Sanctuary Integrated Monitoring Network
Monitoring Project

Long-term Monitoring of Groundfishes in the Monterey Bay National Marine Sanctuary

Principal Investigator(s)

  • Richard Starr
    California Sea Grant
  • Erica Burton
    Monterey Bay National Marine Sanctuary
  • Bob Lea
    California Department of Fish and Wildlife
  • Mary Yoklavich
    NOAA Fisheries
  • Jean DeMarignac
    Monterey Bay National Marine Sanctuary


  • SIMoN
Start Date: September 17, 2003

Because many populations of harvested fish and invertebrates are declining in number and average size despite increasingly stringent fishery regulations, we are developing a long-term monitoring plan to assess changes of benthic fishes and macroinvertebrates in the in the Monterey Bay National Marine Sanctuary (MBNMS). Of special concern in central California is the decreasing population abundance of some of the more than 60 species of Pacific rockfishes (genus Sebastes) in this region. Moreover, even though the Pacific Fisheries Management Council has developed management plans for more than 80 species, it is generally accepted that fisheries are changing populations of non-target species in ways that are not fully understood.

To develop a baseline of information, we conducted visual strip transects using the submersible Delta, to survey fishes and macroinvertebrates in selected deep, rocky continental shelf and slope habitats of the sanctuary in order to characterize and monitor benthic macrofauna and associated habitats. We also conducted opportunistic dives at locations of special interest to the sanctuary to characterize and locate potential future monitoring sites, including a shipwreck. During September 2003 and August 2004, we completed 79 submersible dives at depths ranging from 60 and 350 meters off the Monterey peninsula and Point Sur, in Soquel, Carmel and Partington canyons, and on the Montebello, a sunken oil tanker off Cambria.

We measured changes in fish species composition, size composition, and relative abundance among the different areas surveyed and also over time when comparing our data to similar data collected in 1993 and 1996. We used 82 transects off the Monterey Peninsula for a power analysis to estimate the number of transects that would be needed in the future to detect various levels of change in the mean density of fish at different confidence levels.

Summary to Date

We used 131 transects conducted in 2004 to compare groundfish abundance, size and diversity off Monterey Peninsula and Point Sur from 70 to 120 meters. The two areas were stratified by depth and generally classified as high relief or low relief. The Monterey Peninsula area has historically been fished until it was closed to fishing for rockfishes in 2002. The area of Pt Sur has been less fished because of its remoteness and relatively difficult access. It was also a unique opportunity to develop a baseline of information soon after the rockfish closure and will enable measurement of recovery of the area. Overall species diversity, abundance and sizes, were greater off Point Sur than off the Monterey Peninsula. Off the Monterey Peninsula, the shallower (70-90 m) high-relief rocky areas had lower species diversity than the deeper (90-120 m) low-relief areas. There were many places in which we observed “good rockfish habitat”, but few fish. However, at some locations, especially off Point Sur, we saw larger fish than expected based upon previous surveys.

In 2004 we revisited sites off Monterey Peninsula that were surveyed in 1993 and we compared abundance, species-habitat relationships, and species and size composition of benthic fishes. We observed relatively similar species composition. However, except for yellowtail rockfish (Sebastes flavidus) and squarespot rockfish (Sebastes hopkinsi), mean lengths of all rockfishes were greater in 2004 than in 1993.

We completed 14 submersible dives in three submarine canyons to characterize groundfish assemblages associated with the canyons. The main purposes of these dives was to assess the importance of small-scale refugia to species of benthic rockfishes in Soquel canyon in Monterey Bay; to compare fish assemblage among four depths (75, 150, 250 and 350 meters) in Partington Canyon. Additionally, we used the submersible dives in Partington canyon to search for evidence of sediment transfer in the canyon and groundtruth a seafloor habitat map, which was produced with side scan sonar during summer 2003. We conducted two dives in Carmel Canyon to establish a baseline and to explore other potential monitoring sites.

We completed eight dives on the Montebello, an oil tanker that was torpedoed by a Japanese submarine during World War II off Cambria, CA (December 23, 1941). The objective of these dives included: site reconnaissance for the potential threat posed by this oil tanker adjacent to the sanctuary; characterizing the archeological remains of the Montebello; and characterizing the fish and invertebrate fauna. The data collected during the 2003 dives were compared to data recorded during submersible dives conducted at the Montebello in 1996 to assess biological changes and hull degradation.

Monitoring Trends

  • Rockfishes were dominant at all locations. Three small rockfish species (Sebastes wilsoni, S. hopkinsi, and S. semicinctus) accounted for more than half of the fish abundance at each location. The large numbers of small rockfishes may be an important forage items for larger fishes as we saw numerous predation events on these small species.

    Evidence of regime change: in 2004, we may have observed two northern species, Puget Sound rockfish (Sebastes emphaeus) and redstripe rockfish (Sebastes proriger) rare to this area. Relative to the 1993 surveys, we saw increased numbers of small lingcod, and bocaccio and canary rockfishes which may be attributed to the colder water and recruitment success that has been reported in the last five years for those species.

  • Large groundfish species were more abundant and larger off Point Sur than off the Monterey Peninsula, except for lingcod (Ophiodon elongatus), which was more abundant at an outer ledge area off the Monterey Peninsula.

  • The large rockfish species were larger and more numerous in 2004 than in 1993, whereas the dwarf rockfish species were more abundant in 1993. This may reflect the more stringent fishery regulations that were implemented in the late 1990s.

  • The wreck of the Montebello is an artificial reef that is teeming with fishes and invertebrates, but fishing nets entangled on the wreck are still catching fish.


Submersible surveys are appropriate for determining trends in the abundance and size of fishes in the deep-water portions of the Monterey Bay National Marine Sanctuary and our sampling design was sufficiently robust to enable us to detect statistically significant changes in abundances and sizes of fishes over a ten-year time period. The power analyses we conducted off the Monterey Peninsula and the survey we conducted at the other site provide a baseline for understanding future changes in fish abundances at the depths we surveyed.

The submersible dives provided valuable ground-truthing for existing multibeam and sidescan sonar images. Most of the features on the multibeam maps were accurately positioned but occasionally features shown as hard bottom on interpreted maps were covered with sediment. Low-relief, rocky habitats were occasionally difficult to identify on the current multibeam maps of the Point Pinos and Point Sur areas.

Pending future funding, we will be able to identify long-term trends in species composition, size composition, and relative abundance of groundfish in selected areas of the sanctuary. We can then evaluate their recovery rates in areas that were historically abundant but are now depleted, and compare those with population trends of species in similar habitats that are currently abundant.

Study Parameters

  • Habitat association
  • Range/Biogeography
  • Age & Growth
  • Habitat
  • Diversity
  • Biomass
  • Trophic association
  • Abundance
  • Distribution
  • Density
  • Size structure
  • Stock assessment
  • Temperature
  • Maps
  • Substrate characterization
  • Geological characterization

Study Methods

We are using the Delta submersible to survey fishes and macroinvertebrates in selected rocky habitats on the continental shelf and slope habitats at depths between 75 and 275 meters. Our primary sampling tool for this study, the Delta, is a manned-submersible 4.6 meters in length with 19 viewports. The submersible can reach a maximum speed of 3.5 knots, dive to a depth of 360 meters, and can accommodate a crew of two; a pilot and an observer. The 110 ft R/V Velero is the launch and recovery platform for the submersible.

The submersible is equipped with 3 video cameras and one still digital camera. Two underwater video cameras and power lights are attached to the outside of the submersible. One side-looking HI-8mm video camera is mounted on the starboard-side of the submersible and one forward-facing low-light black and white digital video camera is mounted on the front of the submersible. The camera signals are recorded on mini digital videotape recorders inside the submersible. A hand-held digital camcorder and a high-resolution digital camera are available to the observer inside the submersible. The digital camera is synchronized to an externally mounted strobe on the starboard-side of the submersible.

A pair of lasers, spaced 20 cm apart, is mounted parallel to the starboard video camera, and is used as a reference to measure size of fishes, invertebrates, physical features, and distance. The laser marks on the substrate are visible to the observer and are recorded by the starboard video camera. In addition, a hand-held sonar gun is used by the observer to estimate the distance between the submersible and a particular organism or physical feature.

Submersible equipment also includes a CTD, fathometer, altimeter, compass, and a transducer that emits a sonic signal that is sensed by the tracking system of the support ship. The ship is equipped with a differential Global Positioning System (dGPS), a gyrocompass, and the Delta Oceanographics crew uses ORE Trackpoint II in combination with Winfrog, a state of the art integrated navigation and data management system that records and plots the position of the submersible every 2 seconds. In addition, constant radio contact is maintained between the submersible and the support ship. Using the navigation data, habitat maps, and feedback from the submersible, scientists on the support ship can direct the submersible to targeted areas.

We are following protocols commonly used in other submersible surveys (e.g., Pearcy et al. 1989, Stein et al 1992, Yoklavich et al. 2000, Yoklavich et al. 2002). Visual strip transects, 2 meters wide and 10 minutes in duration, are conducted from the starboard viewport. The submersible travels 1 to 2 meters above the bottom at a speed of approximately 0.5 to 1 knot, depending on conditions (e. g. current, visibility, and habitat complexity). The transect width extends from the base of the starboard-side of the submersible out to 2 meters. A trained observer, looking through 2 starboard viewports, identifies to the lowest taxon possible, counts, and estimates the size to the nearest 5 centimeters of all fishes and macroinvertebrates along the transect. The observer uses the paired lasers to estimate size of fishes where possible, and the sonar gun to determine the transect edge. The observer also remarks on substrate type, morphology, slope, and other relevant habitat information on habitat. The observer’s comments are recorded on the audio channel of the mini digital videotapes. The starboard video camera records the entire transect area except for the area directly under the submersible. However that area is visible to the observer through the lower viewport.

Habitat associated with fishes and macroinvertebrates is characterized following methods commonly used with submersible work (Stein et al 1992, Greene et al. 1999, Yoklavich et al. 2000, Yoklavich et al. 2002). Habitat type is characterized by a primary and a secondary substrate type, more than 50% and 20% of the area viewed, respectively. Substrate types include rock (exposed bedrock and >300 cm), boulder (25 to 300 cm), cobble (0.6 to 25 cm), hash and coarse sand (2-5 mm), and fine sand and mud (<2mm). When algae or sessile invertebrates cover the seafloor, substrate type is defined as organic and classified by the dominant organism. Surface morphology is described as smooth, uneven, sediment ripple or sand wave; and slope is described as low (0 to 5o), medium (5 to 30o), or high (>30o). Surface morphology and slope are also classified using the primary and secondary categories described above.

The front-facing camera is used to complement the habitat characterization from the starboard camera, because the wide angle and orientation of the front-facing camera provide a better view of the habitat associated with the observed organisms. The front-facing camera may also record schooling fish that may flee the submersible area or are above the transect.

Under normal conditions, 4 transects are completed per dive. The submersible has enough battery power to complete 4 to 5 dives per day depending on the dive duration, depth, and weather conditions. After each dive, the observer is debriefed and the videotapes and digital images and backed-up. The data from the videotapes are transcribed into a database and merged with the navigation data.

Descriptive statistics will be calculated for the entire data set, as well as for each transect, dive, location, and substrate type. Species richness, percent dominance, Shannon-Weaver diversity indices and evenness will be calculated for each location and substrate Following Shannon and Weaver (1949), Pielou (1966), Zar (1984) and Krebs (1989).

We will compare species composition using techniques such as the Percent Similarity Index (relative proportions; pair-wise comparisons between communities), or Horn’s (1966) Index of Community Similarity (community overlap). Spearman’s (1904) Rank Correlation will be used to determine if species composition is statistically dissimilar between locations or years. We will compare estimates of size composition of each species among sites and habitat types and between years using techniques such as the Kolmogorov-Smirnov goodness of fit test (Zar 1999).

We will compare relative abundance of species using a variety of paired-sample and multiple-sample techniques. For example, we will use a paired-sample t test to determine if there were differences between transects at the same location in different years. Because of the difficulties of sampling the exact transect location and habitat patches each year, however, we will also analyze our data using several different types of ANOVAs, using a balanced design and log transformation where appropriate. For example, we will conduct a factorial ANOVA using Tukey Post Hoc Multiple Comparisons to determine if there are differences in relative abundance of all fishes between years, geographic locations, substrates, or depths. We will also conduct ANOVAs on specific subsets of the data to eliminate some variables. For example, we will conduct a repeated-measures ANOVA to investigate differences in relative abundance of fishes between 1993 and 2004. These techniques have been used successfully by other researchers who have analyzed submersible surveys over multiple years (e.g. Hixon et al. 1991, Yoklavich et al. 2002)

We will conduct a power analysis to determine the number of submersible transects needed to characterize species composition and detect various levels of change over time. To accomplish this objective, we will first select parameters to test, and then conduct power analyses to determine the sample size required to detect a reasonable experimental effect with a reasonable level of power. For example, we will plot species-acquisition curves to evaluate the number of dives needed to account for various percentages of species observed in the study. We will also conduct power analyses to estimate the number of transects and/or habitat patches needed to detect various levels of probability of correctly rejecting the null hypothesis at various levels of change (e.g. number of transects needed to detect 50% change in fish density at a 5% significance level). We will conduct these analyses at each of our major sampling locations, for each year sampled.

Literature cited

Greene, H.G., M.M. Yoklavich, R.M. Starr, V.M. O’Connell, W.W. Wakefield, D.E. Sullivan, J.E. McRea, Jr. and G.M. Caillet. 1999. A classification scheme for deep seafloor habitats. Oceanologia Acta. 22(6):663-678.

Greene, H.G., M.M. Yoklavich, V.M. O'Connell, R.M. Starr, W.W. Wakefield, C.K. Brylinsky, J.J. Bizzarro, and G.M. Cailliet. 2000. Mapping and Classification of Deep Seafloor Habitats. ICES paper CM 2000/T:08. 11 pp.

Hixon, M.A., B.N. Tissot, and W. Pearcy. 1991. Fish Assemblages of Rocky Banks of the Pacific Northwest. Final Report to US Department of Interior Minerals Management Service, Camarillo, CA 93010.

Horn, H.S. 1966. Measurement of “overlap” in comparative ecological studies. American Naturalist 100:419-424.

Krebs, C. J. 1989. Ecological methodology. HarperCollins Publishers, New York, New York.

Pearcy, W.G., D.L. Stein, M.A. Hixon, E.K. Pikitch, W.H. Barss, and R.M. Starr. 1989. Submersible observations of deep-reef fishes of Heceta Bank, Oregon. Fish. Bull. 91:304-309.

Pielou, E. C. 1966. The measurement of diversity in different types of biological collections. Journal of Theoretical Biology 13: 131–144.

Shannon, C. E. and W. Weaver. 1949. The mathematical theory of communication. University of Illinois Press, Urbana Illinois.

Spearman, C. 1904. The proof and measurement of association between two things. Amer. J. Psychol. 15:72-101.

Stein, D.L., B.N. Tissot, M.A. Hixon, and W. Barss. 1992. Fish-habitat associations on a deep reef at the edge of the Oregon continental shelf. Fish. Bull. 90:540-551.

Yoklavich, M.M., G.M. Cailliet, R.N. Lea, H.G. Greene, R.M. Starr, J. deMarignac, and J. Field. 2002. Deepwater habitat and fish resources associated with the Big Creek Marine Ecological Reserve. CalCOFI Report 43: 120-140.

Yoklavich, M.M., H.G. Greene, G.M. Cailliet, D.E. Sullivan, R.N. Lea, and M. Love. 2000. Habitat associations of deep-water rockfishes in a submarine canyon: an example of a natural refuge. Fish. Bull. 98:25-641.

Zar, J. H. 1999. Biostatistical Analysis. Prentice-Hall, Upper Saddle River, New Jersey.

Figures and Images

Delta submersible prepares to dive. Photo: Schwemmer, CINMS

Except for lingcod (Ophiodon elongatus), large groundfishes densities were higher off Point Sur than off Monterey Peninsula.

Except for lingcod (Ophiodon elongatus), large groundfishes were larger off Point Sur than off Monterey Peninsula.

Groundfish abundance and diversity off Point Sur and Monterey Peninsula in August 2004.

King crabs patrolling abandoned fishing nets entangled on the Montebello.

White plummed anemones (Metridium sp.), colonized the decks of the Montebello.

Large rockfishes (S. miniatus, S.paucispinis, S. ruberrimus) at Point Sur-East.

Cowcod (Sebastes levis) above a rocky table top covered with brachiopods at Point Sur-West.

Halfbanded rockfish (Sebastes semicinctus).