Hawkins et al .: Genetic variation of Sebastes aleutianus and 5 boreahs 



525 



years of age (McDermott, 1994). Rougheye rockfish have 

 been estimated to attain ages in excess of 200 years 

 and shortraker rockfish in excess of 150 years (Munk, 

 2001). These two species are currently managed to- 

 gether as the "shortraker-rougheye" assemblage within 

 waters managed under a North Pacific Fishery Man- 

 agement Council (NPFMC) fishery management plan. 

 Commercial catch levels in NPFMC areas of the Bering 

 Sea, the Aleutian Islands, and the Gulf of Alaska aver- 

 aged 2400 t each year from 1999 to 2001 (Heifetz et al., 

 2002; Spencer and Reuter, 2002). 



The annual catch quota for rockfish and most ground- 

 fish managed by the NPFMC is apportioned among five 

 relatively large geographic areas: the eastern, central, 

 and western Gulf of Alaska, the Aleutian Islands, and 

 the eastern Bering Sea. Previous work in the Gulf of 

 Alaska has indicated geographical segregation of the 

 two rougheye species (Moles et al., 1998; Hawkins et 

 al. 2 ). Based on earlier designations of the International 

 North Pacific Fisheries Commission, area boundaries 

 have little biological basis. If the population structure of 

 a particular species has different geographic boundar- 

 ies than the boundaries of the designated management 

 areas for the species, there is risk of over-harvest. The 

 objective of this study is to examine the population 

 structure of rougheye and shortraker rockfish by using 

 allozyme variation. This is the first population struc- 

 ture study of these two species that encompasses all 

 the North Pacific management areas and most of their 

 biological ranges. 



Methods 



Collection 



Adult rougheye rockfish were collected with bottom 

 trawls from the Gulf of Alaska in 1993, the eastern 

 Bering Sea in 1994, and from the Washington coast in 

 1998. They were also collected by longline from waters 

 north of Unalaska Island in the Aleutian Islands in 

 1996, the central Gulf of Alaska and the northwestern 

 Bering Sea near Russia in 1997, and north of Unalaska 

 Island (Aleutian Islands) and in the eastern and cen- 

 tral Gulf of Alaska in 2001. Shortraker rockfish were 

 collected with bottom trawls from the Gulf of Alaska in 

 1993, the eastern Bering Sea in 1994, and by longline in 

 the northwestern Bering Sea near Russia in 1997. Dates, 

 locations, and sample sizes are reported in Table 1 and 

 Figure 1. 



Approximately 2-3 mL of liver, heart, and muscle 

 were taken from each fish, temporarily stored in either 

 a freezer (-20°C) or in liquid nitrogen, shipped to the 



- Hawkins, S. L., J. Heifetz, J. Pohl, and R. Wilmot. 1997. Un- 

 publ. data. Genetic population structure of rougheye rock- 

 fish (Sebastes aleutianus) inferred from allozyme variation. 

 Alaska Fisheries Science Center, Quarterly Report Feature, 

 July-Aug.-Sept. Auke Bay Laboratory, 11305 Glacier Hwy., 

 Juneau, AK 99801. 



Auke Bay Laboratory, Alaska, and stored at -80°C. Eye 

 tissue was taken from the 1993 Southeast Alaska sam- 

 ples but was not collected during subsequent sampling 

 efforts because initial experimentation yielded limited 

 results from this tissue. Samples of heart tissue were 

 sent to the University of Alaska for DNA analysis. Only 

 liver tissue was taken from the Shumagin and Aleutian 

 Islands rougheye rockfish samples in 2001 (regions 9b, 

 14a, and 16a). The right gill arch and a 4-inch section 

 of the gut were sampled for parasite analysis from the 

 rougheye rockfish 2001 Gulf of Alaska samples. These 

 fish were also photographed, preserved in 10% formalin, 

 and shipped to the Alaska Fisheries Science Center for 

 future morphological studies. 



Laboratory analysis 



Protein enzymes from each sample were separated by 

 horizontal starch-gel electrophoresis as described by 

 Aebersold et al. (1987). Enzymes were screened by stain- 

 ing eye, heart, liver, and muscle tissue on each of six 

 buffer systems (Table 2) by using general staining pro- 

 cedures (Harris and Hopkinson, 1976; Aebersold et al., 

 1987), and Sefrasres-specific procedures (Seeb, 1986). 

 Enzyme screening was designed to detect interspecific 

 allelic mobility differences and to identify intraspecific 

 multilocus enzymes by tissue. Therefore, each tissue 

 type from both rougheye and shortraker rockfish were 

 run together on each gel buffer. Of 47 enzymes screened, 

 23 enzymes representing 29 loci were resolved for all 

 rougheye rockfish except the Russian collection, for 

 which 25 loci were resolved, and the collections from 

 regions 9b, 14a, and 16a, for which only liver samples 

 were taken and 7 loci were resolved (data available 

 from senior author). Twenty-nine loci were resolved for 

 all shortraker rockfish collections except the Russian 

 collection, for which 24 loci were resolved (data avail- 

 able from senior author). The loci used in subsequent 

 analyses and the level of variation are listed in Table 2. 

 Nomenclature for identified loci were assigned according 

 to the American Fisheries Society guidelines for stan- 

 dardization (Shaklee et al., 1990). 



Data analysis 



Fish sampled from stations in close proximity were com- 

 bined to form regional collections (Table 1 and Fig. 1). 

 The software package GENEPOP (vers. 3.4, Montpellier 

 University, Montpellier, France) was used to calculate 

 genotypic frequencies for each region and to test for 

 departure from expected Hardy-Weinberg equilibrium 

 frequencies. Homogeneity of allele frequencies among 

 regional collections was tested with log-likelihood ratio 

 analysis (G-test; Sokal and Rohlf, 1981). F u and F st were 

 calculated with FSTAT (Goudet, 1995). 



Heterogeneity among the collections and within some 

 of the collections of rougheye rockfish was such that the 

 fish were easily divided into two distinct "types" accord- 

 ing to their genotypes at five loci: ACP*, IDDH*, MPI*, 

 PGM-2*, and XO* (Table 3 and data available from 



