.106
0.173
0.063
0.12
0.049
0.001
0.202
0.198
0.052
0.106
0.026
0.001
0.001
0.003
0.168
0.013
0.719
0.195
0.017
0.046
0.324
0.344
0.066
0.598
0.531
0.001
0.002
0.36
0.04
0.098
0.545
0.093
0.001
0.169
QUSH
QUST
QUVE
SAAL
ULAL
ULAM
ULRU
0
7
31
56
0
0
0
3
33
60
15
26
7
14
3
20
22
5
14
7
12
0.183
0.001
0.047
0.576
0.019
0.023
0.004
This excel worksheet shows the rank of each tree species within each group. According
to the importance values, Quercus alba is a strong indicator of the red group,
Liquidambar styraciflua of the green group, Carpinus caroliniana of the turquoise group,
Quercus pinus of the pink group, and Quercus stellata of the yellow group.
Discussion
Through the various methods of vegetative analysis conducted in this study, it has been
found that there are strong correlations between the environmental variables of the Duke
Forest and the woody tree species found within it. Strong indicator species of calcium,
magnesium, and water can be found in axes 2 and 1, and indicators of aluminum in axes
3 and 1. The axes 3 and 2 also contained indicators of water, elevation, magnesium, and
calcium. However, no strong indicator species were found to have a direct correlation
with pH and manganese, which may have resulted from the insufficient abundance of
these corresponding indicator species in the area of study. Further studies researching the
historical history of the land can be conducted on the distribution of woody tree species
in the Duke Forest. Correlations may be discovered between the previous land uses of
plots in the past and their current composition of vegetation.
Literary Works Cited
Jacobs, L. 2004. Multivariate Analysis of High Elevation Red Oak Communities: A
Reassessment of Current Community Classifications.