Rooper and Martin: Comparison of indices of abundance with biomass estimates from trawl surveys 
23 
bottom trawl survey data. This method was applied to 
eight species of rockfish in Alaska for which the data 
from the current bottom trawl survey produce a range 
of coefficients of variation around the mean annual 
abundance estimate. 
Materials and methods 
The data used for these analyses were collected during 
bottom trawl surveys of the Gulf of Alaska (GOA). The 
National Marine Fisheries Service (NMFS), Alaska 
Fisheries Science Center (AFSC), has conducted stan- 
dard bottom trawl surveys on the continental shelf and 
slope since 1980 (von Szalay et ah, 2010). The Gulf 
of Alaska bottom trawl survey is conducted from the 
Islands of Four Mountains (170°W) to Dixon Entrance 
(133°W) (Fig. 1). Surveys were conducted triennially 
between 1993 and 2000 and biennially thereafter; for 
our analysis, AFSC bottom trawl data from 1996 to 2009 
were used (Table 1). The 1996 bottom trawl survey was 
the first for which accurate temperature at depth data 
were available for calculating water column properties 
used in the modeling. In the GOA bottom trawl survey, 
a poly Nor’Eastern high-opening bottom trawl with 
a 24.2-m roller gear footrope constructed with 36-cm 
rubber bobbins separated by 10-cm rubber disks is used 
(Stauffer, 2004). Trawl hauls were conducted at a speed 
of 5.6 km/h (3 knots) for 15 or 30 minutes. Bottom con- 
tact and net dimensions were recorded throughout each 
trawl haul with net mensuration equipment. For these 
analyses, records were used only if trawl performance 
was satisfactory and if the distance fished, geographic 
position, average depth, and water temperature profile 
were recorded. Trawl hauls were deemed satisfactory 
if the net opening was within a predetermined normal 
range, the roller gear maintained contact with the sea- 
floor, and the net suffered little or no damage during 
the tow. Data from a total of 4475 bottom trawl hauls 
were used (Table 1). 
All fish captured during a survey tow were sorted to 
species, counted, measured for total or fork length, and 
the total weight of each species in the catch was deter- 
mined. For large catches, the total catch was weighed 
and subsampled for count and length data. Catch per 
unit of effort (CPUE, no. of fish/ha) for all fish species 
was calculated by using the area swept computed from 
the net width at the wingtips for each tow multiplied 
by the distance towed recorded with global positioning 
systems. Catch data were transformed by using the 
natural log (CPUE+constant) before analyses, hereafter 
shortened to LCPUE. Three constants were examined: a 
constant of 1, a constant of 10% of the mean CPUE val- 
ue, and a constant of 0.5 times the minimum observed 
CPUE value greater than zero. In the case of shortspine 
thornyhead (Sebastolobus alascanus), the constant of 1 
best fit the assumption of normally distributed errors. 
For the other species, a constant of 0.5 multiplied by 
the minimum observed CPUE value greater than zero 
was used. 
Habitat modeling 
Ecological theory predicts that the abundance of a popu- 
lation should be related to the availability of resources 
in the organism’s habitat (Hutchinson, 1957). These 
relationships between habitat and abundance can be 
easily modeled by using generalized linear models or 
generalized additive models, but these methods may 
not be appropriate for nonlinear responses (generalized 
linear models) or may overfit the data (generalized addi- 
tive models), and therefore they may not be robust for 
prediction when applied outside the data set on which 
they are parameterized (Venables and Ripley, 2002). In 
practice and theory, the relationships between animal 
abundance and habitat have typically been described by 
linear relationships, density-dependent functions, and 
dome-shaped curves (May, 1973; Murawski and Finn, 
1988; Friedlander and Parrish, 1998; lies and Beverton, 
2000). Our approach was to parameterize these rela- 
tionships to provide a biologically meaningful model of 
the animal’s relationship with its habitat and thereby 
give robust predictions (Rooper et al., 2005; Rooper and 
Martin, 2009). 
Habitat models for each of eight species of rockfish 
(Table 2) were determined using the two-stage modeling 
methodology of Rooper and Martin (2009). Pacific ocean 
perch CPUE (S. alutus ) was divided into a juvenile com- 
ponent (<250 mm fork length) and an adult component 
(> 250 mm fork length) because individuals at these two 
life history stages are known to prefer different habitats 
(Carlson and Straty, 1981; Rooper et al., 2007; Rooper, 
2008). Juvenile and adult Pacific ocean perch were then 
modeled separately. Recently, the rougheye rockfish (S. 
aleutianus) has been divided into two species: rougheye 
and blackspotted rockfishes (S. melanostictus; Orr and 
Hawkins, 2008). These two species are difficult to posi- 
tively identify in the field and are still evaluated as a 
single species for stock assessment purposes; therefore, 
they were lumped as one species for this analysis. 
Initially, the presence or absence (R) of each species 
in the trawl survey data was used to determine tows 
that were outside the natural range of the species. Data 
from the 1999, 2003, 2005, 2007, and 2009 bottom trawl 
surveys were used to determine the species range be- 
cause these were the only years in which sampling was 
conducted at depths to at least 700 m and across the 
entire GOA region. Depth (D), temperature (T), and lon- 
gitude (L) were the primary variables used to determine 
the range limits for each rockfish species. Continuous 
depth and temperature measurements were collected 
during each trawl haul with calibrated SeaBird (SBE-19 
or SBE-39) microbathythermographs (Sea-Bird Elec- 
tronics, Inc., Bellevue, WA) attached to the headrope 
of the net. Position data (latitude and longitude) were 
collected every second during each bottom trawl tow. 
The average bottom depth and bottom temperature and 
the longitude from the midpoint of each trawl haul were 
used to predict the presence or absence of the species. 
The Gulf of Alaska bottom trawl survey is conducted 
within the middle of the overall range (both from north 
