NOAA Technical Memorandum NMFS-AFSC-233
 

Genetic Stock Composition

Analysis of Chum Salmon Bycatch

Samples from the 2010 Bering Sea

Groundfish Fisheries 

by

C. M. Kondzela, W. T. McCraney, H. T. Nguyen, and J. R. Guyon 

U.S. DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
 

Alaska Fisheries Science Center
 

February 2012 
NOAA Technical Memorandum NMFS 

The National Marine Fisheries Service's Alaska Fisheries Science Center 

uses the NOAA Technical Memorandum series to issue informal scientific and 

technical publications when complete formal review and editorial processing 

are not appropriate or feasible. Documents within this series reflect sound 

professional work and may be referenced in the formal scientific and technical 

literature. 

The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries 

Science Center continues the NMFS-F/NWC series established in 1970 by the 

Northwest Fisheries Center. The NMFS-NWFSC series is currently used by 

the Northwest Fisheries Science Center. 

This document should be cited as follows: 

Kondzela, C. M., W. T. McCraney, H. T. Nguyen, and J. R. Guyon. 

2012. Genetic stock composition analysis of chum salmon bycatch 

samples from the 2010 Bering Sea groundfish fisheries. U.S. Dep. 

Commer., NOAA Tech. Memo. NMFS-AFSC-233, 29 p. 

Reference in this document to trade names does not imply endorsement by 

the National Marine Fisheries Service, NOAA. 
NOAA Technical Memorandum NMFS-AFSC-233
 

Genetic Stock Composition Analysis of 

Chum Salmon Bycatch Samples from the

2010 Bering Sea Groundfish Fisheries
	

by

C. M. Kondzela, W. T. McCraney, H. T. Nguyen, and J. R. Guyon 

Alaska Fisheries Science Center
 

Auke Bay Laboratories
 

17109 Pt. Lena Loop Road

 Juneau, AK 99801
 

www.afsc.noaa.gov

U.S. DEPARTMENT OF COMMERCE 

John E. Bryson, Secretary 

National Oceanic and Atmospheric Administration

 Jane Lubchenco, Under Secretary and Administrator 

National Marine Fisheries Service 

Eric C. Schwaab, Assistant Administrator for Fisheries 

February 2012 
This document is available to the public through: 

National Technical Information Service 

U.S. Department of Commerce 

5285 Port Royal Road 

Springfield, VA 22161 

www.ntis.gov 
 

iii 

ABSTRACT 

A genetic analysis of samples from the chum salmon (Oncorhynchus keta) bycatch of the 

2010 Bering Sea groundfish trawl fishery was undertaken to determine the overall stock 

composition of the sample set. Samples were genotyped for 11 microsatellite markers and results 

were estimated using the current chum salmon microsatellite baseline. In 2010, genetic samples 

were collected as part of the species composition analysis of the Alaska Fisheries Science 

Center’s North Pacific Observer Program. This sampling change for 2010 was an interim 

measure implemented until the systematic sampling protocols are finalized. Consequently, stock 

composition estimates apply to the sample set and may not represent the entire chum salmon 

bycatch. Based on the analysis of 1,048 chum salmon bycatch samples collected throughout the 

2010 Bering Sea trawl fishery, East Asian (38%), North Asian (26%), Western Alaska (14%), 

and Eastern Gulf of Alaska/Pacific Northwest (13%) stocks dominated the sample set, with 

smaller contributions from Upper/Middle Yukon River (7%) stocks. The estimates for the 2010 

chum salmon bycatch sample set were similar to the 2005–2009 chum salmon bycatch estimates, 

suggesting consistency of the regional stock contributions across years. Analysis of temporal 

groupings within the groundfish “B” season revealed changes in stock composition during the 

course of the season with decreasing contribution of Western Alaska and Eastern Gulf of 

Alaska/Pacific Northwest stocks and increasing contribution of North Asian stocks over time, 

but leaves unanswered whether these changes are due to temporal or spatial differences in the 

sample set. 

 

 

v 

CONTENTS
 

ABSTRACT _________________________________________________________________ iii
 

CONTENTS _________________________________________________________________ v 

INTRODUCTION ____________________________________________________________ 1 

SAMPLE DISTRIBUTION _____________________________________________________ 2 

GENETIC STOCK COMPOSITION______________________________________________ 6 

COMPARISON WITH PREVIOUS ESTIMATES ___________________________________ 8 

TEMPORAL STRATIFICATION OF THE BYCATCH SAMPLES ____________________ 10 

SUMMARY ________________________________________________________________ 13 

Sampling Issues____________________________________________________________ 14 

Stock Composition Estimates _________________________________________________ 14 

Temporal Effect on Stock Composition Estimates _________________________________ 15 

Application of These Estimates________________________________________________ 15 

ACKNOWLEDGMENTS _____________________________________________________ 15 

CITATIONS ________________________________________________________________ 17 

APPENDIX_________________________________________________________________ 21 

INTRODUCTION 

It is important to understand the stock composition of salmon caught in Bering Sea 

fisheries because this area is a known feeding habitat for multiple brood years of chum salmon 

(Oncorhynchus keta) from many different localities in North America and Asia (Myers et al. 

2007; Davis et al. 2009; Urawa et al. 2009). Determining the geographic origin of salmon caught 

in federally managed fisheries is essential to understanding the effects that fishing has on chum 

salmon stocks, especially those with conservation concerns. This report includes genetic stock 

identification results for the chum salmon bycatch samples collected from the 2010 U.S. Bering 

Sea groundfish trawl fishery. National Marine Fisheries Service (NMFS) geographical statistical 

areas associated with the groundfish fishery are shown in Figure 1 and are used later in the report 

to describe the spatial distribution of the chum salmon bycatch and genetic samples. 

Figure 1. -- Statistical areas associated with the Bering Sea-Aleutian Island groundfish fishery. 
 

2 

We present the stock composition estimates for the 2010 chum salmon bycatch samples 

collected from the Bering Sea; however, it is important to recognize the limitations imposed by 

the sampling distribution and the genetic baseline. Hence, this report is divided into six sections: 

Introduction, Sample Distribution, Genetic Stock Composition, Comparison with Previous 

Estimates, Temporal Stratification of the Bycatch Samples, and Summary. For additional 

background and methods, this report is intended to be supplemented with the chum salmon 

reports prepared previously for the 2005–2009 Bering Sea trawl fisheries (Guyon et al. 2010; 

Marvin et al. 2011; Gray et al. 2010; Gray et al. 2011a,b). The chum salmon bycatch, designated 

as non-Chinook in the NMFS database, comprises over 99% of the total non-Chinook bycatch 

(NPFMC 2005). 

SAMPLE DISTRIBUTION 

Genetic samples were collected as part of the species composition analysis of the Alaska 

Fisheries Science Center’s (AFSC) North Pacific Observer Program in 2010 for the AFSC’s 

Auke Bay Laboratories. This sampling change from previous years is an interim measure 

implemented until the systematic sampling protocols recommended by Pella and Geiger (2009) 

are finalized. Chum salmon axillary processes (for genetic analysis) and scales (for ageing) were 

collected throughout the season and stored in coin envelopes that were labeled, frozen, and 

shipped to the Auke Bay Laboratories. The majority of the chum salmon bycatch genetic 

samples were derived from the primarily mid-water walleye pollock (Theragra chalcogramma) 

trawl fishery (91% pollock, 2% Pacific cod (Gadus macrocephalus), 2% other, and 5% 

unknown); however, the actual target was not determined until after the season and annotated as 

the most common catch in a haul or offload. In addition, a vessel can theoretically participate in 
3 

various fisheries on a particular cruise before an offload. For these reasons, results are presented 

as the stock composition of the Bering Sea Aleutian Island groundfish trawl fishery for 2010. 

In 2010, an estimated 14,965 chum salmon were incidentally taken as bycatch in the 

Bering Sea groundfish fisheries (NMFS 2011). This number is ~90% less than the average of 

142,931 non-Chinook salmon taken in the fisheries between 1994 and 2010 and ~78% less than 

the median of 66,994 (Fig. 2). The final genetic sample set for the 2010 chum bycatch was 1,048 

fish from statistical areas 509-543 which represented a sampling rate of 7.03% of the 14,912 

chum salmon caught in those areas. This is the highest chum salmon bycatch sampling rate 

observed from 2005 to 2010, whereas the second highest was 4.15% for the 2008 season. Bycatch 

800,000 

700,000 

600,000 

500,000 

400,000 

300,000 

200,000 

100,000 

0 

Chum Salmon Bycatch 

1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 

Year 

Figure 2. -- Yearly estimates for the non-Chinook salmon bycatch from the Bering Sea 

groundfish trawl fishery (NMFS 2011). 

Biases and errors associated with the collection of genetic samples from the bycatch are 

well documented, and have the potential to affect stock composition estimates (Pella and Geiger 

2009). Methods to collect representative samples are being implemented by the Alaska Fisheries 

Science Center to reduce sampling error and bias. Potential biases associated with the 

successfully genotyped 2010 chum salmon bycatch sample set were evaluated by visually 
 

4 

comparing the genetic sample distributions with the overall bycatch estimates. Temporal bias by 

statistical week ending on Sunday was minimal (Fig. 3) when samples were pooled across 

management areas. However, temporal biases were evident at finer spatial scales (Fig. 4). For 

example, statistical area 521 was overrepresented early in the “B” season (weeks 25-27). For 

samples collected from offloads in which the vessel fished in multiple areas, the sample location 

of the entire catch of a fishing trip was identified by the location of the first haul because 

generally fishing locations were in close proximity to each other. 

2010 Chum Salmon Bycatch (14,912) 

2500
 

2000
 

1500
 

1000
 

500
 

0
 

Genetic samples Bycatch 

0 5 10 15 20 25 30 35 40 45 50 

2010 Chum Bycatch Genetic Samples (1,048) 

200 

160 

120 

80 

40 

0 

0 5 10 15 20 25 30 35 40 45 50 

Statistical week 

Figure 3. -- Number of Bering Sea chum salmon bycatch and genetic samples from 2010 by 

statistical week. Total numbers of chum salmon caught in the Bering Sea groundfish 

trawl fishery (top panel) in areas 509-543 compared with the available 1,048 genetic 

samples (bottom panel). Weeks 3-23 correspond to the groundfish “A” season, 

whereas weeks 24-43 correspond to the “B” season, the demarcation of which is a 

vertical line. 
 

5 

509 513 517 519 521 524 543 541 

2010 Chum Salmon Bycatch 

1600 

1200 

800 

400 

0 

2010 Chum Salmon Genetic Samples 120 

0 5 10 15 20 25 30 35 40 45 50 

Bycatch 

0 5 10 15 20 25 30 35 40 45 50 

Genetic samples 

80 

40 

0 

Statistical week 

Figure 4. -- Number of Bering Sea chum salmon bycatch and genetic samples from 2010 by 

statistical week and NMFS area. Not shown in the chum salmon bycatch are an 

estimated 36 fish from area 514 and 11 fish from area 523. Two fish from area 521 

for statistical weeks 9 and 11, and two fish from area 543 for statistical week 27 are 

not shown for the genetic sample set. Weeks 4-23 correspond to the groundfish “A” 

season, whereas weeks 24-43 correspond to the “B” season, the demarcation of 

which is a vertical line. NMFS statistical areas are designated in the legend. 
6 

GENETIC STOCK COMPOSITION
 

DNA was extracted from the axillary processes of the chum salmon bycatch genetic 

samples and microsatellite genotyping was performed as described previously (Guyon et al. 

2010). Briefly, samples were genotyped for the following 11 microsatellite loci: Oki100 

(Beacham et al. 2009a), Omm1070 (Rexroad et al. 2001), Omy1011 (Spies et al. 2005), One101, 

One102, One104, One114 (Olsen et al. 2000), Ots103 (Nelson and Beacham 1999), Ots3 (Greig 

and Banks 1999), Otsg68 (Williamson et al. 2002), and Ssa419 (Cairney et al. 2000). Thermal 

cycling for the amplification of DNA fragments with the polymerase chain reaction (PCR) was 

performed on a dual 384-well GeneAmp PCR System 9700 (Applied Biosystems, Inc.). Samples 

from the PCR reactions were diluted into 96-well plates for analysis by a 16-capillary, 36 cm 

array on the ABI 3130xl Genetic Analyzer. Genotypes were double-scored with GeneMapper 4.0 

software (Applied Biosystems, Inc.) and exported to Excel spreadsheets (Microsoft, Inc.) for 

further analysis. 

A total of 1,152 samples from the 2010 chum salmon bycatch were analyzed, of which 

1,048 samples were successfully genotyped for 8 or more of the 11 loci and analyzed in 

GENALEX (Peakall and Smouse 2006) for data integrity. Previous simulation analyses have 

demonstrated that a set of 8 selected loci can provide similar levels of stock resolution as the 

entire set of 11 loci (Gray et al. 2010); this is also supported by results reported in the literature 

for other loci sets (Beacham et al. 2009b). The remaining 1,048 samples had genetic information 

for an average of 10.81 loci (out of 11). There were 908 samples with data for all 11 loci, 102 

with 10 loci, 22 with 9 loci, and 16 with 8 loci. There were four individual allele calls observed 

that were not present in the chum salmon baseline; those alleles and the associated haplotype 

were changed to “no calls” for further analysis. 
 

 

7 

For the mixture files, allele designations were converted to match those in the Fisheries 

and Oceans Canada (DFO) chum salmon microsatellite baseline (Beacham et al. 2009b,c). 

Genotypes from converted mixtures were then exported from Excel as text files, and C programs 

were used to format the data into both SPAM and BAYES mixture files. Stock compositions 

were determined by comparing mixture genotypes with those from reference baseline 

populations. As described previously (Gray et al. 2010), baseline populations were grouped into 

the following six regions: East Asia, North Asia, Western Alaska, Upper/Middle Yukon, 

Southwest Alaska, and the Eastern Gulf of Alaska/Pacific Northwest (Prince William Sound to 

Washington State). A listing of the individual populations grouped by region is shown in the 

Appendix. 

As with previous chum bycatch analyses (Guyon et al. 2010; Marvin et al. 2011; Gray et 

al. 2010; Gray et al. 2011a,b), stock composition analysis for the 2010 chum bycatch samples 

was performed with both the SPAM and BAYES software by using previously published 

procedures (ADF&G 2003, Pella and Masuda 2001). Because the SPAM estimates were in close 

agreement with the BAYES estimates, the SPAM estimates are not shown. BAYES software 

uses a Bayesian algorithm to produce stock composition estimates and can account for missing 

alleles in the baseline (Pella and Masuda 2001). BAYES stock composition estimates based on 

data from all 11 loci were derived for the six regional groupings (Table 1). For each analysis, six 

Monte Carlo chains starting at disparate values of stock proportions were configured such that 

95% of the stocks came from one designated region with weights equally distributed among the 

stocks of that region. The remaining 5% was equally distributed among remaining stocks from 

all other regions. For all estimates, a flat prior of 0.002625 (calculated as 1/381) was used for all 

381 populations. The stock composition analyses were completed for a chain length of 10,000 
 

 

 

8 

with the first 5,000 deleted during the burn-in phase. Convergence of the chains to posterior 

distributions of stock proportions was determined with Gelman and Rubin shrink statistics, 

which were all 1.05 or less (Table 1), conveying strong convergence to a single posterior 

distribution (Pella and Masuda 2001). 

Table 1. -- Regional BAYES stock composition estimates for 1,048 chum salmon samples from 

the bycatch of the 2010 season Bering Sea groundfish trawl fishery. BAYES 

estimates utilized information from all 11 loci. BAYES mean estimates are provided 

with standard deviations (SD), 95% credible intervals, median estimate, and the 

associated Gelman and Rubin shrink statistic. 

BAYES Region Mean SD 2.5% Median 97.5% Shrink 

East Asia 0.377 0.016 0.346 0.377 0.409 1.00 

North Asia 0.263 0.018 0.229 0.263 0.299 1.02 

Western Alaska 0.140 0.016 0.109 0.140 0.172 1.05 

Upper/Middle Yukon 0.073 0.010 0.055 0.073 0.094 1.01 

Southwest Alaska 0.018 0.008 0.002 0.018 0.034 1.01 

Eastern GOA/PNW 0.129 0.012 0.105 0.129 0.154 1.00 

COMPARISON WITH PREVIOUS ESTIMATES 

The stock composition results from the analysis of the 2010 chum salmon bycatch 

samples were similar to previous estimates (Fig. 5, upper panel), although differences within 

individual regions were apparent between years. The primary difference in the stock composition 

of the chum salmon bycatch samples appears to be the higher contribution from East Asia in 

more recent years. However, caution must be used in comparisons across years as there are 

differences in where and when genetic bycatch samples were collected from year-to-year. The 

1994-1995 chum bycatch sample estimates were produced with allozyme data (Wilmot et al. 

1998), whereas the 2005 (Guyon et al. 2010), 2006 (Marvin et al. 2011), 2007 (Gray et al. 

2011a), 2008 (Gray et al. 2011b), and 2009 (Gray et al. 2010) chum salmon bycatch sample 
 

9 

Percentage 

45 

40 

35 

30 

25 

20 

15 

10 

5 

0 

1994 

1995 

2005 

2006 

2007 

2008 

2009 

2010 

0 

50 

100 

150 

200 

Numbers of fish x 1000 

1994 (94,548) 

1995 (21,875) 

2005 (709,387) 

2006 (325,181) 

2007 (97,351) 

2008 (16,901) 

2009 (47,497) 

2010 (14,965) 

East Asia North Asia Western AK Upper/Mid Yukon SW Alaska Eastern GOA/PNW 

Figure 5. -- Comparison of yearly stock composition estimates of available genetic samples from 

the Bering Sea chum salmon bycatch. Percentages in top panel; numbers of fish in 

bottom panel. The 1994-1995 estimates were derived with allozyme loci, and the 

2005–2010 estimates were produced with DNA-based loci. 95% BAYES credible 

intervals are shown for the DNA-based analyses. Error bars are based on only the 

genetic BAYES credible intervals and do not include errors associated with the 

overall annual bycatch size estimation or potential biases in sample distribution. 

Total estimated chum salmon bycatch from the Bering Sea groundfish fisheries is 

shown in parenthesis in the bottom figure legend. 
10 

estimates were derived from DNA-based microsatellite loci. The allozyme (77 populations) and 

microsatellite DNA (381 populations) baselines have data from many of the same populations 

and have similar regional groupings. When yearly stock composition estimates are extrapolated 

to the total bycatch from the Bering Sea groundfish fisheries, it is apparent that the effect of the 

bycatch on chum salmon populations is influenced by the overall size of the bycatch (Fig. 5, 

lower panel). 

TEMPORAL STRATIFICATION OF THE BYCATCH SAMPLES 

An understanding of the temporal distribution of the chum salmon bycatch is important. 

For example, if the samples are randomly distributed or represent a distribution that can be 

described mathematically, temporally biased estimates could be adjusted with respect to the 

overall bycatch rate. Likewise, if the bycatch stock distribution changes consistently over time, 

the bycatch could be managed in a manner to minimize effects on critical stocks. 

 As with the 2005–2009 analyses, the 2010 sample set was temporally split into three 

“B” season time periods: early, middle, and late (Table 2, Fig. 6). Stock composition analyses 

for 2010 and similar temporal strata of the 2005–2009 year chum salmon bycatch sample sets are 

included for comparison purposes (Fig. 7). Results from this analysis should be used cautiously 

because sample spatial differences are apparent in the 2010 time-stratified sample set (Fig. 6) as 

compared with the 2005–2009 time stratified sample sets. These differences could affect the 

stock composition estimates. 
11 

Table 2. -- Temporal groupings from the 2010 chum salmon bycatch genetic sample sets for 

which temporal information was available and which samples fell between those 

sample collection dates. 

Weeks Dates Number of 

samples 

24-29 June 12 – July 25 594 

30-34 July 26 – August 29 297 

35-41 August 30 – October 11 128 

2010 Chum Salmon Genetic Samples
 

0 

40 

80 

120 

Genetic samples 

509 513 517 519 521 524 

20 25 30 35 40 45 

Statistical week 

Figure 6. -- Genetic samples from the 2010 chum salmon bycatch identified by early (blue), 

middle (brown), and late(green) temporal groupings. NMFS statistical areas are 

designated in the legend. 
 

 

 

12 

0 

0.2 

0.4 

0.6 

East Asia North Asia 

Stock proportion 

Early Middle Late 

2005 2006 2007 2008 2009 2010 2005 2006 2007 2008 2009 2010 

0.5 

0.4 

0.3 

0.2 

0.1 

0 

Western Alaska Upper/Middle Yukon Eastern GOA/PNW 

Figure 7. -- BAYES stock composition estimates and 95% credible intervals for the early, 

middle, and late periods (defined in Table 2) from the 2005–2010 chum salmon 

bycatch. The 95% credible intervals for the 2005 Eastern GOA/PNW grouping are 

not shown because this region represents a sum of the SE Alaska/N. BC, Skeena, and 

BC/Washington groupings used in the 2005 analysis (Guyon et al. 2010). Not shown 

is the SW Alaska region for which estimates never exceeded 5.6%. 

Stock proportion

2005 2006 2007 2008 2009 2010 2005 2006 2007 2008 2009 2010 2005 2006 2007 2008 2009 2010 
13 

BAYES stock composition estimates were made as described previously for each of the 

three temporal strata for each year. Gelman and Rubin shrink statistics were in all cases below 

1.09 and suggested strong convergence to a single posterior distribution. The stock composition 

estimates differed between time periods (Fig. 7). As reported previously with the 2005–2009 

chum salmon bycatch samples (Guyon et al. 2010; Marvin et al. 2011; Gray et al. 2010; Gray et 

al. 2011a,b), there was a shift in the regional contributions of the 2010 chum salmon sample 

stock composition estimate over time, with East Asian and North American stocks more 

dominant in the early sampling and fish from North Asia more dominant in the later sampling 

period. However, the prevalence of fish from the eastern Gulf of Alaska/Pacific Northwest 

region in the early part of the season (Weeks 24-29) apparent in 2008 and 2009 was not repeated 

in 2010. The contribution of fish from North Asia in the latest period (Weeks 35-41) was double 

that from the early periods and resulted in the highest level observed for this region across the 6-

year time period. The higher contribution from East Asia in the earliest period may be due to an 

increase in sampling in area 521 during the early part of the “B” season. Relatively small sample 

sets can bias the stock composition estimates, but the overall trends were repeatable across years 

and were also observed for chum salmon bycatch samples analyzed from the 1994-1995 years 

(Wilmot et al. 1998). This demonstrates that the stock composition of the chum salmon bycatch 

changes during the course of the season, but leaves unanswered whether these changes are due to 

temporal or spatial differences in the sample sets. 

SUMMARY 

Stock composition estimates of the salmon bycatch in the Bering Sea groundfish fisheries 

are needed for fishery managers to understand the impact of these fisheries on salmon 

populations, particularly those in western Alaska. This report provides a stock composition 
 

14 

analysis of a set of 1,048 individuals sampled from the 2010 chum salmon bycatch. The 

limitations and results of this analysis are summarized below. 

Sampling Issues 

We highlight the inherent spatial and temporal biases in the 2010 sample set (Figs. 3 and 

4), which may limit the application of the genetic sample stock composition estimate to the entire 

2010 chum salmon bycatch. NMFS recently published regulations implementing Amendment 91 

to the fishery management plan for groundfish of the Bering Sea and Aleutian Islands 

Management Area (75 FR 53026, August 30, 2010) which requires that all salmon taken as 

bycatch in the Bering Sea pollock fishery be sorted by species and counted to ensure compliance 

with the salmon bycatch caps for the pollock fishery. This new regulation will provide additional 

opportunity for observers to collect representative samples from the salmon bycatch for genetic 

analysis, and improve the capability to characterize the origin of salmon taken as bycatch in the 

Bering Sea pollock fishery. 

Stock Composition Estimates 

Overall, the genetic samples collected from the 2010 bycatch of Bering Sea chum salmon 

were predominantly from Asian stocks (64%) although substantial contributions were also from 

Western Alaska (14%), Upper/Middle Yukon (7.3%), and Eastern GOA/PNW (12.9%). These 

stock proportions are similar to previous estimates and follow the trend of increasing 

contribution from East Asia; however, there appeared to be a lower contribution from eastern 

Gulf of Alaska/Pacific Northwest. Given the differences in where and when genetic bycatch 

samples were collected from year-to-year, caution must be used in making comparisons across 

years. 
 

 

15 

Temporal Effect on Stock Composition Estimates 

A temporal analysis was completed to determine whether stock compositions differed 

across the fishing season. This was limited to a time-stratified analysis of the bycatch from the 

pollock “B” season, when the majority of chum salmon are intercepted. In 2010, Asian-derived 

chum salmon were predominant across all three sampling times; fish from northern Asia were 

predominant in the late sampling time. As in most other years, the contribution of fish from 

North America decreased throughout the “B” season. For the most part, stock composition 

estimates differed in a consistent manner between years, suggesting temporal stratification of 

chum salmon stocks in the Bering Sea and/or changes in sampling or fishing locations. 

Application of These Estimates 

The extent to which any salmon stock is impacted as the bycatch in the Bering Sea trawl 

fishery is dependent on many factors including 1) the overall size of the bycatch, 2) the age of 

the salmon caught in the bycatch, 3) the age of the returning salmon, and 4) the total escapement 

of the affected stocks taking into account lag time for maturity and returning to the river. As 

such, a higher stock composition estimate one year does not necessarily infer greater impact than 

a smaller estimate in another year. 

ACKNOWLEDGMENTS 

The baseline used for these analyses was obtained through a web portal sponsored by 

Fisheries and Oceans Canada and developed in the Molecular Genetics Laboratory with genetic 

loci identified in a number of laboratories. This document was peer reviewed by AFSC and 

external reviewers for which we are especially grateful. 

17 

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chum salmon bycatch in the Bering Sea pollock fishery. Alaska Dep. Fish Game Spec. 

Publ. No. SP 09-08. 

Pella, J., and M. Masuda. 2001. Bayesian methods for analysis of stock mixtures from genetic 

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19 

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21 

APPENDIX
 

Appendix -- Chum salmon populations in the Fisheries and Oceans Canada (DFO) microsatellite 

baseline with the regional designations used in the analyses of this report. 

DFO number Population name Region number Region 

41 Abashiri 

215 Avakumovka 

40 Chitose 

315 Gakko_River 

292 Hayatsuki 

44 Horonai 

252 Kawabukuro 

313 Koizumi_River 

300 Kushiro 

37 Miomote 

391 Namdae_R 

231 Narva 

298 Nishibetsu 

293 Ohkawa 

297 Orikasa 

214 Ryazanovka 

312 Sakari_River 

311 Shari_River 

36 Shibetsu 

299 Shikiu 

253 Shiriuchi 

310 Shizunai 

217 Suifen 

35 Teshio 

39 Tokachi 

38 Tokoro 

314 Tokushibetsu 

291 Toshibetsu 

296 Tsugaruishi 

316 Uono_River 

309 Yurappu 

218 Amur 

207 Anadyr 

384 Apuka_River 

382 Bolshaya 

380 Dranka 

223 Hairusova 

378 Ivashka 

213 Kalininka 

225 Kamchatka 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

1 

2 

2 

2 

2 

2 

2 

2 

2 

2 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

East Asia 

North Asia 

North Asia 

North Asia 

North Asia 

North Asia 

North Asia 

North Asia 

North Asia 

North Asia 
22 

DFO number Population name Region number Region 

219 Kanchalan 2 North Asia 

379 Karaga 2 North Asia 

294 Kikchik 2 North Asia 

209 Kol_ 2 North Asia 

233 Magadan 2 North Asia 

211 Naiba 2 North Asia 

295 Nerpichi 2 North Asia 

381 Okhota 2 North Asia 

212 Oklan 2 North Asia 

222 Ola_ 2 North Asia 

386 Olutorsky_Bay 2 North Asia 

228 Ossora 2 North Asia 

224 Penzhina 2 North Asia 

385 Plotnikova_R 2 North Asia 

221 Pymta 2 North Asia 

220 Tauy 2 North Asia 

383 Tugur_River 2 North Asia 

226 Tym_ 2 North Asia 

230 Udarnitsa 2 North Asia 

290 Utka_River 2 North Asia 

208 Vorovskaya 2 North Asia 

387 Zhypanova 2 North Asia 

348 Agiapuk 3 Western Alaska 

376 Alagnak 3 Western Alaska 

3 Andreafsky 3 Western Alaska 

357 Aniak 3 Western Alaska 

301 Anvik 3 Western Alaska 

80 Chulinak 3 Western Alaska 

347 Eldorado 3 Western Alaska 

358 George 3 Western Alaska 

307 Gisasa 3 Western Alaska 

371 Goodnews 3 Western Alaska 

288 Henshaw_Creek 3 Western Alaska 

339 Imnachuk 3 Western Alaska 

361 Kanektok 3 Western Alaska 

362 Kasigluk 3 Western Alaska 

328 Kelly_Lake 3 Western Alaska 

340 Kobuk 3 Western Alaska 

343 Koyuk 3 Western Alaska 

363 Kwethluk 3 Western Alaska 

336 Kwiniuk_River 3 Western Alaska 

303 Melozitna 3 Western Alaska 

373 Mulchatna 3 Western Alaska 

372 Naknek 3 Western Alaska 

330 Niukluk 3 Western Alaska 

329 Noatak 3 Western Alaska 

345 Nome 3 Western Alaska 
23 

DFO number 

302 

Population name 

Nulato 

Region number 

3 

Region 

Western Alaska 

374 Nunsatuk 3 Western Alaska 

13 Peel_River 3 Western Alaska 

322 Pikmiktalik 3 Western Alaska 

331 

346 

Pilgrim_River 

Shaktoolik 

3 

3 

Western Alaska 

Western Alaska 

341 Snake 3 Western Alaska 

368 

375 

154 

Stuyahok_River 

Togiak 

Tozitna 

3 

3 

3 

Western Alaska 

Western Alaska 

Western Alaska 

342 Unalakleet 3 Western Alaska 

344 

8 

89 

86 

87 

28 

82 

81 

7 

5 

88 

85 

2 

59 

181 

90 

10 

6 

439 

83 

4 

1 

9 

84 

360 

333 

Ungalik 

Big_Creek 

Big_Salt 

Black_River 

Chandalar 

Chandindu 

Cheena 

Delta 

Donjek 

Fishing_Br 

Jim_River 

Kantishna 

Kluane 

Kluane_Lake 

Koyukuk_late 

Koyukuk_south 

Minto 

Pelly 

Porcupine 

Salcha 

Sheenjek 

Tatchun 

Teslin 

Toklat 

Alagoshak 

American_River 

3 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

4 

5 

5 

Western Alaska 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Upper/Middle Yukon 

Southwest Alaska 

Southwest Alaska 

366 

354 

Big_River 

Coleman_Creek 

5 

5 

Southwest Alaska 

Southwest Alaska 

355 Delta_Creek 5 Southwest Alaska 

359 

332 

365 

Egegik 

Frosty_Creek 

Gertrude_Creek 

5 

5 

5 

Southwest Alaska 

Southwest Alaska 

Southwest Alaska 

370 Joshua_Green 5 Southwest Alaska 

364 Meshik 5 Southwest Alaska 

283 

369 

Moller_Bay 

Pumice_Creek 

5 

5 

Southwest Alaska 

Southwest Alaska 
24 

DFO number Population name Region number Region 

367 Stepovak_Bay 5 Southwest Alaska 

335 Sturgeon 5 Southwest Alaska 

350 Uganik 5 Southwest Alaska 

334 Volcano_Bay 5 Southwest Alaska 

356 Westward_Creek 5 Southwest Alaska 

239 Ahnuhati 6 Eastern GOA/PNW 

69 Ahta______ 6 Eastern GOA/PNW 

155 Ain_ 6 Eastern GOA/PNW 

183 Algard 6 Eastern GOA/PNW 

58 Alouette 6 Eastern GOA/PNW 

325 Alouette_North 6 Eastern GOA/PNW 

270 Andesite_Cr 6 Eastern GOA/PNW 

428 Arnoup_Cr 6 Eastern GOA/PNW 

153 Ashlulm 6 Eastern GOA/PNW 

156 Awun 6 Eastern GOA/PNW 

133 Bag_Harbour 6 Eastern GOA/PNW 

164 Barnard 6 Eastern GOA/PNW 

16 Bella_Bell 6 Eastern GOA/PNW 

79 Bella_Coola 6 Eastern GOA/PNW 

49 Big_Qual 6 Eastern GOA/PNW 

201 Big_Quilcene 6 Eastern GOA/PNW 

281 Bish_Cr 6 Eastern GOA/PNW 

198 Bitter_Creek 6 Eastern GOA/PNW 

103 Blackrock_Creek 6 Eastern GOA/PNW 

390 Blaney_Creek 6 Eastern GOA/PNW 

138 Botany_Creek 6 Eastern GOA/PNW 

264 Buck_Channel 6 Eastern GOA/PNW 

169 Bullock_Chann 6 Eastern GOA/PNW 

61 Campbell_River 6 Eastern GOA/PNW 

323 Carroll 6 Eastern GOA/PNW 

78 Cascade 6 Eastern GOA/PNW 

76 Cayeghle 6 Eastern GOA/PNW 

42 Cheakamus 6 Eastern GOA/PNW 

398 Cheenis_Lake 6 Eastern GOA/PNW 

51 Chehalis 6 Eastern GOA/PNW 

19 Chemainus 6 Eastern GOA/PNW 

47 Chilliwack 6 Eastern GOA/PNW 

392 Chilqua_Creek 6 Eastern GOA/PNW 

117 Chuckwalla 6 Eastern GOA/PNW 

139 Clapp_Basin 6 Eastern GOA/PNW 

107 Clatse_Creek 6 Eastern GOA/PNW 

118 Clyak 6 Eastern GOA/PNW 

62 Cold_Creek 6 Eastern GOA/PNW 

77 Colonial 6 Eastern GOA/PNW 

353 Constantine 6 Eastern GOA/PNW 

168 Cooper_Inlet 6 Eastern GOA/PNW 

197 County_Line 6 Eastern GOA/PNW 
25 

DFO number Population name Region number Region 

12 Cowichan 6 Eastern GOA/PNW 

414 Crag_Cr 6 Eastern GOA/PNW 

161 Dak_ 6 Eastern GOA/PNW 

259 Dana_Creek 6 Eastern GOA/PNW 

123 Date_Creek 6 Eastern GOA/PNW 

250 Dawson_Inlet 6 Eastern GOA/PNW 

91 Dean_River 6 Eastern GOA/PNW 

261 Deena 6 Eastern GOA/PNW 

170 Deer_Pass 6 Eastern GOA/PNW 

46 Demamiel 6 Eastern GOA/PNW 

210 Dipac_Hatchery 6 Eastern GOA/PNW 

319 Disappearance 6 Eastern GOA/PNW 

269 Dog-tag 6 Eastern GOA/PNW 

177 Draney 6 Eastern GOA/PNW 

114 Duthie_Creek 6 Eastern GOA/PNW 

427 East_Arm 6 Eastern GOA/PNW 

266 Ecstall_River 6 Eastern GOA/PNW 

94 Elcho_Creek 6 Eastern GOA/PNW 

193 Ellsworth_Cr 6 Eastern GOA/PNW 

203 Elwha 6 Eastern GOA/PNW 

276 Ensheshese 6 Eastern GOA/PNW 

263 Fairfax_Inlet 6 Eastern GOA/PNW 

32 Fish_Creek 6 Eastern GOA/PNW 

429 Flux_Cr 6 Eastern GOA/PNW 

102 Foch_Creek 6 Eastern GOA/PNW 

179 Frenchman 6 Eastern GOA/PNW 

227 Gambier 6 Eastern GOA/PNW 

96 Gill_Creek 6 Eastern GOA/PNW 

166 Gilttoyee 6 Eastern GOA/PNW 

145 Glendale 6 Eastern GOA/PNW 

135 Gold_Harbour 6 Eastern GOA/PNW 

11 Goldstream 6 Eastern GOA/PNW 

66 Goodspeed_River 6 Eastern GOA/PNW 

136 Government 6 Eastern GOA/PNW 

205 Grant_Creek 6 Eastern GOA/PNW 

100 Green_River 6 Eastern GOA/PNW 

450 GreenRrHatchery 6 Eastern GOA/PNW 

237 Greens 6 Eastern GOA/PNW 

141 Harrison 6 Eastern GOA/PNW 

438 Harrison_late 6 Eastern GOA/PNW 

64 Hathaway_Creek 6 Eastern GOA/PNW 

234 Herman_Creek 6 Eastern GOA/PNW 

17 Heydon_Cre 6 Eastern GOA/PNW 

407 Hicks_Cr 6 Eastern GOA/PNW 

400 Homathko 6 Eastern GOA/PNW 

411 Honna 6 Eastern GOA/PNW 

204 Hoodsport 6 Eastern GOA/PNW 
26 

DFO number Population name Region number Region 

185 Hooknose 6 Eastern GOA/PNW 

406 Hopedale_Cr 6 Eastern GOA/PNW 

412 Hutton_Head 6 Eastern GOA/PNW 

278 Illiance 6 Eastern GOA/PNW 

152 Inch_Creek 6 Eastern GOA/PNW 

146 Indian_River 6 Eastern GOA/PNW 

92 Jenny_Bay 6 Eastern GOA/PNW 

115 Kainet_River 6 Eastern GOA/PNW 

144 Kakweiken 6 Eastern GOA/PNW 

268 Kalum 6 Eastern GOA/PNW 

395 Kanaka_Cr 6 Eastern GOA/PNW 

402 Kano_Inlet_Cr 6 Eastern GOA/PNW 

162 Kateen 6 Eastern GOA/PNW 

389 Kawkawa 6 Eastern GOA/PNW 

95 Kemano 6 Eastern GOA/PNW 

192 Kennedy_Creek 6 Eastern GOA/PNW 

238 Kennell 6 Eastern GOA/PNW 

351 Keta_Creek 6 Eastern GOA/PNW 

101 Khutze_River 6 Eastern GOA/PNW 

126 Khutzeymateen 6 Eastern GOA/PNW 

282 Kiltuish 6 Eastern GOA/PNW 

93 Kimsquit 6 Eastern GOA/PNW 

187 Kimsquit_Bay 6 Eastern GOA/PNW 

419 Kincolith 6 Eastern GOA/PNW 

273 Kispiox 6 Eastern GOA/PNW 

106 Kitasoo 6 Eastern GOA/PNW 

99 Kitimat_River 6 Eastern GOA/PNW 

275 Kitsault_Riv 6 Eastern GOA/PNW 

163 Kitwanga 6 Eastern GOA/PNW 

271 Kleanza_Cr 6 Eastern GOA/PNW 

437 Klewnuggit_Cr 6 Eastern GOA/PNW 

21 Klinaklini 6 Eastern GOA/PNW 

418 Ksedin 6 Eastern GOA/PNW 

125 Kshwan 6 Eastern GOA/PNW 

423 Kumealon 6 Eastern GOA/PNW 

112 Kwakusdis_River 6 Eastern GOA/PNW 

436 Kxngeal_Cr 6 Eastern GOA/PNW 

127 Lachmach 6 Eastern GOA/PNW 

262 Lagins 6 Eastern GOA/PNW 

131 Lagoon_Inlet 6 Eastern GOA/PNW 

448 LagoonCr 6 Eastern GOA/PNW 

167 Lard 6 Eastern GOA/PNW 

160 Little_Goose 6 Eastern GOA/PNW 

50 Little_Qua 6 Eastern GOA/PNW 

413 Lizard_Cr 6 Eastern GOA/PNW 

119 Lockhart-Gordon 6 Eastern GOA/PNW 

176 Lower_Lillooet 6 Eastern GOA/PNW 
27 

DFO number Population name Region number Region 

137 Mace_Creek 6 Eastern GOA/PNW 

242 Mackenzie_Sound 6 Eastern GOA/PNW 

116 MacNair_Creek 6 Eastern GOA/PNW 

55 Mamquam 6 Eastern GOA/PNW 

121 Markle_Inlet_Cr 6 Eastern GOA/PNW 

27 Martin_Riv 6 Eastern GOA/PNW 

338 Mashiter_Creek 6 Eastern GOA/PNW 

109 McLoughin_Creek 6 Eastern GOA/PNW 

178 Milton 6 Eastern GOA/PNW 

194 Minter_Cr 6 Eastern GOA/PNW 

254 Mountain_Cr 6 Eastern GOA/PNW 

111 Mussel_River 6 Eastern GOA/PNW 

157 Naden 6 Eastern GOA/PNW 

337 Nahmint_River 6 Eastern GOA/PNW 

444 Nakut_Su 6 Eastern GOA/PNW 

14 Nanaimo 6 Eastern GOA/PNW 

122 Nangeese 6 Eastern GOA/PNW 

422 Nass_River 6 Eastern GOA/PNW 

399 Necleetsconnay 6 Eastern GOA/PNW 

113 Neekas_Creek 6 Eastern GOA/PNW 

321 Neets_Bay_early 6 Eastern GOA/PNW 

320 Neets_Bay_late 6 Eastern GOA/PNW 

173 Nekite 6 Eastern GOA/PNW 

104 Nias_Creek 6 Eastern GOA/PNW 

143 Nimpkish 6 Eastern GOA/PNW 

53 Nitinat 6 Eastern GOA/PNW 

191 Nooksack 6 Eastern GOA/PNW 

186 Nooseseck 6 Eastern GOA/PNW 

318 NorrishWorth 6 Eastern GOA/PNW 

159 North_Arm 6 Eastern GOA/PNW 

377 Olsen_Creek 6 Eastern GOA/PNW 

184 Orford 6 Eastern GOA/PNW 

287 Pa-aat_River 6 Eastern GOA/PNW 

260 Pacofi 6 Eastern GOA/PNW 

56 Pallant 6 Eastern GOA/PNW 

65 Pegattum_Creek 6 Eastern GOA/PNW 

48 Puntledge 6 Eastern GOA/PNW 

98 Quaal_River 6 Eastern GOA/PNW 

147 Quap 6 Eastern GOA/PNW 

108 Quartcha_Creek 6 Eastern GOA/PNW 

199 Quinault 6 Eastern GOA/PNW 

110 Roscoe_Creek 6 Eastern GOA/PNW 

397 Salmon_Bay 6 Eastern GOA/PNW 

195 Salmon_Cr 6 Eastern GOA/PNW 

134 Salmon_River 6 Eastern GOA/PNW 

200 Satsop 6 Eastern GOA/PNW 

236 Sawmill 6 Eastern GOA/PNW 
28 

DFO number Population name Region number Region 

410 Seal_Inlet_Cr 6 Eastern GOA/PNW 

158 Security 6 Eastern GOA/PNW 

130 Sedgewick 6 Eastern GOA/PNW 

393 Serpentine_R 6 Eastern GOA/PNW 

317 Shovelnose_Cr 6 Eastern GOA/PNW 

249 Shustnini 6 Eastern GOA/PNW 

206 Siberia_Creek 6 Eastern GOA/PNW 

25 Silverdale 6 Eastern GOA/PNW 

196 Skagit 6 Eastern GOA/PNW 

274 Skeena 6 Eastern GOA/PNW 

171 Skowquiltz 6 Eastern GOA/PNW 

447 SkykomishRiv 6 Eastern GOA/PNW 

132 Slatechuck_Cre 6 Eastern GOA/PNW 

43 Sliammon 6 Eastern GOA/PNW 

15 Smith_Cree 6 Eastern GOA/PNW 

54 Snootli 6 Eastern GOA/PNW 

180 Southgate 6 Eastern GOA/PNW 

26 Squakum 6 Eastern GOA/PNW 

142 Squamish 6 Eastern GOA/PNW 

128 Stagoo 6 Eastern GOA/PNW 

265 Stanley 6 Eastern GOA/PNW 

52 Stave 6 Eastern GOA/PNW 

396 Stawamus 6 Eastern GOA/PNW 

409 Steel_Cr 6 Eastern GOA/PNW 

424 Stewart_Cr 6 Eastern GOA/PNW 

416 Stumaun_Cr 6 Eastern GOA/PNW 

327 Sugsaw 6 Eastern GOA/PNW 

324 Surprise 6 Eastern GOA/PNW 

75 Taaltz 6 Eastern GOA/PNW 

30 Taku 6 Eastern GOA/PNW 

18 Takwahoni 6 Eastern GOA/PNW 

251 Tarundl_Creek 6 Eastern GOA/PNW 

149 Theodosia 6 Eastern GOA/PNW 

22 Thorsen 6 Eastern GOA/PNW 

129 Toon 6 Eastern GOA/PNW 

279 Tseax 6 Eastern GOA/PNW 

202 Tulalip 6 Eastern GOA/PNW 

97 Turn_Creek 6 Eastern GOA/PNW 

430 Turtle_Cr 6 Eastern GOA/PNW 

247 Tuskwa 6 Eastern GOA/PNW 

165 Tyler 6 Eastern GOA/PNW 

33 Tzoonie 6 Eastern GOA/PNW 

124 Upper_Kitsumkal 6 Eastern GOA/PNW 

140 Vedder 6 Eastern GOA/PNW 

70 Viner_Sound 6 Eastern GOA/PNW 

45 Wahleach 6 Eastern GOA/PNW 

172 Walkum 6 Eastern GOA/PNW 
29 

DFO number Population name Region number Region 

73 Waump 6 Eastern GOA/PNW 

232 Wells_Bridge 6 Eastern GOA/PNW 

352 Wells_River 6 Eastern GOA/PNW 

105 West_Arm_Creek 6 Eastern GOA/PNW 

267 Whitebottom_Cr 6 Eastern GOA/PNW 

326 Widgeon_Slough 6 Eastern GOA/PNW 

277 Wilauks_Cr 6 Eastern GOA/PNW 

120 Wilson_Creek 6 Eastern GOA/PNW 

401 Worth_Creek 6 Eastern GOA/PNW 

60 Wortley_Creek 6 Eastern GOA/PNW 

248 Yellow_Bluff 6 Eastern GOA/PNW 

434 Zymagotitz 6 Eastern GOA/PNW 

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