NOAA Technical Memorandum NMFS-AFSC-366

J. A. Whittle, C. M. Kondzela, Hv. T. Nguyen, K. Hauch, D. Cuadra, 

and J. R. Guyon

Genetic Stock Composition Analysis 

of Chum Salmon from the Prohibited 

Species Catch of the 2016 Bering Sea 

Walleye Pollock Trawl Fishery and 

Gulf of Alaska Groundfish Fisheries 

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Alaska Fisheries Science Center

January 2018

doi:10.7289/V5/TM-AFSC-366
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:

Whittle, J. A., C. M. Kondzela, Hv. T. Nguyen, K. Hauch, D. Cuadra, 

and J. R. Guyon. 2018. Genetic stock composition analysis of chum 

salmon from the prohibited species catch of the 2016 Bering Sea 

walleye pollock trawl fishery and Gulf of Alaska groundfish fisheries. 

U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-366, 56 p.

Document available: http://www.afsc.noaa.gov/Publications/AFSC-TM/NOAA-TM-AFSC-366.pdf

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

the National Marine Fisheries Service, NOAA.
January 2018

NOAA Technical Memorandum NMFS-AFSC-366

by

J. A. Whittle, C. M. Kondzela, Hv. T. Nguyen, 

K. Hauch, D. Cuadra, and J. R. Guyon

Auke Bay Laboratories

Alaska Fisheries Science Center 

National Marine Fisheries Service

National Oceanic and Atmospheric Administration

17109 Pt. Lena Loop Road

Juneau, AK 99801

www.afsc.noaa.gov

U.S. DEPARTMENT OF COMMERCE

Wilbur L. Ross Jr., Secretary

National Oceanic and Atmospheric Administration

 RDML Timothy Gallaudet (ret.), Acting Under Secretary and Administrator

National Marine Fisheries Service

 Chris Oliver, Assistant Administrator for Fisheries 

doi:10.7289/V5/TM-AFSC-366

Genetic Stock Composition Analysis 

of Chum Salmon from the Prohibited 

Species Catch of the 2016 Bering Sea 

Walleye Pollock Trawl Fishery and 

Gulf of Alaska Groundfish Fisheries
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 the prohibited species catch (PSC) of chum salmon (Oncorhynchus 

keta) collected during 2016 from the federally managed walleye pollock (Gadus 

chalcogrammus) trawl fishery in the Bering Sea and from the federal groundfish fisheries in the 

Gulf of Alaska (GOA) was undertaken to determine the overall stock composition of the sample 

sets. Samples were genotyped for 11 microsatellite markers from which stock contributions were 

estimated using the current chum salmon microsatellite baseline. In 2016, one genetic sample was 

collected for every 30.6 chum salmon caught in the Bering Sea midwater trawl fishery. The 

evaluation of sampling in the Bering Sea based on time, location, and vessel indicated that the 

genetic samples were representative of the total chum salmon PSC in the Bering Sea. The 

majority of the 114 chum salmon samples from the A-season were from Northeast Asia (37%) 

and Eastern GOA/Pacific Northwest (PNW) (37%) stocks. Based on the analysis of 2,701 chum 

salmon collected throughout the B-season, the largest stock groups in the catch were Eastern 

GOA/PNW (35%) and Northeast Asia (31%), followed by Western Alaska (19%), Southeast Asia 

(9%), Upper/Middle Yukon (5%), and Southwest Alaska (< 2%) stocks. The chum salmon caught 

in the Bering Sea in 2016 shared general patterns of stock distribution with those from past years, 

but differed by some finer-scale spatiotemporal strata. Of the 473 chum salmon samples from the 

GOA groundfish fisheries, the highest proportion was from Eastern GOA/PNW (93%) stocks, 

similar to previous years. 

 

 

v 

CONTENTS 

ABSTRACT ................................................................................................................................. iii 

INTRODUCTION.......................................................................................................................... 1 

SAMPLE DISTRIBUTION ........................................................................................................... 3 

Bering Sea ............................................................................................................................... 3 

Gulf of Alaska ......................................................................................................................... 8 

LABORATORY ANALYSES ..................................................................................................... 10 

GENETIC STOCK COMPOSITION........................................................................................... 13 

COMPARISON WITH PREVIOUS ESTIMATES ..................................................................... 17 

Bering Sea ............................................................................................................................. 17 

Gulf of Alaska ....................................................................................................................... 20 

TEMPORAL STRATIFICATION............................................................................................... 20 

SPATIAL STRATIFICATION .................................................................................................... 23 

SUMMARY ................................................................................................................................. 29 

Sampling Issues..................................................................................................................... 30

 Bering Sea ...................................................................................................................... 30 

Gulf of Alaska ................................................................................................................ 30 

Stock Composition Estimates ................................................................................................ 31

 Bering Sea ...................................................................................................................... 31 

Gulf of Alaska ................................................................................................................ 32 

Temporal and Spatial Effects ................................................................................................ 32 

Application of Estimates ....................................................................................................... 33 

ACKNOWLEDGMENTS ............................................................................................................ 35 

CITATIONS................................................................................................................................. 37 

APPENDICES.............................................................................................................................. 43 

 

 

INTRODUCTION 

Pacific salmon (Oncorhynchus spp.) are prohibited species in the federally managed 

Bering Sea and Gulf of Alaska (GOA) groundfish fisheries, which are subject to complex 

management rules (NPMFC 2017a,b) that are in part designed to reduce prohibited species catch 

(PSC). It is important to understand the stock composition of Pacific salmon caught in these 

fisheries, which take place in areas that are known feeding habitat for multiple brood years of 

chum salmon (O. 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 (NPFMC 2012). 

In this report, we present the genetic stock composition estimates for the samples of 

chum salmon PSC collected during 2016 from the U.S. Bering Sea walleye pollock (Gadus 

chalcogrammus) trawl fishery and the GOA groundfish fisheries. In the Bering Sea, the pollock 

fishery accounted for more than 98.8% of the total chum salmon taken in the groundfish fisheries 

(NMFS 2017). In the GOA, the majority (56%) of the chum salmon were caught in the pollock 

trawl fishery, with the remainder caught in other groundfish fisheries (NMFS 2016). 

The National Marine Fisheries Service (NMFS) reporting areas associated with the 

groundfish fisheries are shown in Figure 1 and are presented later to describe the spatial 

distribution of the chum salmon catch and genetic samples. The data reporting tool, Alaska 

Fisheries Information Network (AKFIN1), developed by the Pacific States Marine Fisheries 

Commission (PSMFC) simplifies access to fishery information associated with the genetic 

samples of salmon PSC and is useful for organizing sample datasets at the finer resolution of 

1 AKFIN website 
2 

ADF&G groundfish statistical areas (Fig. 1). The AKFIN reports were used to construct spatialtemporal sets of genetic samples along the outer continental shelf from the 2016 chum salmon 

PSC. 

Figure 1. -- NMFS reporting areas associated with the Bering Sea-Aleutian Island and Gulf of 

Alaska groundfish fisheries are numbered and outlined in black. The ADF&G 

groundfish statistical areas are outlined in light gray. 

For additional background and methods, this report is intended to be supplemented with 

the chum salmon reports prepared previously for the 2005-2015 Bering Sea trawl fisheries 

(Guyon et al. 2010; Marvin et al. 2011; Gray et al. 2010, 2011a,b; Kondzela et al. 2012, 2013, 

2016, 2017; Vulstek et al. 2014; Whittle et al. 2015). The chum salmon PSC is designated as non-
 

 

 

 

 

3 

Chinook (O. tshawytscha) in the NMFS database and comprises over 95% of the non-Chinook 

category in the Bering Sea (NPFMC 2007). 

SAMPLE DISTRIBUTION 

Bering Sea 

Genetic samples were collected from the chum salmon caught in the Bering Sea pollock 

fishery by the Alaska Fisheries Science Center’s (AFSC) North Pacific Groundfish and Halibut 

Observer Program (Observer Program) in 2016 for analysis at the AFSC’s Auke Bay 

Laboratories (ABL). Sampling was changed in 2011 from previous years (Faunce 2015, Cahalan 

et al. 2014) to implement a systematic sampling protocol recommended by Pella and Geiger 

(2009). With a goal to sample every 30th chum salmon, axillary processes (for genetic analysis) 

and scales (for ageing) were collected throughout the season. 

In 2016, an estimated 343,001 non-Chinook salmon (referred to hereafter as “chum 

salmon” because 99.9% of the non-Chinook salmon were chum salmon) were caught in the 

pollock-directed trawl fisheries and represent the third largest catch of chum salmon in the 

pollock fisheries since 1994 (NMFS 2017). This catch is substantially larger than the 1994-2015 

average of 144,113 chum salmon and more than four times the median of 79,009 (Fig. 2). As in 

previous years, nearly all of the chum salmon were caught during the pollock B-season (10 June 

to November 1) (Fig. 3) in NMFS reporting areas 509-524 (Fig. 1). During the A-season, 

approximately 3,726 chum salmon, 1% of the total Bering Sea chum salmon PSC, were caught. 

Of the chum salmon caught in the 2016 pollock trawl fishery, genetic samples were collected 

from 11,219 fish (NMFS 2016), which represents a sampling rate of 1 of every 30.6 chum 

salmon (or 3.3% of the chum salmon catch). This sampling rate is nearly identical to that in 

2011-2015, the first 5 years of representative sampling. 
 

 

 

4

800 

600 

400 

200 

0 

Year 

 Figure 2. -- Yearly estimates for the non-Chinook salmon prohibited species catch (PSC) from the 

Bering Sea pollock-directed trawl fisheries (NMFS 2017). The solid horizontal line 

represents mean PSC and the dashed line represents median PSC, 1994-2015. 

Biases and errors associated with past collections of genetic samples from the salmon 

PSC have the potential to affect stock composition estimates (NMFS 2009, Pella and Geiger 

2009). The systematic sampling protocols recommended by Pella and Geiger (2009) were 

implemented in the Bering Sea pollock fisheries in 2011 to reduce sampling error and bias, the 

efficacy of which was evaluated by comparing the genetic sample distributions and the overall 

PSC estimates with Chi-square tests. Low sample sizes in some time/area combinations were 

pooled prior to testing: Early, Middle, and Late time periods (weeks 24-29, 30-34, and 35-43) and 

two areas (NMFS reporting areas aggregated: 509, 513, and 516; and 521, 523, and 524). 

Temporal bias by statistical week ending on Sunday was minimal (Fig. 3) when samples were 

pooled across management areas (χ2

 = 8.49, 24 d.f., P > 0.99). During the B-season, temporal 

biases were also minimal at finer spatial scales (Fig. 4; χ2 = 7.86, 6 d.f., P = 0.25). The NMFS and 

ADF&G reporting area is known for samples collected at the haul-level from at-sea processors 

(hauls), but due to the uncertainty of catch location for samples collected at the trip-level from Number of fish × 1,000 

Bering Sea 

chum salmon PSC 

1994 1996 1998 2000 2002 2004 2006 2008 2010 2012 2014 2016 
 

 

 

5 

shore-side processors (offloads) in which deliveries may contain mixed hauls from multiple 

reporting areas, the reporting area of the chum salmon catch from offloads was identified as the 

area where most of the pollock were caught during a fishing trip. 

0 

400 

800 

1,200 

1,600 

2,000 

0 

10 

20 

30 

40 

50 

60 

Genetic samples 

Chum catch × 1,000 

Chum catch (342,820) 

Genetic samples (11,219) 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct 

0 5 10 15 20 25 30 35 40 45 

Statistical week 

Figure 3. -- Number of Bering Sea chum salmon caught (solid line) and genetic samples collected 

(dashed line) from the 2016 Bering Sea pollock trawl fishery by statistical week. 

Weeks 1-23 correspond to the A-season, whereas weeks 24-43 correspond to the Bseason, the demarcation of which is a vertical line. 
 

 

6 

70,000 

60,000 

50,000 

40,000 

30,000 

20,000 

10,000 

0 

24-25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40-43 

Chum salmon PSC 

509/513/516 517 519 521/523/524 

June July August September 

Number of fish Number of fish 

Statistical week 

2,000 

1,600 

1,200 

800 

400 

0 

Statistical week 

Figure 4. -- Number of Bering Sea chum salmon caught (top) and genetic samples collected 

(bottom) from the 2016 Bering Sea pollock B-season by statistical week and NMFS 

reporting area (designated in the legend). 

The systematic collecting protocol was also evaluated by comparing the total number of 

chum salmon caught on each vessel to the number of genetic samples collected from each vessel. 

Chum salmon 

genetic samples 

June July August September 

24-25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40-43 
 

 

 

 

7 

The chum salmon catch was subsampled for genetic samples across a large range of chum 

salmon catch per vessel (Fig. 5). The sampling ratio of numbers of chum salmon caught to 

numbers of genetic samples per vessel was 30.4 ± 2.6 fish (mean ± S.D.; unweighted by 

proportion of bycatch each vessel caught), which is close to the protocol sampling goal of one 

genetic sample collected from every 30th chum salmon caught. All 102 vessels that participated 

in the midwater trawl fishery during the A- and B-seasons caught chum salmon. In 2016, about 

43% of the chum salmon PSC was counted from at-sea hauls and 57% from shoreside offloads. 

By vessel, the 1:30 ratio of genetic sampling did not differ between hauls and offloads (t-test; 

P = 0.33). 

1,000 

800 

600 

400 

200 

0 

Number of chum salmon PSC per vessel 

Figure 5. -- Bering Sea chum salmon catch and genetic samples from the 2016 Bering Sea pollock 

A- and B-seasons. Number of genetic samples collected from the total number of 

chum salmon caught from each of 102 vessels; black diagonal line represents the 

expected sampling rate. 

Number of genetic samples 

Correlation coefficient, r > 0.99 

0 5,000 10,000 15,000 20,000 25,000 30,000 
 

 

 

 

 

8 

Gulf of Alaska 

The estimated PSC of chum salmon in the GOA (NMFS 2016) is 1-2 orders of magnitude 

lower than in the Bering Sea and has been a lower management priority than the typically larger 

catches of Chinook salmon (e.g., Guthrie et al. 2017). In 2016, chum salmon samples were 

collected in the GOA (AFSC 2015) primarily from the pollock trawl fishery, which caught about 

56% of the chum salmon PSC in the GOA (Fig. 6). The majority of chum salmon from the nonpollock fisheries were caught between the B and C pollock seasons (May 31-August 24; Fig. 7) in 

the arrowtooth flounder, sablefish, rockfish, and halibut fisheries. This is the third year in a row 

that the number of chum salmon genetic samples collected from the GOA groundfish fisheries 

was large enough to run a mixed-stock analysis. Approximately 26% of the chum salmon caught 

in the pollock fisheries were collected for genetic samples, whereas less than 1% of chum salmon 

caught in other GOA groundfish fisheries were sampled. The available sample set included 507 

samples from the pollock fishery from NMFS reporting areas 610, 620, and 630 during primarily 

the pollock C- and D-seasons2

, and 2 samples from other fisheries (Figs. 1, 7, 8). 

2

 Pollock caught in Gulf of Alaska Western and Central Regulatory Areas (NMFS reporting areas 610-630): Aseason (Jan. 20 to Mar. 10), B-season (Mar. 10 to May 31), C-season (Aug. 25 to Oct. 1), D-season (Oct. 1 to Nov. 

1), published in the Federal Register. 
 

 

 

9 

Number of chum salmon 

2,000 

1,600 

1,200 

800 

400 

0 

2016 GOA groundfish fisheries 

Hook-and-line Non-pelagic trawl Pelagic trawl 

Bottom pollock 

Midwater pollock 

Arrowtooth flounder 

Halibut 

Rockfish 

Sablefish 

Figure 6. -- Estimated number of chum salmon caught (N = 3,518) in the 2016 Gulf of Alaska 

groundfish fisheries by target species. The 17 chum salmon caught in the Pacific cod, 

shallow-water flatfish, and flathead sole fisheries are not shown. 

0 

100 

200 

300 

400 

500 

Number of chum salmon 

A B C D 

Jan Feb Mar Apr May Jun Jul Aug Sep Oct 

0 5 10 15 20 25 30 35 40 45 

Statistical week 

Figure 7. -- Number of chum salmon caught (blue plus black) and genetic samples collected 

(black) from the 2016 Gulf of Alaska groundfish fisheries by statistical week. Grayed 

areas with letter designations approximate the NMFS management seasons for 

pollock in the Western and Central Regulatory Areas (NMFS reporting areas 610-

630). 
 

 

10 

Number of genetic samples 

300 

250 

200 

150 

100 

50 

0 

NMFS areas 

610 

620 

630 

Prior to C C (Aug 25-Sep 30) D (Oct 1-31) 

Gulf of Alaska pollock season 

Figure 8. -- Number of chum salmon genetic samples collected from the 2016 Gulf of Alaska 

groundfish fisheries by pollock season and NMFS reporting areas. 

LABORATORY ANALYSES 

Chum salmon samples from the Bering Sea pollock B-season were subsampled in order to 

minimize laboratory costs while limiting potential bias of mixed-stock estimates. The total sample 

set of 11,043 chum salmon was sorted by cruise, haul or offload, and specimen number, and every 

4th sample was selected for analysis (see Whittle et al. 2015 for subsampling effects). DNA was 

extracted from the axillary processes of 2,762 chum salmon sampled in the B-season, all of the 

121 chum salmon sampled in the A-season, and all of the 509 chum salmon sampled in the GOA 

groundfish fisheries. An additional 573 samples were selected for the 4-cluster spatial analysis to 

increase the sample sizes to approximately 200 samples in each time-area category. 

DNA extraction and microsatellite genotyping was performed as described previously 

(Guyon et al. 2010). 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, 
 

11 

One102, One104, One114 (Olsen et al. 2000), Ots103 (Beacham et al. 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 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 48-capillary, 36 cm 

array on the ABI 3730xl Genetic Analyzer (Applied Biosystems, Inc.). Genotypes were doublescored with GeneMapper 5.0 software (Applied Biosystems, Inc.). 

Of the 3,947 chum salmon bycatch samples from the Bering Sea and GOA, 97% were 

successfully genotyped for 8 or more of the 11 loci for an average of 10.9 loci (Table 1). Four 

duplicate genotypes were detected in the Bering Sea bycatch samples with GenAlEx 6.5 (Peakall 

and Smouse 2006, 2012); one sample of each duplicate pair was removed from further analysis. 

Twenty-four GOA samples were determined to be non-chum and were removed from further 

analysis. The weekly distribution of genetic samples collected in the field during the B-season 

and those further subsampled and analyzed did not differ from the total number of chum salmon 

caught based on the NMFS observer sampling protocol (Table 2; AFSC 2015). 

Table 1. -- Number of genetic samples analyzed for chum salmon from the 2016 Bering Sea 

pollock trawl fishery and Gulf of Alaska groundfish fisheries. 

Number loci Genetic samples

 11 3,619 

10 136 

9 31 

8 31 

<8 130 
 

 

 

 

 

12 

Table 2. -- Observed number of samples (N) from the B-season and Chi-square tests for 

goodness of fit used to compare 1) the weekly distribution of genetic samples 

collected with the expected number of samples (total chum salmon caught per 

week/30), and 2) the samples genotyped and analyzed with 1⁄4 of the samples 

expected. Weeks 41-43 were pooled to provide sample sizes > 4 in all time 

categories. 

 Sample set N X2 d.f. P-value 

 Collected vs. expected 11,094 7.60 17 0.97 

 Genotyped vs. 1⁄4 expected 2,762 3.05 17 > 0.99 

 Analyzed vs. 1⁄4 expected 2,701 8.06 17 0.97 

Quality control of sample handling and genotyping was examined by reanalyzing 8.4% of 

the samples: DNA was plated from the eight samples in the left-most column of each elution plate 

for a total of 344 samples that were then processed for genotyping as described above. Genotypes 

from the quality control dataset were then compared to the genotypes of the original dataset 

(Table 3). The genotyping error was low; across 11 loci there were a total of 114 differences in 

7,074 alleles between the original and quality control datasets, which represented an overall 

discrepancy rate of 1.61%. 

Table 3. -- Number of allele differences by locus between the original and quality control 

datasets for 2016 Bering Sea midwater pollock trawl fishery and Gulf of Alaska 

groundfish fisheries samples with non-questionable genotypes. 

Number alleles Number allele Percent 

Locus compared differences difference 

Oki100 622 18 2.89 

Omm1070 640 24 3.75 

Omy1011 644 9 1.40 

One101 624 27 4.33 

One102 624 12 1.92 

One104 648 3 0.46 

One114 652 3 0.46 

Ots103 652 4 0.61 

Ots3 676 7 1.04 

OtsG68 642 4 0.62 

Ssa419 650 3 0.46 
 

 

 

 

13

 GENETIC STOCK COMPOSITION 

For the mixture genotypes, allele designations were standardized to match those in the 

Fisheries and Oceans Canada (DFO) chum salmon microsatellite baseline (Beacham et al. 

2009b,c). Standardized genotypes were saved as text files, and C++ or FORTRAN programs were 

used to format the data into mixture files compatible with software used for stock composition 

estimation. Stock compositions were determined by comparing mixture genotypes with allele 

frequencies from reference baseline populations. As described previously (Gray et al. 2010), with 

minor changes to regional group names, baseline populations were grouped into six regions: 

Southeast Asia, Northeast Asia, Western Alaska, Upper/Middle Yukon, Southwest Alaska, and 

the Eastern GOA/Pacific Northwest (PNW) (Fig. 9). The regional groups were selected based on 

principal coordinate and simulation analyses as described in Guyon et al. (2010). A listing of the 

individual populations grouped by region is provided in Appendix I. 
14 

SE Asia 

NE Asia 

W AK 

Up/Mid Yukon 

SW AK 

EGOA/PNW 

Figure 9. -- Six regional groups of baseline chum salmon populations used in this report. 

As with previous analyses of chum salmon PSC (Guyon et al. 2010; Marvin et al. 2011; 

Gray et al. 2010, 2011a,b; Kondzela et al. 2012, 2013, 2016, 2017; Vulstek et al. 2014; Whittle 

et al. 2015), the stock composition analysis for the 2016 chum salmon samples was performed 

with maximum-likelihood (SPAM 3.7 software; ADF&G 2003) and Bayesian (BAYES software; 

Pella and Masuda 2001) procedures. The conditional maximum likelihood approach in SPAM 

compares the mixture genotypes directly with the baseline. In contrast, the Bayesian method uses 

an algorithm that can account for “missing” alleles in the baseline; that is, typically low 

frequency alleles present but not sampled in the baseline populations (Pella and Masuda 2001). 

Because the maximum-likelihood estimates were in close agreement with the Bayesian estimates, 

the maximum-likelihood estimates are not shown. BAYES stock composition estimates based on 

data from all 11 loci were derived for the six regional groups (Table 4; Appendix II). For all 

estimates, the Dirichlet prior parameters for the stock proportions were defined by region to be 

1/(GCg), where Cg is the number of baseline populations in region g, and G is the number of 
 

 

 

15 

regions3. For each analysis, six MCMC chains of 100,000 iterations (burn-in of 50,000) were run 

starting at disparate values of stock proportions 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. 

Convergence was assessed with Gelman-Rubin shrink factors, which were all 1.00-1.05 (Table 4; 

Appendix II), conveying strong convergence to a single posterior distribution (Gelman and Rubin 

1992, Pella and Masuda 2001). A basic overview of the Bayesian method used for mixed-stock 

analysis in our report is presented in Appendix III. 

The stock composition estimates were summarized by the mean, standard deviation, 

median, 95% credible interval (2.5th and 97.5th percentile of the MCMC iterates in the posterior 

output), and P = 0, which is the probability that a stock composition estimate is effectively zero 

(Munro et al. 2012). The P = 0 statistic is the frequency of the last half of the MCMC iterates of 

each chain combined that were less than a threshold that is calculated as 0.5 divided by the 

number of the chum salmon caught corresponding to the estimated proportion. This threshold is 

the value that would result in the estimated number of fish being rounded to zero fish when stock 

proportions are expanded to numbers of chum salmon caught. This statistic may be more useful 

than the credible interval for assessing the presence or absence of minor stocks. For example, the 

P = 0 value associated with the Upper/Middle Yukon stock estimate from the A-season sample 

set (Table 4) indicates that there is a 98.6% probability that essentially zero chum salmon from 

this stock were caught in this season. 

3

 In analyses prior to the 2013 chum salmon PSC analysis, a flat prior (1/381) was assigned to each baseline 

population. Priors defined by region may reduce bias due to differences in how densely regions are represented by 

baseline populations. 
 

 

 

 

16 

Table 4. -- Regional stock composition estimates of chum salmon collected from 2016 trawl 

fisheries. BAYES mean estimates are provided with standard deviations (S.D.), 

95% credible intervals, median estimate, P = 0 statistic (values > 0.5 are shaded), 

and the Gelman-Rubin shrink factor. 

A. Bering Sea pollock trawl fishery, A-season, (PSC = 3,726, n = 114) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink 

SE Asia 726 0.195 0.039 0.124 0.193 0.277 0 1.00 

NE Asia 1,388 0.372 0.061 0.257 0.372 0.496 0 1.00 

W Alaska 117 0.032 0.026 0 0.027 0.094 0.155 1.00 

Up/Mid Yukon 15 0.004 0.008 0 0.001 0.027 0.986 1.00 

SW Alaska 93 0.025 0.032 0 0.009 0.105 0.451 1.02 

E GOA/PNW 1,387 0.372 0.057 0.261 0.372 0.485 0 1.01 

B. Bering Sea pollock trawl fishery, B-season, (PSC = 339,094, n = 2,701) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink 

SE Asia 29,908 0.088 0.006 0.077 0.088 0.100 0 1.00 

NE Asia 103,254 0.305 0.011 0.282 0.304 0.327 0 1.00 

W Alaska 65,411 0.193 0.011 0.172 0.193 0.214 0 1.00 

Up/Mid Yukon 18,006 0.053 0.007 0.041 0.053 0.067 0 1.00 

SW Alaska 4,374 0.013 0.004 0.006 0.012 0.022 0 1.00 

E GOA/PNW 118,174 0.349 0.010 0.328 0.348 0.369 0 1.00 

C. Gulf of Alaska groundfish fisheries, (PSC = 3,518, n = 473) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink 

SE Asia 37 0.010 0.005 0.002 0.010 0.023 0.759 1.00 

NE Asia 92 0.026 0.010 0.009 0.025 0.049 0.006 1.00 

W Alaska 62 0.018 0.007 0.006 0.017 0.034 0.062 1.00 

Up/Mid Yukon 4 0.001 0.003 0 0.000 0.009 1.000 1.00 

SW Alaska 55 0.016 0.009 0.001 0.015 0.036 0.257 1.00 

E GOA/PNW 3,268 0.929 0.015 0.898 0.930 0.955 0 1.00 
 

 

 

17 

COMPARISON WITH PREVIOUS ESTIMATES 

Bering Sea 

This was the second year in a row that the sample set from the A-season was large enough 

for genetic analysis. The stock composition results from 2016 were similar to 2015 for all regions, 

with the exception of Southeast Asia, which had a significantly larger stock contribution in 2016 

than in 2015 (Fig. 10). 

0.0 

0.1 

0.2 

0.3 

0.4 

0.5 

0.6 

SE Asia NE Asia Western AK Upper/Middle 

Yukon 

SW Alaska Eastern 

GOA/PNW 

Stock proportion 

Bering Sea A-season 

pollock fishery 2015 (n=142) 

2016 (n=114) 

Figure 10. -- Stock composition estimates and 95% BAYES credible intervals for the 2015 and 

2016 chum salmon genetic samples from the Bering Sea pollock A-season. 

The stock composition results from the analysis of the 2016 chum salmon samples 

collected during the B-season were similar to the results from past years for four of the six 

regions, prior to and after systematic sampling was in effect (Fig. 11, upper panel). The two 

exceptions to this pattern were Southeast Asia stocks, which were lower than in previous years, 

and Eastern GOA/PNW stocks, which were higher than in years prior to systematic sampling. In 

2016, Northeast Asia and Eastern GOA/PNW dominated the regional contributions. The extent to 

which year-to-year differences in regional stock contributions are attributable to differences in 
 

 

18 

fishing locations and times or migration patterns of chum salmon is beyond the scope of this 

report. However, with systematic sampling of the Bering Sea chum salmon PSC in place, the role 

of these factors on the year-to-year variation of stock estimates will be easier to determine. 

The 1994-1995 chum salmon stock composition estimates were produced with allozyme 

data (Wilmot et al. 1998), whereas the 2005-2016 estimates were derived from DNA-based 

microsatellite loci (Guyon et al. 2010; Marvin et al. 2011; Gray et al. 2010, 2011a,b; Kondzela 

et al. 2012, 2013, 2016, 2017; Vulstek et al. 2014; Whittle et al. 2015). The allozyme (77 

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

same populations and have similar regional groups. 

The large variation in total chum salmon caught across the years (Fig. 2) is reflected in 

the high standard errors of the mean number of chum salmon caught by region (unweighted by 

year) when stock composition estimates are extrapolated to the total chum salmon PSC from the 

Bering Sea groundfish fisheries (Fig. 11, lower panel). Since 2011, the genetic samples have 

been collected systematically, resulting in the numerical extrapolations being relatively free of 

sample bias. The location and timing of collections prior to 2011 was not always representative 

of the entire chum salmon PSC within a given year. 
 

19 

0.0 

0.1 

0.2 

0.3 

0.4 

Stock proportion 

Bering Sea 

pollock fishery 

mean 1994, 1995, 2005-2010 

mean 2011-2015 

2016 

0 

20 

40 

60 

80 

100 

120 

SE Asia NE Asia Western AK Upper/Middle SW Alaska Eastern 

Numbers of fish 

× 1,000 

mean 1994, 1995, 2005-2010 (166,140) 

mean 2011-2015 (162,107) 

2016 (347,139) 

Yukon GOA/PNW 

Figure 11. -- Comparison of the 2016 Bering Sea chum salmon stock composition estimates with 

the estimates from 2011 to 2015 (systematic sampling) and the unweighted mean 

estimates from 1994, 1995, and 2005-2010 (nonsystematic sampling). Proportions in 

top panel (B-season); numbers of fish (A+B seasons) in bottom panel, which for 

comparison purposes across years are based on the total chum salmon caught in all 

groundfish fisheries (NMFS 2017). Standard errors of the mean estimates are shown 

for the combined years; 95% BAYES credible intervals are shown for the 2016 

analysis. Error bars are based on only the mixed-stock analyses and do not include 

errors associated with the overall annual PSC estimation or potential biases in 

sample distribution. Total chum salmon caught in the Bering Sea groundfish 

fisheries is shown in parentheses in the bottom figure legend; 1994-2010 are 

estimates and 2011-2016 are censuses. 
 

20 

Gulf of Alaska 

In 2016, for the third year in a row, samples from the PSC of chum salmon from the 

GOA groundfish fisheries were available for genetic analysis. The stock composition estimates 

of the 2016 GOA samples were nearly identical to the 2014-2015 estimates, with more than 90% 

of the contribution from Eastern GOA/PNW stocks (Fig. 12). In all three years, the contributions 

from all other regions were 0-5%; chum salmon from the Upper/Middle Yukon and Southwest 

Alaska regions were not present in the GOA samples in any of the three years (0.71-1.00 “P = 0” 

values; Appendix II). 

0.0 

0.2 

0.4 

0.6 

0.8 

1.0 

SE Asia NE Asia Western AK Upper/Middle 

Yukon 

SW Alaska Eastern 

GOA/PNW 

Stock proportion 

Gulf of Alaska 

groundfish fisheries 

2014 

2015 

2016 

Figure 12. -- Stock composition estimates and 95% BAYES credible intervals for the 2014-2016 

chum salmon genetic samples from the Gulf of Alaska groundfish fisheries. 

TEMPORAL STRATIFICATION 

Resolving the temporal distribution of the chum salmon PSC is important for better 

understanding the seasonal impacts of the pollock trawl fishery on salmon stocks. If the chum 

salmon stock distribution changes consistently over time, it may be possible to manage the 
 

21 

pollock fishery in a manner that minimizes effects on critical salmon stocks. This section is 

limited to analyses of the Bering Sea samples.

 Mixture analyses of samples from both the A- and B-season provided an opportunity to 

compare stock contributions on the broader time scale of winter versus summer/fall. Although the 

dominant contribution from both seasons was from Eastern GOA/PNW and Northeast Asia 

stocks, there were significant differences in the stock contributions from other regions, 

particularly Southeast Asia, Western Alaska, and Upper/Middle Yukon (Tables 4A,B). 

As with the 2005-2015 analyses, the 2016 Bering Sea sample set from the B-season was 

split into three time periods: Early, Middle, and Late (Table 5). Stock composition estimates were 

made as described previously for each of the three temporal strata (Appendix II). 

Table 5. -- Temporal groups from the genetic sample sets of chum salmon caught in the 2016 

Bering Sea, B-season pollock fishery. 

Time period Weeks Dates Number of samples 

Early 24-29 June 10 – July 16 453 

Middle 30-34 July 17 – August 20 1,333 

Late 35-43 August 21 – October 22 915 

The stock composition of chum salmon caught in the Bering Sea pollock fishery changed 

during the course of the season (Fig. 13). In 2016, genetic samples differed across the three time 

periods within three of the five regional groups. The contribution from Southeast Asia decreased 

significantly after the Early time period to a low level during the Middle and Late time periods, 

the Eastern GOA/PNW contribution increased across time, nearly doubling between the Early and 

Late time periods, and the Western Alaska contribution decreased slightly between the Middle 

and Late time periods. The slight increase in the Northeast Asia contribution after the Early time 
22 

period was not significant, and the Upper/Middle Yukon contribution was stable over the three 

time periods. 

The averages of the 2005-2015 stock compositions for similar temporal strata are 

included for comparison purposes (Fig. 13). Some differences in the stock contributions by time 

period were observed between the 2016 and the 2005-2015 chum salmon samples. The 

contribution from Eastern GOA/PNW stocks during the Middle and Late time periods in 2016 

was notably higher than in previous years. The contribution from Southeast Asia during the 

Middle and Late time period in 2016 was lower than the average of previous years. The 

proportion of the chum salmon catch contributed by Western Alaska was higher during the 

Middle and Late time periods, and the Upper/Middle Yukon contribution was similar to that 

observed in previous years. Results from the temporal analysis should be used cautiously 

because spatial differences exist in the time-stratified sample sets and these differences are 

known to affect the stock composition estimates. 
 

 

 

 

23 

Middle Late 

Stock proportion 

Early 

0.4 

0.3 

0.2 

0.1 

0.0 

2005-2015 2016 2005-2015 2016 2005-2015 2016 2005-2015 2016 2005-2015 2016 

SE Asia NE Asia W Alaska Up/Mid Yukon EGOA/PNW 

Figure 13. -- Stock composition estimates for the 2005-2015 (mean ± S.E.) and 2016 (± 95% 

BAYES credible intervals) chum salmon samples for the Early, Middle, and Late 

periods of the B-season (defined in Table 5). Not shown is the Southwest Alaska 

region for which estimates never exceeded 5.6%. 

SPATIAL STRATIFICATION 

Resolution of the spatial distribution of the chum salmon PSC is also important for better 

understanding the impacts of the pollock trawl fishery on salmon stocks. This section is limited to 

analyses of the Bering Sea fishery samples. In 2016, for the sixth year, the Observer Program 

undertook a complete census of chum salmon caught in the Bering Sea pollock trawl fisheries. 

About 43% of the chum salmon catch was counted and sampled at shoreside processing facilities. 

Of the shoreside offloads, about 60% of the chum salmon catch was from vessels that fished in 

one ADF&G statistical area during a trip. For the 40% of chum salmon catch offloaded from 

vessels that fished in multiple ADF&G statistical areas during a trip (17% of total chum salmon 
 

 

24 

catch), the area assigned to an offload was the area where the highest weight of pollock was 

caught. 

The 2016 Bering Sea genetic samples from the B-season were split into two areas (see 

Fig. 1): the U.S. waters of the Bering Sea west of 170°W (areas 521, 523, and 524), and the 

southeastern Bering Sea east of 170°W (areas 509, 513, 516, 517, and 519). Stock compositions 

for the two spatial strata were estimated as described previously (Fig. 14; Appendix II). The 

contribution of stocks differed between the two spatial strata in a manner similar to that observed 

in 2015, with the exception of the Northeast Asia and Eastern GOA/PNW regions (Kondzela et al. 

2017), which had nearly identical stock proportions between the two areas in 2016 but different 

proportions in 2015. Almost two-thirds of the contribution in the southeastern Bering Sea was 

from North American stocks, primarily from the Eastern GOA/PNW and Western Alaska regions. 

The contribution in the area west of 170°W was divided nearly evenly between North American 

and Asian stocks. 

0 

0.1 

0.2 

0.3 

0.4 

0.5 

Stock proportion 

2016 Bering Sea 

pollock fishery West of 170°W (n = 369) 

East of 170°W (n =2,332) 

SE Asia NE Asia Western AK Upper/Middle SW Alaska Eastern 

Yukon GOA/PNW 

Figure 14. -- Stock composition estimates and 95% BAYES credible intervals for the 2016 chum 

salmon genetic samples collected during the B-season from the U.S. waters of the 

Bering Sea west of 170°W (aggregate area 521/523/524) and the southeastern Bering 

Sea east of 170°W (aggregate area 509/513/516/517/519). 
 

 

 

 

 

 

25 

To better understand the chum salmon stock distribution across both time and space, the 

2016 samples from NMFS reporting area 517 were compared across Early, Middle, and Late time 

periods and samples from NMFS reporting area 521 were compared across Early and Middle time 

periods (Table 6). Samples from all other areas/time periods were not included due to small 

sample sizes. 

Table 6. -- Spatial and temporal groups from the 2016 chum salmon genetic samples for the 

NMFS reporting areas and time periods (Table 5) with sufficient number of samples 

for analysis. 

Reporting area Time period Number of samples 

517 Early 262 

Middle 1,024 

Late 840 

521 Early 102 

Middle 225 

Stock compositions were estimated for each spatial and temporal stratum as described 

above (Fig. 15; Appendix II). The major differences in regional stock contributions between area 

517 and 521 mirror those observed in samples from east and west of 170°W (Fig. 14). Within 

each area some regional contributions varied across time. In area 517, Southeast Asia stocks had 

the highest contribution during the Early time period, and decreased to a low level during the 

Middle and Late time periods. Northeast Asia stocks increased after the Early time period, 

although the 95% credible intervals overlap. Western Alaska stocks increased during the Middle 

time period, although the 95% credible intervals overlap, and then decreased during the Late time 

period. Eastern GOA/PNW stocks increased across all time periods. In area 521, the Southeast 

Asia stocks decreased five-fold and Eastern GOA/PNW stocks more than doubled after the Early 

time period. As in previous years, the contribution from Upper/Middle Yukon and Southwest 
26 

Alaska stocks was absent or low in all time periods and both areas. It should be noted that the 

numbers of fish from a region within a given area may not change over time, but the proportion 

will change if fish from other regions move into or out of the area. 

The similarity of stock distributions among the areas and time periods may be due at least 

in part to vessels fishing near area boundaries. For example, the southern corner of area 521 

shares the northwestern edge of area 517. Latitude and longitude information was not available 

for many samples, so the locations of the chum salmon samples within each area are unknown. 

In addition, about 17% of the total chum salmon PSC was sampled from offload deliveries in 

which vessels fished in multiple areas. Thus, for an unknown proportion of the chum salmon 

samples, the area designation may not be correct. 
 

 

27 

0.0 

0.1 

0.2 

0.3 

0.4 

0.5 

0.6 

Stock proportion 

Area 517 Early 

Middle 

Late 

0.0 

0.1 

0.2 

0.3 

0.4 

0.5 

0.6 

Stock proportion 

Area 521 Early 

Middle 

SE Asia NE Asia Western AK Upper/Mid SW Alaska Eastern 

Yukon GOA/PNW 

Figure 15. -- Stock composition estimates and 95% BAYES credible intervals for the 2016 chum 

salmon genetic samples collected during the B-season from NMFS reporting area 

517 for the Early, Middle, and Late time periods and from NMFS reporting area 521 

for the Early and Middle time periods (Table 6). 

In an effort to better understand the distribution of chum salmon stocks in the Bering Sea 

PSC from the pollock fishery, stock composition estimates were obtained from four spatial 

clusters–based on ADF&G statistical areas–of chum salmon samples collected along the 

continental shelf edge during Early (statistical weeks 24-32) and Late (statistical weeks 33-43) 
 

 

 

 

 

 

 

28 

time periods (Table 7; Appendix IV). There were fewer differences in stock estimates along the 

continental shelf and across time periods in 2016 (Fig. 16; Appendix II) than in 2015. In the Early 

time period, the pattern of stock proportions was similar between the two years. In 2016 there was 

a gradient of stock proportions along the continental shelf with a higher proportion of chum 

salmon from Asian stocks in the more northern portion of the fishery and a higher proportion of 

chum salmon from North American stocks in the southeastern portion of the fishery, nearest to the 

Alaska Peninsula. In the Late time period, the 2016 stock proportions for all six regions were 

nearly constant across the continental shelf, unlike the pattern observed in 2015 in which the 

Eastern GOA/PNW stock dominated Clusters 1-3 of the fishery. The two exceptions in 2016 were 

the higher proportions of Western Alaska stocks in Cluster 1 and Southeast Asia stocks in 

Cluster 4. 

Table 7. -- Collection information for the four spatial clusters of chum salmon caught in two time 

periods, Early (weeks 24-32) and Late (weeks 33-43), during the 2016 B-season of the 

Bering Sea pollock fishery and analyzed for genetic stock composition. 

 Time Samples Samples 

Cluster period received analyzed 

1 Early 3,653 1,043 

Late 2,788 681 

2 Early 440 185 

Late 2,167 535 

3 Early 970 230 

Late 470 178 

4 Late 187 184 
 

 

29 

Figure 16. -- Stock composition estimates of chum salmon from four spatial clusters of samples 

collected along the continental shelf edge during Early (Weeks 24-32) and Late 

(Weeks 33-43) time periods from the 2016 Bering Sea pollock fishery. The four 

clusters of ADF&G statistical areas in which samples were collected in at least one 

year from 2013 to 2016 are highlighted in gray; ADF&G areas in which samples 

were collected in 2016 from at least 3 vessels are indicated with a dot. The sample 

size of the Early time period for the fourth cluster was too small for analysis. 

SUMMARY 

Stock composition estimates of the salmon caught 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 the genetic stock 

composition analyses of the 2016 chum salmon PSC based on 3,344 samples genotyped from the 
 

 

 

30 

Bering Sea and 473 samples genotyped from the GOA fisheries. The limitations and results of this 

analysis are summarized below and in Appendix II. 

Sampling Issues 

Bering Sea 

We highlight the reduced spatial and temporal biases in the Bering Sea 2016 sample set 

(Figs. 3 and 4) that were inherent in collections before 2011. Reduction of those biases improves 

the application of the 2016 genetic sample stock composition estimates to the entire chum 

salmon PSC. Implementation of Amendment 91 to the North Pacific Fishery Management 

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

Management Area4 requires that all salmon caught in the Bering Sea pollock fishery be sorted by 

species and counted to ensure compliance with the salmon PSC limits for the pollock fishery. This 

regulation led to the collection of representative samples from 98.2% of the chum salmon caught 

in this fishery for genetic analysis in 2016 (Fig. 5), and improved the capability to characterize the 

origin of salmon caught in the Bering Sea pollock fishery. 

Gulf of Alaska 

The GOA groundfish fisheries are complex and not all groundfish catches in the GOA are 

subject to observer coverage. The number of chum salmon caught in GOA federal fisheries is 

much lower than in the federal fisheries of the Bering Sea; however, recent expansion of sampling 

salmon PSC in the GOA5

 provided, for the third year, a small sample set for genetic analysis. The 

distribution of chum salmon PSC samples is not representative of the groundfish fisheries as a 

4 75 FR 53026, August 30, 2010. 5

 Amendment 93 to the NPFMC fishery management plan for GOA groundfish (77 FR 42629, July 20, 2012). 
 

31 

whole. Most of the genetic samples (98%) were from the pollock trawl fishery, which in 2016 

caught just over half the chum salmon PSC in the GOA. 

Stock Composition Estimates 

Bering Sea 

As in past years, only a very small portion of the total chum salmon PSC was caught 

during the 2016 A-season in, but given the relatively high salmon bycatch in 2016, a small sample 

set was available for the second year in a row for genetic analysis. Most of the samples (74%) 

were from Eastern GOA/PNW and Northeast Asia stocks (Table 4A). Except for an increase in 

the proportions from Southeast Asia stocks in 2016, the proportions from other regions were 

similar in 2015 and 2016 (Fig. 10). 

Nearly two-thirds of the genetic samples collected from chum salmon caught in the Bseason 2016 Bering Sea pollock fishery were from North America, with the majority from 

Eastern GOA/PNW (35%), followed by Western Alaska (19%), stocks. The contribution from 

Asian stocks was predominantly from Northeast Asia (31%) (Table 4B). The stock proportions 

from Southeast Asia were significantly lower than in previous years, while Eastern GOA/PNW 

proportions were higher than in years prior to systematic sampling (Fig. 11). Contributions from 

all other regions were similar to previous years, and the low contribution from Southwest Alaska 

continued in 2016. Although chum salmon samples in 2016 were collected representatively from 

the pollock fishery, there were differences in where and when genetic samples were collected 

from previous years, so that caution must be used in making year-to-year comparisons. 
32 

Gulf of Alaska 

As in the previous two years, the stock proportions of the 2016 chum salmon PSC from 

the GOA had a very different pattern than that observed in the Bering Sea. In the GOA groundfish 

fisheries, 93% of the chum salmon sampled were from Eastern GOA/PNW stocks (Table 4C; 

Fig. 12). The remaining contributions from the other five regions were very low, 0-5%. 

Temporal and Spatial Effects 

The A-season stock compositions differed from those of the B-season primarily by a 

higher contribution from Southeast Asia stocks and lower contributions from Western Alaska and 

Upper/Middle Yukon stocks (Table 4A,B); differences were minor in other regional estimates. 

Whether the differences are due to the spatial contraction of the pollock fleet during the A-season 

or to seasonal differences in the oceanic distribution of chum salmon is unknown. 

The finer-scale time-stratified analysis of the chum salmon samples was limited to the 

pollock B-season, when the majority of chum salmon are intercepted in the Bering Sea. As in 

previous years, stock composition estimates of the 2016 chum salmon catch changed across the 

three sampling periods, suggesting a shift in the temporal stratification of chum salmon stocks in 

the Bering Sea, changes in fishing or sampling locations, or both (Fig. 13). By time period, some 

differences were observed in the stock composition estimates of chum salmon PSC collected in 

2016 and in previous years, notably for the Middle and Late time periods for Southeast Asia, 

Western Alaska, and Eastern GOA/PNW stocks. 

Spatial analysis suggested that the majority of the chum salmon from U.S. waters of the 

Bering Sea east of 170°W originated from North American stocks, primarily from the Eastern 

GOA/PNW region. West of 170°W, the chum salmon originated from nearly equal contributions 

of Asian and North American stocks (Fig. 14). The proportion of chum salmon from Southeast 
 

 

 

 

33 

Asia stocks in the western area was higher than that in the southeastern Bering Sea, whereas the 

proportion of chum salmon from North America, particularly from Western Alaska stocks, was 

higher in the southeastern Bering Sea. 

An examination of chum salmon stock estimates on both spatial and temporal strata of 

the Bering Sea pollock fishery during the B-season indicates that stocks are not uniformly 

distributed (Figs. 15, 16). In general, the proportion of stocks from Asia are higher in the more 

northwestern areas of the fishery and stocks from North America, particularly from the Eastern 

GOA/PNW region, are more abundant later in the season, although these patterns of stock 

distribution were more evident in the previous year. 

Application of Estimates 

The extent to which any salmon stock is impacted by the Bering Sea and GOA trawl 

fisheries is dependent on many factors including 1) the overall size of the PSC, 2) the age of the 

salmon caught, 3) the age composition of the salmon stocks at return, 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 imply greater impact than a 

smaller estimate in another year. 
 

34 
 

 

 

35 

ACKNOWLEDGMENTS 

Salmon tissue samples were collected by observers deployed through the AFSC’s 

Fisheries Monitoring and Analysis Division (FMA). Fishery information was provided by the 

FMA, Pacific States Marine Fisheries Commission (PSMFC), and NMFS Alaska Regional Office 

(AKR). Particular thanks go to Rob Ames and Bob Ryznar of PSMFC who created the AKFIN 

reports that facilitate access to salmon bycatch data in tabular and graphical form, and to Julie 

Blair (FMA) for support to PSMFC. Hanhvan Nguyen and Scott Vulstek of ABL assisted with 

data analyses. Through ABL-affiliated contracts, Dione Cuadra and Kate Hauch assisted in the 

laboratory, and Maxwell Marsh assisted with proofing the report. The baseline used for these 

analyses was obtained through a web portal sponsored by Fisheries and Oceans Canada and 

developed in their Molecular Genetics Laboratory with genetic loci identified in a number of 

laboratories. This document was reviewed by the AFSC, with special thanks to Jordan Watson 

and Jim Lee. 
36 
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43 

APPENDICES 

45 

Appendix Table I. -- Chum salmon populations in the Fisheries and Oceans Canada (DFO) 

microsatellite baseline with the regional designations used in the analyses 

of this report. 

DFO Reg DFO Reg 

num. Population name num. Region num. Population name num. Region 

41 Abashiri 1 SE Asia 213 Kalininka 2 NE Asia 

215 Avakumovka 1 SE Asia 225 Kamchatka 2 NE Asia 

40 Chitose 1 SE Asia 219 Kanchalan 2 NE Asia 

315 Gakko_River 1 SE Asia 379 Karaga 2 NE Asia 

292 Hayatsuki 1 SE Asia 294 Kikchik 2 NE Asia 

44 Horonai 1 SE Asia 209 Kol 2 NE Asia 

252 Kawabukuro 1 SE Asia 233 Magadan 2 NE Asia 

313 Koizumi_River 1 SE Asia 211 Naiba 2 NE Asia 

300 Kushiro 1 SE Asia 295 Nerpichi 2 NE Asia 

37 Miomote 1 SE Asia 381 Okhota 2 NE Asia 

391 Namdae_R 1 SE Asia 212 Oklan 2 NE Asia 

231 Narva 1 SE Asia 222 Ola 2 NE Asia 

298 Nishibetsu 1 SE Asia 386 Olutorsky_Bay 2 NE Asia 

293 Ohkawa 1 SE Asia 228 Ossora 2 NE Asia 

297 Orikasa 1 SE Asia 224 Penzhina 2 NE Asia 

214 Ryazanovka 1 SE Asia 385 Plotnikova_R 2 NE Asia 

312 Sakari_River 1 SE Asia 221 Pymta 2 NE Asia 

311 Shari_River 1 SE Asia 220 Tauy 2 NE Asia 

36 Shibetsu 1 SE Asia 383 Tugur_River 2 NE Asia 

299 Shikiu 1 SE Asia 226 Tym_ 2 NE Asia 

253 Shiriuchi 1 SE Asia 230 Udarnitsa 2 NE Asia 

310 Shizunai 1 SE Asia 290 Utka_River 2 NE Asia 

217 Suifen 1 SE Asia 208 Vorovskaya 2 NE Asia 

35 Teshio 1 SE Asia 387 Zhypanova 2 NE Asia 

39 Tokachi 1 SE Asia 348 Agiapuk 3 W Alaska 

38 Tokoro 1 SE Asia 376 Alagnak 3 W Alaska 

314 Tokushibetsu 1 SE Asia 3 Andreafsky 3 W Alaska 

291 Toshibetsu 1 SE Asia 357 Aniak 3 W Alaska 

296 Tsugaruishi 1 SE Asia 301 Anvik 3 W Alaska 

316 Uono_River 1 SE Asia 80 Chulinak 3 W Alaska 

309 Yurappu 1 SE Asia 347 Eldorado 3 W Alaska 

218 Amur 2 NE Asia 358 George 3 W Alaska 

207 Anadyr 2 NE Asia 307 Gisasa 3 W Alaska 

384 Apuka_River 2 NE Asia 371 Goodnews 3 W Alaska 

382 Bolshaya 2 NE Asia 288 Henshaw_Creek 3 W Alaska 

380 Dranka 2 NE Asia 339 Imnachuk 3 W Alaska 

223 Hairusova 2 NE Asia 361 Kanektok 3 W Alaska 

378 Ivashka 2 NE Asia 362 Kasigluk 3 W Alaska 
46 

DFO Reg DFO Reg 

num. Population name num. Region num. Population name num. Region 

328 Kelly_Lake 3 W Alaska 6 Pelly 4 U/M Yukon 

340 Kobuk 3 W Alaska 439 Porcupine 4 U/M Yukon 

343 Koyuk 3 W Alaska 83 Salcha 4 U/M Yukon 

363 Kwethluk 3 W Alaska 4 Sheenjek 4 U/M Yukon 

336 Kwiniuk_River 3 W Alaska 1 Tatchun 4 U/M Yukon 

303 Melozitna 3 W Alaska 9 Teslin 4 U/M Yukon 

373 Mulchatna 3 W Alaska 84 Toklat 4 U/M Yukon 

372 Naknek 3 W Alaska 360 Alagoshak 5 SW Alaska 

330 Niukluk 3 W Alaska 333 American_River 5 SW Alaska 

329 Noatak 3 W Alaska 366 Big_River 5 SW Alaska 

345 Nome 3 W Alaska 354 Coleman_Creek 5 SW Alaska 

302 Nulato 3 W Alaska 355 Delta_Creek 5 SW Alaska 

374 Nunsatuk 3 W Alaska 359 Egegik 5 SW Alaska 

13 Peel_River 3 W Alaska 332 Frosty_Creek 5 SW Alaska 

322 Pikmiktalik 3 W Alaska 365 Gertrude_Creek 5 SW Alaska 

331 Pilgrim_River 3 W Alaska 370 Joshua_Green 5 SW Alaska 

346 Shaktoolik 3 W Alaska 364 Meshik 5 SW Alaska 

341 Snake 3 W Alaska 283 Moller_Bay 5 SW Alaska 

368 Stuyahok_River 3 W Alaska 369 Pumice_Creek 5 SW Alaska 

375 Togiak 3 W Alaska 367 Stepovak_Bay 5 SW Alaska 

154 Tozitna 3 W Alaska 335 Sturgeon 5 SW Alaska 

342 Unalakleet 3 W Alaska 350 Uganik 5 SW Alaska 

344 Ungalik 3 W Alaska 334 Volcano_Bay 5 SW Alaska 

8 Big_Creek 4 U/M Yukon 356 Westward_Creek 5 SW Alaska 

89 Big_Salt 4 U/M Yukon 239 Ahnuhati 6 E GOA/PNW 

86 Black_River 4 U/M Yukon 69 Ahta 6 E GOA/PNW 

87 Chandalar 4 U/M Yukon 155 Ain 6 E GOA/PNW 

28 Chandindu 4 U/M Yukon 183 Algard 6 E GOA/PNW 

82 Cheena 4 U/M Yukon 58 Alouette 6 E GOA/PNW 

81 Delta 4 U/M Yukon 325 Alouette_North 6 E GOA/PNW 

7 Donjek 4 U/M Yukon 270 Andesite_Cr 6 E GOA/PNW 

5 Fishing_Br 4 U/M Yukon 428 Arnoup_Cr 6 E GOA/PNW 

88 Jim_River 4 U/M Yukon 153 Ashlulm 6 E GOA/PNW 

85 Kantishna 4 U/M Yukon 156 Awun 6 E GOA/PNW 

2 Kluane 4 U/M Yukon 133 Bag_Harbour 6 E GOA/PNW 

59 Kluane_Lake 4 U/M Yukon 164 Barnard 6 E GOA/PNW 

181 Koyukuk_late 4 U/M Yukon 16 Bella_Bell 6 E GOA/PNW 

90 Koyukuk_south 4 U/M Yukon 79 Bella_Coola 6 E GOA/PNW 

10 Minto 4 U/M Yukon 49 Big_Qual 6 E GOA/PNW 
47 

DFO Reg DFO Reg 

num. Population name num. Region num. Population name num. Region 

201 Big_Quilcene 6 E GOA/PNW 269 Dog-tag 6 E GOA/PNW 

281 Bish_Cr 6 E GOA/PNW 177 Draney 6 E GOA/PNW 

198 Bitter_Creek 6 E GOA/PNW 114 Duthie_Creek 6 E GOA/PNW 

103 Blackrock_Creek 6 E GOA/PNW 427 East_Arm 6 E GOA/PNW 

390 Blaney_Creek 6 E GOA/PNW 266 Ecstall_River 6 E GOA/PNW 

138 Botany_Creek 6 E GOA/PNW 94 Elcho_Creek 6 E GOA/PNW 

264 Buck_Channel 6 E GOA/PNW 193 Ellsworth_Cr 6 E GOA/PNW 

169 Bullock_Chann 6 E GOA/PNW 203 Elwha 6 E GOA/PNW 

61 Campbell_River 6 E GOA/PNW 276 Ensheshese 6 E GOA/PNW 

323 Carroll 6 E GOA/PNW 263 Fairfax_Inlet 6 E GOA/PNW 

78 Cascade 6 E GOA/PNW 32 Fish_Creek 6 E GOA/PNW 

76 Cayeghle 6 E GOA/PNW 429 Flux_Cr 6 E GOA/PNW 

42 Cheakamus 6 E GOA/PNW 102 Foch_Creek 6 E GOA/PNW 

398 Cheenis_Lake 6 E GOA/PNW 179 Frenchman 6 E GOA/PNW 

51 Chehalis 6 E GOA/PNW 227 Gambier 6 E GOA/PNW 

19 Chemainus 6 E GOA/PNW 96 Gill_Creek 6 E GOA/PNW 

47 Chilliwack 6 E GOA/PNW 166 Gilttoyee 6 E GOA/PNW 

392 Chilqua_Creek 6 E GOA/PNW 145 Glendale 6 E GOA/PNW 

117 Chuckwalla 6 E GOA/PNW 135 Gold_Harbour 6 E GOA/PNW 

139 Clapp_Basin 6 E GOA/PNW 11 Goldstream 6 E GOA/PNW 

107 Clatse_Creek 6 E GOA/PNW 66 Goodspeed_River 6 E GOA/PNW 

118 Clyak 6 E GOA/PNW 136 Government 6 E GOA/PNW 

62 Cold_Creek 6 E GOA/PNW 205 Grant_Creek 6 E GOA/PNW 

77 Colonial 6 E GOA/PNW 100 Green_River 6 E GOA/PNW 

353 Constantine 6 E GOA/PNW 450 GreenRrHatchery 6 E GOA/PNW 

168 Cooper_Inlet 6 E GOA/PNW 237 Greens 6 E GOA/PNW 

197 County_Line 6 E GOA/PNW 141 Harrison 6 E GOA/PNW 

12 Cowichan 6 E GOA/PNW 438 Harrison_late 6 E GOA/PNW 

414 Crag_Cr 6 E GOA/PNW 64 Hathaway_Creek 6 E GOA/PNW 

161 Dak_ 6 E GOA/PNW 234 Herman_Creek 6 E GOA/PNW 

259 Dana_Creek 6 E GOA/PNW 17 Heydon_Cre 6 E GOA/PNW 

123 Date_Creek 6 E GOA/PNW 407 Hicks_Cr 6 E GOA/PNW 

250 Dawson_Inlet 6 E GOA/PNW 400 Homathko 6 E GOA/PNW 

91 Dean_River 6 E GOA/PNW 411 Honna 6 E GOA/PNW 

261 Deena 6 E GOA/PNW 204 Hoodsport 6 E GOA/PNW 

170 Deer_Pass 6 E GOA/PNW 185 Hooknose 6 E GOA/PNW 

46 Demamiel 6 E GOA/PNW 406 Hopedale_Cr 6 E GOA/PNW 

210 Dipac_Hatchery 6 E GOA/PNW 412 Hutton_Head 6 E GOA/PNW 

319 Disappearance 6 E GOA/PNW 278 Illiance 6 E GOA/PNW 
48 

DFO Reg DFO Reg 

num. Population name num. Region num. Population name num. Region 

152 Inch_Creek 6 E GOA/PNW 50 Little_Qua 6 E GOA/PNW 

146 Indian_River 6 E GOA/PNW 413 Lizard_Cr 6 E GOA/PNW 

92 Jenny_Bay 6 E GOA/PNW 119 Lockhart-Gordon 6 E GOA/PNW 

115 Kainet_River 6 E GOA/PNW 176 Lower_Lillooet 6 E GOA/PNW 

144 Kakweiken 6 E GOA/PNW 137 Mace_Creek 6 E GOA/PNW 

268 Kalum 6 E GOA/PNW 242 Mackenzie_Sound 6 E GOA/PNW 

395 Kanaka_Cr 6 E GOA/PNW 116 MacNair_Creek 6 E GOA/PNW 

402 Kano_Inlet_Cr 6 E GOA/PNW 55 Mamquam 6 E GOA/PNW 

162 Kateen 6 E GOA/PNW 121 Markle_Inlet_Cr 6 E GOA/PNW 

389 Kawkawa 6 E GOA/PNW 27 Martin_Riv 6 E GOA/PNW 

95 Kemano 6 E GOA/PNW 338 Mashiter_Creek 6 E GOA/PNW 

192 Kennedy_Creek 6 E GOA/PNW 109 McLoughin_Cr 6 E GOA/PNW 

238 Kennell 6 E GOA/PNW 178 Milton 6 E GOA/PNW 

351 Keta_Creek 6 E GOA/PNW 194 Minter_Cr 6 E GOA/PNW 

101 Khutze_River 6 E GOA/PNW 254 Mountain_Cr 6 E GOA/PNW 

126 Khutzeymateen 6 E GOA/PNW 111 Mussel_River 6 E GOA/PNW 

282 Kiltuish 6 E GOA/PNW 157 Naden 6 E GOA/PNW 

93 Kimsquit 6 E GOA/PNW 337 Nahmint_River 6 E GOA/PNW 

187 Kimsquit_Bay 6 E GOA/PNW 444 Nakut_Su 6 E GOA/PNW 

419 Kincolith 6 E GOA/PNW 14 Nanaimo 6 E GOA/PNW 

273 Kispiox 6 E GOA/PNW 122 Nangeese 6 E GOA/PNW 

106 Kitasoo 6 E GOA/PNW 422 Nass_River 6 E GOA/PNW 

99 Kitimat_River 6 E GOA/PNW 399 Necleetsconnay 6 E GOA/PNW 

275 Kitsault_Riv 6 E GOA/PNW 113 Neekas_Creek 6 E GOA/PNW 

163 Kitwanga 6 E GOA/PNW 321 Neets_Bay_early 6 E GOA/PNW 

271 Kleanza_Cr 6 E GOA/PNW 320 Neets_Bay_late 6 E GOA/PNW 

437 Klewnuggit_Cr 6 E GOA/PNW 173 Nekite 6 E GOA/PNW 

21 Klinaklini 6 E GOA/PNW 104 Nias_Creek 6 E GOA/PNW 

418 Ksedin 6 E GOA/PNW 143 Nimpkish 6 E GOA/PNW 

125 Kshwan 6 E GOA/PNW 53 Nitinat 6 E GOA/PNW 

423 Kumealon 6 E GOA/PNW 191 Nooksack 6 E GOA/PNW 

112 Kwakusdis_River 6 E GOA/PNW 186 Nooseseck 6 E GOA/PNW 

436 Kxngeal_Cr 6 E GOA/PNW 318 NorrishWorth 6 E GOA/PNW 

127 Lachmach 6 E GOA/PNW 159 North_Arm 6 E GOA/PNW 

262 Lagins 6 E GOA/PNW 377 Olsen_Creek 6 E GOA/PNW 

131 Lagoon_Inlet 6 E GOA/PNW 184 Orford 6 E GOA/PNW 

448 LagoonCr 6 E GOA/PNW 287 Pa-aat_River 6 E GOA/PNW 

167 Lard 6 E GOA/PNW 260 Pacofi 6 E GOA/PNW 

160 Little_Goose 6 E GOA/PNW 56 Pallant 6 E GOA/PNW 
 

 

 

 

 

 

 

49 

DFO Reg DFO Reg 

num. Population name num. Region num. Population name num. Region 

65 Pegattum_Creek 6 E GOA/PNW 324 Surprise 6 E GOA/PNW 

48 Puntledge 6 E GOA/PNW 75 Taaltz 6 E GOA/PNW 

98 Quaal_River 6 E GOA/PNW 30 Taku 6 E GOA/PNW 

147 Quap 6 E GOA/PNW 18 Takwahoni 6 E GOA/PNW 

108 Quartcha_Creek 6 E GOA/PNW 251 Tarundl_Creek 6 E GOA/PNW 

199 Quinault 6 E GOA/PNW 149 Theodosia 6 E GOA/PNW 

110 Roscoe_Creek 6 E GOA/PNW 22 Thorsen 6 E GOA/PNW 

397 Salmon_Bay 6 E GOA/PNW 129 Toon 6 E GOA/PNW 

195 Salmon_Cr 6 E GOA/PNW 279 Tseax 6 E GOA/PNW 

134 Salmon_River 6 E GOA/PNW 202 Tulalip 6 E GOA/PNW 

200 Satsop 6 E GOA/PNW 97 Turn_Creek 6 E GOA/PNW 

236 Sawmill 6 E GOA/PNW 430 Turtle_Cr 6 E GOA/PNW 

410 Seal_Inlet_Cr 6 E GOA/PNW 247 Tuskwa 6 E GOA/PNW 

158 Security 6 E GOA/PNW 165 Tyler 6 E GOA/PNW 

130 Sedgewick 6 E GOA/PNW 33 Tzoonie 6 E GOA/PNW 

393 Serpentine_R 6 E GOA/PNW 124 Upper_Kitsumkal 6 E GOA/PNW 

317 Shovelnose_Cr 6 E GOA/PNW 140 Vedder 6 E GOA/PNW 

249 Shustnini 6 E GOA/PNW 70 Viner_Sound 6 E GOA/PNW 

206 Siberia_Creek 6 E GOA/PNW 45 Wahleach 6 E GOA/PNW 

25 Silverdale 6 E GOA/PNW 172 Walkum 6 E GOA/PNW 

196 Skagit 6 E GOA/PNW 73 Waump 6 E GOA/PNW 

274 Skeena 6 E GOA/PNW 232 Wells_Bridge 6 E GOA/PNW 

171 Skowquiltz 6 E GOA/PNW 352 Wells_River 6 E GOA/PNW 

447 SkykomishRiv 6 E GOA/PNW 105 West_Arm_Creek 6 E GOA/PNW 

132 Slatechuck_Cre 6 E GOA/PNW 267 Whitebottom_Cr 6 E GOA/PNW 

43 Sliammon 6 E GOA/PNW 326 Widgeon_Slough 6 E GOA/PNW 

15 Smith_Cree 6 E GOA/PNW 277 Wilauks_Cr 6 E GOA/PNW 

54 Snootli 6 E GOA/PNW 120 Wilson_Creek 6 E GOA/PNW 

180 Southgate 6 E GOA/PNW 401 Worth_Creek 6 E GOA/PNW 

26 Squakum 6 E GOA/PNW 60 Wortley_Creek 6 E GOA/PNW 

142 Squamish 6 E GOA/PNW 248 Yellow_Bluff 6 E GOA/PNW 

128 Stagoo 6 E GOA/PNW 434 Zymagotitz 6 E GOA/PNW 

265 Stanley 6 E GOA/PNW 

52 Stave 6 E GOA/PNW 

396 Stawamus 6 E GOA/PNW 

409 Steel_Cr 6 E GOA/PNW 

424 Stewart_Cr 6 E GOA/PNW 

416 Stumaun_Cr 6 E GOA/PNW 

327 Sugsaw 6 E GOA/PNW 
 

 

 

 

 

50 

Appendix II. -- Regional stock composition estimates of chum salmon samples from the 2016 

Bering Sea (BS) midwater pollock trawl fishery and the Gulf of Alaska (GOA) 

groundfish fisheries. Estimated number of prohibited species catch (PSC), 

BAYES mean estimates, standard deviations (SD), 95% credible intervals, 

median estimate, the probability that the stock estimate is equal to zero (P = 0; 

values > 0.5 are shaded; Munro et al. 2012), and the Gelman-Rubin shrink factor 

are reported. For each stratum, PSC is the number of chum salmon reported as 

caught and n is the number of genetic samples used in the analysis. Early season 

is Weeks 24-29, Middle season is Weeks 30-34, and Late season is Weeks 35-

43. For the analyses of four spatial clusters, the Early time period is Weeks 24-

32 and the Late time period is Weeks 33-43. 

GOA Total sample set (PSC = 3,518, n = 473) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 37 0.010 0.005 0.002 0.010 0.023 0.759 1.00 

NE Asia 92 0.026 0.010 0.009 0.025 0.049 0.006 1.00 

W Alaska 62 0.018 0.007 0.006 0.017 0.034 0.062 1.00 

Up/Mid Yukon 4 0.001 0.003 0 0.000 0.009 1.000 1.00 

SW Alaska 55 0.016 0.009 0.001 0.015 0.036 0.257 1.00 

E GOA/PNW 3,268 0.929 0.015 0.898 0.930 0.955 0 1.00 

BS A-season sample set (PSC = 3,726, n = 114) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 726 0.195 0.039 0.124 0.193 0.277 0 1.00 

NE Asia 1,388 0.372 0.061 0.257 0.372 0.496 0 1.00 

W Alaska 117 0.032 0.026 0 0.027 0.094 0.155 1.00 

Up/Mid Yukon 15 0.004 0.008 0 0.001 0.027 0.986 1.00 

SW Alaska 93 0.025 0.032 0 0.009 0.105 0.451 1.02 

E GOA/PNW 1,387 0.372 0.057 0.261 0.372 0.485 0 1.01 

BS B-season sample set (PSC = 339,094, n = 2,701) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 29,908 0.088 0.006 0.077 0.088 0.100 0 1.00 

NE Asia 103,254 0.305 0.011 0.282 0.304 0.327 0 1.00 

W Alaska 65,411 0.193 0.011 0.172 0.193 0.214 0 1.00 

Up/Mid Yukon 18,006 0.053 0.007 0.041 0.053 0.067 0 1.00 

SW Alaska 4,374 0.013 0.004 0.006 0.012 0.022 0 1.00 

E GOA/PNW 118,174 0.349 0.010 0.328 0.348 0.369 0 1.00 
 

 

 

 

 

 

 

51 

Appendix II. -- Continued. 

BS Early season sample set (PSC = 56,835, n = 453) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 15,885 0.280 0.022 0.237 0.279 0.325 0 1.00 

NE Asia 13,453 0.237 0.025 0.189 0.236 0.287 0 1.00 

W Alaska 10,497 0.185 0.023 0.142 0.184 0.230 0 1.00 

Up/Mid Yukon 4,348 0.077 0.015 0.049 0.076 0.108 0 1.00 

SW Alaska 659 0.012 0.007 0.002 0.011 0.027 0.006 1.00 

E GOA/PNW 11,992 0.211 0.021 0.172 0.211 0.253 0 1.00 

BS Middle season sample set (PSC = 166,973, n = 1,333) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 9,534 0.057 0.007 0.044 0.057 0.072 0 1.00 

NE Asia 50,943 0.305 0.016 0.274 0.305 0.337 0 1.00 

W Alaska 37,936 0.227 0.016 0.197 0.227 0.259 0 1.00 

Up/Mid Yukon 7,597 0.046 0.010 0.027 0.045 0.067 0 1.00 

SW Alaska 2,521 0.015 0.006 0.006 0.015 0.027 0 1.00 

E GOA/PNW 58,457 0.350 0.015 0.322 0.350 0.379 0 1.00 

BS Late season sample set (PSC = 115,286, n = 915) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 4,727 0.041 0.008 0.028 0.041 0.057 0 1.01 

NE Asia 37,076 0.322 0.020 0.283 0.322 0.362 0 1.01 

W Alaska 17,962 0.156 0.017 0.122 0.156 0.191 0 1.00 

Up/Mid Yukon 6,018 0.052 0.011 0.033 0.052 0.074 0 1.01 

SW Alaska 2,444 0.021 0.010 0.006 0.020 0.042 0 1.01 

E GOA/PNW 47,060 0.408 0.019 0.372 0.408 0.445 0 1.01 

BS area 517 sample set (PSC = 263,180, n = 2,126) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 17,001 0.065 0.006 0.053 0.065 0.077 0 1.00 

NE Asia 80,586 0.306 0.013 0.281 0.306 0.332 0 1.00 

W Alaska 55,478 0.211 0.012 0.188 0.211 0.235 0 1.00 

Up/Mid Yukon 13,422 0.051 0.007 0.037 0.051 0.066 0 1.00 

SW Alaska 3,948 0.015 0.005 0.006 0.014 0.027 0 1.00 

E GOA/PNW 92,745 0.352 0.012 0.330 0.352 0.375 0 1.00 
 

 

 

 

 

 

52 

Appendix II. -- Continued. 

BS area 517 Early season sample set (PSC = 32,564, n = 262) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 7,451 0.229 0.028 0.177 0.228 0.285 0 1.00 

NE Asia 7,529 0.231 0.034 0.167 0.230 0.300 0 1.00 

W Alaska 6,431 0.198 0.032 0.138 0.197 0.262 0 1.00 

Up/Mid Yukon 3,094 0.095 0.022 0.055 0.094 0.141 0 1.00 

SW Alaska 860 0.026 0.013 0.006 0.025 0.057 0.001 1.00 

E GOA/PNW 7,203 0.221 0.028 0.168 0.220 0.279 0 1.00 

BS area 517 Middle season sample set (PSC = 124,946, n = 1,024) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 5,298 0.042 0.007 0.029 0.042 0.058 0 1.00 

NE Asia 38,358 0.307 0.018 0.271 0.307 0.344 0 1.00 

W Alaska 33,660 0.269 0.018 0.234 0.269 0.306 0 1.00 

Up/Mid Yukon 4,098 0.033 0.011 0.013 0.033 0.055 0 1.00 

SW Alaska 1,674 0.013 0.007 0.003 0.012 0.029 0 1.00 

E GOA/PNW 41,857 0.335 0.016 0.303 0.335 0.367 0 1.00 

BS area 517 Late season sample set (PSC = 105,670, n = 840) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 4,692 0.044 0.008 0.030 0.044 0.061 0 1.01 

NE Asia 33,032 0.313 0.021 0.272 0.313 0.355 0 1.01 

W Alaska 16,971 0.161 0.018 0.127 0.160 0.197 0 1.00 

Up/Mid Yukon 5,410 0.051 0.011 0.032 0.051 0.074 0 1.01 

SW Alaska 1,849 0.018 0.009 0.004 0.016 0.039 0 1.01 

E GOA/PNW 43,716 0.414 0.020 0.375 0.414 0.453 0 1.00 

BS area 521 sample set (PSC = 44,785, n = 329) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 9,405 0.210 0.024 0.165 0.209 0.259 0 1.00 

NE Asia 15,536 0.347 0.032 0.286 0.346 0.411 0 1.00 

W Alaska 3,807 0.085 0.023 0.045 0.083 0.137 0 1.00 

Up/Mid Yukon 2,656 0.059 0.019 0.023 0.059 0.097 0.001 1.00 

SW Alaska 237 0.005 0.007 0 0.003 0.023 0.455 1.01 

E GOA/PNW 13,149 0.294 0.028 0.241 0.293 0.349 0 1.00 
 

 

 

53 

Appendix II. -- Continued. 

BS area 521 Early season sample set (PSC = 12,955, n = 102) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 5,809 0.448 0.052 0.350 0.448 0.552 0 1.00 

NE Asia 3,927 0.303 0.052 0.206 0.302 0.408 0 1.00 

W Alaska 803 0.062 0.040 0.008 0.054 0.155 0.000 1.00 

Up/Mid Yukon 479 0.037 0.029 0 0.035 0.100 0.135 1.00 

SW Alaska 40 0.003 0.007 0 0.000 0.024 0.927 1.00 

E GOA/PNW 1,897 0.146 0.038 0.079 0.144 0.229 0 1.00 

BS area 521 Middle season sample set (PSC = 31,449, n = 225) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 2,790 0.089 0.021 0.052 0.087 0.134 0 1.05 

NE Asia 11,925 0.379 0.039 0.302 0.379 0.457 0 1.01 

W Alaska 3,123 0.099 0.027 0.050 0.098 0.157 0 1.00 

Up/Mid Yukon 2,393 0.076 0.022 0.038 0.075 0.123 0 1.00 

SW Alaska 236 0.008 0.010 0.000 0.004 0.033 0.414 1.00 

E GOA/PNW 10,985 0.349 0.036 0.281 0.349 0.421 0 1.00 

BS east of 170°W sample set, areas 509, 513, 516, 517, 519 (PSC = 289,278, n = 2,332) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 20,192 0.070 0.006 0.059 0.070 0.082 0 1.00 

NE Asia 86,986 0.301 0.012 0.277 0.301 0.325 0 1.00 

W Alaska 60,719 0.210 0.012 0.187 0.210 0.233 0 1.00 

Up/Mid Yukon 15,968 0.055 0.007 0.041 0.055 0.071 0 1.00 

SW Alaska 4,252 0.015 0.005 0.006 0.014 0.026 0 1.01 

E GOA/PNW 101,132 0.350 0.011 0.328 0.350 0.371 0 1.00 

BS west of 170°W sample set, areas 521, 523, 524 (PSC = 49,816, n = 369) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 9,968 0.200 0.023 0.157 0.200 0.246 0 1.00 

NE Asia 16,982 0.341 0.031 0.281 0.341 0.401 0 1.00 

W Alaska 3,916 0.079 0.021 0.043 0.077 0.124 0 1.00 

Up/Mid Yukon 2,934 0.059 0.016 0.029 0.058 0.092 0 1.00 

SW Alaska 404 0.008 0.008 0 0.006 0.027 0.228 1.01 

E GOA/PNW 15,617 0.314 0.027 0.262 0.313 0.369 0 1.00 
 

 

 

54 

Appendix II. -- Continued. 

Cluster 1 Early sample set (PSC= 111,336, n=1,043) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 10,198 0.092 0.010 0.074 0.091 0.111 0 1.00 

NE Asia 25,585 0.230 0.017 0.198 0.230 0.263 0 1.00 

W Alaska 26,754 0.240 0.018 0.205 0.240 0.277 0 1.00 

Up/Mid Yukon 7,883 0.071 0.013 0.047 0.070 0.097 0 1.00 

SW Alaska 2,193 0.020 0.007 0.008 0.019 0.034 0 1.00 

E GOA/PNW 38,734 0.348 0.016 0.316 0.348 0.380 0 1.00 

Cluster 1 Late sample set (PSC= 88,941, n=681) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 2,055 0.023 0.007 0.012 0.023 0.038 0 1.00 

NE Asia 28,479 0.320 0.023 0.275 0.320 0.367 0 1.00 

W Alaska 21,622 0.243 0.023 0.199 0.243 0.288 0 1.00 

Up/Mid Yukon 4,136 0.047 0.014 0.023 0.045 0.076 0 1.02 

SW Alaska 1,103 0.012 0.008 0.002 0.011 0.031 0.001 1.00 

E GOA/PNW 31,556 0.355 0.020 0.316 0.355 0.395 0 1.00 

Cluster 2 Early sample set (PSC= 13,045, n=185) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 2,244 0.172 0.030 0.118 0.171 0.232 0 1.00 

NE Asia 4,246 0.326 0.045 0.240 0.325 0.416 0 1.00 

W Alaska 2,269 0.174 0.042 0.098 0.172 0.260 0 1.00 

Up/Mid Yukon 1,144 0.088 0.029 0.036 0.087 0.147 0 1.00 

SW Alaska 111 0.009 0.013 0 0.002 0.044 0.590 1.00 

E GOA/PNW 3,032 0.232 0.034 0.169 0.231 0.302 0 1.00 

Cluster 2 Late sample set (PSC= 73,346, n=535) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 4,980 0.068 0.012 0.046 0.067 0.093 0 1.00 

NE Asia 25,612 0.349 0.026 0.298 0.349 0.402 0 1.01 

W Alaska 9,784 0.133 0.020 0.096 0.133 0.174 0 1.00 

Up/Mid Yukon 2,230 0.030 0.010 0.014 0.029 0.053 0 1.03 

SW Alaska 2,340 0.032 0.012 0.012 0.031 0.059 0 1.01 

E GOA/PNW 28,400 0.387 0.024 0.341 0.387 0.435 0 1.01 
 

55 

Appendix II. -- Continued. 

Cluster 3 Early sample set (PSC= 29,591, n=320) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 7,229 0.244 0.026 0.195 0.244 0.297 0 1.00 

NE Asia 8,463 0.286 0.031 0.227 0.286 0.348 0 1.00 

W Alaska 2,110 0.071 0.022 0.033 0.070 0.118 0 1.00 

Up/Mid Yukon 1,033 0.035 0.017 0.002 0.034 0.071 0.016 1.00 

SW Alaska 346 0.012 0.008 0 0.010 0.030 0.048 1.01 

E GOA/PNW 10,413 0.352 0.030 0.295 0.352 0.411 0 1.00 

Cluster 3 Late sample set (PSC= 15,170, n=178) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 1,330 0.088 0.022 0.049 0.086 0.135 0 1.00 

NE Asia 5,159 0.340 0.043 0.258 0.339 0.427 0 1.00 

W Alaska 1,661 0.110 0.032 0.053 0.108 0.177 0 1.00 

Up/Mid Yukon 1,141 0.075 0.025 0.032 0.073 0.129 0 1.00 

SW Alaska 438 0.029 0.018 0.001 0.027 0.071 0.028 1.00 

E GOA/PNW 5,440 0.359 0.040 0.284 0.358 0.438 0 1.00 

Cluster 4 Late sample set (PSC= 6,931, n=184) 

Region Est. num. Mean SD 2.5% Median 97.5% P=0 Shrink Factor 

SE Asia 1,143 0.165 0.030 0.109 0.164 0.228 0 1.00 

NE Asia 2,134 0.308 0.045 0.223 0.307 0.399 0 1.00 

W Alaska 925 0.133 0.033 0.073 0.132 0.203 0 1.00 

Up/Mid Yukon 234 0.034 0.018 0.004 0.032 0.075 0.012 1.00 

SW Alaska 73 0.011 0.015 0 0.004 0.053 0.588 1.00 

E GOA/PNW 2,422 0.350 0.039 0.274 0.349 0.428 0 1.00 
 

 

56 

Appendix III. -- Basic overview of Bayesian mixed-stock analysis (MSA) pertinent to the 

analysis of the chum salmon prohibited species catch (PSC). 

MSA requires three components: 

1. A mixture containing genotypes of samples of unknown origin (e.g., chum salmon PSC 

samples). 

2. A baseline of allele frequencies of potentially contributing stocks in the mixture (same 

genetic markers as the mixture). The baseline is typically comprised of stock groups6, 

populations that are grouped due to genetic similarity, geographic proximity, or political 

boundaries. For the chum salmon PSC we used the 381-population, 11-locus 

microsatellite baseline from Fisheries and Oceans Canada (DFO), with populations 

grouped into six regions. 

3. A method to compare the mixture to the baseline to estimate the proportions of baseline 

populations, or more commonly stock groups, in the mixture. Two methods were used in 

our study: 

a. Maximum-likelihood method in program SPAM (Debevec et al. 2000; ADF&G 

2003). For the chum salmon PSC samples, the likelihood method typically 

estimates stock proportions similar to those produced by the Bayesian method. A 

comparison of the stock proportions produced by the two methods provides a 

quality control check on the MSA. 

b. Bayesian method in program BAYES (Pella and Masuda 2001), described below. 

MSA using the BAYES program requires several steps: 

1. Assign parameters of the prior distribution for the unknown stock proportions. Typically 

an uninformative prior with parameters equal to 1/number of stocks is used unless 

independent information is available for setting an informative prior. If stock-group 

estimates are made, then an uninformative prior for the stock-group proportions is set 

(parameters equal to 1/GCg where G is the number of groups and Cg is the number of 

baseline populations in group g). 

2. Choose the number of Markov chain Monte Carlo (MCMC) samples to simulate from the 

posterior distribution of stock proportions (depends on the data, but 50,000 to 100,000 is 

commonly used in our salmon mixed-stock applications). 

3. Run several sets of MCMC samples (at least 3 “chains”) with disparate values of initial 

mixture stock proportions such that most of the contribution comes from one stock or 

stock group. In the chum salmon PSC analyses, six chains were used, the first of which 

was started with 95% of the contribution coming from the first baseline region and 5% 

from all other regions. The other chains were similarly started. 

6

 Depending upon the context, stock groups are sometimes referred to as reporting groups or regional groups. 
57 

4. Evaluate convergence of stock proportion estimates to the posterior distribution. Two 

diagnostics implemented in the BAYES program help gauge convergence. Increase the 

number of MCMC samples until the stock estimates converge. 

a. Within chains: the Raftery and Lewis (1996) diagnostic is useful for determining 

the number of MCMC samples required to estimate quantiles of the posterior 

distribution with a specified accuracy and probability. 

b. Across chains: the Gelman and Rubin (1992) diagnostic compares the variation 

within a single chain for a given parameter (e.g., unknown stock proportion) to 

the total variation among chains and summarizes the two measures by a univariate 

statistic called the shrink factor. A shrink factor near 1 is consistent with 

convergence of the samples to the posterior distribution. A shrink factor >1.2 may 

indicate lack of convergence. 

5. Once convergence is determined, the MCMC samples of stock composition estimates are 

combined from all chains and summarized (e.g., mean, median, standard deviation, 2.5% 

and 97.5% quantiles), typically from the last half of the chains to remove the influence of 

the initial values. 
 

58 

Appendix IV. -- Four spatial clusters of ADF&G groundfish statistical areas7 of chum salmon 

PSC sampled from 2013 to 2016 during the B-season of the Bering Sea 

midwater pollock trawl fishery and analyzed for genetic stock composition. The 

areas sampled in 2016 in which at least three fishing vessels are represented are 

in bold (Fig. 16). 

Cluster 1: 625504, 625531, 625600, 625630, 635501, 635504, 635530, 635600, 635630, 645434, 

645501, 645502, 645530, 645600, 645630, 645700, 655409, 655410, 655430, 655500, 

655530, 655600, 655630, 655730, 665336, 665401, 665403, 665404, 665430, 665500, 

665530, 665600, 665630, 665700 

Cluster 2: 675430, 675500, 675530, 675600, 675630, 675700, 675730, 685500, 685530, 685600, 

685630, 685700, 685730 

Cluster 3: 695530, 695600, 695631, 705530, 705600, 705630, 705701, 705730, 715600, 715630, 

715700, 715730, 725630, 725700, 725730, 735630, 735700, 735730, 745730 

Cluster 4: 705830, 715800, 725800, 725830, 735800, 735830, 735900, 735930, 745800, 745830, 

745900, 745930, 755830, 755900, 755930, 756000, 765830, 765900, 765930, 766000, 

766030, 775900, 775930, 776000, 776030, 785930, 786000, 786030 

7 http://www.adfg.alaska.gov/index.cfm?adfg=fishingCommercialByFishery.statmaps 
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Copies of this and other NOAA Technical Memorandums are available from the 

National Technical Information Service, 5285 Port Royal Road, Springfield, VA 22167 

(web site: www.ntis.gov). Paper and electronic (.pdf) copies vary in price. 

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