21 
Comparison of habitat-based indices 
of abundance with fishery-independent 
biomass estimates from bottom trawl surveys 
Email address for contact author: Chris.Rooper@noaa.gov 
Alaska Fisheries Science Center 
National Marine Fisheries Service 
National Oceanic and Atmospheric Administration 
7600 Sand Point Way NE 
Seattle, Washington 981 1 5 
Abstract — Rockfish species are noto- 
riously difficult to sample with multi- 
species bottom trawl survey methods. 
Typically, biomass estimates have 
high coefficients of variation and 
can fluctuate outside the bounds of 
biological reality from year to year. 
This variation may be due in part 
to their patchy distribution related 
to very specific habitat preferences. 
We successfully modeled the distribu- 
tion of five commercially important 
and abundant rockfish species. A 
two-stage modeling method (model- 
ing both presence-absence and abun- 
dance) and a collection of important 
habitat variables were used to predict 
bottom trawl survey catch per unit of 
effort. The resulting models explained 
between 22% and 66% of the variation 
in rockfish distribution. The models 
were largely driven by depth, local 
slope, bottom temperature, abundance 
of coral and sponge, and measures 
of water column productivity (i.e., 
phytoplankton and zooplankton). A 
year-effect in the models was back- 
transformed and used as an index 
of the time series of abundance. 
The abundance index trajectories of 
three of five species were similar to 
the existing estimates of their bio- 
mass. In the majority of cases the 
habitat-based indices exhibited less 
interannual variability and similar 
precision when compared with strati- 
fied survey-based biomass estimates. 
These indices may provide for stock 
assessment models a more stable 
alternative to current biomass esti- 
mates produced by the multispecies 
bottom trawl survey in the Gulf of 
Alaska. 
Manuscript submitted 17 February 2011. 
Manuscript accepted 30 August 2011. 
Fish. Bull. 110:21-35 (2012). 
The views and opinions expressed 
or implied in this article are those of the 
author (or authors) and do not necessarily 
reflect the position of the National Marine 
Fisheries Service, NOAA. 
Christopher N. Rooper (contact author) 
Michaell H. Martin 
Abundance indices from fishery-inde- 
pendent surveys of marine fish species 
are widely used to determine trends 
in species abundance. Most broad- 
scale surveys are designed to estimate 
abundance for multiple species and 
have been an important data source 
for producing fisheries stock assess- 
ments for commercially exploited 
species. A problem in estimating the 
biomass for an individual species in a 
multispecies survey occurs for species 
not evenly distributed over the survey 
area or when the sample allocation (in 
terms of either locations or number of 
samples) is not ideal for estimating 
the abundance of the species in ques- 
tion. These two problems affect fish 
that have affinities for specific habitat 
types so that the availability of the 
fish to the survey may change with 
habitat type (Cordue, 2007). Addi- 
tionally, this situation is especially 
true for bottom trawl surveys where 
all habitat types may not be sampled 
equally with the survey gear (Zim- 
mermann, 2003). 
One solution may be habitat-based 
surveys of abundance for fish spe- 
cies with strong habitat affinities. 
For these species, habitat-based 
abundance indices have a clear ad- 
vantage over other methods because 
they incorporate prior knowledge of 
fish distributions, such as habitat- 
based surveys for cowcod ( Sebastes 
levis ) and yelloweye rockfish (S. ru- 
berrimus ) (O’Connell and Carlile, 
1993; Yoklavich et al., 2007). These 
surveys produce fishery independent 
estimates of biomass that are based 
on applying the mean density within 
a habitat to the total area that the 
habitat comprises in the ecosystem. 
Rockfish are difficult species to as- 
sess in Alaska and along the U.S. 
west coast owing to their patchy dis- 
tribution and strong habitat affinities 
(Clausen and Heifetz, 2002; Rooper 
et al., 2007). Stratified, random bot- 
tom trawl surveys are commonly 
used for these species, and typically 
catch-per-unit-of-effort data for each 
species are expanded across entire 
strata to estimate a total biomass for 
a species (e.g., Wakabayashi et al., 
1985). Strata are typically defined 
as regions of similar bathymetry or 
geographical features. For example, 
in the Gulf of Alaska, three types of 
strata have generally been defined: 
the continental shelf, continental 
slope, and gullies intruding on the 
continental shelf. 
Trawl surveys generally produce 
highly variable and unstable biomass 
estimates for rockfish species. Part of 
this is due to the multispecies nature 
of the sample allocation and stratifi- 
cation schemes, which lead to inter- 
survey differences in the amount and 
types of habitat sampled from year to 
year. For example, an area commonly 
referred to as the “Snakehead” has 
historically been an important area 
for the commercial rockfish fishery 
in the Gulf of Alaska, producing a 
substantial portion of the rockfish 
catch in some years (Clausen and 
Heifetz, 2002). The number of sta- 
tions randomly selected in the bottom 
trawl survey at the “Snakehead” has 
