AULA TEÓRICO-PRÁTICA ECOLOGIA DE RECURSOS/ECOLOGY

AULA TEÓRICO-PRÁTICA
ECOLOGIA DE RECURSOS/ECOLOGY OF RESOURCES
BIOLOGIA MARINHA (2º CICLO)
TITLE: Analysis of the impact of clam dredge fishery on
the benthic assemblages
AIMS:
Use the PRIMER software for the data treatment
Analyse the results (MDS, ANOSIM, DIVERSITY, AB
PLOTS)
Discuss the changes in the benthic assemblages caused
by the fishing impact.
RATIONALE:
Lagos and Vilamoura are two sites in the coast of Algarve
(South Portugal). At Vilamoura a continuous bivalve
fishing activity, using dredges, impacts on the bottom. At
Lagos, the intensive dredge fishing led to a depletion of
the bivalve stocks in the area and to a stop in fishing
activities.
18 macrofauna samples were collected with corers at
both sites, by divers, in June 2002. Samples were sieved
by 1mm mesh sieves and specimens were identified to
the lowest possible taxonomic level.
The list and abundance of taxa identified and counted,
transformed to square meter, was compiled in an Excel
data sheet, Fishing-impacts.xls.
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PRIMER SOFTWARE:
The
PRIMER
(Plymouth
Routines
In
Multivariate
Ecological Research) is a package developed at the
Plymouth Marine Laboratory for the study of community
structure and intended for use by ecologists, without
needing a strong background in statistics. The software
was developed by Bob Clarke and Richard Warwick.
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Data analysis with PRIMER software:
1- Import data from EXCEL to PRIMER:
Open (select Excel files); Unselect option “Include
Title”, Ok
(only if species are not in rows Select: Samples as
“Rows”)
2- Verify if the matrix is ready for PRIMER: species
should be in rows, and samples in columns. If not it is
needed to TRANSPOSE the matrix – it can be done
with the Excel or with the PRIMER (DATA,
TRANSPOSE). Matrix should look like the following:
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3- Link samples to factors (eg. Site, level of impact, etc)
Select EDIT; FACTORS. Again, select Factors; Add;
Add factor name (add factors names: site, OK. Repeat
to add another factor name: impact, OK;)
Add factors:
IMPACT: Lagos “--" replicate 1 – 18; “Vilamoura
“++” replicate 1- 18
SITE:, Lagos - replicate 1 – 18; Vilamoura replicate 1- 18
For faster filling of the rows, after opening the Factors
options, fill the first cell and then mark the area (nº of
rows) to be filled (including the first cell with the factor).
Select EDIT and “FILL DOWN”. Use “VALUE” for repeating
one value, or “PATTERN”, for repeating a series of values.
Select OK.
Save file as fishing-impacts.pri
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4- Calculate the similarity matrix – basic step for further
calculations of MDS, CLUSTER and ANOSIM analysis.
Select DATA (main menu); Similarity, “Samples”,
“Bray-Curtis similarity” and choose as Transformation
“LOG(X+1) “ – needed to eliminate the weight of zeros
in the samples
Save file as fishing-impacts .sid .
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5- “Multidimensional scaling” MDS” Analysis
Select “ANALYSE” (main menu); “MDS”, “plot graph”,
select nº restarts (10 default); OK
Rotate the graph just by moving the mouse on the
graph.
Verify the stress value –the better the adjustment the
lower the value – stress should be less than 0.15.
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6- Configure the MDS plot
With the mouse pointer on the graph, use the right
button to select “properties”. Example: select “None”
in “symbols” and “Factor level” in “label”. Select one
“factor name”, eg. site; OK.
Test different options and copy the outputs to a Word
file.
Test with 3D view
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7- Associate the abundance of each taxa to the factor
(site, impact, etc)
Need to have the original Primer file open (fishingimpacts.pri). Then, with the mouse on top of the
graph, use the right button to select “properties”.
Select “Bubble value 2D” in “symbols”, and “Factor
level” in “label”. In the “bubble plot area” select taxa;
then OK. Test different taxa. To add the name of the
taxa to the graph – as title – open properties, select
“MORE” and write the name for the graph.
Save results to the Word file.
8 – CLUSTER Analysis
The similarity matrix needs to be open/selected
(fishing-impacts.sid). Select ANALYSE (main menu)
and then, CLUSTER; OK. Click on the union between
different branches to change the plot. Open the
properties menu (mouse on top of graph) and select “use
factor”. Select “factor name”, eg . site and then OK.
Copy graphs to the Word file.
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8 – Similarity analysis (ANOSIM)
The similarity matrix (fishing-impacts.sid) needs to
be open/selected and selected (click on top with the
mouse). Select ANALYSE (main menu), “ANOSIM”. In the
“output area” select “Histogram”.
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Output to PRIMER results file
Global Test
Sample statistic (Global R): 0,938
Significance level of sample statistic: 0,1%
Number of permutations: 999 (Random sample from
134596)
Number of permuted statistics greater than or equal to
Global R: 0
“Global R” indicates the level of similarity between sites.
The higher the global R value (max=1), more different are
the samples. High global R indicated that the distribution of
the data is not random, and therefore indicates that some
factor is affecting the distribution and making it different
from a complete random distribution – the similarity is low
and the sites are different.
The “significance level %” indicates the confidence level of
the analysis (as much smaller is the % - varying between 0
and 1 - better is the confidence of the analysis).
Copy graphs and results to the Word file.
8- Analysis of the structuring taxa
Open the initial matrix fishing-impacts.pri. Select
ANALYSE (main menu); SIMPER and choose the “factor
name”, eg: site; OK. Copy results to the Word file.
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9 – K-dominance plots
Open the files lagos abund log.pri and lagos
biomass log.pri
Select the abundance file.
With both files open, select in both files the site (eg.
Lagos) by clicking on the top of the respective column in
both files, so that they become highlighted.
With the lagos abund log.pri file selected (active), select
ANALISE (main menu); DOMINANCE PLOT; ABUNDANCE
AND BIOMASS DATA (ABC) – select the “Biomass
worksheet” - lagos biomass log.pri. In the Plot type area
select “Cumulative”; OK
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Copy graphs to the Word file (green – abundance;
blue – biomass). Impact situation if the abundance
dominates the biomass.
Repeat the analysis and graph with the Vilamoura files
vilamoura abund log.pri and vilamoura biomass
log.pri
11- Diversity indices
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Open the file fishing-impact.pri.
Open the aggregation file (for taxonomic distinctness)
– fishing-impacts-agr.agg.
Select (activate) file fishing-impact.pri .
Select ANALYSE, DIVERSE, Other (ex. select indices
Margalef-d, and Pielou-J´), Shannon-Weaver (H), Simpson
(1-lambda) e Taxdiv (delta) (select first option Tax div).
Select “Results to worksheet”.
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Save file as fishing-impact-div.pri.
With this file open, Select EDIT factor, Add factor
(site).
Then, Select Data Average; Averaged factor (select
site); OK. Copy output to an Excel file and save it as
fishing-impacts-divers.xls. Make graphs using the Excel.
Copy graphs and results to the Word file.
QUESTIONS FOR DISCUSSION
1 – Are the two sites similar or different, regarding the
macrofauna assemblages? What type of analysis and
results support your decision?
2 – Can you say anything about the level of impact of the
benthic fishing gears on the macrofauna, in the study
areas?
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3 – If you have to propose an impact indicator based on the
macrofauna assemblages, what would you propose?
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