28 
Fishery Bulletin 110(1) 
Table 5 
The predicted and observed presence and absence of each rockfish species based 
Gulf of Alaska bottom trawl survey data. 
on the niche prediction model for the 1996-2009 
Species 
Predicted absent 
Predicted present 
Dusky rockfish 
Observed absent 
2777 
1293 
(Sebastes variabilis) 
Observed present 
193 
212 
Harlequin rockfish 
Observed absent 
2878 
1421 
( Sebastes variegatus ) 
Observed present 
62 
114 
Northern rockfish 
Observed absent 
3126 
802 
( Sebastes polyspinis ) 
Observed present 
338 
209 
Juvenile Pacific ocean perch 
Observed absent 
2078 
1566 
(Sebastes alutus) 
Observed present 
183 
648 
Shortspine thornyhead 
Observed absent 
3071 
135 
( Sebastolobus alascanus) 
Observed present 
492 
777 
Adult Pacific ocean perch 
Observed absent 
2485 
642 
( Sebastes alutus ) 
Observed present 
525 
823 
Rougheye and blackspotted rockfish 
Observed absent 
2709 
895 
(Sebastes aleutianus and S. Melanostictus ) 
Observed present 
209 
662 
Shortraker rockfish 
Observed absent 
4063 
124 
( Sebastes borealis ) 
Observed present 
66 
222 
Sharpchin rockfish 
Observed absent 
4039 
174 
(Sebastes zacentrus) 
Observed present 
158 
104 
The habitat model-based abundance index did not 
track the CPUE estimated from the stratified random 
sampling formulae particularly well in the cases of 
Pacific ocean perch and rougheye and blackspotted rock- 
fish (Fig. 4). The two indices of abundance were well 
correlated for sharpchin rockfish, shortraker rockfish 
and shortspine thornyhead, for which the habitat index 
mirrored the stratified estimate (Fig. 4). In most cases, 
the habitat-based index appeared to be smoother than 
was predicted by the trawl survey biomass estimate. 
The correlations between the habitat indices and the 
biomass estimates from the bottom trawl survey ranged 
from -0.20 to 0.80. The most notable deviation occurred 
for adult Pacific ocean perch for which the model-based 
index was negatively correlated with the biomass es- 
timate (although the relationship was insignificant). 
The precision of estimates was generally higher for the 
model-based indices of CPUE than for the stratified 
random sampling estimates, with the exception of the 
estimates for shortspine thornyhead. The precision of 
the model-based estimates was also consistent across 
the time series, as opposed to the variable estimates 
determined for Pacific ocean perch with the survey 
data, for example. 
Discussion 
The lack of significant spatial patterns in the residuals 
implies that the spatial autocorrelation detected in other 
analyses of trawl survey data (Swartzman et al., 1992) 
could be the result of spatial autocorrelation in habi- 
tat distribution. For example, regions of medium slope 
generally occur on the shelf break in a contiguous area. 
Because medium slope areas are the preferred habitat 
for adult Pacific ocean perch, the autocorrelation in their 
distribution may be a function of the autocorrelation in 
the slope variable. Additionally, the slope variable itself 
was derived from kriging the bathymetry data for the 
Gulf of Alaska. Thus, the autocorrelation of slope values 
may have accounted for any spatial autocorrelation in 
the LCPUE data. 
An interesting result was that the time series of the 
habitat model index tended to be smoother for most 
species than the biomass estimates calculated directly 
from the trawl survey. This result implies that the in- 
terannual variation in the biomass estimate may be at 
least in part related to interannual variability in the 
habitats sampled, rather than to the effects of fishing 
mortality, natural mortality, or recruitment. Because of 
their long-lived nature and low natural mortality, it is 
unlikely that any of the rockfish populations examined 
could truly vary as much as the survey-based biomass 
estimate implies. For example, the Pacific ocean perch 
biomass estimated by the survey ranged from 820,000 
t in 2001 to 457,000 t in 2003 to 766,000 t in 2005, a 
range that seems unlikely given the long life span and 
old age at maturity of this species. The habitat-based 
abundance index predicts a smooth increase in Pacific 
ocean perch abundance over this time period, an in- 
crease that is probably more consistent with the biol- 
ogy of the organism. In the Gulf of Alaska both Pacific 
ocean perch and the rougheye and the blackspotted 
rockfish complex are managed by using age-structured 
models. These models incorporate natural mortality 
estimates, recruitment functions, catch and age data 
