UNITED STATES DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration 

NATIONAL MARINE FISHERIES SERVICE 

Alaska Fisheries Science Center 

7600 Sand Point Way N.E. 

Bldg. 4, F/AKC 

Seattle, Washington 98115-0070 

DATE: March 12, 2008 

MEMORANDUM FOR: Douglas Mecum 

Acting Alaska Regional ';_d'}YnistratoV-..J, 

FROM: t (Douglas 

Science & 

P. 

Research 

De Master 

Director, 

~ 

Alaska Region 

SUBJECT: Lynn Canal Herring ESA Petition: Transmittal of 

Biological Review Team Report 

I am pleased to submit the report of AFSC's Biological Review Team entitled, Status 

Review ofPacific herring (Clupea pallasii) in Lynn Canal, Alaska. The report 

incorporates the results of a peer review ofits contents that was conducted by seven 

independent scientific experts (three non-federal, four federal) who were selected in 

compliance with the requirements ofthe Data Quality Act and the corresponding NOAA 

Information Quality Guidelines (NOAA IQ Guidelines). 

The BRT concluded that Pacific herring in Lynn Canal are not a distinct population 

segment (DPS) as defined by the ESA. Examination of all available data by the BRT did 

not convince the majority ofmembers that herring in Lynn Canal were markedly discrete 

from other populations ofthe same taxon in southeast Alaska. In addition, no members 

perceived Lynn Canal herring to be significant with respect to the taxon, although all 

recognized the importance ofherring to the local ecosystem. A risk analysis was not 

conducted for Lynn Canal herring because the BRT did not find them to be a DPS. 

Please let me know ifthere are items in the report needing to be clarified or otherwise 

addressed, or if the Center may be offurther assistance in this matter. 

Enclosure 

cc: Kaja Brix, AKR/PRD 

Usha Varanasi, NWC/SD 
Status Review of 

Lynn Canal Herring 

(Clupea pallasii) 

Mark G. Carls 

Chairman, editor, and author 

Alaska Fisheries Science Center 

Auke Bay Laboratories 

17109 Pt. Lena Loop Rd. 

Juneau, AK 

& 

Scott W. Johnson 

Mandy R. Lindeberg 

A. Darcie Neff 

Pat M. Harris 

Contributing authors 

Alaska Fisheries Science Center 

Auke Bay Laboratories 

& 

Robin Waples 

Contributing author 

Northwest Fisheries Science Center 

2725 Montlake Blvd E. 

Seattle, WA 

& 

members of the 

Biological Review Team 

Mark G. Carls, Jeffrey T. Fujioka, Richard G. Gustafson, Scott W. Johnson 

Erika Phillips, Stanley D. Rice, Johanna Vollenweider, Robin S. Waples 

Bruce L. Wing, & Jamie N. Womble 

March 2008 

i 
Acknowledgements 

This document was prepared at the request of the Regional Office of the National Marine 

Fisheries Service. The purpose is to review the status of Lynn Canal herring and to determine if 

Lynn Canal herring are a distinct population segment of Pacific herring as defined by the 

Endangered Species Act. To accomplish this goal, the National Marine Fisheries Service 

assembled a knowledgeable biological review team: Mark G. Carls, Jeffrey T. Fujioka, Scott 

W. Johnson, Stanley D. Rice, Johanna Vollenweider, and Bruce L. Wing at the Alaska Fisheries 

Science Center; Richard G. Gustafson and Robin S. Waples at the Northwest Fisheries Science 

Center; Jamie N. Womble, National Park Service; and Erika Phillips at the Alaska Regional 

Office. We thank all team members for their contributions. The Alaska Department of Fish and 

Game (ADFG), the agency that manages Pacific herring in Alaska, provided considerable data 

and advice; important assistance was obtained from Marc Pritchett and Kevin Monagle and we 

thank them for this. Analysis of some of these data were contracted to Brian Bue, formerly at 

ADFG, and we thank him for his assistance. 

ii 
Table of Contents 

List of Tables ................................................................................................................................ iii 

List of Figures ............................................................................................................................... iii 

Chapter contents ..............................................................................................................................v 

List of Tables 

3.1. Mean growth rates in SEAK Pacific herring stocks ...........................................................3.17 

4.1. Seine hauls, fish catch, temperature, and salinity in SEAK................................................4.15 

4.2. Summary of major ShoreZone habitat classifications ........................................................4.16 

List of Figures 

2.1. Pacific herring illustration...................................................................................................2.20 

2.2 a,b. Global distribution of Pacific herring ...........................................................................2.21 

2.3. Herring stocks in the eastern north Pacific .........................................................................2.22 

2.4 a,b. Herring spawning movement, small and large scale.....................................................2.23 

2.5. Comparison of spawning fidelity rates among areas in British Columbia .........................2.25 

2.6. Offshore herring in the Gulf of Alaska ..............................................................................2.26 

3.1. Pacific herring spawning locations and management areas in SEAK ................................3.18 

3.2. Relationship between geographic area and fidelity in British Columbia ...........................3.19 

3.3. Lynn Canal management area as defined by ADFG ..........................................................3.20 

3.4. Seasonal Pacific herring biomass change in Lynn Canal ...................................................3.21 

3.5. Biomass estimates in tons for Lynn Canal herring .............................................................3.22 

3.6. Total nautical miles of herring spawn in Lynn Canal.........................................................3.23 

3.7. Relationship between biomass estimates obtained by dive survey and aerial survey ........3.24 

3.8. Estimated historical biomass of Lynn Canal herring..........................................................3.25 

3.9 a,b. Pacific herring age structure in SEAK..........................................................................3.26 

3.10. Larval herring distribution in SEAK.................................................................................3.28 

3.11. Juvenile Pacific herring distribution in SEAK..................................................................3.29 

3.12. Adult non-spawning Pacific herring distribution in SEAK ..............................................3.30 

3.13. Total herring biomass and human harvest at major spawning locations in SEAK...........3.31 

3.14. Genetic measures involving SEAK herring......................................................................3.32 

3.15. Spawn timing by location in SEAK..................................................................................3.33 

3.16. Range of spawn timing in Pacific herring aggregations along North America ................3.34 

3.17. Typical sea surface temperature gradient in SEAK in spring...........................................3.35 

3.18 a,b. Differences in recruitment in SEAK herring ..............................................................3.36 

3.19. Length-at-age data from 1929...........................................................................................3.38 

iii 
3.20. Relationship between age and body size among SEAK herring stock .............................3.39 

3.21 a,b. Differences among Pacific herring weight-at-age in SEAK .......................................3.40 

3.22. Trends in size (length) at age in SEAK Pacific herring stocks.........................................3.42 

3.23. Cohort growth in northern SEAK.....................................................................................3.43 

3.24. Vertebrae number in SEAK herring .................................................................................3.44 

3.25. Pacific herring migration in SEAK...................................................................................3.45 

4.1. Ten study areas for herring in SEAK..................................................................................4.17 

4.2. Locations of beach seine sites sampled for herring in SEAK.............................................4.18 

4.3. Berners Bay: ShoreZone coastal habitat maps...................................................................4.19 

4.4. Shoreline kilometers of herring spawn in Lynn Canal .......................................................4.20 

4.5. Berners Bay: ADFG records of herring spawn..................................................................4.21 

4.6. Location and habitat type of beach seine sites in Berners Bay...........................................4.22 

4.7. Favorite Channel: ShoreZone coastal habitat maps...........................................................4.23 

4.8. Favorite Channel: ADFG records of herring spawn..........................................................4.24 

4.9. Location and habitat type of beach seine sites in Favorite Channel...................................4.25 

4.10. Auke Bay: ShoreZone coastal habitat maps.....................................................................4.26 

4.11. Auke Bay: ADFG records of herring spawn....................................................................4.27 

4.12. Location and habitat type of beach seine sites in Auke Bay.............................................4.28 

4.13. Tenakee Inlet: ShoreZone coastal habitat maps...............................................................4.29 

4.14. Tenakee Inlet: ADFG records of herring spawn..............................................................4.30 

4.15. Location and habitat type of beach seine sites in Tenakee Inlet.......................................4.31 

4.16. Northern Sitka Sound: ShoreZone coastal habitat maps..................................................4.32 

4.17. Northern Sitka Sound: ADFG records of herring spawn.................................................4.33 

4.18. Location and habitat type of beach seine sites in Northern Sitka Sound..........................4.34 

4.19. Central Sitka Sound: ShoreZone coastal habitat maps ....................................................4.35 

4.20. Central Sitka Sound: ADFG records of herring spawn ...................................................4.36 

4.21. Location and habitat type of beach seine sites in Central Sitka Sound ............................4.37 

4.22. Southern Sitka Sound: ADFG records of herring spawn.................................................4.38 

4.23. Location and habitat type of beach seine sites in Southern Sitka Sound..........................4.39 

4.24. Craig: ShoreZone coastal habitat map .............................................................................4.40 

4.25. Craig: ADFG records of herring spawn...........................................................................4.41 

4.26. Location and habitat type of beach seine sites in Craig....................................................4.42 

4.27. Duke Island: ShoreZone coastal habitat maps .................................................................4.43 

4.28. Duke Island: ADFG records of herring spawn ................................................................4.44 

4.29. Location and habitat type of beach seine sites in Duke Island .........................................4.45 

4.30. Kah Shakes: ShoreZone coastal habitat maps..................................................................4.46 

4.31. Kah Shakes: ADFG records of herring spawn.................................................................4.47 

4.32. Location and habitat type of beach seine sites in Kah Shakes..........................................4.48 

4.33. General global sea surface temperature distribution.........................................................4.49 

4.34. Sea surface temperature in SEAK.....................................................................................4.50 

4.35. ShoreZone bioareas for SEAK..........................................................................................4.51 

4.36. Alaska marine ecoregions.................................................................................................4.52 

5.1. Summary of biological information......................................................................................5.1 

iv 
Chapter 1. Executive summary ..................................................................................................1.1 

Introduction..............................................................................................................................1.1 

Deliberation..............................................................................................................................1.2 

Conclusion ...............................................................................................................................1.2 

Reference .................................................................................................................................1.3 

Chapter 2. Pacific herring life history and ecology .....................................................................2.1 

Distribution ..............................................................................................................................2.1 

 Habitat requirements................................................................................................................2.1 

Trophic interactions .................................................................................................................2.2 

Reproduction............................................................................................................................2.2 

Mortality and survival..............................................................................................................2.3 

 Diurnal movements..................................................................................................................2.6 

 Migratory movements..............................................................................................................2.7 

 Factors limiting productivity....................................................................................................2.8 

Genetics....................................................................................................................................2.8 

 Stocks, populations, metapopulation .......................................................................................2.9 

References..............................................................................................................................2.11 

Figures....................................................................................................................................2.20 

Chapter 3. Description of Pacific herring in Lynn Canal and southeastern Alaska ....................3.1 

Abstract....................................................................................................................................3.1 

Introduction .............................................................................................................................3.1 

Lynn Canal herring ..................................................................................................................3.2 

 Pacific herring biomass in Lynn Canal...............................................................................3.3 

 Age structure, age structured models, and estimation of recruitment.................................3.4 

Estimate discrepencies........................................................................................................3.4 

 SEAK herring...........................................................................................................................3.4 

Distribution .........................................................................................................................3.4 

Age structure.......................................................................................................................3.5 

Genetics...............................................................................................................................3.6 

 Spawn timing ......................................................................................................................3.6 

Biomass...............................................................................................................................3.7 

 Recruitment.........................................................................................................................3.7 

Size-at-age and growth rate ................................................................................................3.8 

 Morphological or meristic variability .................................................................................3.9 

Migration...........................................................................................................................3.10 

Metapopulation .................................................................................................................3.11 

 Summary................................................................................................................................3.11 

References..............................................................................................................................3.12 

Table ......................................................................................................................................3.17 

Figures....................................................................................................................................3.18 

Chapter 4. Pacific herring habitat in southeastern Alaska ...........................................................4.1 

Abstract....................................................................................................................................4.1 

Introduction .............................................................................................................................4.1 

v 
 Pacific herring habitat utilization in SEAK .............................................................................4.1 

 Comparisons among study areas..............................................................................................4.2 

Lynn Canal...............................................................................................................................4.2 

Berners Bay.........................................................................................................................4.2 

Favorite Channel.................................................................................................................4.3 

Auke Bay ............................................................................................................................4.4 

Tenakee Inlet............................................................................................................................4.5 

Sitka .........................................................................................................................................4.6 

Northern Sitka Sound..........................................................................................................4.6 

Central Sitka Sound ............................................................................................................4.6 

Southern Sitka Sound..........................................................................................................4.7 

Craig.........................................................................................................................................4.7 

Duke Island ..............................................................................................................................4.8 

Kah Shakes Cove .....................................................................................................................4.8 

 Sea surface temperature and climate........................................................................................4.9 

Marine zoogeographic provinces.............................................................................................4.9 

 Summary................................................................................................................................4.10 

References..............................................................................................................................4.12 

Tables.....................................................................................................................................4.15 

Figures....................................................................................................................................4.17 

Chapter 5. Are Lynn Canal herring a discrete population segment? ...........................................5.1 

Abstract....................................................................................................................................5.1 

Introduction .............................................................................................................................5.1 

Endangered Species Act .....................................................................................................5.1 

Evaluation of discreteness...................................................................................................5.2 

Evaluation of significance...................................................................................................5.2 

DPS decision by the BRT ........................................................................................................5.2 

Are Lynn Canal herring discrete? ............................................................................................5.3 

Evidence against discreteness.............................................................................................5.3 

Evidence for discreteness....................................................................................................5.5 

Are SEAK herring discrete? ....................................................................................................5.6 

Evidence for SEAK discreteness ........................................................................................5.6 

 Are SEAK herring significant with respect to the taxon?........................................................5.7 

References................................................................................................................................5.8 

Figure .....................................................................................................................................5.10 

Appendix A, Summary of Pacific herring genetic studies...........................................................A.1 

Appendix B, Analysis of ADFG age-length-weight data ............................................................B.1 

vi
 

Chapter 1 

Executive Summary 

Mark G. Carls 

Introduction 

On April 2, 2007 the National Marine Fisheries Service (NMFS) received a petition from 

the Sierra Club to list Pacific herring (Clupea pallasii) in Lynn Canal as endangered or 

threatened under the Endangered Species Act (ESA). The agency found that the petition 

presented substantial scientific and commercial information indicating the petitioned action may 

be warranted and initiated a status review (NMFS 2007). 

The purpose of this document was to review the status of Lynn Canal herring and 

specifically to determine if Lynn Canal herring are a Distinct Population Segment (DPS) of 

Pacific herring as defined by the ESA. To accomplish this goal, NMFS assembled a 

knowledgeable biological review team (BRT): Mark G. Carls, Jeffrey T. Fujioka, Scott W. 

Johnson, Stanley D. Rice, Johanna Vollenweider, and Bruce L. Wing, at the Alaska Fisheries 

Science Center; Richard G. Gustafson and Robin S. Waples at the Northwest Fisheries Science 

Center; Jamie N. Womble, National Park Service; and Erika Phillips at the Alaska Regional 

Office. The Alaska Department of Fish and Game (ADFG), the agency that manages Pacific 

herring in Alaska, provided considerable data and advice; important assistance was obtained 

from Marc Pritchett and Kevin Monagle. Analysis of some of these data were contracted to 

Brian Bue, formerly at ADFG. Additional data were obtained from various sources, generally 

associated with scientific papers or reports. 

After compiling and analyzing pertinent data, the BRT met on January 29, 2008 to 

discuss them and to determine if Lynn Canal herring are a DPS as defined by the ESA or if not, 

to determine the DPS to which Lynn Canal herring belong. In order to be classified as a DPS, a 

vertebrate population must fulfill two criteria – discreteness and significance. To be considered 

“distinct,” a population, or group of populations, must first be “discrete” from other populations 

and then “significant” to the entire taxon (species or subspecies) to which it belongs. Evaluation 

was based on criteria in the ESA; a population segment of a vertebrate species may be 

considered discrete if it is markedly separated from other populations of the same taxon as a 

consequence of physical, physiological, ecological, or behavioral factors. Quantitative measures 

of genetic or morphological discontinuity may also provide evidence of this separation. A 

population may also be considered discrete if it is delimited by international governmental 

boundaries, between which exist differences in control of exploitation, management of habitat, 

conservation status, or regulatory mechanisms that are significant in light of Section 4(a)(1)(D) 

of the ESA. 

Under the ESA, once a population segment is determined to be discrete under one or 

more of the above conditions, its biological and ecological significance to the taxon must then be 

considered. Criteria that can be used to assess whether the discrete population segment is 

significant include: 1) persistence of the discrete population segment in an ecological setting 

unusual or unique for the taxon; 2) evidence that loss of the discrete population segment would 

result in a significant gap in the range of a taxon; 3) evidence that the discrete population 

segment represents the only surviving natural occurrence of a taxon that may be more abundant 

elsewhere as an introduced population outside its historic range; or, 4) evidence that the discrete 

population segment differs markedly from other populations of the species in its genetic 

1.1 
characteristics. A discrete population segment needs to satisfy only one of these criteria to be 

considered significant. However, the list of criteria is not exhaustive; other criteria may be used 

as deemed appropriate. The ESA and NMFS do not provide any guidance on what these 

additional criteria might be. 

Deliberation 

To examine the possibility that Lynn Canal herring are discrete, the BRT first briefly 

reviewed southeastern Alaska (SEAK) habitat, climate, and utilization by Pacific herring, thus 

allowing discussion of Lynn Canal herring in context. 

Marine habitat in SEAK is variable, yet Pacific herring essentially occupy all of it. 

Organics and semi-protected, partially mobile substrate are the most common shore type and 

habitat class among all areas. Marine waters of SEAK are characterized by an inshore-offshore 

salinity gradient and a north-south temperature gradient. Inside waters are more estuarine, more 

protected from wave action, and have more extreme seasonal fluctuations in temperature and 

salinity than outside waters. Herring were captured in essentially all areas of SEAK; occasional 

capture failures were interpreted as insufficient sampling, not an absence of herring. Eelgrass 

meadows, kelp communities, sand-gravel beaches, and bedrock outcrops comprise a continuum 

of habitat types available to herring throughout southeastern Alaska. The percent shoreline extent 

of kelps (canopy and understory) and eelgrass are less in Lynn Canal than in all other areas but 

herring continue to spawn in Berners Bay and juveniles continue to utilize nearshore habitats in 

Auke Bay, Favorite Channel, and Berners Bay. 

Beaches Pacific herring spawn on are not continuous in SEAK; some are repeatedly 

utilized, thus ADFG eventually began to manage herring in these areas as discrete stocks. 

However, available biological data, including genetics, spawn timing, biomass, recruitment, 

growth, meristics, and migration do not identify definitive divisions among SEAK stocks, rather 

apparent geographic groupings were variable and often rather arbitrary. Limited tagging studies 

within SEAK demonstrate fish migrate and mix over most of the region but were not designed to 

study spawning fidelity. Migration data from British Columbia, a region to the south of SEAK 

and reasonably similar in structure and climate, were used to roughly predict repeat spawning 

fidelity of herring stocks in SEAK; these approximations suggest considerable mixing among 

stocks (about 60 to 80%), possibly explaining the lack of definitive differences among stocks and 

suggesting that SEAK herring are part of an interrelated metapopulation. Clearly more work 

remains to understand the relationships among SEAK herring stocks, such as more detailed 

genetic analysis and more detailed, spawn-oriented and seasonal tagging studies. 

Conclusion 

The BRT concluded that Pacific herring in Lynn Canal are not a DPS as defined by the 

ESA. Examination of all available data by the BRT did not convince the majority of members 

that herring in Lynn Canal were markedly discrete from other populations of the same taxon in 

SEAK (the vote was 6 to 4). In addition, no members perceived Lynn Canal herring to be 

significant with respect to the taxon (although all recognized the importance of herring to the 

local ecosystem), thus even if the team had concluded that Lynn Canal herring were discrete the 

ESA significance criterion precludes its definition as a distinct population segment. A risk 

analysis was not completed for these fish because the BRT did not find that Lynn Canal herring 

are a DPS 

1.2 
The team concluded the smallest defensible DPS that includes Lynn Canal is SEAK. 

Although the team recognized the possibility that there may be subdivisions within SEAK, 

available biological data are either too incomplete or too similar to definitively separate herring 

populations within this region. The southern limit of the DPS, Dixon Entrance, is identified by 

genetic differences between herring in SEAK and those in British Columbia and by differences 

in parasitism between herring stocks north and south of the Queen Charlotte Islands. Genetics 

did not provide a definitive northern separator, rather the northern border is defined by a physical 

barrier: mobile, open ocean beaches are inadequate as spawning and rearing habitat. The 

northern boundary is near Icy Point. Glacier Bay and Lynn Canal are both included in the SEAK 

Pacific herring DPS. 

The BRT based its decision on the best available science, yet recognizes that the science 

behind these decisions is imperfect. They also recognize that precautionary management of 

animals and ecosystems is a wise approach that goes beyond the language of the ESA. 

Precautionary management is the current stance of ADFG, the agency responsible for Pacific 

herring in Lynn Canal; the fishery has not been open since 1982. The information assembled in 

this report will further enable ADFG to appropriately manage this stock and it will enable 

Federal agencies responsible for the permitting of shoreline development to manage Lynn Canal 

herring in a precautionary manner. 

Reference 

NMFS 2007. Endangered and threatened species; notice of finding on a petition to list the Lynn 

Canal stock of Pacific herring as a threatened or endangered species. Fed Regist 72(174): 

51619-51621. 

1.3 
 

Chapter 2 

Pacific herring (Clupea pallasii) life history and ecology 

Mark G. Carls 

Pacific herring (Clupea pallasii): body elongate, depth about 4.5 into standard length, 

considerably and variably compressed. Head compressed about 4.0 to 4.5 into standard length. 

Mouth terminal, moderate in size, and directed moderately upward, upper jaw extending to around 

middle of eye. Teeth, none on jaws, a patch of fine teeth on volmer. Interorbital space slightly 

rounded, about 1.3 into eye. Eye diameter about equal to snout and about 3. 5 to 4.0 into length of 

head. Opercles smooth (Hart 1973). 

Pacific herring are one of about 330 species of fish classified within the family Clupeidae 

(Whitehead 1985). Pacific and Atlantic herring are the northernmost clupeids and the only ones 

in Arctic waters (Hay et al. 2001). They are dark bluish green to olive on the dorsal surface and 

fade to silver on the sides and belly (Fig. 2.1). Adult herring total length ranges from 13 to 46 cm 

and increases with latitude (Hart 1973; Garrison and Miller 1982; Emmett et al. 1991; 

Mecklenburg et al. 2002). For example, herring are rarely >25 cm in British Columbia; lengths 

>30 cm are common in Togiak (Hart 1973; Brazil 2007). Maximum age also increases with 

latitude. Until recently, Pacific, Atlantic, and Baltic herring were considered separate subspecies 

instead of species (Clupea harengus harengus, C. h. pallasii, and C. h. membras, respectively) 

(Hay et al. 2001; Mecklenburg et al. 2002). 

Distribution 

The species ranges from northern Baja California to the Arctic (Beaufort Sea) in the 

eastern Pacific (Mecklenburg et al. 2002) (Fig. 2.2). Pacific herring on the Asian coast range 

from Korea to the estuary of the Lena River in the Arctic Ocean (Laptev Sea) (Hart 1973). 

However, Pacific herring apparently mix with Atlantic herring as far west as the Barents sea, 

where two genetically different groups have been described (Jorstad 2004). Pacific herring 

populations in the Barents Sea, White Sea, and Kara Sea are apparently relics from an earlier 

dispersion of Pacific herring into the Atlantic associated with Pleistocene glaciation and are 

considered subspecies of C. pallasii (McQuinn 1997). Herring likely originated in the Atlantic 

Ocean and moved through the Bering Strait into the Pacific during the Pliocene (about 3 million 

years ago) (Novikov et al. 2001). In the postglacial period about 5000 y ago, Pacific herring 

dispersed and were distributed along the estuaries of the northern ocean, reaching the White Sea 

and some northern Norwegian fjords (Derjugin 1929; Jorstad et al. 1984; Novikov et al. 2001). 

Habitat requirements 

The habitat requirements of Pacific herring are diverse. For example, three different life 

history forms of Pacific herring are recognized in the northwestern Pacific: 1) a long-lived, 

migratory sea form; 2) a coastal form that undergoes little or no migration; and 3) a lagoon 

Pacific herring that is associated throughout its life with low salinity estuarine areas (Hay et al. 

2001). Some Baltic herring also inhabit low salinity areas (<5 ppt) (Hay et al. 2001). Resident 

and migratory forms are thought to inhabit British Columbia and Washington (Taylor 1964; 

Trumble 1983; Hay 1985). Habitat requirements vary considerably with life stage and 

seasonally within life stage as should become clear in the ensuing text. Also clear is their 

adaptability; eggs for example, are not preferentially spawned on a single type of substrate, 

2.1 
rather whatever substrate is available at selected spawning sites is acceptable to these fish. How 

herring choose their repeatedly utilized spawning sites is a long-standing, unresolved puzzle. 

Trophic interactions 

Pacific herring are relatively small, schooling, abundant, mobile planktivores (forage 

fish) that provide a key link between lower trophic levels (typically crustaceans and small fish) 

and higher tropic levels [whales, sea lions, birds, and other fish; (Hart 1973; Hourston and 

Haegele 1980; Bakun 2006)]. Their position between first- or second-order consumers and 

larger predators essentially guarantees that the herring population is responsive to seasonal, 

oceanographic, and climate-driven changes in producer (phytoplankton) and predator 

populations and distributions. Intra- and interspecific competition are also important factors with 

an important nuance: herring may prey on early life stages of their predators, leading to trophic 

instability and possible abrupt regime shifts (Bakun 2006). Thus, the balancing act between 

trophic worlds explains in part why this relatively short-lived fish (about 20 y maximum) 

generally survives no more than 9 y (Ware 1985; Hay et al. 2001) and why population 

abundance is highly variable. However, survival during earlier life stages may be an even more 

important influence on population size; strongly recruiting year classes typically influence 

population size and age structure until senescence. Early life stages are particularly vulnerable to 

physical variability, resulting in high inter-annual variability and reproductive success (Bakun 

2006). 

Reproduction 

From the human perspective, spawning is arguably the crucial event in the herring life 

cycle, for this is when the reproductive biomass concentrates in predictable, distinct regions at 

predictable times (Hay and Outram 1981) and is most easily enumerated. Spring spawning 

herring also represent a rich source of food for at least 25 vertebrate predators just emerging 

from winter (Willson and Womble 2006). Some species may consume only eggs, others both 

eggs and fish, and some consume adult fish only. Pacific herring are gonochoristic, oviparous, 

and iteroparous with external fertilization and spawn once a year (Emmett et al. 1991; Hay et al. 

2001). Fecundity increases with female size, producing on average 19,000 eggs annually at 19 

cm standard length and 29,500 at 22 cm (Hart 1973). Unfertilized Pacific herring eggs are about 

1.0 mm in diameter; fertilized eggs are 1.2-1.5 mm in diameter (Outram 1955; Hart 1973; 

Hourston and Haegele 1980). 

Adult herring typically congregate near spawning grounds weeks or months in advance of 

spawning and leave immediately thereafter, though some herring remain in inside waters near 

spawning grounds throughout the year (Haegele and Schweigert 1985). Ripe and spent herring 

can travel considerable distances in a short period of time [150 km in 6 d and 350 km in 16 d, 

respectively (Haegele and Schweigert 1985)]. 

Spawning areas (inlets, sounds, bays, and estuaries) are typically protected from ocean 

surf, probably an adaptation to minimize egg loss (Haegele and Schweigert 1985). No spawning 

has been reported in the relatively unsheltered Gulf of Alaska shoreline between northern 

southeastern Alaska and Yakutat or between Yakutat and Prince William Sound (Fig. 2.3). 

Herring typically spawn along the same shoreline each year although areas spawned can shift at 

various scales (e.g., small scale movement in Berners Bay or larger scale movement among Kah 

Shakes, Cat Island, and Annette Island in southeastern Alaska (SEAK) in the 1990s; Fig 2.4). 

Also variable are the volume of eggs deposited and shoreline spawn distances, easily visible 

2.2 
because the milt turns water milky white. For example, cumulative miles of spawn in Seymour 

Canal ranged from about 14 to 31 km between 1985 and 1989 (Bergmann et al. 1993). 

Herring apparently do not favor specific vegetation types, rather the type of vegetation 

utilized is a function of spawn depth and the type of vegetation found in a given area (Haegele 

and Schweigert 1985). Adherent eggs are deposited on eelgrass, kelp, rockweed, other seaweed 

and sometimes rock, pilings, or trash (Hart 1973). Soft sediment is avoided (Stacey and 

Hourston 1982; Lassuy 1989). Herring in Lynn Canal spawn more heavily on large brown kelps 

(e.g., Laminaria, Alaria) than on eelgrass (Zostera marina) (Blankenbeckler and Larson 1987). 

Deposition depth ranges from high tide to subtidal; in Prince William Sound, 90% of the eggs 

are deposited between -2 and +5 m mean lower low water (Brown and Carls 1998). However, 

<25% of the spawn typically becomes exposed to air by tidal movement (in British Columbia) 

and this for only about 10% of the total incubation time (Haegele et al. 1981). 

Spawn timing is related to winter and spring sea surface temperatures (Brown and Carls 

1998) and varies according to latitude; it begins in November in the southern part of the range 

(California) and extends to August in the north (Kotzebue Sound, Alaska) (Lassuy 1989; Emmett 

et al. 1991). Spawning temperature ranges from 3.0°C to 12.3°C on the Pacific coast of North 

America (Scattergood et al. 1959). However, other factors may also influence spawn timing, 

such as tides (Hay 1990; Hay et al. 2001). Spawning typically occurs within a 3 to 6 week 

period within a given geographical area (Haegele and Schweigert 1985). Both males and 

females contact the substrate during spawning (Haegele and Schweigert 1985). Single spawning 

events are generally completed within 1 to 3 d (Hay 1985). Two or more spawning events are 

common at a given location; larger fish spawn before smaller, presumably younger fish, and 

these spawning events may be separated by 10 to 15 d (Hay 1985). Eggs hatch in 11 to 12 d at 

10.7o C, 14 d at 8.5o C and 28 to 40 d at 4.4o C (Outram 1955). The optimal incubation 

temperature is roughly 5 to 9oC (Alderdice and Velsen 1971; Ojaveer 2006). 

Herring eggs are euryhaline; the optimal salinity range for fertilization is about 12 to 24 

ppt; sperm motility is reduced at low and high salinities [4 to 8 ppt and 28 to 32 ppt, respectively 

(Griffin et al. 1998)]. Maximum embryo survival was reported at 13 to 19 ppt and a spawning 

range of 8 to 28 ppt is typical (Alderdice and Velsen 1971). However at 32 ± 1 ppt, we routinely 

observed good fertility (80 to 96%), successful hatch (generally about 80%) and viable larvae 

(>95%) in herring from SEAK and Prince William Sound (Johnson et al. 1997). 

Mortality and survival 

Herring eggs must survive both ‘top down’ and ‘bottom up’ predation. Egg mortality is 

high (about 75%, range 67 to 100%) and tends to be greatest in upper intertidal areas and lowest 

at intermediate depths (Palsson 1984; Rooper et al. 1999). The amount of time eggs are exposed 

to air may be related to susceptibility to wave action and predation by birds and hypoxia, 

desiccation, and air-water temperature differentials: exposure to ultraviolet light may also 

increase risk factors for eggs in the upper intertidal (Alderdice and Velsen 1971; Hunter et al. 

1979; Alderdice and Hourston 1985; Rooper et al. 1999). Crabs, sea anemones, sea cucumbers, 

and snails consume significant amounts of herring eggs (Haegele 1993). Perhaps lower survival 

at the lowest spawn depths (compared to the optimal intermediate depths) can be explained by 

greater access time by water-oriented predators because immersion time is longer and possibly 

because lower incubation temperatures prolong that access. In addition, low oxygen and 

microorganism invasions may kill large numbers of eggs; eggs in the middle of multiple layers 

2.3 
 

have reduced survival (Alderdice and Hourston 1985; Hay 1985). Surviving herring eggs hatch 

as larvae and are advected from natal areas by water movement. 

Newly hatched larvae carry a yolk sac that is typically depleted in the first week and to 

survive they must begin feeding before depletion of endogenous energy stores and irreversible 

starvation. At 6 to 10oC, irreversible starvation occurs about 1 week after yolk resorption 

(McGurk 1984). The earliest larval stages begin feeding on invertebrate eggs and small 

zooplankton such as copepods, invertebrate eggs, and diatoms (Hart 1973). While the larval 

Pacific herring grow and congregate nearshore (generally in water <5 m deep) through their first 

summer, they continue to live mainly on copepods but may also eat other crustaceans, barnacle 

larvae, mollusk larvae or young fishes (Hart 1973; Brown and Carls 1998). 

Larval mortality is caused by advection, predation, limited food availability, and other 

factors (McGurk 1993; McGurk et al. 1993; Norcross and Frandsen 1996). Loss of planktonic 

stages caused by diffusive and advective processes may explain large variations in population 

abundance; geographic patterns may be partially maintained in areas that limit egg and larval 

advection (Sanvicente-Anorve et al. 2006). A broad range of invertebrates and fish prey upon 

larvae by filtration, entrapment (e.g., ctenophores and jellyfish), or targeted feeding (Hart 1973; 

Alderdice and Hourston 1985). Suitable food must be located before irreversible starvation 

occurs if larvae are to survive. This observation forms the basis of the critical period hypothesis 

(Hjort 1914), that larval survival is the prime determinant of year-class strength, dependent on 

larval transition from endogenous to exogenous food. Low growth rates result in a longer 

exposure time for mortality through predation or transport out of favorable oceanographic 

regions (Cushing 1990; Leggett and DeBlois 1994). A longer larval period could result in poor 

condition for juvenile herring that must prepare for winter (Paul et al. 1998; Foy and Paul 1999; 

Norcross et al. 2001). Transport offshore can lead to increased mortality from lack of food, 

salinity intolerance, or increased predation pressure (Stevenson 1962; Alderdice and Hourston 

1985; Schweigert et al. 1985; McGurk 1989; Wespestad and Moksness 1990). The larval stage 

may be the determinant of year class strength (Norcross et al. 2007). 

When herring larvae become nektonic, they are able to swim to favorable habitats rather 

than follow currents (Gallego and Heath 1994). Metamorphosis to juveniles begins when larvae 

reach approximately 26 mm total length (about 10 weeks in Prince William Sound) and is 

complete by about 35 mm (Hourston and Haegele 1980; Hay 1985; Brown and Carls 1998; 

Stokesbury et al. 2002). Juveniles form and maintain schools as their primary defense against 

predation (Blaxter and Hunter 1982; Pitcher 1986) and spend the first two three years of their 

lives in nearshore waters (Tanasichuk et al. 1993; Hay et al. 2001). They occupy a variety of 

nearshore habitat types including steep bedrock outcrops, eelgrass, kelps, and sand-gravel 

beaches (Johnson and Thedinga 2005). Copepods remain an important food for juvenile herring. 

From August to October, age 0 juvenile herring survival depends on food availability, 

competition, predation, and disease (Stokesbury et al. 2002). Schooling is a mechanism that 

helps minimize the risks of the first three. During winter, as temperature and light decrease, food 

supply becomes limited and both young and adult year classes stop feeding functionally (Blaxter 

and Holiday 1963; Hay et al. 1988; Huse and Ona 1996; Paul et al. 1998). 

To survive, juveniles must escape predation and accumulate sufficient energy for winter 

starvation. Predation is the greatest source of mortality for age 0 juvenile herring from the time 

of metamorphosis through fall (Stokesbury et al. 2000; Stokesbury et al. 2002). Sufficient 

energy storage to maintain age 0 and age 1 juveniles over winter is critical to juvenile herring 

survival in Prince William Sound and likely throughout northern waters. Food availability 

2.4 
declines in winter [the highest percentage of empty stomachs is in December (Norcross et al. 

2001) and fish in cold regions often fast or reduce feeding (Blaxter and Holiday 1963; Hay et al. 

1988; Paul et al. 1998)]. Consequently, whole body energy content drops over winter; YOY 

juveniles either consume relatively less energy than adults during this period or only those with 

the highest energy content in the fall survive (Paul et al. 1998). Juveniles begin recruiting to the 

adult population at about age 3 in the Gulf of Alaska (age 4 in the Bering Sea) (Williams and 

Quinn 2000; Hay et al. 2001). Age of first maturity increases with latitude, as early as 2 y in 

California, and as late as 8 y in the Bering Sea (Spratt 1981; Brazil 2007). 

Apparent natural mortality is lower at the onset of adulthood than in juvenile and 

senescent adults, thus the overall mortality function is U-shaped (Vetter 1988; Hampton 2000; 

Tanasichuk 2000). The relationship between size and predation may in part explain declining 

natural mortality rates as herring approach adulthood. Increased body size may be a survival 

strategy to avoid predation (Houde 1997; Pedersen 1997) and larger-bodied juvenile herring are 

more likely to have sufficient energy reserves to survive winter starvation periods (Foy and Paul 

1999; Stokesbury et al. 1999; Metcalfe and Monaghan 2003). Schooling is another survival 

strategy, common both to juveniles and adults. It is apparently an anti-predator tactic that 

increases survival odds for individual fish and schooling may have a sentry effect by increasing 

awareness of predators (Blaxter 1985). Schooling may increase feeding effectiveness and have 

hydrodynamic, migration, reproduction, and learning advantages (Freon et al. 2005). Survival of 

adult herring is dependent on both intrinsic and extrinsic factors; these are related because 

populations adapt to extrinsic pressures (Reznick et al. 2002; Reznick et al. 2006). 

Intrinsic factors that may influence adult fish survival include growth rate, body size, 

genetics, reproductive effort, and senescence. Growth rate and longevity are influenced by water 

temperature (Terzibasi et al. 2007). Pacific herring are relatively small [about 70 g at maturation 

(≥3 y) and 200 g maximum in the oldest age classes]; growth becomes asymptotic at roughly 10 

y (Tanasichuk 2000). The total herring lifespan is fairly short (6 or 7 y in extreme southern 

populations to 20 y or more in northern populations), consistent with the typical relationship 

between life span and body size among all species (Roff 1992; Hay et al. 2001; Metcalfe and 

Monaghan 2003). Genetic heritage determines how fast fish grow, how they utilize and store 

energy, their innate behavior, reproduction, and lifespan, and thus is arguably the central intrinsic 

factor. Reproductive stress and age-related reduction in metabolic efficiency might destabilize 

homeostasis and predispose adult herring to death (Woodhead 1979; Tanasichuk 2000). In 

particular, Tanasichuk (2000) demonstrates that increasing proportions of surplus energy in 

Pacific herring are allocated to gonads and argues that this demonstrates progressively greater 

reproductive strain in aging fish. However, because the rate of somatic growth becomes 

asymptotic, allocation of proportionally more energy to reproduction might simply mean that 

proportionately less energy is required for growth, leaving relatively more for reproduction 

without necessarily causing life-threatening physiological stress. Senescence, representing a 

combination of genetic heritage, accumulating physiological defects, and possibly growth 

history, ultimately limits individual lifespans. In fish species with gradual senescence (such as 

herring), age-dependent organ and cellular degeneration occur, including loss of muscle fiber and 

endocrine abnormalities (Patnaik et al. 1994; Terzibasi et al. 2007), probably a result of the 

progressive failure of physiological repair mechanisms to repair damage and maintain 

homeostatis (Valdesalicil and Cellerino 2003). These factors explain increased mortality rates as 

mature fish age. 

2.5 
Extrinsic (habitat) factors responsible for adult herring mortality include predation, 

starvation, disease, inter-specific competition, and contaminants. These in turn are influenced by 

ocean conditions, climate change, and intricate ecological relationships involving predators, 

prey, and intra- and inter-specific competition. This leads to a complex question: can the 

relative importance of each source of natural mortality be determined? The solution is not easy 

and may be impossible; natural mortality is one of the most difficult parameters to assess in fish 

populations (Vetter 1988; Tanasichuk 2000; Hewitt and Hoenig 2005). Most dead fish disappear 

without a trace. Instead of biologically based estimates of natural mortality, stock assessment 

models depend on modeled parameters or other estimates (Tanasichuk 2000; Cotter et al. 2004). 

Diurnal movements 

Diurnal movement in herring presumably evolved to maintain maximal access to prey, 

avoid predators, and conserve energy by digesting at colder temperatures. Adult herring schools 

remain near the seabed during daylight hours and move to the surface at dusk (Blaxter and 

Holiday 1963; Blaxter 1985; Hay et al. 2001). Feeding activity increases as the fish near the 

surface; as light levels decrease, visual attraction among school members relaxes and the fish 

disperse (Blaxter 1985). Small, less cohesive schools are best for optimum foraging (Blaxter and 

Hunter 1982). Herring can apparently switch to filter feeding during the night if particle sizes 

are suitable (Blaxter 1985). Many invertebrate prey follow a diel cycle and are most 

concentrated near the surface at night, suggesting this is an opportune place and time for herring 

to feed. Peak feeding is at dawn and dusk and herring actively feed on the way up and down in 

the water column, giving them access to a wide variety of foods and currents (Zusser 1958). 

The swim bladder (or gas or air bladder) may play a role in herring buoyancy and be 

advantageous for diel movement. Herring, as are all clupeids, physostomous; the swim bladder 

has both stomach and anal ducts. Herring cannot excrete gas, rather they acquire it at the surface 

by swallowing air (Brawn 1962; Blaxter and Batty 1984; Thorne and Thomas 1990). This gas 

may persist for weeks or months, depending on the pressure regime (Blaxter and Batty 1984). 

Some researchers indicate swim bladders are rarely filled to volumes sufficient for neutral 

buoyancy, even at the surface (Blaxter and Batty 1984). Others conclude that herring can adjust 

their density through changes in swim bladder volume and that the swim bladder acts as a 

hydrostatic organ at least in fish near the surface (Brawn 1962). In theory, sufficient intake of 

surface air is unlikely to yield neutral buoyancy at depth, rather herring may adjust to an 

intermediate depth, thus minimizing energy expenditure by compensatory movement (Brawn 

1962). Under this scenario, herring would expend energy to reach the intermediate depth [about 

60 m (Thorne and Thomas 1990)] and they would expend energy at greater depths to offset 

gravity. Herring release some gas as they ascend but most gas is released after reaching the 

depth where they remain throughout the night suggesting adjustment to reach neutral buoyancy 

(Thorne and Thomas 1990). Intriguingly, a recent study suggests that Pacific herring produce 

rapid sound bursts associated with anal bubble expulsion (either from the gut or swim bladder) 

and that these sounds may have a social function (Wilson et al. 2004). In any case, the variable 

air volume in herring swim bladders means acoustic reflectivity varies, thus influencing 

population assessment by hydroacoustic measurement, thus careful compensation for varying 

target strength is required. 

2.6 
 

Migratory movements 

Most adult herring tend to migrate between summer feeding areas on shelf waters to 

overwintering areas, often in protected nearshore water, and then to spawning locations (Hay et 

al. 2001). Juvenile herring remain isolated in bays through their first two winters in northern 

areas such as Prince William Sound and do not begin migratory behavior until they recruit to the 

adult population (Stokesbury et al. 2000). [First year juveniles (age 0+) school together and do 

not associate with larger juveniles (age 1+)]. Adult herring form small dynamic feeding schools 

in summer that move extensively to utilize relatively ephemeral aggregations of copepods 

(Kvamme et al. 2000; Sigler and Csepp 2007). In late fall, copepod densities are reduced and 

herring begin to aggregate into large schools and migrate to wintering areas (Huse and Ona 

1996). The shift to wintering depths may be linked to breakup of the thermocline (Carlson 

1980). Herring move little in wintering areas, apparently to conserve energy (Sigler and Csepp 

2007), though as noted earlier, they can swim > 150 km/week immediately before or after 

spawning. 

Herring schools have coherence. Individuals from different schools do not simply mix 

and migrate randomly, rather there is a positive association among tagged individuals released at 

the same site that can persist for several years (Hay and McKinnell 2002). An alternative 

explanation, that fish mix randomly and then home to specific spawning sites is not supported 

because the degree of homing (fidelity) to specific locations is low [Fig. 2.5; (Hay et al. 2001)]. 

Thus, there must be cohesion among conspecific herring, a phenomenon recognized in some 

other pelagic fish [e.g., yellowfin tuna] but the biological mechanisms for this cohesion are 

unclear (Hay and McKinnell 2002). An alternative, speculative, explanation is that because 

herring rarely segregate as individuals, small groups of fish may remain together as schools mix, 

thus the social behavior that binds individuals together may operate without requiring individual 

recognition of conspecifics (Hay and McKinnell 2002). 

“If conspecifics associate together, it follows from the results that there may be a 

level of structure, perhaps dynamic and subtle, that occurs in large aggregations of 

herring that prevents thorough mixing. If so, large aggregations of herring typical of 

summer feeding concentrations could represent conglomerations of different populations, 

with different biological origins, destinations, and other characteristics. In B.C. [British 

Columbia] and most other areas inhabited by herring, dense aggregations also form 

during the overwintering period. In general, these aggregations appear to be larger but 

fewer in number and spatial scale than aggregations observed at other times of the year, 

particularly during spawning periods (Hay and McCarter 1997). This indicates that when 

these aggregations break up, herring move into smaller components and move away, 

perhaps to spawning or feeding areas. Therefore, we think that it is reasonable to assume 

that herring from different origins could merge or "appear" to merge into large loose 

aggregations. Subsequently they might dissociate into smaller units that retain some or 

much of the original membership. This would explain the patterns of matched tag 

recoveries observed after considerable periods (>200 days) and spatial ranges (>100 

n.mi.). This interpretation supports the view that smaller aggregations may consist of fish 

with some common heritage, although not necessarily genetic. If so, when such small 

aggregations of relatively homogeneous fish (conspecifics) join with others to form larger 

conglomerations, they may not mix thoroughly. If so, conglomerations may confound 

attempts to take representative biological samples random[ly] from such mixtures. 

Instead such conglomerations of herring may contain components that exhibit a range of 

different biological attributes, such as different sizes and ages, nutritional states and 

2.7 
conditions, and maturation schedules, and perhaps even some form of spatial imprinting 

for approximate spawning sites (McQuinn 1997; Hay et al. 2001). It follows that 

fisheries directed on such mixed groups would have uncertain consequences, with the 

risk of relatively higher mortality among the smaller components.” (Hay and McKinnell 

2002) 

Factors limiting productivity 

Available energy (food) and sheltering from predation likely play critical roles in 

population productivity and these factors likely vary among life stages. Larval mortality may be 

the primary determinant of Pacific herring population recruitment and growth (Hjort 1914; 

Norcross et al. 2007). The hydrodynamic and meteorological events that influence water 

movement affect year class recruitment by affecting the vertical stability of the water column, 

thereby providing concentrations of suitable food (Lasker 1978), and by affecting transport of 

larvae to areas of good or bad food supply and predator fields (Fortier and Leggett 1982; Frank 

and Leggett 1982; Crecco et al. 1983; Crecco and Savoy 1984; Lambert and Ware 1984; Leggett 

et al. 1984; Sherman et al. 1984), estuarine nursery areas (Nelson et al. 1977; Shaw et al. 1985), 

and areas of recruitment to adult stocks (Bailey 1981; Parrish et al. 1981; Boltz and Lough 1984; 

Power 1986). Juvenile herring require adequate nearshore habitat to survive and the abundance 

of this habitat is likely to play a critical role in population success. 

Adult herring may not be confined to spawning-related areas such as SEAK, rather they 

may range onto the continental shelf, thus greatly expanding feeding opportunities [inferred from 

Hay (Hay 2008)]. Although utilization of continental shelf waters by SEAK herring has not been 

documented, herring have been captured on shelf waters throughout the Gulf of Alaska, 

including areas near SEAK (Fig. 2.6). This suggests that like other eastern Pacific herring 

stocks, the habitat of SEAK herring may be considerably larger than is generally assumed. 

Genetics 

There is good evidence that some populations of Pacific herring in some geographic areas 

are locally distinctive genetically, albeit on a scale that is modest compared to the differences 

found between the two major lineages of Pacific herring. Atlantic and Pacific herring are 

characterized by genetic differences that are consistent with a separation of a few million years 

(Grant 1986). Within Pacific herring, by far the largest genetic distinction is between 

populations from Asia and the Bering Sea versus those inhabiting the remainder of North 

America (Fig. 2.2a) (Grant and Utter 1984). With the exception of some differentiated 

populations from the Alaskan Peninsula, genetic differences among localities within these two 

major lineages are smaller by an order of magnitude or more (Grant 1986). Among herring from 

the Alaska Peninsula to California, some very modest evidence of population structure exists 

[estimated with protein electophoresis (Grant and Utter 1984; Kobayashi 1993)]. Herring from 

some geographic areas can be distinguished in a statistical sense from herring from other areas 

(Burkey 1986; Schweigert and Withler 1990; Beacham et al. 2002; Bentzen 2004; Small et al. 

2005). However, in some instances allele frequency differences between years were as large or 

larger than those between localities: temporal DNA variation among spawning aggregations 

may dominate the genetic variability at spatial scales of about 700 km (Seeb et al. 1999). In one 

case (Cherry Point herring in Washington), temporally replicated samples provided consistent 

evidence for population subdivision. Physical or behavioral isolation may explain consistent 

genetic differences. See Appendix A for a more complete review of Pacific herring genetics. 

2.8 
Large populations might be demographically independent but have only very modest 

levels of population genetic differentiation. At presumably neutral markers such as those 

discussed here, population genetic differentiation (as measured by indices such as FST) is a 

function of the product of the effective population size (Ne) and the migration rate (m = fraction 

of the population that migrates each generation) (Gustafson et al. 2006). Based on Wright’s 

(Wright 1978) commonly used (albeit very rough) approximation that at equilibrium, FST = 

1/(1+4Nem), the FST = 0.0032 reported by (Beacham et al. 2002) for NE Pacific herring implies 

Nem ~ 78 migrant individuals per generation. In a small population, that could represent a high 

migration rate (m), but in a population with 106

 individuals it equates to m = 7.8 x 10-5 – that is, 

less than one individual in ten thousand is a migrant each generation. Because of the inverse 

relationship between FST and Nem and the numerous assumptions underlying Wright’s formula, 

robust estimation of migration parameters associated with low FST values is very difficult 

(Waples 1998; Whitlock and McCauley 1999), so any quantitative estimates should be treated 

with caution. Nevertheless, the point remains that in very large populations, very low levels of 

genetic differentiation could be associated with migration rates that have little influence in 

shaping the demographic parameters of the population. That is, large populations might be 

demographically independent but have only very modest levels of population genetic 

differentiation. Whether this scenario represents one in which it is reasonable to identify 

different ‘populations’ is not a question that has a single, scientifically correct answer; rather, the 

conclusions drawn for any practical application should be guided by desired 

conservation/management goals and the concept of ‘population’ that is most suitable to that 

application (Waples and Gaggiotti 2006). 

Stocks, populations, metapopulation 

The pan-Pacific herring population is a composite of many smaller stocks and is 

consistent with the metapopulation concept. Herring populations in the eastern Pacific consist of 

a relatively large number (>20) of relatively small populations (most <100,000 t) (Hay et al. 

2001). Several herring stocks are evident along the Gulf of Alaska, including several population 

centers in British Columbia, SEAK, Yakutat, Prince William Sound, Kodiak, Cook Inlet, and 

along the Aleutian chain (Fig. 2.3). Herring in the Bering Sea are distinctly different from 

populations in the Gulf of Alaska and more southern regions of the eastern Pacific; they 

complete longer migrations, grow to 500 g (about twice the size of herring in the Gulf of 

Alaska), and are genetically distinct (Grant and Utter 1984; Williams and Quinn 2000; Hay et al. 

2001) (Fig. 2.2a). Allozyme data also suggest differences among herring in south-central Alaska 

including those in SEAK and stocks in British Columbia (Grant and Utter 1984). 

Two of the central characteristics of a metapopulation as originally defined were that 

local subpopulations are linked by migration and are subject to periodic extinction (extirpation) 

and recolonization (Levins 1969; Levins 1970). Consequently, not all suitable habitats would be 

simultaneously occupied. This ideal metapopulation included the assumptions that 

subpopulations have independent dynamics, that the exchange rate between subpopulations is so 

low that it has no affect on local subpopulation dynamics, and that all habitat patches have equal 

isolation and equal area (Levins 1970). In practice, most of these assumptions have been relaxed 

and no real metapopulation has been identified that satisfies all these criteria (Hanski and 

Simberloff 1997). 

Local subpopulations within a metapopulation are spatially structured and migration 

among the subpopulations has some effect on local subpopulation dynamics (Hanski and 

2.9 
Simberloff 1997). The underlying concept in the many refinements to the original 

metapopulation model is that “persistence of species depends on their existence as sets of local 

populations, largely independent yet interconnected by migration” (Harrison and Taylor 1997). 

Others have advocated that linkage of local- and regional-scale population processes beyond 

extinction-recolonization analysis can be considered under the metapopulation concept for 

marine fishes and that “the critical feature of metapopulations is the coupling of spatial scales, 

whereby local populations experience partially independent dynamics but receive some 

identifiable demographic influence from other populations” (Kritzer and Sale 2004). 

An ‘adopted-migrant’ variant of the metapopulation hypothesis applied to Atlantic 

herring suggests that juveniles that associate with and synchronize their maturation with adult 

schools will adopt the migration and homing patterns of the adults (McQuinn 1997). Thus local 

spawning populations are maintained by “repeat rather than natal homing to spawning areas, 

while local population persistence is ensured through the social transmission of migration 

patterns and spawning areas from adults to recruiting individuals” (McQuinn 1997). Under the 

adopted-migrant hypothesis, hydrographic forces on larvae and the effects of schooling of 

juveniles lead the majority of individuals to spawn in their native population. Thus differences 

in the mean values of meristic and morphometric measurements that reflect environmental 

differences during development are maintained, although strays from other populations are 

adopted by local populations and gene flow is significant(McQuinn 1997). The adopted-migrant 

hypothesis is consistent with genetic studies on Atlantic herring that have not observed 

temporally persistent differences, since no genetic differences would be expected between 

Atlantic herring populations with the hypothesized level of gene flow (McQuinn 1997). 

Although this metapopulation concept and adopted-migrant hypothesis were first formulated for 

Atlantic herring, they have equal application in the case of Pacific herring (Gustafson et al. 

2006). Along these lines, several investigators have provided evidence indicating the major 

migratory stocks of Pacific herring in British Columbia are spatially structured and interact as a 

metapopulation (Ware et al. 2000; Ware and Schweigert 2001; Ware and Schweigert 2002; Ware 

and Tovey 2004). Dispersal rate and straying in both Atlantic and Pacific herring appear to be 

density dependent and increase with abundant recruitment, resulting in periodic waves of 

dispersal that radiate throughout the metapopulation (Huse et al. 2002; Ware and Schweigert 

2002). 

To be considered a metapopulation a system must meet the following two criteria: 1) 

local populations must be shown to exchange low levels of individuals, and 2) extinction and 

recolonization must be documented (Smedbol 2002). Both of these metapopulation criteria have 

been met, for example, by Georgia Basin Pacific herring to the south of SEAK. Evidence 

supporting the hypothesis that the five major migratory stocks of British Columbia Pacific 

herring form a spatially structured metapopulation include: 1) the spatially fragmented 

distribution of spawning habitat (Hay et al. 1989; Ware et al. 2000; Hay and McCarter 2004), 2) 

evidence of disappearance and recolonization events (Ware and Tovey 2004), 3) evidence of 

significant migration (straying) between the five main stock assessment regions as indicated by 

tagging data (Hay et al. 1999; Ware et al. 2000; Hay et al. 2001), and 4) high levels of gene flow 

as shown by DNA microsatellite analyses (Beacham et al. 2001; Beacham et al. 2002). 

2.10 
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2.11 
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2.14 
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2.16 
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2.18 
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2.19 
I 

mgc 

Fig. 2.1. Pacific herring (Clupea pallasii); actual photo (anterior) combined with a colorized 

scientific drawing (Hart 1973). 

2.20 
07 

1 \ ,11, lei 1=~ .. ~I 

::~::,)r.~t 

O.G4~=~0~0~.J'=""'=o;,a~1?-=o,to,.,=.......,oo Gtm~Jlc dlstonce IO) 

ARCTIC OCEAN 

OCEAN 

Fie. 13. Schernalic view of 1hc distribution of herring throughout 1he ea~tcrn North Allantic. Amie. and Pacific oceans. Spa" ning location an..i 

di tributions of Arctic herring arc not well documcmcd; therefore, size.5 of the circles arc not intended to rcprc~cnt either the range or abu ndance ,r 

these waters. 

Relative likelihood 

o1 occurence 

- 0 .80 - 1.00 

0.60 - 0 .79 

0.40 - 0.59 

0 .20 - 0 ,3 9 

0 .01 - 0 .19 

Fig. 2.2a. Global distribution of Pacific herring [adapted from Hay (1985)]. The genetic distance 

inset is from Grant and Utter (1984) (protein allozyme analysis); the red ellipses on the map 

identify these groupings. 

Fig. 2.2b. Global distribution of Pacific herring generated by FishBase (unreviewed; 

http://fishbase.sinica.edu.tw/tools/aquamaps/receive.php). 

2.21 
• 

... 

• 

~ 

• 

• 

• 

• 

• 

• 

• .. 

• 

• 

•••• 

• 

·central Alaska/ / 

/• 

• 

*" , ___ .,-' 

British Columbia 

PAC\F\C OCEAN 

California 

Fig. 2.3. Herring stocks in the eastern North Pacific, separated by solid, dashed, or dotted lines. 

The dark areas indicate the approximate centers of spawning and overwintering [from (Hay et al. 

2001)]. The area circled in red has been defined as a discrete population segment using 

Endangered Species Act (ESA) criteria (Stout 2001; Gustafson et al. 2006). 

2.22 
N 

A 

5 

Kilometers 

Fig. 2.4a. Small scale spawning movement in Berners Bay 1976 (blue) and 1977 (red). 

2.23 
 

-1978 1984 - 1985 

1991 -1992 1993 -1994 

Fig. 2.4b. Large scale spawning movement in the Kah Shakes, Cat Is., and Annette Island area 

of SEAK. Red indicates spawning location (Pritchett 2006). 

2.24 
0 

0 

[1.5 

[l.0 

Region 

0 

a 

0 0 

0 

Statistical 

Area 

D 

0 

0 0 0 

1 

Section 

Geographica~ scale 

0 

a 

0 

oCI 

o 

0 

D 

Location 

Fig. 2.5. Redrawn from Hay et al. (1999). “Comparison of fidelity rates by regions, statistical 

areas, sections, and locations. The array of small points (jittered horizontally to reduce overlap) 

each represent the mean fidelity of different geographic units within each geographic category 

(i.e., there are 6 regions and 6 points). Some of the highest points in the statistical area and 

section categories are based on very small sample sizes. The larger circles represent the overall 

mean fidelity for each geographic category” (Hay et al. 1999). Regions vary from 3000 to 10000 

km2

, statistical areas from 500 to 2500 km2, and most sections are <300 km2 (Hay et al. 2001). 

2.25 
Alaska 

Fig. 2.6. Offshore herring in the Gulf of Alaska. Purple symbols are adult herring (Orsi et al. 

2007; Farley 2008); blue symbols are juvenile herring (Orsi et al. 2007; Orsi 2008). Illustrated 

groupings (red ellipses) are based on allozyme analysis by Grant and Utter (1984); herring 

collected in Helm Bay, Lynn Canal, Yakutat Bay, Prince William Sound and west of Kodiak 

were included in that analysis. 

2.26 
 

Chapter 3 

Description of Pacific herring in Lynn Canal and southeastern Alaska 

Mark G. Carls 

Abstract 

All life stages of Pacific herring (Clupea pallasii) utilize much of southeastern Alaska 

(SEAK) waters as habitat. The beaches used for spawning are not continuous; some are 

repeatedly utilized, thus the Alaska Department of Fish and Game (ADFG) eventually began to 

manage herring in these areas as discrete stocks. However, available data do not identify 

definitive divisions among SEAK stocks, rather apparent geographic groupings were variable 

and often rather arbitrary. Limited tagging studies within SEAK demonstrate fish migrate and 

mix over most of the region but were not designed to demonstrate repeat spawning fidelity. 

Migration data from British Columbia, a region to the south of SEAK and reasonably similar in 

structure and climate, are used here to roughly predict repeat spawning fidelity at SEAK stock 

scales; these approximations suggest considerable mixing among stocks (59 to 84%), possibly 

explaining the lack of definitive differences among stocks and suggesting that SEAK herring are 

part of an interrelated metapopulation. Clearly more work remains to understand the 

relationships among SEAK herring stocks, such as more detailed genetic analysis and more 

detailed, spawn-oriented and seasonal tagging studies. 

Introduction 

Pacific herring in southeastern Alaska (SEAK) are managed as discrete stocks by the 

Alaska Department of Fish and Game (ADFG; Fig. 3.1). Management boundaries are based on 

major historic spawning areas. These boundaries are not contiguous, and how stocks outside 

them relate to identified stocks is unclear and unknown. Estimated stock areas range from about 

100 to 1100 km2

 (water only). Of these, the Sitka management area is the largest, Lynn Canal is 

second and Craig is third. 

In this chapter Lynn Canal herring are examined first, then herring throughout SEAK are 

examined to place Lynn Canal herring in context. Migration studies competed in British 

Columbia are used to roughly predict spawning fidelity within SEAK, a topic that has not been 

addressed by research in SEAK. For each of the variables considered (distribution, biomass, 

recruitment, size at age (a surrogate for growth rate), spawn timing, morphological variability, 

migration, and genetics) the question is asked, are there substantial differences among stocks, 

and if so do these differences form a cohesive pattern? The underlying goal is to determine if 

separately managed SEAK herring stocks are one population or metapopulation, or if they are 

sufficiently different to be considered separate populations. 

Herring spawning fidelity studies in British Columbia provide estimates of conditions in SEAK 

The spawning fidelity of Pacific herring has been extensively studied in British Columbia 

but not in SEAK. These fidelity estimates can reasonably be used to interpret conditions in 

SEAK. Located adjacently, both domains stretch along the north Pacific in the Gulf of Alaska, 

about 860 km (SEAK) to 900 km (British Columbia). Both are temperate rain forests bounded 

on the east by coastal mountains, ice fields and glaciers. Both have complex coastlines with 

many islands and fjords. Both domains may be partially or wholly in the same zoogeographic 

province (see Chapter 4 for a more complete discussion of this topic), although located further to 

the south, average water temperatures in British Columbia are likely warmer than those in SEAK 

3.1 
(e.g., Chapter 4, Figs 4.33 and 4.34). The distance between ‘outside’ and ‘inside’ waters (those 

along the Pacific Ocean and those along the mainland behind barrier islands) is roughly 100 to 

150 km in SEAK. This distance is more variable in British Columbia, roughly 15 to 190 km, 

where the outside barrier islands are larger, fewer in number, and do not completely shield the 

mainland from the Gulf of Alaska as they do in SEAK. 

On large scales, fidelity of Pacific herring approaches 100% and declines to near 0 as 

geographic scales decline to beach size [Chapter 2, Fig. 2.5; (Hay et al. 1999)]. This suggests 

that fish that mingle in summer areas mix and do not all return to the same spawning beaches. 

However, a nonrandom association of herring over considerable distances for up to several years 

is evident (Hay and McKinnell 2002), suggesting that herring schools have coherence; 

individuals from different schools do not simply mix and migrate randomly. (See Chapter 2 for 

a more complete discussion of school interaction.) 

To roughly estimate spawning fidelity in SEAK, the relationship between fidelity and 

area in British Columbia was estimated by regression. Mean fidelity was estimated from the 

original x-y plot of Hay et al. (1999) using CAD. Areas for each category (water only) were 

reported by Hay and McKinnell (2002); the smallest area (“location”) was estimated by dividing 

the mean region size by the number of locations (1800). Regression of ln(fidelity) against 

ln(area) was used to estimate the relationship between fidelity and area; r2

 = 0.975 (Fig. 3.2) and 

the resultant equation was used to roughly predict the spawning fidelity of SEAK stocks. The 

approximations are considered rough for two reasons 1) application of observations from one 

large geographic region to another and 2) scatter in the British Columbia data is high (Chapter 2, 

Fig. 2.5), though central tendencies at the smallest scales are rather clear. 

Lynn Canal herring 

The historic Lynn Canal spawning area, as defined by ADFG ranges from Berners Bay 

south to Taku Harbor and encompasses an area of about 950 km2 (Fig 3.3). The Lynn Canal 

Pacific herring stock was one of the larger stocks in SEAK prior to 1983 [third in the 1930s; 

(Rounsefell and Dahlgren 1935)] but declined through the 1970s and has been depressed since 

1982 (Pritchett et al. 2008). Studies by Carlson (1980), who summarized earlier work and is 

frequently referenced, focused his study primarily on a considerably smaller subset (16%) of this 

region (Fig. 3.3). Spawning in Lynn Canal was previously distributed from Juneau (Auke Bay) 

north to Berners Bay; since 1990, however, most spawning has been concentrated in Berners Bay 

north of Cascade Point and from Point Bridget south to Mab Island (Moulton 1999). Summer 

feeding areas are on the west side of Douglas Island with most fish found at depths of 5 and 37 

m, whereas in winter, herring move into deeper waters and remain in dense concentrations near 

the bottom (73 to 110 m) (Carlson 1980). Herring biomass in Lynn Canal peaks in winter 

(December to February, variable among years) and decreases sharply thereafter (Sigler and 

Csepp 2007) (Fig. 3.4). The fish move around during this period; schools formed in the 

Benjamin Island area in November, then shifted south toward Amalga Trench (Sigler and Csepp 

2007). Because marine mammal activity (in winter) was confined to these areas, the authors 

assumed few herring were elsewhere. They also assumed that observed herring were all from 

Lynn Canal because the nearest stocks occur “more than 100 km away.” [Actual distance to the 

nearest spawning stock, in Port Frederick, is about 60 km, and distances to the nearest summer 

feeding areas are <5 km (near Point Retreat on the Mansfield Peninsula) to 24 km (Couverden 

Island), less than the net average yearly movement of herring, 89 km (Hay et al. 2001; Hay and 

McKinnell 2002).] Herring have utilized Fritz Cove in winter for three decades but abundance in 

3.2 
 

Auke Bay has declined, offset by an increase near Benjamin Island and in the Amalga Trench 

(Carlson 1980; Sigler and Csepp 2007). The submarine gully in this area is apparently critical 

winter habitat for the Lynn Canal herring stock and presumably offers benefits by reducing 

energy expenditure (sheltering from tidal currents) and predation (lower light levels may reduce 

predation by visual feeders) (Sigler and Csepp 2007). 

Pacific herring biomass in Lynn Canal 

Accurate biomass estimates for Pacific herring stock in Lynn Canal do not exist, though 

available data do indicate the present status. Biomass estimates of Lynn Canal herring have been 

made intermittently since the winter of 1971 to 1972 beginning with hydroacoustics (ADFG), 

although the estimates are most likely not comparable for all years (Fig. 3.5). Winter surveys 

had the apparent advantage of observing large aggregations of herring in deep water, a situation 

advantageous to echo integration techniques. Efforts during the first four years of surveys 

concentrated on equipment development and survey design while the remaining years used 

designed systematic surveys. Harvest quotas for the Lynn Canal herring sac roe fishery were 

based on these biomass estimates; fishery performance indicated that they were overestimates. 

In addition, recent work by Sigler and Csepp (2007) demonstrated a seasonal abundance pattern 

of herring in the Lynn Canal area with winter aggregations being much greater than the number 

of herring remaining in the spring to spawn (Fig. 3.4). Possibly herring from outside the Lynn 

Canal area also winter in the trench, and although the need to conserve energy during winter 

argues against this hypothesis, herring seem to disappear from wintering areas and reappear at 

often distant spawning areas (Thorne 2008). 

Biomass estimates based on actual herring spawn by dive survey are better indicators of 

the true biomass and these surveys were conducted in the Juneau area during the mid to late 

1980s (Fig. 3.5). Unfortunately, because the Lynn Canal herring biomass is at a level much 

lower than the threshold required for a commercial fishery and the limited stock assessment 

resources of ADFG are typically used in areas where fisheries are likely to occur, these surveys 

are incomplete and have recently been confined to Berners Bay. 

Aerial surveys provide the longest time series of relative herring abundance data for the 

Lynn Canal area (Fig. 3.6). These data are collected by mapping observed spawning activity 

along the coastline. Survey frequency and the area to be flown are not standardized and as such, 

the total nautical miles of spawn observed for a given year can be a function of weather and 

survey effort. In addition, not all areas where spawning is observed are of equal value in regards 

to spawning requirements; the type of substrate is important as well as the width of usable 

substrate. No reliable observations of spawn intensity are available from aerial surveys. 

Because of these limitations biomass observations are typically not made using aerial surveys 

alone. 

Uncertainty is high in Lynn Canal biomass estimates. An estimate of the historic 

biomass of spawning herring in Lynn Canal was made using the eight estimates of spawning 

biomass from the dive surveys (Fig. 3.5) and the time series of nautical miles of spawn obtained 

from the aerial survey program (Fig. 3.6). The estimated tons of herring per nautical mile of 

spawn was considerably greater in the mid to late 1980s than what has been observed recently 

(256 tons of herring per nautical mile of spawn for the mid to late 1980s compared to 130 tons 

recently; Fig. 3.7). This disparity could be due to the differences in areas used for spawning 

between the time periods, where and how intensely the aerial surveys were conducted, as well as 

differences in herring biomass. However, given the small amount of data and high variance, 

3.3 
these estimates are not statistically different (P = 0.802). An average of the estimated tons of 

herring per nautical mile of spawn (176 tons) was used to estimate the historic spawning biomass 

time series (Fig. 3.8). Although this method may underestimate the early years and overestimate 

the more recent years, it is based on data collected during the spring spawning season. Earlier 

biomass estimates relied heavily on winter hydroacoustics, which most likely dramatically 

overestimated the spawning biomass, led to overfishing, and contributed to the stock collapse. 

Perhaps the most obvious result of the limited and variable data is that Lynn Canal biomass 

estimates are uncertain (Fig. 3.8). 

Age structure, age structured models, and the estimation of recruitment 

There are insufficient data available to construct an age structured model for the Lynn 

Canal herring population (Fig. 3.9) (Carlile et al. 1996; Quinn and Deriso 1999). Approximately 

10 years of good biomass estimates and corresponding age composition estimates would be 

required to begin modeling this population. Typically, ADFG reliably ages herring in Southeast 

Alaska through age 8 with ages greater than age 8 grouped into a group called age 8+. Ten years 

of complete data would allow for observation of two complete cohorts. 

Estimate discrepencies 

An apparent discrepancy in estimated Lynn Canal herring biomass by ADFG (Carlile et 

al. 1996) (Fig. 3.5) and Sigler and Csepp (2007) (Fig. 3.4); alternatively it may be due to method 

differences, differences in observation timing coupled with possible outmigration, or inclusion of 

juvenile fish in the Sigler and Csepp (2007) data set. Peak estimates by Sigler and Csepp (2007) 

were roughly 400 times greater than those estimated from ADFG (Carlile et al. 1996; Pritchett 

2007) data. Adjustment for juveniles in estimates of Sigler and Csepp (2007), roughly 5 to 20% 

of the total biomass, does not explain the difference between estimates. Apparently each time 

series can be considered an index of biomass and may form a time series consistent with itself 

but not necessarily with other data sets. At least some of the ADFG hydroacoustic data were 

collected in March (Moberly and Thorne 1974), likely missing the peak biomass observed more 

recently (Sigler and Csepp 2007) and differences between acoustic gear types, survey strategies, 

and other unknown factors may also contribute to the discrepancy. 

SEAK herring 

Distribution 

Herring are ubiquitous throughout SEAK and utilize this habitat at all life stages (e.g., 

Fig. 3.1). Shoreline is utilized for spawning and egg incubation primarily in spring; there are 

many spawning aggregations throughout SEAK with the greatest biomass near Sitka (Fig. 3.1). 

(At least 9 of these aggregations are fished commercially.) Glacier Bay may be the only major 

area in SEAK without spawning, though northern Lynn Canal may also generally fall into this 

category. Bays and inlets along both the outer coast (e.g., Sitka) and inner coast (e.g., Lynn 

Canal) are utilized for spawning. In general, herring that spawn on the outer coastal areas are 

more productive than those in inside waters (Pritchett 2005). 

Limited larval habitat utilization data have been collected in SEAK. Most larval studies 

have focused on Glacier Bay (Arimitsu et al. 2007; Piatt 2008) and Auke Bay (Haldorson et al. 

1986; Haldorson et al. 1987; Haldorson et al. 1988); few other data exist (Fig. 3.10). Despite the 

limited surveys, we suspect many bays in SEAK are utilized by larval herring as rearing habitat 

3.4 
as they are elsewhere, such as Prince William Sound (Stokesbury et al. 1999; Stokesbury et al. 

2000). Advection will control the destinations of these weak swimmers and bays proximal to 

spawning areas are logical places to expect larvae. Even bays without spawning events, such as 

Glacier Bay provide evidence of rearing habitat (with the caveat that the presence of larvae in the 

bay does not necessarily mean they will survive there). However, juveniles are also well 

represented in Glacier Bay, strongly suggesting it is adequate habitat. (Larvae, juveniles, and 

adults were categorized by size, <35 mm = larvae, 35-180 mm = juveniles, and >180 mm = 

adults). Larvae are also advected offshore from SEAK (Fig. 3.10) and based on observations in 

British Columbia and Prince William Sound, these are likely to die from lack of food, salinity 

intolerance, or increased predation pressure (Stevenson 1962; Alderdice and Hourston 1985; 

Stocker et al. 1985; McGurk 1989; Wespestad and Moksness 2002; Norcross et al. 2007). Peak 

larval abundances are in May or June in Auke Bay (Haldorson et al. 1986; Haldorson et al. 1987; 

Haldorson et al. 1988). 

Juvenile herring evidently utilize many of the bays in SEAK as rearing habitat (Fig. 

3.11). Sampling for juvenile herring in SEAK is more thorough than for larvae, though again 

coverage is not complete. Capture of juvenile herring by nearshore seine hauls is hit or miss; 

relative herring abundances tend to be high when a school is captured and low when schools are 

missed by the net. The incidence of capture in one study was about 132 times out of 600 hauls 

(Johnson 2007). In Glacier Bay, an area repeatedly resampled for 5 y (1999 to 2004), juveniles 

evidently utilize the entire area and were captured more often than not (Arimitsu et al. 2007; 

Piatt 2008). 

Non-spawning adult Pacific herring are likely widespread throughout SEAK (Fig. 3.12). 

Although non-spawning sampling has been confined to limited areas [the summer reduction 

fishery in the 1930s (Rounsefell and Dahlgren 1933; Rounsefell and Dahlgren 1935; Skud 1963; 

Carlson 1977), winter hydroacoustic surveys generally in the vicinity of Juneau (Vollenweider 

2008), and midwater trawls completed in Glacier Bay (Arimitsu et al. 2007)], anecdotal evidence 

suggests most of the waters in SEAK are utilized by Pacific herring throughout the year. More 

detail, and particularly comprehensive coverage of winter and summer schooling areas 

segregated by season, is desirable and would contribute to the general understanding of species 

utilization and population structure within SEAK. 

The contemporary distribution of herring in SEAK is not identical to that in the past. At 

one time Kootznahoo Inlet (near Angoon) was of great importance (Rounsefell and Dahlgren 

1935) but spawning activity is not even monitored there today. On the other hand, Sitka Sound 

and San Alberto Bay (near Craig) were considered the largest stocks in the 1930s (Rounsefell 

and Dahlgren 1935) and that is also true today (Fig. 3.13). Icy Strait was important herring 

habitat in the summer in the 1930s (Rounsefell and Dahlgren 1935) as it is today (Arimitsu et al. 

2007). The distribution of herring plants in the 1900s may provide a rough index of historic 

herring distribution; however, where commercial fishing occurred was influenced by plant 

location and fishing intensity was less on large stocks impractically distant from the plants 

(Rounsefell and Dahlgren 1935). 

Age structure 

As in other herring populations (Williams and Quinn 2000; Funk 2007), strong age 

classes generally occur every few years in SEAK stocks (Fig. 3.9). For example, strong year 

classes (cohorts) were evident beginning in 1980, 1987, and 1996 at Kah Shakes. Synchrony 

among stocks is evident, consistent general patterns in the North Pacific Ocean and strongly 

3.5 
influenced by environmental conditions (Hollowed et al. 1987). For example, synchronous 

strong year classes were evident in 1996 in every SEAK stock except Sitka (Fig. 3.9). 

Interestingly, the largest, most actively growing stock (Sitka) is apparently the least reliant of all 

SEAK stocks on strong year classes. 

Genetics 

Current data do not support definitive genetic differences among SEAK stocks (Fig. 

3.14). Available genetic data for SEAK stocks is largely peripheral to studies focused on other 

areas (Beacham et al. 2002) or on population separation on a coarse scale (Grant and Utter 

1984); these do not suggest differences among SEAK populations. The first of these studies was 

a Pacific Ocean scale allozyme survey that provided modest evidence of population structure 

among herring from the Alaska Peninsula to California (Grant and Utter 1984). Within the 

northern Gulf of Alaska, herring near Kodiak, Yakutat, and Lynn Canal were grouped together; 

herring from Helm Bay (Cleveland Peninsula, north of Ketchikan) were grouped with 

populations to the south. Later, a microsatellite study identified genetic differences between 

herring in SEAK and British Columbia; SEAK samples included fish from Sitka, Kirk Point and 

Mary Island (in the Kah Shakes area), and Seymour Canal (Beacham et al. 2002). Genetic work 

on SEAK herring stocks is ongoing at the Auke Bay Laboratory but data collection and analysis 

are not complete. 

Spawn timing 

Differences in spawn timing suggest possible northern and southern groupings of SEAK 

herring (Fig. 3.15). The primary cause is likely temperature; marine waters of SEAK are 

characterized by an inshore-offshore salinity gradient and a north-south temperature gradient 

(Quast 1968; Murphy and Orsi 1999). 

Pacific herring respond to their thermal environment; residence within a given area will 

drive spawning behavior. Most spawning in SEAK occurs between mid-March and mid-April; 

in Lynn Canal, herring spawn from late April to early May (Davidson et al. 2005; Pritchett 2006; 

Coonradt 2008). To understand how spawn timing in SEAK relates to spawning elsewhere in 

the eastern Pacific, the relationship between latitude and spawn timing was examined from 

California to Kotzebue Sound. Approximate latitudes were added to the data (Rounsefell 1930; 

Chapman et al. 1941; Miller and Schmidtke 1956; Scattergood et al. 1959; Skud 1960; Alderdice 

and Velsen 1971; Barton and Wespestad 1980; Hourston 1980; ADFG 1985; Hay 1985; 

Lemberg et al. 1997; Davidson et al. 2005) summarized by (Stout et al. 2001). All spawn dates 

were expressed as Julian days; negative values are those that extend into the previous year (e.g., 

December spawning in California). Data from SEAK data were updated from recent sources; 

data from Yakutat were unavailable (Davidson et al. 2005; Pritchett 2006; Coonradt 2008). 

Midpoint data were regressed against latitude. To compare timing specifically in SEAK with the 

overall pattern, data were divided into two groups, SEAK only and all other eastern Pacific 

herring and analyzed with analysis of covariance (latitude × midpoint × group). 

The time Pacific herring spawn in the eastern Pacific Ocean is correlated with latitude (r 

= 0.950, P < 0.001). The relationship between latitude and spawn timing within SEAK was the 

same as all other eastern Pacific herring (slopes were not significantly different; P = 0.262, Fig. 

3.16). Spawning throughout SEAK may be slightly earlier than predicted by the general 

relationship (P = 0.003); however, spawn timing in bordering areas (just north and south of 

SEAK) entirely overlapped timing in SEAK, suggesting the latter result may have little meaning. 

3.6 
Clearly, spawn timing in SEAK conforms to the overall cline evident along the coast and 

a spawn timing cline exists within SEAK (r = 0.918; Fig. 3.15 to 3.17). Temperature is likely the 

primary driver (Brown and Carls 1998). For example, annual sea surface temperatures are 

highest near the equator and decrease toward the poles (NOAA 2008), strong evidence that 

temperature gradients occur throughout the analysis region and within SEAK. 

Spawn timing in SEAK is broader than captured by ADFG data, though the official data 

set likely by far captures most of the spawning activity. Only large scale spawning events are 

recorded in these data. Spawning outside the spring timing has been observed over many years. 

Spawning was observed in mid June (Gut Bay, Baranof Island) in the 1930s. In recent years, we 

have observed Pacific herring spawning in Auke Bay in June [1997, 2000, 2003; (Wing 2008)]. 

To the best of our knowledge, no one has attempted to record this additional spawning activity in 

SEAK. Rounsefell and Dahlgren (1935) imply that small groups of herring such as these may be 

nonmigratory residents, different in habit to the earlier migratory spawners. 

Biomass 

Temporal changes in biomass are not synchronous among SEAK herring stocks, 

suggesting at least some level of discreteness among them. Since the 1990s, herring spawning 

biomass in SEAK has increased in several stocks (Sitka Sound, Hoonah Sound, Seymour Canal, 

Craig, Ernest Sound); shown no trend (Hobart Bay / Port Houghton, Lynn Canal) or fluctuated 

(Tenakee, West Behm Canal; Figs. 3.8 and 3.13). The largest herring spawning biomass in 

SEAK is at Sitka, presently >4 times that of any other stock. Only one stock appears to be in 

decline (Kah Shakes) but this is likely not true. The Kah Shakes stock has moved from place to 

place over a many year period and is now spawning on Annette Island, outside the jurisdiction of 

ADFG, hence is unavailable for biomass estimates (see Chapter 2, Fig. 2.4b for an example). 

There are no apparent geographic groupings among increasing, fluctuating, or static stocks (not 

illustrated). In particular, temporal changes in Lynn Canal biomass are not synchronous with 

nearby stocks (Sitka, Hoonah Sound, and Seymour Canal). Unfortunately, biomass estimates for 

other nearby stocks are not available for comparison [Olivers Inlet (within the Lynn Canal 

Management Area), Port Frederick, and Lisianski Inlet]. Asynchronous biomass changes 

suggest that herring do not simply randomly disperse into areas with lower population density 

and there is no evidence that Lynn Canal herring are being repopulated by excesses from nearby, 

growing populations. 

Recruitment 

Recruitment synchrony, analyzed with multidimensional analysis (Williams and Quinn 

2000), suggests divisions among SEAK herring, though coverage was not comprehensive (only 

Seymour Canal, Sitka Sound, Craig, and Kah Shakes were represented) and results differed 

among the several analyses provided (Figs. 3.18). Neither Lynn Canal nor Yakutat herring were 

included in the analysis. Geographic divisions suggested by recruitment synchrony do not 

follow the thermal gradient pattern, but how temperature may influence synchrony is unknown, 

and relative thermal conditions in SEAK through annual cycles remains to be described. 

Differences in recruitment among SEAK stocks may divide the area into two or three 

regions (Fig 3.18). Comparison of recruitment similarities within SEAK was based on an 

analysis by Williams and Quinn (2000); data were obtained from several sources (Reid 1971; 

Funk et al. 1992; Schweigert et al. 1997; Williams and Quinn II 1998), and included samples 

from British Columbia north to Norton Sound (Alaska). Sites included in SEAK were Seymour 

3.7 
Canal, Sitka Sound, Craig, and Kah Shakes. [An additional ‘site’ was designated SEAK in their 

analysis (Williams and Quinn 2000); this is simply the sum of recruitment at Sitka and Craig and 

is not an independent measure.] Conspicuously absent from the analysis was Lynn Canal 

recruitment. Several multidimensional analyses and dendograms provided slightly differing 

results. Division may indicate differences between “inside” and “outside” populations, the latter 

directly exposed to the Gulf of Alaska and the former protected by barrier islands. However, the 

analysis provides no insight regarding the northern portion of SEAK and Lynn Canal in 

particular. A more complete data set for SEAK is available [ADFG; (Pritchett 2007)] and is 

currently under examination but insufficient time precluded a more detailed analysis and, as 

explained earlier, recruitment in Lynn Canal is not estimable, so the expanded data set does not 

improve the interpretation of this particular area. 

Size-at-age and growth rate 

Some size-at-age data suggest no consistent geographic differences among herring in 

SEAK, another suggests division but does not include northern SEAK. Four data sets were 

available to compare size-at-age within SEAK: 1) data from 1929 and 1930 (Rounsefell and 

Dahlgren 1935), 2) a relatively small experimental data set collected for research purposes 

(Johnson et al. 1997; Carls et al. 1998), 3) data ranging from Nome, Alaska, to British Columbia 

(Williams and Quinn 2000), and 4) raw data from ADFG (Pritchett 2007). The fourth set is the 

largest and most comprehensive. No geographic groupings were evident in the 1929 and 1930 

length data (e.g., Fig. 3.19, illustrating the year of the most comprehensive coverage). No 

distinct geographic groupings emerged from the limited experimental set. Shelter Island (Lynn 

Canal) and Sitka fish were generally the largest at a given age; Seymour Canal fish tended to be 

the smallest but overlapped Cat Island (Kah Shakes) fish in some year classes (Fig 3.20). An 

analysis of weights by Williams and Quinn (2000) suggests southern and central divisions but 

did not include Lynn Canal fish [samples were collected from Seymour Canal, Sitka Sound, 

Craig, and Kah Shakes (Fig. 3.21)]. Based on applicable, completed analyses, the size at age of 

Lynn Canal herring did not differ from other nearby stocks. 

The current trend in size-at-age in SEAK herring stocks is downward and there is no 

evidence that Lynn Canal stock is different from the others (Fig. 3.22). To determine trends, 

mean deviation from mean length [by stock and age; ADFG dataset (Pritchett 2007)] were 

calculated; age classes were restricted to 3 through 8 to avoid poor resolution (few fish) in 

younger and older year classes [(Williams and Quinn 2000); see Appendix B for complete 

analysis detail]. Size at age has been decreasing for several decades in some stocks, e.g., Kah 

Shakes. In others there was a general increase in the 1980s or 1990s; all are now in apparent 

decline (Fig 3.22). 

Growth rates were not significantly different among SEAK Pacific herring stocks (P = 

0.577, Fig. 3.23 and Table 3.1). Growth rates were estimated by cohort (year class) for each 

stock [ADFG data, (Pritchett 2007)]; analysis was restricted cohorts with ≥15 length 

measurements in ≥3 y to provide robust estimates (see Appendix B for complete analysis detail). 

The number of growth estimates for each stock ranged from 3 to 24 (Table 3.1); Lynn Canal had 

the fewest estimates. Mean growth rates ranged from 0.107 to 0.142 ln(mm)/ln(year) and varied 

significantly among cohorts, though most slopes were similar. The same conclusion, that growth 

rate does not vary significantly among stocks, was reached when only cohorts common to those 

in Lynn Canal (1983, 1995, and 1996) were analyzed (P = 0.223). 

3.8 
One interpretation of the growth data is that herring are too mobile to develop meaningful 

size differences among SEAK stocks. If there is a consistent thermal gradient in SEAK, as 

suggested by satellite sensing and spawn timing, and fish remain within given areas for extended 

periods, then a relationship between latitude (or longtitude) and fish size might develop. 

Correlation of length to either was not obvious in the Rounsefell and Dahlgren (1935) study r = 

0.150 and r = 0.559, respectively. Clearly in this analysis longtitude appears to be more 

important; however, inspection suggests there is no relationship and that two outlying values 

drive the apparent relationship. When these forcing points are removed, r = 0.214 [data from 

table 9 of Rounsefell and Dahlgren (1935), age 4 fish in 1929, the most comprehensive set]. The 

failure of fish growth to respond to the typical thermal gradient in SEAK may suggest significant 

movement from location to location. 

Morphological or meristic variability 

The number of vertebrae a herring develops is negatively correlated with temperature (r = 

-0.85) (Rounsefell and Dahlgren 1932; Rounsefell and Dahlgren 1935), thus allowing possible 

discrimination among SEAK stocks presumptively sensitive to a temperature gradient through 

the region. From samples collected between 1928 and 1931 and partitioned by year class, 

Rounsefell and Dahlgren (1935) concluded that there is more than one herring population in 

SEAK; age and gender did not influence results. However, their “evidence tending to prove a 

lack of admixture in samples from the individual localities” is not detailed enough for further 

analysis and is not completely convincing. The entire analysis would have been more 

compelling if the effect of sample year had been included as a factor in their ANOVA. 

Vertebrae number in fish from Juneau were generally not different from those elsewhere in 

SEAK (unknown in Yakutat), except the 1926 year class differed significantly from that in 

Petersburg; differences among the 1925 and 1927 year classes were not significant (Rounsefell 

and Dahlgren 1935). 

Differences in vertebrae number suggest perhaps three geographic groups in SEAK, 

southern, central, and northern (Fig. 3.24). These boundaries, however, are highly subjective. 

Lower counts in the southern grouping may be driven by warmer spring temperatures; the 

highest counts in the central region may in part be caused by an occasional relatively cool central 

water mass as the region warms (Fig. 3.17). Relatively low vertebrae counts were also observed 

in the north but there were also some low counts in central SEAK. Counts in central SEAK (in 

the general vicinity of Cape Ommaney) were variable and changed among year classes. Thus, 

any tendency for linkage between capture location and thermal history appears to be weak, 

though admittedly the relationship between temperature (observed 2005 to 2007 by satellite) and 

vertebrae count (1928 to 1931) is speculation and is not proven. 

Herring stocks in SEAK probably cannot be definitively distinguished by vertebrate 

count because a) the fish are too mobile, resulting in a mixed population (see also section 

“migration”) or b) because thermal conditions within localized regions are not stable enough to 

develop a coherent signal, or c) the link between temperature and vertebrae number is not 

sufficient for a definitive outcome (r2

 = 0.72), or d) a combination of these and other unknown 

factors (Fig 3.24). There was no numerical correlation between vertebrae number and latitude (r2 

= 0.076 for the 1926 year class and r2 = 0.002 for the 1927 year class, the two sets where n > 5). 

Migration 

3.9 
Migration studies suggest herring from most of SEAK mix during the summer (Fig. 3.25) 

(Rounsefell and Dahlgren 1933; Rounsefell and Dahlgren 1935; Dahlgren 1936; Skud 1963; 

Carlson 1977); however, these studies were not designed to measure fidelity among spawning 

stocks. Instead, fish were tagged and released from spawning locations and observed in a 

summer fishery concentrated within a single area (near the southern end of Baranof Island). Fish 

tagged with either small metal operculum strap tags or internal belly tags were released near 

Sitka and Craig between 1932 and 1935 (Rounsefell and Dahlgren 1933; Rounsefell and 

Dahlgren 1935; Dahlgren 1936). Relatively few fish were tagged in the first year of study, 

<4000; recovery times ranged from 2 to 149 d. Increased numbers of fish were released in 

subsequent years, about 41 000 in 1935, and fish were recovered over a 5 y period (Skud 1963). 

Most fish were released in spring, coincident with spawning, and captured in the summer, thus 

linking spawning grounds and summer feeding areas. An additional study was completed 

between 1960 and 1962; some fish were released in the area of previous study, others from Auke 

Bay (n = 615) and Seymour Canal (n = 1142). Fish from the latter sites were also captured near 

southern Baranof Island (Carlson 1977). Tag recovery ranged from 0 to 0.8% in the latter study 

and from 0 to 8% in the former; belly tags were superior to operculum tags (Dahlgren 1936). An 

alternative tagging method, coded-wire tags, was more recently but incompletely explored 

(Krieger 1982). The migration patterns of Yakutat herring have never been studied. 

The mixing of southern SEAK herring with other SEAK stocks is unknown; the weak 

evidence of segregation [lack of tag recapture (Carlson 1977)] is insufficient to conclude mixing 

does not occur because few fish were tagged. Furthermore, percent tag recovery was related to 

the approximate distance between release and capture in that study (r2

 = 0.613) and fish released 

in the southernmost area (Cleveland Peninsula) were furthest from capture locations. Herring 

released from some sites were not recaptured and although the authors of the studies involved 

suggest this is evidence against migration (Rounsefell and Dahlgren 1933; Rounsefell and 

Dahlgren 1935; Dahlgren 1936; Carlson 1977), it is more likely evidence of an insufficient study 

design (relatively few fish were released and recapture was constrained to a single, limited 

geographic area). Not recovered were fish from Auke Bay [n = 1572; (Dahlgren 1936)], Cape 

Bendel [n = 1820; (Rounsefell and Dahlgren 1933; Rounsefell and Dahlgren 1935)], and the 

Cleveland Peninsula [near Ketchikan; n = 527; (Carlson 1977)]. Given the small release 

numbers and an average recapture rate of about 3% [derived from (Dahlgren 1936) and 

consistent with the more extensive tagging experience in British Columbia (mean annual rate 

2.7%, range 0.5 to 11%; (Hay et al. 1999)], recapture of between 6 and 55 fish could be expected 

from these sites under average conditions. Given that only a limited area was searched for tags, 

the failure to recapture any of these fish is not surprising and cannot be used as evidence that 

they were isolated from other SEAK stock. Indeed, migration was evident in a subsequent 

release of Auke Bay herring [1961; (Carlson 1977)], demonstrating the limitations of data from 

the earlier release. Similarly, fish released at Cornwallis Point (Carlson 1977), 21 km from Cape 

Bendel, were recaptured; given the apparent migratory pathways of other fish (such as from 

Seymour Canal), there is no reason to believe the intervening Keku Strait represents a 

geographic barrier. 

One author (who is often cited in this context) concluded that Lynn Canal herring spend 

the entire year in the same general vicinity (Carlson 1980), unlike the more migratory 

populations in Sitka, Craig, and British Columbia. Although there is some evidence that nonmigratory resident stocks may exist (Hay et al. 1999), we question the veracity of this 

conclusion, particularly because the same author reported movement of tagged fish from Auke 

3.10 
Bay to Frederick Sound, south of Admiralty Island (Carlson 1977) where they mixed with stocks 

from other locations. The recovery of two fish tagged in Auke Bay does not imply two herring 

made the migration because herring remain in schools; single herring are presumably highly 

vulnerable to predation. As previously noted, Carlson (Carlson 1980) confined his surveys to a 

relatively small area and did not provide compelling evidence that fish remained within this 

narrow boundary. 

Mixed summertime stocks do not eliminate the possibility that individual schools remain 

coherent and go their separate ways after summer. Tagging studies completed in SEAK were 

designed to only detect movement from spawning grounds to one summer feeding area. Thus, 

although they demonstrate that herring mix in this feeding area, they do not demonstrate that fish 

become mixed on spawning grounds, i.e., they do not eliminate the possibility that individual 

schools remain coherent and separate after summer. However, more extensive tagging studies in 

British Columbia strongly suggest some degree of mixing, albeit nonrandom, and that individual 

fish do not always return to the same spawning area (Hay et al. 1999; Hay et al. 2001; Hay and 

McKinnell 2002). 

Estimates of territorial size suggest Pacific herring in most of SEAK can potentially be 

described as a single population. Pacific herring can move considerable distances, evident both 

in SEAK (up to 200 km) and net yearly movement in BC (up to 300 km, mean 89 km) (Dahlgren 

1936; Hay and McKinnell 2002). Assuming these measured distance are radii of circles, the 

average territorial range is about 180 km and the maximum is 600 km, implying potential 

territorial areas of 25,000 to 280,000 km2

 (assuming circumscribed areas are entirely water). 

The BC record confirms these estimates are within reason; fidelity of herring is high (~88%) 

from a regional perspective, where regions represent areas of about 3000 to 10,000 km2 (Hay et 

al. 2001). An ellipse bounding the entire observed area of migration in SEAK and extending 

north to Berners Bay is 31,600 km2

 (water only; Fig. 3.25), well within estimated territorial 

bounds but greater than the maximum region size in BC. 

Metapopulation 

Herring in SEAK are likely part of the eastern Pacific metapopulation: a) local stocks 

within SEAK exchange at least low levels of individual fish, suggested by tagging studies (Skud 

1963; Carlson 1977), b) stocks have been depressed to near zero and recovered, such as at 

Tenakee (Fig. 3.13), c) spawning habitat is spatially fragmented into numerous areas (Davidson 

et al. 2006) (Fig 3.1), and d) gene flow is likely high because no differences in alleles are 

evident across SEAK or in British Columbia and genetic structure varies temporally at spatial 

scales of about 700 km (Grant and Utter 1984; Seeb et al. 1999). Herring size at age and 

recruitment data provide limited evidence of population differences at smaller scales (Williams 

and Quinn 2000) but also support the metapopulation concept because groupings were consistent 

with geography. In the latter study, some SEAK herring (Sikta) grouped most closely with those 

in Prince William Sound, others (Seymour Canal, Kah Shakes, and Craig) were grouped more 

closely with Prince Rupert stock in British Columbia. 

Summary 

A variety of data do not evidence of separation among SEAK herring stocks, rather 

apparent geographic grouping were variable and often rather arbitrary. Limited tagging studies 

within SEAK demonstrate fish migrate and mix over most of the region but were not designed to 

determine repeat spawning fidelity. Migration data from British Columbia, a region to the south 

3.11 
of SEAK and reasonably similar in structure and climate, are used here to roughly predict repeat 

spawning fidelity at SEAK stock scales; these approximations predict considerable mixing 

among stocks (59 to 84%), possibly explaining the lack of definitive differences among stocks 

and suggesting that SEAK herring are part of an interrelated metapopulation. 

To definitively understand migration and spawning behavior in SEAK, fish must be 

tagged and recovered on spawning grounds in ensuing years. Future tagging efforts could rely 

on physical tags as has been done in the past or some alternative technique, such as mass otolith 

marking could be used. The point is, if we truly wish to understand the population structure of 

Pacific herring in SEAK, a large-scale, multi-year study is necessary and it will require the 

cooperation of commercial fishing operations to be feasible. An ongoing, detailed genetic 

analysis of SEAK herring stocks may provide sufficient data for greater understanding; it may 

also lead to additional questions. 

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3.16 
Table 3.1. Mean growth rates [ln(mm)/ln(year)] in SEAK Pacific herring stocks. The 

data represented here are a subset of ADFG data (Pritchett 2007), fish captured during 

active spawn between March and May, thus describing local spawning stocks as closely 

as possible. (These selection criteria identified 78,971 fish of 188,628 in the database, 

42%. Examination of a second category, pre-spawning fish captured within the same 

time period, is recommended. Time constrains have precluded this analysis.) 

95% 

mean confidence 

stock n rate bounds 

Sitka 18 0.127 0.114 0.139 

Lynn Canal 3 0.142 0.098 0.186 

Craig 12 0.115 0.100 0.130 

Ernest Sound 9 0.110 0.087 0.133 

Hobart-Houghton 12 0.107 0.079 0.135 

Hoonah 10 0.114 0.097 0.130 

Kah Shakes 19 0.134 0.117 0.151 

Seymour Canal 24 0.136 0.121 0.151 

West Behm 14 0.107 0.090 0.124 

Tenakee 12 0.123 0.103 0.143 

3.17 
Sound 

Craig - Klawock 

Lynn Canal 

Seymour Canal 

Hobart - Houghton 

Fig. 3.1. Pacific herring spawning locations and management areas in SEAK (Carlson 1980; 

Grant and Utter 1984; Leon 1993; Herbert and Carlile 2002; Davidson et al. 2005; Pritchett 

2005; Pritchett 2007). The red symbols are spawning data for herring from an Alaska 

Department of Fish and Game database (Pritchett 2006), 1964 through present, although time 

series are not continuous, particularly prior to the 1970s. Orange symbols are other reported 

spawn sites not mapped by ADFG. Management boundaries approximate where the managers 

may be conducting fisheries, historically where spawn has occurred for particular spawning 

stocks, and are for information purposes only; i.e. they are places where managers look for 

spawn and where a fishery might occur. 

3.18 
0 

Fidelity (%) 

100 

80 

60 

40 

20 

0 

0 2000 4000 6000 

Area (square kilometers) 

Fig. 3.2. Relationship between geographic area and herring fidelity in British Columbia (r2 = 

0.975, P = 0.013) (Hay et al. 1999). 

3.19 
A 

Hyd roacoustics 

~ Summer 

~ Winter 

ubset studied 

iiJ Carlson (1980 

Herring spawn 

--2000 - present 

--1990- 1999 

--1980- 1989 

1972 - 1979 

ynn Canal 

Man gement area 

20 

Kilometers 

Fig. 3.3. Lynn Canal Management area as defined by ADFG (Pritchett et al. 2008) and the 

subset studied by Carlson (1980) (yellow). Non-spawning herring located by acoustic survey are 

indicated in green (summer) or blue (winter). Spawning is color coded by decade; however these 

lines often overlap and not all temporal detail is visible. 

3.20 
Fig. 3.4. Seasonal Pacific herring biomass change in Lynn Canal (Sigler and Csepp 2007); data 

were converted to short tons to be consistent with units used by ADFG. Noted in the text, there 

is a large discrepancy between these biomass estimates and those of ADFG (e.g., Figs. 3.4 and 

3.7). 

0 

5000 

10000 

15000 

20000 

25000 

30000 

35000 

40000 

Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar Apr May 

month 

Biomass, short tons 

2001-2002 

2002-2003 

2003-2004 

3.21 
Fig. 3.5. Biomass estimates in tons for Lynn Canal herring, southeast Alaska (Moberly and 

Thorne 1974; Pritchett 2007). 

 

• 

···0 ··· 

- -.6.- -

14000 Winter Hydroacoustics 

Biomass Estimate (tons) 12000 

10000 

8000 

6000 

4000 

2000 

0 

1950 

Spawn Dep - Juneau Area 

Spawn Dep - Berners Area 

1960 1970 1980 1990 2000 2010 

Year 

3.22 
Fig. 3.6. Total nautical miles of herring spawn observed by year for aerial surveys of the Lynn 

Canal area, Southeast Alaska (Carlile et al. 1996; Pritchett 2007). 

3: 

"' a. 

(/) 

-

0 

1/1 

QJ 

2 

"' 

u 

.... 

::, 

z 

"' 

30 

25 

20 

15 

10 

5 

0 

1950 1960 

• 

1970 1980 

Year 

JL1neaL1 Area 

--e-- Berne rs Bay Area 

1990 2000 2010 

C 

3.23 
Fig 3.7. Relationships between the biomass estimates for Lynn Canal herring obtained from dive 

surveys (y) and the nautical miles of spawn obtained from aerial surveys (x). 

3.24 

0 

.. .. .. .. .... .. .. .. .. . .. ..... .. ..... .... 

0 -.. ... .. -.. .. .. -..... 

0 

___ 

o _________________________ _ 6 

Lynn Canal Herring 

Biomass Estimate (tons) 

8000 

7000 

6000 

5000 

4000 

3000 

2000 

1000 

0 

1983-1988 Surveys 

2004-2007 Surveys Slopes:

 1983-88 Surveys = 256

 2004-07 Surveys = 130

 All Surveys = 176 

0 2 4 6 8 10 12 14 

Nautical Miles of Spawn 
Fig. 3.8. Estimated historical biomass of Lynn Canal herring using miles of spawn observed 

during aerial surveys and the estimated biomass obtained from dive surveys. The aerial survey 

estimate is based on the the slope describing all surveys, 176 tons/mile (Fig. 3.6). The vertical 

bars identify 95% confidence bounds. 

3.25 

---+---

0 

t:. 

Estimated Biomass (tons) 

13000 

11000 

9000 

7000 

5000 

3000 

1000 

-1000 

1950 1960 1970 1980 1990 2000 2010 

Adjusted Aerial 

Spawn Dep - Juneau Area 

Spawn Dep - Berners Area 

Year 
0 

0 

8 

$ 0 

0 

6 

0 0 o 

003-00 A8o§0

Va ~~ o o . • . . 0 

0 0 0 

0 0 0 ~ 6 0 .. 

0 

0 

0 

0 gcP • 0 

0 0 

9? 

0 0 

0 0 

0 

0~ 0 

6 CJ 

s ; ; : · oc;? . ~~0 0 °: 6 av. 0 ; g 

0 

0 O 

0 

0 o 0 0 0 

0 0 ° 0 

0 0 

0 0 

8 0 

0 0 

0 0 

0 

0 

0 

0 

0 

0 

0 

O 0 

0 0 

0 0 

0 0 

0 

0 

0 

0 

0 

0 

0 

0 

0 

0 

0 

8 

0 

0 0 o 

8 8? 8 8 

Fig. 3.9a. Pacific herring age structure in northern SEAK. The data represented here are a 

subset of ADFG data (Pritchett 2007), fish captured during active spawn between March and 

May, thus describing local spawning stocks as closely as possible. (These selection criteria 

identified 78,971 fish of 188,628 in the database, 42%. Examination of a second category, prespawning fish captured within the same time period is recommended. Time constrains have 

precluded this analysis.) 

16 Lynn Canal 

12 

8 

4 

0 

16 Seymour Canal 

12 

8 

4 

0 

16 Tenakee 

12 

8 

4 

0 

16 Hoonah Sound 

12 

8 

4 

0 

16 Hobart-Houghton 

12 

8 

4 

0 

1980 1985 1990 1995 2000 2005 2010 

year 

Percent at age

3.26 
o JoPO 

0 o 

.. 

0 • 

0 . ?o::R· ; 0 0 

~ . 0 8 

•• 0 

. . • . 0 

0 • 0 0 0 O oo 0 0Q•O,Q_O 

0· 00QQ005uo 

:a· A og'g'8?s' O o g8o_, o . ~ ~ a . 

0 U ·O0oo 

• 0 

. • 0 0 

• • • 0 0 0 

Qo• ,ooQ•oOQO t6o~eg68~8~~? 

0 • 

~rD~ ~ 8 §_ 8 8 OJ~ 0 8 oFig. 3.9b. Pacific herring age structure in central and southern SEAK. 

16 Sitka Sound 

12 

8 

4 

0 

16 Craig 

12 

8 

4 

0 

16 Kah Shakes 

12 

8 

4 

0 

16 West Behm 

12 

8 

4 

0 

16 Ernest Sound 

12 

8 

4 

0 

1980 1985 1990 1995 2000 2005 2010 

year 

Percent at age 

3.27 
Fig. 3.10. Larval herring distribution in SEAK. Data are not synoptic and do not represent total 

habitat utilization; years are combined (Mattson and Wing 1978; Haldorson et al. 1986; 

Haldorson et al. 1987; Haldorson et al. 1988; Haldorson and Collie 1991; Wing et al. 1997; 

Johnson 2003; Arimitsu et al. 2007; Johnson 2007). Most observation efforts have been focused 

in Glacier Bay [1999 to 2004; (Arimitsu et al. 2007)], Sitka [1989 to 1990 (Haldorson and Collie 

1991)], and Auke Bay [1986 to 1988; (Wing and Reid 1972; Haldorson et al. 1986; Haldorson et 

al. 1987; Haldorson et al. 1988)]. Those in Haines and Saginaw Bay were collected in 1972 

(Mattson and Wing 1978). Offshore larvae were collected in 1990 (Wing et al. 1997). Some 

larvae are captured in ongoing habitat assessment research although these nets are too coarse for 

efficient larval capture (Johnson 2003; Johnson 2007). 

3.28 
Fig. 3.11. Juvenile Pacific herring distribution in SEAK. Observation in Glacier Bay was 

extensive [1999 to 2004 (Arimitsu et al. 2007; Piatt 2008)]. Sampling in other SEAK habitat 

was less comprehensive (Johnson 2003; Johnson 2007; Orsi et al. 2007; Cieciel 2008; MuretWoody 2008; Orsi 2008). 

3.29 
 

Spring ' summer, or fall 

Winter 

Fig. 3.12. Adult non-spawning Pacific herring distribution in SEAK (Rounsefell and Dahlgren 

1933; Rounsefell and Dahlgren 1935; Skud 1963; Carlson 1977; Arimitsu et al. 2007; Orsi et al. 

2007; Farley 2008; Orsi 2008; Vollenweider 2008). Not all areas have been sampled. 

3.30 
--- 25,000 • Kah Shakes/Cat Island j 25,000 • Hobart Bay/Port Houghton Biomass Biomass 

20,000 ~ Kah Shakes/Cat Island Catch 20,000 ~ Hobart Bay/Port Houghton Catch 

15,000 15,000 

10,000 10,000 

5,000 5,000 

0 oeeeee.e,e~Sh~ 

t~ 

"' "' "' '° '° '° '°' '° '° '° '° '° '° "' "' "' <O <O <O <O <O <O <O <O <O <O 0 0 0 0 0 0 00 00 ? 00 00 <O <O '£ <O <O 0 0 i g: 00 ~ O> 00 :g ~ '£ <O <O 0 0 0 i "' "' 00 0 "' 0, 00 0 "' "' O> 00 0, 00 0 "' -, 

[ • W. Behm Caoal Bk>mass 25,000 • Seymour Canal Biomass 

- 20,000 ~ W. Behm Canal Catch 20,000 ~ Seymour Canal Catch "' 15,000 ~ 15,000 •• ~ 10,000 1 ~ 10,000 

Cl) 5,000 ... 5,000 •• 

0 0 s.,,, ..... ,~ 0 

- '° '° <O '° '° '° '° "' "' "' <O <O '° <O <O '° '° '° <O <O <O 0 0 0 <O <O "' "' "' 0 0 0 

Cl) 00 00 ? 00 00 <O <O '£ <O <O 0 0 i 00 00 ? 00 00 <O <O '£ <O <O 0 0 0 i "' "' 00 0 "' 0, 00 0 "' 0 "' 0, 00 0 "' "' 00 0 "' 

nl 

(.) 

en 25,000 25,000 1 6 Hoooah s°""' Bl~as, I - 20,000 20,000 

C: ~ Hoonah Sound Catch 

Cl) 15,000 15,000 • ... • ~ 10,000 10,000 

5,000 5,000 

"C • 0 0 

Cl> 

~-

co <D ~ <D ~ ~ ~ <D "' "' "' ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ 

(!) (!) (!) (!) (!) (!) 0 0 0 (!) "' "' "' "' "' "' "' "' "' "' "' "' 0 0 0 

- 00 00 ~ 00 00 <O <O <O <O <O 0 0 0 00 00 ~ 00 00 <O <O <O <O <O 0 0 i 0 0 "' 0, 00 0 "' ,,, "' 00 0 "' ,,, 0 "' 0, 00 0 "' ,,, "' 00 0 "' 

C: 

- Ernest Sound Cl) • Biomass • Sitka Biomass 

z 20,000 ~ Ernest Sound Catch 120,000 

0 15,000 ~ Sitka Catch 

110,000 • I- 10,000 100,000 

5,000 • • • 90,000 

0 ~ <> ~ 80.000 

<O <O <O <O <O <O <O <O <O <O "' 0 "' 0 0 "' 00 00 ? 00 00 <O <O '£ <O <O 0 0 i 70,000 • 0 "' "' 00 0 "' "' 00 0 "' 

25,000 • Tenakee Inlet Biomass 

60,000 j 

50,000 

20,000 ~ Tenakee Inlet Catch 40,000 -

15,000 30,000 • •• 10,000 20,000 4 • 

5,000 10,000 

0 0 

L '° <O '° <O <O <O '° '° '° '° "' "' "' '° '° '° <O <O '° '° '° 0 0 0 <O <O 0 "' "' "' 0 0 00 00 ~ 00 00 <O <O '£ <O <O 0 0 ~ 00 00 ? 00 00 <O <O '£ <O <O 0 0 0 i "' "' 00 0 "' "' 00 0 "' 0 "' "' 00 0 "' "' 00 0 "' 

YEAR 

Fig. 3.13. Total mature herring biomass (tons) and human harvest (tons) at major spawning 

locations in SEAK (Carlile 2003; Pritchett 2007). See Fig. 3.7 for Lynn Canal biomass. 

Biomass is characterized with smoothed data [4235H method; (Velleman and Hoaglin 1981)]. 

3.31 
& Utter (1984) 

Lynn Canal 

Management Area 

Fig. 3.14. Genetic measures involving SEAK herring. Blue ellipses are the result of a Pacific 

Ocean scale allozyme analysis (Grant and Utter 1984) and the red ellipse is the SEAK grouping 

estimated by microsatellite analysis (Beacham et al. 2002). 

3.32 
edian 

• 94.5- 100.0 

• 100.0 - 104.5 

• 104.5 - 119.0 

• 119.0 - 123.0 

• 123.0 - 132.8 

N 

A 

100 

Kilometers 

Fig. 3.15. Spawn timing (median Julian days) by location in SEAK (Davidson et al. 2005; 

Pritchett 2006; Coonradt 2008). The question mark indicates missing information. Circled areas 

divide the data into earlier and later spawning groups. Areas range from 11,500 to 37,800 km2 

(water only); predicted herring spawning fidelity is 100% in areas this size [derived from Hay et 

al. (Hay et al. 1999)]. 

3.33 
 Fig. 3.16. Range of spawn timing of Pacific herring aggregations along the west coast of North 

America. Data from Stout et al. (Stout et al. 2001), a compilation of other authors (Hourston 

109-; Rounsefell 1930; Chapman et al. 1941; Miller and Schmidtke 1956; Scattergood et al. 

1959; Skud 1960; Alderdice and Velsen 1971; Barton and Wespestad 1980; ADFG 1985; Hay 

1985; Lemberg et al. 1997; Davidson et al. 2005). SEAK data were updated (Davidson et al. 

2005; Pritchett 2006; Coonradt 2008) and approximate latitude was added with reference to 

original work. Vertical bars indicate the range of spawn timing with symbols at the midpoints. 

r = 0.950 

200 

Mid spawn date (Julian day) 150 

100 

r = 0.918 

50 

NE Pacific 

SEAK only 

0 

30 40 50 60 

North latitude (degrees) 

70 

3.34 
 

35 40 45 50 55 

I I I I I I I ii I !F-C I I I I I I 

0 2 4 6 8 10 12 14 

Sea Surface Temperature 

Fig. 3.17. Typical sea surface temperature gradient in SEAK in spring. 

3.35 
Fig. 3.18a. Differences in recruitment suggest herring in SEAK can be subdivided into more 

than one region. Illustrated areas are based on Figures 4 (red), 7 (black), 8 and 9 (blue) in 

Williams and Quinn (2000); see Fig. 3.17b. Question marks indicate missing information. 

Delineated areas entirely within SEAK range from 1100 to 49,500 km2

 (water only); predicted 

herring spawning fidelity ranges from 41 to 100% in areas this size [derived from Hay et al. 

(1999)]. 

3.36 
i 

R 

Figu N -t. Scattell}lot of U1c fin.; two dimensions from a metric 

multidimensional scaling analysis of Bering Sea and NE Pacific 

herring recruitment estimates. 

......... , 

Metric t.05, Mlnhaltan Distance 

VarianceE,ipllined·5591A, 

.... :~ \ ~ 

i 

t..·· ...... ~i °'1 .\ 

( t&M 

\ 

\ w:,ci 

" 

! 

i 

\cc SCG,/ ................ · 

... 

'\ ... ._ ... .,' 

r:::·~\) 

\ ..... '?_'!.0-/ 

100 

... 

.. 

Figure 7. Dendroi:rom from divisive hierarchical anal1·sis of 

NE Pacific herring recruitment estimates. 

4 6 

PIIIIS 

SIT 

SEAi< 

SEY 

KAH 

CRG 

PR 

8 

KOO 

QCI 

Height 

10 12 14 

i 

Figure 8, Scattell}lot of first two dimensions from a metric 

multidimensional scaling analysis of NE Pacific herring 

recruitment estimates corresponding to the 1978-1993 year 

classes. 

,I' ..... 

/ : /'1Wti 

,' : ; i 

i i I ;' 

I ' / / : WM/ 

i••,/ ,_, 

-· 

Figure 9. Dendrogram from divisive hierarchical analysis of 

NE Pacific herring rccnoitmcm c,1ima1cs corresponding to 

the 1978-1993 year classes. 

2 

SIT 

SEAK 

KAH 

PR 

VCI 

SOG 

3 

CRG 

Height 

4 

KOO 

OCI 

5 6 

i 

i 

) 

l 

Fig. 3.18b. Recruitment analysis figures from Williams and Quinn (2000). SEAK = SIT + CRG 

in this analysis. 

3.37 
Age 4 

Median length (mm) 

176.0 - 186.9 

186.9 • 194.5 

• 194.5 - 199.2 

• 199.2 • 207.1 

• 207.1 - 214.8 

~ 

.rr-0 ' <. 1 ' I ~ ·· 

Fig. 3.19. Length-at-age data from 1929, year class 4 (Rounsefell and Dahlgren 1935), do not 

suggest definitive separation among herring in SEAK. 

3.38 
Fig. 3.20. Relationship between age and body size among SEAK herring stock (Johnson et al. 

1997; Carls et al. 1998). Shelter Island is within the Lynn Canal management area; Cat Island is 

near Kah Shakes. Symbol size is related to number of fish; the smallest symbols represent single 

fish; interpretation of such data obviously requires caution. 

3.39 

... 

• 

300 

270 

gth (mm) 240 Fork len 210 

180 

150 

200 

Shelter Is. 

Sitka Sound 

Cat Is. 

Seymour Canal 

150 

ht (g) 

100 

Somatic wet weig

50 

0 

3 4 5 6 7 8 

Age 

9 10 11 
.rr-0 

' ~j I 

Fig. 3.21a. Differences among Pacific herring weight-at-age in SEAK. Illustrated areas are 

based on Williams and Quinn (2000) weight at age analysis. Question marks indicate missing 

information. The circled area in SEAK is 34,000 km2

 (water only); predicted herring spawning 

fidelity is 100% in an area this size [derived from Hay et al. (1999)]. 

3.40 
rvos, . nan CKs~e 

~l'lilng<t l::4pl.-:iin~ ; 89' ~ 

t<.00 

I I I I I • I 

-1;:,«'0 Q 

(ity 

Fig. 3.21b. Figure 10 of Williams and Quinn (2000). Metric multidimensional scaling analysis 

of Pacific herring weight-at-age data for ages 3 to 8 from the Bering Sea and NE Pacific. SEAK 

= SIT + CRG in this analysis. 

3.41 
20 

HOB LYN 

10 

ERN 

0 TEN SEY 

-10 

-20 

-30 

20 

KAH 

CRG BEH 

10 

HOO 

0 

-10 

SIT 

-20 

-30 

1975 1985 1995 2005 1975 1985 1995 2005 

Year Year 

Length deviation (mm) Length deviation (mm) 

Fig. 3.22. Trends in size (length) at age in SEAK Pacific herring stocks; Lynn Canal (LYN), 

Seymour Canal (SEY), Tenakee (TEN), Hobart-Houghton (HOB), Ernest Sound (ERN), Craig 

(CRG), Hoonah Sound (HOO), Sitka Sound (SIT), Kah Shakes (KAH), and West Behm Canal 

(BEH). The data represented here are a subset of ADFG data (Pritchett 2007), fish captured 

during active spawn between March and May, thus describing local spawning stocks as closely 

as possible. (These selection criteria identified 78,971 fish of 188,628 in the database, 42%. 

Examination of a second category, pre-spawning fish captured within the same time period is 

recommended. Time constrains have precluded this analysis.) 

3.42 
r 

300 Lynn Canal Seymour Canal 

250 

200 

150 

100 

300 Tenakee Sitka 

250 

200 

150 

Standard length (mm) Standard length (mm) 

100 

1980 1985 1990 1995 2000 2005 1980 1985 1990 1995 2000 2005 

year year 

Fig. 3.23. Cohort growth in northern SEAK (power model); growth in remaining SEAK stocks 

is not illustrated. Individual cohorts are distinguished by color, symbol shape, and symbol fill. 

Symbol sizes correspond to the number of measurements (the largest indicate >100, the smallest 

≤10). The data represented here are a subset of ADFG data (Pritchett 2007), fish captured during 

active spawn between March and May, thus describing local spawning stocks as closely as 

possible. (These selection criteria identified 78,971 fish of 188,628 in the database, 42%. 

Examination of a second category, pre-spawning fish captured within the same time period is 

recommended. Time constrains have precluded this analysis.) 

3.43 
• 51.96- 52.11 

• 52.11 - 52.26 

• 52.26 - 52.33 

• 52.33 - 52.40 

• 52.40 - 52.51 

• 52.51 - 52.63 

• 52.63 - 52.80 

All years 

Fig. 3.24. Vertebrae number in SEAK herring (Rounsefell and Dahlgren 1935). Symbol sizes 

are largest for the earliest year classes so that variability in vertebrate number is evident for each 

location. The question mark indicates missing information. Circled areas divide SEAK into 

three possible regions, northern, southern, and central, the latter with a somewhat higher 

vertebrae count. Admittedly these divisions are highly subjective. Circled areas range from 

3800 to 15,200 km2 (water only); predicted herring spawning fidelity ranges from 69 to 100% in 

areas this size [derived from Hay et al. (1999)]. 

3.44 
Fig. 3.25. Pacific herring migration in SEAK, observed by tagging studies (Rounsefell and 

Dahlgren 1933; Rounsefell and Dahlgren 1935; Dahlgren 1936; Skud 1963; Carlson 1977). 

Question marks indicate missing or incomplete information. The circled area identifies the 

approximate area of known mixing and is 31,600 km2 (water only); predicted herring spawning 

fidelity within an area this large is 100% [derived from Hay et al. (1999)]. 

3.45 
Chapter 4 

Pacific herring habitat in southeastern Alaska 

Scott W. Johnson, Mandy R. Lindeberg, A. Darcie Neff, and Pat M. Harris 

Abstract 

Marine habitat in southeastern Alaska (SEAK) is variable, yet Pacific herring essentially 

occupy all of it. Organic sediment and semi-protected, partially mobile substrate are the most 

common shore type and habitat class among all areas. Marine waters of SEAK are characterized 

by an inshore-offshore salinity gradient and a north-south temperature gradient. Inside waters 

are more estuarine, more protected from wave action, and have more extreme seasonal 

fluctuations in temperature and salinity than outside waters. Herring were captured in essentially 

all areas of SEAK; occasional capture failures were interpreted as insufficient sampling, not an 

absence of herring. Eelgrass meadows, kelp communities, sand-gravel beaches, and bedrock 

outcrops comprise a continuum of habitat types available to herring throughout SEAK. The 

percent shoreline extent of kelps (canopy and understory) and eelgrass are reduced in Lynn 

Canal compared to all other areas but herring continue to spawn in Berners Bay and juveniles 

continue to utilize nearshore habitats in Auke Bay, Favorite Channel, and Berners Bay. 

Introduction 

Because all life stages of Pacific herring (Clupea pallasii) are responsive to climatic and 

oceanographic conditions, areas that this species inhabits are linked to population survival and 

success. Spawn timing, for example, is related to winter and spring sea surface temperatures 

(Lassuy 1989; Emmett et al. 1991; Brown and Carls 1998). Hatching must coincide with 

sufficient zooplankton abundance or larvae will starve and survival may be the principal 

determinant of year class strength (Hjort 1914; McGurk 1984; Norcross et al. 2001). These fish, 

particularly first year juveniles, must accumulate enough energy before winter to survive winter 

starvation (Paul et al. 1998). 

In this chapter, we focus on herring habitat and how it varies by region in southeastern 

Alaska (SEAK). The specific goal is to determine if habitat in Lynn Canal is unique or discrete 

compared to other areas. Ten areas with a history of known herring populations were used in 

habitat comparisons (Fig. 4.1). Lynn Canal was divided into three study areas (Berners Bay, 

Favorite Channel, and Auke Bay) and Sitka Sound was divided into three areas (northern, 

central, and southern). The other study areas were Tenakee Inlet, Craig, Duke Island, and Kah 

Shakes Cove (Fig. 4.1). Within each area we examined shore type, habitat class, extent of 

vegetation types (e.g., kelp, eelgrass), environmental data (temperature, salinity), general fish 

distributions, and historical herring spawning areas. The selection of the 10 areas was also based 

on the availability of data from three major datasets [ShoreZone aerial imagery (Harney et al. 

2007), Nearshore Fish Atlas of Alaska (Nearshore Fish Atlas of Alaska. 2007) and ADFG 

spawning surveys (Leon 1993; Herbert and Carlile 2002; Davidson et al. 2005; Pritchett 2006)]. 

The habitat and shore type classifications referenced in this report are based on the 

classifications used by the Alaska ShoreZone program. There are 35 shore type classes; such as 

rock cliff, organic sediment, and man-made [Table 4.1; (Howes et al. 1994)]. Habitat 

classification relates dominant structuring processes (e.g., fluvial, glacial, and wave energy) to 

biologically based estimates of exposure (Table 4.2). A complete description of ShoreZone 

methods and habitat classifications is presented in Harney et al. (2007). 

4.1 
Pacific herring habitat utilization in SEAK 

Juvenile herring occupy a variety of habitat types including steep bedrock outcrops, 

eelgrass, kelps, and sand-gravel beaches in SEAK. In surveys from 1998 to 2007, mean catch 

per seine haul for herring was greatest in bedrock outcrops, followed by kelp, eelgrass, and sand 

and gravel beaches (Fig. 4.2) (Johnson et al. 2005; Nearshore Fish Atlas of Alaska. 2007). In 

brief, bedrock outcrops are usually steep and located in exposed locations on the outside of bays– 

Laminaria and Alaria are usually attached to bedrock faces; eelgrass meadows are typically 

located inside protected bays and inlets in soft substrates of sand, silt, or mud; understory kelps 

(Laminariales) occupy more exposed locations, often near the entrance of bays; and sand or 

gravel beaches with no rooted vegetation are generally “pocket beaches” found inside protected 

bays–algae (e.g., filamentous) is occasionally present. Characteristic of schooling fishes, herring 

were captured infrequently with a beach seine (<20% of all hauls) but often in large numbers 

(Johnson et al. 2005; Johnson and Thedinga 2005). After hatching in spring, larvae scatter 

widely, both nearshore and offshore. At metamorphosis juvenile herring move into nearshore 

water [in late July and early August in Auke Bay (Jones 1978)] and spend the first three years of 

their lives in nearshore waters (Tanasichuk et al. 1993) 

Herring tolerate a wide range of temperatures and salinities. Juvenile herring were 

captured in nearshore habitats throughout SEAK in seawater temperatures that ranged from 

4.0°C to 16.9°C [Table 4.3; (Johnson and Lorenz)]. Temperature profiles from several locations 

in northern SEAK, including Lynn Canal, exhibited a similar pattern; mean monthly 

temperatures were usually lowest in March (about 4°C) and highest in August or September 

[about 13°C; (NMFS. 1974; Johnson and Thedinga 2005)]. Herring were captured in nearshore 

habitats throughout SEAK in salinities that ranged from about 7 PSS to 33 PSS (practical salinity 

scale) [Table 4.3; (Johnson and Lorenz)]. 

In Lynn Canal, herring commence spawning when sea-surface temperatures (SST) 

increase to 5 to 6°C (Carlson 1980). Sea surface temperatures in Auke Bay increased about 

0.024°C per year between 1976 and 2004 (Wing et al. 2006). The greatest freshwater input is 

from April to November; surface salinity is highest (31 PSS) in March and usually lowest (10-15 

PSS) in late July or August. Herring spawn from late April to early May in Lynn Canal, a time 

of relatively high salinity (USDA 2004). 

Comparisons among study areas 

For each study area, there are three maps: a four-panel map with shore type, habitat 

class, kelp distribution, and eelgrass distribution based on ShoreZone aerial imagery (see 

Appendix I for definitions); a four-panel map showing historical herring spawn locations from 

the early 1970s to 2007 [ADFG surveys (Pritchett 2006)]; and a map showing beach seine 

capture locations of juvenile herring by habitat type, overall fish species composition, and 

temperature data (not available for all areas) from NOAA Fisheries (Nearshore Fish Atlas of 

Alaska. 2007). On the ShoreZone imagery maps, boundaries included in habitat descriptions are 

depicted by large Xs. Study areas are described from north to south in SEAK (Fig. 4.1). 

Lynn Canal 

Berners Bay 

The Berners Bay study area includes 89.3 km of shoreline (excludes Berners River delta) 

from Point Sherman to Sunshine Cove (Fig. 4.3a). Shoreline outside of Berners Bay is 

dominated by wide platforms with gravel beaches which are semi-protected and partially mobile. 

4.2 
Inside Berners Bay, beaches are dominated by organic sediment and wide sand and gravel flats. 

Dominant organic sediment (27%) are primarily associated with estuary habitats (29%) and other 

areas of the bay are mainly semi-protected, protected, or partially mobile (Figs. 4.3a,b). Less 

common shore types within the classification “other” (40%) represent 22 separate classes which 

are not dominated by one class or a uniquely different class (Fig. 4.3a). Semi-exposed or 

exposed habitats are not found in this area. The shoreline extent of kelps is dominated by Fucus 

(57%) followed by Alaria (34%), understory kelps (14%), and canopy kelps (5%) (Fig. 4.3c). 

Eelgrass is present on only about 5% of the shoreline (Echo Cove and Bridget Cove) (Fig. 4.3d), 

and total area of all eelgrass beds is about 10 ha (Harris et al. In prep). Limited development has 

occurred in Berners Bay (man-made or modified shoreline is <1% or 174 m) but future activities 

may include the enlargement of a marine terminal at Slate Creek Cove (Fig. 4.3a) to service the 

Kensington Gold Mine (Harris et al. 2005) and construction of an access road from Juneau to 

Skagway. 

The Lynn Canal herring population has declined since the 1950s; mean shoreline extent 

of spawn averaged roughly 15 km in the 1950s compared to about 5 km in the 2000s (Fig. 4.4) 

(Williams et al. 2004). In 2007, about 12 km of spawn was observed in Lynn Canal (Alaska 

Department of Fish and Game. 2007). Presently, most Lynn Canal herring spawn in the vicinity 

of Berners Bay. In the 1970s and 1980s, herring spawned from south of Point Sherman to 

Sunshine Cove (Figs. 4.5a,b), whereas in the 1990s and 2000s, spawning was concentrated along 

the eastern shore of Berners Bay and from Point Bridget to Bridget Cove (Figs. 4.5c,d). No 

significant spawning in any year has been observed in Echo Cove on kelp or eelgrass 

Juvenile herring utilize eelgrass and kelp in Berners Bay. Nearly 9,000 herring were 

captured in 16 of 54 beach seine hauls from 1998 to 2006; mean fish size was 44 mm FL (Fig. 

4.6) (Nearshore Fish Atlas of Alaska. 2007). No herring were captured in northern Berners Bay 

on sand-gravel substrates void of vegetation. In addition to herring, 41 other species were 

captured; dominant species included young-of-the year (YOY) chum salmon (Oncorhynchus 

keta), coho salmon (O. kisutch) smolts, tubesnout (Aulorhynchus flavidus), and crescent gunnel 

(Pholis laeta) (Fig. 4.6). Temperature profiles in Berners Bay followed seasonal patterns similar 

to other areas in SEAK; mean monthly temperatures were usually lowest in February or March 

and highest in July or August (Fig. 4.6). 

Favorite Channel 

The Favorite Channel study area includes 60.7 km of shoreline from Sunshine Cove to 

Lena Point (Fig. 4.7a). The shoreline within Favorite Channel is dominated by rock ramps with 

gravel (21%), sand and gravel flats (10%), and by wide platforms with gravel (9%) that range 

from mostly semi-protected (53%) to protected (13%) from wave action, with partially mobile 

sediments. Estuaries (19%) and semi-protected shorelines with immobile substrates (8%) are 

also common in this area (Figs. 4.7a,b). Shore types within the classification “other” (60%) 

represent 20 separate classes mostly comprised of gently sloping wide sand and gravel flats that 

are concentrated near the Eagle River Delta and where most of the estuarine habitat is present 

(Fig. 4.7a). Semi-exposed or exposed habitats are not found in this area. The shoreline extent of 

kelps is dominated by Fucus (57%) followed by Alaria (27%), and understory kelps (26%); 

canopy kelps are absent (Fig. 4.7c). Eelgrass is present on less than 2% of the shoreline 

(Sunshine Cove and Tee Harbor) (Fig. 4.7d); total area of all eelgrass beds is about 1.4 ha (Harris 

et al. In prep). Development along Favorite Channel (man-made or modified shoreline is 1% or 

552 m) is mostly limited to residential homes concentrated in Lena Cove and Tee Harbor. A 

4.3 
major Steller sea lion (Eumetopias jubatus) haulout is located on Benjamin Island (Fig. 4.7a); up 

to 800 sea lions may use this haulout from October to June (Thedinga et al. 2006). 

Historically, spawning has been concentrated on the eastern side of Favorite Channel 

with no significant spawning on any of the nearby islands (Shelter Island, Lincoln Island) (Fig. 

4.8a). In the 1970s, herring spawned along most of the shoreline from Sunshine Cove to Tee 

Harbor (Fig. 4.8a), whereas in the 1980s spawning was sparse and concentrated near Sunshine 

Cove and Tee Harbor (Fig. 4.8b). Spawning was almost nonexistent in the 1990s and sparse and 

concentrated near Sunshine Cove in the 2000s (Figs. 4.8c,d). 

Juvenile herring use bedrock, kelp, and sand-gravel habitats in Favorite Channel. Nearly 

5,000 herring were captured in 16 of 95 beach seine hauls from 2001 to 2006; mean fish size was 

55 mm FL (Fig. 4.9) (Nearshore Fish Atlas of Alaska. 2007). In addition to herring, 37 other 

species were captured in Favorite Channel; dominant species included Pacific sand lance 

(Ammodytes hexapterus), walleye pollock (Theragra chalcogramma), tubesnout, and YOY pink 

salmon (O. gorbuscha) (Fig. 4.9). Temperature profiles in Favorite Channel followed seasonal 

patterns similar to other areas in SEAK; mean monthly temperatures were usually lowest in 

February or March and highest in July or August (Fig. 4.9). 

Auke Bay 

The Auke Bay study area includes 52.1 km of shoreline between Lena Point and Outer 

Point on Douglas Island (Fig. 4.10a). The shoreline within Auke Bay is dominated by gently 

sloping sand and gravel flats (23%), organic sediment (14%), estuaries (16%), and rock ramps 

with gravel and sand beaches (10%). These beaches are mostly semi-protected-partially mobile 

(43%), or semi-protected (8%) from wave action with mobile sediments and protected-partially 

mobile (8%) substrates (Figs. 4.10a,b). Less common shore types within the classification 

“other” (45%) represent 22 separate classes which are not dominated by one class or a uniquely 

different class (Fig. 4.10a). Steep rock cliffs and semi-exposed shoreline are mostly absent in 

this area. The shoreline extent of kelps is dominated by Fucus (60%) followed by Alaria (12%), 

and understory kelps (10%); canopy kelps are absent (Fig. 4.10c). Eelgrass is present on about 

6% of the shoreline (Fig. 4.10d), and total area of all eelgrass beds in Auke Bay is about 8 ha 

(Harris et al. In prep). Auke Bay has a history of public, private, and commercial development 

including a ferry terminal, marina, docks, and housing complexes–about 16% of the shoreline 

has been subject to man-made alterations (Figs. 4.10a,b). 

In the 1970s, most herring spawned in the vicinity of Indian Point, whereas in the 1980s 

spawning was concentrated near the present day marina (Figs. 4.11a,b). No significant spawning 

has occurred in Auke Bay since the 1980s (Figs. 4.11c,d). Historical spawning beaches overlap 

with public, private, and commercial development (Figs. 4.11a,b). In addition, historical 

spawning locations were near or in eelgrass beds (Figs. 4.10d, 4.11a,b). Loss of eelgrass from 

development in Auke Bay is unknown. Anecdotal evidence suggests that the size of the eelgrass 

bed in Auke Nu Cove (Fig. 4.10d) was about 5.7 ha in the early 1980s (USCOE. 1984) compared 

to 1.9 ha in 2007 (Harris et al. In prep). 

Presently, juvenile herring still utilize eelgrass in Auke Bay. Over 800 herring were 

captured in 11 of 39 beach seine hauls from 1999 to 2007; mean fish size was 42 mm FL (Fig. 

4.12) (Nearshore Fish Atlas of Alaska. 2007). Herring may use other habits in Auke Bay but 

they have not been sampled. In addition to herring, 36 other species were captured in Auke Bay; 

dominant species included YOY chum and pink salmon, tubesnout, crescent gunnel, and 

threespine stickleback (Gasterosteus aculeatus) (Fig. 4.12). Temperature profiles in Auke Bay 

4.4 
 

followed seasonal patterns similar to other areas in SEAK; mean monthly temperatures were 

usually lowest in February or March and highest in July or August (Fig. 4.12). 

Tenakee Inlet 

The Tenakee Inlet study area includes 116.0 km of shoreline between East Point and 

Tenakee Springs on the north side of the inlet and between South Passage Point and Saltery Bay 

on the south side of the inlet (Fig. 4.13a). The shoreline within Tenakee Inlet is dominated by 

organic sediment (42%) and estuarine habitats (45%). Gently sloping sand and gravel flats 

(20%) and wide platforms with gravel and sand (11%) are also common shore types. Habitat 

classifications in addition to dominating estuaries include protected with partially mobile (27%), 

semi-protected with partially mobile (4%), and semi-protected with mobile substrates (Figs. 

4.13a,b). Less common shore types within the classification “other” (27%) represent 20 separate 

classes which are not dominated by one class or a uniquely different class (Fig. 4.13a). Habitat 

information is not currently available for the southern shoreline outside Tenakee Inlet, a known 

spawning area for herring. The shoreline extent of kelps is dominated by Fucus (54%) followed 

by understory kelps (44%), Alaria (6%), and canopy kelps (1%) (Fig. 4.13c). Eelgrass and 

surfgrass are present on about 57% and 1% of the shoreline (Fig. 4.13d). Development is 

minimal in Tenakee Inlet (man-made or modified shoreline is <1% or 526 m) and concentrated 

near the small community of Tenakee Springs with a population of about 100 people (Fig. 

4.13a). 

Records of herring spawn in Tenakee Inlet are limited to 1998 and later; most spawning 

has been on the south side of the inlet. In 1998, 1999, and 2000 most spawning was between 

Trap Bay and Basket Bay (Figs. 4.14a,b). In 2001, spawning was concentrated from Corner Bay 

to Saltery Bay (Fig. 4.14b). From 2002 to 2007, spawning occurred along much of the shoreline 

from Basket Bay to Saltery Bay (Figs. 4.14c,d). Based on the shoreline extent of eelgrass and 

kelp in Tenakee Inlet, herring likely spawn on both vegetation types. 

Herring were not captured in Tenakee Inlet in 20 beach seine hauls from 1998 to 2006 

(Fig. 4.15) (Nearshore Fish Atlas of Alaska. 2007). A total of 28 species were captured; 

dominant species included YOY chum and pink salmon, threespine stickleback, crescent gunnel, 

and Pacific cod (Gadus macrocephalus) (Fig. 4.15). Temperature profiles in Tenakee Inlet (Crab 

Bay) followed seasonal patterns similar to other areas in SEAK; mean monthly temperatures 

were usually lowest in February or March and highest in July or August (Fig. 4.15). 

Sitka 

Northern Sitka Sound 

The northern Sitka Sound study area includes 314.2 km of shoreline encompassed by 

Sinitsin Cove, Kane Island, Lisianski Point, and Mountain Point (Fig. 4.16a). The shoreline 

within the northern Sitka Sound study area contains organic sediment (22%) and estuarine 

habitats (22%), narrow sand and gravel beaches (17%), and rock ramps with gravel (9%). Less 

common shore types within the classification “other” (52%) represent 27 separate classes of 

which sand and gravel flats or fans and rock cliffs with gravel beaches are prevalent (Fig. 4.16a). 

Dominate habitats include protected partially mobile (33%), estuaries, semi-protected partially 

mobile (17%), and protected immobile (7%) substrates (Figs. 4.16a,b). Less common habitat 

classifications within “other” (21%) are mostly current dominated habitats. The shoreline extent 

of kelps is dominated by Fucus (86%) followed by understory kelps (70%), canopy kelps (17%), 

and Alaria (12%) (Fig. 4.16c). Eelgrass and surfgrass are present on 39% and 1% of the 

4.5 
 

shoreline (Fig. 4.16d). Shoreline development is sparse in northern Sitka Sound (man-made or 

modified shoreline is <1% or 780 m) and limited mostly to cabins; ferry and recreational boat 

traffic can be high, especially in summer with the community of Sitka nearby. 

From the 1960s to the 1990s, most spawning occurred on the north end of Partofshikof 

Island, southern Krestof Island, northern Halleck Island, and in the vicinity of Lisianski 

Peninsula (Figs. 4.17a,b,c). Since 2000, spawning has been much more extensive, especially in 

2005, when almost all of northern Sitka Sound was covered with spawn (Fig. 4.17d). Based on 

the shoreline extent of eelgrass and kelp in northern Sitka Sound, herring likely spawn on both 

vegetation types. 

Juvenile herring utilize bedrock, eelgrass, and sand-gravel habitats in northern Sitka 

Sound; herring likely also use kelp but only one kelp site was sampled. Over 5,000 herring were 

captured in 19 of 53 beach seine hauls from 1998 to 2006; mean fish size was 94.2 mm FL (Fig. 

4.18) (Nearshore Fish Atlas of Alaska. 2007). In addition to herring, 45 other species were 

captured in northern Sitka Sound; dominant species included YOY chum and pink salmon, 

shiner perch (Cymatogaster aggregata), and Pacific sand lance (Fig. 4.18). No thermograph data 

are available from northern Sitka Sound. 

Central Sitka Sound 

The central Sitka Sound study area includes 369.3 km of shoreline from Lisianski Point 

to the vicinity of Redoubt Bay (excludes Silver Bay, Deep Bay, Redoubt Bay) (Fig. 4.19a). The 

shoreline within central Sitka Sound area has rock ramps with gravel (14%), rock cliffs (13%) 

and narrow rock ramp (13%) beaches. Less common shore types within the classification 

“other” (54%) represent 26 separate classes of which steep cliffs with gravel, sand and gravel 

flats or fans and estuaries are prevalent (Fig. 4.19a). Dominate habitats include semi-protectedpartially mobile (29%), protected-partially mobile (15%), semi-protected-immobile (15%), and 

estuaries (5%) (Figs. 4.19a,b). Less common habitat classifications within “other” (29%) are not 

dominated by one class or a uniquely different class but semi-exposed habitats are present. The 

shoreline extent of kelps is dominated by Fucus (83%) followed by understory kelps (69%), 

Alaria (38%), and canopy kelps (38%) (Fig. 4.19c). Eelgrass and surfgrass are present on 32% 

and 11% of the shoreline (Fig. 4.19d). Shoreline development is concentrated around the 

community of Sitka (man-made or modified shoreline is 7% or 24,082 m). Sitka has a 

population of about 9,000 people; recreational and commercial boat traffic is high, especially 

during the summer months and numerous cabins are located on many islands in Sitka Sound. 

In the 1960s and 1970s, most spawning occurred from Lisianski Peninsula (including 

Katlian Bay) and Middle Island south to the community of Sitka and in the vicinity of Eastern 

Channel (Fig. 4.20a). From the 1980s to the 2000s, spawning occurred throughout central Sitka 

Sound including Silver Bay and Deep Inlet in 2005 (Figs. 4.20b,c,d). Based on the shoreline 

extent of eelgrass and kelp in northern Sitka Sound, herring likely spawn on both vegetation 

types. 

Juvenile herring utilize bedrock, eelgrass, kelp, and sand-gravel habitats in central Sitka 

Sound. Nearly 1,500 herring were captured in 10 of 58 beach seine hauls from 1998 to 2006; 

mean fish size was 84.6 mm FL (Fig. 4.21) (Nearshore Fish Atlas of Alaska. 2007). In addition 

to herring, 47 other species were captured in northern Sitka Sound; dominant species included 

shiner perch, YOY chum and pink salmon, and Pacific sand lance (Fig. 4.21). Temperature 

profiles from central Sitka Sound (Sandy Cove) followed seasonal patterns similar to other areas 

4.6 
in SEAK; mean monthly temperatures were usually lowest in February or March and highest in 

August or September (Fig. 4.21). 

Southern Sitka Sound 

Shore type and habitat class information is not available for southern Sitka Sound. 

Shoreline extent of kelps and eelgrass is likely very similar to northern and central Sitka Sound. 

Shoreline development is sparse in southern Sitka Sound; there are a few cabins and recreational 

boat traffic from the nearby community of Sitka is limited. 

In the 1970s and 1990s most spawning was in the vicinity of Redoubt Bay and the 

Necker Islands (Figs. 4.22a,c). In the 1980s, spawning occurred from Redoubt Bay into West 

Crawfish Inlet (Fig. 4.22b). Since 2000, spawn has been extensive and in some years continuous 

throughout all of southern Sitka Sound (Fig. 4.22d). 

About 3,000 herring were captured in only 1 of 23 beach seine hauls in southern Sitka 

Sound from 1998 to 2006; mean fish size was 31.3 mm FL (Fig. 4.23) (Nearshore Fish Atlas of 

Alaska. 2007). In addition to herring, 35 other species were captured in southern Sitka Sound; 

dominant species included Pacific cod, bay pipefish (Syngnathus leptorhynchus), shiner perch, 

and juvenile greenling (Hexagrammidae) (Fig. 4.23). No thermograph data is available from 

southern Sitka Sound. 

Craig 

The Craig study area includes 426.1 km of shoreline from Blanquizal Island to Craig 

(Fig. 4.24). Only shore type information is currently available for this area. The shoreline 

within the Craig area has organic sediment (19%) associated with estuaries, sand and gravel flats 

(17%), and rock ramps with gravel and sand (16%) beaches (Fig. 4.24). Less common shore 

types within the classification “other” (47%) represent 19 separate classes of which narrow sand 

and gravel beaches are prevalent including rock platforms with sand and gravel and rock ramps 

with gravel. Although not assessed, kelps and eelgrass are common habitat types in the Craig 

area (Murphy et al. 2000). Shoreline development is concentrated near the community (manmade or modified shoreline is 1% or 3,701 m); Craig has a population of about 1,400 people. 

In the 1970s, spawning was concentrated on the western side of Wadleigh and Fish Egg 

Islands only (Fig. 4.25a) and in the 1980s expanded to include San Christoval Channel and San 

Fernando Island (Fig. 4.25b). Spawning has been relatively consistent since the 1990s in the 

vicinity of Wadleigh Island, Fish Egg Island, San Fernando Island, and San Juan Bautista Island 

(Figs. 4.25c,d). 

Juvenile herring utilize eelgrass, kelp, and sand-gravel habitats near Craig. Nearly 9,000 

herring were captured in 15 of 76 beach seine hauls from 1998 to 1999; mean fish size was 43.8 

mm FL (Fig. 4.26) (Nearshore Fish Atlas of Alaska. 2007). In addition to herring, 45 other 

species were captured; dominant species included YOY pink salmon, Pacific sand lance, bay 

pipefish, threespine stickleback, and crescent gunnel (Fig. 4.26). No thermograph data is 

available from Craig. 

Duke Island 

The Duke Island study area includes 163.4 km of shoreline from Ryus Bay to Duke Point 

(includes Mary Island) (Fig. 4.27a). The shoreline within the Duke Island area contains organic 

sediment (27%) and estuarine habitats (21%), sand and gravel flats (14%), and wide platforms 

with gravel and sand beaches (12%). Less common shore types within the classification “other” 

4.7 
(47%) represent 16 separate classes of which wide platforms and ramps with gravel beaches are 

prevalent in the more exposed areas (Fig. 4.27a). Dominant habitats include semi-protected, 

partially mobile (56%), estuaries (21%), protected, partially mobile (16%) and semi-exposed, 

partially mobile (3%) beaches (Figs. 4.27a,b). The shoreline extent of kelps is dominated by 

Fucus (92%) followed by understory kelps (81%), canopy kelps (28%), and Alaria (23%) (Fig. 

4.27c). Eelgrass and surfgrass are present on 32% and 3% of the shoreline (Fig. 4.27d). 

Shoreline development is absent in the vicinity of Duke Island (man-made or modified shoreline 

is 0%). 

In the 1970s and 1980s, spawning was very sparse and limited to the eastern shore of 

Annette Island near Crab Bay (Figs. 4.28a,b). In the 1990s, spawning was extensive and 

included the eastern shore of Annette Island, Mary Island, Cat Island, and northern Duke Island 

(Fig. 4.28c). Since 2000, spawning has been sparse and limited mainly to Annette Island and 

Mary Island (Fig. 4.28d). Based on the shoreline extent of eelgrass and kelp near Duke Island, 

herring likely spawn on both vegetation types. 

Herring were not captured in the Duke Island area; sampling was limited, however, to 

only three beach seine hauls in 2007 (Fig. 4.29) (Nearshore Fish Atlas of Alaska. 2007). A total 

of 28 species were captured; dominant species included YOY chum and pink salmon, crescent 

gunnel, English sole (Parophrys vetulus), and juvenile flatfish (Fig. 4.29). No thermograph data 

is available from Duke Island. 

Kah Shakes Cove 

The Kah Shakes Cove study area includes 68.3 km of shoreline from near Black Island to 

Foggy Point (excludes Boca de Quadra) (Fig. 4.30). Only shore type information is currently 

available for this area. The shoreline within the Kah Shakes Cove area has wide platforms with 

gravel and sand (22%) beaches, sand and gravel flats (21%), and beaches with organic sediment 

(11%) associated with estuarine habitats (Fig. 4.30). Less common shore types within the 

classification “other” (46%) represent 18 separate classes of which wide platforms and ramps 

with gravel beaches are prevalent in the more exposed areas. Shoreline development is absent in 

the vicinity of Kah Shakes Cove (man-made or modified shoreline is 0%). 

From the late 1970s through the1990s, spawning was concentrated on either side of the 

entrance of Boca de Quadra north to Black Island and south to Foggy Bay (Figs. 4.31a,b,c). 

Since 2000, spawning has been sparse and limited from Boca de Quadra south to Foggy Bay 

(Fig. 4.31d). No spawning information is available after 2003. 

Only six herring were captured in the Kah Shakes Cove area; sampling was limited, 

however, to only four beach seine hauls in 2007 (Fig. 4.32) (Nearshore Fish Atlas of Alaska. 

2007). In addition to herring, 20 other species were captured; dominant species included shiner 

perch, YOY pink salmon, kelp perch (Brachyistius frenatus), bay pipefish, and copper rockfish 

(Sebastes caurinus) (Fig. 4.32). No thermograph data is available from Kah Shakes Cove. 

Sea surface temperature and climate 

Solar energy input drives global temperatures and because the greatest net radiative gain 

is at the equator, a general temperature gradient is established from equatorial to polar regions. 

Sea surface temperatures are correlated with air temperatures [e.g., (Rounsefell and Dahlgren 

1932)], explaining general sea surface temperature patterns Fig. 4.33. Southeast Alaska stretches 

about 860 km along the eastern Pacific in a primarily north-south orientation, thus a general sea 

surface temperature gradient is expected through the region, consistent with observation. Marine 

4.8 
waters of SEAK are characterized by an inshore-offshore salinity gradient and a north-south 

temperature gradient (Quast 1968; Murphy and Orsi 1999). Inside waters are more estuarine, 

more protected from wave action, and have more extreme seasonal fluctuations in temperature 

and salinity than outside waters (Pickard 1967; Pickard and Emery 1982; Rosenthal et al. 1982). 

Sea surface temperatures measured by infrared or microwave radiometry by satellites (Wentz et 

al. 2000) support these observations and suggest that a north-south thermal gradient is typical in 

SEAK and that inside waters may be cooler than outside waters at corresponding latitudes (Fig. 

4.34). 

Marine Zoogeographic Provinces 

Distribution patterns of fauna in the northeastern Pacific and Bering Sea can be described 

in terms of zoogeographic provinces (Briggs 1974). Each province represents a distinct set of 

environmental conditions and species that have lived together during recent evolutionary history 

(Allen and Smith 1988). The coastal region from Puget Sound to Sitka, Alaska is considered a 

transition zone and is classified as either one of two provinces; Aleutian or Oregonian by some 

(Briggs 1974). The southern boundary of the Oregonian Province is generally recognized as 

Point Conception, California, and the northern boundary of the Aleutian Province is similarly 

recognized as either Nunivak or the Aleutian Islands (Allen and Smith 1988). Briggs (1974) 

placed the boundary between the Oregonian and Aleutian Provinces at Dixon Entrance in 

southern Southeast Alaska, based on the well-studied distribution of mollusks, but indicated that 

distributions of fishes, echinoderms, and algae gave evidence for placement of this boundary in 

the vicinity of Sitka, Alaska. Peden and Wilson (1976) investigated the distributions of inshore 

fishes in British Columbia and found Dixon Entrance to be of minor importance as a barrier to 

fish distribution. A more likely boundary between these faunas may occur near either Sitka, 

Alaska, or Cape Flattery, Washington (Peden and Wilson 1976; Allen and Smith 1988). 

ShoreZone mapping has identified geographic bioareas with unique indicator and 

associated species in Alaska. For example, SEAK can be divided into four bioareas based on 

differences in bioband occurrence, species composition within biobands, and geographic 

boundaries (Fig. 4.35). Additional bioareas will develop as further ShoreZone mapping of 

SEAK is completed. Briefly, the Yakutat Bioarea (SEYA) is characterized by sparse biota, high 

wave exposure, and few canopy kelps. The Icy Strait Bioarea (SEIC) is the only area with 

significant amounts of the dragon kelp bioband (Alaria fistulosa). The Lynn Canal Bioarea 

(SEFJ) has milky, glacial-fed inlets, many with coralline reds in the red algae bioband, especially 

in areas with semi-protected exposures. The Sitka Bioarea (SESI) has fully marine waters with a 

wide range of wave exposures and a lush mixture of canopy kelps, particularly the giant kelp 

bioband (Macrocystis integrifolia). 

An alternative marine ecoregion proposal (Piatt and Springer 2007) divides SEAK into 

northern and southern zones (Fig. 4.36); these correspond almost exactly with the two divisions 

suggested by the spawn timing of Pacific herring (Fig. 3.15). Divisions among marine 

ecoregions were based on biological indicators, topographic, bathymetric, and oceanographic 

features such as persistent fronts. The relationship between marine ecoregions and the 

preliminary and incomplete Shorezone bioareas is unclear; at present the Shorezone approach 

will result in a greater number of divisions. Both schemes are subject to modification and 

perhaps ultimately both schemes will be used to inform the other or be merged. 

Distinct distribution patterns are evident for some fauna and flora in SEAK. For 

example, black rockfish (S. melanops) and shiner perch are absent in northern inside waters near 

4.9 
Juneau, but are relatively common in inside and outside waters south of Sitka, Alaska (Johnson 

2003). Similarly, the Juneau area is more strongly dominated if not richer in both arcticamphiboreal and western North Pacific taxa of marine algae than near Sitka–cooler waters near 

Juneau than on the outer coast of the Alaska Panhandle may partially explain differences in 

distribution patterns of some marine algae (Lindstrom et al. 1986). 

Summary 

From a habitat perspective, ShoreZone mapping, historical spawning records, and 

nearshore fish sampling reveal no obvious pattern in habitat use by herring–adult and juvenile 

herring use a wide range of geographical areas (inside and outside waters), habitat types, beach 

exposures, temperatures, salinities, and vegetation types. 

ShoreZone mapping revealed similarities and differences in habitat between Lynn Canal 

and other areas. For example, organic sediment and semi-protected, partially mobile substrate 

are the most common shore type and habitat class among all areas, whereas the percent shoreline 

extent of kelps (canopy and understory) and eelgrass is less in Lynn Canal than in all other areas 

(Table 4.4). These results are not surprising given differences in topography, oceanography, 

wave exposure, and glacial influence among areas. For example, turbid effluent from glacial 

rivers may partially explain the absence or near absence of eelgrass in some bays and inlets on or 

near the mainland (McRoy 1968). Nearshore, vegetated habitats are available to herring in 

Lynn Canal, however, and lack of vegetation does not seem to be a factor in limiting fish from 

spawning, especially in historical spawning areas such as Favorite Channel and north of Berners 

Bay. 

Physical habitat parameters such as temperature and salinity can also play an important 

role for all life stages of herring. Spawn distribution and juvenile catch data in SEAK show that 

herring utilize a wide range of sea surface temperatures (SST) and salinities. Marine waters of 

SEAK are characterized by an inshore-offshore salinity gradient and a north-south temperature 

gradient (Quast 1968; Murphy and Orsi 1999). Inside waters are more estuarine, more protected 

from wave action, and have more extreme seasonal fluctuations in temperature and salinity than 

outside waters (Pickard 1967; Pickard and Emery 1982; Rosenthal et al. 1982). Observed 

patterns in SST in Lynn Canal (Berners Bay) (Fig. 4.6) were similar to observations in earlier 

years (NMFS. 1974) and similar to observations at other areas–maximum and minimum 

temperatures usually reach about 12°C to 14°C in August or September and 3°C to 5°C in 

February or March. Thus, changes in SST are probably not a reason why herring declined in 

Lynn Canal. 

The possibility that human shoreline development has caused the Lynn Canal herring 

population to decline has been suggested but the evidence does not support this hypothesis. The 

decline in the Lynn Canal herring population occurred slowly from 1950 to 1980 prior to most 

major development projects, somewhat more rapidly from 1980 to 1990, and has remained 

relatively low and stable the last 25 years (Fig. 4.4). Development has long been considered a 

factor in the decline of Lynn Canal herring, particularly from loss of habitat in Auke Bay. Auke 

Bay has the highest percentage (16%) of human altered shoreline of any area (Table 4.4). Loss 

of habitat from development, however, does not explain fluctuations of the herring population in 

Tenakee Inlet; shoreline development in this area is minimal to nonexistent (Table 4.4). In 

addition, central Sitka Sound supports a robust herring population even with the second highest 

percentage (7%) of man-made alteration of shoreline. Decline of herring spawning in Auke Bay 

also does not account for the near absence of spawning in nearby Favorite Channel; herring used 

4.10 
to spawn extensively along the eastern shore of Favorite Channel until 1990 and the shoreline 

has remained relatively undisturbed. 

Nearshore fish sampling showed that two to three fish species comprised the majority of 

the total catch at all areas. Herring were captured in all areas except Tenakee Inlet and Duke 

Island; juvenile herring were probably present in these two areas but not captured due to limited 

sampling. In areas where herring were captured, herring comprised from 1% (Kah Shakes Cove) 

to 70% (southern Sitka Sound) of the total catch. In Lynn Canal, herring comprised from 5% 

(Auke Bay) to 36% (Berners Bay) of the total catch. The spatially large and consistent capture 

of mostly age-0 herring in shallow water habitats of SEAK provides evidence of the importance 

of the nearshore as juvenile habitat. Some of the other abundant fish species captured with 

herring were YOY chum and pink salmon, tubesnouts, and crescent gunnels. Herring larvae and 

juveniles are eaten by many fish species, but no unusual or large fish predator populations were 

observed in any nearshore area. 

Eelgrass meadows, kelp communities, sand-gravel beaches, and bedrock outcrops 

comprise a continuum of habitat types available to herring throughout SEAK (Johnson et al. 

2005; Nearshore Fish Atlas of Alaska. 2007). The shoreline extent of some of these habitat types 

may be less in Lynn Canal than in other areas, but herring continue to spawn in Berners Bay and 

juveniles continue to utilize nearshore habitats in Auke Bay, Favorite Channel, and Berners Bay. 

With some habitat types such as eelgrass comprising only about 3% of 235 km of shoreline 

surveyed from Auke Bay to Berners Bay (Harris et al. In prep) and spawning limited mostly to 

Berners Bay (e.g., Cascade Point), habitat protection should be a management priority for the 

preservation of Lynn Canal herring. 

References 

Alaska Department of Fish and Game. 2007. Juneau herring season summary for 2007. 

http://documents.cf1.adfg.state.ak.us/AdfgDocument.po?DOCUMENT=11379. 

Allen, J. M. and G. B. Smith 1988. Atlas and zoogeography of common fishes in the Bering 

Sea and northeastern Pacific. NOAA Technical Report, National Oceanic and 

Atmospheric Administration, National Marine Fisheries Service: 1-151. 

Briggs, J. C. 1974. Marine zoogeography. New York, NY, McGraw-Hill Book Company. 

Brown, E. D. and M. G. Carls 1998. Pacific herring (Clupea pallasi). Rest Notebook, 

EVOSTC: 1-8. 

Carlson, H. R. 1980. Seasonal distribution and environment of Pacific herring near Auke Bay, 

Lynn Canal, southeastern Alaska. Trans Am Fish Soc 109(1): 71-78. 

Davidson, W., D. Gordon, K. Monagle and D. Harris 2005. Northern southeast Alaska herring 

spawn-on-kelp pound fishery, 2005. Fishery Management Report No. 05-11, Alaska 

Department of Fish and Game: 29. 

Emmett, R. L., S. L. Stone, S. A. Hinton and M. E. Monaco 1991. Distribution and abundance 

of fishes and invertebrates in West Coast estuaries, Volume II: species life history 

summaries. ELMR. Rockville, MD, NOAA/NOS SEA Division: 329. 

Harney, J. N., M. Morris and J. R. Harper 2007. ShoreZone coastal habitat mapping protocol 

for the Gulf of Alaska. Sidney, BC., Coastal & Ocean Resources, Inc. 

Harris, P. M., S. W. Johnson, L. G. Holland, A. D. Neff, J. F. Thedinga and S. D. Rice 2005. 

Hydrocarbons and fisheries habitat in Berners Bay, Alaska: baseline monitoring 

4.11 
associated with the Kensington Gold Mine, U.S. Department of Commerce. AFSC 

Processed Report 2005-06: 1-44. 

Harris, P. M., A. D. Neff, S. W. Johnson and J. F. Thedinga In prep. Eelgrass habitat and faunal 

assemblages in the City and Borough of Juneau, Alaska, U.S. Department of Commerce, 

AFSC Report. 

Herbert, K. and D. Carlile 2002. Southeast Alaska/Yakutat annual herring research report, 

2000/2001 season. Alaska Fish Game Regional Information Report No. IJ02-36: 1-146. 

Hjort, J. 1914. Fluctuations in the great fisheries of northern Europe. Rapp P-V Reun Cons Int 

Explor Mer 20: 1-228. 

Howes, D. E., J. R. Harper and E. H. Owens 1994. Physical shore-zone mapping system for 

British Columbia. Victoria, BC, BC Ministry of Environment, Lands and Parks: 71. 

Johnson, S. M., ML; Csepp, DJ; Harris, PM; Thedinga, JF 2003. Survey of fish assemblages in 

eelgrass and kelp habitats of southeastern Alaska U.S. Department of Commerce, NOAA 

Technical Memorandum NMFS AFSC-139: 1-50. 

Johnson, S. W. and J. M. Lorenz Unpublished data, NOAA Fisheries, Auke Bay Laboratory. 

Johnson, S. W., A. D. Neff and J. F. Thedinga 2005. An atlas on the distributiion and habitat of 

common fishes in shallow nearshore waters of southeastern Alaska, U.S. Department of 

Commerce, NOAA Technical Memorandum NMFS-AFSC-157: 1-89. 

Johnson, S. W. and J. F. Thedinga 2005. Fish use and size of eelgrass meadows in southeastern 

Alaska: a baseline for long-term assessment of biotic change. Northwest Sci 79: 141-

155. 

Jones, J. D. 1978. Growth of larval Pacific herring in Auke Bay, Alaska in 1975 and 1976. 

Juneau, AK, University of Alaska, Juneau. Masters: 23. 

Lassuy, D. M., D 1989. Species profiles. Life histories and environmental requirements of 

coastal fishes and invertebrates (Pacific Northwest). Pacific herring US Fish Wildl. Serv. 

Biol. Rep. 82(11.126); US Army Corps of Engineers TR-EL-82-4: 1-18. 

Leon, H. 1993. Stock discreteness of Pacific herring (Clupea harengus pallasi) in southeast 

Alaska. Seattle, WA, University of Washington. Master of Science: 128. 

Lindstrom, S. C., N. I. Calvin and J. R. Ellis 1986. Benthic marine algae of the Juneau, Alaska 

area. Contrib Nat Sci 6: 1-10. 

McGurk, M. D. 1984. Effects of delayed feeding and temperature on the age of irreversible 

starvation and on the rates of growth and mortality of Pacific herring larvae. Mar Biol 

84(1): 13-26. 

McRoy, C. P. 1968. The distribution and biogeography of Zostera marina (eelgrass) in Alaska. 

Pac Sci 22: 507-513. 

Murphy, J. M. and J. A. Orsi 1999. Physical oceanographic observations collected aboard the 

NOAA ship John C. Cobb in the northern region of southeastern Alaska, 1997 and 1998, 

U.S. Dept of Commerce. NMFS-AFSC Proc. Rep. 99-02: 239. 

Murphy, M. L., S. W. Johnson and D. J. Csepp 2000. A comparison of fish assemblages in 

eelgrass and adjacent subtidal habitats near Craig, Alaska. AK Fish Res Bull 7: 11-21. 

Nearshore Fish Atlas of Alaska. 2007. http://www.fakr.noaa.gov/habitat/fishatlas/ National 

Oceanics and Atmospheric Administration, National Marine Fisheries Service. 

NMFS. 1974. Lynn Canal: a resource assessment. Juneau, AK, U.S. Department of Commerce, 

NMFS. Prepared for the Alaska Power Administration: 172. 

Norcross, B. L., E. D. Brown, R. J. Foy, M. Frandsen, S. M. Gay, T. C. Kline, D. M. Mason, E. 

V. Patrick, A. J. Paul and K. D. E. Stokesbury 2001. A synthesis of the life history and 

4.12 
ecology of juvenile Pacific herring in Prince William Sound, Alaska. Fish Oceanogr 10: 

42-57. 

Paul, A. J., J. M. Paul and E. D. Brown 1998. Fall and spring somatic energy content for 

Alaskan Pacific herring (Clupea pallasi Valenciennes 1847) relative to age, size and sex. 

J Exp Mar Biol Ecol 223(1): 133-142. 

Peden, A. E. and D. E. Wilson 1976. Distribution of intertidal and subtidal fishes of northern 

British Columbia and southeastern Alaska. Syesis 9: 221-248. 

Piatt, J. F. and A. M. Springer 2007. Marine ecoregions of Alaska. Long-term ecological 

change in the northern Gulf of Alaska. R. B. Spies. Amsterdam, Elsevier: 522-526. 

Pickard, G. L. 1967. Some oceanographic characteristics of the larger inlets of southeast 

Alaska. J Fish Res Bd Can 24: 1475-1506. 

Pickard, G. L. and W. J. Emery 1982. Descriptive physical oceanography: an introduction. 

New York, NY, Pergamon Press. 

Pritchett, M. 2006. Historic spawn herring database. Alaska Department of Fish and Game, 

Juneau, AK. 

Quast, J. C. 1968. New records of thirteen Cottoid and Blennoid fishes for southeast Alaska. 

Pac Sci 22: 482-487. 

Rosenthal, R. J., L. Haldorson, L. J. Field, V. M. O'Connell, M. G. LaRiviere, J. Underwood and 

M. C. Murphy 1982. Inshore and shallow offshore bottomfish resources in the 

southeastern Gulf of Alaska 1981-82. Alaska Coastal Research. Sitka, AK: 1-166. 

Rounsefell, G. A. and E. H. Dahlgren 1932. Fluctuations in the supply of herring, Clupea 

pallasii, in Prince William Sound, Alaska. Bull US Bureau Fish XLVII: 263-291. 

Tanasichuk, R. W., A. H. Kristofferson and D. V. Gillman 1993. Comparison of some life 

history characteristics of Pacific herring (Clupea pallasi) from the Canadian Pacific 

Ocean and Beaufort Sea. Can J Fish Aquat Sci 50(5): 964-971. 

Thedinga, J. F., S. W. Johnson and D. J. Csepp 2006. Nearshore fish assemblages in the vicinity 

of two Steller sea lion haulouts in southeastern Alaska. Sea lions of the world. A. W. 

Trites, S. K. Atkinson, D. P. DeMaster, L. W. Fritz, T. S. Gelatt, L. D. Rea and K. M. 

Wynne. Fairbanks, AK, University of Alaska, Fairbanks: 269-284. 

USCOE. 1984. Juneau, Alaska boat harbor improvements, final detailed project report and 

environmental impact statement. U.S. Army Engineer District, Alaska, ATTN: Records 

Manager, PO Box 6898, Elmendorf Airforce Bace, US Army Corps of Engineers (Alaska 

District). 1-85. 

USDA 2004. Kensington gold project, draft supplemental environmental impact statement, Vol. 

1 of 2, U.S. Department of Agriculture, Forest Service. 

Wentz, F. J., C. Gentemann, D. Smith and D. Chelton 2000. Satellite measurements of sea 

surface temperature through clouds. Science 288(5467): 847-850. 

Williams, G. D., L. K. O'Rourke and W. H. Pearson 2004. Reconnaissance evaluation of 

ecological effects to forage fish populations associated with Juneau access improvements 

project. Sequim, WA, Battelle Marine Sciences Laboratory, PNWD-3419: 50. 

Wing, B. L., M. M. Masuda and S. G. Taylor 2006. Time series analyses of physical 

environmental data records from Auke Bay, Alaska, U.S. Department of Commerce, 

NOAA Technical Memorandum NMFS-AFSC-166: 75. 

4.13 
SUBSTRATE SEDIMENT WIDTH SLOPE COASTAL CLASS NO. 

STEEP (>20°) n/a 

WIDE (>30m) INCLINED (5-20°) Rock Ramp, wide 1 

ROCK N/A FLAT (<5°) Rock Platform, wide 2 

STEEP (>20°) Rock Cliff 3 

NARROW (<30 m) INCLINED (5-20°) Rock Ramp, narrow 4 

FLAT(<S0

) Rock Platform, narrow 5 

STEEP (>20°) n/a 

WIDE (>30m) INCLINED (5-20°) Ramp with gravel beach, wide 6 

GRAVEL FLAT (<5°) Platfo1T11 with gravel beach, wide 7 

STEEP (>20°) Cliff with gravel beach 8 

NARROW (<30 m) INCLINED (5-20°) Ramp with gravel beach 9 

FLAT (<5°) Platfo1T11 with gravel beach 10 

STEEP (>20°) n/a 

WIDE (>30m) INCLINED (5-20°) Ramp w gravel & sand beach, wide 11 

ROCK& SAND & FLAT (<5°) Platform with G&S beach, ~de 12 

SEDIMENT GRAVEL STEEP (>20°) Cliff with gravel/sand beach 13 

NARROW (<30 m) INCLINED (5-20°) Ramp with gravel/sand beach 14 

FLAT (<5°) Platfo1T11 with graveVsand beach 15 

STEEP (>20°) n/a 

WIDE (>30m) INCLINED (5-20°) Ramp with sand beach, wide 16 

SANO FLAT (<5°) Platform with sand beach, wide 17 

STEEP (>20°) Cliff with sand beach 18 

NARROW (<30 m) INCLINED (5-20°) Ramp with sand beach, narrow 19 

FLAT (<5°) Platform with sand beach, narrow 20 

WIDE (>30m) FLAT (<5°) Gravel flat, wide 21 

GRAVEL STEEP (>20°) n/a 

NARROW (<30 m) INCLINED (5-20°) Gravel beach, narrow 22 

FLAT (<5°) Gravel flat or fan 23 

STEEP (>20°) n/a 

SAND WIDE (>30 m) INCLINED (5-20°) n/a 

& FLAT (<5°) Sond & gravel flot or fun 24 

SEDIMENT GRAVEL STEEP>20°) n/a 

NARROW (<30 m) INCLINED (5-20°) Sand & gravel beach, narrow 25 

FLAT (<5°) Sand & gravel flat or fan 26 

STEEP (>20°) n/a 

WIDE (>30m) INCLINED (5-20°) Sand beach 27 

FLAT (<5°) Sand flat 28 

SANO /MUD FLAT 1<5°) Mudflat 29 

STEEP (>20°) n/a 

NARROW (<30m) INCLINED (5-20°) Sand beach 30 

FLATl<S0 ) n/a n/a 

ORGANICS n/a n/a Estuaries 31 

ANTHRO- Man-made n/a n/a Man-made oermeable 32 

POGENIC n/a Man-made, impermeable 33 

CHANNEL Current n/a n/a Channel 34 

GLACIER Ice n/a n/a Glacier 35 

Table 4.1. Classification of shore types (based on ShoreZone protocol). 

4.14 
Biological Exposure Catego

Structw·ing Substrate Coastal Type Description Very Semi- Semi- 

Mobility Exposed Exposed exposed protected P

Process VE E SE SP 

Rock or 

The epibiota in the immobile mobility categories is influenced 

by the wave exposureatlhe site. In high wave exposures. only 10 20 30 40 

Immobile Rock & Sediment solid bedrock shorelines 

will be classified as 'immobile'. At the 

VE I E I SF, I SP I 

orSedimeJtt lowest wave exposures, even pebbl el cobble beaches 

may show 

lush epibiota. indicaline an immobile Habitat Class. 

These units desa-ibc the combination of sediment 

mobility 

observed. That is, a sediment beach that is bare in the upper half 

of the intertidal wilh biobands occurring on the lower beach 

Pa,tially- Rock & Sediment would be classed as ·~rtially mobile' . This pattern is seen at 11 21 31 41 

Wave Energy mobile orSedimeJtt moderate wave exposures, VE P E p SE P SP P 

Units wilh immobile bedrock outcrops intermingled with bare mobile sediment bead1es, as can be seen at higher wave 

exoosures. could also be classified as 'Da1tiallv mobile'. 

These categories arc intended to show lhe 'bare sediment 

beaches', 

where no epibenlhic macrobiota are observed. Very 12 22 32 42 

Mobile Sediment fine sediment may be mobile even at lhe lowest wave 

exposures, while at U1e highest wave exposures, large-sized VE M EM SE M SP M 

boulders 

will be 

mobile and bare of epibiota. 

Fluvial/Estuarine 

Units classified as the 'e~uary' types always include wetland 13 23 33 43 

Estuary/Wetland biobands in the upper intertidal, are always associatedwiU1 a Processes freshwata- stream or river and often show a delta form. Estuary VEE EE SEE SP E 

units are usuallv in lower wave exoosure cate2ories. 

Current- Species assemblages observed in salt-water channels are 14 24 34 

44 

Current energy dominated 51.ructtJred by current energy ralher than by wave energy, 

Currmt-dominated sites are limited in distribution and are rare VE C EC SEC SP C 

channel habitats. 

In a few places in coa!tal Alaska, saltwater glaciers form the 15 25 35 45 

Glacial processes 

Glacier intertidal habitat. The;e Habitat Classes are rare and include a 

small percentage of the shoreline length. VEG EG SE G SP G 

Anthropogenic - Impermeable man-made Habitats arc intended to specifically 16 26 36 

46 

Impermeable note units classified as Coastal Class 33. VEX EX SEX SPX 

i\.fan-m odified 

Anthropogenic - Permeable man-made Habitats are intended to specifically note 17 27 37 47 

Permeable shore units classified~ Coastal Class 32. VEY E y SEY SPY 

Units classified as Lagoons in the Secondary Habitat Class 

contain brackish or saltv water !hat is contained wilhin a basin 18 28 38 48 

Lagoon 

Lagoon that has limited drainage. They arc often associated with 

wetlands and may include wetland biobands in lhe upper VE L EL SE L SP L 

intertidal. 

4.15 
 

Total catch 

 Mean 

Area Temperature Mean salinity 

No. hauls All spp. Herring °C (PSS) 

Berners Bay* 54 24,339 8,804 8.3 - 12.8 16.9 - 18.3 

Favorite Channel* 95 16,891 4,638 4.0 - 12.4 17.6 - 32.6 

Auke Bay* 39 16,625 873 6.9 - 12.7 11.3 - 30.8 

Sweetheart Creek 2 4,074 3,910 9.9 - 10.8 6.8 - 7.7 

Farragut Bay 1 374 246 9.2 11.7 

Flat Cove 2 5,412 5,358 13.8 33.6 

Sitka Sound north* 53 31,098 5,145 6.5 - 13.3 22.4 - 31.0 

Sitka Sound central* 58 23,722 1,472 6.3 - 13.7 19.7 - 33.0 

Sitka Sound south* 23 4,370 3,050 14.2 23.7 

Hamilton Bay 4 24,128 23,804 14.4 - 16.9 29.9 - 30.6 

Dakaneek Bay 2 6,493 4,400 12.7 - 14.8 31.2 - 31.3 

Craig* 76 28,952 651 9.7 - 12.5 25.4 - 27.5 

Kah Shakes Cove* 1 509 6 13.6 19.3 

Total 410 186,987 62,356 

Table 4.3. Total number of beach seine hauls, total fish catch (all spp.), total herring catch, and 

mean temperature and salinity (practical salinity scale) ranges at several areas throughout SEAK 

from 1998 to 2007 (Johnson and Lorenz). Asterisk denotes herring study areas discussed in 

detail in this report. 

4.16 
Table 4.4. Summary of major ShoreZone habitat classifications found within the BRT study areas. Percentages 

4.30. 

Berners Favorite Auke Northern Central Southern 

Bay Channel Bay Tenakee Sitka Sitka Sitka Crai

Total Shoreline (km) 89.3 60.7 52.1 116.0 314.2 369.3 NA 426.

Shore Type 

manmade 0% 0% 8% 0% 0% 6% NA 1% 

other 40% 60% 45% 27% 52% 54% NA 47% 

organic sediment 27% 14% 42% 68% NA 19% 

wide platform with gravel 19% 9% NA 

sand and gravel flat 14% 10% 23% 20% NA 17% 

ramp with gravel beach 21% 9% 14% NA 

ramp with gravel and sand 10% NA 16% 

wide platform with gravel and 

sand 11% NA 

narrow sand and gravel 17% NA 

rock cliff 13% NA 

narrow rock ramp 13% NA 

Habitat Class 

manmade 0% 1% 16% 0% 0% 7% NA NA 

other 8% 6% 9% 7% 21% 29% NA NA 

Semi-exposed partially mobile 

Semi-protected partially mobile 37% 53% 43% 17% 17% 29% NA NA 

semi-protected mobile 8% 4% NA NA 

semi-protected immobile 10% 8% 15% NA NA 

protected partially mobile 16% 13% 8% 7% 33% 15% NA NA 

protected immobile 7% NA NA 

estuary 29% 19% 16% 45% 22% 5% NA NA 

Kelps 

Canopy kelps 5% 0% 0% 10% 17% 38% NA NA 

Understory kelps 14% 26% 11% 44% 70% 69% NA NA 

Alaria (intertidal) 34% 27% 13% 6% 12% 38% NA NA 

Fucus 57% 57% 64% 54% 86% 83% NA NA 

Seagrasses 

Eelgrass 6% 2% 6% 57% 39% 32% NA NA 

surfgrass 0% 0% 0% 1% 1% 11% NA NA 

4.17 
Berners Bay 

Lynn Canal Favorite Channel 

Auke Bay 

Tenakee 

Inlet 

Canada northern 

Sitka central Alaska Sound 

southern 

Kah Shakes 

Craig Gulf of Alaska 

Figure 4.1. Ten study areas for herring in SEAK identified by the Lynn Canal herring Biological 

Review Team (BRT). 

Cove 

Duke Is. 

4.18 
• Beach seine sites without Pacific herring captured 

• Beach seine sites with Pacific herring captured 

 

 

 

250 

0 100 200 300 

Summary (1998-2007) 

Total catch: 76,388 fish 

Occurrence: 132 of 667 seine hauls = 20% 

Mean fork length: 63.7 mm (n = 1,820) 

Canada Gulf of Alaska 

Alaska 

Nearshore Fish Atlas 

100

80 

60 

40 

20 

146 

180 

243 

98 

l

ype %

Mean catch per hau200 

tat t

s 

 habi

n = 132 haul

150 

100 

50 

0 0

Occurrence by

Bedrock Eelgrass Kelp Sand 

Figure 4.2. Locations of beach seine sites sampled for herring in SEAK from 1982 to 2007; 

summary data (1998-2007) and bar graph from Nearshore Fish Atlas of Alaska (2007). Numbers 

above bars are number of seine hauls. Other data sources are Orsi and Landingham (1985), and J. M. 

Lorenz, NOAA Fisheries, ABL, Juneau, AK unpublished data. 

4.19 
A N B 

Berners River 

Delta Pt. Sherman 

A A 

N 

8% 

Habitat Class 

Shore Type BC Class --SP _P • Stff9oPro1oc:tod P:uti~lly Mobiat • 32 1 ltm 

--31 • Otg:iink:s . 24.4 km --P _P. P'fotect•d Partially Mobile. 14.7 km 

--7 • VIAot pl.atl'ormWlth gro\111 ba:ich• 16.8 km --SP _I · S.mi-ProtK11d lnmobie • 8.7 km 

--24 • Saftd and gravel rl:ll • 12.4 km - Estu1u~ • 26.2 km 0 1 2 6 

--32 :i ~ 33 • M:inrmde • 0.8 J:m --ManrNda • 0.2 km - =--===---'°- ... Tolal Shoreline 89.J km Total Shoreline 89.3 km --Oho, · 3S.6 lrim --Othtr • 7Akrn 

C 

A 

N D 

A 

N 

.. 

70 

., 

50 

30 

20 

10 

0 

Futus 

Kelps 

-- Fueus-51 .3km 

Alnirl3 0nt&rtidalJ • 30.4 km Seagrasses 

-- Undentory K•lps • 12.6 km 0 

- =--=

1 

==--6 Ktomectrs. --Eelgrass - 5.0 km 0 

- =--=

1 2 

__ ~nopy Kolp, . 4.3 km O • -- Surfgr,us. o km ==--- ... Total Shoreline 89.3 Tota l S horelin e 89.3 km --Stu,:fyArH --Study Area 

Slate Creek 

Cove 

Cascade Pt. 

Pt. St. Marys 

Echo Pt. Bridget Cove 

Bridget 

Cove Mab Is. 

Sunshine 

Cove 

 of Shoreline %

Figure 4.3. Berners Bay: ShoreZone coastal habitat maps. Proportions of dominant habitat classes 

are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel C (kelps), and 

panel D (seagrasses). For definitions of ShoreZone habitat classifications see Appendix A. 

4.20 
25 

C 

3: 

n, 

a. 20 V') 

-0 

1/'l 

Q) 15 

10 

5 

0 

1950 1960 

• 

1970 1980 

Year 

~ Junea u Area 

--e-- Bern ers Bay Area 

1990 2000 2010 

30 

Figure 4.4. Shoreline kilometers of herring spawn in Lynn Canal from 1951 to 

2007 (Pritchett 2007). 

4.21 
Herring Spawn 

-- Juneau_ 1972 

--Joo@au_ 1973 

-- Juneau_ 1974 

--Juneau_ 1975 

-- Jooeau_ 1976 

-- Juneau_ 19TT 

-- Juneau_ 1978 

--Juneau_ 1979 

--Juoe1;111,1_ 1990 

--Juneau_ 1991 

-- Juneaiu_ 1992 

--Juneau_1993 

-- Juneaiu_1994 

--Juneau_1995 

--Juneau_ 1998 

--Juneau_ 1997 

--JuMau_ 1998 

-- June!ill.J_ 1999 

' 

• Kilomet,m; 

N 

A 

N 

A 

Herring Spawn 

--Jooeau_1980 

--Juneau_ 1981 

-- Jooeau_ 1982 

-- J111eau_1983 

-- Juneeu_1984 

-- Jl.W'l~_ 1985 

--Jooeau_1986 

--J111eau_ 1987 

--Juneau_1988 

-- JIX!eau_ 1989 

--Juneau_2000 

-- Jur-.eau_2001 

--Juneau_2002 

--Juneau_2003 

--Juneau_2004 

--Juneau_2005 

--Jur-.eau_2006 

--Juneau_2007 

' -- Bemefs_Bay_2001 

--Bemer5_8~_200s 

i==:= 

N 

A 

' 

~ 

N 

A 

Pt. Sherman 

A (1970’s) 

Berners River 

Delta 

Slate Creek 

Cove 

Berners 

Bay 

B (1980’s) 

Berners 

Bay 

Pt. St. Marys 

Cascade Pt. 

Pt. Bridget 

Echo 

Cove 

Bridget 

Cove Mab Is. 

Sunshine Cove 

C (1990’s) 

Berners 

Bay 

D (2000’s) 

Berners 

Bay 

Figure 4.5. Berners Bay: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some panels 

may not have spawn records for each year in a given decade. Refer to each panel’s legend for color 

coded, annual spawn records. 4.22 
N 

0 

A 

• 

0 

0 

0 

)C. (pme TreataweS .gvA

D 

• 

D 

D 

D 

• 

0 ••o•-=---=:::::::i-• 1 2 3 4 

Kilometers 

Pt. Sherman 

Thermograph 

Herring 

Eelgrass 

Kelp 

Bedrock 

Sand-Gravel 

Berners Bay 

Herring summary (1998-06) 

Total catch: 8,804 fish 

Occurrence: 16 of 54 hauls = 30% 

Mean fork length: 43.8 mm (n = 187) 

16.0 

14.0 

12.0 

10.0 

8.0 

6.0 

4.0 

2.0 4

5

5

6

6 

0

0

0

0

0

unbugb-

-r

J

Fe

A

Fe

Ap

Cacsade Point 

Echo Cove 

Bridget Cove 

Berners River 

Delta 

C) o mp ( tertewaaen saeM

Slate Creek 

Cove 

Berners 

Bay 

Pt. St. Marys 

Cascade Pt. 

Chum salmon 

Pacific herring 

Crescent gunnel 

Species composition 

Tubesnout 

Coho salmon Bridget 

Cove 

37 other species 

Total catch all species = 24,339 

Sunshine 

Cove 

Pt. Bridget 

Mab Is. 

Echo 

Cove 

Figure 4.6. Location and habitat type of beach seine sites in Berners Bay (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 54 seine hauls from 1998 to 2006. Seawater 

temperature is from three locations within Berners Bay. 

4.23 
A 

N A ove 

Yankee Cove 

A B N 

Sunshine C

Benjamin 

Is. Eagle River 

Delta 

Amalga 

Harbor 

Favorite 

Channel 

Tee 

Harbor 

Shelter 

Is. Lena 

Cove 

Lena Pt. Habitat Class Shore Type BC Class 

--SP _P - S•n'I-Proltded Por1~1ty Mobile· 31 .9 km --9- Ramp with gravel beach. 12.5 km - P _P • Protected Pa.rtiaUy Mobh • 8. 1 km 

24 - Sand and gravel Rat - 5.8 km 

--==- --SP _I • Semi-Protected lrmiobiN - 4.8km 

--7 - Wide pfal0<m with gravel beach - 5.2 km 4 0 ' --Estuary- 117km 

--32 and 33 - Manmade - 0,2 km --M,nm.tdie. O 6 km Tolal Shoreline --60-· .7 k:m -

Total 

-==- Shoreline 60.7 km 

--Other - 36.9 

---.. , km --01:hor • 3.6 km 

N N C A D A 

'·

60 

---------~--~ 

•• 

50 !! --~----~_._-_-_-_-_-_-_-_ .....JO 

20 i !~ ~ 1 to Ii ... 0 0.1 

.. OA 

0.2 

0 Kelps 

-- FIK.u5 • 34.8 km 

\ -- A&arlil (intertidal) - 16.4 km Seagrasses 

-- Underslory Kel~ • 16.0 km 0 - ' - Eelgran • 1.0km ' -- C=iinopy Kelp,.. o km --$wfg1.is.s - O km Tolal Sho-- -Ton,1 Shorelioe 60

Stl,.IClyArt:a 

-==-reline 60 7 k:m \ km 

--

-· .

--&udyA.re.ii 

-==---""""""' .7 

Figure 4.7. Favorite Channel: ShoreZone coastal habitat maps. Proportions of dominant habitat 

classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel C 

(kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 

4.24 
A 

N Sunshine Cove Herring Spawn Herring Spawn 

A (1970’s) -- Juneau_1972 A 

N 

--J111eeu_ 1980 

Yankee Cove -- Juneau_ 1973 -- Jl.S'IBau_ 1981 

--Jooeau_1974 -- Juneau_1982 

--Juneau_ 1975 -- Juneau_1983 

-- Juneau_ 1976 --Juneau_ 1984 

--J1.11eau_19n -- JLl"leau_198S 

Benjamin --Jl.W'leau_1978 -- Jooeau_ 1986 

Is. --Jooeau_ 1979 -- Juneau_1987 

--JIXl8au_1988 

Eagle River --Juneau_ 1989 

Delta 

Amalga Lincoln Harbor Is. 

Favorite 

Channel 

Shelter Tee 

Is. Harbor 

Lena 

Cove 

Lena Pt. 

A 

N Herring Spawn Herring Spawn 

Juneau_ 1990 A 

N 

-- --Ju ... au..2000 

--Juneau_ 1991 --Ju...eau_2001 

--Juneau_ 1992 --J\Jr)e,ill,l_20()2 

--Juneau_ 1993 --Juneao_2003 

--Juneau_ 1994 --Jurteau_2004 

--Juneau_199S 

--Juneau_ 1996 

--Juneau_1997 

--Juneau_1998 

--Juneau_ 1999 

/\\ • Kilomet.e,s 

B (1980’s) 

C (1990’s) D (2000’s) 

Figure 4.8. Favorite Channel: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some panels 

may not have spawn records for each year in a given decade. Refer to each panel’s legend for color 

coded, annual spawn records. 4.25 
6 

• 

D 

D 

D 

D 

• 

0 

0 

• 0 

. 

~ 

2 3 

N 

A 

4 

Kilometers 

Sunshine Cove 

Yankee Cove 

Favorite Channel 

Herring summary (2001-06) 

Total catch: 4,638 fish 

Occurrence: 16 of 95 hauls = 17% 

Mean fork length: 55.2 mm (n = 392) 

Thermograph 

Herring 

Eelgrass 

Kelp 

Bedrock 

Sand-Gravel 

Benjamin 

Is. 

o Mean seawater temp. ( C)16 

14 Eagle River 

Delta 12 

10 

8 

6 

4 

2 

0 Amalga Aug 02 Jan 03 July 03 Jan 04

Harbor 

Favorite 

Channel 

Pacific herring 

Pacific sand lance 

Walleye pollock 

Tubesnout 

Pink salmon 

33 other species 

Species composition 

Shelter 

Is. 

Tee 

Harbor 

Lena 

Cove 

Total catch all species = 16,891 

Lena Pt. 

Figure 4.9. Location and habitat type of beach seine sites in Favorite Channel (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 95 seine hauls from 2001 to 2006. Seawater temperature is 

from Benjamin Island. 4.26 
A 

N 

A 

N 

.• .,. 

~ Auke Auke 

Bay Bay 

9% 

45% 

8% 8% 10% 8% 

Habitat Class Shore Type BC Class --SP _P • Serri-P,otecced Partially Mobile - 22..5 km 

-- 24 . S1nd and gra'lcl flat. 12,2 km --P_P- Protoded Pnrtfal>, MoMo-4.3km 

--31 . Organics . 7,3 km --SP _M • Solff-Protoctod Mobllo • -1.1 km 

-- 14 • Ramp with gravel and sand beach • 5.0 km 0 0 32 and 33. Manmade 4.0 km ::15 -- m: •'==-- EsMlcy-8.4 km 3 0 0 5 3 Kllometers -- Kllomet•rs M.>nmade • 8.3 km m:::1•==' -- Total Shorellne 52.1km Total Shorellne 52.1km --~, - 23.5km --Olher - 4.5 llm 

N N 

'-' 

\c A A 

Auke 

Bay 

.. " 

IN 

j 

• ! .. 

•o+--a---

,. 

" 

Kelps 

-- Fucus • 33.3 km 

AJaria (inlertldail) - 6.5 km Seagrasses 

-- Understory Kelps - 5.5 km Eelgras.s - 3.0 km 0 0 OS 1 3 

-- ps - 0 km -==-

OS 1 

== 3 

Canopy Kel --Kllomet•rs Surf grass - O km -==-==--Kllomelars 

-- Total Shoreline 52.1km Total Shorellne 52.1km Study Alea Study Area 

Auke Bay 

Marina Ferry 

Terminal Auke Nu 

Cove 

Indian Pt. 

Lena Pt. 

Douglas 

Outer Pt. Island 

Figure 4.10. Auke Bay: ShoreZone coastal habitat maps. Proportions of dominant habitat 

classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel C 

(kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 

4.27 
Herring Spawn Herring Spawn 

--Juneau_ 1sn --Juneau_ 1980 

--Juneau_ 1973 --Juneau_ 1981 

-- Jur-.eau_ 1974 --Juneau_ 1982 

--Junieau_ 1975 --Juneau_ 1983 

--.kmeau_ 1978 --Juneau_ 1984 

--Juooau_ ,en --Juneau .. 1985 

--Juneau_ 1978 --Juneau_ 1986 

--JurlHU_1979 --Juneau_ 1987 

--Juneau_ 1988 

--Juneau_ 1989 

0 N 0 

D 

N 

• K.IIOITlll!!let!ii 

A D • KilOll'lll!ltefS 

A 

Herring Spawn Herring Spawn 

--Juneau_2000 --Juneau_ 1890 

--Juneau_ 2001 --Juneau_ 1991 

--Jur.au_2002 --JullE!au_199'2 

--Juneau_2003 --Juneau_ 1993 

--June.au_2004 --Juneau_ 1894 

--Juneau .. 2005 --.h.meau_1995 

--.Juneau .. 2006 -- Juneau_ 1996 

--Jul'.e.81.l_2007 --Jul)eau_ 1997 

~ ~ 

(\ {). (\ {). 

\ \ 

A 

N N 

• KJIOITlll!!tel'!J 

A 

A (1970’s) B (1980’s) 

Auke Bay 

Ferry Marina 

Lena Pt. Auke Nu Terminal Cove 

Indian Pt. 

Auke Auke 

Bay Bay 

Outer Pt. Douglas 

Island 

C (1990’s) D (2000’s) 

Auke Auke 

Bay Bay 

Figure 4.11. Auke Bay: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some 

panels may not have spawn records for each year in a given decade. Refer to each panel’s legend 

for color coded, annual spawn records. 4.28 
I N Auke Bay 

0 

A 

• 

0 

0 

0 

 (C)per Temateawve. SA

" 

D 

D 

D 

D 

D 

• 

O 

-

0.5 

-

1 2 3 

Kilometers 

Thermograph 

Herring summary (1999-07) 

Herring Total catch: 873 fish 

Occurrence: 11 of 39 hauls = 28% Eelgrass Mean fork length: 42 mm (n = 88) 

Kelp 

Bedrock Auke Bay Lena Pt. Marina Sand-Gravel Auke Nu Ferry 

Cove Terminal 

Indian Pt. Auke 

Bay 

16.0 

14.0 

12.0 

10.0 

8.0 

6.0 

4.0 

2.0 

04

05

07

06

06

-Jul

an-

-Jul

an-

-Jul

JJ

Jan07 

C) o mp (eer tatan seaweM

Species composition Outer Pt. 

Chum salmon 

Douglas Island 

Tubesnout 

Crescent gunnel 

Threespine stickleback 

Pink salmon 

Pacific herring 

31 other species 

Total catch all species = 16,625 

Figure 4.12. Location and habitat type of beach seine sites in Auke Bay (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 39 seine hauls from 1999 to 2007. Seawater 

temperature is from Indian Pt. 4.29 
A 

A 

N B 

A 

N 

7%, 

4o/, 

20o/. 

Habitat Class 

Shore Type BC Class o 

--=, s J e --P _P - Proteeted Partially Mobile . 31.7 km 0 15 J • -- 3t - Orgnnics • •7.91un --SP_P - Semi-PfotK:ted Partially Moblle- - 19.6 km Total Shoreline 116.0 km 

--=

Total Sho

=---·

reline 116.0 

t(Jlomet,<Of1, km - -- 24 - Sand alld gravel 11.11 • 23--2 km 

=---··-· --SP_M • Seml.PrOIK"ledMobiJ.e - 4.1 km 

-- 12 .\Mdepla1k>1m withgraH l 11od u ndbeach - 12,Slt.m --Es1ua.ty • 52.0 km 

-- 32 . Manmade . 0..5 km --Manmade - 0.5 km 

--Olller - lt,9km --Other -8.1 km 

C 

A 

N D 

A 

N 

Fucus Al:irl :i Unden:rory Canopy 

Kelps a 1 s J £ 0 15 l • Fucus - 62A km --=Tota l S

=-hore--· lin e 11 6.0 km 

~ Sea grasses To1al Shoreline 116.0 km 

Al.u l.11 (lntHtklal) . 6.5 km 

-· --==---·""""''"" --Eelgr~u-S6.5km -- Undtt$10ry Kt:lp$ . 51.1 km 

__ Conopyt<ejps- 1.1 km --Surlgr.11.u .0.8 km 

- - Study Area --Slud)'AIH 

East Pt. 

Chatham 

Strait 

Tenakee Springs 

South 

Passage Pt. 

Trap Saltery Bay Bay 

Corner 

Bay Baranof 

Island 

Crab Bay 

 of Shoreline %

 of Shoreline %

Figure 4.13. Tenakee Inlet: ShoreZone coastal habitat maps. Proportions of dominant habitat 

classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel C 

(kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 

4.30 
A 

N 

Herring Spawn Herring Spawn 

--Tenakee_lnkn_ 1998 --Tenakee_lnlel2000 

--Tena1tee_1n1tt_ 1999 --Tenak.ee_lnle1_2001 

A 

N 

Herring Spawn Herring Spawn --Telloilkee_lnleL2004 

--Tenakee_lnleL2002 --Tenakeie_lnlet_200S 

--Tenakee_lnlet_2003 --Teoakee_lnleL2006 

--Tenak&e_lnleL2007 

0 t 2 3 -4 0 1 2 3 4 K~ometers l<ilom,,ie,s 

A (1998 - 99) B (2000 - 01) 

East Pt. 

Tenakee Springs 

Saltery Bay Chatham 

Strait 

South 

Passage Pt. 

Trap Bay 

Crab Bay Corner 

Bay 

Basket 

Bay 

Baranof 

Island 

C (2002 - 03) D (2004 - 07) 

Figure 4.14. Tenakee Inlet: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some panels 

may not have spawn records for each year in a given decade. Refer to each panel’s legend for color 

coded, annual spawn records. 4.31 
A

N 

0 

• 

0 

0 

D 

D o

D 

emp. ( C)

T

D 

ater w

D 

Avg. Sea

• 

4 

Kilometers 

Tenakee Inlet 

Herring summary (1998-06) 

Total catch: 0 fish 

Occurrence: 0 of 22 hauls = 0% 

Mean fork length: NA East Pt. 

Tenakee Springs Saltery Bay Chatham 

Strait 

Tenakee Inlet 

South 

Passage Pt. 

Trap Bay 

Crab Bay Corner 

Bay 

Baranof 

Island 

Thermograph 

Herring 

Basket 

Eelgrass Bay 

Kelp 

Bedrock 

Sand-Gravel 

Species composition 

Pink salmon 

Threespine stickleback 

Chum salmon 

Crescent gunnel 

Pacific cod 

23 other species 

16 

) 14 

C12 

10 

ater temp (o 

8 

wae

6 

an se

4 

M

2 

0 

 01

02 

Total catch all species = 18,547 

July

Nov 01

Mar 02

July Nov 03

Mar 03

Figure 4.15. Location and habitat type of beach seine sites in Tenakee Inlet (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 22 seine hauls from 1998 to 2006. Seawater temperature is 

from Crab Bay. 4.32 
Si

A 

N N 

Baranof 

Island nitsin Kane 

A 

Cove Is. Neva 

Strait 

St. John Baptist 

Bay 

Partofshikof 

Is. 

Nakwasina Kruzof Halleck Sound Is. Is. 

Krestof 

Is. 

Lisianski 

Pt. 

Mountain Pt. 

Habitat Class 

Shore Type BC Class --P _P . Protected Partially Mobile • 103.7 km 

-- 31 • O!gan~• . 68.0 km Sitka --SP _P . Semi-Prole<:ted Partially Mobile. 52.8 km 

Sound 25 - Narrow $clod arld g,a,,..e,I beach . 51 .9 km --P _I - Ptot&cted Immobile-. 23.0 km 

--9. Ramp with gravel boeac:h. 28.9 km 0 1 2 -- E>tuary • 68.8 km 0 I 2 

--32 • Manmade • 0 .8 km -- Manmade • 0.5 km Tolal Shorellne 31-4.2 km Total Shoreline 314.2 km 

-- Other. 163.6 km -- Other. 65,4 km 

A 

N 

A 

N 

., 

" ----------, 

i: 

~ ,. 

...

~ 20 

~ 

.. 

15 

Kelps 

' 

0 - --- -------·· 

-- Fucus. • 269.9 km 

-- Alarla (1nlel1idal) - 36.9 km Sea grasses 

-- Unde~tory Kelps - 221.5 km 0 1 2 - Eelgrass - 121. 1 km 0 I 2 

__ Canop)' Kelps - 53.1 l(m --Surf grass - 4,3 km Tolal Shoreline 314.2 km Total Shoreline 314.2 km 

-- Study Area -- StudyP-lea 

Figure 4.16. Northern Sitka Sound: ShoreZone coastal habitat maps. Proportions of dominant 

habitat classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel 

C (kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 4.33 
Herring Spawn 

--Sitlca_1980 

--Silka_1981 

--S.tka_1982 

--Sitka_ 1983 

--Sitka_ 1984 

--Sitka_1985 

--Sitka_ 1972 --Sitk8_1986 

--Si11<a_197S --Sitka_1987 

--Sitka_1976 --$itkB_1988 

--Sitka_1977 --Sitko_ 1989 

--Sitka_ 1978 

--Sitka_ 1979 

--Sitka_2000 

--Sitka_2001 

--S.tka_2002 

--S,tka_2003 

--Sitka_2004 

- - Sitka_200S 

--Sitko_ 1996 --\Ne.sl_St;rata_2005_shorel 

--Sitk.a_1997 --S.lk0_2008 

--Si1ka_1998 --Sitk8_2008_Sutwly_O..y 

--Sitka_ 1999 --$rtka_2007 

A 

N 

A 

N 

Sinitsin A (1964-67) (1970’s) B (1980’s) Cove 

Kane 

Is. 

Neva 

Strait 

St. John Baptist 

Bay 

Partofshikof 

Is. Baranof 

Island 

Halleck Kruzof Krestof Nakwasina Is. Is. Sound Sound 

Krestof 

Is. 

Lisianski 

Pt. 

Mountain Pt. Sitka 

Sound 

C (1990’s) D (2000’s) 

Figure 4.17. Northern Sitka Sound: ADFG records of herring spawn (Pritchett 2007). Panel A shows 

spawn records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some 

panels may not have spawn records for each year in a given decade. Refer to each panel’s legend for 

color coded, annual spawn records. 4.34 
o A 

0 

• 

0 

0 

D 

D 

D ' 

• 

D 

~·Ob? f:) 

• 

1 2 

(J 

3 4 0 Kilometers t 

·· -=--=--c::=- A 

N 

Thermograph Northern Sitka Sound 

Herring summary (1998 - 2006) 

Herring Total catch: 5,145 fish 

Occurrence: 19 of 53 hauls = 36% 

Eelgrass Mean fork length: 94.2 mm (n = 198) Sinitsin 

Cove Kelp 

Bedrock 

Kane 

Sand-Gravel Is. 

Neva 

Strait 

Baranof St. John Baptist Island Bay Partofshikof 

Is. 

Kruzof 

Is. Krestof Halleck Sound Is. 

Nakwasina 

Sound 

Species composition 

Pink salmon 

Krestof 

Shiner perch Is. 

Pacific sand lance 

Pacific herring Lisianski 

Pt. Chum salmon 

41 other species Mountain Pt. Sitka 

Sound 

Total catch all species = 31,098 

Figure 4.18. Location and habitat type of beach seine sites in Northern Sitka Sound (see legend). Herring 

are summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 53 seine hauls from 1998 to 2006. 

4.35 
N K

. 

A 

N 

atlian Bay 

Lisianski 

Pt

A Tolal Shoreline J69.3 ltm Tota l Shoreline 369.J km 

0 1 2 4 0 1 2 4 1111111c:::::i1111111- 1<,1om,ce" 1111111c:::::i1111111-Ktom!'len1 

Middle Baranof 

Is. Island Silver 

Bay 

Sitka l 

Deep 

Inlet 

Eastern Channel 

Pirate 

Cove Sandy 

Cove 

54% 

Povorotni Pt. 15% 

6% 

Redoubt Bay 'ri;,• ~' 

Habitat Class -~ Shore Type BC Class --SP _P - Sefd.P10lected Pamally Mobh - 107 .0 t m 

-. --9 - Ramp with gravel buch • 53,5 km --P _P - Protecied Partialy Mobile • S.SA km 

3 - Rock cliff - 49.0 km --SP _I - Seml-ProlecM!d lnwnobile - 54.3 km 

--4 • N.trrow rock ramp • 46.7 km --Eslua,y - lt.S WI 

--32 and 33 - Manmad• - 23.3 km --M.lrtlt'ladfJ-24.l b'll 

--ou~ r - 196.8 km --other - 108.1 km 

A 

N 

A 

N 

Tolal Shoreline 369.3 ltm Tota l Shoreline 369.J km 

0 

-

1 

=

2 

--

4 

""""''"" 0 1 2 

l 

"

.. ,0 ---------•I 

1 25 

0 20 

~ t5 

; 10 

' 

Kelps 

-- Fut\ls • 304.9 km 

Alarla (1ntc-rtldal) - 141 .7 km Seagrasses 

-- Unden;lory Kelps - 253.2 km --Eelgra:ss - 117.6km 

Canopy Kelps - 141.5 km --Surfgrass - 39.5 km 

--Study A rea -- Sludy A rea 

Figure 4.19. Central Sitka Sound: ShoreZone coastal habitat maps. Proportions of dominant 

habitat classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel 

C (kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 

4.36 
Herring Spawn Herring Spawn 

A (1964-67) -- SiOca_1964 B (1980’s) --Silka_ 1980 

Katlian Bay (1970’s) --Silka_ 1965 --Si1ka_ 1981 

Lisianski --Si1ka_ 1966 --Si1ka_1ss2 

Pt. -- $ilka_1967 --Silko_ 1983 

--Sioko_ 1970 --S11ka_ 1984 

--Si1ka_1971 --Silka_ 1985 

--Silko_1872 --SllkD_ 19&e 

- - Silka_ 1975 --Silka_1987 

--Silka_ 1976 --Si1ka_ 1988 

--Silka_ 1977 --SiU<a_1989 Middle --SiU<a_1978 Is. Baranof --Sitka_ 1979 

'' Isl

!I 

""•. . and 

•. ' 

Sitka 

Sitka 

Sound 

Silver 

Deep Bay Pirate Eastern Channel Inlet Cove 

Sandy 

Cove 

Povorotni Pt. 

A 

N 

A 

N 

Redoubt Bay • Kllom!lers 

Herring Spawn Herring Spawn 

C (1990’s) --Silka_1990 D (2000’s) --Sitka_2000 

-- &lka_1991 --Srtl<a_2001 

--Silka_ 1992 --Snko_2002 

--Silka_1993 --Si1ka_2003 

--Si1ka_1994 --Sitka_2004 

--Silko_1995 --Sill<a_2005 

--Stka_1996 --Sitt:a_2006 

--Si•ka_ 1997 --Sllko_2007 

--Silka_1998 

--SiOi:a_ 1999 

A 

N 

• ......... . A 

N 

.....,, ... 

Figure 4.20. Central Sitka Sound: ADFG records of herring spawn (Pritchett 2007). Panel A shows 

spawn records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some 

panels may not have spawn records for each year in a given decade. Refer to each panel’s legend for 

color coded, annual spawn records. 4.37 
)C. (pme TerateawS .vgA

,...~·.:i 9-•.. • 

) 

..... 

· ,:J> 

.fa 

•'-J J"\. -

·u· 

O

~ , .

t, 

• . .... 

~ ~ ~ .. ~ 

Katlian Bay 

Lisianski 

Pt. 

Central Sitka Sound 

Herring summary (1998 - 2006) 

Total catch: 1,472 fish 

Occurrence: 10 of 58 hauls = 17% 

Mean fork length: 84.6 mm (n = 95) 

Thermograph 

Herring 

Eelgrass 

Kelp 

Bedrock 

Sand-Gravel 

14.0 

12.0 

10.0 

8.0 

6.0 

4.0 

2.0 1

1

2

2

3

3 

0

0

0

0

0

0

unugbugb-

-r

J

A

Fe

A

Fe

Ap

Sandy Cove 

Pirate Cove 

C) o mp ( tertewaaen s

Middle 

aeM

Is. 

Baranof 

Island 

Sitka 

Sitka 

Sound 

Eastern Channel Silver 

Bay Pirate Species composition 

Cove 

Sandy 

Shiner perch 

Cove 

Povorotni Pt. 

Redoubt 

Bay 

Pink salmon 

Chum salmon 

Pacific sand lance 

Pacific herring 

43 other species 

Total catch all species = 23,722 

Figure 4.21. Location and habitat type of beach seine sites in Central Sitka Sound (see legend). Herring 

are summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 58 seine hauls from 1998 to 2006. Seawater temperature is 

from two locations within Central Sitka Sound. 

4.38 
Herring Spawn 

--Silka_t980 

Herring Spawn - S,1ka_19s1 

--Sllka_t970 - S,1ka_t982 

--Silka_t971 - Silk8_196J 

--Silka_t972 - S,1ka_19e, 

--Silka_t975 - Silka_ 1985 

--Silka_t976 - Solka_1988 

-- Sitka_1977 N - S,lka_1987 N --Sllka_t978 

--Sitka_1979 

0 I 2 3 4 

.......... 

A - Silka_1988 

- 5'tka_t989 

0 1 2 3 4 

Kiornetef'S 

A 

f 

Herring Spawn 

--Sitka_t990 

--Sitka_1991 Herring Spawn 

--Silka_t992 - Silka_2000 

--Sitka_1993 - Silka_2001 

--Sitka_1994 - Si11<a_2002 

--Sitka_t995 - Silka_200J 

--Silka_t996 - Sitka_2004 

--Si11<a_t997 N 

--Silka_t998 

--Silka_1999 

0 1 2 3 4 

Klome1ers. 

A - Si11<a_2005 N 

- Sitka_2006 

- Sitka_2007 

0 1 2 l 4 _,..,,..,. 

A 

A (1970’s) Redoubt B (1980’s) 

Bay Kidney Taigud Cove Is 

Kanga Bay 

Biorka 

Is. Baranof 

Island Hot 

Springs 

Bay 

West Crawfish 

Inlet 

Necker 

Is. 

C (1990’s) D (2000’s) 

Figure 4.22. Southern Sitka Sound: ADFG records of herring spawn (Pritchett 2007). Panel A shows 

spawn records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some 

panels may not have spawn records for each year in a given decade. Refer to each panel’s legend for 

color coded, annual spawn records. 4.39 
Southern Sitka Sound Thermograph Herring summary (1998 - 2006) 

Redoubt Total catch: 3,050 fish Herring Bay Occurrence: 1 of 23 hauls = 4% 

·--~&\ 

~ -· 

~ . 

-·,~

. 

" -- /)::; ' 

{) 

•

.'·

a ' 

--~ 

•

. 

' 

I 

+ . • !Jo .. 

o D 41 ,c:J 

.. o 

9 , I 

' , 

1> " 

4 

Kilometers 

Kidney 

Mean fork length: 31.3 mm (n = 50) Cove Eelgrass 

Taigud 

Is. Kelp 

Bedrock 

Sand-Gravel 

Kanga 

Bay 

Biorka Hot Is. Springs 

Bay 

Baranof 

Island 

West Crawfish 

Inlet 

Necker 

Is. 

Species composition 

Pacific herring 

Pacific cod 

Bay pipefish 

Shiner perch 

Juvenile greenling 

31 other species 

Total catch all species = 4,370 

Figure 4.23. Location and habitat type of beach seine sites in Southern Sitka Sound (see legend). Herring 

are summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 23 seine hauls from 1998 to 2006. 

4.40 
A 

N Shore Type BC Class A 

31 - Organics - 81 .9 km 

--- 24 - Sand and gravel flat - 72.4 km Prince of 

Whales --- 14 - Ramp with gravel and sand beach - 68.2 km Island 

--- 32 - Manmade - 3.7 km 

--- Other -199.9 km 

1% 16% 

Blanquizal Is. Wadleigh 

Is. 

Klawock 

San Fernando Fish Egg Island Craig Is. 

•• 

• 

San Juan 

Bautista 

Is. 

0 1 2 4 __ [) --===--• Kilometers 

Total Shoreline 426.1 km 

Figure 4.24. Craig: ShoreZone coastal habitat map. Proportion of dominant shore types are 

delineated in panel A. ShoreZone information for Habitat Class, kelps, and seagrasses are currently 

unavailable. For definitions of ShoreZone habitat classifications see Appendix A. 

4.41 
~ Herring Spawn Herring Spawn 

A (1970’s) --Craig_ 1970 --Craq_ 1980 

--Craig_1971 

~~ --Craig_1981 

-- --Craig_ 1982 Cralg_1972 

-- --Cra;g_ 1983 Craig_1973 

--Craig_1984 --Craig_1974 --Cralg_1985 --Cralg_1977 --Craig_l986 --Cralg_1978 --Crag_ 1987 

--Craig_1979 

Prince of 

Whales 

Island Big Salt 

Lake Blanquizal 

Is. 

Wadleigh 

Is. 

Klawock 

San Fernando 

Is. 

Fish Egg 

Is. 

Craig 

San Juan 

Bautista 

Is. 

4 

Kilometefl A 

N 

Herring Spawn Herring Spawn 

--Craig_ 1990 --cra1g_2000 

--Cro,g_ 1991 --cra;g_2001 

- - Craig_ 1992 --Cralg_2002 

--c,,,;g_ 1993 --Craig_2003_base_map 

--Craig_199-4 --CraiQ_2003 

--cra1g_1995 --Cn1111..2004 

--c,,,;g_ 1998 --Cralg_2005 

--Craig_ 1997 --Craig_2006 

--cra1g_2001 

N 

, ' 4 

KBome1ers 

a A 

B (1980’s) 

C (1990’s) D (2000’s) 

Figure 4.25. Craig: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn records 

for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some panels may not 

have spawn records for each year in a given decade. Refer to each panel’s legend for color coded, 

annual spawn records. 4.42 
<.) () 

q 

Q 

~~ ~ 

4 0 (j 

Kilometers 

Craig Species composition Herring summary (1998 - 1999) Pink salmon 

Total catch: 8,804 fish Pacific sand lance Occurrence: 15 of 76 hauls = 20% 

Mean fork length: 43.8 mm (n = 187) Bay pipefish 

Threespine stickleback 

Thermograph 

Crescent gunnel 

Herring Prince of 

Whales Pacific herring Eelgrass Island 

Kelp 40 other species 

Bedrock 

Sand-Gravel 

Blanquizal Is. 

Total catch all species = 28,952 

Big Salt 

Lake 

Wadleigh 

San Fernando 

Is. 

Is. 

Craig 

San Juan 

Bautista 

Is. 

Is. 

Klawock 

Fish Egg 

Figure 4.26. Location and habitat type of beach seine sites in Craig (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 76 seine hauls from 1998 to 1999. 

4.43 
N N Shore Type BC Class Habitat Class A B -- 31 • Org;anic:s. 43.8 km '( --SP _P • Seml•Pfoteded Pou1AJly Mobil'• 90.2 km 

--24 • Sand ,1nd gravel ft,11 • 22.1 km 

A --P_P· Proteded PD~1Jy MobJ&- 26,7 km 

A -- 12 -Wide platform withgt.1vel and sand beach -20.2 kn "· -- se_P. Soml•E-posed P.,rtouy Mo1>1i. - s,7 km 

-- Manmade , O k_m -- Estu;iry • 33.7km 

--Other • 77,3 km -- M.lnmacS. - Okm 

--OU~r - 7.2 k.m 

Crab 

Bay 

• 

Annette ) Cat 

Is • • • . 

Felice Strait ~~ 

Is. \ 

~ Reef 

Ha ,_J" 

/--· rbor 

Ryus Duke Pt. 

Bay 

0 

,.J --==- Tot.a l Shoreline --4 - 4 

63., km f ' -===- KilOmeto&rl. 1""""'''·" --

t' Total ShDf'eline 163., km ~ 

N N Kelps Seagrasses C D Fucus • 151.0 tcm ... '( - Eelgran • 52.7 km 

AJaria (intertidal) - 37.3 km 

A --SUrtgran - 5.2 km 

A -- Underslory Kelps -132.7 km --studyArea 

-- Canopy Kelps , 45, 1 km 

... 

-- s1udy A1H 

~ 

j .. "Ii •

•• 

• 

~ # ,. I 

I F 1111a1~ Ab,b U mlKl.hM)' canopy 

<, 

) 

~· .:....,,v, 4 ._:r,:1 - F a 1 2 4 

- -===---KilQmete,a Tot

-==-

al Sho

--

reline 16

'"-· 

3 .. 4 km • 1' Tota l Shoreline 163.4 km ~ of Shoreline %

Figure 4.27. Duke Island: ShoreZone coastal habitat maps. Proportions of dominant habitat 

classes are delineated in four panels - panel A (Shore Type), panel B (Habitat Class), panel C 

(kelps), and panel D (seagrasses). For definitions of ShoreZone habitat classifications see 

Appendix A. 

4.44 
Herring Spawn Herring Spawn 

-- ks_ann_1sn -- k,_ann_1980 

-- -- ks_ann_ 1981 .. _-...1978 

-- ks_ann_1979 ,. -- k5_ann_1982 , . -- ks_enn_ 1983 

-- ks_a,n_ 1984 

-- ks_ann_ 1985 

-- ks_ann_ 1986 

-- ks_ann_ 1987 

-- ks_arm_ 1988 

-- ks_ann_ 1989 

i;5!)_ ..... b"" . ':'-·- ,., 

-- ks._ann_ 1990a --k5_ann_2000 

-- ks_ann_ 199CIJ --1a_a,n_2001 

-- k:s_ann_,991 r, --k!i_ann_2002 

-- ks_a,,n._1992 --ks_ann_2003 

--Ks_ann_ 1993 -- snn~e_2004 

-- ks._ann_ 199-4 

-- ks_ann_ 1995 

-- ks_ann_ 1996 

-- ks_81'ln_ 1997 

-- ks_-,n_ 1998 

-- ks_ann_ 1999 

A (1970’s) B (1980’s) 

Crab Bay 

Mary 

Is. 

Annette 

Is. 

Cat 

Is. 

Felice Strait 

Reef Ryus Harbor Bay 

Duke Is. 

Duke Pt. 

C (1990’s) D (2000’s) 

Figure 4.28. Duke Island: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2007. Some panels 

may not have spawn records for each year in a given decade. Refer to each panel’s legend for color 

coded, annual spawn records. 

4.45 
(l 0 

c:!!J o ___ {) ~· '> 

:··-·~ . •, . ,~· 

A 

N 

3 

Duke Island 

Herring summary (2007) 

Total catch: 0 fish 

Occurrence: 0 of 3 hauls = 0% 

Mean fork length: NA 

Species composition 

Thermograph 

Herring 

Eelgrass 

Kelp 

Bedrock 

Sand-Gravel 

Crab Bay 

Pink salmon 

Crescent gunnel 

Mary Chum salmon 

Is. 

English sole 

Juvenile flatfish 

23 other species 

Cat 

Is. Total catch all species = 1,028 

Annette Felice Strait 

Is. 

Ryus Reef 

Bay Harbor 

Duke Is. 

Duke Pt. 

Figure 4.29. Location and habitat type of beach seine sites in Duke Island (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 3 seine hauls from 2007. 

4.46 
Black 

A 

N 

Is. 

Bullhead 

Cove 

Revillagigedo 

Channel 

46% 

0% 11% Foggy 

• Bay 

Shore Type BC Class Foggy Pt. 

--- 12 - Wide platform with gravel and sand beach - 15.1 km 

--- 24 - Sand and gravel flat - 14.2 km 

--- 31 - Organics - 7.7 km 

--- Manmade - 0 km 0 0.5 1 2 

-c:::=---Kilometers --- other- 31 .2 km 

Total Shoreline 68.3 km 

Figure 4.30. Kah Shakes: ShoreZone coastal habitat map. Proportion of dominant shore types 

are delineated in panel A. ShoreZone information for Habitat Class, kelps, and seagrasses are 

currently unavailable. For definitions of ShoreZone habitat classifications see Appendix A. 

4.47 
Herring Spawn Herring Spawn 

-- ks_1976 -- ks_arV1_1980 

-- ks_aon_19n -- ks_ann_1981 

--lr.S_ann_ 1978 --kS_ilOO_ 1982 

-- ks_ann_1979 --ks_aM_ 1983 

--ks_ann_ 1984 

-- ks_arv1_1985 

-- ks_aM_1986 

-- ks_ill'V'l_1987 

-- ks_arw,_1988 

-- ks_ann_ 1989 

, ,..,._ ,";,·, 

A 

N 

A 

N 

Herring Spawn Herring Spawn --ks_an.n_ 1990a 

-- ks_ann_2000 -- ks_ar\n_ 1990b -- ks_ann_2001 --l!J;_ann_ 1991 

-- ks_ann_2003 -- ks_Wln_ 1992 

--~s_t992 

-- ks_arm_ 1993 

-- ks_ann_ 1994 

-- kS_ann_ 1995 {}, 

--ks_ann_ 1996 

-- ks_arm_ 1997 

--ks_ann_ 1998 

-- ks_ar.n_ 1999 , ,,,._ , ,,._ 

A 

N 

A 

N 

Black 

Is. A (1970’s) B (1980’s) 

Boca de Quadra 

Bullhead 

Cove 

Kah Shakes 

Revillagigedo Cove 

Channel 

Foggy 

Bay 

Foggy 

Pt. 

C (1990’s) D (2000’s) 

Figure 4.31. Kah Shakes: ADFG records of herring spawn (Pritchett 2007). Panel A shows spawn 

records for 1970’s, panel B for 1980’s, panel C for 1990’s, and panel D for 2000– 2003. Some panels 

may not have spawn records for each year in a given decade. Refer to each panel’s legend for color 

coded, annual spawn records. 4.48 
0 

• 

0 

(} 0 

.· ~--

D 

D 

D 

D 

• 

• 

• 

N \. 

0 

A 

--

2 3 

Black 

Is. Kah Shakes 

Herring summary (2007) 

Total catch: 6 fish 

Occurrence: 1 of 4 hauls = 25% Thermograph Mean fork length: 136.2 mm (n = 6) 

Herring 

Eelgrass 

Kelp 

Bedrock 

Boca de Quadra Sand-Gravel 

Revillagigedo Bullhead 

Channel Cove 

Kah Shakes 

Cove 

Species composition 

Shiner perch 

Pink salmon 

Kelp perch 

Foggy Bay pipefish Bay 

Copper rockfish 

Foggy Pacific herring Pt. 

15 other species 

Total catch all species = 509 

Figure 4.32. Location and habitat type of beach seine sites in Kah Shakes (see legend). Herring are 

summarized by total catch, percent occurrence, and mean fork length. Seine catch data (pie graph) 

represents the percent species composition of 1 seine haul from 2007. 

4.49 
GODAS SST (5m), Ann 

9ON 

unit: "C 

75N 

6ON ~ • ,,.,,,r 

45N 

80N 

15N 

EQ 

15S • 

30S 

45S 

6OS 

75S 

90S30H tlOE SOE 12OE 15DE 1BO 15OW 120W 90W tlOW 3OW 0 30E 

0 z 4 a 8 10 12 14 16 18 20 22 24 26 28 

Fig. 4.33. General global sea surface temperature distribution (15). 

4. 50 
30 35 40 45 50 55 

; I I I ' i i I I I ' I ' 

!F'-C 

0 2 4 6 B 10 12 14 

Sea Surface Temperature 

Fig. 4.34. Sea surface temperature in SEAK illustrating the general pattern of warmest waters in the 

south and coolest toward the north and inside waters (16). 

4.51 
Southeast Alaska Bioareas 

SECR • SE Alaska -- Craig 

SEMJ • SE Alaska - Misty Fjords 

SESI • SE Alaska - Sitka 

SEFJ • SE Alaska -- Lynn Canal 

SEIC • SE Alaska - Icy Strait 

SEYA • SE Alaska - Y a kutat 

-- Mapped Shoreline 

Gulf of Alaska 

N 

0 25 50 100 150 200 250 

KIiometers A 

Figure 4.35. ShoreZone bioareas for SEAK. Delineation of further bioareas pending 

completion of habitat mapping but projected with hatched lines. 

4.52 
7 

2 

4 

3 

Fig. 4.36. Alaska Marine Ecoregions (Piatt and Springer 2007); North Pacific Current – Alaska Stream 

Loop (2), eastern Gulf of Alaska transitional (3), eastern Gulf of Alaska slope (4), Prince of Wales shelf 

and inside waters (5), Chichagof shelf and inside waters (6), northern Gulf of Alaska slope (7), and 

northern Gulf of Alaska shelf (8). 

4.53 
 

 

Chapter 5 

Are Lynn Canal herring a discrete population segment (DPS)? 

Mark G. Carls, Jeffrey T. Fujioka, Scott W. Johnson 

Stanley D. Rice, Johanna Vollenweider, & Bruce L. Wing 

Alaska Fisheries Science Center, Auke Bay Laboratories, Juneau, AK 

and 

Richard G. Gustafson & Robin S. Waples 

Northwest Fisheries Science Center, Seattle, WA 

and 

Jamie N. Womble 

National Park Service, Juneau, AK 

and 

Erika Phillips 

Alaska Regional Office, Juneau, AK 

Abstract 

Pacific herring in Lynn Canal are not a distinct population segment (DPS) as defined by 

the Endangered Species Act (ESA). Examination of all available data by the biological review 

team (BRT) did not convince the majority of members that herring in Lynn Canal were markedly 

discrete from other populations of the same taxon in southeast Alaska (SEAK). No members 

perceived Lynn Canal herring to be significant with respect to the taxon (although all recognized 

the importance of herring to the local ecosystem). Available biological data were either 

incomplete or were too similar to definitively separate herring populations within SEAK, thus 

the team concluded that the smallest defensible DPS that includes Lynn Canal is SEAK. The 

southern limit of the DPS, Dixon Entrance, is identified by genetic differences between herring 

in SEAK and those in British Columbia. The northern border is defined by a physical barrier, 

mobile open ocean beaches inadequate as spawning and rearing habitat; the oceanward boundary 

is near Icy Point. Glacier Bay and Lynn Canal are both included in the SEAK DPS. The team 

did not rule out the possibility that SEAK might be subdivided into smaller DPS units if more 

detailed data collected in the future thus indicate. 

Introduction 

Endangered Species Act (ESA) 

For the purpose of the ESA, Congress has defined a species as “any subspecies of fish or 

wildlife or plants, and any distinct population segment of any species of vertebrate fish or 

wildlife which interbreeds when mature.” Guidance on what constitutes a distinct population 

segment (DPS) is provided by the joint NMFS-USFWS interagency DPS policy (61 FR 4722, 

February 7, 1996). In order to be classified as a DPS, a vertebrate population must fulfill two 

criteria – discreteness and significance. To be considered “distinct,” a population, or group of 

populations, must first be “discrete” from other populations and then “significant” to the taxon 

(species or subspecies) to which it belongs. 

The fundamental species question addressed by the Biological Review Team for this 

status review was “does the Lynn Canal herring stock comprise a distinct population segment 

(DPS) as defined under the Endangered Species Act?” The Team’s approach to answering this 

question is described in this chapter. Prior to the commencement of this status review, Pacific 

herring stocks in Southeast Alaska had not been examined in detail for DPS structure. However, 

5.1 
several herring studies conducted in the North Pacific helped the BRT evaluate population 

discreteness and significance, shedding light on whether or not Pacific herring in Lynn Canal are 

a distinct population segment as defined under the ESA. 

Evaluation of discreteness 

As stated previously, a population segment of a vertebrate species may be considered 

discrete if it is markedly separated from other populations of the same taxon as a consequence of 

physical, physiological, ecological, or behavioral factors. Quantitative measures of genetic or 

morphological discontinuity may also provide evidence of this separation. A population may 

also be considered discrete if it is delimited by international governmental boundaries, between 

which exist differences in control of exploitation, management of habitat, conservation status, or 

regulatory mechanisms that are significant in light of Section 4(a)(1)(D) of the ESA. Because 

the focus of this status review document is the scientific assessment of population structure, the 

Biological Review Team focused on the available scientific evidence for population discreteness. 

Evaluation of significance 

Once a population segment is determined to be discrete under one or more of the above 

conditions, its biological and ecological significance to the taxon must then be considered. 

Criteria that can be used to assess whether the discrete population segment is significant include: 

1. Persistence of the discrete population segment in an ecological setting unusual or unique 

for the taxon; 

2. Evidence that loss of the discrete population segment would result in a significant gap in 

the range of a taxon; 

3. Evidence that the discrete population segment represents the only surviving natural 

occurrence of a taxon that may be more abundant elsewhere as an introduced population 

outside its historic range; or 

4. Evidence that the discrete population segment differs markedly from other populations of 

the species in its genetic characteristics. 

A discrete population segment needs to satisfy only one of these criteria to be considered 

significant. However, the list of criteria is not exhaustive; other criteria may be used as deemed 

appropriate. 

DPS decision process by the BRT 

The fundamental goal was to determine if Lynn Canal herring are a DPS and if not, to 

identify the DPS that includes Lynn Canal herring. The ESA discreteness question was 

examined first. To understand Lynn Canal in its physical and biological context, data review 

(detailed in Chapters 2 to 4) began at large geospatial scales and moved toward smaller scales, 

ending with Lynn Canal. After determining that Lynn Canal herring were not discrete, i.e., not 

markedly different from nearby stocks, the BRT determined the smallest discrete geographic 

area supported by the data (SEAK) and debated the significance of this area with respect to the 

taxon. 

5.2 
Structure among Pacific herring at large and small scales 

Genetic differences and known herring mobility provided the largest scale evidence of 

differences among Pacific herring subpopulations (Chapter 2, Fig. 2.2). In particular, the genetic 

differences between herring in Asia, the Bering Sea, and those in the Gulf of Alaska (Grant and 

Utter 1984; Kobayashi 1993; O'Connell et al. 1998) are consistent with herring migration ability; 

the maximum observed yearly net movement of tagged fish ranges from nearly 200 km (SEAK) 

to 300 km (British Columbia) and the average net movement is about 90 km (Dahlgren 1936; 

Hay and McKinnell 2002). Thus, genetic drift among populations located thousands of 

kilometers apart is understandable. Recruitment and biomass data corroborate differences 

among populations; Bering Sea herring are much different than those along the GOA and in 

British Columbia (Williams and Quinn 2000). Herring in the northern Gulf of Alaska (Kodiak 

through Lynn Canal) may be distinct from those further south (Helm Bay near Ketchikan 

through San Francisco) (Grant and Utter 1984). However, this allozyme study (Grant and Utter 

1984) was not designed to discriminate among SEAK stock and a more detailed microsatellite 

study found a modest genetic difference between herring in SEAK and those from the Queen 

Charlotte Islands and northern British Columbia (Beacham et al. 2002). (Sample locations in 

SEAK included Sitka, Seymour Canal, and the vicinity of Kah Shakes, south of Ketchikan.) 

Evidence for genetic structure in populations east and south of the Alaska Peninsula is relatively 

weak: genetic differences among populations covering the large geographic area from San 

Francisco to Kodiak Island are only about 1/10th as large as those between Gulf of Alaska and 

Bering Sea populations (Grant and Utter 1984; Kobayashi 1993). 

The other biological variables available for comparison within SEAK (migration, spawn 

timing, vertebrae number, recruitment, and size-at-age) provided modest and often conflicting 

evidence of discreteness among stocks. (See Chapter 3 for a complete discussion and Fig. 5.1 

for a summary map.) Geospatial interpretation of these data was generally highly subjective and 

variable; geospatial coverage was often incomplete. No clear divisions emerged among herring 

in SEAK when available biological variables were overlain. In this context, we turned our 

attention to Lynn Canal herring. 

Are Lynn Canal herring discrete? 

Based on the available evidence, the BRT concluded 6 to 4 that Lynn Canal herring are 

not discrete; i.e., they are not markedly different from other stocks in SEAK (Fig. 5.1). The 

boundaries accepted for Lynn Canal are the ADFG management boundaries, ranging from 

Berners Bay south to Taku Harbor and encompassing Douglas Island and portions of northern 

Admiralty Island, notably Oliver Inlet where spawning frequently occurs (Fig. 3.2). 

Evidence against discreteness 

• There are no known genetic differences between Lynn Canal stock and others in SEAK. 

o Several studies have included herring from SEAK (Grant and Utter 1984; Grant 

1986; Kobayashi 1993; Beacham et al. 2002). Lynn Canal herring were included 

in one of these (an allozyme study) but sampling within SEAK was generally 

insufficient to draw conclusions. 

o The microsatellite DNA study by Beacham et al. (2002) was the most detailed 

genetic analysis; they concluded that SEAK herring differ from herring in British 

Columbia but did not provide a detailed comparison of samples (Sitka, Kirk Point, 

Mary Island, and Seymour Canal) within SEAK. 

5.3 
 

• Spawn timing in Lynn Canal does not differ from the timing in other northern SEAK 

stocks, rather spawn timing appears to partition into an early southern group and a later 

northern group. 

• Comparison of Lynn Canal herring recruitment to other SEAK stocks was not available 

at the time of the decision and more data are required before recruitment is estimable 

(Chapter 3). 

o However, incomplete evidence suggests year class strength in Lynn Canal may be 

synchronous with that in other SEAK stocks (Fig. 3.9) 

• Growth rates in Lynn Canal, based on the limited amount of data at the time of the 

decision (Rounsefell and Dahlgren 1935; Johnson et al. 1997; Carls et al. 1998; Williams 

and Quinn 2000), are not different from elsewhere in SEAK. (Subsequent analysis of 

ADFG data further substantiates this conclusion.) 

o Variation in median lengths [age 4 herring in 1929; (Rounsefell and Dahlgren 

1935)] did not suggest divisions among SEAK herring stocks. 

o Lynn Canal lengths and weights at age were not unusual [1994 to 1995; (Johnson 

et al. 1997; Carls et al. 1998)]. 

o Analysis of weight-at-age by Williams and Quinn (2000) suggested growth rates 

in a broad portion of SEAK were similar; however, this analysis did not include 

Lynn Canal fish. 

o Given the consistency among the data analyzed to date, marked differences 

between Lynn Canal herring and other SEAK stock were not expected in the 

unanalyzed ADFG data set at the time of the BRT decision. Preliminary analysis 

of 78,971 measurements from the ADFG data set supports the original decision; 

 Current trends in size at age (length) in all SEAK herring stocks is 

downward and there is no evidence Lynn Canal stock differs from the 

others. 

 Growth rates do not vary significantly among SEAK herring stocks 

• Vertebrae number in Lynn Canal herring is consistent with nearby areas (Rounsefell and 

Dahlgren 1935). 

o Vertebrae number generally does not provide clear separation within SEAK 

stocks. 

• Lynn Canal herring mix with other SEAK herring in summer feeding areas (Carlson 

1980). 

o However, limited tagging data do not rule out the possibility that stocks remain 

segregated on spawning grounds. 

• Herring occupy nearby waters adjacent to the Lynn Canal area and these populations may 

be functionally continuous. 

o Predicted herring fidelity within an area the size of the Lynn Canal management 

area is about 40%, suggesting considerable exchange with surrounding stocks is 

plausible. [This estimate is based on the assumption that tagging data averaged 

over the five managed stocks of herring in British Columbia can be used to 

predict fidelity in SEAK and is intended only as a rough measure; it is based on 

central tendancies in the British Columbia data. Scatter in the British Columbia 

data is high and observed fidelity ranged from about 0 to 100% at this scale (950 

km2

, water only).] 

5.4 
o The nearest spawning stock, in Port Frederick, is located ~60 km from the Lynn 

Canal stock, well within net average yearly herring movement [89 km, (Hay et al. 

2001; Hay and McKinnell 2002)]. 

 Herring can travel considerable distances in short periods of time; e.g., 

ripe, prespawning herring moved 150 km in 6 d and spent fish moved 350 

km in 16 d (Haegele and Schweigert 1985). 

• Habitat in Lynn Canal is not markedly different from habitat elsewhere in SEAK. 

o Measured temperatures are not unique (Chapter 4, Table 4.1) 

o Expected temperatures are not unique (Chapter 3, Fig. 3.17; Chapter 4, Fig. 4.34) 

o Measured salinities are not unique (Chapter 4, Table 4.1) 

o The area is not isolated by features that impede water exchange or act as 

migration barriers. 

o There is generally less macroalgae cover in Lynn Canal than elsewhere in SEAK 

and there are differences in communities between Lynn Canal and other bioareas 

in SEAK (Chapter 4, Fig. 4.35). However, this does not appear to limit spawning 

or modify herring behavior; herring are euryhaline, eurythermal, and spawn on a 

wide variety of substrates (Chapters 2 and 4). 

• Lynn Canal herring do not have unusual or elevated polynuclear aromatic hydrocarbon 

(PAH) contaminant loads (Carls et al. 1998; Carls et al. 1999). 

o PAH loads in adult herring collected near Shelter Island were low and were not 

consistent with either petrogenic or pyrogenic contamination. 

 Mean total PAH = 17 ng/g wet weight in ovaries and muscle tissue [the 

95% confidence bounds were 15 to 20 ng/g (parts per billion), n = 49 

(Carls et al. 1998)]. 

 Mean total PAH concentrations were 14 ± 2, 23 ± 3, and 11 ± 4 ng/g wet 

weight for ovaries or eggs from Shelter Island (Lynn Canal), Cat Island, 

and Seymour Canal, respectively (the error term is standard error; n = 15, 

6, and 4, respectively). 

o Human shoreline development (presumably elevating the relative potential for 

contaminant discharge and physical disruption), is greatest in the Lynn Canal 

management area (8%). However Sitka Sound is the second most developed area 

(6%) and is utilized by the largest and increasing herring biomass in SEAK 

(Chapter 4, Table 4.2). 

 Note; we cannot eliminate the possibility that shoreline development 

reduces stock biomass wherever it occurs. Rather, we are suggesting the 

2% development difference between Lynn Canal and Sitka habitat 

disturbance does not explain the very different population loss and growth 

trajectories at the two locations. 

Evidence for discreteness 

• Lynn Canal is a consistent spawning area, not contiguous with adjacent spawning areas. 

o Repeat spawning in a given area suggests utilization by the same fish 

 Caveats: 

• No tagging studies have documented spawning fidelity in SEAK 

5.5 
• The nearest spawning stock, in Port Frederick, is located ~60 km 

from Lynn Canal stock, well within net average yearly herring 

movement [89 km, (Hay et al. 2001; Hay and McKinnell 2002)]. 

• Predicted herring fidelity for the Lynn Canal Management Area is 

about 40%, implying exchange with surrounding fish is likely. 

o Herring are found year round in this location. 

• Temporal changes in biomass are not synchronous with nearby stocks (Figs. 3.8 and 

3.13). 

o Sitka Sound, Hoonah Sound, and Seymour Canal stock biomasses have increased 

since the 1990s. 

o Tenakee Inlet stock biomass has fluctuated up and down since the 1990s. 

o Lynn Canal stock biomass has generally been steady since1990 (as has that at 

Hobart Bay / Port Houghton). 

o This suggests that herring do not randomly disperse into areas with lower 

population density, i.e., there is no evidence that Lynn Canal herring are being 

repopulated by excesses from nearby, growing populations. 

• Persistence of depressed stock abundance 

o Lynn Canal stock has been depressed since the 1980s. 

 Fishing ended in 1982 (Blankenbeckler and Larson 1987; Pritchett et al. 

2008); there are indications that overfishing caused the stock collapse. 

 Other suggested causes are increased marine mammal populations, human 

shoreline development, waste discharge (e.g., sewage), contaminant 

discharge, and boat activity. 

o Typical recolonization time is about 11 y (range 5 to 35 y) for herring in British 

Columbia (Ware and Tovey 2004). 

Are SEAK herring discrete? 

Not only was the BRT unable to definitively distinguish Lynn Canal herring from the 

remainder of SEAK, they could not identify any definitive divisions among SEAK stocks in 

general. Divisions among regions within SEAK were ambiguous at best (Fig. 5.1). However, 

SEAK herring can reasonably be distinguished from other Pacific herring to the north with 

genetic differences (e.g., the Bering Sea) and because the open beaches between SEAK and other 

northern herring habitat (e.g., Yakutat and Prince William Sound) represent a physical barrier 

between spawning populations. (These beaches are exposed to ocean surf and thus are not 

suitable spawning or rearing habitat.) The oceanward boundary for SEAK as defined here is in 

the vicinity of Icy Point, some 30 km north of Cross Sound and about 200 km south of Yakutat. 

However, the BRT recognizes this northern boundary cannot be rigorously proven at present and 

that the DPS may be larger than defined. Glacier Bay and Lynn Canal were both included within 

the northernmost part of the SEAK DPS. The southern limit of SEAK, Dixon Entrance, is 

identified by genetic differences between herring in SEAK and those in British Columbia. The 

team did not rule out the possibility that SEAK might be subdivided into smaller DPS units if 

more detailed data collected in the future thus indicate. 

5.6 
Evidence for SEAK discreteness 

Using ESA questions designed to determine discreteness, the BRT concluded that SEAK 

herring are discrete. Herring in SEAK are markedly separated from other Pacific herring as a 

consequence of physical barriers, genetics, and ecological differences. 

• SEAK herring are isolated to the north by barrier beaches. 

o Pacific herring do not utilize beaches exposed to ocean surf for spawning. 

o To our knowledge, no spawning has been reported in the relatively unsheltered 

Gulf of Alaska shoreline between northern SEAK and Yakutat or between 

Yakutat and Prince William Sound. 

o The gap between other SEAK habitat and Yakutat is about 200 km (Icy Point to 

Yakutat). The gap between Yakutat and Zaikof Bay in Prince William Sound is 

about 400 km, a distance greater than documented maximum annual migration 

distances [300 km; (Hay and McKinnell 2002)]. 

• A natural biological boundary between herring populations coincides with the 

international boundary separating SEAK and British Columbia. 

o SEAK herring are genetically different from those in British Columbia (Beacham 

et al. 2002). 

o Parasitism differs among herring north and south of this border (Arthur and Arai 

1980), though this is a coarse measure because few sites were sampled, thus this 

measure yields ambiguous boundary position estimates. 

o Different biological zones are apparent along the coast, probably a result of both 

thermal (north-south) and salinity (east-west) gradients (Chapter 4). 

• A thermal gradient is clearly evident through British Columbia and SEAK. 

o Temperatures in SEAK are colder than in British Columbia 

o SEAK has tidewater glaciers, British Columbia does not, chilling the water and 

increasing turbidity and possibly nutrients. 

o SEAK mainland topography is heavily influenced by snowfields and glaciers; this 

is less prevalent in British Columbia 

Are SEAK herring significant with respect to the taxon? 

Using the questions posed by the ESA to evaluate significance, the BRT concluded that 

SEAK herring are significant. The population persists in a unique habitat intermediate between 

areas further south and further north. Loss of SEAK herring would result in a significant gap in 

the range of the taxon and SEAK herring are genetically different from herring in British 

Columbia. 

• Does the discrete population persist in habitat unusual or unique for the taxon? 

o Yes, based on the evidence stated for discreteness, SEAK is a unique habitat, 

intermediate between warmer southern habitat along the eastern Pacific and 

cooler habitat to the north. 

• Would loss of this population segment result in a significant gap in the range of the 

taxon? 

o Yes, loss of fish in an area this large will result in a gap in the taxon. 

o The area involved exceeds normal territorial size of herring by more than a factor 

of 2 and the distance of SEAK from Cross Sound to Dixon Entrance (roughly 500 

5.7 
km) exceeds the presumptive exposed beach barrier distance between Prince 

William Sound and Yakutat (400 km). 

• Does SEAK represent the only surviving natural occurrence of Pacific herring? 

o No, herring occupy natural habitat around the Pacific Ocean as far south as 

California in N. America and Korea in Asia and north into the Arctic Ocean, 

extending nearly to Norway (Chapter 2, Fig. 2.2). 

• Do SEAK stock differ genetically from other Pacific herring stock? 

o Yes and no. Evidence suggests that SEAK stock is different from British 

Columbia stock (Beacham et al. 2002) but not different from nearby Gulf of 

Alaska stocks to the north and west (Grant and Utter 1984). One study found 

evidence of genetic structure within Prince William Sound (Burkey 1986), raising 

the possibility a more detailed study with modern techniques may reveal 

differences between these stocks and SEAK stock. However, subsequent study 

demonstrated that DNA data provide no evidence of stable differentiation among 

Pacific herring populations within sea basins on spatial scales of up to ~700 km, 

rather temporal variation was dominant (Seeb et al. 1999). 

References 

Arthur, J. R. and H. P. Arai 1980. Studies on the parasites of Pacific herring (Clupea harengus 

pallasi Valenciennes): a preliminary evaluation of parasites as indicators of geographical 

origin for spawning herring. Can J Zool 58: 521-527. 

Beacham, T. D., J. F. Schweigert, C. MacConnachie, K. D. Le, K. Labaree and K. M. Miller 

2002. Population structure of herring (Clupea pallasi) in British Columbia determined 

by microsatellites, with comparisons to southeast Alaska and California, Fisheries and 

Oceans Canada, Canadian Science Advisory Secretariat. 

Blankenbeckler, D. and R. Larson 1987. Pacific herring (Clupea harengus pallasi) harvest 

statistics, hydroacoustical surveys, age, weight, and length analysis, and spawning ground 

surveys for southeastern Alaska, 1980-1983. Juneau, Alaska Department of Fish and 

Game, Division of Commercial Fish. Technical Data Report 202: 121. 

Burkey, C. J. 1986. Population structure of Pacific herring (Clupea harenqus pallasi) in Eastern 

Prince William Sound, Alaska, University of Alaska, Juneau. masters. 

Carls, M. G., G. D. Marty, T. R. Meyers, R. E. Thomas and S. D. Rice 1998. Expression of 

viral hemorrhagic septicemia virus in prespawning Pacific herring (Clupea pallasi) 

exposed to weathered crude oil. Can J Fish Aquat Sci 55(10): 2300-2309. 

Carls, M. G., S. D. Rice and J. E. Hose 1999. Sensitivity of fish embryos to weathered crude 

oil: Part I. Low-level exposure during incubation causes malformations, genetic damage, 

and mortality in larval Pacific herring (Clupea pallasi). Environ Toxicol Chem 18(3): 

481-493. 

Carlson, H. R. 1980. Seasonal distribution and environment of Pacific herring near Auke Bay, 

Lynn Canal, southeastern Alaska. Trans Am Fish Soc 109(1): 71-78. 

Dahlgren, E. H. 1936. Further developments in the tagging of the Pacific herring, Clupea 

pallasii. J Conseil 11: 229-247. 

5.8 
Grant, W. S. 1986. Biochemical genetic divergence between Atlantic, Clupea harengus, and 

Pacific, C. pallasi, herring. Copeia 1986: 714-719. 

Grant, W. S. and F. M. Utter 1984. Biochemical population genetics of Pacific herring (Clupea 

pallasi). Can J Fish Aquat Sci 41(6): 856-864. 

Haegele, C. W. and J. F. Schweigert 1985. Distribution and characteristics of herring spawning 

grounds and description of spawning behavior. Can J Fish Aquat Sci 42: 39-55. 

Hay, D. E., P. B. McCarter and K. S. Daniel 2001. Tagging of Pacific herring Clupea pallasi 

from 1936-1992: a review with comments on homing, geographic fidelity, and straying. 

Can J Fish Aquat Sci 58(7): 1356-1370. 

Hay, D. E. and S. M. McKinnell 2002. Tagging along: association among individual Pacific 

herring (Clupea pallasi) revealed by tagging. Can J Fish Aquat Sci 59(12): 1960-1968. 

Johnson, S. W., M. G. Carls, R. P. Stone, C. C. Brodersen and S. D. Rice 1997. Reproductive 

success of Pacific herring, Clupea pallasi, in Prince William Sound, Alaska, six years 

after the Exxon Valdez oil spill. Fish Bull 95(4): 748-761. 

Kobayashi, T. 1993. Biochemical analyses of genetic variability and divergence of populations 

in Pacific herring. Bull Nat Res Inst Far Seas Fish 30: 1-77. 

O'Connell, M., M. C. Dillon, J. M. Wright, P. Bentzen, S. Merkouris and J. Seeb 1998. Genetic 

structuring among Alaskan Pacific herring populations identified using microsatellite 

variation. J Fish Biol 53(1): 150-163. 

Pritchett, M., K. Monagle and D. Harris 2008. Berners Bay area herring research, 2007, Alaska 

Department of Fish and Game, Division of Commercial Fisheries: 1-10. 

Rounsefell, G. A. and E. H. Dahlgren 1935. Races of herring, Clupea pallasii, in southeastern 

Alaska. Bull Bureau Fish 17. 

Seeb, J., S. E. Merkouris, L. W. Seeb, J. B. Olsen, P. Bentzen and J. M. Wright 1999. Genetic 

discrimination of Prince William Sound herring populations. Anchorage, AK, Alaska 

Department of Fish and Game, Genetics Laboratory: 1-111. 

Ware, D. M. and C. Tovey 2004. Pacific herring spawn disappearance and recolonization 

events, Fisheries and Oceans Canada, Canadian Science Advisory Secretariat: Online at 

http://www.dfo-mpo.gc.ca/csas/CSAS/DocREC/2004/RES2004_008_E.pdf. 

Williams, E. H. and T. J. Quinn 2000. Pacific herring, Clupea pallasi, recruitment in the Bering 

Sea and northeast Pacific Ocean, I: relationships among different populations. Fish 

Oceanogr 9(4): 285-299. 

5.9 
Fig. 5.1. Summary of biological information (colored overlays); migration, spawn timing, 

vertebrae number, recruitment, and weight at age, together with stock management areas (black 

polygons). The blue ellipses are genetic groupings estimated with allozyme analysis (Grant and 

Utter 1984); the red ellipse is the SEAK grouping (microsatellite) estimated by Beacham et al. 

(2002). Question marks indicate missing information. 

Biological Variable 

- migration patterns 

- Spawn timing 

recruitment synchrony 

- weight-at-age 

- vertebrae number 

Lynn Canal 

Management Area 

5.10 
Appendix A 

Summary of Pacific herring genetic studies 

Robin Waples 

Over the last three decades, a number of molecular genetic studies have considerably 

advanced the understanding of the population structure of herring. Based on the level of 

differentiation observed at 40 allozyme loci, Grant (Grant 1986) estimated that Pacific herring 

(Clupea pallasii), and Atlantic herring (C. harengus) have been isolated since the mid to late 

Pliocene. This estimated divergence time is consistent with results of a subsequent study based 

on ribosomal DNA (Domanico et al. 1996). 

 Within C. pallasii, the contrast between populations from Asia and the eastern Bering 

Sea versus those from the rest of North America provides by far the strongest evidence for 

population genetic differentiation (Grant and Utter 1984)—with genetic differences about onetenth as large as those between Pacific and Atlantic herring (Grant 1986). These two studies 

considered 21 populations from Asia (Korea, Japan, USSR), northeast and southeast Bering Sea, 

the Gulf of Alaska (including Lynn Canal), and the eastern North Pacific (from Helm Bay to San 

Francisco). Kobayashi (Kobayashi 1993), based on almost 2400 individuals from 18 populations 

from the Yellow Sea to California sampled for 25 allozyme loci, and O’Connell et al. (O'Connell 

et al. 1998), based on 350 herring from 7 locations from Norton Sound to Prince William Sound 

assayed for 5 microsatellite loci, also identified the Bering Sea – Gulf of Alaska split as 

representing the major genetic feature within Pacific herring. 

Considering only populations east and south of the Alaska Peninsula, evidence for 

population genetic structure is relatively weak. Both Grant and Utter (Grant and Utter 1984) and 

Kobayashi (Kobayashi 1993) found that genetic differences among populations covering the 

large geographic area from San Francisco to Kodiak Island were only about 1/10th as large as 

those between Gulf of Alaska and Bering Sea populations. Within this large area in the eastern 

North Pacific, a number of studies have looked at more fine-scale population genetic structure. 

In a master’s thesis, Burkey (Burkey 1986) evaluated genetic structure within eastern 

Prince William Sound herring based on 14 allozyme loci and samples taken in 1979 to 1981 

from both the winter bait/food and spring sac-roe fisheries. Burkey (Burkey 1986) found no 

statistically significant allele frequency differences between samples within fisheries, between 

years within fisheries, or between fisheries. The O’Connell et al. (O'Connell et al. 1998) study 

cited above included four collections from Prince William Sound, each consisting of 50 fish 

sampled in one year only. They found little evidence for population structure among the samples 

from St Matthew’s Bay, Fish Bay, and Rocky Bay, but the sample from Port Chalmers was 

genetically distinct from the other Prince William Sound samples. [There were no obvious 

differences in size at age among fish sampled by Johnson et al. (Johnson et al. 1997) from these 

same four locations in the same year,1995; reproductive success was good and did not vary 

significantly among location.] 

In British Columbia, Schweigert and Withler (Schweigert and Withler 1990) used 7 

allozyme loci to examine relationships among 12 samples (> 1000 fish total) taken in sac-roe 

fisheries in 1985 and 1986 from three geographic areas (Strait of Georgia, west coast Vancouver 

Island, and north coast). Although they found statistically significant heterogeneity of allozyme 

allele frequencies among the three areas and among regions within the Strait of Georgia, the 

absolute levels of differentiation were modest. Furthermore, a gene diversity analysis showed 

that temporal differences between years within collection sites were nearly as large as 

A.1 
 

differences between sites within years. Schweigert and Withler (Schweigert and Withler 1990) 

also reported results of restriction enzyme analysis of mtDNA from a much smaller number (31) 

of individuals collected in 1984. This small study provided no evidence of major population 

subdivision but had little power to detect subtle differences. 

Beacham et al. (Beacham et al. 2002) presented results of a much more ambitious study 

of variation at 13 microsatellite loci among 20,000 herring taken from spawning aggregations at 

83 localities (75 in British Columbia, 5 in SE Alaska, one from Washington (Cherry Point), and 

two from California). About a third of the locations were sampled in more than one year. In 

agreement with results reported by previous authors for allozymes, the overall level of 

differentiation was very low (FST = 0.00321). Beacham et al. (Beacham et al. 2002) found no 

evidence of stock structure within a number of the geographic areas they sampled (W. Queen 

Charlotte Islands, North Coastal, Central Coastal, Johnstone Strait, W. Vancouver Island). 

Samples from a few locations (Skidegate Inlet and Louscoone Inlet (Q. Charlotte Islands), and 

Portage Inlet/Esquimault Harbour (Strait of Georgia)) were locally distinctive. Beacham et al. 

(Beacham et al. 2002) also found evidence for some modest differences between herring from 

different geographic regions (Johnstone Strait vs other B.C. populations; S.E. Alaska vs Queen 

Charlotte Islands and Northern B.C.; California vs B.C.). Except for the comparisons involving 

the samples from Skidegate Inlet and Portage Inlet/Esquimault Harbour, allele frequency 

differences between temporal samples from the same locality were as larger or larger than those 

for geographic comparisons between localities. 

In a brief unpublished report for WDFW, Bentzen (Bentzen 2004) provided a 

“Preliminary summary” of analysis of mtDNA sequences from 458 herring from five localities in 

Puget Sound, including one (Cherry Point) sampled in two years. Samples from Norton Sound, 

Prince William Sound, British Columbia (Denman/Hornby), and San Francisco Bay were also 

included as outgroups. The two most common haplotypes were found in all populations. An 

analysis of molecular variance (AMOVA) found no significant differences among all the 

samples combined. After lumping some rare haplotypes, however, the analysis was repeated and 

(barely) statistically significant differences were found among the Puget Sound collections. 

Including the more geographically distant B.C., Alaskan and Californian samples in the analysis 

increased the level of differentiation (and the significance level of the heterogeneity test) only 

slightly. Pairwise tests indicated that the pooled samples from Cherry Point were the most 

distinctive within Puget Sound. 

Small et al. (Small et al. 2005) used data for 12 microsatellite loci to examine genetic 

variation in samples of over 1000 herrring from five sites in Puget Sound, one in southern Strait 

of Georgia, and one in California. An AMOVA found significant evidence for population 

structure, with variance associated with geography about twice as large as that associated with 

temporal samples from the same locality. Geographic differences were primarily due to two 

populations (Cherry Point and Squaxin Pass) for which temporal samples showed a consistent 

pattern of genetic differentiation. In Cherry Point, the isolating mechanism appears to be an 

unusually late spawn timing, whereas it was hypothesized that physical isolation was responsible 

for the relative distinctiveness of samples from Squaxin Pass. In a subsequent master's study, 

Mitchell (2006) examined temporal patterns of population structure with 12 microsatellite DNA 

loci over the years 1999-2005 in many of the same populations surveyed by Small et al (2005). 

Herring samples from Cherry Point remained genetically differentiated over this time period; 

1 FST takes values between 0 and 1 and indicates the fraction of overall genetic variance that is due to differences 

among samples. 

A.2 
however, no significant genetic differences were found between Squaxin Pass and other Puget 

Sound samples in 2005, with the exception of Cherry Point (Mitchell 2006). 

No studies focused specifically on herring from Southeast Alaska, although samples from 

that area were included in studies by Grant and Utter (Grant and Utter 1984), Kobayashi 

(Kobayashi 1993), and Beacham et al.(Beacham et al. 2002). As noted above, Beacham et al. 

(Beacham et al. 2002) found evidence for modest differences between herring sampled from S.E. 

Alaska and those from the Queen Charlotte Islands and Northern B.C. The Grant and Utter 

(Grant and Utter 1984) study is the only one to report data for Lynn Canal herring; they did not 

comment on this sample specifically, and a review of their results does not suggest anything 

particularly distinctive about Lynn Canal herring. 

Discussion 

Collectively, results summarized above have demonstrated the following points: 

• Atlantic and Pacific herring are characterized by genetic differences that are consistent 

with a separation of a few million years. 

• Within Pacific herring, by far the largest genetic distinction is found between populations 

from Asia and the Bering Sea versus the rest of North America. With the exception of 

some differentiated populations from the Alaskan Peninsula, genetic differences among 

localities within these two major lineages are smaller by an order of magnitude or more. 

• Among herring from the Alaska Peninsula to California, some very modest evidence of 

population structure exists. Herring from some geographic areas can be distinguished in 

a statistical sense from herring from other areas. 

• Some studies included temporal replication of samples from specific areas; in some cases 

allele frequency differences between years were as large or larger than those between 

localities. In other cases, (e.g., Cherry Point and perhaps Squaxin Pass) these replicated 

samples provide consistent evidence for population subdivision. Physical or behavioral 

isolation may explain consistent genetic differences. There is good evidence, therefore, 

that some populations in some geographic areas are locally distinctive genetically, albeit 

on a scale that is modest compared to the differences found between the two major 

lineages of Pacific herring. 

Gustafson et al. (Gustafson et al. 2006) included a useful discussion of some factors that 

influence how one should interpret genetic data for Pacific herring, or for any species with very 

large population sizes. Some of those points are summarized here. At presumably neutral 

markers such as those discussed here, population genetic differentiation (as measured by indices 

such as FST) is a function of the product of the effective population size (Ne) and the migration 

rate (m = fraction of the population that migrates each generation). Based on Wright’s (Wright 

1978) commonly used (albeit very rough) approximation that at equilibrium, FST = 1/(1+4Nem), 

the FST = 0.0032 reported by Beacham et al. (Beacham et al. 2002) for NE Pacific herring 

implies Nem ~ 78 migrant individuals per generations. In a small population, that could represent 

a high migration rate (m), but in a population with 106

 individuals it equates to m = 7.8 x 10-5 – 

that is, less than one individual in ten thousand is a migrant each generation. Because of the 

inverse relationship between FST and Nem and the numerous assumptions underlying Wright’s 

formula, robust estimation of migration parameters associated with low FST values is very 

difficult (Waples 1998; Whitlock and McCauley 1999), so any quantitative estimates should be 

treated with caution. Nevertheless, the point remains that in very large populations, very low 

A.3 
levels of genetic differentiation could be associated with migration rates that have little influence 

in shaping the demographic parameters of the population. That is, large populations might be 

demographically independent but have only very modest levels of population genetic 

differentiation. Whether this scenario represents one in which it is reasonable to identify 

different ‘populations’ is not a question that has a single, scientifically correct answer; rather, the 

conclusions one draws for any practical application should be guided by the 

conservation/management goals one is trying to achieve and the concept of ‘population’ that is 

most suitable to that application (Waples and Gaggiotti 2006). 

References 

Beacham, T. D., J. F. Schweigert, C. MacConnachie, K. D. Le, K. Labaree and K. M. Miller 

2002. Population structure of herring (Clupea pallasi) in British Columbia determined 

by microsatellites, with comparisons to southeast Alaska and California, Fisheries and 

Oceans Canada, Canadian Science Advisory Secretariat. 

Bentzen, P. 2004. Analysis of mtDNA polymorphism in Puget Sound herring: A preliminary 

summary provided for WDFW. March 13, 2004, memorandum. Portland, OR, National 

Marine Fisheries Service, Protected Resources Division. 

Burkey, C. J. 1986. Population structure of Pacific herring (Clupea harenqus pallasi) in Eastern 

Prince William Sound, Alaska, University of Alaska, Juneau. masters. 

Domanico, M. J., R. B. Phillips and J. F. Schweigert 1996. Sequence varation in ribosomal 

DNA of Pacific (Clupea pallasi) and Atlantic herring (Clupea harengus). Can J Fish 

Aquat Sci 53: 2418-2423. 

Grant, W. S. 1986. Biochemical genetic divergence between Atlantic, Clupea harengus, and 

Pacific, C. pallasi, herring. Copeia 1986: 714-719. 

Grant, W. S. and F. M. Utter 1984. Biochemical population genetics of Pacific herring (Clupea 

pallasi). Can J Fish Aquat Sci 41(6): 856-864. 

Gustafson, R. G., J. Drake, M. J. Ford, J. M. Myers, E. E. Holmes and R. S. Waples 2006. 

Status review of Cherry Point Pacific herring (Clupea pallasii) and updated status review 

of the Georgia Basin Pacific herring distinct population segment under the Endangered 

Species Act. Seattle, WA, Northwest Fisheries Science Center: 182. 

Johnson, S. W., M. G. Carls, R. P. Stone, C. C. Brodersen and S. D. Rice 1997. Reproductive 

success of Pacific herring, Clupea pallasi, in Prince William Sound, Alaska, six years 

after the Exxon Valdez oil spill. Fish Bull 95(4): 748-761. 

Kobayashi, T. 1993. Biochemical analyses of genetic variability and divergence of populations 

in Pacific herring. Bull Nat Res Inst Far Seas Fish 30: 1-77. 

Mitchell, D. M. 2006. Biocomplexity and metapopulation dynamics of Pacific herring (Clupea 

pallasii) in Puget Sound, Washington. Seattle, University of Washington. Masters: 75. 

O'Connell, M., M. C. Dillon, J. M. Wright, P. Bentzen, S. Merkouris and J. Seeb 1998. Genetic 

structuring among Alaskan Pacific herring populations identified using microsatellite 

variation. J Fish Biol 53(1): 150-163. 

Schweigert, J. F. and R. E. Withler 1990. Genetic differentiation of Pacific herring based on 

enzyme electrophoresis and mitochondrial DNA analysis. Am Fish Soc Symp 7: 459-

469. 

Small, M. P., J. L. Loxterman, A. E. Frye, J. F. Von Bargen, C. Bowman and S. F. Young 2005. 

Temporal and spatial genetic structure among some Pacific herring populations in Puget 

Sound and the southern Strait of Georgia. Trans Am Fish Soc 134(5): 1329-1341. 

A.4 
Waples, R. S. 1998. Separating the wheat from the chaff: patterns of genetic differentiation in 

high gene flow species. J Hered 89(5): 438-450. 

Waples, R. S. and O. Gaggiotti 2006. What is a population? An empirical evaluation of some 

genetic methods for identifying the number of gene pools and their degree of 

connectivity. Mol Ecol 15: 1419-1439. 

Whitlock, M. C. and D. E. McCauley 1999. Indirect measures of gene flow and migration: FST 

doesn’t equal 1/(4Nm+1). Heredity 82: 117-125. 

Wright, S. 1978. Evolution and the genetics of populations. Chicago, University of Chicago 

Press. 

A.5 
 

 

Appendix B 

Analysis of ADFG age-length-weight data 

Data 

• Were supplied by ADFG. 

• Data structure is complex 

o e.g., many collection sites, times, collection methods, variable levels of fish 

maturity, age, gender. 

Data restrictions 

• Analysis was restricted to fish length 

o This avoids probable mass changes before, during, and after spawning 

• Data were restricted to months of spawn (March, April, May) 

o The majority of the data were collected in either March-April or April May 

o Distribution of these collection times corresponded exactly to sites classified as 

either relatively early or relative late spawners in southeastern Alaska (Fig. 3.14). 

• Data were restricted to collections at active spawning. 

o This ensured that measured fish were spawners at or near capture sites, not 

transients 

o This should minimize variance in fish condition at the time of measurement 

• Data were restricted to records where fish ages were determined (the vast majority of the 

data) and where age>2. 

• Several likely errors were detected (length of mature fish <50 mm); these data were 

excluded. 

Results 

• Number of samples 

stock n months years n years 

Sitka 18294 Mar – Apr 1983 – 2007 19 

Lynn Canal 2395 Apr – May 1983 – 2007 7 

Craig 7169 Mar – Apr 1981 – 2007 15 

Ernest Sound 3319 Apr 1988 – 2007 10 

Hobart-Houghton 5777 Apr – May 1995 – 2007 12 

Hoonah Sound 5533 Apr – May 1981 – 2007 13 

Kah Shakes 11091 Mar – Apr 1997 – 2006 21 

Seymour Canal 13153 Apr – May 1997 – 2007 24 

West Behm 7189 Apr 1995 – 2007 13 

Tenakee 5051 Apr – May 1983 – 2007 13 

total 78971 

• Initial results, 3-factor ANOVA (year × age × sex) 

P 

year 0.0001 sig 

age 0.0001 sig 

B.1 
 sex 0.5555 not sig 

year*age 0.0001 sig 

year*sex 0.4743 not sig 

age*sex 0.8598 not sig 

year*age*sex 0.7525 not sig 

• preliminary conclusion: gender is not important, drop this parameter from the model 

Size at age trend analysis 

• Purpose: compare trends in length at age 

• Method 

o calculate deviations from mean length (mean by stock, age) (Fig. B.1) 

o summarize by plotting mean deviates vs year where age>2 and age<8. 

 Age was restricted because relatively few fish were present in older year 

classes (the minimum n = 30 in the final analysis) 

o Cubic splines (of mean time series) were the best general description of trends 

• Results 

o Stocks are grouped by geographic adjacency (Fig. B.2) 

o Size at age is currently declining at all sites 

o An increase in size at age was evident in the 1980s or 1990s at some sites 

o Trends in Lynn Canal herring were about the same as those in Seymour Canal 

Growth rate 

• Purpose: compare growth rates among SEAK herring stock 

• Model 

o Regress ln(length) on ln(year – base year) by stock and cohort (power model) 

o Cohort = observation year – (fish age – 3) 

o Base year = cohort – 1 

o Growth rate was not estimated for cohorts where the number of measurements 

was not ≥ 15 in at least 3 y. 

• Results 

o The number of growth rate estimates for each stock ranged from 3 to 24 (see Fig. 

B.1 and Table B.1). 

o Lynn Canal had the fewest estimates. 

o Mean growth rates ranged from 0.107 to 0.142 [ln(mm)/ln(year)] and were not 

significantly different among stocks (P = 0.577). 

• Two-factor ANOVA (stock × cohort) was disconnected (growth of all 

cohorts was not estimable in all stocks), thus the model could only be run 

without an interaction term. 

• Growth rate differences among cohorts were significant (P < 0.001). 

• The same conclusion, that growth rate does not vary significantly among 

stocks (P = 0.223), is reached when the analysis is restricted to cohorts 

where growth rates in Lynn Canal were estimable (1983, 1995, and 1996). 

B.2
Table B.1. Mean cohort growth rates by stock [ln(mm)/ln(year)]. 

mean 95% confidence 

stock n rate bounds 

Sitka 18 0.127 0.114 0.139 

Lynn Canal 3 0.142 0.098 0.186 

Craig 12 0.115 0.100 0.130 

Ernest Sound 9 0.110 0.087 0.133 

Hobart-Houghton 12 0.107 0.079 0.135 

Hoonah 10 0.114 0.097 0.130 

Kah Shakes 19 0.134 0.117 0.151 

Seymour Canal 24 0.136 0.121 0.151 

West Behm 14 0.107 0.090 0.124 

Tenakee 12 0.123 0.103 0.143 

B.3 
Fig. B.1. Example length data, summarized with means by age class and overlain with 

deviation in length (estimated across age classes 3 through 8). 

Sitko 

25 20 

23 

10 

E E 

E210 E 

C 

0 

0 

u 

L 

_g190 _c 

0, 

C 

QJ 

_J 

10 

170 

Age 3 

20 

150 

130 -+-~~~~--~~~~~~~~~--~~~~~~~--+---- 0 

1975 1980 1985 1990 1995 2000 2005 

Year 

B.4 
Fig. B.2. Smoothed mean (±SE) trends in length at age in SEAK herring stocks. 

20 

HOB LYN 

(mm) 

10 

on 

ERN 

tia

0 

Length devi

TEN SEY 

-10 

-20 

-30 

20 

±-=-="='=-==2==:::::i:7 -:~[IJ="='=-==2==:::::i:_ 

KAH 

CRG BEH 

(mm) 

10 

HOO 

on tia

0 

th devi

-10 

Leng

SIT 

-20 

-30 

1975 1985 1995 2005 1975 1985 1995 2005 

Year Year 

B.5 
Fig. B.3. Cohort growth in northern SEAK (power model). Individual cohorts are distinguished 

by color, symbol shape, and symbol fill. Symbol sizes correspond to the number of 

measurements (the largest indicate >100, the smallest ≤10). 

300 Lynn Canal Seymour Canal 

250 

 (mm) Standard length 200 

150 r 

100 

300 Tenakee Sitka 

250 

(mm) h Standard lengt 200 

150 

100 

1980 1985 1990 1995 2000 2005 1980 1985 1990 1995 2000 2005 

year year 

B.6