SUPPLEMENTARY MATERIAL
Decline in top predator body size and changing climate alter
trophic structure in an oceanic ecosystem
Nancy L. Shackell 1*, Kenneth T. Frank1, Jonathan A. D. Fisher1,2, Brian Petrie1 and
William C. Leggett2
1
Ocean Sciences Division, Bedford Institute of Oceanography, PO Box 1006, Dartmouth,
NS B2Y 4A2, Canada
2
Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
* To whom correspondence should be addressed
E-mail: Nancy.Shackell@dfo-mpo.gc.ca
Data Supplement
Files in this Data Supplement:

(a) Research Vessel Survey Sampling Methodology, (b) CPR survey, (c) Top
Predator Size Methodology, (d) Table S1 provides the common and scientific
name of fish species within functional groups and their associated % contributions
to total biomass from 1970-2008, (e) Table S2 provides summary of final models
exploring the effect of lagging predictors and (f) Effect of size on burst speed
swimming.

Figure S1 shows the study area. Figure S2 shows time series of standardized
anomalies of the response and independent variables. Figure S3 shows the
diagnostic plots of model summarized in Table 1 of main text. Figure S4 shows
the annual cumulative commercial catch at length for NAFO Div. 4X haddock
(black line) versus the cumulative summer RV survey catch at length for selected
years.
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(a) Research Vessel Survey Sampling Methodology
The RV survey uses a stratified random sampling design comprised of forty-eight strata,
defined by geographic location and depth. Samples (tows) are allocated to each stratum in
proportion to area. Each set consists of the deployment of a standard, Western IIA bottom
trawl with a 19 mm cod-end liner, towed at a constant speed of 3.5 knots for
approximately 30 minutes. The swept area of one set is equal to 0.04 km2. The survey is
conducted around the clock, randomly within strata and among years. Our analysis is
restricted to offshore shelf waters of the western Scotian Shelf in NAFO (Northwest
Atlantic Fisheries Organization) Division 4X (figure S1). Thirteen RV survey strata were
pooled within this area for the analyses. This area includes the primary spawning and
nursery area for the majority of the groundfish species evaluated in this study (Shackell &
Frank 2000) and it has been the principal location of mobile gear fishing (and associated
landings) in the region.
(b) CPR survey
The Continuous Plankton Recorder survey has been conducted by ships of opportunity at
a nominal sampling interval of 1 month since 1961 and uses a high-speed plankton net to
sample the surface abundance of phytoplankton and zooplankton
(http://www.sahfos.org). We used data from the geographic area overlapping the western
Scotian Shelf as provided to the Department of Fisheries and Oceans, Canada. The
available data are not continuous, and there is a gap from 1974 to 1990. All data from the
CPR were processed to account for seasonality and expressed as counts per sample. We
omitted years when less than 5 months had been sampled. For those years with a
sufficient minimum number of months (>5), we used the average of the preceding and
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following months, following Head & Sameoto (2007) to impute missing values. In the
event of two adjacent missing months, we used the long-term monthly average. We
calculated an annual index by taking the average of all months within a year. Thus, the
annual signals were comparable across years.
(c) Top Predator Size
To build a community-level indicator of fish size, we used several sources of information
(i) mean mass and mean length were derived from weight-at-length-frequency
distributions, and (ii) growth rate as indexed by length and mass at age 6 were derived
from length-at age distributions. To create a composite index, we calculated average
anomalies, weighted by species biomass, within functional groups for all size indices and
then calculated the annual average anomaly of all size indices as an index of annual top
predator size. The average anomaly of top predator size represents the aggregate,
community-level variability of size and growth.
(i) Mean length and mean mass: Body size data were derived from RV survey annual
abundance at length frequency distributions. Length frequency distributions, and
weight/length relationships were available for most fish species, but not for plankton or
macroinvertebrates. Body size of small benthivores was not estimated. Abundances in
each length class (>18cm) were converted to weight by using species-specific annual
weight/length regression coefficients, estimated from the RV survey data. When annual
species-specific estimates of the weight/length coefficients were missing, the average
value for adjacent years was used. For each functional group, species weights (or
numbers) were pooled into length classes to create functional group weight-at-length or
numbers–at-length frequency distributions. Annual average mean weight was calculated
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as the biomass-weighted average mean weight of all length classes. Annual average mean
length was calculated as biomass-weighted average mean length of all length classes.
(ii) Growth: Gadus morhua (cod), Melanogrammus aeglefinus (haddock), Pollachius
virens (pollock) and Merluccius bilinearis (silver hake) have been consistently aged each
year of the RV survey, enabling growth rate (size-at-age) to be calculated.
References
1. Shackell, N. L. & Frank, K. T. 2000 Larval fish diversity on the Scotian Shelf.
Can. J. Fish. Aquat. Sci. 57, 1747–1760.
2. Head, E. J. H. & Sameoto, D. D. 2007 Inter-decadal variability in zooplankton
and phytoplankton abundance on the Newfoundland and Scotian shelves. DeepSea Res. II 54, 2686-2701.
(d) Table S1.
Common and scientific name of fish species within six functional groups and their %
contributions to functional group biomass and total finfish biomass from 1970-2008.
Values less than 0.009 % depicted as 0.00.
Common name
Scientific name
% of
%of
Group
Total
biomass biomass
Large Benthivore
haddock
Melanogrammus aeglefinus
86.35
20.53
thorny skate
Amblyraja radiata
4.64
1.10
American plaice
Hippoglossoides platessoides
3.68
0.87
4
Atlantic wolffish
Anarhichas lupus
3.37
0.80
winter skate
Leucoraja ocellata
0.95
0.23
barndoor skate
Dipturus laevis
0.80
0.19
ocean pout
Zoarces americanus
0.11
0.03
Northern hagfish
Myxine glutinosa
0.08
0.02
wrymouth
Cryptacanthodes maculatus
0.03
0.01
witch flounder
Glyptocephalus cynoglossus
29.62
0.47
winter flounder
Pseudopleuronectes americanus
25.83
0.41
yellowtail flounder
Limanda ferruginea
25.56
0.40
little skate
Leucoraja erinacea
11.04
0.17
smooth skate
Malacoraja senta
7.96
0.13
spiny dogfish
Squalus acanthias
42.39
15.56
pollock
Pollachius virens
30.73
11.28
cod
Gadus morhua
13.80
5.07
white hake
Urophycis tenuis
5.91
2.17
cusk
Brosme brosme
2.83
1.04
monkfish
Lophius americanus
2.42
0.89
halibut
Hippoglossus hippoglossus
1.39
0.51
sea raven
Hemitripterus americanus
0.51
0.19
turbot
Reinhardtius hippoglossoides
0.02
0.01
Medium Benthivore
Piscivore
Zoopiscivore
redfish
Sebastes sp.
80.66
25.28
silver hake
Merluccius bilinearis
17.15
5.38
Red hake
Urophycis chuss
1.76
0.55
long-fin hake
Phycis chesteri
0.22
0.07
offshore hake
Merluccius albidus
0.21
0.06
Planktivore
5
Atlantic herring
Clupea harengus
64.08
3.87
Atlantic argentine
Argentina silus
30.95
1.87
Atlantic mackerel
Scomber scombrus
4.70
0.28
alewife
Alosa pseudoharengus
0.12
0.01
butterfish
Peprilus triacanthus
0.09
0.01
Northern sand lance
Ammodytes dubius
0.05
0.00
Atlantic saury
Scomberesox saurus
0.00
0.00
Small Benthivore
longhorn sculpin
Myoxocephalus octodecemspinosus
47.07
0.26
blackbelly rosefish
Helicolenus dactylopterus
27.81
0.15
lumpfish
Cyclopterus lumpus
15.41
0.09
American shad
Alosa sapidissima
4.23
0.02
fourspot flounder
Hippoglossina oblonga
3.82
0.02
marlin-spike grenadier
Nezumia bairdii
0.84
0.00
mailed sculpin
Triglops murrayi
0.43
0.00
fourbeard rockling
Enchelyopus cimbrius
0.18
0.00
longnose greeneye
Parasudis truculenta
0.14
0.00
Gulf stream flounder
Citharichthys arctifrons
0.07
0.00
alligatorfish
Aspidophoroides monopterygius
0.00
0.00
arctic hookear sculpin
Artediellus uncinatus
0.00
0.00
Atlantic spiny lumpsucker
Eumicrotremus spinosus
0.00
0.00
snake blenny
Lumpenus lampretaeformis
0.00
0.00
shortnose greeneye
Chlorophthalmus agassizi
0.00
0.00
radiated shanny
Ulvaria subbifurcata
0.00
0.00
Atlantic soft pout
Melanostigma atlanticum
0.00
0.00
Atlantic hookear sculpin
Artediellus atlanticus
0.00
0.00
(e) Table S2.
Results of final lagged models of changes in aggregate prey biomass as a function of
lagged predator biomass, predator size, SST and stratification linear regressions. Final
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models were selected by examining the marginal sums-of -squares (SS) and the use of
Akaike’s Information Criterion (AIC ) in stepwise regressions as a guide to which
variables could be dropped from the model. Predator biomass and SST were dropped
from each model. Predictors, slopes, slope standard errors (SE), probability of slope not
=0 (Prob), and adjusted R2 values are indicated. The Marginal Sums of Squares (SS)
reflect the SS accounted for by each independent variable after all other terms have been
accounted for. The variance inflation factor (VIF) reflects how the magnitude of variance
is inflated due to correlated independent variables; The Corr of errors refers to the
temporal correlation of residuals from the model at lag 1, and the Durbin Watson statistic
(D-W) represents a test of whether that autocorrelation significantly different from 0. The
boot-stapped probability-value is in parentheses.
Lag
Predictor
0
1
2
3
4
Intercept
TopPredSize
Stratification
Residual SE/SS
DF
Intercept
TopPredSize
Stratification
Residual SE/SS
on df
Intercept
TopPredSize
Stratification
Residual SE/SS
DF
Intercept
TopPredSize
Stratification
Residual SE/SS
DF
Intercept
TopPredSize
Stratification
Slope
-0.16
-0.84
0.39
0.59
Marginal
SS
SE
0.10
0.14
0.10
12.90
5.26
12.02
Pr
1.03E-01
5.25E-07
3.99E-04
Adj.R2
VIF
Corr of
Errors
Lag1
D-W
(Pr)
0.65
1.08
0.27
1.40 (0.04)
0.12
1.73(0.31)
0.35
1.12(0.002)
0.36
1.18(0.002)
35
-0.12
-0.81
0.37
0.66
0.11
0.16
0.11
10.99
4.66
14.73
2.86E-01
1.54E-05
2.41E-03
0.57
1.09
34
-0.11
-0.84
0.46
0.64
0.11
0.18
0.14
9.05
4.28
13.64
3.01E-01
4.72E-05
2.89E-03
0.60
1.21
33
-0.05
-0.77
0.51
0.64
0.11
0.19
0.17
6.55
3.69
13.01
6.74E-01
3.37E-04
5.05E-03
0.58
1.34
32
0.00
-0.73
0.54
0.12
0.22
0.21
4.87
2.73
9.77E-01
2.20E-03
1.80E-02
0.54
1.51
7
Residual SE/SS
on df
0.66
31
13.55
0.37
1.19(0.002)
(f) Effect of size on burst speed swimming
To examine the effect of size reduction on predator abilities, we used information
compiled on FishBase (http://www.fishbase.org/manual/english/fishbase
the_swimming_and_speed_tables.htm). From their Fig. 53, we estimated the relationship
between burst swimming speed (swimming that could be maintained for a few seconds
only but important for capturing prey) and body length. Using the size range applicable to
our data set (18cm-112cm), the linear equation was Log (Burst Speed cm/s) = 1.68*Log
(Length (cm)) +0.84; R2=0.53.
Supplementary Figure Legend
Figure S1. Scotian Shelf, Northwest Atlantic. Shaded area outlines the western Scotian
Shelf study area.
Figure S2. Time series of standardized anomalies of Prey biomass (Prey_BM), Predator
size (Pred_Size), Stratification, Sea surface temperature (SST) and Predator biomass
(Pred_BM). Lines are 3-yr running means. Plots are presented in 2 panels for clarity.
Legends are inset.
Figure S3. Diagnostic plots of model described in Table 1 (main text).
Figure S4. Annual cumulative commercial catch at length for NAFO Div. 4X haddock
(line on left) versus the cumulative summer RV survey catch at length (line on right) for
selected years. The difference between the curves illustrates the difference between what
is caught by the fishing industry and by the RV survey. Before 1990, the fishery caught
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fish that were up to 8 cm larger than what was available, this value rose to 25 cm in 1995.
Note how the shape of the curve of the RV survey changes over time, reflecting a
proportional loss of larger fish.
Fig S1
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Fig S2
10
Fig S3
11
Fig S4
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