describing the habitat of atlantic salmon...
TRANSCRIPT
![Page 1: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/1.jpg)
Describing the habitat of Atlantic salmon parr(Salmo salar) using the common spatial dependence between fish abundance andenvironmental variables: validation and application of a new multi-scale method
Guillaume Guénard – [email protected]
Pierre LegendreDaniel Boisclair
Département de sciences biologiquesUniversité de Montréal
![Page 2: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/2.jpg)
Atlantic salmon
• Anadromous migratory• Juveniles (parr) are stream dwelling• Most wild stocks are at risk in North
America
![Page 3: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/3.jpg)
Atlantic salmon
• Anadromous migratory• Juveniles (parr) are stream dwelling• Most wild stocks are at risk in North
America
Deterioration of habitat (spawning and feeding)
![Page 4: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/4.jpg)
2 Objectives
1. Develop a method to integrate spatial information about environmental descriptors to improve habitat models
2. Build models that describe the habitat used by Atlantic salmon parr
![Page 5: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/5.jpg)
Modeling fish abundance using multiple linear regression
Abundance = Descriptors · b
Observations:Sampling in space
Availability of information: GPS location systems, etc.
What about using this information for modelingpurposes?
![Page 6: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/6.jpg)
PCNM variables
1. Truncated matrix of distances among sites2. Correct the matrix (Euclidean)3. Number of PCNM variables = n – 14. Sine-shaped spatial variables5. Orthogonal to one another6. Each PCNM variable has a mean of 0
)1()1(2
−⋅+≈
niLn
iλ
![Page 7: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/7.jpg)
-0.10
-0.05
0.00
0.05
0.10
PC
NM
var
iabl
e va
lue
-0.10
-0.05
0.00
0.05
0.10
-0.10
-0.05
0.00
0.05
0.10
Position (km)
0 1 2 3 4 5 6-0.10
-0.05
0.00
0.05
0.10
Scale
6200 m
775 m
123 m
62 m
![Page 8: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/8.jpg)
Basic idea
If both the fish abundance and a habitat descriptor show high correlation to a given PCNM variable:
1. They are likely to have a common spatial dependence at the scale described by this PCNM variable.
2. This descriptor is suitable for predicting fish abundance at this spatial scale.
![Page 9: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/9.jpg)
Method
• Least-square codependence analysis withrespect to PCNM variables (matrix W)
][]'[][]'[][']['
,, xxxxyyyyxxyy
iiii
iixy −−⋅−−
−−= WWC W�
Cy,x,W is the vector of scale-dependant correlations between the fish abundances (y) and the habitat descriptor (x).
� : Hadmard product
![Page 10: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/10.jpg)
Method
• Calculate a pivotal statistic to test the significance of each coefficient of vector C using permutations
( )( ) ( )�� −−−⋅−−−
−−−−=
ikkiskki
iisi
kkisisxy
xxxxyyyy
xxyypnt sk
2,,
2
,,,
2
]['][]['][
][']['1
ww
www
�
![Page 11: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/11.jpg)
Permutation testing
Two permutation approaches are possible
• Permute y and x together (pairwise) with respect to W.
H0: variables y and x are correlated but their correlation is not spatially dependent.
• Permute y and x independently.H0: variables y and x are neither correlated nor
spatially dependent.
![Page 12: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/12.jpg)
Corrections for multiple testing
1. Non-sequential Šidák correction of p-values
kpp )1(1' −−=
1)1(1' −−−−= stepkpp
2. Sequential Šidák correction of p-values
![Page 13: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/13.jpg)
Stepwise testing procedure1. Compute all Cy,x,W coefficients.2. Sort them in decreasing order of absolute
values.3. Test the first or subsequent coefficient(s)
for significance.4. Use a correction for multiple testing in the
test of subsequent coefficients.
5. Repeat from step 3 as long as coefficients are significant. Stop when a non-significant coefficient is found.
![Page 14: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/14.jpg)
Simulation results
![Page 15: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/15.jpg)
Estimation of type I error rate of the test, using independent permutationsand sequential correction, for 3 commonly-used significance levels (α)
Number of observations along transect
0 20 40 60 80 100 120
Type
I er
ror r
ate
0.001
0.01
0.1
1
α = 0.1α = 0.05α = 0.01
χ2 = 7.8
![Page 16: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/16.jpg)
Results of all simulations using independant pairs of randomvariables
7.8SequentialIndependent
16.9Non-sequentialIndependent
14.4SequentialPairwise
17.7Non-sequentialPairwise
χ²11CorrectionPermutation
![Page 17: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/17.jpg)
Results
Simulating type II error rate, using pairs ofvariables with know common spatial dependence…
…remains to be done!
![Page 18: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/18.jpg)
Predicting Salmon parr relative abundance
���
�
���
�
−⋅−−⋅−−
=]['
][]'[][]'[ˆ
,
,,,,,
kkis
xykkikkiiisks xx
xxxxyyyysk
wC
wy w
�=s
ksk ,ˆˆ yy �=k
kyy ˆˆ
![Page 19: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/19.jpg)
0 1 250 2 500 3 750 5 000625Meters
Application to habitat modeling
Sainte-Marguerite River, Québec
Study area
![Page 20: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/20.jpg)
Sampling
1. Salmon parr counted by snorkling2. Mean water velocity and depth3. Substrate composition: 6 grain size classes4. Size of sampling unit in the river: 20 m
![Page 21: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/21.jpg)
Results
![Page 22: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/22.jpg)
Codependence spectrum between fish abundanceand mean water depth
Scale (m)
100 1000
Cab
unda
nce,
mea
n de
pth
-0.10
-0.05
0.00
0.05
0.10
![Page 23: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/23.jpg)
Codependence spectrum between fish abundanceand m ean water velocity
Scale (m)
100 1000
Cab
unda
nce,
mea
n ve
loci
ty
-0.10
-0.05
0.00
0.05
0.10
![Page 24: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/24.jpg)
Codependence spectrum between fish abundanceand percentage of fine substrates (0.5 - 4 m m )
Scale (m)
100 1000
Cab
unda
nce,
% fi
ne s
ubst
rate
s
-0.10
-0.05
0.00
0.05
0.10
![Page 25: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/25.jpg)
Codependence spectrum between fish abundanceand percentage of gravels (4 - 32 m m )
Scale (m)
100 1000
Cab
unda
nce,
% g
rave
ls
-0.10
-0.05
0.00
0.05
0.10
![Page 26: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/26.jpg)
Codependence spectrum between fish abundanceand percentage of pebbles (32 - 64 m m)
Scale (m)
100 1000
Cab
unda
nce,
% p
ebbl
es
-0.10
-0.05
0.00
0.05
0.10
![Page 27: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/27.jpg)
Codependence spectrum between fish abundanceand percentage of small boulders (0.25 - 1m )
Scale (m)
100 1000
Cab
unda
nce,
% s
mal
l bou
lder
s
-0.10
-0.05
0.00
0.05
0.10
![Page 28: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/28.jpg)
O bserved and raw predicted fish abundance using m eanwater velocity, depth, substra te com position
Position a long river stretch (km )
0 1 2 3 4 5 6
Abu
ndan
ce (f
ish.
20m
-1 s
trech
)
0
2
4
6
8
10
12
14O bserved abundancePredicted abundance
![Page 29: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/29.jpg)
Observed vs. predicted local fish abundance
Observed local abundance (fish.20m-1)
0 2 4 6 8 10 12 14
Pre
dict
ed lo
cal a
bunc
ance
(fis
h.20
m-1
)
0
2
4
6
8
10
12
14 R² using codependence = 26.4%
R² using multiple regression = 9.5%
![Page 30: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/30.jpg)
Conclusions
1. The spatial distribution of an environmental descriptor also containsinformation.
2. This information can be used to improve prediction of Atlantic salmon parr distribution.
3. Further simulations have to be done to determine type II error rate and the statistical power of the method.
![Page 31: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/31.jpg)
The End
![Page 32: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/32.jpg)
Supplementary explanations
� �
� �
= =
= =
−⋅−
−⋅⋅−⋅=
n
i
n
iii
n
i
n
iijiiji
xy
xxyy
xxyy
j
1 1
22
1 1,,
,,
)()(
)()( wwC w
( )( )���
�
���
�−⋅−⋅−= −
= =� � 1
,,,1 1
2,
2, ][')()(ˆ kkisxy
n
i
n
ikkiisks xxxxyy
skwCwy w �
�=ks
ks,
,ˆˆ yy
![Page 33: Describing the habitat of Atlantic salmon parrbiol09.biol.umontreal.ca/ESA_SS/Guenard_et_al_talk.pdf · Observed vs. predicted local fish abundance Observed local abundance (fish.20m-1)](https://reader034.vdocuments.us/reader034/viewer/2022042804/5f5154eee5f918157102be57/html5/thumbnails/33.jpg)
Supplementary explanations
][]'[][]'[
]['][',, xxxxyyyy
xxyy
iiii
ijijwxy j −−⋅−−
−−=
wwC
�
]['
][]'[][]'[]['
,
,,,,,
kkis
xykkikkiiiisks xx
xxxxyyyyyy sk
−⋅−−⋅−−
=−=w
Cwb w
���
�
���
�
−⋅−−⋅−−
==]['
][]'[][]'[ˆ
,
,,,,,,
kkis
wxykkikkiiiskssks xx
xxxxyyyysk
wC
wbwy
�=s
ksk ,ˆˆ yy �=k
kyy ˆˆ