Title: Multivariate analysis of community structure data
1Multivariate analysis of community structure data
Colin Bates UBC Bamfield Marine
Sciences Centre
2Goals
- To understand the ideas behind multivariate
community structure analysis. - To understand how to perform these analyses in
PRIMER. - To be prepared to analyse and interpret your
class data later today.
3What are multivariate statistics?
Statistics that allow us to look at how multiple
variables change together
4What are multivariate statistics?
Statistics that allow us to look at how multiple
variables change together EG How do 50 species
in a community react to an environmental
perturbation?
5What are multivariate statistics?
- Statistics that allow us to look at how multiple
variables change together - EG How do 50 species in a community react to an
environmental perturbation? - 50 ANOVAs?
-
6What are multivariate statistics?
- Statistics that allow us to look at how multiple
variables change together - EG How do 50 species in a community react to an
environmental perturbation? - 50 ANOVAs? No
- Multivariate stats allow us to condense
information for simplicity
7When might I use this type of analysis?
- For a multi-species community, you may wish to
- pull order from complex systems
- visualize these patterns
- comparisons over time and space
- test hypotheses
8The vehicle
9Example Seaweed Communities at Cape Beale
- Is flora different at two close sites, each
exposed to different wave intensity?
10Data collection
112. Data Analysis
Step 1 Entering your data into PRIMER
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15How to analyze this type of data?
1. Diversity indices
16How to analyze this type of data?
1. Diversity indices Yet, most diversity indices
do not consider species identity
17How to analyze this type of data?
1. Diversity indices Yet, most diversity indices
do not consider species identity
Multivariate community structure analyses
18Analysis flow
samples
species
sample similarities
ordination
How?
are sites different?
19Analysis flow
samples
species
sample similarities
ordination
Calculate Bray Curtis Similarity ? gives a
triangular similarity matrix
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23within
within
between
24Analysis flow
samples
species
sample similarities
ordination
How?
are sites different?
25Visualizing similarities
Ordination maps similarity relationships
between samples
26nMDS ordination example
27nMDS ordination example
Distance between points reflects relative
similarity!
28Nonmetric multidimensional scaling (nMDS)
the future of ordination is in nonmetric
multidimensional scaling McCune Grace, 2002
Nonmetric no axes Multidimensional represents
relationships between multiple variables in two
or three dimensions Scaling the ratio between
reality and representation
29How does nMDS work?
nMDS uses the RANK ORDER of similarity
relationships between samples
A1 is closer to A2 than it is to A3
30How does nMDS work?
Then, nMDS tries to place points in 2 (or 3)
dimensional space to represent this ranked order
A3
A1 is closer to A2 than it is to A3
A1
A2
31How does nMDS work?
Then, nMDS tries to place points in 2 (or 3)
dimensional space to represent this ranked order
A1 is closer to A2 than it is to A3
32How accurate is the nMDS map?
- Sometimes the nMDS cant represent all
relationship accurately - this is reflected by a
high STRESS value
33How accurate is the nMDS map?
- Sometimes the nMDS cant represent all
relationship accurately - this is reflected by a
high STRESS value
If Stress Value 0.0 perfect map 0.1 decent
map 0.2 ok map 0.3 dont bother
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similarity in sim. matrix
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distance on nMDS
34Main points about ordination!
- Ordination is a way to visualize how similar
your samples are - - nMDS tries to represent visually the rank order
within the underlying similarity matrix - all that matters is the relative distance
between points. - stress value allows you to estimate quality of
the nMDS
sample similarities
ordination
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42Obviously distinct groups
43Less obvious! Are they really different?
44Analysis flow
samples
species
sample similarities
ordination
are sites different?
45Analysis flow
samples
species
sample similarities
ordination
How?
are sites different?
46Are groups different?
Analysis of Similarities a statistical approach
exposed
sheltered
47Are groups different?
Analysis of Similarities a statistical approach
Ho sites the same
Ha sites are different
exposed
sheltered
48If Ho (sites the same) true
Similarity within Similarity between
49If Ha (sites different) true
Similarity within gt Similarity between
50Are groups different?
Analysis of Similarities a statistical approach
51Are groups different?
Analysis of Similarities a statistical approach
52If Ho (sites the same) true
Similarity within Similarity between
0
53If Ha (sites different) true
Similarity within gt Similarity between
1
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57To simulate null distribution
58To simulate null distribution
Similarity within Similarity between
59To simulate null distribution
Similarity within Similarity between
Calculate R
60To simulate null distribution
Similarity within Similarity between
Calculate R
61.477
621
P
0.001
999
.477
63Analysis flow
samples
species
sample similarities
ordination
How?
are sites different?
64Sites are different why?
- We will use the SIMPER routine
- - Similarity Percentages
- Basically indicates which species are responsible
for the patterns that we see.
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71Data analysis summary
samples
species
sample similarities
nMDS
are sites different?
How? SIMPER
ANOSIM