NOAA Technical Memorandum NMFS-NWFSC-80

Conservation

of North Pacific Rockfishes:

Ecological Genetics and 

Stock Structure

Proceedings of the Workshop

March 2–3, 2004

Seattle, Washington

April 2007

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
NOAA Technical Memorandum

NMFS Series

The Northwest Fisheries Science Center of the National 

Marine Fisheries Service, NOAA, uses the NOAA Technical Memorandum NMFS series to issue informal scientific 

and technical publications when complete formal review 

and editorial processing are not appropriate or feasible due 

to time constraints. Documents published in this series may 

be referenced in the scientific and technical literature.

The NMFS-NWFSC Technical Memorandum series of the 

Northwest Fisheries Science Center continues the NMFSF/NWC series established in 1970 by the Northwest & 

Alaska Fisheries Science Center, which has since been 

split into the Northwest Fisheries Science Center and the 

Alaska Fisheries Science Center. The NMFS-AFSC Technical Memorandum series is now being used by the Alaska 

Fisheries Science Center.

Reference throughout this document to trade names does 

not imply endorsement by the National Marine Fisheries 

Service, NOAA.

This document should be cited as follows:

Berntson, E.A., P.S. Levin, and P.C. Moran (editors). 

2007. Conservation of North Pacific rockfishes: Ecological 

genetics and stock structure. Proceedings of the workshop, 

March 2-3, 2004, Seattle, Washington. U.S. Dept.

Commer., NOAA Tech. Memo. NMFS-NWFSC-80, 80 p.
NOAA Technical Memorandum NMFS-NWFSC-80

Conservation

of North Pacific Rockfishes:

Ecological Genetics and 

Stock Structure

Proceedings of the Workshop

March 2–3, 2004

Seattle, Washington

Edited by Ewann A. Berntson, Phil S. Levin,* and Paul Moran

Northwest Fisheries Science Center

Conservation Biology Division

Fishery Resource Analysis and Monitoring Division

2725 Montlake Boulevard East

Seattle, Washington 98112

April 2007

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

*
Most NOAA Technical Memorandums

NMFS-NWFSC are available online at the 

Northwest Fisheries Science Center

web site (http://www.nwfsc.noaa.gov)

Copies are also available from:

National Technical Information Service

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phone orders (1-800-553-6847)

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ii
Table of Contents 

Executive Summary .....................................................................................................................................v

Acknowledgments......................................................................................................................................vii

Themes of the Workshop Highlight Management Advances in the Application of Genetic 

Methods to Stock Assessment Paul Moran ................................................................................................1

Literature Review of Genetic Structure in North Pacific Rockfishes Ewann A. Berntson .........................6

Tribal Fisheries: Role of Stock Structure in Regional Management Rob Jones.......................................15

Movement and Activity Patterns of Rockfish Christopher G. Lowe ........................................................17

Toward Establishing Patterns of Connectivity for Kelp Rockfish: Geographic Structure in 

Elemental Signatures in Larval Otoliths and a Review of Potential Proxies for Natal Signatures 

Jennifer E. Caselle and Robert R. Warner.................................................................................................22

Stable Isotope Analyses of Otoliths and the Stock Structure of Yelloweye Rockfish 

Yongwen Gao, Farron R. Wallace, and Tien-Shui Tsou............................................................................27

Population Structure in Black Rockfish: A Comparison of Otolith Microchemistry and DNA 

Microsatellites Jessica A. Miller and Alan L. Shanks...............................................................................32

Fish and Chips: Genetic Identification of Rockfish Larvae and Juveniles John R. Hyde.........................35

Integrated Methods to Converge on Estimates of Larval Dispersal Cynthia A. Taylor............................42

MHC Evolution in Rockfishes Andres Aguilar and John Carlos Garza..................................................44

Microsatellites Reveal Regional Genetic Structure and Effective Population Size in Darkblotched 

Rockfish Daniel Gomez-Uchida and Michael A. Banks...........................................................................47

Population Structure of Puget Sound Rockfish Assessed with Mitochondrial DNA and 

Microsatellites Jennifer A. Hempelmann, Christiane H. Biermann, Erik E. Sotka, and Daniel Halos....52

Genetic Markers Distinguish Populations of Black Rockfish in the Gulf of Alaska Lisa W. Seeb ..........57

Genetic Studies of Rockfish: Identification, Relationships, and Population Structure 

Anthony J. Gharrett, Zhuozhuo Li, Andrew P. Matala, Andrew K. Gray, Jonathan Heifetz, 

Milton S. Love, and Arthur W. Kendall, Jr. ...............................................................................................61

Conservation Genetics of Rockfishes: The West Coast’s Most Species-rich and Imperiled 

Genus of Fishes Russell D. Vetter.............................................................................................................67

Appendix A: Rockfish Microsatellite Loci in GenBank............................................................................73

iii
iv
Executive Summary 

On 2 and 3 March 2004, the Conservation Biology Division and Fishery Resource 

Analysis and Monitoring Division sponsored a workshop at NOAA’s Northwest Fisheries 

Science Center (NWFSC) in Seattle. The specific goals of the workshop were as follows:

• To bring together researchers and managers to help define current conservation problems 

and to provide an understanding of current opportunities (and limitations) of technologies 

such as molecular genetic methods and stable isotope analysis; 

• To foster interactions between ecologists and geneticists and to promote collaborations 

that address long-standing conservation and recovery problems; and 

• To prioritize conservation research and provide suggestions for future research needs. 

Approximately 50 scientists attended the workshop from a variety of institutions, 

including federal, state, tribal, and academic. The workshop was organized into two days of 

presentations with ample opportunity for open discussion. Presentations covered a range of 

topics including ecology, microchemistry, genetics, stock structure, policy, and conservation, as 

do the presentation summaries included here. Many of the presentation summaries cover 

measuring movement of individual rockfish over the short and long term, using elemental or 

isotopic analysis over short periods, and using molecular methods to study movements over 

evolutionary time. The summaries also address systematic relationships, many in the context of 

larval identification. 

Speakers presented diverse management and research perspectives, and identified a 

number of research priorities as they highlighted their current work. Given the precipitous 

decline of multiple rockfish species in the last 15 years, there is great opportunity for the 

incorporation of techniques, both new and traditional, to further the assessment, conservation, 

and recovery of North Pacific rockfishes. The perspective gained in this workshop is likely to be 

of general interest in applying genetic methods to stock assessment and marine conservation. 

v
vi
Acknowledgments 

Contemporary rockfish biologists owe a great debt of gratitude to the nineteenth and 

early twentieth century ichthyologists who first described these remarkably diverse and 

fascinating creatures. In 1829 George Cuvier coined the genus name Sebastes, “magnificent,” in 

Greek. Other pioneers such as William O. Ayres, Charles Girard, Theodore Gill, and Julius B. 

Phillips described the systematics and ecology of key species and laid the foundation for current 

investigations of genetics, stock assessment, and general biology. Although the role of these 

historical personalities is central to rockfish research today, one contemporary rockfish biologist 

has done more than any single individual to foster admiration and interest in rockfishes. Milton 

Love has done for rockfishes what Ethelwyn Trawavas and Tony Ribbink did for East African 

cichlids. He made them accessible, interesting, and important to scientists and the lay public. 

Rockfishes are very cool indeed! 

For their facilitation and encouragement of this workshop, we also offer thanks to 

Elizabeth Clarke, director of the Fishery Resource Analysis and Monitoring (FRAM) Division, 

and Michael J. Ford, director of the Conservation Biology Division. The FRAM Division and 

NOAA Fisheries Service’s Protected Resources Division provided funding to host this meeting. 

Arlene Frazier of FRAM generously contributed to logistics and organization. 

vii
viii
Themes of the Workshop Highlight Management 

Advances in the Application of Genetic Methods 

to Stock Assessment 

Paul Moran 

Northwest Fisheries Science Center 

Conservation Biology Division 

2725 Montlake Boulevard East 

Seattle, Washington 98112 

paul.moran@noaa.gov 

Precipitous declines in abundance of multiple rockfish (Sebastes spp.) species over the 

past 15 years have motivated efforts to improve stock-specific management. The hope is that 

genetic methods, microchemistry, telemetry, and other techniques that track the movement of 

individuals can refine stock-specific management to allow harvest (and bycatch) of abundant 

stocks while protecting and restoring depleted species and stocks. It is not yet clear how recently 

developed genetic tools will benefit groundfish conservation in general and rockfish stock 

assessment in particular. Considerable potential exists; however, rockfish species often present 

significant challenges to sampling and study design for genetic research. Species ranges are 

geographically broad and typically lack obvious breeding aggregates. Although many rockfish 

species are sedentary, pelagic larvae provide substantial opportunity for dispersal. There is some 

expectation for isolation by distance, but the geographic scale of that isolation is often unclear. It 

is difficult to know how individual fish samples (e.g., trawls) should be grouped into putative 

populations or stocks.1

 Where data are available, some species show evidence of relatively 

fine-scale population structure, whereas others show widespread gene flow. 

Significant recent progress has been made toward addressing goals for rockfish genetics 

research that Russ Vetter identified more than 5 years ago (SWFSC 2006). Although he 

presented these goals as being of specific interest to the California Marine Life Protection Act, 

they are equally relevant to rockfish research in general. Vetter identified the following 

priorities throughout the ranges of multiple rockfish species: 1) characterize species and 

subgeneric relationships within the genus Sebastes, 2) identify larvae, and 3) define unit stocks 

for rockfish species. 

 

1

 Population is a biological term that denotes a group of freely interbreeding individuals partially or completely 

isolated from other such groups within a species. A stock is a management unit that typically identifies a group 

that is demographically linked. Stocks often coincide with populations or groups of populations within species but 

may include multiple species (see discussion of cryptic species, e.g., Genetic Studies of Rockfish: Identification, 

Relationships, and Population Structure, p. 61, and Conservation Genetics of the Rockfishes: The West Coast’s 

Most Species-Rich and Imperiled Genus of Fishes, p. 67). 

1
These goals are clearly interrelated and although Vetter, his students, and others have 

done much to address these issues, this workshop underscored specific areas that need additional 

work. Gharrett et al. (Genetic Studies of Rockfish: Identification, Relationships, and Population 

Structure, p. 61) propose almost the exact same research priorities for molecular genetic studies 

in rockfishes: 1) improved descriptive phylogenetics, 2) larval identification, and 

3) elucidation of population structure. Gharrett et al. state that improved species identification, 

high throughput markers, and improved systematics of Asian species are high priorities, but that 

the most work is needed in analysis of population structure within species. Population genetic 

structure is directly related to the movement of individuals among locations along with their 

subsequent reproductive success. Although these demographic connections are central to 

biologically sound stock assessment, conservation, and recovery, managers generally have 

incomplete demographic information about their stocks. Another important and related 

application of population genetic studies is to evaluate the evolutionarily effective population 

size of rockfish populations to examine genetic diversity relative to census size (Microsatellites 

Reveal Regional Genetic Structure and Effective Population Size in Darkblotched Rockfish, 

p. 47). 

The goals of this workshop were threefold. First, we sought to use presentations and 

discussion to define the central issues in rockfish conservation as related to stock structure. 

Second, we hoped to give attendees some sense of the capabilities and the limitations of current 

molecular (and other) methods. Finally, we hoped the workshop would lead to collaborations 

and partnerships among harvest managers, ecologists, and geneticists. Toward this last goal we 

cast a broad net of invitations with hopes of bringing together different agencies and interests 

including tribal, state, federal, and academic scientists, managers, and public policy advocates. 

We take the diversity of presentations and wide-ranging discussions as an indication of success. 

The need for accurately estimating stock structure is understood and appreciated in the 

research and management community, and the level of interest in this topic was reflected in the 

workshop’s substantial attendance. For example, sustainable harvest and effective bycatch 

management require some understanding of the biological populations that are impacted. Such 

an understanding allows direction of harvest toward abundant populations and away from 

depressed or sensitive groups. Likewise, risk assessment, conservation, and recovery planning 

require the same kind of biological foundation. A first step in conservation genetics is to identify 

the units that are being conserved. Rarely are entire species represented by a single population, 

and individual populations almost certainly have different demographic trajectories (some might 

say by definition, e.g., McElhany et al. 2000). A potential liability of stock-specific management 

might be further depression of coast-wide abundance, that is, each stock is fished closer to the 

limit of sustainability. However, this concern is more appropriately directed at the application of 

new population genetic data. Instead, the issue would seem to be what harvest levels are allowed 

on those individual stocks. Alternatively, to limit harvest on abundant populations due to 

ignorance about the biological underpinnings of management units seems socially unacceptable 

if such biological information could be obtained. 

Similarly an understanding of stock structure and dispersal is essential for designing, 

monitoring, and evaluating marine protected areas (MPAs) (Botsford et al. 2001, Palumbi 2003, 

Sale et al. 2005). If MPAs are too widely dispersed, then populations are isolated and may suffer 

inbreeding depression (Carson and Hentschel 2006). If individual MPAs support large 

2
populations anyway, then inbreeding is not an issue. However, vast differences exist among 

species with respect to dispersal distances and population size (including census size, genetic 

effective population size, and the ratio of those parameters). These differences in dispersal 

underscore the complexity of optimizing the design of MPAs to benefit many diverse species. 

Perhaps most important in the future, a basic understanding of population genetics is 

essential for effective artificial propagation (see Tribal Fisheries: The Role of Stock Structure in 

Regional Management, p. 15). Although the specific issues differ, population structure is as 

important to conservation programs (e.g., supplementation and gene banking) and fishery 

enhancement as it is to harvest management. The point is that, depending on the scale of the 

program, artificial propagation can have profound impacts on gene flow among groups that 

might have been isolated over recent evolutionary time (relative to generation time and rates of 

adaptive divergence among populations—again widely different among species). Artificial 

propagation also can reduce genetic diversity by amplifying a relatively small slice of the total 

diversity in the population (Ryman and Laikre 1991). Broodstock collections must often balance 

the desire to fully capture the diversity within the population of interest, yet not combine distinct 

and adaptively diverged populations. In some cases it is unclear whether a captive breeding or 

supplementation program is at greater risk for inbreeding or outbreeding. Indeed some programs 

suffer both effects simultaneously. Management challenges in Pacific salmon (Oncorhynchus

spp.) strongly suggest that it is better to plan ahead than to begin large artificial propagation 

programs without considering the genetic implications. Although experience in salmon may be 

of limited utility in rockfish genetics due to fundamental differences in biology and genetic 

structure, it is worth considering the concerns that have developed in salmon artificial 

propagation. From concern over altering the metapopulation structure and genetic connectivity 

among populations to domestication selection and reduction of life history diversity, the salmon 

experience provides an initial framework for developing risk assessment in rockfish artificial 

propagation. 

Another lesson from salmon genetics related to logistics rather than biology is that 

multilaboratory standardization of genetic markers and genotyping conventions is essential for 

addressing large-scale, multijurisdictional conservation and fishery management problems 

(Moran et al. 2006). It is very inefficient for individual laboratories to forge ahead, each with 

their own suite of nonoverlapping markers. Laboratories are best served by early agreement on a 

common suite of markers and standardized allele designations. Markers should be appropriate to 

the task. Microsatellite loci are suitable for fine-scale descriptive population genetic work, 

whereas mitochondrial DNA or single-copy nuclear genes might be suited for systematic 

relationships or species identification. The markers need the right power of resolution, need to 

be portable among laboratories, and need to be cost effective. Genetic standardization requires 

some initial investment of time and effort, and experience has shown that little progress is 

typically made in the absence of specific management objectives. Multilaboratory 

standardization generally requires extensive sharing of tissue or DNA samples and sharing of 

unpublished data. Sample and data sharing can raise issues of stewardship and ownership of 

samples and unpublished data. 

Selecting markers is a critical element of interlaboratory standardization. If no markers 

are shared, then only limited combined analyses are possible. An almost immediate question is 

whether to use neutral or nonneutral markers. All that is needed for many applications is 

3
discrimination of particular groups of fish. For example, managing harvest of fish from different 

stocks taken in mixed fisheries simply requires differentiating among potential source 

populations. In many applications, it does not matter whether markers are neutral. Indeed 

nonneutral markers are sometimes substantially more powerful than neutral markers (Miller et al. 

2001, 2002). For most other applications, however, neutrality is an important prerequisite, for 

example, effective population size estimates, dispersal distances and gene flow among semiisolated populations, and other issues related directly and indirectly to stock assessment. 

Whether markers are neutral or nonneutral is less important than considering how the markers 

are to be employed and what limitations are present in particular applications. 

The future of genetics in rockfish stock assessment appears full of opportunity. Results 

presented in this workshop demonstrate real utility in rockfish management. Substantial new 

biological insight has been obtained related to demographics and movement of individuals, a 

cornerstone of stock assessment. Ecological genetics is at a critical juncture with rockfishes and 

other nonmodel organisms for several reasons. Molecular genetic techniques have matured to 

the point that extremely powerful data can now be obtained on a wide range of spatial and 

temporal genetic relationships. Along with the maturation of molecular methods, computing 

power has increased exponentially. These new tools and resources have contributed to a rebirth 

and reapplication of some important statistical methods. In particular, Bayesian methods of 

inference are now widely used for parameter estimation in complex multivariate problems. A 

major challenge, and an area of considerable current insight and creativity, involves developing 

efficient sampling strategies and algorithms that rapidly and efficiently explore posterior 

distributions without becoming trapped in local optima. It seems likely that as computing and 

molecular methods become more powerful, population genetic analysis is likely to gravitate 

toward analysis of individual fish. A statistical analogy would be to move from analysis of 

discrete variables (allele frequencies in population segments) to continuous variables (genetic 

relatedness among individuals relative to various biotic and abiotic correlates). Multivariate 

analysis of genetic data in a broad ecological context will be desirable in order to make 

generalizations about species distributions and connectivity between stocks. 

This proceedings volume is organized much like the workshop, with summaries 

representing each of the presentations. One exception is a literature review, by organizer and 

editor Ewann A. Berntson, that expands on some of the points introduced here related to recent 

developments in rockfish genetics. The presentation summaries reflect a diversity of 

management and research perspectives. Most are concerned with movement of individuals, 

whether measured over short periods using elemental or isotopic analysis, or whether 

considering the net effect of those movements over evolutionary time, as measured with genetic 

methods. Numerous authors also address systematic relationships, often in the context of larval 

identification. The topics presented closely reflect the research priorities identified above and 

significant progress is reported here and in recent peer-reviewed literature (see Literature Review 

of North Pacific Rockfish Genetic Structure, p. 6). Nevertheless, a great deal of potential 

remains for using genetic methods for stock assessment, conservation, and recovery. The 

presentation summaries included here bring some of that potential to fruition. 

4
References 

Botsford, L. W., A. Hastings, and S. D. Gaines. 2001. Dependence of sustainability on the configuration 

of marine reserves and larval dispersal distance. Ecol. Lett. 4:144–150. 

Carson, H. S., and B. T. Hentschel. 2006. Estimating the dispersal potential of polychaete species in the 

Southern California Bight: Implications for designing marine reserves. Mar. Ecol. Prog. Ser. 

316:103–113. 

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000. Viable 

salmonid populations and the recovery of evolutionarily significant units. U.S. Dept. Commer., 

NOAA Tech. Memo. NMFS-NWFSC-42. 

Miller, K. M., T. D. Beacham, and R. E. Withler. 2002. Use of neutral and adaptive genetic variation in 

the management and conservation of Pacific salmon. ICES Rep. CM 2002/U:17. 

Miller, K. M., K. H. Kaukinen, T. D. Beacham, and R. E. Withler. 2001. Geographic heterogeneity in 

natural selection on an MHC locus in sockeye salmon. Genetica 111:237–257. 

Moran, P., D. J. Teel, E. S. LaHood, J. Drake, and S. Kalinowski. 2006. Standardizing multi-laboratory 

microsatellite data in Pacific salmon: An historical view of the future. Ecol. Freshw. Fish 

15:597–605. 

Palumbi, S. R. 2003. Population genetics, demographic connectivity, and the design of marine protected 

areas. Ecol. Appl. 13:S146–S158. 

Ryman, N., and L. Laikre. 1991. Effects of supportive breeding on the genetically effective population 

size. Conserv. Biol. 8:888–890. 

Sale, P. F., R. K. Cowen, B. S. Danilowicz, G. P. Jones, J. P. Kritzer, K. C. Lindeman, S. Planes, N. V. C. 

Polunin, G. R. Russ, Y. J. Sadovy, and R. S. Steneck. 2005. Critical science gaps impede use of 

no-take fishery reserves. Trends Ecol. Evol. 20(2):74–80. 

SWFSC (Southwest Fisheries Science Center). 2006. Rockfish genetics—stock structure. Online at 

http://swfsc.noaa.gov/textblock.aspx?Division=FRD&id=1090&ParentMenuId=39 [accessed 28 

November 2006]. 

5
Literature Review of Genetic Structure 

in North Pacific Rockfishes 

Ewann A. Berntson 

Northwest Fisheries Science Center 

Conservation Biology Division 

2725 Montlake Boulevard East 

Seattle, Washington 98112 

ewann.berntson@noaa.gov 

Rockfishes (Sebastes spp.) are important members of the groundfish community in the 

Pacific and Atlantic oceans. Approximately 74 species of rockfish are found in the northeast 

Pacific, and several have been a documented component of commercial fisheries since the 

mid-nineteenth century (Love et al. 2002). A great deal of effort is devoted to the management 

of rockfish species. Nine of the 74 rockfish species have been thoroughly assessed through the 

Pacific Fisheries Management Council in previous years, and two additional rockfish species 

were assessed in 2005. In 2000 seven species were designated overfished by the National 

Marine Fisheries Service: bocaccio (S. paucispinis), Pacific ocean perch (S. alutus), canary 

rockfish (S. pinniger), cowcod (S. levis), widow rockfish (S. entomelas), yelloweye rockfish 

(S. ruberrimus), and darkblotched rockfish (S. crameri). Much of the information needed for 

completing these assessments for the remaining species simply is not available. 

Effective fisheries management decisions must be based on a solid biological foundation. 

A thorough understanding of life history and ecology may be difficult to acquire for marine fish 

species, which often have populations that cover large territories and may differ in distribution 

with life stage. In the absence of such information, a species (and sometimes multiple species) 

will be managed as a single, homogenous unit. If that species is actually comprised of separate 

stocks, however, overfishing may deplete portions of the species with little chance of rebuilding 

from the remaining stocks. Current fishing practices, which also are a concern to fisheries 

managers and conservation biologists, may bring genetic changes that will have substantial 

consequences for fish populations, relating to overall size, size and age at maturity, and genetic 

diversity. Genetic changes may be slow to reverse and will not be on a time scale relevant to 

fisheries managers (Stokes and Law 2000). 

Recent advances in the field of genetics have given fishery managers some important 

tools in the pursuit of more biologically relevant management practices. Two general categories 

of genetic techniques have been used to address questions relating to stock management: 

1) protein-based allozyme electrophoresis, and 2) DNA sequence-based techniques, including the 

direct comparison of sequences, restriction fragment length polymorphisms (RFLPs), and 

microsatellite analyses (hypervariable, noncoding regions of nuclear DNA). DNA 

sequence-based techniques usually exhibit greater levels of variation than allozymes, and they 

have the added advantage of requiring minute amounts of tissue so individuals can be sampled 

6
nondestructively. Studies utilizing sequence-based techniques can be found increasingly in the 

recent literature (Gharrett et al. 2004). Different techniques have different levels of resolution 

for population studies, but all can be useful for assessing the health of marine populations. 

Genetics can lend insight into attributes such as population subdivisions, sex- and 

life-stage-specific migration patterns, and effective population size, which may be significantly 

different from the census size (Hauser et al. 2002). Genetics also can be useful in the basic 

identification of species, which can be difficult in species groups such as rockfish; adults of some 

rockfish species closely resemble each other and many larvae and juveniles are morphologically 

indistinguishable. A 1998 commercial catch report from a Northwest Fisheries Science Center 

Groundfish Research Plan showed 1,699 mt (12% of the overall rockfish caught in the Pacific 

Ocean) listed as “unspecified rockfishes” (NMFS 2000). The lack of species identification will 

be an impediment to acquiring the accurate ecological information required for designing proper 

management policies. Allozyme electrophoresis has been used successfully in species 

identification (Seeb 1986, Seeb and Kendall 1991, LeClair and Buckley 2001), as have DNA 

sequence-based techniques (Rocha-Olivares 1998, Rocha-Olivares et al. 2000, Gharrett et al. 

2001, Gray et al. 2006, Li et al. 2006a). Descriptive studies of genetic variation among species 

also can provide information useful to fisheries managers by recounting the demographic history 

of a species, investigating species or subspecies differences (Gharrett et al. 2004), and 

identifying introgression or hybridization when it occurs between species. This information can 

help create a better ecological picture for management decisions. 

Species-level and Phylogenetic Questions 

Molecular techniques have proven useful at multiple levels in rockfish: broad-scale 

phylogenetics, species identification, finer-scale speciation, introgression, and population 

dynamics. Allozyme information generated by Seeb (1986) was combined with cytochrome b

sequences to provide evidence that rockfish constitute one of the few marine examples of a 

species flock (Johns and Avise 1998)—a species-rich yet relatively similar grouping 

differentiating within a short amount of time. These similarities, in part, have created difficulties 

for taxonomists and systematists studying this group. Genetic analyses can help elucidate 

relationships among closely related species. Narum et al. (2004) used microsatellite markers to 

show clear evidence for differentiation between gopher rockfish (S. carnatus) and black-andyellow rockfish (S. chrysomelas), a sympatric species pair that differ primarily in color. 

Comparisons of mitochondrial DNA (mtDNA) control region sequences for gopher rockfish and 

black-and-yellow rockfish have suggested that the speciation processes may be ongoing within 

rockfish (Alesandrini and Bernardi 1999). Without an understanding of current species 

groupings, managers will be unable to accurately model fisheries stocks. 

Phylogenetic analyses will help elucidate relationships among closely related species. 

Molecular information, primarily mitochondrial sequence information and RFLPs, was used to 

create phylogenies for thornyheads (Sebastolobus spp.) (Stepien et al. 2000), the Sebastes 

subgenera Sebastomus (Rocha-Olivares et al. 1999a, 1999b), and Pteropodus (Li et al. 2006b). 

Nuclear sequences were used to examine the phylogeny of rockfish as a whole (Asahida et al. 

2004), and similar levels of divergence were found compared to studies using mtDNA (Gharrett 

et al. 2001). Asahida et al. (2004) found many of the Asian species clustering together, divergent 

from most of the North American species. 

7
Introgression may be an important factor in the population dynamics and genetic 

diversity for rockfish. Seeb (1998) used allozyme and RFLP analyses to detect striking changes 

in allele frequencies in the subgenus Pteropodus (gopher rockfish, quillback rockfish 

[S. maliger], and brown rockfish [S. auriculatus]) over very short (70 km) distances within Puget 

Sound in the absence of any obvious barriers to gene flow; however, when the Puget Sound 

populations were removed from the analyses, no measurable differentiation was detected from 

Washington to Alaska. Seeb suggested that introgression occurs among these three species 

within Puget Sound, and that it may contribute to overall genetic diversity within the genus as a 

whole. A microsatellite study of brown rockfish came to the same conclusions regarding 

potential introgression among these three species in Puget Sound (Buonaccorsi et al. 2005). The 

authors hypothesize that introgression may occur more readily in areas with low population 

numbers. As rockfish populations drop, introgression may play a larger role for other rockfish 

species in other areas. Introgression will need to be considered in stock assessments. 

Population-level Questions 

Genetic studies that may help identify population differentiation and stock structure 

within commercially important species are perhaps of most interest to fisheries managers. A 

handful of species have been examined with stock structure in mind. Allozyme studies have 

proven useful in some species: two stocks were identified for canary rockfish (S. pinniger) 

(Wishard et al. 1980), significant geographic variation was found within brown rockfish (Seeb 

1998), and two groups of sympatric rougheye rockfish (S. aleutianus) also were delineated 

(Hawkins et al. 1997, 2005). An additional study using mtDNA sequences and microsatellite 

loci found the same two rougheye rockfish groups, and the authors suggested they are likely 

different species—a greater difference between mitochondrial haplotypes exists between the two 

groups than can be found between other pairs of rockfish species (Gharrett et al. 2005, 2006). 

Mitochondrial RFLP analysis of mtDNA (ND-3/ND-4 and 12S/16S ribosomal RNA [rRNA] 

genes) showed divergences within 8 of 15 rockfish species tested from the eastern Gulf of 

Alaska (Gharrett et al. 2001). Mitochondrial control region sequences have shown significant 

population differentiation in blue rockfish (S. mystinus) from Washington to California (Cope 

2004), and in rosethorn rockfish (S. helvomaculatus) from California to the Gulf of Alaska 

(Rocha-Olivares and Vetter 1999). A distinct genetic break was identified for rosethorn rockfish 

at the divergence of the Alaska Current and the California Current. Control region sequences 

also demonstrated high levels of diversity within species in thornyhead populations (longspine 

thornyhead [Sebastolobus altilevis] and shortspine thornyhead [S. alascanus]) in the northern 

Pacific, with most individuals having unique haplotypes (Stepien et al. 2000). Mitochondrial 

sequences showed this diversity where earlier allozyme studies (Siebenaller 1978) did not. Each 

of these studies provides specific information that has immediate relevance to fishery 

management in general and stock assessment in particular. 

Five rockfish species from the western Pacific were investigated using mtDNA sequences 

and amplified fragment length polymorphisms (AFLP) analyses—another sequence-based 

technique for measuring genetic diversity across the entire genome. Higuchi and Kato (2002) 

demonstrated variation in the nucleotide diversity of usu-mebaru (S. thompsoni), togotto-mebaru

(S. joyneri), mebaru (S. inermis), kurosoi (S. schlegeli), and S. owstoni. The authors concluded 

that this technique might be suitable for stock structure analysis in future studies. A second 

study used mtDNA sequences and AFLPs to distinguish among three color morphotypes within 

8
mebaru (Kai et al. 2002). Both methods indicated some gene flow among the types, however, 

which suggested to the authors that introgression may be occurring or that speciation of the three 

was very recent. 

Microsatellite analyses currently are the most useful technique for measuring 

within-species genetic variation. The high levels of variability and relative ease and speed of 

analysis make microsatellites an obvious choice for efforts to delineate stock structure. In 

addition it is likely that microsatellite loci shown to be variable within one species also may be 

variable within other, closely related species. Several loci have been published recently for use 

in rockfish, and have potential for use in determining stock structure. A summary of currently 

published loci and the species for which they have proven to be variable, along with measured 

heterozygosities and references, is provided in Appendix A (p. 73). 

Studies utilizing microsatellite loci to identify potential stock structure are becoming 

more prevalent in published literature. Genetic diversity correlating to geographic distance has 

been shown for grass rockfish (S. rastrelliger) (Buonaccorsi et al. 2004) and brown rockfish 

(Buonaccorsi et al. 2005) from the eastern Pacific, as well as usu-mebaru populations from Japan 

(Sekino et al. 2001). Previous mtDNA sequence analyses were unable to detect population 

subdivisions within usu-mebaru (Sekino et al. 2001). A recent microsatellite study detected 

spatial structure in darkblotched rockfish from Washington to California and also focused on a 

discussion of the effects of pooling small sample sizes (Gomez-Uchida and Banks 2005). 

Microsatellite analyses of quillback rockfish from Puget Sound to southeast Alaska indicated 

genetic structure also (Burr 1999). Quillback rockfish from Washington State are managed 

currently as a single stock, but Burr suggested this decision should be revisited if further 

sampling confirms these findings (Burr 1999). A study of bocaccio using microsatellites 

detected population structure consistent with the California Current flow regimes along the 

coastline and suggested restricted movement of juveniles and adults (Matala et al. 2004a). 

Bocaccio population numbers now are 2–3% of those measured in 1969 (Love et al. 2002). 

Given the rapidly declining bocaccio populations, any successful conservation efforts must 

consider the potential existence of genetic structure. 

The literature contains several examples of studies using multiple techniques to analyze 

population structure, some of which have been mentioned above. In some cases, but not all, 

results from the different techniques agree. Copper rockfish (S. caurinus) and quillback rockfish 

were studied using allozymes and mtDNA (Seeb 1998) and microsatellites (Buonaccorsi et al. 

2002). Seeb (1998) found significant genetic differentiation over the whole range with 

particularly strong shifts in allozyme frequencies in quillback rockfish from Puget Sound. 

Introgression was suggested as a possible explanation (as mentioned previously). Copper 

rockfish microsatellite analyses also showed evidence of significant population subdivision in 

fish sampled from southern California to British Columbia including the Puget Sound 

(Buonaccorsi et al. 2002). Another example of concordance among techniques is in the Mexican 

rockfish (S. macdonaldi, the southernmost rockfish from the northeast Pacific Ocean), which 

ranges from California south to Baja, Mexico, including the Gulf of California (Rocha-Olivares 

et al. 2003). Mitochondrial DNA sequence information (Bernardi et al. 2003) and microsatellites 

(Rocha-Olivares et al. 2003) showed no significant differentiation among sampling sites. Small 

amounts of genetic partitioning suggested the possibility of recent dispersal rather than current 

gene flow or an older founder effect (Rocha-Olivares et al. 2003). In a third example an 

9
allozyme study looked at yellowtail rockfish (S. flavidus) collected from the northeast Pacific 

coastline and found no genetic differentiation (Wishard et al. 1980). This result was largely 

confirmed using mtDNA RFLPs (McGauley and Mulligan 1995). 

The literature also holds examples of multiple genetic analyses differing in their 

conclusions for a given species. Microsatellite analyses of shortraker rockfish (S. borealis), 

found on the Pacific Rim from California to Japan showed population structure in Alaskan 

waters not addressed by current stock divisions (Matala et al. 2004b), where a second study 

using allozymes found no genetic differentiation (Hawkins et al. 2005). Two allozyme studies 

(Wishard et al. 1980, Seeb and Gunderson 1988) and one microsatellite study (Withler et al. 

2001) examined populations of Pacific ocean perch. Wishard et al. (1980) distinguished three 

different stocks along the northeast Pacific coastline, whereas Seeb and Gunderson (1988) found 

only slight amounts of genetic variation across a similar area. The microsatellite study found 

evidence for three distinct populations from coastal sites in British Columbia (Withler et al. 

2001). The higher levels of variation of microsatellite loci gave Withler et al. (2001) the ability 

to distinguish these populations on a much smaller geographic scale than the allozyme studies 

could. Below we discuss considerations of the characteristics and performance of different 

marker classes, and interpretation of analysis results. 

Issues of Concern in Genetic Stock Assessments 

Genetic techniques can be extremely useful, if not essential, in determining stock 

structure of marine fish species. There are some important caveats, however, for the 

understanding and appropriate use of genetic information in devising management policies. 

Techniques with lower variability, such as allozyme electrophoresis, may show a given 

population to be homogenous over a given range, where more-variable microsatellite loci may 

show finely detailed genetic structure. Therefore a result showing no detectable genetic variation 

does not necessarily mean that the populations in question are homogenous. Analyses using 

multiple techniques (genetic and otherwise) and sampling over time can help determine which 

populations may be truly homogeneous. 

The interpretation of levels of genetic differentiation found also must be done carefully, 

particularly in species that have the potential for high levels of gene flow. One of the most 

commonly used methods for estimating the level of gene flow among populations is the 

calculation of the FST parameter, which compares the proportion of genetic variation found 

within populations to that found among populations. The interpretation of FST is based on 

several assumptions, however: the number of subpopulations is infinite, the effective population 

size is the same in every subpopulation, breeding is random within each subpopulation, 

migration rates are small and constant for every subpopulation, the genes chosen are selectively 

neutral, and no mutation occurs (Waples 1998). These assumptions will be violated for any 

biological organism studied, more severely for some than others. In species experiencing 

relatively high rates of gene flow, genetic differentiation and the calculated FST values will be 

low, and violations of the assumptions will become more significant. In addition FST values will 

vary among loci and over time, so better estimates of true rates of gene flow will come from the 

analysis of multiple loci, on populations sampled over multiple time periods. 

10
The significance of FST values to the development of management policies should be 

examined carefully for each case. Very few migrants per generation are required to produce low 

FST values, seemingly indicating stocks experiencing near panmixia; however, the minimum 

level of migration necessary to produce near genetic homogenization would be insignificant for 

rebuilding stocks depleted through overfishing, at least on time scales of interest to fisheries 

managers. The calculations may be statistically significant but demographically irrelevant. 

Additional information on the ecology and life history of the species, specifically direct 

measurement of dispersal rates if possible, may be necessary to adequately determine the ability 

of neighboring populations to recover from depletion (Waples 1998). 

With increasing fishing pressures worldwide, many species are experiencing dwindling 

numbers. Genetic techniques can be extremely useful in determining stock structure for marine 

fish species, a key component of successful management plans. The literature contains a few 

genetic studies of some rockfish species in the North Pacific, utilizing primarily allozyme 

electrophoresis, mitochondrial RFLP and direct sequence comparisons, and microsatellite 

analyses. While each of these analyses can provide important information for determining 

genetic patterns within species, microsatellite analyses hold much promise for delineating 

genetic differentiation on small geographic scales. Multiple microsatellite loci have now been 

developed, so we are poised for an explosion of new data for multiple species. With a solid 

understanding of the advantages and concerns regarding genetic information, fisheries 

management practices could benefit greatly from this additional information as it becomes 

available. Ultimately however, the utility of genetic information will rely on the willingness of 

managers to incorporate such information. 

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Li, Z., A. K. Gray, M. S. Love, A. Goto, T. Asahida, and A. J. Gharrett. 2006b. A key to selected 

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population genetic structure of bocaccio. N. Am. J. Fish. Manag. 24:1189–1202. 

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cytochrome b gene sequence in the species-rich genus Sebastes (Teleostei, Scorpaenidae) and its 

utility in testing the monophyly of the subgenus Sebastomus. Mol. Phylogenet. Evol. 

11:426–440. 

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zoogeography of the rockfish subgenus Sebastomus (Sebastes, Scorpaenidae) based on 

mitochondrial cytochrome b and control region sequences. Mol. Phylogenet. Evol. 11:441–458. 

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variation in the Mexican rockfish Sebastes macdonaldi. Sci. Mar. 67:451–460. 

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98:353–363. 

Rocha-Olivares, A., and R. D. Vetter. 1999. Effects of oceanographic circulation on the gene flow, 

genetic structure, and phylogeography of the rosethorn rockfish (Sebastes helvomaculatus). Can. 

J. Fish. Aquat. Sci. 56:803–813. 

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thesis. Univ. Washington, Seattle. 

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auriculatus, S. caurinus, and S. maliger. J. Hered. 89:393–403. 

13
Seeb, L. W., and D. R. Gunderson. 1988. Genetic variation and population structure of Pacific ocean 

perch (Sebastes alutus). Can. J. Fish. Aquat. Sci. 45:78–88. 

Seeb, L. W., and A. W. Kendall, Jr. 1991. Allozyme polymorphisms permit the identification of larval 

and juvenile rockfishes of the genus Sebastes. Environ. Biol. Fishes 30:191–201. 

Sekino, M., N. Takagi, M. Hara, and H. Takahashi. 2001. Analysis of microsatellite DNA 

polymorphisms in rockfish Sebastes thompsoni and application to population genetic studies. 

Mar. Biotechnol. 3:45–52. 

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Waples, R. S. 1998. Separating the wheat from the chaff: Patterns of genetic differentiation in high gene 

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Mar. Biol. 139:1–12. 

14
Tribal Fisheries: Role of Stock Structure 

in Regional Management 

Rob Jones 

Northwest Indian Fisheries Commission 

Fishery Management and Planning Services 

6730 Martin Way East 

Olympia, Washington 98516 

rjones@nwifc.org 

Treaty fisheries are conducted in fixed areas known as usual and accustomed stations and 

grounds (U&As). The tribes have always managed each area-based fishery separately—

concentrating their fishing in areas of highest abundance while ensuring that abundance remains 

relatively stable over time. The four coastal tribes (Makah, Quileute, Hoh, and Quinault) with 

treaty rights to groundfish conduct four major groundfish fisheries, all of which currently face 

constraints due to interactions with overfished rockfish (Sebastes) species. The primary fisheries 

are midwater trawling for Pacific whiting (hake [Merluccius productus]) and yellowtail rockfish 

(S. flavidus) plus setline fisheries for Pacific halibut (Hippoglossus stenolepis Schmidt) and 

sablefish (Anoplopoma fimbria). Midwater trawl fisheries are primarily constrained by bycatch 

of canary rockfish (S. pinniger) and widow rockfish (S. entomelas), while setline fisheries are 

constrained due to interactions with both species. 

Presently there is little abundance data for most groundfish species in the Pacific Fishery 

Management Council’s Groundfish Fishery Management Plan. Even less is known about the 

structure of most rockfish stocks. Thus the current management regime treats virtually all 

groundfish species as coast-wide stocks. Seven rockfish species are currently classified as 

overfished and are subject to rebuilding plans. These rebuilding plans are projected to take 

decades, in some cases close to 100 years. Other rockfishes could be designated as overfished as 

data become available. The restrictions faced under rebuilding affect most of the groundfish 

fisheries and even some of the nongroundfish fisheries along the coast. 

Some relief has been realized by applying different management strategies to distinct 

stocks within a population. When a species shows biological differences within its overall range, 

it is beneficial to manage those different segments of the population separately in order to 

prevent localized depletion. This strategy also prevents restrictions in areas that are far removed 

from the regions where overfishing actually occurs or where fishing strategies are drastically 

different. Delineating and managing to stock differences provides local opportunities rather than 

coast-wide restrictions. 

Collection of genetic, stable isotope, and trace element samples from fishery landings 

coupled with location data from logbooks could aid in answering important questions about 

stock structure. The Makah Tribe’s proposed rockfish enhancement project also would help 

15
delineate stock structure for some species. Understanding stock structure, competitive 

interactions within and between species, and mechanisms of genetic drift or isolation are critical 

first steps to effectively accelerating rebuilding while avoiding the mistakes of some salmon 

hatcheries in the past. While this approach is being proposed for a few of the most constraining 

overfished species, the resultant knowledge would have broad application in transitioning to 

more effective regional and ecosystem-based management. 

As management evolves from single-species management to a management strategy that 

accounts for ecosystem interactions and essential fish habitat (EFH), it is of paramount 

importance that the necessary data are collected and incorporated into the management process. 

Legal mandates must be met whether or not the information to properly fulfill them is available. 

This evolution of management could exacerbate the current groundfish crisis if ecosystems are 

defined arbitrarily or EFH designation is not properly tied to production (i.e., regional depletion 

could worsen where stock structure is poorly understood or marine protected areas 

inappropriately sited). 

Tribal fisheries have been managed regionally within the U&As for eons. Applying this 

approach all along the coast in concert with an ecosystem-based management regime, if properly 

implemented, could reduce the instances of regional stock depletions and allow for faster 

rebuilding times for overfished rockfish species. Comanagement of rockfish fisheries will 

benefit from increasing understanding of ecosystem dynamics, such as stock structure and the 

role of habitat in fish production through collaboration of federal, state, and tribal scientists. 

Better understanding of rockfish stock structure could provide all West Coast groundfish 

fisheries the benefits of opportunities afforded by regional management rather than constraints 

resulting from coast-wide restrictions. 

16
Movement and Activity Patterns of Rockfish 

Christopher G. Lowe 

California State University, Long Beach 

Department of Biological Sciences 

1250 Bellflower Boulevard 

Long Beach, California 90840 

clowe@csulb.edu 

The understanding of the movement and activity patterns of rockfish (Sebastes spp.) has 

increased considerably over the past 50 years due to advances in technology (Lowe and Bray 

2006). Although technological advances have led to more effective harvest of many species, the 

lack of sufficient knowledge of fish movements has hampered management and conservation 

measures. Nevertheless quantifying movement patterns of fishes poses serious challenges 

because movements vary over spatial and temporal scales, and among and within species, 

populations, and even individuals. 

Methods for Quantifying Movements of Rockfish 

A variety of tools have been used to quantify and evaluate movements of rockfish over 

these various scales, but no one tool is adequate for resolving movements over various scales. 

Fishing catch data have been used to determine stock movement or distribution, but due to biases 

in fishing method or the fishery, this technique cannot adequately resolve movements, only 

distribution of a population or stock. Tag and recapture methods often rely on fishery 

participation and are useful in determining movement patterns of a population, yet these 

techniques cannot resolve fine-scale movements and their success is fishing dependent. In situ 

monitoring via diver, remotely operated vehicle, or submersible observations has evolved as a 

powerful tool in quantifying movements of small, reef-associated species and factors that may 

influence movements of fishes (i.e., habitat composition, social influences, diel changes); 

however, this technique cannot provide longer-term data sets because of the short duration over 

which observations can be made. Some of the greatest advancements in studying fish 

movements have been due to the advent of remote-sensing technologies (e.g., sonar, acoustic 

telemetry tracking, acoustic telemetry monitoring, and satellite telemetry). Remote-sensing 

methods are good for resolving movements of tagged individuals over varying spatial and 

temporal scales; however, these methods are expensive and often limited in sample size and the 

size of fish that can be instrumented with tags (Matthews et al. 1990, Lowe et al. 2003). 

Genetics and other types of “natural” tags (i.e., parasites) are powerful tools in resolving 

population-scale movements, but are also limited by sampling and collecting tissues (Lowe and 

Bray 2006) (Table 1). 

17
Table 1. Advantages and disadvantages of methods used to quantify the spatial and temporal variability 

of movements of marine fish. 

Method 

Spatial 

resolution 

Temporal 

resolution Advantages Disadvantages 

Fishing/ 

catch data 

Ocean wide Long term 

(years, decades) 

Population level, 

dispersal potential 

Fishery dependent, 

sampling biased 

Standard tag 

and recapture 

Ocean wide Short term 

(days) to long 

term (years) 

Population level, 

inexpensive, can be 

used to gather growth 

data 

Spatial and temporal 

poor resolution, fishery 

dependent, sampling 

biased 

In situ 

observations 

Fine scale 

(≈10–1,000 m2

) 

Short term 

(<12 hours) 

Individual level, direct 

observation of 

movements 

Influence behaviors, 

too short in duration 

Sonar Fine scale 

(≈1–100s m2

) 

Short term 

(<few hours) 

Population or 

individual, can observe 

entire school and 

species composition 

Expensive, time 

consuming, limited in 

duration, may influence 

schooling behavior 

Acoustic 

telemetry 

tracking 

Fine scale 

(≈10–10,000 m2

) 

Short term 

(hours–days) 

Individual level, 

can quantify habitat 

use, home range 

size, activity patterns 

Expensive, labor 

intensive, limited in the 

size of fish that can be 

tagged 

Acoustic 

telemetry

monitoring 

Larger scale 

(≈100 m2

–km2) 

Long term 

(<6 years) 

Individual level, 

can observe conspecific 

interactions, site 

fidelity 

Expensive, limited in 

size of fish that can be 

tagged 

Satellite 

telemetry

Larger scale 

(100 km–ocean 

wide) 

Long term 

(<1 year) 

Individual level, 

can also record 

depth and temperature; 

best for wide-ranging, 

surface-oriented 

species 

Expensive, limited in 

size of fish that can be 

tagged, tag retention 

duration, poor spatial 

resolution (>60 nmi) 

Natural tags 

(genetics, 

parasites) 

Large scale 

(100 km–ocean 

wide) 

Long term 

(>1 year) 

Population level, good 

for identifying 

populations and degree 

of population 

movement 

Fishery dependent, 

expensive, usually 

lacking in spatial 

resolution 

Factors Influencing Movements of Rockfish 

Aside from larval dispersal and seasonal migrations, most juvenile and adult rockfish are 

thought to use home ranges, areas used on a daily basis (Love et al. 2002). Surprisingly very few 

studies actually have quantified home range behavior in rockfish (Larson 1980a, 1980b, 1980c, 

Matthews 1990, Matthews et al. 1990, Starr et al. 2000, 2002). In general it is thought that fish 

most closely associated with complex habitats tend to move less than those more loosely 

associated with habitat. Although resource availability largely influences this relationship, there 

also appears to be a large amount of variability in behavior between species and individuals 

18
(Figure 1). Nevertheless the general differences in movements are likely associated with 

energetic trade-offs between finding food and mates, and avoiding predation or unsuitable 

abiotic conditions (Lowe and Bray 2006). 

Depending on life history, it is also thought that many fish exhibit some sort of 

ontogenetic shift in home range or activity space size (Love et al. 2002, Lowe and Bray 2006). 

Early life history for most rockfish utilizes planktonic dispersal, after which larvae settle and 

recruit to juvenile or adult habitat. Two differing models of ontogenetic space use may be 

proposed based on whether the species exhibits territorial behavior as an adult, which has been 

demonstrated for some reef-associated rockfishes (Larson 1980b, 1980c). For nonterritorial 

species, newly settled individuals may generally have small home ranges based on their lower 

energy requirements and food availability, whereas larger individuals may increase their home 

ranges or activity spaces as they get larger to accommodate increased energy demand and 

reduced prey availability (Mace et al. 1983). The opposite trend is likely seen from territorial 

species, where newly settled individuals are frequently displaced from adult home ranges and 

territories. As a result, juveniles must continuously move to avoid conflicts or predation. As 

individuals get larger, they are better able to hold and defend territories, thereby reducing their 

home range or activity space requirements (Lowe and Bray 2006). In addition many of the same 

trade-offs have likely influenced the evolution of activity patterns seen in rockfish. 

Figure 1. Theoretical model of home range or activity space size relative to affinity to complex 

substratum for various assemblages of fish. High complexity substratum would include habitat 

offering high rugosity and relief (e.g., rock reef), whereas low complexity substratum would have 

low rugosity and relief (e.g., sand and mud). 

19
Conclusions 

Development of new technology and techniques has significantly furthered knowledge of 

rockfish movement and activity, and it is likely these advances will continue. Because of the 

economic importance of many rockfish species, the need to understand fish behavior has 

increased, particularly for its application in resource and fisheries management. While we have a 

better understanding of the proximate mechanisms that influence movement and activity pattern 

in fish, we still do not thoroughly understand the ultimate mechanisms behind these behaviors. 

In addition, while research has been done to examine the movement patterns of larger fish, still 

relatively little is known about movements and space use by small fish. Further investigation of 

ontogenetic shifts in movement patterns, home range behavior, and the factors that influence 

shifts in home ranges of rockfish will provide a better understanding of stock structure. This 

information could be extremely valuable to resource managers in developing better fisheries 

management models and when establishing marine protected areas. 

References 

Larson, R. J. 1980a. Competition, habitat selection, and the bathymetric segregation of two rockfish 

(Sebastes) species. Ecol. Monogr. 50:221–239. 

Larson, R. J. 1980b. Influence of territoriality on adult density in two rockfishes of the genus Sebastes. 

Mar. Biol. 58:123–132. 

Larson, R. J. 1980c. Territorial behavior of the black-and-yellow rockfish and gopher rockfish 

(Scorpaenidae, Sebastes). Mar. Biol. 58:111–122. 

Love, M. S., M. Yoklavich, and L. Thorsteinson. 2002. The rockfishes of the northeast Pacific. 

University of California Press, Berkeley. 

Lowe, C. G., and R. N. Bray. 2006. Fish movement and activity patterns. In L. G. Allen, D. J. Pondella 

II, and M. H. Horn (eds.), The ecology of California marine fishes: California and adjacent 

waters, p. 524–553. University of California Press, Berkeley. 

Lowe, C. G., D. T. Topping, D. P. Cartamil, and Y. P. Papastamatiou. 2003. Movement patterns, home 

range, and habitat utilization of adult kelp bass (Paralabrax clathratus) in a temperate no-take 

marine reserve. Mar. Ecol. Prog. Ser. 256:205–216. 

Mace, G. M., P. H. Harvey, and T. H. Clutton-Brock. 1983. Vertebrate home-range size and energetic 

requirements. In I. R. Swingland and P. J. Greenwood (eds.), The ecology of animal movement, 

p. 32–53. Oxford University Press, New York. 

Matthews, K. R. 1990. A telemetric study of the home ranges and homing routes of copper and quillback 

rockfishes on shallow rocky reefs. Can. J. Zool. 68:2243–2250. 

Matthews, K. R., T. P. Quinn, and B. S. Miller. 1990. Use of ultrasonic transmitters to track demersal 

rockfish movements on shallow rocky reefs. In N. C. Parker, R. C. Giorgi, D. B. Heidinger, D. B. 

Jester, Jr., E. D. Prince, Jr., and G. A. Winans (eds.), Fish-marking techniques, p. 375–379. 

American Fisheries Society, Bethesda, MD. 

20
Starr, R. M., J. N. Heine, J. M. Felton, and G. M. Cailliet. 2002. Movements of bocaccio (Sebastes 

paucispinis) and greenspotted (Sebastes chlorostictus) rockfishes in a Monterey submarine 

canyon: Implications for the design of marine reserves. Fish. Bull. 100:324–337. 

Starr, R. M., J. N. Heine, and K. A. Johnson. 2000. Techniques for tagging and tracking deepwater 

rockfishes. N. Am. J. Fish. Man. 20:597–609. 

21
Toward Establishing Patterns of Connectivity 

for Kelp Rockfish: Geographic Structure in 

Elemental Signatures in Larval Otoliths and a 

Review of Potential Proxies for Natal Signatures 

Jennifer E. Caselle and Robert R. Warner 

University of California, Santa Barbara 

Department of Ecology, Evolution, and Marine Biology 

Santa Barbara, California 93106 

caselle@lifesci.ucsb.edu 

One of the most important yet least understood aspects of marine populations is the 

degree to which they are connected via larval dispersal. The pathways of larval transport and the 

extent to which populations are seeded from local or distant sources have important 

consequences for population replenishment, colonization of new habitats, and resiliency to 

harvest. In addition knowledge of the spatial patterns of connectivity can help in the design and 

placement of marine protected areas. 

Knowledge of connectivity among marine populations lags behind that for populations of 

other animals such as mammals or birds, due mainly to the difficulty of artificially tagging and 

recapturing small marine larvae. Jones et al. (1999) studied the chemical tagging of coral reef 

fish egg masses on an island in the Great Barrier Reef. Recruited individuals were later 

captured, and from the number of returns it was estimated that 15–65% of the total recruitment to 

the island was from local production. Such tagging studies, while important, are necessarily 

limited in spatial scale. 

We focus on the use of natural tags, specifically trace element signatures in the hard parts 

(e.g., otoliths and statoliths) of marine organisms. The idea behind using natural tracers in the 

ocean to track larvae is based on the presumption that the chemical composition of the water is 

extremely variable, especially near the coast (Bruland 1983, Donat and Bruland 1995). As 

larvae travel through water masses with differing chemical composition, elements are taken up 

into the otoliths. Our general approach is to attempt to characterize local signatures over a wide 

geographic area. We are investigating the spatial scales over which these local signatures vary, 

as well as their stability through time. If local signatures can be mapped in space and time, the 

next step is to collect recruits from target areas, analyze the signature in the natal portion of the 

otolith, and assign them to particular source populations. 

Most published work on natal assignment has focused on species that migrate between 

relatively discrete habitat types such as estuaries, rivers, or enclosed bays and open coastal 

habitats (Thorrold et al. 1998, Gillanders 2002, Swearer et al. 2003). One would expect 

detectable geographical variation in otolith elemental composition in these systems due to 

22
substantial gradients in salinity, temperature, and trace element inputs. Because it is possible 

that gradients in oceanographic conditions along open coasts may often be too subtle to register 

in a natural tag (but see Campana et al. 1994, Patterson et al. 2001), we focus on open coastal 

regions of central and southern California, where there are abrupt and distinctive spatial patterns 

in oceanographic conditions (Harms and Winant 1998). 

Otoliths are calcium carbonate (mainly aragonite) structures in the inner ear canal of fish 

and are used for balance and hearing. Three important features of otoliths allow us to analyze 

chemical signatures in order to assess residency in different water masses (Campana and 

Thorrold 2001): 

1. The time of deposition can be estimated by counting the daily increments found in many 

otoliths. 

2. Because the aragonitic structure is metabolically inert and not reworked, there is likely to 

be no resorption or change in the elemental composition of an area of the otolith once it is 

deposited. 

3. The calcium carbonate and trace elements are taken up from the ambient water, so the 

trace elemental concentration in the otolith should reflect the environmental 

characteristics of the water (Secor et al. 1995, Campana and Thorrold 2001). 

We address two questions. What is the magnitude and scale of spatial variation in source 

signatures in otoliths? And, are there feasible methods for estimating this variation that do not 

rely on larval otolith collection? 

We briefly review progress made in measuring source signatures directly using 

prepelagic larval otoliths of the kelp rockfish (Sebastes atrovirens) and indirectly using three 

potential proxies: seawater, resin-based elemental accumulators, and the outermost edges of 

otoliths of resident kelp rockfish adults. 

Collection and analytical chemistry methods are given in detail in Warner et al. (2005). 

Results 

The most direct approach to assessing a local or source signature is to measure it directly 

from the otoliths of larvae still resident at the natal location. To do this we focused on species 

that are ovoviviparous, such as the rockfish, or those that lay benthic egg masses. Rockfish 

larvae begin to form otoliths prior to parturition, and larvae can be harvested from near-term 

pregnant females in the field. 

Using laser ablation inductively coupled plasma mass spectrometry on kelp rockfish 

larval otoliths, we found significant spatial variation in multielement natal signatures between 

regions and sites separated by only tens of kilometers (Warner et al. 2005). For many but not all 

elements, variation was consistent between the 2 years of the study. 

The obvious advantage of using larval otoliths to measure source signatures is that the 

signature is preserved throughout life and can later be directly measured in the core region of the 

otolith of older life stages. For the goal of assigning juveniles or adults onto maps of potential 

23
source signatures, this technique provides the most unequivocal and direct measure; however, 

capturing pregnant female fish or locating egg masses in the field is difficult, labor intensive, and 

may be impossible in some systems (e.g., for deepwater rockfish). In addition the isolation and 

preparation of larval otoliths for laser-based inductively coupled plasma mass spectrometry is 

initially difficult (as protocols are developed) and will remain time consuming throughout any 

project. Thus we investigated the development of a suitable proxy—one that is more easily 

sampled than larval otoliths and captures the local trace element environment as recorded in the 

otolith. 

We first investigated trace element incorporation into resin-based elemental 

accumulators—diffusive gradients in thin films or DGT (Zhang and Davison 2000). DGT 

consists of an open-pore hydrogel layer backed with a chelex binding agent and is used for the 

quantitative determination of metals in situ. Because of the nature of the binding agent in DGT 

as currently designed, not all elements detectable in larval otoliths were extractable from DGT 

samples. Of the four elements that were detectable in both DGT and larval otoliths, two showed 

significant regional variation in DGT, but only one (manganese, Mn) had a qualitatively similar 

spatial pattern as the larval otoliths (Warner et al. 2005). 

DGT is an ideal field sampler because it can be placed in known locations and easily 

collected at predetermined frequencies. Although DGT eliminates the biological sampling 

problem and integrates elemental chemistry over time like an otolith, as currently designed it 

does not uptake many of the elements that are incorporated and easily detectable in otoliths. 

This issue may be overcome by designing a resin-based elemental accumulator with new 

properties. Analytically DGT must be run using solution-based techniques while larval otoliths 

can be analyzed using laser ablation. Direct comparison of concentrations will require 

calibration studies. 

We also collected seawater samples at the same times and locations as DGT samples and 

larval otoliths. Seawater and larval otoliths had five detectable elements in common. Of those 

five, three varied significantly among regions but only one (Mn) showed a spatial pattern similar 

to larval otoliths (Warner et al. 2005). Seawater tended to show higher within-year temporal 

variability than larval otoliths or other proxies, likely because water samples are taken at specific 

points in time (every 2 weeks in this study). Increasing the frequency of sampling, even 

approaching continuous sampling, could reduce this variability and may still prove easier than 

collecting larvae. Analytically seawater is problematic because of extremely low elemental 

concentrations and the calibration issues that exist when comparing between solution and laserbased techniques also must be addressed for comparisons between seawater and otoliths. 

Finally we collected adult kelp rockfish at the same locations as larvae in both years of 

the study. We analyzed the outermost edges of the adult otoliths and compared them to larval 

otolith. Concentrations of most trace elements at the edges of otoliths of adults were 

considerably lower than levels found in larvae. Only three elements were detectable in the edges 

of adult otoliths and all three also were found in larval otoliths. Of the three elements, two 

varied significantly among regions but only in one of the two years. In general there was little 

similarity in spatial patterns between adult otolith edges and larval otoliths (Warner et al. 2005). 

24
For species with limited home ranges as adults, such as many rockfish (Love et al. 2002), 

the outer edge of the adult otolith could conceivably provide a measure of elemental 

concentrations similar to larval otoliths forming at the same time and location. This could 

provide some advantage because adults are often easier to collect than preparturition larvae or 

egg masses. However, physiological differences between adults and larvae appear to result in 

differences in elemental uptake, and this limits the utility of using adult data as proxies for larval 

signatures. 

Conclusions 

Microchemical composition of fish larvae otoliths collected at their natal sites (before 

pelagic dispersal) shows significant spatial variation at scales of tens of kilometers along an open 

coastline (Warner et al. 2005). This result opens the possibility of creating a spatial map of natal 

signatures, although more information is needed about the spatial and temporal scales of 

variability in natal signatures. 

Drawing a spatial map would be considerably simplified if natal otolith signatures could 

be predicted from knowledge of local water chemistry or otolith chemistry of adults from the 

same area. Unfortunately, we found little correspondence between such potential proxies and the 

natal signatures, indicating that currently available proxy measures are inadequate to characterize 

natal otolith chemistry. 

References 

Bruland, K. W. 1983. Trace elements in sea water. In J. P. Riley and R. Chester (eds.), Chemical 

oceanography, vol. 8, p. 157–220. Academic Press, New York. 

Campana, S. E., A. J. Fowler, and C. M. Jones. 1994. Otolith elemental fingerprinting for stock 

identification of Atlantic cod (Gadus morhua) using laser-ablation ICPMS. Can. J. Fish. Aquat. 

Sci. 51:1942–1950. 

Campana, S. E., and S. R. Thorrold. 2001. Otoliths, increments, and elements: Keys to a comprehensive 

understanding of fish populations? Can. J. Fish. Aquat. Sci. 58:30–38. 

Donat, J. R., and K. W. Bruland. 1995. Trace elements in the oceans. In B. Salbu and E. Steinnes (eds.), 

Trace elements in natural waters, p. 247–281. CRC Press, Boca Raton, FL. 

Gillanders, B. M. 2002. Connectivity between juvenile and adult fish populations: Do adults remain near 

their recruitment estuaries? Mar. Ecol. Prog. Ser. 240:215–223. 

Harms, S., and C. D. Winant. 1998. Characteristic patterns of the circulation in the Santa Barbara 

Channel. J. Geophys. Res. 103:3041–3065. 

Jones, G. P., M. J. Milicich, M. J. Emslie, and C. Lunow. 1999. Self-recruitment in a coral reef fish 

population. Nature 402:802–804. 

Love, M. S., M. Yoklavich, and L. Thorsteinson. 2002. The rockfishes of the northeast Pacific. 

University of California Press, Berkeley. 

25
Patterson, W. F., III, H. J. Cowan, Jr., C. A. Wilson, and N. Julien. 2001. Discriminating between age-0 

red snapper, Lutjanus campechanus, nursery areas in the northern Gulf of Mexico using otolith 

microchemistry. Proc. Gulf Caribb. Fish. Inst. 52:74–86. 

Secor, D. H., A. Henderson-Arzapalo, and P. M. Piccoli. 1995. Can otolith microchemistry chart 

patterns of migration and habitat utilization in anadromous fishes? J. Exp. Mar. Biol. Ecol. 

192:15–34. 

Swearer, S. E., G. E. Forrester, M. A. Steele, A. J. Brooks, and D. W. Lea. 2003. Spatio-temporal and 

interspecific variation in otolith trace-elemental fingerprints in a temperate estuarine fish 

assemblage. Estuar. Coast. Shelf Sci. 56:1111–1123. 

Thorrold, S. R., C. M. Jones, P. K. Swart, and T. E. Targett. 1998. Accurate classification of juvenile 

weakfish (Cynoscion regalis) to estuarine nursery areas based on chemical signatures in otoliths. 

Mar. Ecol. Prog. Ser. 173:253–265. 

Warner, R. R., S. E. Swearer, J. E. Caselle, M. Sheehy, and G. Paradis. 2005. Natal trace-elemental 

signatures in the otoliths of an open-coast fish. Limnol. Oceanogr. 50:1529–1542. 

Zhang, H., and W. Davison. 2000. Direct in situ measurements of labile inorganic and organically bound 

metal species in synthetic solutions and natural waters using diffusive gradients in thin films. 

Anal. Chem. 72:4447–4457. 

26
Stable Isotope Analyses of Otoliths and 

the Stock Structure of Yelloweye Rockfish 

Yongwen Gao 

Makah Fisheries Management 

PO Box 115 

Neah Bay, Washington 98357 

gaoy@olypen.com 

Farron R. Wallace 

Washington Department of Fish and Wildlife 

48 Devonshire Road 

Montesano, Washington 98563 

wallafrw@dfw.wa.gov 

Tien-Shui Tsou 

Washington Department of Fish and Wildlife 

600 Capitol Way North 

Olympia, Washington 98501 

tsoutt@dfw.wa.gov 

A lack of genetic differentiation in marine fish populations is a common problem in stock 

structure studies (Grant et al. 1987). Possible reasons may include the large population size of 

marine fish reducing the importance of genetic drift in producing genetic differences between 

populations, the original low genetic differentiation of marine fish as compared to freshwater fish 

and salmon, and the migration of marine fish erasing the effects of genetic drift (Ward 2000). As 

an alternative, stable isotope ratio analysis (18O/16O or δ18O and 13C/12C or δ13C) in otoliths has 

proven informative and useful for determining discrete stock structure of marine fish along the 

Pacific West Coast (e.g., Gao et al. 2001, Gao and Beamish 2003, Gao et al. 2004). The basic 

principle is that otolith layers are deposited in or very close to oxygen isotopic equilibrium with 

the ambient seawater where a fish lived, and faithfully record the environmental fluctuations 

throughout the life history of the animal. Thus stable oxygen isotope ratios extracted from 

otoliths can provide information about habitat alteration, water temperature, migration, and 

climate regime shifts experienced by an individual fish (e.g., Devereux 1967, Kalish 1991, Gao 

2002). Stable carbon isotope ratios in otoliths are generally precipitated in isotopic 

disequilibrium with the ambient seawater, but can record changes in metabolism of the fish and 

dietary shifts (e.g., Mulcahy et al. 1979, Fry 1988, Schwarcz et al. 1998). Therefore if fish 

spawn or live at different localities with different δ18O and δ13C values, these isotopic variations 

would be signatures that are characteristics of different areas or of different spawning stocks. 

Yelloweye rockfish (Sebastes ruberrimus) are considered overfished (Methot et al. 2002), 

and this resulted in serious concerns and management restrictions (PFMC 2002). The life history 

27
features of this species include extreme longevity (maximum age of 120 years) and strong 

association with high relief, hard bottom substrates. To examine their stock structure, 200 

sagittal otoliths of yelloweye rockfish were collected off the Washington and Oregon coast 

(Figure 1) and were analyzed for stable oxygen and carbon isotope ratios. The affinity for hard 

bottom substrates and age of the fish led us to extract two aragonite powder samples from each 

otolith during microsampling. One sample was taken from the nucleus of yelloweye rockfish 

Figure 1. Location map showing the yelloweye rockfish otolith sampling along the Washington and 

Oregon coast. The dotted line is the depth range of 183 m. 

28
Figure 2. Stable isotopic composition of otolith nuclei of yelloweye rockfish from Washington (open 

circles) and Oregon (solid circles) coast. 

otoliths (the starting time of the life history) and the other was taken from the fifth annual zone 

(assuming age-5 if validated). Data of otolith nuclei can provide information on the natal 

sources and spawning stock separation of the fish (Gao et al. 2001), whereas the isotopic 

signatures from age-1 to age-5 would indicate their behavior over the sampling period. 

Among the 200 otoliths analyzed, δ18O values of yelloweye rockfish ranged from −0.5 to 

2.2‰ Vienna Peedee belemnite (VPDB), while δ13C values of the same otoliths ranged from 

−6.5 to −0.1‰ VPDB. There were no isotopic differences in otolith nuclei (Figure 2), 

suggesting there might be a single spawning stock for yelloweye rockfish along the Washington 

and Oregon coast. However, the distinct isotopic differences between samples from otolith 

nuclei and the fifth annual zones (Figure 3) indicated that the fish might move to different 

habitats as they grow. Compared to the fifth annual zones, the isotopic values between 

Washington and Oregon samples were significantly different (t-test, p < 0.0001 for δ18O, and 

p < 0.0001 for δ13C). Interestingly, the difference appeared mainly in δ13C, not in δ18O, 

suggesting that the food sources or composition of the two areas might be slightly different. 

In conclusion yelloweye rockfish might be a single coast-wide population as the Pacific 

Fishery Management Council currently manages it. From age-1 to age-5, the fish might change 

their habitat or associated bottom substrates for different levels of food. These isotopic 

interpretations and conclusions seem in agreement with genetic studies and observations of 

underwater video for this species,2

 but differ from results of sablefish (Anoplopoma fimbria) 

otoliths coast wide (Gao et al. 2004). 

 

2

 J. Tagart, Washington Dept. of Fish and Wildlife, Olympia, WA. Pers. commun., 30 June 2003. 

29
Figure 3. Isotopic comparison between samples from otolith nuclei (open circles) and the fifth annual 

zones (open squares) from the Washington coast. 

References 

Devereux, I. 1967. Temperature measurements from oxygen isotope ratios of fish otoliths. Science 

155:1684–1685. 

Fry, B. 1988. Food web structure on Georges Bank from stable C, N, and S isotopic compositions. 

Limnol. Oceanogr. 33:1182–1190. 

Gao, Y. W. 2002. Regime shift signatures from stable oxygen isotopic records of otoliths of Atlantic cod 

(Gadus morhua). Isotopes Environ. Health Stud. 38:100–113. 

Gao, Y. W., and R. J. Beamish. 2003. Stable isotopic composition of otoliths from tagged Pacific 

halibut, Hippoglossus stenolepis. Environ. Biol. Fishes 67:101–109. 

Gao, Y. W., S. Joner, and G. Bargmann. 2001. Stable isotopic composition of otoliths in identification of 

spawning stocks of Pacific herring (Clupea pallasi) in Puget Sound. Can. J. Fish. Aquat. Sci. 

58:2113–2120. 

Gao, Y. W., S. Joner, R. Svec, and K. Weinberg. 2004. Stable isotopic comparison in otoliths of juvenile 

sablefish (Anoplopoma fimbria) from waters off the Washington and Oregon coast. Fish. Res. 

68:351–360. 

Grant, W. S., C. Zhang, T. Kobayashi, and G. Stahl. 1987. Lack of genetic stock discretion in Pacific 

cod (Gadus macrocephalus). Can. J. Fish. Aquat. Sci. 44:490–498. 

Kalish, J. M. 1991. Oxygen and carbon stable isotopes in the otoliths of wild and laboratory-reared 

Australian salmon (Arripis trutta). Mar. Biol. 110:37–47. 

30
Methot, R., F. Wallace, and K. Piner. 2002. Status of yelloweye rockfish off the U.S. West Coast in 

2002. Appendix: Status of the Pacific Coast groundfish fishery through 2002 and recommended 

acceptable catches for 2003. Stock assessment and fishery evaluation. (Available from Pacific 

Fishery Management Council, 7700 NE Ambassador Place, Suite 200, Portland, OR 97201.) 

Mulcahy, S. A., J. Killingley, C. Phleger, and W. Berger. 1979. Isotopic composition of otoliths from 

a bentho-pelagic fish, Coryphaenoides acrolepis, Macrouridae: Gadiformes. Oceanol. Acta 

2:423–427. 

PFMC (Pacific Fishery Management Council). 2002. New information on West Coast rockfish may lead 

to significant cuts in several fisheries. Pacific Fishery Management Council, Portland, OR. 

Online at http://www.pcouncil.org/groundfish/gfnewinfo.html [accessed 24 October 2006]. 

Schwarcz, H. P., Y. Gao, S. Campana, D. Browne, M. Knyf, and U. Brand. 1998. Stable carbon isotope 

variations in otoliths of cod (Gadus morhua). Can. J. Fish. Aquat. Sci. 55:1798–1806. 

Ward, R. D. 2000. Genetics in fisheries management. In A. M. Sole-Cava, C. A. M. Russo, and J. P. 

Thorpe (eds.), Marine genetics: Developments in hydrobiology, p. 191–201. Kluwer Academic, 

Norwell, MA. 

31
Population Structure in Black Rockfish: 

A Comparison of Otolith Microchemistry and 

DNA Microsatellites 

Jessica A. Miller and Alan L. Shanks 

Oregon State University 

Hatfield Marine Science Center 

Coastal Oregon Marine Experiment Station 

2030 SE Marine Science Drive 

Newport, Oregon 97365 

jessica.miller@oregonstate.edu 

Otolith microchemistry and DNA microsatellites are relatively recent technological 

advances that can provide information on individual movements and population structure in 

marine fishes. Although both techniques have been touted as being among the most powerful 

means to distinguish among fish populations in recent years, the two techniques are rarely 

combined in the same study. Otolith microchemistry has the potential to provide information on 

individual movements and exchange among groups of fish within a generation, whereas 

microsatellite data can provide information on population connectivity over longer periods. 

The black rockfish (Sebastes melanops) is a long-lived, viviparous species with an 

extended pelagic larval duration (3–5 months) and a broad continental distribution along the 

northeast Pacific Ocean. Marine species with extended larval durations are assumed to have 

widespread dispersal and little population structure. We combined otolith microchemistry and 

DNA microsatellites to estimate the relative movements of juvenile and adult black rockfish and 

to test for evidence of genetic structure along the Oregon and Washington coast. 

We examined otolith elemental composition in juvenile and adult black rockfish collected 

from locations 120 to 460 km apart, between Grays Harbor, Washington, and Brookings, 

Oregon. In 2001 and 2002 we examined elements in juvenile otoliths at three regions: core, edge, 

and midway between the core and edge. Each otolith region represents a distinct life history 

period, including 1) egg and early larval, 2) pelagic larval, and 3) late larval and early juvenile 

periods. In 2001 elements in adult otoliths were examined at the core (which represents on 

average the initial 4 months of life) and edge (which represents the collection year). 

Significant differences in metal to calcium ratios (i.e., Mg:Ca, Mn:Ca, Zn:Ca, Sr:Ca, and 

Ba:Ca) were found among collection locations for both juveniles and adults at each otolith region 

sampled. Discriminant function analyses based on geochemical signatures consistently group 

greater than 85% (jackknifed = 74%) of juveniles and greater than 75% (jackknifed = 68%) of 

adults to collection location throughout their life history (Tables 1 and 2). For the juveniles we 

considered four alternatives to explain the relatively high classification accuracy of individuals to 

32
Table 1. The percentage of juvenile black rockfish accurately classified to collection location based on 

discriminant function analyses (DFA) using otolith elemental composition. The collection site, 

year of collection, otolith region (i.e., early larval, larval, and juvenile), percent correctly 

assigned, and the jackknifed percent correctly assigned (in parentheses) are presented. 

DFA % correct (jackknifed % correct) 

Site 

Early 

larval Larval Juvenile 

Site 

average 

2001

Grays Harbor, WA 88 (59) 100 (76) 100 (94) 96 (76) 

Cape Arago, OR 89 (81) 89 (75) 93 (89) 90 (82) 

Lone Ranch, OR 80 (40) 60 (50) 70 (40) 70 (43) 

Average 86 (60) 83 (67) 88 (74) 85 (67) 

2002

Tillamook Bay, OR 91 (87) 100 (91) 95 (86) 95 (88) 

Cape Arago, OR 78 (78) 88 (88) 88 (83) 85 (83) 

Lone Ranch, OR 83 (78) 74 (70) 83 (70) 80 (73) 

Average 84 (81) 87 (83) 88 (80) 87 (81) 

Table 2. Site classification success based on both otolith microchemistry and DNA microsatellites. 

Collection sites and sample size are presented. For otolith microchemistry, the percent correctly 

assigned, jackknifed percent correctly assigned (in parentheses), and average percent are 

presented for the otolith core (1st year) and the edge (collection year). For DNA microsatellites, 

site classification success was based on resampled allele frequencies (N = 1,000). Ten iterations 

per population were generated and averaged for 5 and 7 loci. The percent correct (±SD) and the 

total averages are presented. 

Percentage correct 

(jackknife % correct) 

Percentage correctly 

classified 

Site 

Sample 

size 1st year

Collection 

year Average 5 loci 7 loci 

Grays Harbor, WA 22 77 (59) 67 (62) 70 (61) 59.7 ± 2.1 68.9 ± 1.0 

Cape Arago, OR 26 81 (73) 50 (46) 66 (60) 72.7 ± 1.4 86.2 ± 0.7 

Gold Beach, OR 28 100 (89) 89 (89) 95 (89) 43.5 ± 1.2 68.4 ± 2.1 

Brookings, OR 17 71 (65) 76 (53) 74 (59) 79.5 ± 1.5 N/A 

Total average 82 (72) 71 (63) 77 (68) 63.1 ± 0.6 74.6 ± 0.6 

collection location throughout the early life history based on otolith elemental data: 1) fish stayed 

together relative to other collection locations (i.e., did not mix), 2) fish did not move appreciable 

distances alongshore, 3) both 1 and 2, or 4) fish from the same location followed similar 

dispersal pathways. Parturition dates within each collection site, estimated from otolith 

increment analysis of juveniles, were spread over a 22–66 day period. Therefore larvae could 

not have remained together since parturition because they were not released at the same time. 

Furthermore the predominant alongshore surface current over the continental shelf undergoes a 

seasonal reversal within the study area, and there is a spring transition when conditions shift 

33
from primarily downwelling to persistent upwelling along the coast. Given that black rockfish 

females usually release larvae during late winter and juveniles arrive in nearshore areas between 

May and August, it is difficult to envision a larval dispersal pathway that would persist over a 

22–66 day period in this ocean regime. We suggest that a more parsimonious explanation is that 

the majority of juveniles collected at these geographic locations did not mix, even between 

locations 120 km apart. Similarly, the adult otolith microchemistry data also indicate limited 

mixing among individuals collected at these geographic locations. 

Limited alongshore movements of larval, juvenile, and adult black rockfish may 

contribute to genetic divergence along the Oregon and Washington coast. Therefore we 

completed DNA microsatellite analysis on the same fish used in otolith chemical analysis.3 We 

examined seven microsatellites and found significant genetic differences among adults collected 

340–460 km apart (FST = 0.018 ± 0.007) and no evidence for isolation by distance. There was no 

evidence of population structure in juveniles (FST = 0.003 ± 0.003) and weak evidence for 

isolation by distance (p = 0.05). WHICHLOCI4

 was used to classify adults to collection location 

based on allele frequencies. On average 69% of adults were correctly classified to collection 

location (Table 2). 

The relatively high site classification accuracy of juveniles and adults based on otolith 

microchemistry suggests minimal alongshore movement (i.e., <120 km) for the majority (≈70%) 

of black rockfish used in this study. Such limited movements may contribute to the genetic 

structure observed in black rockfish collected 340–460 km apart. This type of comparative 

approach can provide corroborative information on population structure as well as identify 

potential isolating mechanisms. Such information is important for population ecology and 

fisheries management and conservation. 

The lack of information on the extent of exchange among populations hinders current 

management and conservation efforts. There is relatively little quantitative information on how 

far marine fish larvae disperse and the proportion of individuals that disperse widely. The 

maintenance of genetic diversity within a population may not be in jeopardy if greater than 10% 

of the new recruits come from external sources. The recovery of a depleted population, however, 

depends not only on the size and proximity of adjacent populations but also on the proportion of 

larvae from those populations that disperse widely enough to provide new recruits to the depleted 

population. Therefore the rate of recovery of such a population could be substantially slower in 

a species where typically 80%, compared with 20%, of the successful recruits are generated 

internally. Similarly, such principles apply in the design of marine reserves. Successful reserve 

design requires knowledge of the mean dispersal distance as well as the proportion of successful 

recruits generated within a reserve. Much of the debate surrounding marine reserve design (i.e., 

are single, larger reserves more successful than networks of smaller reserves) will remain largely 

theoretical until more specific information on larval dispersal is generated. 

 

3

 This work was completed with Michael Banks of the Marine Fisheries Genetics Laboratory at Oregon State 

University’s Hatfield Marine Science Center in Newport. 4

 WHICHLOCI is available online at http://marineresearch.oregonstate.edu/genetics/whichloci.htm [accessed 16 

November 2006]. 

34
Fish and Chips: Genetic Identification 

of Rockfish Larvae and Juveniles 

John R. Hyde 

Scripps Institution of Oceanography 

8604 La Jolla Shores Drive 

La Jolla, California 92037 

john.hyde@noaa.gov 

Ichthyoplankton sampling can be an informative tool for understanding temporal and 

spatial dynamics of spawning events. These early life stages are useful as they can be utilized as 

measures of spawning biomass (Ralston et al. 2003) and reproductive output. Rockfish 

(Sebastes spp.) along the West Coast are an important commercial and recreational fishery, with 

several species currently identified as overfished. Of the approximately 60 species that are 

known to occur within the California Cooperative Oceanic Fisheries Investigations (CalCOFI) 

study area, only 6 are currently identified at the larval stage. This is due primarily to the 

interspecific overlap of meristic and morphologic characters and the intraspecific plasticity of 

these characters. For this reason the majority of rockfish larvae are lumped together as Sebastes 

species in the CalCOFI data series. This grouping represents the fourth most abundant fish 

group in this data set (Moser et al. 2001). Clearly current identification techniques are 

inadequate and perhaps through the use of genetic techniques we can resolve this difficulty. 

The use of genetics for identification purposes requires a full understanding of 

interspecific divergence and intraspecific DNA variation. To this end it is necessary to have 

reference data for every species that occurs within and adjacent to the study area. Also it is 

necessary to have data from multiple individuals of each of the species to understand the 

intraspecific variation. It has been difficult to obtain DNA sequence data for several of the 

rockfish species because they are rarely found in fisheries and may be represented by only a few 

type specimens. For these species I have developed a protocol to obtain DNA from formalin 

preserved museum specimens. This protocol has allowed me to complete a DNA sequence 

database for all of the currently identified species in the eastern Pacific Ocean (Figure 1). 

Interspecific genetic divergence for these species ranges from 0.1% to 8.7%. Sequencing of the 

cytochrome b gene from multiple individuals of each of the species has allowed me to measure 

intraspecific variation. For eastern Pacific Ocean species the variation found ranges from 0 to 

4.2% but is predominantly below 1%. Higher levels of intraspecific genetic variation can be 

viewed in several ways. First, genetically isolated populations can accumulate added variation 

by genetic drift, higher than normal variation at a gene being indicative of species with limited 

dispersal potential, and multiple genetically distinct populations. Second, high levels of 

variation can be expected when two species are mistakenly analyzed as one, a possibility when 

cryptic species exist but are unable to be separated by traditional meristic criteria. In my analysis 

of intraspecific variation I have come across two cases where an argument for the existence of 

cryptic species can be made. 

35
Figure 1. Minimum evolution phylogenetic tree for mitochondrial cytochrome b and 16S genes from 

rockfish found in the eastern Pacific Ocean generated using MEGA2 (v2.1, Kumar 2001), Kimura 

2-parameter model, and 1,000 bootstrap replicates. Branch nodes with bootstrap support greater 

than 60% are labeled. Helicolenus hilgendorfii (GenBank accession number NC_003195) is used 

as the outgroup to root the tree. 

36
The stripetail rockfish (S. saxicola), a small, fishery insignificant species, shows a fixed 

1.7% divergence between sequence clades (cytochrome b data, Figure 1). Current sample 

collections seem to support a north-south barrier coincident with the northern Channel Islands in 

the Southern California Bight (SCB), close to the Oregonian-Californian biogeographic faunal 

break at Point Conception (Briggs 1974). Using microsatellite markers to test for reproductive 

isolation between these two mitochondrial clades, I found highly significant differences at all 

five loci examined (genic differentiation, Fisher’s exact test as implemented in Genepop v3.4 

[Raymond and Rousset no date]: locus SR7-2.2 [p = 0.0000], SR7-7.3 [p = 0.0000], SR7-25.4 

[p = 0.0000], SR11-103.6 [p = 0.0001], SR16-5.8 [p = 0.0025] Chi2 = ∞, df = 10, highly 

significant). Significance was maintained between samples from both clades taken in a zone of 

co-occurrence in the Santa Barbara Channel, however, further sampling in this region is 

necessitated due to small sample size (n = 17). Maintenance of genetic heterogeneity within an 

area of sympatry would suggest that these two mitochondrial clades should be viewed as separate 

species. 

The vermilion rockfish (S. miniatus) shows a split similar to that of the stripetail rockfish 

with two clades separated by a 1.5% fixed genetic divergence (cytochrome b data, Figure 1). It 

is of particular interest that both of these clades are only 1.2% different from the canary rockfish 

(S. pinniger). They are more different from each other than either is from the recognized sister 

species. Unlike the stripetail rockfish, the vermilion rockfish has no clear geographic separation 

yet between the clades. This could be an artifact of inadequate sample size both north and south 

of the SCB. Members of both clades are found in the SCB in nearshore kelp forests and offshore 

submarine ridges. As done with stripetail rockfish, microsatellites were used to examine 

reproductive isolation between these two mitochondrial clades. Again significant differences 

were found at all loci examined (genic differentiation, Fisher’s exact test as implemented in 

Genepop v3.4 [Raymond and Rousset no date]: locus SR7-2.2 [p = 0.0000], SR7-7.3 [p = 

0.0000], SR7-25.4 [p = 0.0000], SR16-5.8 [p = 0.0000], SR15-8.9 [p = 0.0000] Chi2 = ∞, df = 

10, highly significant). Overall FST (Weir and Cockerham 1984) and RST (Rousset 1996) values 

are 0.0544 and 0.2384 respectively when comparing the two mitochondrial clades. A 

comparison with canary rockfish using the same microsatellites indicates similar genetic distance 

between either vermilion clade or canary rockfish (FST of 0.0673 and 0.0331, RST of 0.4614 and 

0.3526). These results, plus the maintenance of genetic heterogeneity in sympatry, suggest that 

these clades should be viewed as distinct species despite the lack of traditional meristic and 

morphologic characters to separate them. Clearly this can cause difficulty in management of 

fishery important species such as the vermilion rockfish. Since both of the cryptic species 

mentioned are found primarily within the SCB, this region should be viewed and managed 

separately from the rest of the coast due to its complex and seasonably variable oceanography. 

Also the majority of rockfish species found in the eastern Pacific Ocean are found here, 

suggesting a center of speciation most likely caused to some degree by historic variability in 

oceanographic conditions and sea level. 

With an adequate understanding of the genetic variation within and between species it 

becomes possible to assign species identification to larvae based on DNA sequence data alone. 

Traditionally this would involve sequencing a large portion of DNA and subsequent 

phylogenetic analysis of this sequence with a set of reference data. While robust, this method is 

time consuming and expensive. Though a useful tool, DNA sequencing is not applicable for the 

throughput that would be needed to analyze the material usually collected from a typical 

37
ichthyoplankton survey. For this, autapomorphic genetic characters—nucleotide sites that are 

unique to single species—can be exploited to effectively minimize sequence analysis from 

hundreds of bases to one or two. Careful analysis of the reference data set of DNA sequences 

allows species-specific probes to be designed for a variety of assays. Ideally probes are unique 

for single species, but in some cases this is not possible and several probes may be used in 

concert with identity inferred through the use of a dichotomous key. Once species-specific 

probes have been designed, the format of the identification assay can take several forms 

depending on the number of taxa to be examined and budgetary constraints. 

The first assay is the simplest and cheapest but can identify the least number of taxa. 

Through use of a universal forward primer in conjunction with a set of species-specific probes as 

reverse primers, a polymerase chain reaction (PCR) is performed to amplify a portion of DNA 

using the universal primer and the matching species-specific primer (Rocha-Olivares 1998, Hyde 

et al. 2005). Because only a single fragment is generated, the assay can be designed to produce a 

different size fragment for each taxon. The unique size of the resulting fragment is then 

diagnostic for the identity of the unknown. Amplicon size can be easily determined by 

electrophoresis on an agarose gel and subsequent comparison to a set of standards. Because size 

resolution is limited, a finite number of taxa can be assayed in this manner. In my experience, as 

many as 8–10 taxa can be reliably included in an assay of this type. Figure 2 depicts such an 

assay designed to identify members of the Sebastes subgenus Pteropodus. Assays of this manner 

are rapid (identification in 3 hours) and relatively inexpensive (less than $0.50 per sample). 

Following this design, an assay was designed for shipboard identification of billfish (family 

Figure 2. Agarose minigel depicting the results of a species-specific multiplex PCR developed for the 

Pteropodus subgenus. Each lane represents DNA from reference specimens of the indicated 

species queried using this assay. 

38
Istiophoridae) eggs and larvae off the island of Hawaii from ichthyoplankton samples within 3 

hours of acquisition (Hyde et al. 2005). In field application, this method was sensitive and 

robust and yielded valuable information including the first description of fertilized eggs of the 

shortbill spearfish (Tetrapturus angustirostris). 

The second assay utilizes DNA array technology. DNA arrays spotted on epoxy slides 

allow potentially thousands of taxa to be screened simultaneously. In preliminary work, we have 

developed an array to screen for 20 species of rockfish, a fraction of the potential available using 

this platform. The slide is spotted with a series of unique capture probes, each spot containing 

thousands of capture probes designed to bind to the species-specific probe for a single taxon. 

Identification of an unknown is accomplished by the incorporation of a fluorescent molecule into 

the species-specific probe that matches exactly to the unknown DNA sample. The label is 

incorporated using a technique called allele-specific primer extension, which utilizes Taq DNA 

polymerase to add a labeled deoxynucleotide to the probe bound to the unknown DNA (Chen 

et al. 2000). Under sufficiently stringent conditions, this incorporation occurs only when the 

probe and DNA template are an exact match. This reaction is then applied to the DNA array 

slide where the now labeled probe is captured by a specific capture probe on the surface of the 

slide. The DNA array is then imaged on a fluorescent scanner. Identity is accomplished by 

matching of the fluorescent spot against the known x-y coordinates of the capture probes for 

individual taxa. Figure 3 shows an image of the 20 species DNA array queried with DNA from 

3 species of rockfish; spots for each species are replicated 10 times. Though this method is 

capable of identifying countless taxa, it has some limitations when compared to the previous 

method. Because more steps are involved, the time required is slightly greater and the potential 

for sample error is increased. Also, the cost of consumables and equipment is greater using this 

method, but the more expensive equipment (array printer and reader) is commonly available for 

use at local universities. 

Use of genetic techniques for identification of ichthyoplankton samples is the future for 

larval and egg surveys. The consistency and high throughput of these assays will ultimately 

speed sample processing while adding additional taxa and reducing error rates. The ability to 

cheaply and rapidly analyze survey samples will greatly increase the number of questions that 

can be addressed and answered using the early life stages of fish. The speed at which some 

assays can be performed allows near real-time sample identification and can be used to adjust 

survey parameters to adaptively sample areas where species of interest have been located. 

39
Figure 3. Image of 20 species DNA array probed with DNA from 3 species: stripetail rockfish 

(S. saxicola), cowcod (S. levis), and chilipepper (S. goodei). Spots containing species-specific 

capture probes are replicated 10 times. 

40
References 

Briggs, J. C. 1974. Marine zoogeography. McGraw-Hill, New York. 

Chen, J., M. A. Iannone, M. S. Li, J. D. Taylor, P. Rivers, A. J. Nelson, K. A. Slentz-Kessler, A. Roses, 

and M. P. Weiner. 2000. A microsphere-based assay for single nucleotide polymorphism 

analysis using single base chain extension. Genome Res. 10:549–557. 

Hyde, J. R., E. Lynn, R. Humphreys, Jr., M. Musyl, A. P. West, and R. Vetter. 2005. Shipboard 

identification of fish eggs and larvae by multiplex PCR, and description of fertilized eggs of blue 

marlin, shortbill spearfish, and wahoo. Mar. Ecol. Prog. Ser. 286:269–277. 

Kumar, S., K. Tamura, I. Jakobsen, and M. Nei. 2001. MEGA2: Molecular Evolutionary Genetics 

Analysis software. Arizona State University, Biodesign Institute, Tempe. Online at 

http://www.megasoftware.net/mega2.html [accessed 23 October 2006]. 

Moser, H. G., R. L. Charter, P. E. Smith, D. A. Ambrose, W. Watson, S. R. Charter, and E. M. Sandknop. 

2001. Distributional atlas of fish larvae and eggs in the Southern California Bight region: 

1951–1998. CalCOFI Atlas No. 34. 

Ralston, S., J. R. Bence, M. B. Eldridge, and W. H. Lenarz. 2003. An approach to estimating rockfish 

biomass based on larval production, with application to Sebastes jordani. Fish. Bull. 

101(1):129–146. 

Raymond, F., and F. Rousset. No date. Genepop on the web. Online at http://wbiomed.curtin.edu.au/ 

genepop/ [accessed 22 November 2006]. 

Rocha-Olivares, A. 1998. Multiplex haplotype-specific PCR: A new approach for species identification 

of the early life stages of rockfishes of the species-rich genus Sebastes Cuvier. J. Exp. Mar. Biol. 

Ecol. 231:279–290. 

Rousset, F. 1996. Equilibrium values of measure of population subdivision for stepwise mutation 

processes. Genetics 142:1357–1362. 

Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. 

Evolution 38:1358–1370. 

41
Integrated Methods to Converge on Estimates 

of Larval Dispersal 

Cynthia A. Taylor 

Illumina, Inc. 

9885 Towne Centre Drive 

San Diego, California 92121 

ctaylor@illumina.com 

Connectivity at relevant scales for management and conservation of many marine species 

occurs through dispersal of larvae. By understanding dispersal in the pelagic early life history 

phase, we can hope to identify barriers to dispersal, recognize conditions that contribute to 

successful year-classes of marine species, and characterize potential functioning of marine 

protected areas to better manage harvested stocks. A variety of methods are used to examine 

pelagic larval dispersal, including chemical tagging (Jones et al. 1999), otolith microchemistry 

(Swearer et al. 1999), physically following late-stage pelagic fish larvae (Leis and Carson-Ewart 

1997), and direct larval observations (Shanks et al. 2003). The cross section of methods have 

shown that larvae of many species have a lower realized dispersal (and in some cases, natal 

fidelity) than their time in the pelagic realm might suggest. 

Genetic methods, an indirect method of assessing larval dispersal, have been especially 

useful to identify limitations to gene flow within the range of rockfish (Sebastes) species 

including the Pacific ocean perch (S. alutus) (Seeb and Gunderson 1988, Withler et al. 2001), the 

rosethorn rockfish (S. helvomaculatus) (Rocha-Olivares and Vetter 1999), and species within the 

nearshore S. Pteropodus subgenus (Buonaccorsi et al. 2002). 

The goal of this study was to assess dispersal and connectivity in the Southern California 

Bight (SCB) and throughout the range of depth-limited rockfish using a combination of indirect 

and direct methods. Kelp rockfish (S. atrovirens) populations were examined for evidence of 

genetic structure using 8 coastal and 5 island locations from central California to Baja California, 

Mexico, using 7 microsatellite loci and 611 adult individuals. Although no significant 

population structure was detected among all populations treated separately, significant 

differences were found when populations were pooled based on hydrographic regions identified 

using average sea surface temperature at the time of spawning and pelagic dispersal (FST = 

0.002). An isolation-by-distance pattern of gene flow among coastal and nearshore island 

comparisons (Mantel Test, p = 0.01) appeared to drive this structure. An estimate of average 

dispersal was calculated using the relationship between the regression of the isolation by distance 

and linearized density (see Rousset 1997) at 5–9 km for coastal and nearshore island populations. 

Larval distributions were examined directly by collecting early stage (3–16 mm) rockfish 

samples through the California Cooperative Oceanic Fisheries Investigations (CalCOFI) surveys, 

completing species-specific identifications on larvae by comparing sequence data to a reference 

42
database of adults for the mitochondrial cytochrome b gene, and ageing the larvae using otolithbased methods on the most abundant species in the survey, squarespot rockfish (S. hopkinsi). An 

analysis of covariance showed a significant pattern of higher abundance and younger larvae 

(mean = 9.2 days) within eddies in the SCB, and lower abundance and older larvae (mean = 

15.6 days) outside eddies (F1 = 26.13, p < 0.001). For positive stations of the oldest postflexion 

larvae, 83% (5 of 6 positive stations) were found near (within 20 km of being over) adult habitat. 

By “tracking” larvae from 1-day-old distributions over natal habitat where they are released by 

the adults and by examining distributions of aged larvae relative to these natal stations, an overall 

estimate of dispersal for the 41-day pelagic period was calculated to be 27 km. Using a 

combination of morphological and molecular methods, 23 additional species were identified 

from the same cruise, and the youngest larval distributions were examined for concordance with 

the eddies and adult habitat. The results suggest an overall pattern of retention of these early 

stage larvae within the SCB and limitation to dispersal beyond that expected for the time in the 

pelagic stage for both the nearshore kelp rockfish and the more offshore but also depth-limited 

squarespot rockfish. These data, collected using integrated methods of direct ichthyoplankton 

observations and indirect genetic methods, support previous work on many species suggesting 

that pelagic fish larvae have a lower realized dispersal than expected considering the length of 

their pelagic dispersal period. 

References 

Buonaccorsi, V. P., C. A. Kimbrell, E. A. Lynn, and R. D. Vetter. 2002. Population structure of copper 

rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of larval 

dispersal. Can. J. Fish. Aquat. Sci. 59:1374–1384. 

Jones, G. P., M. J. Milicich, M. J. Emslie, and C. Lunow. 1999. Self-recruitment in a coral reef fish 

population. Nature 402:802–804. 

Leis, J. M., and B. M. Carson-Ewart. 1997. In situ swimming speeds of the late pelagic larvae of some 

Indo-Pacific coral-reef fishes. Mar. Ecol. Prog. Ser. 159:165–174. 

Rocha-Olivares, A., and R. D. Vetter. 1999. Effects of oceanographic circulation on the gene flow, 

genetic structure, and phylogeography of the rosethorn rockfish (Sebastes helvomaculatus). Can. 

J. Fish. Aquat. Sci. 56:803–813. 

Rousset, F. 1997. Genetic differentiation and estimation of gene flow from F-statistics under isolation by 

distance. Genetics 145:1219–1228. 

Seeb, L. W., and D. R. Gunderson. 1988. Genetic variation and populations structure of the Pacific 

ocean perch (Sebastes alutus). Can. J. Fish. Aquat. Sci. 45:78–88. 

Shanks, A., B. A. Grantham, and M. H. Carr. 2003. Propagule dispersal distance and the size and 

spacing of marine reserves. Ecol. Appl. 13:S159–S169. 

Swearer, S. E., J. E. Caselle, D. W. Lea, and R. R. Warner. 1999. Larval retention and recruitment in an 

island population of a coral-reef fish. Nature 402:799–802. 

Withler, R. E., T. D. Beacham, A. D. Schulze, L. J. Richards, and K. M. Miller. 2001. Co-existing 

populations of Pacific ocean perch, Sebastes alutus, in Queen Charlotte Sound, British Columbia. 

Mar. Biol. 139:1–12. 

43
MHC Evolution in Rockfishes 

Andres Aguilar 

University of California, Merced 

School of Natural Sciences 

PO Box 2039 

Merced, California 95344 

aaguilar2@ucmerced.edu 

John Carlos Garza 

Southwest Fisheries Science Center 

Santa Cruz Laboratory 

110 Shaffer Road 

Santa Cruz, California 95060 

carlos.garza@noaa.gov 

The major histocompatibility complex (MHC) is a multigene family found in vertebrates. 

The MHC contains genes that are involved in the processing and presentation of antigens to cells 

of the immune system, and are critical to any cell-mediated immune response. MHC class II 

genes are specifically responsible for the presentation of exogenous or extracellular antigens to 

the immune system. Genetic variation at MHC class II genes is known to be important in 

pathogen resistance and may also be important in mate choice. The MHC has only been studied 

in a relatively small number of fish species, and has not yet been looked at in rockfishes 

(Sebastes spp.). Isolation of MHC genes in rockfishes will provide insight into the genomic 

organization of MHC genes in higher teleosts, general modes of MHC evolution in fishes, and a 

valuable tool for the study of selection, mate choice, and population genetics in rockfishes. Our 

objectives are to 1) isolate MHC class II genes from a variety of rockfish species, 2) perform 

phylogenetic analysis of rockfish and other teleost MHC sequences, 3) determine whether 

nonsynonymous substitution rates are elevated compared to synonymous substitutions, and 

4) test for locus-specific amplification. 

Rockfish tissue samples were obtained from NMFS trawls and longline collections. 

DNA was extracted using standard protocols. Polymerase chain reaction (PCR) primers were 

designed to amplify a portion of the MHC class IIB gene, from intron 1 to exon 2 (~500 base 

pairs [bp] fragment). PCR products were then subcloned and sequenced. An additional set of 

PCR primers were designed based on intron 1 sequence, and amplified on six greenspotted 

rockfish (S. chlorostictus) and stripetail rockfish (S. saxicola) individuals to test for locusspecific amplification. Phylogenetic analysis and estimation of nonsynonymous (amino acid 

replacement, dn) and synonymous (silent, ds) substitution rates was done with MEGA2 (Kumar 

2001) for exon 2 fragments only. 

MHC class IIB gene fragments were isolated from six rockfish species: aurora rockfish 

(S. aurora), blackgill rockfish (S. melanostomus), copper rockfish (S. caurinus), greenspotted 

44
rockfish, halfbanded rockfish (S. semicinctus), and stripetail rockfish. Multiple loci were that 

phylogenetic isolated from each of the species. Some sequences contained frameshift mutations, 

leading to an incorrect open reading frame, indicating that pseudogenes may be present in the 

rockfish MHC. Figure 1 shows analysis revealed a distinct cluster of rockfish MHC genes when 

Figure 1. Neighbor-joining tree, estimated using the Tamura-Nei distance measure, for all rockfish MHC 

class IIB alleles (exon 2) and MHC alleles from other teleost species. Numbers next to nodes 

indicate percentage of support from 500 bootstrap replicates. Species codes follow. Rockfishes: 

ARRA: aurora rockfish; BLGL: blackgill rockfish; COPP: copper rockfish; GSPT: greenspotted 

rockfish; HBRK: halfbanded rockfish; STRK: stripetail rockfish; nonrockfish species: Anha: 

Aulonocara hansbaenschi; Fuhe: mummichog (Fundulus heteroclitus); Gaac: threespine 

stickleback (Gasterosteus aculeatus); Icpu: channel catfish (Ictalurus punctatus); Mosa: striped 

bass (Morone saxitilis); Ongo: pink salmon (Oncorhynchus gorbuscha); Onke: chum salmon (O. 

keta); Onki: coho salmon (O. kisutch); Pama: red seabream (Pagrus major); Xima: southern 

platyfish (Xiphophorus maculatus); Stvi: walleye (Stizostedion vitreus, now Sander vitreum). 

45
Table 1. The nonsynonymous (d ) and synonymous (d ) substitution rates for the MHC class IIB alleles 

isolated from greenspotted rockfish and stripetail rockfish and all rockfish species used in this 

study. Standard errors are given in parentheses.

n s

Species dn ds dn:ds

Greenspotted rockfish 0.187 (0.036) 0.035 (0.013) 5.34 

Stripetail rockfish 0.175 (0.033) 0.056 (0.019) 3.13 

All rockfish 0.299 (0.038) 0.086 (0.024) 2.66 

compared to other teleost MHC sequences. Transspecific allelism, indicative of a history of 

balancing selection, is evident in the comparison of Sebastes MHC alleles (Figure 1). 

Redesigning of primers based on intron 1 sequence data gave locus-specific amplification for 

two of the species: greenspotted rockfish and stripetail rockfish. Elevated dn:ds ratios were found 

for a comparison of all rockfish MHC genes (Table 1) as well as for the alleles isolated from 

greenspotted rockfish and stripetail rockfish. 

The number of MHC loci appears to be variable across rockfish species. This is evident 

by the number of unique sequences that were isolated from each of the rockfish species. This 

finding of multiple MHC class II loci within rockfish has also been found in other teleost species 

(e.g., cichlids [Cichlidae] and sticklebacks [Gasterosteidae]). Elevated dn:ds ratios indicate that 

positive selection has been operating on rockfish MHC sequences, demonstrating historical 

selection and possible functionality to the genes isolated. Preliminary results suggesting locusspecific amplification in two species (greenspotted rockfish and stripetail rockfish) gives hope 

for further molecular evolutionary and population genetic studies of MHC class IIB genes in 

rockfishes. 

This is a work in progress, as we are continuing in the isolation of MHC sequences from 

a larger number of rockfish species. We also plan to verify locus-specific amplification through 

mother-offspring comparisons. We are also establishing genotyping methods (i.e., single strand 

conformational polymorphism, or SSCP) for MHC in rockfishes to conduct population-level 

studies of MHC variation in rockfishes. 

References 

Kumar, S., K. Tamura, I. Jakobsen, and M. Nei. 2001. MEGA2: Molecular evolutionary genetics 

analysis software. Arizona State University, Biodesign Institute, Tempe. Online at 

http://www.megasoftware.net/mega2.html [accessed 23 October 2006]. 

46
Microsatellites Reveal Regional Genetic 

Structure and Effective Population Size 

in Darkblotched Rockfish 

Daniel Gomez-Uchida and Michael A. Banks 

Oregon State University 

Hatfield Marine Science Center 

Coastal Oregon Marine Experiment Station 

2030 SE Marine Science Drive 

Newport, Oregon 97365 

daniel.gomez-uchida@lifetime.oregonstate.edu 

michael.banks@oregonstate.edu 

The broad diversity among rockfishes (Sebastes spp.) complicates the tasks of fisheries 

management and conservation in the northeastern Pacific. An undesired outcome of historical 

exploitation of this fish complex (see a review in Parker et al. 2000) has been a growing number 

of species declared overfished. Darkblotched rockfish (S. crameri) is in that delicate status, 

inhabiting deep areas of the continental shelf and slope. Low biomass estimates of darkblotched 

rockfish in 1999 (below 25% of the virgin stock) required the implementation of a conservation 

area from Washington to California, which also restricted catches on other shelf and slope 

rockfishes, resulting in serious economic impacts to coastal fishing communities. Extensive 

knowledge of darkblotched rockfish population dynamics is thus necessary to support 

management strategies such as marine reserves, which may enhance rockfish stock productivity 

(Lubchenco et al. 2003). 

Molecular population genetics provides an understanding of rockfish population 

dynamics in an evolutionary context. One primary question is whether the long pelagic stage 

(2 months) of darkblotched rockfish in surface waters (Love et al. 2002) allows effective mixing 

of individuals by ocean currents on a large scale (e.g., from Washington to northern California). 

From a conservation standpoint, to determine whether eggs, larvae, juveniles, or adults are 

exported or retained from or within an area is key for marine reserve design (Hellberg et al. 

2002). Microsatellites have demonstrated that highly variable markers may offer more analytical 

resolution to address this question in rockfish biology (e.g., Roques et al. 2002). Increased 

resolving power through microsatellites, however, requires larger sample sizes as well as 

repeated sampling over time in order to give a significant statistical signal (Waples 1998). 

Effective population size (Ne) is another parameter of interest in conservation, as it 

assesses the number of successful breeders. If the effective size is too small, it may jeopardize 

the long-term viability of a population through inbreeding depression (Frankham 1995). 

Employing the so-called temporal method in long-lived fishes has shown that Ne can be several 

orders of magnitude smaller than census sizes (N) (Hauser et al. 2002, Turner et al. 2002), which 

47
might be explained by a large individual variance in reproductive success (Hedgecock 1994), 

among several causes. Despite the importance of effective population size for conservation 

genetics, no estimates of this parameter are available for rockfishes in the northeast Pacific. 

Here we present results from molecular, population, genetic, and demographic analyses 

of darkblotched rockfish, collected during 2001 and 2002 NOAA Fisheries annual shelf and 

slope surveys along the northeastern Pacific coast. Our first objective was to determine whether 

darkblotched rockfish samples were drawn from a genetically panmictic or subdivided 

population. To accomplish this goal, 1,268 rockfishes caught between 48°N and 39°N latitude 

were genotyped across seven microsatellite loci: Sma10, Sma11 (Wimberger et al. 1999); Sal1, 

Sal3 (Miller et al. 2000); and Spi4, Spi10, and Spi12 (Gomez-Uchida et al. 2003). HardyWeinberg model fit and Wright’s F-statistics were calculated to measure genetic variation within 

and among samples (LeClair and Buckley 2001). Using FST as an estimate of genetic distance, 

we tested the hypothesis of isolation by distance using pairwise FST/(1 − FST) and geographic 

distance values. We then used an Unweighted Pair Group Method with Arithmetic Mean 

(UPGMA) cluster analysis to visualize distinct genetic groups using Cavalli-Sforza’s chord 

distance (Felsenstein 1993). Results indicated a weak signal of genetic differentiation in the 

2001 and 2002 original collections. 

We thus investigated pooling genotypes across locations, creating larger samples 

comparable in size, based on genetic similarity and geographic proximity, in order to increase 

resolution. This exercise is summarized in Table 1, which shows that pooling across both years 

(see Pooled 2001–2002 column) maximized the number of significant loci among five combined 

samples: Washington (WA), northern Oregon zone 1 (NOR1), northern Oregon zone 2 (NOR2), 

southern Oregon (SOR), and northern California (NCA). Also, a statistically significant pattern 

of isolation by distance was revealed; however, FST values remained relatively constant overall, 

reflecting low levels of genetic differentiation, regardless of sample sizes (Table 1). Three 

significant clusters from the five samples can be identified in the UPGMA phenogram of 

Figure 1. 

Our second objective was to compute an estimate of effective population size for the 

entire darkblotched rockfish population from Washington to California. We preferred a 

panmictic approach despite our previous findings, because the temporal method for overlapping 

generations (Jorde and Ryman 1995) relies on allele frequencies calculated on each cohort or 

Table 1. Summary statistics, genetic indices of differentiation, and statistical fit to isolation-by-distance 

model for raw and pooled collections of darkblotched rockfish.

Raw

2001 

Raw

2002 

Pooled

2001 

Pooled

2002 

Pooled 

2001–2002 

Number of samples 17 16 8 6 5 

Mean sample size ± SD 25.7 ± 7.2 48.8 ± 34.1 54.3 ± 8.5 128.7 ± 33.6 231.6 ± 52.3 

Number of significant loci* 0 0 2 1 5 

FST 0.001 –0.001 0.002 0.000 0.001 

Isolation-by-distance 

model fit (R2

; P-value) 

0.015; 0.15 0.032; 0.053 0.066; 0.19 0.052; 0.24 0.52; 0.015 

*After Bonferroni’s adjustment for multiple k tests (loci), k = 7, P < 0.0071. 

48
Figure 1. Distribution map of NOAA Fisheries Service 2001 shelf (gray triangles) and 2002 slope (black 

squares) sample sites in the northeastern Pacific, and associated UPGMA tree drawn from pooled 

samples across years (see Table 1 and text) using Cavalli-Sforza’s chord distance. Numbers on 

the tree are percentage of bootstrap support for each branch (WA = Washington; NOR1 = 

northern Oregon zone 1; NOR2 = northern Oregon zone 2; SOR = southern Oregon; NCA = 

northern California). 

49
year-class. Under subdivision, we reasoned that allele frequencies might have been biased as 

result of low cohort sample size within each of the three previously described clusters (Figure 1). 

Demographic parameters such as survival-at-age and reproductive success-at-age are also 

required for estimating effective size. NOAA Fisheries Service ageing teams determined 

individual age from otolith readings. Demographic parameters were obtained from available 

stock assessments (Rogers et al. 2000) and published literature (Nichol and Pikitch 1994). 

Because low frequency alleles can also bias Ne estimation, we used a binning procedure Turner

et al. (2001) developed. The harmonic mean of numbers-at-age across 40 years of fishery data 

was calculated as darkblotched rockfish census population size (N) (Rogers et al. 2000). From 

1911 to 2000 (calendar years), 30 cohorts were found. Nonetheless, 97% of the sample was 

concentrated among seven cohorts born between 1994 and 2000. Only these year-classes were 

used during the estimation of Ne. Estimates were approximately three orders of magnitude 

smaller than census size (Ne = 20,954; N = 22,984,049), with a confidence interval for 

Ne = [11,977, 32,400]. 

We derive two main conclusions from this study. First, we were able to reveal a pattern 

of genetic differentiation in darkblotched rockfish, ranging from Washington to northern 

California, by simulating larger samples that increased statistical resolution. Despite 

documenting low levels of genetic differentiation for darkblotched rockfish, we identified three 

distinct subpopulations as well as a pattern of isolation by distance. These findings should be 

taken into account in future management measures, since this species has been defined as a 

single fishery unit. Second, we found that effective population size was at least three orders of 

magnitude smaller than census sizes, which challenges the intuitive notion that large marine fish 

populations are “immune” to loss of genetic variation (Hauser et al. 2002). Only several 

thousand darkblotched breeders rather than millions in the whole population support current 

conservation initiatives to rebuild this overexploited rockfish stock. 

References 

Felsenstein, J. 1993. PHYLIP (phylogeny inference package), version 3.57c. Univ. Washington, 

Department of Genetics, Seattle. 

Frankham, R. 1995. Conservation genetics. Ann. Rev. Genet. 29:305–327. 

Gomez-Uchida, D., E. A. Hoffman, W. R. Ardren, and M. A. Banks. 2003. Microsatellite markers for 

the heavily exploited canary (Sebastes pinniger) and other rockfish species. Mol. Ecol. Notes 

3:387–389. 

Hauser, L., G. J. Adcock, P. J. Smith, J. H. Bernal Ramirez, and G. R. Carvalho. 2002. Loss of 

microsatellite diversity and low effective population size in an overexploited population of New 

Zealand snapper (Pagrus auratus). Proc. Natl. Acad. Sci. 99:11742–11747. 

Hedgecock, D. 1994. Does variance in reproductive success limit effective population sizes of marine 

organisms? In A. R. Beaumont, Genetics and evolution of aquatic organisms, p. 122–134. 

Chapman and Hall, London. 

Hellberg, M. E., R. S. Burton, J. E. Neigel, and S. R. Palumbi. 2002. Genetic assessment of connectivity 

among marine populations. Bull. Mar. Sci. 70:273–290. 

50
Jorde, P. E. and N. Ryman. 1995. Temporal allele frequency change and estimation of effective size in 

populations with overlapping generations. Genetics 139:1077–1090. 

LeClair, L. L., and R. M. Buckley. 2001. Electrophoretic identification of juvenile rockfish (genus 

Sebastes) recruiting to drifting algae and seagrass habitats off the Washington coast. Northwest 

Sci. 75:53–60. 

Love, M. S., M. Yoklavich, and L. Thorsteinson. 2002. The rockfishes of the northeast Pacific. 

University of California Press, Berkeley. 

Lubchenco, J., S. R. Palumbi, S. D. Gaines, and S. Andelman. 2003. Plugging a hole in the ocean: The 

emerging science of marine reserves. Ecol. Appl. 13(1):S3–S7. 

Miller, K. M., A. D. Schulze, and R. E. Withler. 2000. Characterization of microsatellite loci in Sebastes 

alutus and their conservation in congeneric rockfish species. Mol. Ecol. 9:240–242. 

Nichol, D. G. and E. K. Pikitch. 1994. Reproduction of darkblotched rockfish off the Oregon coast. 

Trans. Am. Fish. Soc. 123:469–481. 

Parker, S. J., S. A. Berkeley, J. T. Golden, D. R. Gunderson, J. Heifetz, M. A. Hixon, R. Larson, 

B. M. Leaman, M. S. Love, J. A. Musick, V. M. O’Connell, S. Ralston, H. J. Weeks, and 

M. M. Yoklavich. 2000. Management of Pacific rockfish. Fisheries 25(3):22–29. 

Rogers, J. B., R. Methot, T. L. Builder, K. Piner, and M. Wilkins. 2000. Status of the darkblotched 

rockfish (Sebastes crameri) resource in 2000. Appendix: Status of the Pacific coast groundfish 

fishery through 2000 and recommended acceptable biological catches for 2001. (Available from 

Pacific Fishery Management Council, 7700 NE Ambassador Place, Suite 200, Portland, OR 

97201.) 

Roques, S., J. M. Sevigny, and L. Bernatchez. 2002. Genetic structure of deep-water redfish, Sebastes 

mentella, populations across the North Atlantic. Mar. Biol. 140(2):297–307. 

Turner, T. F., L. A. Salter, and J. R. Gold. 2001. Temporal-method estimates of Ne from highly 

polymorphic loci. Conserv. Genet. 2:297–298. 

Turner, T. F., J. P. Wares, and J. R. Gold. 2002. Genetic effective size is three orders of magnitude 

smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops 

ocellatus). Genetics 162(3):1329–1339. 

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. 

Wimberger, P., J. Burr, A. Lopez, and P. Bentzen. 1999. Isolation and characterization of twelve 

microsatellite loci for rockfish (Sebastes). Mar. Biotech. 1:311–315. 

51
Population Structure of Puget Sound Rockfish 

Assessed with Mitochondrial DNA 

and Microsatellites 

Jennifer A. Hempelmann 

Northwest Fisheries Science Center 

Conservation Biology Division 

2725 Montlake Boulevard East 

Seattle, Washington 98112 

jennifer.hempelmann@noaa.gov 

Christiane H. Biermann 

Portland State University 

Department of Biology 

1719 SW 10th Avenue 

Portland, Oregon 97207 

biermann@pdx.edu 

Erik E. Sotka 

Stanford University 

Hopkins Marine Station 

120 Oceanview Boulevard 

Pacific Grove, California 93950 

sotka@stanford.edu 

Daniel Halos 

University of Washington 

Friday Harbor Laboratories 

620 University Road 

Friday Harbor, Washington 98250 

danhalos@gmail.com 

Historically, rockfishes (Sebastes spp.) and other large vertebrates have played 

fundamental roles in the ecology of nearshore communities in the northeast Pacific (Dayton et al. 

1998). However, over the last three decades, many ecologically and commercially important 

large rockfish species along the northeastern coastlines of the Pacific Ocean have rapidly 

declined in abundance to a fraction of their original biomass (Gunderson 1997). This decline can 

be attributed in part to a popular recreational and commercial fishery of rockfish that arose in the 

late 1960s and early 1970s and peaked at over 200 million tons in the early 1990s along the west 

coast of North America (Laidig et al. 1996, Love et al. 2002). In stark contrast to declines in the 

large rockfishes, a “dwarf” rockfish that has no commercial value or recreational interest—the 

52
Puget Sound rockfish (S. emphaeus)—has exploded in population size by several orders of 

magnitude over the same time period (Fulmer et al. in press). The concern for managers is that 

huge aggregations of these “dwarf” rockfish may impede the recovery of larger and more 

commercially valuable rockfish species through competition. 

Even though it is informative to study a nonfished species in addition to its exploited 

congeners, few studies have focused on Puget Sound rockfish. This study uses sequences from 

the mitochondrial control region and alleles from two microsatellite loci to quantify gene flow 

among five Puget Sound rockfish populations separated by 10–120 km in Washington waters 

(Figure 1) and to assess whether there was a genetic signature of recent population expansion. 

Our examination of the mitochondrial control region revealed a great deal of genetic 

variation within populations of Puget Sound rockfish (Table 1). Fifty-six haplotypes—only 

16 of which were shared by two or more individuals—were sequenced from the 127 total 

individuals. On average, individuals differed by approximately 1% (±0.1% SD; Table 1). A 

phylogenetic analysis delineated two major clades within Puget Sound rockfish, distinguished by 

two transitions and one transversion (genealogy not shown). 

Sea 

WSd 

FHL 

PGe

Shaw

Seattle

~100km

San 

Juan 

Islands 

Figure 1. Collection locations (shown in white boxes). 

Sea = Off Boeing Creek, Seattle 

WSd = West side of San Juan Island, off Eagle Cove 

FHL = East side of San Juan Island, near Friday Harbor Laboratories 

PGe = Point George, South of Shaw Island 

Shaw = North of Shaw Island, Broken Point 

53
Table 1. Indices of genetic diversity, haplotype frequencies, and tests for population expansion (Tajima’s 

D-statistics and Fu’s F-statistics) among populations of the Puget Sound rockfish. 

Tajima’s 

D-test Fu’s F-test 

Population n 

Number of 

haplotypes 

Number of 

unique 

haplotypes 

Proportions 

of clades 

(A:B) 

Nucleotide 

diversity 

(±SD) D 

pvalue F 

pvalue 

FHL 28 22 14 0.71:0.29 0.012(±0.002)

PGe 32 17 5 0.78:0.22 0.008(±0.003)

Shaw 25 20 7 0.80:0.20 0.010(±0.002)

Westside 19 15 8 0.79:0.21 0.012(±0.002)

Seattle 23 17 6 0:70:0.30 0.012(±0.002)

Total 127 56 40 0.76:0.24 0.010(±0.002) −2.03 0.021 −47.91 <0.001

Despite the considerable genetic variation within Puget Sound rockfish, there was little 

evidence of population subdivision across localities, which were separated by up to 120 km

(Figure 1). There were no significant differences in the frequencies of the 16 shared haplotypes 

and no differences in the relative proportions of the two control region clades, which occurred at 

all locations in approximately a 70:30 mix. An analysis of molecular variance (AMOVA) of the 

mitochondrial DNA (mtDNA) sequences indicated no significant differentiation among 

populations. An AMOVA analysis of the two microsatellite loci, which presumably evolve more 

quickly than mtDNA, also displayed no significant population subdivision. 

Because it is unlikely that the noncoding control region locus is under strong selection, 

the observed genetic homogeneity among these populations of Puget Sound rockfish is probably 

the consequence of broad gene flow among populations, or a recent cessation of gene flow and 

incomplete lineage sorting. We currently believe that there is substantial gene flow among 

rockfish populations from the San Juan Islands and Puget Sound, because even the more quickly 

evolving microsatellite loci displayed no genetic differentiation with reasonable sample sizes 

(n = 15 to 27 per locus per population). A more definitive conclusion may be reached with 

higher sample sizes and more loci. 

The mtDNA sequence data contain a signal of population expansion that appears to 

reflect a relatively old expansion into the Puget Sound region. Analysis of the mitochondrial 

control region data indicated more new mutations than would be expected from the number of 

segregating sites (Tajima’s D = −2.03, p = 0.021) or from the number of alleles (Fu’s F = 

−47.91, p < 0.001; Table 1). Because it is unlikely that the noncoding locus is under selection, 

these negative D and F values likely indicate an expanding population. 

A mismatch distribution analysis (see Lessios et al. 2001) confirmed the results of the 

Tajima’s D-tests and Fu’s F-tests and provided an estimate of the time since expansion began. 

From the mismatch analysis (Figure 2), we estimate that the time since the expansion began in 

Puget Sound is approximately 12,770 years before present—with a large confidence interval, 

however. The notion that the expansion began approximately 12 thousand years ago (KYA) 

matches very closely with estimates of when habitats became available in Puget Sound after the 

retreat of the last glacial maximum (Pielou 1991). 

54
Figure 2. Mismatch distribution of Puget Sound rockfish mtDNA control region sequences. 

In summary, we have detected apparently high gene flow among populations of rockfish 

in Puget Sound and the Northwest Straits and detected a genetic signal of population expansion 

that was likely initiated with the postglacial colonization of the Georgia Basin about 12 KYA. 

The most pressing work that remains is to assess whether the high densities of this “dwarf” 

rockfish may alter the course of recovery of the larger, commercially valuable species. In 

particular, a focus on the feeding ecologies and interactions among adult Puget Sound rockfish 

and juvenile individuals of the larger rockfish species should reveal whether these fish guilds 

compete for food and habitat and thus whether such competition may impede the recovery of the 

larger rockfish. Alternatively, if Puget Sound rockfish are regularly eaten as prey by larger 

rockfish (Love et al. 2002), then large abundances of Puget Sound rockfish may actually 

accelerate recovery of larger rockfish. 

Acknowledgments 

This project was generated during a spring 2003 research apprenticeship course at Friday 

Harbor Laboratories at University of Washington. Jennifer Hempelmann received financial 

support from the Mary Gates Endowment. Erik Sotka was supported in part by the Andrew W. 

Mellon Foundation. We thank R. Buckley and the Washington Department of Fish and Wildlife 

for help with fishing. 

References 

Dayton, P. K., M. J. Tegner, P. B. Edwards, and K. L. Riser. 1998. Sliding baselines, ghosts, and 

reduced expectations in kelp forest communities. Ecol. Appl. 8:309–322. 

Fulmer, J., D. R. Gunderson, L. LaFrance, B. S. Miller, B. Goetz, and W. A. Palsson. In press. Changes 

in growth and recruitment of the Puget Sound rockfish (Sebastes emphaeus) in northern Puget 

Sound. In J. Heifetz, J. DiCosimo, A. J. Gharrett, M. S. Love, V. M. O’Connell, and R. D. 

Stanley (eds.), Biology, assessment, and management of North Pacific rockfishes. Alaska Sea 

Grant, University of Alaska Fairbanks. 

55
Gunderson, D. R. 1997. Spatial patterns in the dynamics of slope rockfish stocks and their implications 

for management. Fish. Bull. 95:219–230. 

Laidig, T. E., K. M. Sakuma, and M. N. Nishimoto. 1996. Description of pelagic larval and juvenile 

stripetail rockfish, Sebastes saxicola (family Scorpaenidae), with an examination of larval 

growth. Fish. Bull. 94:289–299. 

Lessios, H. A., M. J. Garrido, B. D. Kessing. 2001. Demographic history of Diadema antillarum, a 

keystone herbivore on Caribbean reefs. Proc. R. Soc. Lond. B 268:2347–2353. 

Love, M. S., M. Yoklavich, and L. Thorsteinson. 2002. The rockfishes of the northeast Pacific. 

University of California Press, Berkeley. 

Pielou, E. 1991. After the Ice Age: The return to life to glaciated North America. University of Chicago 

Press, Chicago. 

56
Genetic Markers Distinguish Populations 

of Black Rockfish in the Gulf of Alaska 

Lisa W. Seeb 

Alaska Department of Fish and Game 

Division of Commercial Fisheries 

Gene Conservation Laboratory 

333 Raspberry Road 

Anchorage, Alaska 99518 

lisa_seeb@fishgame.state.ak.us 

The understanding of the genetic structure of discrete stocks and the biological 

significance of local depletions is a central feature of conservation and restoration of 

commercially exploited fisheries resources. Marine organisms represent unusual challenges in 

the study of population genetics. Adult marine organisms may make extensive migrations over 

huge distances and have highly dispersive larval and early life history stages. 

Rockfish (Sebastes spp.) stocks are harvested extensively in Alaska by both commercial 

and sport fisheries, but like rockfishes throughout the North Pacific, they are easily 

overharvested and slow to rebuild due to longevity and delayed maturation (Love et al. 2002). 

The harvest for nearshore rockfishes in the northern Gulf of Alaska primarily occurs in state 

waters, and black rockfish (S. melanops) represent an important component of that fishery. 

Schools of adults often aggregate over shallow rocky areas making them particularly susceptible 

to fishing. The State of Alaska has sole management and assessment responsibility for black 

rockfish, since it was believed that the species was not adequately assessed by the trawl surveys 

conducted by the National Marine Fisheries Service (NMFS). 

In this study, we surveyed the population structure of 10 populations of black rockfish 

ranging from the Alaska Peninsula across the Gulf of Alaska. We also included a representative 

population from Washington State as an outgroup (Table 1, Figure 1). Samples were collected 

by hook and line and from commercial and sport fish sampling. Target sample sizes were set at 

100, but realized sample sizes varied from 24 to 130 individuals. Fin clips from individual fish 

were nonlethally sampled, placed in ethanol, and shipped to the laboratory for analysis. 

DNA was extracted using a rapid precipitation method; all microsatellite analyses were 

conducted on an Applied Biosystems (ABI) 377 automated sequencer (Applied Biosystems, 

Foster City, California). Individuals were analyzed for 10 microsatellite loci including tri- and 

tetranucleotide loci cloned from black rockfish (Sme 2, 3, 4, 5, 8, 9, 11, 14, ADFG unpubl. data) 

and dinucleotide loci from quillback rockfish (S. maliger) (Sma 1, 3; Wimberger et al. 1999). A 

wide range of variation was observed at the 10 loci with the number of alleles per locus varying 

from 8 to 48 (Table 2). Overall, 235 alleles were observed. 

57
Table 1. Collection locations of black rockfish. 

Location N 

Collection 

date 

Washington 30 1998 

Southeast Alaska—Sitka 100 1999 

Yakutat 130 2003 

Prince William Sound 48 2000 

Resurrection Bay 24 1998 

Kodiak Island—East 100 1998 

Kodiak Island—West 86 1998 

Alaska Peninsula—Chignik 100 2000 

Alaska Peninsula—Sand Point 60 1999 

Alaska Peninsula—Akutan 100 1999 

To evaluate the relationships among sites, FST was calculated among all collections as 

well as pairwise between collections using FSTAT version 2.9.3 (Goudet 2001). Significant 

population structure was detected with an overall value of FST of 0.008 (P = 0.01). This level of 

structure, although low, is consistent with previous studies of rockfish species over broad 

geographic ranges based on microsatellite loci. For example, Buonaccorsi et al. (2002), 

surveying copper rockfish (S. caurinus) from California to British Columbia, estimated an FST of 

0.007. 

Figure 1. Map of collection sites for black rockfish. 

58
Table 2. Microsatellite loci, number of alleles and locus source for black rockfish. 

Locus 

Number of 

alleles 

GenBank accession 

number or source 

Sme 2 25 AF142484 

Sme 3 38 AF142485 

Sme 4 34 AF142486 

Sme 5 13 AF142487 

Sme 8 15 AF142490 

Sme 9 24 AF142491 

Sme 11 18 AF142493 

Sme 14 8 AF142587 

Sma 1 12 Wimberger et al. 2000 

Sma 3 48 Wimberger et al. 2000 

Overall 235 

A matrix of pairwise FST values between all pairs of populations was computed. 

Population structure was visualized using multidimensional scaling (MDS) of the pairwise 

values as implemented in NtSYS (Exeter Software, Setauket, New York) to reduce the 

dimensionality of the interpopulation distances to three-dimensional space. Two major clusters 

are apparent in the multidimensional scaling, a large cluster of populations ranging from the 

Alaska Peninsula through the central Gulf of Alaska and a second cluster of populations ranging 

from Yakutat to the Washington population from the Pacific Northwest (Figure 2). These data 

suggest an isolation by distance model with a distinct discontinuity between Prince William 

Sound and the Yakutat. 

Figure 2. MDS using pairwise FST values for 10 populations of black rockfish from the Gulf of Alaska 

and Washington coast. 

59
References 

ADFG (Alaska Department of Fish and Game). Unpubl. data. Ten microsatellite loci including tri- and 

tetranucleotide loci cloned from black rockfish. (Available from Alaska Dept. Fish and Game, 

333 Raspberry Rd., Anchorage, AK 99518.) 

Buonaccorsi, V. P., C. A. Kimbrell, E. A. Lynn, and R. D. Vetter. 2002. Population structure of copper 

rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of larval 

dispersal. Can. J. Fish. Aquat. Sci. 59:1374–1384. 

Goudet, J. 1995. FSTAT (version 1.2): A computer program to calculate F-statistics. J. Hered. 

86:485–486. 

Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 

2.9.3). Updated from Goudet (1995). Online at http://www2.unil.ch/popgen/softwares/fstat.htm. 

Love, M. S., M. Yoklavich, and L. Thorsteinson. 2002. The rockfishes of the northeast Pacific. 

University of California Press, Berkeley. 

Wimberger, P., J. Burr, A. Gray, A. Lopez, and P. Bentzen. 1999. Isolation and characterization of 

twelve microsatellite loci for rockfish (Sebastes). Mar. Biotech. 1:311–315. 

60
Genetic Studies of Rockfish: Identification, 

Relationships, and Population Structure 

Anthony J. Gharrett, Zhuozhuo Li, Andrew P. Matala, and Andrew K. Gray 

University of Alaska Fairbanks 

School of Fisheries and Ocean Sciences, Juneau Center 

11120 Glacier Highway 

Juneau, Alaska 99801 

a.gharrett@uaf.edu 

Jonathan Heifetz 

National Marine Fisheries Service 

Auke Bay Laboratory 

11305 Glacier Highway 

Juneau, Alaska 99801 

jon.heifetz@noaa.gov 

Milton S. Love 

University of California, Santa Barbara 

Marine Science Institute 

Santa Barbara, California 93106 

love@lifesci.ucsb.edu 

Arthur W. Kendall, Jr. 

National Marine Fisheries Service 

7600 Sand Point Way NE 

Seattle, Washington 98115 

art.kendall@noaa.gov 

The species-rich genus of rockfish (Sebastes spp.) continues to provide many challenges 

to fisheries scientists. More than 60 species are indigenous to the Pacific coast of North America 

and over 100 occur worldwide (Kendall 2000). Rockfishes are important to commercial and 

recreational fisheries, and their numbers and diversity indicate that they are important and 

complex components of the marine ecosystem. The challenges of rockfish result both from the 

large number of species and their often close similarities. 

Although the life history and ecology of many rockfish species have been studied in 

detail, little information is available for the majority of species. In addition to the number of 

species, some of which are cryptic and others probably unrecognized (Seeb 1986), the 

ontogenetic progression of rockfish obfuscates study efforts. Female rockfish are viviparous. In 

the marine environment, larvae develop through a series of transformations until, as juveniles, 

they begin to take on adult characteristics. It is not yet possible to identify visually the species of 

61
many larvae and identification of some juveniles is difficult. Consequently, the early life history 

of those species is unknown. These problems, related directly to the systematics of the rockfish 

genus, make it difficult to determine environmental influences on their abundances and roles in 

the marine ecosystem. 

The planktonic nature and dispersal of rockfish larvae also create questions about the 

sources of rockfish production. Because dispersal of larvae is related to oceanic processes, the 

nature of the population structure is not immediately obvious for a particular species. The 

population structure of different species may vary substantially because of the variety of life 

histories. Knowledge of the population structure translates to practical questions when fisheries 

scientists attempt to manage fish for harvest, to conserve species, or to protect them from 

environmental or anthropogenic influences. These questions involve the population genetics of 

rockfish species. 

Approach 

We have addressed a broad array of questions concerning systematics and population 

structure using studies involving genetic analysis. We have examined the genetic diversity 

among species and characterized the genetic composition within and among selected species of 

rockfish. The underlying concept is that evolutionarily related individuals share common 

ancestry but often exhibit some genetic divergence. At the molecular level, the overall DNA 

base sequence (or gene products) of two related species should be similar, but because of 

divergence in nucleotide sequences there are some differences. Ordinarily, more differences 

accumulate as divergence between species (or populations) increases. 

Our work had three major facets. The basis of the species identification work involved 

development of restriction site maps in regions of the mitochondrial DNA that include the 

nicotinamide adenine dinucleotide, reduced form (NADH), dehydrogenase subunit-3 and 

subunit-4 genes (ND3/ND4 region), and the 12S and 16S ribosomal RNA (rRNA) genes 

(12S/16S region). Those data also provided preliminary data for phylogenetic comparisons 

among rockfish species as well as with two other scorpaenids, shortspine thornyheads 

(Sebastolobus alascanus) and Helicolenus hilgendorfii. In the second facet, we applied our 

database to identify to species larval and juvenile rockfish collected in ichthyoplankton and 

juvenile surveys. The third facet of the project was to examine the potential of mitochondrial 

DNA (mtDNA) and microsatellite variation to detect population structure. 

Results 

Our first studies examined interspecific mtDNA variation in Sebastes rockfish. The 

systematics of rockfish, the assignment of subgenera, and the relationships between Asian and 

North American species have not been thoroughly evaluated since the advent of molecular 

methods. We mapped restriction sites in the mtDNA ND3/ND4 and 12S/16S regions and used 

the presence or absence of sites as characters for comparisons among species. We began by 

examining the most common species in the eastern Gulf of Alaska (GOA). We were able to 

distinguish all 15 rockfish species included in the study; although all were distinct, black 

rockfish (S. melanops) was similar to yellowtail rockfish (S. flavidus) (both subgenus 

Sebastosomus), harlequin rockfish (S. variegatus) was similar to sharpchin rockfish 

62
(S. zacentrus) (both subgenus Allosebastes), and quillback rockfish (S. maliger) was similar to 

copper rockfish (S. caurinus) (both subgenus Pteropodus) (Gharrett et al. 2000). Subsequently, 

we extended our survey of rockfish species and included species from Asian and both the 

southern and northern North American ranges. 

With these samples we addressed questions about 1) the integrity of the subgenus 

Pteropodus, which has representatives both in Asia and along the North American coast, and 

their relationship to species in other subgenera (e.g., Mebarus), and 2) the monophyly of 

subgenera within rockfish. We discovered that Asian and North American Pteropodus and 

Mebarus species are distinct (Li et al. 2006a). In addition, several of the subgenera (e.g., 

Acutomentum and Allosebastes) are probably not monophyletic (Li et al. 2006b). Mitochondrial 

DNA has unique markers because mtDNA is clonal and matrilineally inherited. Nuclear markers 

provide an independent evolutionary snapshot, and we initiated a study of microsatellite flanking 

regions. The rationale was that these sequences are unlikely to be heavily influenced by natural 

selection. The flanking regions in aggregate would provide sequences that reflect generalized 

divergence among species. That work also indicated that Asian rockfish species represented 

lineages separate from their North American congeners (Asahida et al. 2004). 

From the information that restriction site data provided, the majority of more than 

70 species of rockfish could be unequivocally identified. Only a few small groups of species 

(usually groups of two or three) could not be resolved. One of the challenges rockfish present is 

that the larvae and many small juveniles are difficult or impossible to identify visually. 

Consequently, we applied the species-identifying mtDNA methods to collections of juveniles 

from the Southern California Bight (SCB) and the GOA and to several ichthyoplankton 

collections from Southeast Alaska. In all of the studies, collaborators (M. Nishimoto in 

California and A. Kendall and B. Wing in Alaska) examined the morphology of the specimens in 

an effort to develop or confirm morphological means to identify these small fish. Morphological 

identification of the SCB specimens was confirmed, but some species groups like gopher 

rockfish (S. carnatus) and black-and-yellow rockfish (S. chrysomelas) remain indistinguishable 

(Li et al. in press). We successfully extracted DNA from 5-mm preflexion larvae and identified 

them to species or species group, but with exceptions for two species of the subgenus Pteropodus

and possibly sharpchin rockfish, no morphological markers were found that would facilitate field 

identification (Gray et al. 2006). The GOA juveniles were also identified genetically to species 

or species group and many of the fish were identified morphologically. Although some of the 

specimens could not be identified to species, the number of potential species was reduced to two 

to four (Kondzela et al. in press). Consequently, it was possible to use morphology to complete 

the identifications in nearly all cases for juveniles. 

One of the controversies that remains is the relationship between gopher rockfish and 

black-and-yellow rockfish. These species occupy the same range, but seem to be ecologically 

separated. Recently, microsatellite markers have been identified that are probably species 

specific (Narum 2000). Previous studies failed to find fixed differences between the species. 

We examined mtDNA variation within these groups and used an analysis that tested the 

significance of haplotype distributions in a haplotype tree in a context of geographic distribution. 

Although both species have many of the same common haplotypes, their distributions differed, 

especially for presumed ancestral haplotypes, suggesting that one species emerged to the south of 

Point Conception and the other emerged to the North. In addition, comparison of haplotypes of 

63
copper rockfish from its northern (Canada) and southern (Southern California) ranges reveals 

overlap in mtDNA haplotype composition, but frequency differences indicate population 

divergence. 

Knowledge of population structure is important to conservation and management 

missions, and population genetic structure is particularly useful because it can identify maximum 

bounds of production units. For population genetic studies, microsatellites provide a useful tool 

because there are literally thousands in the genome, many are probably neutral and noncoding, 

and they are diploid, which provides information that can be used both to assess their utility and 

is useful in stock separation computations. Consequently, we used microsatellites in separate 

studies of the population genetic structure of bocaccio (S. paucispinis), rougheye rockfish 

(S. aleutianus), shortraker rockfish (S. borealis), and northern rockfish (S. polyspinis). Bocaccio 

along the California coast has been heavily exploited and is in jeopardy. Our work suggests that 

the bocaccio population structure should be considered in making conservation decisions and 

that the structure may be influenced by current patterns. The population structure observed in 

bocaccio is consistent with a neighborhood model in which the distribution of a species is 

relatively continuous, but the distance moved between birth and reproduction is much less than 

the species range (Matala et al. 2004a). Shortraker rockfish also has population structure that 

appears consistent with the neighborhood model (Matala et al. 2004b). 

In our population studies of rougheye rockfish, we were at first puzzled by the absence of 

heterozygotes at one microsatellite locus, but when we observed that two distinct mtDNA 

haplotypes were correlated with the microsatellite expression, it became clear that there were two 

distinct species (Gharrett et al. 2005). Both species of rougheye rockfish (Types I and II) 

(Gharrett et al. in press) also have population structure that appears consistent with the 

neighborhood model. Weak structure was observed in preliminary studies of northern rockfish. 

What Remains to Be Done? 

The results summarized above leave many questions. First, several groupings of rockfish 

cannot yet be distinguished genetically. It is possible that discriminating markers occur in other 

mtDNA regions. Exploration of other regions also should provide markers that increase the 

systematic resolution. In addition to better resolving systematic differences, it would be useful to 

survey nuclear loci. One of the problems with the molecular phylogenies is that they do not 

provide clear relationships near the interior of the tree. To define those relationships, either a 

substantial amount of additional data or data from more strongly conserved sequences would be 

useful. 

Additional markers would also be useful for species identification of larvae and juveniles. 

The RFLP markers could be converted to single nucleotide polymorphism (SNP) markers. SNP 

markers would make processing samples from ichthyoplankton surveys very fast and could alter 

the approach to larval assessment surveys in some areas and make such surveys appropriate in 

other areas. 

The differences between Asian and North American species are intriguing. Although we 

have tissue samples of nearly all of the Asian species, we have not yet analyzed them. The 

64
completion of those analyses will provide interesting information about the evolutionary history 

of rockfish. 

There are more than 70 rockfish species along the North American coast. Many are 

commercially or recreationally valuable; all are important components in the ecosystem. We 

know little about their population structure, but because many are long-lived, they are 

demographically fragile and need to be well understood and carefully managed if we expect 

them to persist. Knowledge of their population genetic structure is an important facet of learning 

about their biology and the basis of their productivity. 

Acknowledgments 

Our work has been supported by the U.S. Geological Survey, the U.S. National Marine 

Fisheries Service Auke Bay Laboratory, the Saltonstall-Kennedy Fund, and the North Pacific 

Research Board. 

References 

Asahida, T., A. K. Gray, and A. J. Gharrett. 2004. Use of microsatellite locus flanking regions for 

phylogenetic analysis: A preliminary study of Sebastes subgenera. Environ. Biol. Fishes 

69:461–470. 

Gharrett, A. J., A. K. Gray, and J. Heifetz. 2000. Identification of rockfish (Sebastes spp.) from 

restriction site analysis of the mitochondrial ND3/ND4 and 12S/16S rRNA gene regions. Fish. 

Bull. 99:49–62. 

Gharrett, A. J., A. P. Matala, E. L. Peterson, A. K. Gray, Z. Li, and J. Heifetz. 2005. Two genetically 

distinct forms of rougheye rockfish are different species. Trans. Am. Fish. Soc. 134:242–260. 

Gharrett, A. J., A. P. Matala, E. L. Peterson, A. K. Gray, Z. Li, and J. Heifetz. In press. Distribution and 

population genetic structure of sibling species of rougheye rockfish. In J. Heifetz, J. DiCosimo, 

A. J. Gharrett, M. S. Love, V. M. O’Connell, and R. D. Stanley (eds.), Biology, assessment, and 

management of North Pacific rockfishes. Alaska Sea Grant, University of Alaska Fairbanks. 

Gray, A. K., A. W. Kendall, Jr., B. L. Wing, M. G. Carls, J. Heifetz, Z. Li, and A. J. Gharrett. 2006. 

Identification and first documentation of larval rockfishes in southeast Alaskan waters was 

possible using mitochondrial markers but not pigmentation patterns. Trans. Am. Fish. Soc. 

135:1–11. 

Kendall, A. W., Jr. 2000. An historical review of Sebastes taxonomy and systematics. Mar. Fish. Rev. 

62:1–23. 

Kondzela, C. M., A. W. Kendall, Jr., Z. Li, D. Clausen, and A. J. Gharrett. In press. Species of juvenile 

rockfish collected in the Gulf of Alaska, 1998–2002. In J. Heifetz, J. DiCosimo, A. J. Gharrett, 

M. S. Love, V. M. O’Connell, and R. D. Stanley (eds.), Biology, assessment, and management of 

North Pacific rockfishes. Alaska Sea Grant, University of Alaska Fairbanks. 

Li, Z., A. K. Gray, M. S. Love, T. Asahida, and A. J. Gharrett. 2006a. Phylogeny of members of the 

rockfish (Sebastes) subgenus Pteropodus and their relatives. Can. J. Zool. 84:527–536. 

65
Li, Z., M. M. Nishimoto, M. S. Love, and A. J. Gharrett. 2006b. Comparing the identification of 

Southern California juvenile rockfishes (genus Sebastes spp.) by restriction site analysis of the 

mitochondrial ND3/ND4 region and by morphological characteristics. Fish. Bull. 104:376–382. 

Li, Z., A. K. Gray, M. S. Love, A. Goto, and A. J. Gharrett. In press. Are the subgenera of Sebastes

monophyletic? In J. Heifetz, J. DiCosimo, A. J. Gharrett, M. S. Love, V. M. O’Connell, and R. 

D. Stanley (eds.), Biology, assessment, and management of North Pacific rockfishes. Alaska Sea 

Grant, University of Alaska Fairbanks. 

Matala, A. P., A. K. Gray, A. J. Gharrett, and M. S. Love. 2004a. Microsatellite variation indicates 

population genetic structure of bocaccio. N. Am. J. Fish. Man. 24:1189–1202. 

Matala, A. P., A. K. Gray, J. Heifetz, and A. J. Gharrett. 2004b. Population structure of Alaskan 

shortraker rockfish, Sebastes borealis, inferred from microsatellite variation. Environ. Biol. 

Fishes 69:201–210. 

Narum, S. 2000. Assortative mating and genetic structure of gopher rockfish (S. carnatus) and blackand-yellow-rockfish (S. chrysomelas): A case of incipient speciation. Master’s thesis. Univ. San 

Diego, San Diego, CA. 

Seeb, L. W. 1986. Biochemical systematics and evolution of the scorpaenid genus Sebastes. Doctoral 

dissertation. Univ. Washington, Seattle. 

66
Conservation Genetics of Rockfishes: 

The West Coast’s Most Species-rich 

and Imperiled Genus of Fishes

Russell D. Vetter 

Southwest Fisheries Science Center 

8604 La Jolla Shores Drive 

La Jolla, California 92038 

russ.vetter@noaa.gov 

More than 70 species of rockfish (Sebastes spp.) occur off the west coast of North 

America at depths from the intertidal to over 500 m. All members of the genus share an 

ovoviviparous system of reproduction with mate selection, copulation, internal fertilization, and 

the gestation and production of live-born young. Relative to broadcast spawning fishes, the 

properties of assortative mating and live bearing may promote reproductive isolation and 

regional retention of larvae. Assortative mating may increase rates of speciation 

(Rocha-Olivares 1999a, 1999b, Narum et al. 2004) and larval retention may promote a high level 

of phylogeographic population structure (Rocha-Olivares and Vetter 1999, Buonaccorsi et al. 

2004). The high numbers of similar species, the potential for cryptic species, and the likelihood 

of regional stock structure make rockfish species difficult to assess and manage but also make 

them good candidates for molecular approaches to their systematics, population structure, and 

ecology. In the early 1990s the Fish Genetics Group at the Southwest Fisheries Science Center 

La Jolla Laboratory targeted rockfish and related scorpaenid fishes for molecular studies of their 

ecology and evolutionary biology. Studies of molecular larval identification (Fish and Chips: 

Genetic Identification of Rockfish Larvae and Juveniles, p. 35) and larval dispersal patterns 

(Integrated Methods to Converge on Estimates of Larval Dispersal, p. 42) are covered elsewhere 

in this volume. First, I summarize studies of the evolution, phylogeny, and subgeneric structure 

of the genus particularly as it informs studies of morphology, biogeography, niche, and early life 

history characteristics. Second, I discuss types of population genetic structure that have been 

observed in different scorpaenid fishes and how this may relate to larval dispersal patterns and 

metapopulation structure. Finally, I discuss the application of molecular studies to inform 

management decisions. 

Classic systematic investigations of the rockfishes noted morphologic similarities and 

differences that led to the description of several taxonomic groupings that have at times been 

elevated to genus-level distinctions although they are presently subsumed within the rockfishes. 

Phylogenetic studies based on mitochondrial DNA (mtDNA) have generally supported 

morphologically based subgeneric lineages with the occasional reassignment of a species that is 

not related by descent but appears similar due to convergent evolution. Cytochrome b sequences 

of 54 rockfish species were originally described by Rocha-Olivares et al. (1999a). Since then 

almost all remaining species have been sequenced (>98 species or taxa, see Fish and Chips: 

67
Genetic Identification of Rockfish Larvae and Juveniles, p. 35). Subsequent studies have sought 

to refine subgeneric groupings, for example, the Sebastosomus (Rocha-Olivares et al. 1999b) and 

Pteropodus (Taylor 1998). Numerous field studies of adults, juveniles, and larvae have also 

attempted to group rockfishes by similarities in adult niches or juvenile life history. For 

example, Lenarz et al. (1995) observed that pelagic juveniles could be grouped by depth of 

occurrence and relative abundance in El Niño and normal years. They noted that these coherent 

groups corresponded to adult guilds such as structure schoolers (fish that tend to congregate near 

large objects like rocky reefs, oil platforms, etc.) and nearshore demersals. It has been 

particularly gratifying that morphological characters and ecological behaviors tend to overlay 

phylogenetic groupings determined by molecular methods. The genetic lineage known as the 

Pteropodus rockfishes directly corresponds to the pelagic juvenile and adult assemblages 

described by Lenarz et al. as the nearshore demersals and the Sebastomas lineage to the structure 

schoolers. The value of considering these subgeneric lineages continues to be a useful 

organizing principle for interpreting field observations. 

Most scorpaenid fishes have a sedentary adult stage with dispersal largely confined to the 

pelagic larval and juvenile stages. The descriptions of various patterns of adult population 

genetic structure have allowed us to infer characteristic patterns of larval dispersal, identify 

geographic or oceanographic barriers to dispersal, and make management recommendations 

regarding population connectivity and appropriate units of management. In a recent book 

chapter (Gunderson and Vetter 2006), I proposed four types of metapopulation structure that 

might be expected in sedentary groundfish species with various pelagic larval dispersal strategies 

(Figure 1). Possible patterns range from broadly dispersing species with no genetic structure to 

non-dispersing species with virtually closed populations and a high degree of genetic structure. 

The shortspine thornyhead (Sebastolobus alascanus) and the longspine thornyhead (S. altivelis) 

produce eggs and have mesopelagic juvenile stages that can last more that a year. They are 

thought to be an example of broad dispersal and recruitment from a common larval pool 

(Figure 1, far left). In this case there is little to no population genetic structure in mitochondrial 

control region DNA (Stepien et al. 2000). A study of population genetic structure in the broadly 

distributed rosethorn rockfish (Sebastes helvomaculatus) shows mesoscale population genetic 

structure with a separation that corresponds with the divergent flows of the Alaska Gyre and the 

California Current (Rocha-Olivares and Vetter 1999) and Figure 2. In this scenario larvae are 

thought to be advected away from their natal habitat but are dispersed via oceanographic features 

(Figure 1, middle left). In other species of rockfishes larvae remain nearshore and may never 

enter advective currents. Studies of copper rockfish (S. caurinus), grass rockfish (S. 

rastrelliger), and brown rockfish (S. auriculatus) all seem to show that in nearshore kelp habitats 

larvae may avoid offshore advective flows and may be largely self-recruiting but with limited 

diffusive dispersal of larvae to neighboring rocky habitats (Buonaccorsi et al. 2002, 2004, 2005). 

This dispersal strategy produces a series of small, stepping-stone metapopulations characterized 

by a strong isolation-by-distance genetic structure (Figure 1, middle right). The pattern of very 

limited dispersal (Figure 1, far right) has not been observed in scorpaenid fishes but has been 

observed in the surfperches (Embiotocidae), which produce large precocious juveniles that do 

not have a pelagic dispersal phase (Bernardi 2000). 

Population genetic studies of rockfishes and related scorpaenid fishes have been used to 

inform management decisions in several important ways: 1) defining appropriate management 

68
Figure 1. Propagule dispersal models and population structure: (far left) broad advective dispersal typical 

of species with extended early planktonic stages; (middle left) mesoscale dispersal typical of 

species whose early life stages develop in the plankton but are retained in an oceanographic 

feature such as the Southern California eddy; (middle right) diffusive dispersal describes 

nearshore species whose eggs and larvae remain in nearshore boundary layers subject to diffusive 

rather than advective flows; and (far right) non-dispersing describes species that produce large 

precocious young capable of swimming and not subject to passive dispersal in currents (after 

Gunderson and Vetter 2006). 

units for stock assessments, 2) defining distinct population segments (DPSs) for Endangered 

Species Act (ESA) listings, and 3) estimating realized larval dispersal distances and the design of 

marine protected area (MPA) networks. The study of copper rockfish (Buonaccorsi et al. 2002) 

formed the basis for declaring Puget Sound populations of copper rockfish as a DPS under the 

procedures of the ESA. Avoiding potential pitfalls in the design of MPAs is illustrated by a 

recent study of grass rockfish (Buonaccorsi et al. 2004). Here we showed that, for nearshore 

rockfish species targeted for management via MPAs, the genetic signal of isolation by distance 

could be used to calculate mean dispersal distances (Figure 3). The finding that these species 

have mean dispersal distances on the order of tens of kilometers is quite remarkable and suggests 

that many small MPAs spaced over shorter distances rather than a few large reserves might be 

more effective for the maintenance of population connectivity. It is politically unrealistic for 

MPAs to be spaced every 10 km. This practical reality suggests that intervening fished areas 

must be managed such that some individuals live to reproduce and act as multigenerational 

stepping stones that can provide genetic connectivity between MPAs. 

69
Figure 2. Map of study area showing the sampling stations (1–12) for rosethorn rockfish. In each 

putative population, pie charts represent the frequency of 10 haplotype classes (A–J) defined by 

ignoring autapomorphic sites. Classes A and I (underlined) belong to clade A. Classes B–H and J 

(boldface) belong to group B. Unique haplotypes can be in either one. In each population solid 

circles in the minimum spanning network indicate the presence of a given haplotype. The major 

oceanographic features of the northeast Pacific are also presented (after Rocha-Olivares and 

Vetter 1999). 

Figure 3. Comparison of isolation-by-distance coastal regression slopes for grass rockfish and copper 

rockfish. For the purpose of comparing slopes the y-intercept was set to zero (after Buonaccorsi 

et al. 2004). 

70
References 

Bernardi, G. 2000. Barriers to gene flow in Embiotoca jacksoni, a marine fish lacking a pelagic larval 

stage. Evolution 54:226–237. 

Buonaccorsi, V. P., C. A. Kimbrell, E. A. Lynn, and R. D. Vetter. 2002. Population structure of copper 

rockfish (Sebastes caurinus) reflects postglacial colonization and contemporary patterns of larval 

dispersal. Can. J. Fish. Aquat. Sci. 59:1374–1384. 

Buonaccorsi, V. P., M. Westerman, J. Stannard, C. Kimbrell, E. Lynn, and R. D. Vetter. 2004. 

Molecular genetic structure suggests limited larval dispersal in grass rockfish, Sebastes 

rastrelliger. Mar. Biol. 145:779–788. 

Buonaccorsi, V. P., C. A. Kimbrell, E. A. Lynn, and R. D. Vetter. 2005. Limited realized dispersal and 

introgressive hybridization influence genetic structure and conservation strategies for brown 

rockfish, Sebastes auriculatus. Conserv. Genet. 6:697–713. 

Gunderson, D., and R. D. Vetter. 2006. Temperate rocky reef fishes. In J. P. Kritzer and P. F. Sale 

(eds.), Marine metapopulations. Academic Press, Boston. 

Lenarz, W. H., D. A. Ventresca, W. M. Graham, F. B. Schwing, and F. Chavez. 1995. Explorations of 

El Niño events and associated biological population dynamics off Central California. CalCOFI 

Rep. 36:106–119. 

Narum, S. R., V. P. Buonaccorsi, C. A. Kimbrell, and R. D. Vetter. 2004. Genetic divergence between 

gopher rockfish (Sebastes carnatus) and black-and-yellow rockfish (Sebastes chrysomelas). 

Copeia 2004(4):926–931. 

Rocha-Olivares, A., C. A. Kimbrell, B. J. Eitner, and R. D. Vetter. 1999a. Evolution of a mitochondrial 

cytochrome b gene sequence in the species-rich genus Sebastes (Teleostei, Scorpaenidae) and its 

utility in testing the monophyly of the subgenus Sebastomus. Mol. Phylogenet. Evol. 

11:426–440. 

Rocha-Olivares, A., R. H. Rosenblatt, and R. D. Vetter. 1999b. Molecular evolution, systematics and 

zoogeography of the rockfish subgenus Sebastosomus (Sebastes, Scorpaenidae) based on 

mitochondrial cytochrome b and control region sequences. Mol. Phylogenet. Evol. 11:441–458. 

Rocha-Olivares, A., and R. D. Vetter. 1999. Effects of oceanographic circulation on the gene flow, 

genetic structure, and phylogeography of the rosethorn rockfish (Sebastes helvomaculatus). Can. 

J. Fish. Aquat. Sci. 56:803–813. 

Stepien, C. A., A. K. Dillon, and A. K. Patterson. 2000. Population genetics, phylogeography, and 

systematics of the thornyhead rockfishes (Sebastolobus) along the deep continental slopes of the 

North Pacific Ocean. Can. J. Fish. Aquat. Sci. 57:1701–1717. 

Taylor, C. A. 1998. Phylogenetics and larval identification of rockfishes (genus Sebastes) using 

mitochondrial DNA techniques. Master’s thesis. San Diego State Univ., San Diego, CA. 

71
72
73

Appendix A: Rockfish Microsatellite Loci 

in GenBank 

GenBank is a collection of publicly available DNA sequences, which is maintained by 

the National Center for Biotechnology Information, a part of the National Institute of Health. 

The following species in the genus Sebastes are identified by scientific name in Table A-1: 

acadian redfish (S. fasciatus)

black rockfish (S. melanops) 

blue rockfish (S. mystinus) 

bocaccio (S. paucispinus) 

brown rockfish (S. auriculatus) 

canary rockfish (S. pinniger) 

China rockfish (S. nebulosus) 

copper rockfish (S. caurinus) 

darkblotched rockfish (S. crameri) 

deepwater redfish (S. mentella) 

dusky rockfish (S. ciliatus) 

grass rockfish (S. rastrelliger) 

kitsunemebaru (S. vulpes) 

Schlegel’s black rockfish (S. schlegeli) 

darkbanded rockfish (S. inermis) 

Norway or small redfish (S. viviparus) 

ocean perch (S. marinus)

Pacific ocean perch (S. alutus) 

quillback rockfish (S. maliger) 

redbanded rockfish (S. babcocki) 

rougheye rockfish (S. aleutianus) 

shortraker rockfish (S. borealis) 

silvergray rockfish (S. brevispinis) 

splitnose rockfish (S. diploproa) 

tiger rockfish (S. nigrocinctus) 

togotto-mebaru (S. joyneri) 

vermilion rockfish (S. miniatus) 

widow rockfish (S. entomelas) 

yellowtail rockfish (S. flavidus) 

yelloweye rockfish (S. ruberrimus) 

goldeye rockfish (S. thompsoni) 
Table A-1. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 indicates 

dash (—) indicates no data. If the variability of the locus was tested in other species, the results are noted here. 

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Sal1 CCAAGTGTTTGTTTGAT 

ATGCTCAGCACAGTAATTA 

tet S. alutus 0.87 Miller et al. 2000 AF153595 Linked to Sal6; 

species tested 

Sal2 CTCTGTTTGGTATTTAACCTG 

GTAAAAGGAATCCACCTAAC 

tet 0.78 Miller et al. 2000 AF153596 Variable in 11 o

Sal3 TCCCCATAAAGACAAACTGTAGC 

ACAGCAGACAGCAGTTCT 

pent 0.83 Miller et al. 2000 AF153597 Variable in all 1

S. auriculatus, S

S. entomelas, S. S. melanops, S. 

S. babcocki, S. aS. mentella

Sal4 GGTGATATGATAGATTGCAG 

AATGATGGACGGATGTATAG 

tet 0.79 Miller et al. 2000 AF153598 Variable in 9 of 

Sal5 GGTGCGAGTGGAAATAATCT 

AATAAAGTTTACTATCTATC 

tet 0.71 Miller et al. 2000 AF153599 Redesigned F pr

ATTCAAGGAC

polymorphic in 1–2 nonoverlapp

Sal6 GGGCGTCCAGGGTTTCCTC 

AATCACCACATGCATCA 

di 0.50 Miller et al. 2000 AF153595 Linked to Sal1; 

species 

Seb9 AAGGCTGACTCTGAGTGGGA 

CTCTGAGTCTATGTATCTGGCT 

di See comments 0.48–

0.96 

Roques et al. 1999 

AF103018 Designed from D

S. fasciatus, S. m

S. viviparus

Seb25 CAGCTTGACGTGAGGGGA 

GTGCCTGTTTAGGGTGTTCTT 

di See comments 0.71–

0.96 

Roques et al. 1999 

AF103023 Designed from D

S. fasciatus, S. m

S. viviparus

Seb30 CTGTTGGACAGATAAAGACGC 

GGTGATATTGCTGCTGGTAGAT 

di See comments 0.60–

0.90 

Roques et al. 1999 

AF103025 Designed from D

S. fasciatus, S. m

S. viviparus

Seb31 GTGAGACCAGTAATAAGGGCA 

TACTTCTCGACTGTGGTG 

di See comments 0.67–

0.93 

Roques et al. 1999 

AF103019 Designed from D

S. fasciatus, S. m

S. viviparus

74
Table A-1 continued. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 

zero and a dash (—) indicates no data. If the variability of the locus was tested in other species, the results are note

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Seb33 CAGATGTTGGTAGACGCAAGCA 

AGTCCAGTGTCCATCCTCCTT 

di See comments 0.89–

1.00 

Roques et al. 1999 

AF103020 Designed from D

S. fasciatus, S. m

S. viviparus

Seb37 GTACAGTCCATTCAGCTTTGA 

AGGGTGTGTGGAAGAAATAGT 

di See comments 0.61–

0.89 

Roques et al. 1999 

AF103022 Designed from D

S. fasciatus, S. m

S. viviparus

Seb45 GAGGAGGAAAAGACTGGACAGA 

GAAAGATGGTGAGCAGCGATGA 

di See comments 0.54–

0.73 

Roques et al. 1999 

AF103021 Designed from D

S. fasciatus, S. m

S. viviparus

Seb46 GCTGATGTTGCTCCTAAAGAA 

CTCTTCATGTCAATCCTGCCT 

di See comments 0.67–

0.87 

Roques et al. 1999 

AF103024 Designed from D

S. fasciatus, S. m

S. viviparus

Sma1 AAGTGAGTGGGTTTCATTGAGATAC 

TACCTGTGTCAGCAAGTAAACTCTG 

di S. maliger — Wimberger et al. 

1999 

AY654593 Appears to amp

S. caurinus, S. a

S. ciliatus, S. boS. paucispinis, a

Sma2 TTACTTGTTTTCTTTGTCTCATGTGG 

CACAGGACTATCAGCAGGGAAG 

di S. maliger 0.47 Wimberger et al. 

1999 

AY654594 Variable in S. ca

S. ciliatus, S. boS. paucispinus, 

Sma3 GCAGACTTACAGCGGTTTCAC 

ACCATCCAGTCATACGAGCAC 

di S. maliger 0.68 Wimberger et al. 

1999 

AY654595 Variable in S. m

S. ruberrimus, SS. borealis, S. aand S. alutus

Sma4 CATAACATATGATGGAAAATAAAACCC 

CAAATTGCCCCCACTGAAG 

tri S. maliger 0.66 Wimberger et al. 

1999 

AY654596 Variable in S. m

S. auriculatus, SS. paucispinis, a

Sma5 ATTCCCACCCACTCACACTT 

GAGATTTCTGGAGTCCACGC 

di S. maliger 0.38 Wimberger 

et al. 1999 

AY654597 Variable in S. m

S. borealis, S. aand S. alutus

Sma6 ATGATGAAGTGTCGGTTGCTC 

AAGGGAGGGCACCCCAAAC 

di S. maliger 0 Wimberger et al. 

1999 

AY654598 Not enough info

variability in oth

Sma7 CATAGGTCATTTCTCAAAGGTGTG 

GAGAAACAAACAGGAACTGAGAGAG 

di S. maliger 0 Wimberger et al. 

1999 

AY654599 Variable in S. m

S. borealis, S. aS. alutus, and H

75
Table A-1 continued. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 

zero and a dash (—) indicates no data. If the variability of the locus was tested in other species, the results are note

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Sma8 TCACACATCGTCTGGCTATTTC 

AATTCTAAAGTCTATGGGGACACG 

di S. maliger 0 Wimberger et al. 

1999 

AY654600 Not enough info

variability in oth

Sma9 GATCACCGTTATTGCTTGAGTG 

CTTTTAACGGTTTTTACCGATAGC 

di S. maliger 0 Wimberger et al. 

1999 

AY654601 Not enough info

variability in oth

Sma10 CAGCAGCATTTGAAGCACATC 

CACCAGTGGAACACACGCAC 

di S. maliger 0.79 Wimberger et al. 

1999 

AY654602 Variable in S. m

S. auriculatus, SS. aleutianus, S. and Helicolenus 

Sma11 AATATGAGGACGGGCAACG 

TAGTAGGAGTGAGCATCGTACCAG 

di S. maliger 0 Wimberger et al. 

1999 

AY654603 Variable in S. ca

S. borealis, S. aand S. alutus

Sma12 AACTGAGAAGAAAAGGGAGCG 

GACAAAGTGGAGCAGAGAGTCC 

irreg. S. maliger 0 Wimberger et al. 

1999 

AY654604 Not enough info

variability in oth

Sme1 GCAACAACTCTGGCACAC 

GTGGAAAAAATGTCCTCCTC 

tet S. melanops — ADFG unpubl. 

data 

AF141663 Primer sequence

GenBank 

Sme2 TGCCAGCTCTTTACTGTTATT 

CATCCTTCACTCCTTCACTC 

tet S. melanops — ADFG unpubl. 

data 

AF142484 Primer sequence

GenBank 

Sme3 CAGCAAGGTAAGAGTAAACTGC 

GCTTTCTGGAGAAGTCGAGT 

tet S. melanops — ADFG unpubl. 

data 

AF142485 Primer sequence

GenBank 

Sme4 GCAGCCAACTACTAACTAACAGC 

TTGCACGCTTTGCTAATGTA 

tet S. melanops — ADFG unpubl. 

data 

AF142486 Primer sequence

GenBank 

Sme5 TGTTTTGCACTATGGAACTGT 

CCAAATTCATCTCAGAACTCTC 

tet S. melanops — ADFG unpubl. 

data 

AF142487 Primer sequence

GenBank 

Sme6 ATTCAAACCTTAGCCACAGT 

CACGGGGATAGATAAAGC 

tet S. melanops — ADFG unpubl. 

data 

AF142488 Primer sequence

GenBank 

Sme7 GGAACTGTGATGCTGGAAAC 

CAGGGAAAACCCCAAACTAT 

tet S. melanops — ADFG unpubl. 

data 

AF142489 Primer sequence

GenBank; ampl

(Young et al. un

Sme8 GGAACTGTGATGCTGGAAAC 

GGGTCAACTATGATGAACGG 

tet S. melanops — ADFG unpubl. 

data 

AF142490 Primer sequence

GenBank 

Sme9 TGATGCACAACACTAAAACAAG 

TCCCTTGGGATCAATAAAGT 

tet S. melanops — ADFG unpubl. 

data 

AF142491 Primer sequence

GenBank 

76
Table A-1 continued. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 

zero and a dash (—) indicates no data. If the variability of the locus was tested in other species, the results are note

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Sme10 TGTTCAAAGGTCAAGGTCACT 

GTGTCGCTGTTTCCACTGT 

tet S. melanops — ADFG unpubl. 

data 

AF142492 Primer sequence

GenBank 

Sme11 GACAATAACCTCCCATGTCTG 

CCCTCGGGATCAATAAAGT 

tet S. melanops — ADFG unpubl. 

data 

AF142493 Primer sequence

GenBank 

Sme12 TGAATTTCCCTCAGGATCAA 

ATGGGAGAACCGTGATCATA 

tet S. melanops — ADFG unpubl. 

data 

AF142494 Primer sequence

GenBank 

Sme13 AACGCTCCGTTTTAGACAGAC 

ATGGAACTGTGTCGCTGTAAA 

tet S. melanops — ADFG unpubl. 

data 

AF142495 Primer sequence

GenBank 

Sme14 TTATACAAAGGACCTCCCCC 

TTCAGATGTCAGGTCACCCT 

tet S. melanops — ADFG unpubl. 

data 

AF142587 Primer sequence

GenBank 

Sme15 TTGAATTTCCCTCTGGATCA 

TGTCGCTTCACACAGGTAGA 

tet S. melanops — ADFG unpubl. 

data 

AF142496 Primer sequence

GenBank 

Spi4 GTCAGAGTTACATAGCGTGCCCT 

GCACTATGGAACTGTGATTCTGGA 

tet S. pinniger 0.86 Gomez-Uchida 

et al. 2003 

AY192599 Variable in S. ru

S. crameri, S. diS. maliger, S. niand S. melanops

Spi6 AGTGGAAGTGAACACGTAGGTTAG 

CACTATGGAACTGTGATGCTGG 

tet S. pinniger 0.94 Gomez-Uchida 

et al. 2003 

AY192600 Variable in S. ne

S. caurinus, S. cS. mystinus, S. mS. miniatus, S. mS. auriculatus

Spi7 CTGTCTTTGTCACTGTAATCATAGTCA 

GATCTGGAGTCAGATGGATAGATG 

tet S. pinniger 0.07 Gomez-Uchida 

et al. 2003 

AY192601 Departure from 

possible null all

S. mystinus, S. m

Spi9 CATTCTTACGCACCGATCTG 

GAGTTTTCTTCATCTCCTTGTATTTT 

tet S. pinniger 0.11 Gomez-Uchida 

et al. 2003 

AY192602 Departure from 

possible null all

S. mystinus, S. mS. flavidus

Spi10 TTTGATGGCCTGAAACTGAG 

GTTCAAACACACAGTAGCTAAACTATC

tet S. pinniger 0.77 Gomez-Uchida 

et al. 2003 

AY192603 Variable in S. ne

S. caurinus, S. cS. mystinus, S. mS. miniatus, S. mS. auriculatus

77
Table A-1 continued. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 

zero and a dash (—) indicates no data. If the variability of the locus was tested in other species, the results are note

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Spi12 GGGAGTATGAGAGAGGATCATGC 

CAATACGCCTCCAAGCTAGATC 

di S. pinniger 0.40 Gomez-Uchida 

et al. 2003 

AY192604 Variable in S. ne

S. caurinus, S. cS. maliger, and 

Spi14 CCAGCAGCTTGGATAGATAGTTAG 

GCTGGAAATACATTACACTGTTTAGTC

tet S. pinniger 0.91 Gomez-Uchida 

et al. 2003 

AY192605 Variable in S. ni

Spi17 TGTTGGTTAATTACATGCTGGA 

TATTCCCAGCAGCTTGGATA 

tet S. pinniger 0.91 Gomez-Uchida 

et al. 2003 

AY192606 Didn't amplify i

Spi18 GTACAAGAAGTTAAAAAGCAAGTTGCAG

GCGTGTTTGCACTAACCTTTGT 

tet S. pinniger 0.76 Gomez-Uchida 

et al. 2003 

AY192607 Variable in S. ca

Sra.5-9 CTTGCTACTGCAGAGTGACTAC 

CCTCATAATAGAGCTTGTAATAACG 

di S. rastrelliger 0.35 Westerman et al. 

2005 

AF269052 

Sra.5-32 GTGAGGAGGTTAAGATGACCG 

AGCACACACGTCTAAAACACT 

di S. rastrelliger — Westerman et al. 

unpubl. data 

AF269053 Primer sequence

GenBank 

Sra.6-52 ATCGGGTGTCCTTCAGTCAG 

CGCTTTAATTTCCCGTTGAA 

di S. rastrelliger — Westerman et al. 

unpubl. data 

AF269057 Primer sequence

GenBank 

Sra.7-2 GAACATCCCTCCTTCCGACGC 

GTCAAACAACTGCAGAATGTTCG 

di S. rastrelliger 0.43 Westerman et al. 

2005 

AF269054 

Sra.7-7 GCATGAAAGTGTATGAAAGGC 

CATGTGATTCTGTGTCTAACTGAG 

di S. rastrelliger 0.72 Westerman et al. 

2005 

AF269055 

Sra.7-25 GACCTTTCCCTGAACACACTCG 

CAAGAGGCGGTGGTGCTGATGG 

di S. rastrelliger 0.85 Westerman et al. 

2005 

AF269056 

Sra.11-

103 

CTTGCAGGTAACGGGAAGG 

GGCTGATGACATTGCAACCTTG 

tri S. rastrelliger — Westerman et al. 

2005 

AF269058 

Sra.15-8 GGAGATGTGCGTGGCTCGTCTGG 

GGGTTTACTCATTGTAGAC 

tet S. rastrelliger 0.87 Westerman et al. 

2005 

AF269059 

Sra.15-

23 

CCCCAAATACTGTCTTGCCAG CCGTCTTGATCCAGATGGTACATGTC 

di S. rastrelliger — Westerman et al. 

unpubl. data 

AF269060 Primer sequence

GenBank; mono

organism 

Sra.16-5 CCATCTGTGCTGAGCTGTCACTG 

GAGAAGAGGCCTACAAGTACC 

tet S. rastrelliger 0.93 Westerman et al. 

2005 

AF269061 

Ssc1 AAGTCAACCCATCAGAAGCTGT 

GGTTGTTCCACTGTGAAGTCTG 

di S. schlegeli 0.07 Yoshida et al. 

2005 

AB058404 

78
Table A-1 continued. Rockfish (Sebastes spp.) microsatellite loci found in GenBank. HO is the observed heterozygosity: 0 

zero and a dash (—) indicates no data. If the variability of the locus was tested in other species, the results are note

Locus Primer sequences (5'–3') 

Repeat 

motif Species HO Sourcea

GenBank 

numberb C

Ssc12 AACACGCTGAACAGAGAACAAA 

GCTCCGACTATAGCTGGTCCTA 

di S. schlegeli 0.84 Yoshida et al. 

2005 

AB058405 

Ssc71 GATCCCTCCTTTCCTTTCAGGAT 

GCCTCATCGCATTGCTACAACA 

di S. schlegeli 0.43 Yoshida et al. 

2005 

AB058409 

Ssc23 AGTGTCATGCCCTCTTCCAG 

CACTCGGCATTCTCACCTCA 

di S. schlegeli 0.90 Yoshida et al. 

2005 

AB058406 

Ssc51 GTGCTGATGGAAAACACTACCA 

GTGACCTTTCCCTGAACACACT 

di S. schlegeli 0.89 Yoshida et al. 

2005 

AB058407 

Ssc69 GGCACCGAGCTCAACCTTACTG 

TGCTGTGACTATTTCCCTCTGGC 

di S. schlegeli 0.82 Yoshida et al. 

2005 

AB058408 

Sth 3A ATGGTGACAAGCTAGCAGTGCATTC 

GACAATGTCCATCTAGGCATGACTG 

di S. thompsoni 0.60 Sekino et al. 

2000 

AB033424 Variable in S. in

S. vulpes

Sth 3B GTCATGCCTAGATGGACATTGTCTAC 

GAGATAAGAGGAGTTTGAAGGCAGAG

di S. thompsoni 0.92 Sekino et al. 

2000 

AB033425 Variable in S. in

Sth 24 AGGACAGGATGTGCCCTTTTACCA 

GCCTCAGAGGCCGATTTCCTTATT 

di S. thompsoni 0.46 Sekino et al. 

2000 

AB033426 Variable in S. jo

Sth 37 TACAGGAAACAAGACCACGGGTACAG 

GCAACATCCCTTTAAGTCACCTGCAG 

di S. thompsoni 0.88 Sekino et al. 

2000 

AB033427 Variable in S. in

S. vulpes

Sth 45 CTGGGACCTAGCCTGATTACAGCA 

AAACTCAGCGACAGCAGACCACA 

di S. thompsoni 0.71 Sekino et al. 

2000 

AB033428 Variable in S. in

Sth 56 CAGCAGCTCCAGTTCAGTGTATGT 

GGATTGATCCTCATGTGGTGCTCT 

di S. thompsoni 0.74 Sekino et al. 

2000 

AB033429 Variable in S. in

S. vulpes

Sth 86 ACCATCACCCACTGTAAACTGCA 

TACCAGGAAACGTCGTGTCTCAA 

di S. thompsoni 0.82 Sekino et al. 

2000 

AB033430 Variable in S. in

Sth 91 TTTCGATATGCTTCGCTAGGGTGTT 

CCATCAAACTGCACCAACAAAGACA 

di S. thompsoni 0.30 Sekino et al. 

2000 

AB033431 Variable in S. in

a ADFG (Alaska Department of Fish and Game). Unpubl. data. Fifteen microsatellite loci including tri- and tetranucleotide loci clon

(Available from Alaska Dept. of Fish and Game, 333 Raspberry Rd., Anchorage, AK 99518.) Gomez-Uchida, D., E. A. Hoffman, W. R. Ardren, and M. A. Banks. 2003. Microsatellite markers for the heavily exploited canar

other rockfish species. Mol. Ecol. Notes 3:387–389. Miller, K. M., A. D. Schulze, and R. E. Withler. 2000. Characterization of microsatellite loci in Sebastes alutus and their conserv

rockfish species. Mol. Ecol. 9:240–242. 

79
Roques, S., D. Pallotta, J.-M. Sevigny, and L. Bernatchez. 1999. Isolation and characterization of polymorphic microsatellite mar

redfish (Teleostei: Scorpaenidae, genus Sebastes). Mol. Ecol. 8:685–702. Sekino, M., N. Takagi, M. Hara, and H. Takahashi. 2000. Microsatellites in rockfish Sebastes thompsoni (Scorpaenidae). Mol. EWesterman, M. E., V. P. Buonaccorsi, J. A. Stannard, L. Galver, C. Taylor, E. A. Lynn, C. A. Kimbrell, and R. D. Vetter. 2005. C

characterization of novel microsatellite DNA markers for the grass rockfish, Sebastes rastrelliger, and cross-species amplification Mol. Ecol. Notes 5:74–76. 

Westerman, M. E., V. P. Buonaccorsi, and R. D. Vetter. Unpubl. data. Isolation and characterization of novel polymorphic micro

grass rockfish, Sebastes rastrelliger. Cited in http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=10179897 [accWimberger, P., J. Burr, A. Gray, A. Lopez, and P. Bentzen. 1999. Isolation and characterization of twelve microsatellite loci for r

Biotechnol. 1:311–315. 

Yoshida, K., M. Nakagawa, and S. Wada. 2005. Multiplex PCR system applied for analyzing microsatellite loci of Schlegel’s bla

schlegeli. Mol. Ecol. Notes 5:416–418. 

Young, S. F., A. W. Pichahchy, and J. F. Von Bargen. Unpubl. data. A microsatellite DNA analysis of population subdivision in y

(Sebastes flavidus) along the Pacific coast of North America. (Available from S. F. Young, Washington Dept. of Fish and Wildlife

b The GenBank database is online at http://www.ncbi.nlm.nih.gov/GenBank [accessed 27 October 2006].

80
Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC79 Lawson, P.W., E.P. Bjorkstedt, M.W. Chilcote, C.W. Huntington, J.S. Mills, K.M.S. Moore, T.E.

 Nickelson, G.H. Reeves, H.A. Stout, T.C. Wainwright, and L.A. Weitkamp. 2007. Identification of 

 historical populations of Coho salmon (Oncorhynchus kisutch) in the Oregon coast evolutionarily significant 

 unit. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-79, 129 p. NTIS number pending.

78 Ruckelshaus, M.H., K.P. Currens, W.H. Graeber, R.R. Fuerstenberg, K. Rawson, N.J. Sands, and J.B. 

Scott. 2006. Independent populations of Chinook salmon in Puget Sound. U.S. Dept. Commer., NOAA 

Tech. Memo. NMFS-NWFSC-78, 125 p. NTIS number PB2007-104920.

77 Sloan, C.A., D.W. Brown, G.M. Ylitalo, J. Buzitis, D.P. Herman, D.G. Burrows, G. Yanagida, R.W. 

Pearce, J.L. Bolton, R.H. Boyer, and M.M. Krahn. 2006. Quality assurance plan for analyses of environmental samples for polycyclic aromatic compounds, persistent organic pollutants, fatty acids, stable isotope ratios, 

lipid classes, and metabolites of polycyclic aromatic compounds. U.S. Dept. Commer., NOAA Tech. Memo. 

NMFS-NWFSC-77, 30 p. NTIS number PB2007-104919.

76 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. U.S. Dept. Commer., NOAA Tech. 

Memo. NMFS-NWFSC-76, 182 p. NTIS number PB2007-104918. 

75 Keller, A.A., B.H. Horness, V.J. Tuttle, J.R. Wallace, V.H. Simon, E.L. Fruh, K.L. Bosley, and D.J.

 Kamikawa. 2006. The 2002 U.S. West Coast upper continental slope trawl survey of groundfish resources

 off Washington, Oregon, and California: Estimates of distribution, abundance, and length composition. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-75, 189 p. NTIS PB2006-111432.

74 Pool, S.S., and R.D. Brodeur. 2006. Neustonic mesozooplankton abundance and distribution in the northern California Current, 2000 and 2002. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-74,

 76 p. NTIS PB2006-109275.

73 Myers, J., C. Busack, D. Rawding, A. Marshall, D. Teel, D.M. Van Doornik, and M.T. Maher. 2006.

 Historical population structure of Pacific salmonids in the Willamette River and lower Columbia River

 basins. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-73, 311 p. NTIS PB2006-109278.

72 Keller, A.A., E.L. Fruh, K.L. Bosley, D.J. Kamikawa, J.R. Wallace, B.H. Horness, V.H. Simon, and 

V.J. Tuttle. 2006. The 2001 U.S. West Coast upper continental slope trawl survey of groundfish resources 

off Washington, Oregon, and California: Estimates of distribution, abundance, and length composition. U.S.

 Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-72, 175 p. NTIS PB2006-109277

71 Nash, C.E., P.R. Burbridge, and J.K. Volkman (editors). 2005. Guidelines for ecological risk assessment of marine fish aquaculture. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-71, 90 p. 

NTIS PB2006-109287.

Most NOAA Technical Memorandums NMFS-NWFSC are available online at the

Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov).