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Identification and Systematics of Rockfishes (Sebastes)
in the Northeast Pacific Ocean

(Quarterly Report for Jan-Feb-Mar 2001)

by Art Kendall and Jay Orr

  picture of rockfish

With slightly over 100 species worldwide and 33 species off Alaska, identifying rockfishes is an ongoing challenge to fishery biologists, fishermen, and casual observers alike.  Although many rockfish species were described in the late 1800s,  new species are still being found today.  This is partly because the characters that distinguish the species are often subtle and confusing.  For convenience, several similar appearing species frequently are lumped in fisheries catch statistics.  Nevertheless, each species has unique biological characteristics and should be managed separately from all other species.

Populations of many rockfish species in the Northeast Pacific Ocean are severely depleted, and rebuilding efforts are called for. For such efforts to be successful, the life history characteristics of each species must be well understood.  This requires that all life history stages—larval, juvenile, and adult—of the species can be accurately identified.  While accurate identification of adults of some rockfish species is difficult, accurate identification of larvae is rarely possible at all.

In response to the need for more accurate identification of rockfishes, scientists at the Alaska Fisheries Science Center (AFSC) have undertaken a variety of collaborative approaches to studying rockfish of the Northeast Pacific.  This article describes several of those studies, the progress that has been made to date, and some of the challenges that remain.

The Rockfish Database

Art Kendall and Jay Orr of the Center’s  Resource Assessment and Conservation Engineering (RACE) Division have been conducting investigations on various aspects of the taxonomy and systematics of Sebastes for several years.  In the process of these studies, they accumulated a large amount of information on characters of Sebastes species worldwide, which they gleaned from the literature used to define the species and subgenera of Sebastes. The primary sources of information on adult Sebastes species were original descriptions and Cramer (1895), Matsubara (1943), and Ishida (1994).  They also reviewed keys and other sources, such as Hitz (1965, and as updated in Hitz (1981)), Chen (1986), Ishida (1984), and Orr et al. (2000) that contained characters of many of the species of Sebastes.  They examined specimens of Sebastes from the North Atlantic, because they could not find adequate descriptions for several of their characters in the literature.  For data on larvae and juveniles, they used original descriptions and compilations of early life history information such as Okiyama (1988), Matarese et al. (1989), and Moser (1996). They also made extensive use of unpublished data and figures by Laroche, particularly for pelagic juvenile pigment.  These data were then compiled and tabulated to create a computerized rockfish database, designed and developed by Lisa Rugen, formerly with the AFSC.

The rockfish database includes data for 98 species of Sebastes, and two species of Sebastiscus with information on geographic distribution, adult morphology, meristics, and head spines. For early life history stages the database includes data on preflexion pigment patterns, postflexion larval characters, and pelagic juvenile pigment patterns.  Photographs of adult rockfish species and illustrations of larvae and juveniles are also included.  Although each datum does not presently link to a specific reference, a bibliography of the references used for the data is also presented.

The database is entered through one of seven sections:

  1. an introduction

  2. a map showing species occurring in various geographic areas

  3. a species-by-species listing of data

  4. a search form to select species having specified character states

  5. a section to compare larval and juvenile illustrations and photographs of adults of several species simultaneously

  6. a list of references used to construct the database plus other references to literature on Sebastes taxonomy and systematics

  7. an acknowledgments section where individuals and organizations who have contributed data and advice for the database are gratefully listed.

Geographic areas of occurrence

Geographic information on each species was collected from the literature and RACEBASE, the RACE Division’s survey database for the Northeast Pacific Ocean and eastern Bering Sea.  This information was binned into 28 geographic areas: 12 in the Northeast Pacific, 13 in the Northwest Pacific, 2 in the North Atlantic, and 1 in the Southern Hemisphere. These 28 areas of occurrence are labeled on an interactive map of the North Pacific Ocean, where clicking on each of the labeled regions displays a drop down list containing the names of rockfish species that occur in the region, their total number, and the options to enter the Species-by-Species section or the Compare Images section of the database.  The list of species in those subsequent sections is then limited to those species for the chosen geographic area.

Species-by-species listing of data

The Species-by-Species section of the rockfish database presents character states  for more than 100 characters displayed respectively for the database’s 100 rockfish species.  Published illustrations of larvae and juveniles and photographs of adults for each species also can be viewed in this section. By selecting from drop-down lists containing  scientific or common names or by entering a species name in an empty field, the subgenus of the species is displayed on screen along with a series of tabs representing criteria specific to the selected species.

The Species-by-Species Geographic Coverage tab leads to a map of the North Pacific, with the areas of occurrence of the selected species shown in red and labeled.  Clicking the Meristics tab displays modal counts of a number of characters for the species, such as number of spines and rays in each fin and vertebrae.  The Head Spines tab leads to a diagram of the dorsal view of a rockfish head with the spines for the particular species (as benthic juveniles) illustrated and labeled.  There is also a note on the relative strength of the head spines in adults.  The Adult Morphology section provides data on morphological features of the species such as mouth size, jaw length, gas bladder, and a color photograph of the species, if available.  Clicking the Cranial Osteology tab displays character states of several features used in early systematic analyses of Sebastes that together define the shape of the skull of the species.

The database contains five early life history tabs.  The Preflexion Pigment tab leads to section of the database containing computerized representations of pigment loci displayed on a template of a  preflexion larva. A total of  27 pigment loci have been identified on preflexion larvae. Illustrations of larvae of each species contained in the database were coded for the presence of pigment at each of these loci.  Clicking the Postflexion Larvae tab reveals information on the morphology and pigment of postflexion larvae.  There are two tabs for pigment on pelagic juveniles: Juvenile Body Pigment and Juvenile Fin Pigment.  The data for these characters come largely from tables in an unpublished manuscript by Wayne Laroche, a specialist in juvenile rockfish morphology who compiled data on juveniles and illustrated larvae and juveniles of several species of rockfish while under contract to the AFSC.  The Larval and Juvenile Images tab shows published drawings of larvae and juveniles of the selected species.  These are grouped three-to-a-page, with the stage of development, size of the specimen, and literature source of the illustration also provided. Illustrations are arranged on screen by stage of development and can be scrolled to view additional images when more than three of a species are available.  Clicking on an individual illustration brings up an enlarged image.  About 365 larval and juvenile illustrations were scanned for this portion of the database.

Search for species with selected characteristics

The Search section of the database allows searches based on known character states of a specimen through a series of drop down lists.  Once all known criteria have been entered, a click of the Search tab queries the database and retrieves the criteria searched on and a list of the species that match those criteria. (Characters in the default “any” or entered as “unknown” are not listed.)  The results of the query then lead the user to either the Species-by-Species or the Compare Images section of the database for the species meeting the selection criteria. Queries are available on adult, larval, and juvenile characters categorized similar to those used with the Species-by-Species listing of data. For example, for a query on an adult specimen,  subgenus,  geographic area, meristic data, cranial osteology, and adult morphology can be specified through a series of drop-down lists, or the characteristic can be typed in. Head spines are handled a little differently.  The eight possible head spines are designated with check boxes, which can be clicked for present (a check mark), absent (default, blank) or unknown (shaded).

The preflexion larval pigment template uses an illustration of a preflexion larva with pigment indicated at each of the 27 loci where pigment may occur. Each of the 27 loci is associated with a numbered box. The boxes are set at the default unknown condition, denoted with a question mark.  Clicking the box once turns it yellow, indicating that pigment is present at that locus. Another click leaves the box white and deletes the pigment area from the drawing, indicating that pigment is absent from that locus. Once the pigment on the drawing matches the pigment pattern of the unknown larva, a query of the database retrieves a report listing the species with that pigment pattern.

Comparing images of several species

The Compare Images section provides comparisons of illustrations of larvae and juveniles or photographs of adults of several species. Photographs of 77 species are currently in the database.   Two drop down options allow selection of species and selection of developmental stage (extrusion, preflexion, flexion or postflexion larvae, juveniles, or adults). Only one developmental stage of as many as 39 species can be selected per query. Once the selections have been made, and the View Images tab has been clicked, the screen displays the images for the selected species and stage, along with the size of the specimen (except for adults) and the source of the image.  The Compare Images function displays up to 39 images per query with a limit of 9 images per screen. Selected species for which there are no images in the database are listed at the top of the screen.  Double clicking on an image returns an enlarged image which can be moved on the screen to reveal other portions of the screen showing the rest of the selected species.  Only one image can be enlarged at a time.  Clicking the X in the upper right of the enlarged image panel returns the image to its original position and size.  Images are initially arranged alphabetically on the screen but can be rearranged by clicking the desired species name in the list under each image.  This replaces the image of the selected species for the one that was there initially; thus, one can view the same image more than once on the  screen.  Only the names of species in the original selection appear under the images.

Current and planned activities

The rockfish database will continue to develop.  The database can be used to store, search on, and display many other kinds of information on rockfishes.  Any information (text or graphic) that can be linked to a species of rockfish and is available for a reasonable number of species (e.g. genetic information) can be added.  Data on nomenclature and ecology have been tabulated and are ready to be added to the database, as well as data on ranges and frequency distributions of meristics.  The quality of the larval and juvenile images in the database needs improvement, and data in several other areas needs to be augmented.  There also are plans to convert the database to a format suitable for the World Wide Web, so it will be available to interested researchers worldwide.

Guides to the Rockfishes of the Northeast Pacific

The rockfishes of the northeast Pacific Ocean north of Mexico comprise five genera, three of which are detailed in the NOAA Technical Memorandum Guide to Rockfishes (Scorpaenidae) of the Genera Sebastes, Sebastolobus, and Adelosebastes of the Northeast Pacific Ocean by Jay Orr,  Mike Brown (also of the Center’s  RACE Division) and Dave Baker (formerly of the Center’s North Pacific Groundfish Fishery Observer Program). The guide was published first in 1998 and an updated version in 2000. The second edition of the guide contains color images of 68 species photographed under natural and electronic flash conditions in the field and includes 21 additional photographs not available when the guide was first published in 1998. Most specimens were photographed immediately after collection; 12 species photographed underwater are also included in a separate section. The second edition includes color photos of all species of Sebastes, Sebastolobus, and Adelosebastes in the U.S. waters of the Pacific Ocean, except for two species, the dwarf red rockfish, Sebastes rufinanus, and semaphore rockfish, S. melanosema, which were collected in the 1970s and known only from the type specimens. These two species are represented by line drawings, produced from published photographs of the types.

Of the guide’s excellent photographs, about 80% were provided by research fishery biologist and photographer Bob Lauth (RACE).  Other photographs were graciously contributed by Ann Cleveland (North Pacific Groundfish Fishery Observer Program), Blaise Eitner (Southwest Fisheries Science Center (SWFC)), Tony Gharrett (University of Alaska), Red Kessler (RACE), Carol Kimbrell (SWFC), Milton Love (University of California, Santa Barbara), Axa Rocha- Olivares (Scripps Institution of Oceanography (SIO)), and H. J. Walker (SIO).

Both editions present key characters useful in identifying rockfishes, including head spine characters, color notes, and meristics.  The most significant characters are highlighted directly on the photos in each species account.  Habitat information is presented for depths and geographic distribution.  Comparative information is presented in a “Similar Species” section to facilitate identification of easily confused species. Both editions of the guide are available on the AFSC Web site ( The first edition at groundfish/rockfishguide/index.htm  
is a navigable HTML document. The second edition is available in PDF format at

A History of Sebastes Systematic Studies

Other studies on the identification of rockfish species at the Center include Art Kendall’s manuscript reviewing the history of Sebastes systematic studies. The paper examines the worldwide history and status of taxonomic studies on Sebastes, and reviews the 23 subgenera that have been erected over the years.  This review of research, which includes morphological and genetic studies, provides a framework against which to evaluate studies using new genetic techniques. The manuscript is scheduled for publication in the Marine Fisheries Review (Kendall, A. W. Jr. A historical review of Sebastes taxonomy and systematics. Mar. Fish. Rev. in press).

The beauty and astonishing diversity of the rockfishes has generated both excitement and bewilderment among scientists who have studied them over the years.  Kendall strives  to capture this sense of scientific discovery as he reviews the history of the studies. He reviews the initial description in the 1770s of a species of Sebastes from the northeast Atlantic and the incredible taxonomic diversity of the genus as more and more species were discovered in Northeast Pacific waters in the late 1800s.  The paper examines the many taxonomic problems the genus Sebastes presents.  For example, early efforts to understand relationships among the species resulted in the erection of several subgenera.  Some biologists accepted these subgenera while others did not.  This generated heated debates in the scientific literature of the late 1800s, but did little to advance our understanding of the relationships among these fishes.  In the mid- 1900s, new genetic techniques were applied to the taxonomy of rockfishes, and progress in understanding population structure of some species was developed.  However, relationships among most of the species within the genus remain elusive even today.  The position of the genus within the order Scorpaeniformes, as well as the limits of the genus and the validity of some species remain unresolved. Ongoing genetic and traditional morphological research offers promise to resolve these problems, but the incredible diversity and wide geographic range of the genus make this an enormous task.

Systematics of the Dusky Rockfishes (Sebastes ciliatus)

picture of light and dark dusky rockfishes

Light (above) and dark dusky rockfishes

Jay Orr and Jim Blackburn (Alaska Department of Fish and Game) have completed a manuscript on the recognition of the light and dark dusky rockfishes as distinct species, based on morphology. Orr also has collaborated with molecular biologists Paul Bentzen (University of Washington (UW)),   J. Andres Lopez (UW), and Peter Wimberger (University of Puget Sound) on studies of the mitochondrial and microsatellite DNA of the two species.  The manuscript describing the two species and presenting taxonomic conclusions will be submitted in 2001.

The two species have been confused by ichthyologists and fishery biologists since their original description.  Both were described in the early 1800s from dried specimens collected from the Aleutian Islands and the Kamchatka Pennisula during the Russian explorations of the mid-1700s.  The species  have recently been identified by general coloration as the light and dark dusky rockfishes.  The light dusky rockfish is a highly variable species, which ranges primarily over the outer continental shelf, while the dark dusky rockfish is a uniformly dark species that is typically found in much shallower water.  Specimens have been examined from throughout the range of both species, including the last remaining type of the ciliatus species complex.  Orr and Blackburn’s study was built upon initial collections made by Blackburn from sites around Kodiak Island, where both species were collected together.  Much additional material was collected during RACE survey cruises in the Gulf of Alaska and Aleutian Islands, where the bulk of the deeper water specimens from the margin of the continental shelf were obtained.  More shallow water specimens were collected during a survey of the inshore waters of Southeast Alaska with members of the AFSC’s Auke Bay Laboratory (ABL).  Especially important among the specimens was the collection of near-shore light duskies with dark duskies. Samples from Kamchatka and the Commander Islands and from Canada were obtained through loans from the Kamchatka Institute of Ecology in Petrapavlovsk and the British Columbia Royal Museum in Victoria, respectively.

Systematics of the Rougheye Rockfishes (Sebastes aleutianus)

Sharon Hawkins (ABL), Jon Heifetz (ABL), and Orr are conducting research into the specific status of rougheye rockfish populations.  The work was initiated by Hawkins and Heifetz as part of a population genetic study of rougheye rockfish populations of Alaska (described in the feature article “Genetic Population Structure of Rougheye Rockfish (Sebastes aleutianus) Inferred from Allozyme Variation,” AFSC Quarterly Report, July-Sept 1997).  The study found highly significant differences in genetics between fish collected from the Aleutian Islands and those collected from the Gulf of Alaska.  Jay will be contributing the morphological and nomenclatural work towards species-level recognition of these populations.

Use of Genetic Techniques to Identify Larval Sebastes

The use of traditional morphological techniques has been largely unsuccessful in identifying the species of Sebastes in plankton collections.  It is relatively easy to identify a larva as belonging to the genus Sebastes, but usually impossible to identify which of the many species it represents.  Genetic techniques which require minute amounts of tissue offer promise in resolving these identification problems.  Because such techniques generally require fresh, unpreserved material, they may not be useful with routine sampling programs, but they can help in establishing the identity of unknown specimens, whose morphology can then be described. This will allow preserved specimens from routine sampling to be identified.

Art Kendall, in collaboration with A.J. Gharrett and University of Alaska graduate student Andy Gray, has been studying the application of genetic techniques they have developed for adult Sebastes to samples of larvae.  During a 1998 field study in Southeast Alaska aboard the NOAA research vessel John N. Cobb,  Kendall, Gray, and Bruce Wing (ABL) collected Sebastes larvae with plankton nets, photographed and sketched them while fresh, and preserved them in fluid for later mitochondrial DNA (mtDNA) analysis.  A total of 67 larvae were subjected to both pigment and genetic analysis.  All larvae were small and were little developed beyond the extrusion stage.  The larvae were grouped into eight pigment groups; genetic analysis found that seven species were represented.  With few exceptions, there was poor agreement between the pigment groups and the genetic identity of these larvae.  Based on this study, identification of larvae using mtDNA analysis is effective, but identification based on pigment remains problematic.  (See: “A comparison of genetic identifications and pigment patterns of Sebastes larvae caught on NOAA ship John N. Cobb cruise 9809: AFSC Proc. Rep. 2001-02.”)

In another study, aboard the Japanese training ship Oshoro Maru in the Bering Sea during summer 1999, Kendall retrieved Sebastes larvae fresh from plankton net collections, sketched them and noted their pigment patterns, and preserved them for later mtDNA analysis in Gharrett’s laboratory.  Three species of larvae were identified genetically, S. alutus (Pacific ocean perch), S. polyspinis (northern rockfish) and S. borealis (shortraker rockfish).  These larvae were larger and better developed than those from the Cobb cruise, and were distinct morphologically.  Larvae of S. alutus were slightly larger than those of S. polyspinis, indicating that S. alutus releases larvae earlier in the year than S. polyspinis does. The morphology of none of these species was well known, and larvae of S. borealis were totally unknown.  Results of this study will lead the way toward identification of these important species in routinely collected plankton samples.

Curation of Rockfishes at the University of Washington

Most of the specimens used in the production of the rockfish guide and examined in the systematics study of dusky and rougheye rockfishes have been preserved as vouchers in the University of Washington Fish Collection. As the result of collaborative work with the collection’s curator Ted Pietsch and research associates, hundreds of specimens of most species of eastern North Pacific rockfishes have been archived and are readily available on loan for examination by researchers around the world.  Records of the cataloged specimens of rockfishes, as well as other vouchers for RACE surveys, are available through the Fish Collection site at

Literature Cited

Chen, L.  1986.  Meristic variation in Sebastes (Scorpaenidae) with an analysis of character association and bilateral pattern and their significance in species separation.  NOAA Tech. Rep. NMFS No. 45. 17 p.

Cramer, F.  1895.  On the cranial characters of the genus Sebastodes (rock-fish).  Proc. Calif. Acad. Sci., ser. 2, vol. 5, no. 1, p. 573-610, pls. 57-70.

Hitz, C. R.  1965.  Field identification of the northeastern Pacific rockfish (Sebastodes).  U.S. Dept. Interior, Fish and Wildl. Serv., Bur. Commer. Fish., Circ. 203.  58 p.

Hitz, C. R.  1981.  Field identification of northeastern Pacific rockfish (Sebastodes). Revised by K. M. Howe, Contrib. No. 11, Coop. Syst. Progr. College Fish. (Univ. Washington) and Northwest Alaska  Fish. Cent. (Natl. Mar. Fish. Serv., NOAA).

Ishida, M. 1984.  Taxonomic study of the sebastine fishes in Japan and its adjacent waters.  M. Sc. Thesis, University of Hokkaido, Hakodate. 245 p.

Ishida, M. 1994.  Phylogeny of the suborder Scorpaenoidei (Pisces: Scorpaeniformes). Bull. Nansei Natl. Fish. Res. Inst. 27: 1-112.

Laroche, W. A. in prep.  Guide to larval and juvenile rockfishes (Sebastes) of North America. 311 p.

Matarese, A. C., A. W. Kendall, Jr., D. M. Blood, and B. M. Vinter. 1989.  Laboratory guide to early life history stages of northeast Pacific fishes. U.S. Dep. Commer., NOAA Tech. Rep. NMFS Circ. 80, 656 p.

Matsubara, K.  1943.  Studies on the Scorpaenoid fishes of Japan. Anatomy, phylogeny and taxonomy, I, II.  Trans. Sigenkagaku Kenkyusyo Nos. 1 and 2.  Tokyo.  486 p.

Moser, H. G. 1996.  Scorpaenidae: scorpionfishes and rockfishes. pp. 733-795. In: H. G. Moser (ed.) The early stages of fishes in the California Current region.  CalCOFI Atlas 33.

Okiyama, M. (ed.) 1988.  An atlas of the early stage fishes in Japan.  Tokai University Press.

Orr, J. W., M. A. Brown, and D. C. Baker. 2000.  Guide to the rockfishes (Scorpaenidae) of the genera Sebastes, Sebastolobus, and Adelosebastes of the northeast Pacific Ocean, second edition. U.S. Dep. Commer.,  NOAA Tech. Memo. NMFS-AFSC-117.  47 p.