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March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island

Assessment of Warty Sea Cucumber Abundance at Anacapa Island

Final Report to:

Resources Legacy Fund Foundation

Grant #13319

March, 2019

Andrew Lauermann, Heidi Lovig, Greta Goshorn

Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.org

TABLE OF CONTENTS
LIST OF FIGURES………………………………………………………………………………………………………………………..2
LIST OF TABLES …………………………………………………………………………………………………………………………3
INTRODUCTION………………………………………………………………………………………………………………………….4
BACKGROUND ……………………………………………………………………………………………………………………………4
PURPOSE…………………………………………………………………………………………………………………………………….5
OBJECTIVES ……………………………………………………………………………………………………………………………….5
SURVEY METHODS ……………………………………………………………………………………………………………………..6
ROV EQUIPMENT AND SAMPLING OPERATIONS ………………………………………………………………………..7
SUBSTRATE AND HABITAT ANNOTATION……………………………………………………………………………………8
INVERTEBRATE ENUMERATION………………………………………………………………………………………………….9
ROV POSITIONAL DATA ……………………………………………………………………………………………………………….9
RESULTS……………………………………………………………………………………………………………………………………..10
SURVEY TOTALS………………………………………………………………………………………………………………………….10
SUBSTRATE AND HABITAT………………………………………………………………………………………………………….11
INVERTEBRATE TOTALS……………………………………………………………………………………………………………..12
WARTY SEA CUCUMBERS…………………………………………………………………………………………………………….13
DISCUSSION…………………………………………………………………………………………………………………………………15
PROJECT DELIVERABLES ……………………………………………………………………………………………………………15
REFERENCES ………………………………………………………………………………………………………………………………16

LIST OF FIGURES

Figure 1. Planned transect lines placed parallel to depth contours at Anacapa Island SMR
and East Fish Camp…………………………………………………………………………………………………………6

Figure 2. Basic ROV strip transect methodology used to collect video data along the sea floor,
showing overlapping base substrate layers produced during video processing and habitat
types (hard, mixed soft) derived from the overlapping substrates…………………………………….8

Figure 3. Density of WSCs per 100m2 in each habitat type for the spring and fall at Anacapa
Island SMR and East Fish Camp. Densities represent the total number of WCSs observed per
100m2 of each habitat type……………………………………………………………………………………………..13

Figure 4. The mean density of WSC (per m2) summarized from 10 meter transect segments
across all habitats by 5 meter depth bin for each season at Anacapa Island SMR and East
Fish Camp. Error bars represent one standard error…………………………………………………………………..14

LIST OF TABLES

Table 1. Survey totals for Anacapa Island SMR and East Fish Camp, including hours of video,
total distance surveyed (kilometers), swept area of transects (hectares), and average,
minimum and maximum depth (meters) by season…………………………………………………………10

Table 2. Percentages of substrates and habitats by season at Anacapa Island SMR and East
Fish Camp. …………………………………………………………………………………………………………………….11

Table 3. Common and taxonomic (species) names of quantified invertebrates for the spring
and fall combined………………………………………………………………………………………………………….12

Table 4. The average, minimum and maximum depth, and the number of warty sea
cucumbers observed at Anacapa SMR and East Fish Camp during the spring and fall. ………13

INTRODUCTION

BACKGROUND

Warty sea cucumbers (WSC), Apostichopus parvimensis, are an important component of the
subtidal zone, feeding on benthic waste and recycling nutrients. WSCs are found in and
adjacent to rocky outcroppings from the shallow intertidal to approximately 60 m deep from
Monterey, California to Bahia Tortugas, Mexico. Within their range in Southern California
and Mexico, dive fisheries catch WSCs for export to Asian markets. Similar to other sea
cucumber fisheries around the world, demand for WSCs seems to be consistently increasing,
while the resource is becoming less abundant. This trend is also evident in California, where
landings data gathered by the California Department of Fish and Wildlife (CDFW) show that
the fishery has declined in both overall catch and catch per unit of effort (CPUE) in recent
years (State of California Fish and Game Commission, 2017).

CDFW scientists have performed SCUBA surveys since 2013 in an effort to increase their
understanding of basic life history information of the species. Results from the surveys have
indicated that WSCs form spawning aggregations each year in the spring and summer. This
coincides with a peak in the number of cucumbers harvested in commercial dive landings,
with approximately 75% of landings occurring during spring and early summer periods.
Based on these findings, the Fish and Game Commission recently adopted a seasonal closure
to protect spawning aggregations of WSCs each year from March 1-June 14.

While seasonal abundance levels have been well documented at SCUBA depths (less than 30
meters), anecdotal reports from commercial fishery participants have suggested that WSCs
display a seasonal migration from deep to shallower water for spawning. However, to what
degree they utilize deeper waters when they are not found in shallow areas or what
proportion of the population moves to shallow areas during spawning remains unknown.
Because of this, CDFW biologists are interested in gathering more data on WSC distribution
and seasonality of abundance to determine the role that deeper, unstudied areas (greater
than 30 meters) play in supporting their populations. This data may be critical, as the
increasingly high demand for WSCs coupled with the lack of information about them makes
them vulnerable to overexploitation.

The Southern California WSC dive fishery occurs near Anacapa Island State Marine Reserve
(Anacapa Island SMR). A differential in WSC densities inside and outside of this Marine
Protected Area (MPA) has been documented by previous dive studies, where WSC were
shown to be much less abundant outside of the MPA than inside (Schroeter et al., 2001,
California Department of Fish and Game, 2007, State of California Fish and Game
Commission, 2017). To better understand seasonal abundance and depth distribution inside
and outside of MPAs and to examine seasonality of abundance deeper than SCUBA depths,
Marine Applied Research and Exploration (MARE) and CDFW conducted a 2-phase
assessment around Anacapa Island in 2018.Sampling was completed using MARE’s remotely
operated vehicle, ROV Beagle. Two study sites were selected, one inside the protection of
Anacapa Island SMR and one outside of the reserve that was subject to fishing. Both sites are
adjacent to CDFW and National Park Service monitoring stations. Each site was sampled
during the spring (phase 1), and fall (phase 2) to survey both WSC spawning and non-
spawning seasons.

PURPOSE

The purpose of this study was to provide CDFW with critical information that will be used to
inform the management of the WSC dive fishery and to further understand the performance
of an MPA in relation to the fishery. Specifically, we ask whether there is evidence of a
seasonal shift in abundance between shallow well studied areas and deeper areas out to the
observed maximum depth range of the species in the study area. In addition, these data will
inform future study design by providing information related to the extent of sampling
needed to accurately characterize WSC populations in both MPAs and fished areas.

OBJECTIVES

1) Estimate WSC density and relative abundance around two study locations off
Anacapa Island during spring and fall seasons.
2) Provide spatial data to CDFW to allow examination of the distribution and depth
range of WSC inside and outside of Anacapa Island SMR.
3) Provide an archive of high quality video transects capturing ecological conditions that
can be used to inform poorly understood aspects of WSC biology (i.e. growth, size
distribution, habitat associations and movement) that are important to future
management efforts.

The following report describes the data collection and post-processing methods used for this
study. Data summary statistics are presented to highlight preliminary survey results and
general trends. A complete dataset was provided to CDFW for further analysis.

SURVEY METHODS

Phase one surveys were performed in the spring, from May 10th – 12th, 2018 and the second
phase, in the fall, from November 18th – 20th, 2018. During each phase, two study sites were
surveyed, Anacapa Island SMR and East Fish Camp around Anacapa Island in the Channel
Islands (Figure 1). Survey sites and planned transect lines were provided to MARE by CDFW.
Transect lines were placed parallel to depth contours and evenly spaced across the target
range of 15 to 60 meters depth (Figure 1). Sites and transects were chosen to target rocky
habitat although the patchy nature of the Anacapa Island reefs ensured that sufficient soft
sediment and mixed habitats were surveyed.

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 6

Figure 1. Planned transect lines placed parallel to depth contours at Anacapa Island SMR
and East Fish Camp.

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 7 ROV EQUIPMENT AND SAMPLING OPERATIONS
MARE’s ROV, the Beagle, was used
to collect data during the survey.
The ROV was operated off of NOAA’s
R/V Shearwater, a National Marine
Sanctuaries research vessel. The

ROV was flown along the pre-
planned transect lines between the

hours of 0800 and 1700. It was
flown off the vessel’s stern using a
“live boat” technique that employed
a 700 lb. depressor weight. Using
this method, the 50 meter tether
allowed the ROV pilot sufficient
maneuverability to maintain a
constant speed and a straight
course down the transect line. The ROV pilot and ship’s helm used real-time video displays
of the location of the ship and ROV to navigate.
For this survey, the Beagle was configured with a forward-facing high definition (HD) video
camera, downward-facing standard definition video camera, and forward facing HD still
camera that collected video and still imagery of WSCs and their surrounding habitats. Photos
were taken of WSCs by scientists when encountered and also automatically at approximately
30 second intervals to capture habitat and other species. The ROV’s on-screen display also
recorded time, depth, altitude, heading, temperature and range. In addition, positional
coordinates were recorded to track the position of the ROV relative to the ship in real time
and to provide the basis for determining length and area of transects for analysis.

POST-PROCESSING METHODS

All data collected by the ROV, along with subsequent observations extracted during post-
processing of the video, were linked in a Microsoft Access® database by time, which was

synced across all data streams at a one second interval. During video post-processing, a
customized computer keyboard was used to input the time of species observations and
habitat characteristics into a Microsoft Access® database.

SUBSTRATE AND HABITAT ANNOTATION

Video was reviewed for six different substrate types: rock, boulder, cobble, gravel, sand and
mud (Green et al. 1999). Each substrate was recorded as a discrete segment by entering the
beginning and ending time. Annotation was completed in a multi-viewing approach, in which
each substrate was recorded independently, capturing the often overlapping segments of
each substrate type (Figure 2). Percent by substrate represents the ratio of the transect lines
that have a given substrate compared to the total line, therefore overlapping substrates can
result in a sum greater than 100%.

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 8

Figure 2. Basic ROV strip transect methodology used to collect video data along the sea floor,
showing overlapping base substrate layers produced during video annotation and habitat
types (hard, mixed soft) derived from the overlapping substrates.

After the video review and annotation process, the substrate data were combined to create
three independent habitat categories: hard, soft, and mixed (Figure 2). Rock and boulder
were categorized as hard substrate types, while cobble, gravel, sand, and mud were
categorized as soft substrates. Hard habitat was defined as any combination of the hard
substrates, soft habitat as any combination of soft substrates, and mixed habitat as any
combination of hard and soft substrates. Habitat percentages sum to 100% and are derived
from substrate types as the proportion of the survey line that contained that specific habitat
type.

INVERTEBRATE ENUMERATION

Video was reviewed for observations of WSCs as well as the following invertebrates of
interest to CDFW scientists: other sea cucumber species, sea stars, sea urchins,
corals/gorgonians, spiny lobster, and keyhole limpets. During the review process, the
forward video camera files were reviewed, and the select macro-invertebrates were
recorded. Each invertebrate observation was entered into a Microsoft Access® database at
the one second time interval when it crossed the bottom of the viewing screen. This insured
that the positional coordinates of the observation were matched exactly with the estimated
position of the ROV.

ROV POSITIONAL DATA

Acoustic tracking systems generate numerous erroneous positional fixes due to acoustic
noise and other errors caused by vessel movement. For this reason, positional data were
post-processed to remove outliers and generate smoothed transects along each survey line
that best represent the true path of the ROV. Estimates of transect length derived from
survey lines processed using this technique have been found to have an accuracy of 1.7 ± 0.5
meters in total length when compared to known lengths between 0 and 100 meters (Karpov
et al. 2006).

ANALYSIS METHODOLOGIES

WARTY SEA CUCUMBER SUMMARIES

Data for WSCs was summarized by habitat type for each site and study season. The density
of WSCs per 100m2 in each habitat type (hard, mixed and soft) for the spring and fall at
Anacapa Island SMR and East Fish Camp were calculated using the following equation:
(Total number of WSCs per habitat type / Total m2 of each habitat type) * 100
Data for WSCs was also summarized by depth by breaking transects into 10 linear-meter
segments. Densities for each segment were calculated using the following equation:
(Total number of WSCs per 10 m segment / Total m2 of each 10 m segment)
Segments were then grouped into depth bins using the average depth per segment and
summarized for each study location and season.

RESULTS

SURVEY TOTALS

Survey effort was similar between sites and sampling periods (Table 1). A total of 15.7 hours
of video was reviewed, 8 hours for the spring survey, and 7.7 hours for the fall survey. Less
distance was surveyed during the spring (10.0 km) than in the fall (12.1 km), where effort
was added to fill in transects that were not surveyed at the East Fish Camp in spring due to
time restrictions (Figure 1). The range of depths surveyed during the spring and fall was
comparable at both sites (Table 1).

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 9

SUBSTRATE AND HABITAT

A summary of substrate and habitat composition for all survey sites and transects is given in
Table 2. Soft habitat was the dominant habitat observed overall, accounting for an average
of 59% of the habitat surveyed at Anacapa Island SMR, and 68% of the habitat observed at
East Fish Camp during both seasons (Table 2). Sand was the dominant substrate observed
within the soft category, accounting for an average of 83% at Anacapa Island SMR, and 86%
at East Fish Camp combined for both seasons. Hard and mixed habitats were less common
individually, however rocky substrate within those categories was relatively common
accounting for an average of 41% at Anacapa Island SMR and 31% at East Fish Camp for both
seasons combined (Table 2).

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 10

Table 2. Percentages of substrates and habitats by season at Anacapa Island SMR and East
Fish Camp.

INVERTEBRATE TOTALS

Total counts for all invertebrates observed at both Anacapa Island SMR and East Fish Camp
are given in Table for both survey sites and seasons combined. There were approximately
75% less WSCs enumerated during the fall than the spring survey (Table 4). Site specific
differences were not presented and data were not analyzed for non-WSC invertebrate
species observed in this study. These data were provided to CDFW scientists for further
analysis.

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 11

Table 3. Common and taxonomic (species) names of quantified invertebrates for the spring
and fall combined.

WARTY SEA CUCUMBERS

Overall, fewer WSCs were observed at East Fish Camp than at Anacapa Island SMR (Table 4).
And, while the largest proportion of habitat surveyed was soft habitat (Table 2), a greater
density of WSCs were found on hard and mixed habitat types (Figure 3). WSCs were also,
more abundant at both Anacapa Island SMR and East Fish Camp during the spring than the
fall (Table 4, Figure 3).

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 12

Table 4. The average, minimum, and maximum depth and the total number of warty sea
cucumbers observed at Anacapa Island SMR and East Fish Camp during the spring and fall.

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 13

As expected, there was a lower mean density of WSCs at East Fish Camp (the fished site) in
all depth bins than at Anacapa Island SMR (the protected site) (Figure 4). Additionally,
there were higher mean densities of WSCs observed at both sites in the 15 to 20 meter
range than at any other depth (Figure 4).

March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island 14

DISCUSSION

The WSC dive fishery around Anacapa Island is not an exception to the pattern seen in other
sea cucumber fisheries, where market demand is increasing as the abundance of the
resource is decreasing (Chavez et al., 2011). The purpose of this study was to provide CDFW
with information to help inform management of the WSC dive fishery by further
understanding the performance of an MPA in relation to the fishery and by quantifying
seasonal WSC abundance to see if they undergo seasonal shifts from shallow to deep.
We looked at the role Anacapa Island SMR (a MPA) may play in providing refugee for this
species by documenting their densities within the SMR and in a nearby fished area. The
results clearly indicated a differential in WSC densities inside and outside the protection of
the MPA, with WSCs being more abundant (~75%) at the MPA site, than the fished site at all
depths and during both survey seasons. These results were consistent with previous results
reported by CDFW SCUBA surveys.
We also quantified WSCs to see if there was evidence of a seasonal shift in abundance
between shallow-water habitats (<30 m) and deep-water habitats (> 30 m). It was found that
anecdotal reports of WSCs exhibiting a seasonal depth migration were not supported by this
study. Although differences in abundance were observed between seasons, with densities
considerably lower in the fall than in the spring, there was no shift in the distribution of
abundance by depth.
In addition, there was no difference in WSC abundance by habitat type between seasons.
Density by habitat type remained proportional between seasons, with no shift from one
habitat type to another. Further study is required to explain the change in WSC abundance
in winter months, when densities in shallower waters decrease drastically.

PROJECT DELIVERABLES

MARE will provide CDFW lead scientist copies of the primary video (forward and downward
facing) and HD still photos for the entire survey on a portable hard drive. Each video and
photo file folder has an accompanying storyboard detailing the ROV name, date, dive
number, location, and transect number. All video recordings contain a timecode audio track
that can be used to automatically extract GPS time from the video.

A copy of the master Microsoft Access database, which contains all the raw and post-
processed data will also be provided to the CDFW lead scientist. These data will include ROV

position (raw and cleaned), ROV sensor readings (depth, temperature, salinity, dissolved
oxygen, forward and downward range, heading, pitch and roll), calculated transect width
and area, substrate and habitat, and invertebrate identifications. Included in the processed
position table are the computed transect identifications for invertebrate transects (see
methods).

REFERENCES

California Department of Fish and Game. 2007. Status of the Fisheries Report, 5. Sea
Cucumbers.

Chavez, E.A., Salgado-Rogel, A.L., Palleiro-Nayar, J. 2011. Stock Assessment of the Wary Sea
Cucumber Fishery (Parastichopus Parvimensis) of NW Baja California. CalCOFI Rep., Vol. 52.

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. Cailliet. 1999. A classification scheme for deep seafloor habitats:
Oceanologica Acta 22(6):663–678.

Gotshall, D.W. 2005. Guide to marine invertebrates – Alaska to Baja California, second
edition (revised). Sea Challengers, Monterey, California, USA.

Karpov, K., A. Lauermann, M. Bergen, and M. Prall. 2006. Accuracy and Precision of
Measurements of Transect Length and Width Made with a Remotely Operated Vehicle.
Marine Technical Science Journal 40(3):79–85.

Schroeter SC., Reed DS., Kushner DJ, Estes JA., Ono DS. 2001. The use of marine reserves in
evaluating the dive fishery for the warty sea cucumber (Apostichopus parvminesis) in
California, U.S.A. Canadian Journal of Fisheries and Aquatic Sciences. 58: 1173-1781.

State of California Fish and Game Commission. July 11, 2017. Initial Statement of Reasons
for Regulatory Action, Title 14 California Code of Regulations, Re: Commercial Taking of
Sea Cucumber.

Veisze, P. and K. Karpov. 2002. Geopositioning a Remotely Operated Vehicle for Marine
Species and Habitat Analysis. Pages 105–115 in Undersea with GIS. Dawn J.
Wright, Editor. ESRI Press.

deepdirk2021-07-20T20:59:41-08:00March 1st, 2019|research|

March 2017 – Survey and Research Priorities for Coastal and Marine Systems of the Northern Channel Islands, CA

Western North American Naturalist HORIZON SCANNING:

SURVEY AND RESEARCH PRIORITIES FOR COASTAL AND MARINE SYSTEMS

OF THE NORTHERN CHANNEL ISLANDS, CALIFORNIA

Manuscript Number: WNAN-D-17-00067R1

Full Title: HORIZON SCANNING: SURVEY AND RESEARCH PRIORITIES FOR COASTAL

AND MARINE SYSTEMS OF THE NORTHERN CHANNEL ISLANDS, CALIFORNIA

Article Type: California Islands Symposium Article

Corresponding Author: Mary Gleason, Ph.D. Nature Conservancy Monterey, California UNITED STATES

Corresponding Author Secondary Information:

Corresponding Author’s Institution: Nature Conservancy

Corresponding Author’s Secondary Institution:

First Author: Mary G. Gleason

First Author Secondary Information:

Order of Authors: Mary G. Gleason

Jennifer E. Caselle

Chris Caldow

Russell Galipeau

Walter Heady

Corinne Laverty

Annie Little

David Mazurkiewicz

Eamon O’Byrne

Dirk Rosen

Stephen Whitaker

Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.org

Order of Authors Secondary Information:

Abstract: Historical marine ecology provides information on past ocean conditions and

community structure that can inform current conservation and management. In an era of rapid global ocean changes, it is critical that managers and scientists ensure sufficient documentation of past and present conditions of resources they manage or study. Documenting, archiving, and preserving historic and contemporary data will provide their colleagues in the future with more information to make robust science- based management decisions. Using a workshop approach, we identified research and archiving priorities to enhance documentation of the past and present conditions of coastal and marine ecosystems of the northern Channel Islands in California. We identified a variety of types of historical data (e.g., archeological data, oral histories, environmental records, imagery) that should be preserved and analyzed to better understand past coastal and marine ecosystems around the northern Channel Islands. Continuing with long-term monitoring programs is also important for establishing baselines to inform contemporary management decisions and compare with future conditions. We underscore the role that individual scientists and managers working in the northern Channel Islands must play in documenting their work, archiving data, and preserving specimens in museums and institutions. Our case study for the northern Channel Islands provides a guide for how scientists should be documenting past and present conditions for marine resources around the world. Robust documentation of such conditions will give future scientists, managers, and other stakeholders the information needed to navigate what are sure to be increasingly complex management challenges.

HORIZON SCANNING: SURVEY AND RESEARCH PRIORITIES FOR COASTAL AND MARINE SYSTEMS OF THE NORTHERN CHANNEL ISLANDS, CALIFORNIA

Gleason, M.G. 1*, J. E. Caselle2, C. Caldow3, R. Galipeau4, W. Heady1, C. Laverty5, A. Little6, D. Mazurkiewicz4, E. O’Byrne1, D. Rosen7, and S. Whitaker4

1The Nature Conservancy, 201 Mission St., San Francisco, CA, USA 2 Marine Science Institute, University of California, Santa Barbara, CA, 93106 3 Channel Islands National Marine Sanctuary, University of California Santa Barbara Ocean Science Education Building 514, MC 6155, Santa Barbara, CA 93106-6155 4 Channel Islands National Park, 1901 Spinnaker Dr., Ventura, CA 93001 5 Natural History Museum of Los Angeles County, 900 Exposition Blvd., Los Angeles, CA 90007 6 U.S. Fish and Wildlife Service, 1901 Spinnaker Dr., Ventura, CA 93001 7 Marine Applied Research and Exploration, 1230 Brickyard Cove Rd. #101, Richmond, CA 94801

*Corresponding author: mgleason@tnc.org

Running Head: Coastal and marine information for the century ahead

ABSTRACT
Historical marine ecology provides information on past ocean conditions and community
structure that can inform current conservation and management. In an era of rapid global ocean
changes, it is critical that managers and scientists ensure sufficient documentation of past and
present conditions of resources they manage or study. Documenting, archiving, and preserving
historic and contemporary data will provide their colleagues in the future with more information
to make robust science-based management decisions. Using a workshop approach, we identified
research and archiving priorities to enhance documentation of the past and present conditions of
coastal and marine ecosystems of the northern Channel Islands in California. We identified a
variety of types of historical data (e.g., archeological data, oral histories, environmental records,
imagery) that should be preserved and analyzed to better understand past coastal and marine
ecosystems around the northern Channel Islands. Continuing with long-term monitoring
programs is also important for establishing baselines to inform contemporary management
decisions and compare with future conditions. We underscore the role that individual scientists
and managers working in the northern Channel Islands must play in documenting their work,
archiving data, and preserving specimens in museums and institutions. Our case study for the
northern Channel Islands provides a guide for how scientists should be documenting past and
present conditions for marine resources around the world. Robust documentation of such
conditions will give future scientists, managers, and other stakeholders the information needed to
navigate what are sure to be increasingly complex management challenges.

INTRODUCTION

Coastal and marine ecosystems are being subjected to increasing impacts due to human activities
such as resource extraction, pollution, and anthropogenic climate changes that pose significant
threats to ecological processes, biodiversity, ecosystem health and food security (Worm et al.
2009; Hoegh-Guldburg and Bruno 2010; Cózara et al. 2014; Greene 2016). Understanding and
responding to these impacts represents a significant challenge to the scientific and conservation
communities, in part because of unique attributes of the marine environment. The pace of some
indicators of climate change (e.g., species shifts) may be faster in marine ecosystems, especially
mid-latitude upwelling ecosystems, relative to many other systems (Burrows et al. 2011; Doney
et al. 2012). Additionally, the scale of chemical and material transport in the ocean is generally
quite large (i.e., many kilometers). Due to the fluid nature of marine ecological processes, spatial
boundaries are dynamic across time and over many different parameters. The “openness” of
marine systems, with species distributions defined by dynamic water bodies and broad dispersal

and movement patterns, affects connectivity of populations, genetics, trophic interactions, and
the ability to protect and restore those populations (Kinlan and Gaines 2003; Carr et al. 2003).
Ownership and access issues are also markedly different in the marine environment than on land.
Additionally, we know relatively little about marine ecosystems, especially deeper zones,
compared to terrestrial ecosystems. This is because ocean ecosystems are difficult to access,
require the development of new tools, and, as a result, are expensive to study. Coastal
ecosystems, occupying a relatively narrow zone at the intersection of land and sea, have their
own unique conservation challenges and are subject to stressors from both land and sea, as well
as looming threats from sea level rise (Scavia et al. 2002; Sloan et al. 2007; Heberger et al.
2011).

Overcoming the special challenges of research in coastal and marine ecosystems and collecting
baseline data and information for informed management are essential. We need information on
the current status of resources and the processes affecting them, as well the natural variability
and responses of systems to specific environmental or anthropogenic-based changes. To better
equip and inform natural resource decision-making today and into the future, Morrison et al. (in
press) highlight the accountability that scientists and managers have to ensure data pertaining to
past and present conditions of the resources in their charge are collected and archived. Historical
marine ecology provides information on past ocean conditions and community structure that
informs our current understanding of conservation status, recovery targets, and management
needs (Jackson et al. 2001; Lotze et al. 2006; McClenachan et al. 2012). As memories fade,
records are lost, conditions change, and baselines shift it is important to do what we can now to
document and secure information from the past and present. Global change will bring added

complexity and challenges to stewardship of the coastal and marine environment, but we suggest
that a strong and easily accessible record and documentation of past and current conditions will
give stakeholders and decision-makers in the future the kind of valuable information they will
need. What future managers will ultimately do with this information from the past is hard to
predict and will be context-specific. However, there is a growing understanding that making
resource management decisions, such as how to maintain populations or communities in their
current state or whether to bring an ecosystem back to an earlier state, will benefit from an
understanding of baseline conditions, trajectories of historic change, and the impacts of humans
on observed changes (McClenachen 2012; Thurstan et al. 2015).

As a first stage in this process, we undertook an inquiry to examine the current state of
documentation of past and present conditions of the coastal and marine ecosystems of the
northern Channel Islands of California (USA), an area of high conservation value and of
management and scientific interest. Our inquiry focused on three questions: How can we better
document past conditions? How can we better document present conditions? And, how can we
build support for data collection and archiving that can be used to make more informed
management decisions today and into the future? Our inquiry was conducted as part of a broader
effort to assess research and archiving needs and opportunities for the California Islands
(Morrison et al., in revision). Our assessment presents a case study of, and a template for, how
this type of inquiry can be applied to marine resources elsewhere.

MANAGEMENT AREA AND RESOURCES OF INTEREST

The Santa Barbara Channel region is highly variable, sitting at the confluence of warm- and
cold-water ocean currents, which results in an important biogeographic transition zone for many
marine organisms (Hickey 1998; Hamilton et al. 2010). The ocean waters around the northern
Channel Islands are some of the most protected in the world, lying within the federal Channel
Islands National Marine Sanctuary (henceforth, the “Sanctuary”) and the Channel Islands
National Park. In addition to the federal designations, the State of California established a
network of 13 marine protected areas (MPAs) in 2003, 11 of which are no-take reserves
(Figure1; Airame et al. 2003; Gleason et al. 2013).

While much of the marine environment around the islands is protected from extractive activities,
large areas still support extractive activities, such as recreational and commercial fishing, that are
likely to grow in importance as human population increases. In addition, this region experiences
impacts from other sources including shipping (e.g., noise, whale strikes, pollution), land-based
pollutants carried offshore, offshore oil and gas development, tourism, and climate impacts (e.g.,
warming water temperatures, ocean acidification, sea level rise).

Santa Barbara Island, while geographically grouped with the southern Channel Island
archipelago, is included in this overview due to this shared management boundary and research
history. We assumed that as we identified questions and information needs related to this
jurisdictional unit, the geographic area of interest may scale outward depending on the specific
resource or question of interest. For example, connectivity issues in the marine environment, as
described above, may lead to conservation strategies that transcend political boundaries.
Similarly, conservation of particularly threatened species or habitats might dictate research
priorities at spatial scales larger than this study area boundary.
Coastal and marine resources

The coastal and marine ecosystems and resources in the northern Channel Islands are important
for their biodiversity values and relevance to the people who have lived, worked, and recreated
around the islands and their waters both currently and historically. As an ecoregional transition
zone, marine biodiversity is quite high, containing species with both northern (cold water) and
southern (warm water) affinities. The coastal bluffs and shorelines around the northern Channel
Islands include habitats such as coastal scrub, small wetlands, pocket beaches, intertidal rocky
habitats, and offshore rocks and islets. Each island supports unique vegetative communities on
the coastal margins (such as coastal bluff scrub, coastal sage scrub, and chaparral) and rare
endemic plant species; much of the coastal vegetation has been altered by human activities and is
in some stage of recovery. Coastal areas provide grounds for colonies of seabirds such as Ashy
Storm-Petrel (Oceanodroma homochroa), California Brown Pelican (Pelecanus occidentalis),
Brandt’s Cormorant (Phalacrocorax pencillatus), Pigeon Guillemot (Cepphus columba),
Cassin’s Auklet (Ptychoramphus aleuticus), Scripps’s Murrelet (Synthliboramphus scrippsi), and
others. These areas are also important for marine mammal rookeries and haul-outs for species

Study area boundary

We defined our study area as the waters around the northern Channel Islands, and used the
federal Sanctuary boundary as the demarcation (Figure 1). This is akin to using the management
unit of an individual island or protected area as a focal area for determining research and
documentation priorities for terrestrial resources. The Sanctuary encompasses 1,110 square
nautical miles (1,470 square miles or 3,807 km2) of water from mean high tide to six nautical
miles offshore of Santa Barbara, Anacapa, Santa Cruz, Santa Rosa, and San Miguel Islands.

such as California sea lion (Zalophus californianus), northern fur seal (Callorhinus ursinus),
northern elephant seal (Mirounga angustirostris), and others (NCCOS 2005).

Offshore, the marine environment can be characterized by different depth zones (e.g., inner shelf

0-30m, middle shelf 30-100m, outer shelf 100-200m, meso-benthal slope 200-500m, and bathy-
benthal slope >500m), different substrate types (e.g., silt, sand, cobble, bedrock), the presence of

submerged aquatic vegetation (e.g., eelgrass and surfgrass) or macroalgae (e.g., kelp forests).
The waters in the Sanctuary around the northern Channel Islands range from intertidal to
approximately 1,600 meters in depth, with bathymetric complexity in the form of submarine
canyons and pinnacles, and important deep sea coral and sponge communities. Similarly, there
are different pelagic zones (e.g., bathypelagic, mesopelagic, and epipelagic) characterized by
their depth, physical oceanographic parameters, and frontal boundaries. These marine
ecosystems support a diverse array of algal, invertebrate, fish, seabird, and marine mammal
populations. Important fishery species include spiny lobster (Panulirus interruptus), market
squid (Loligo opalescens), sea cucumbers, urchins, many species of rockfish (Sebastes spp.),
lingcod (Ophiodon elongatus), sanddabs (Citharichthys spp.), sheephead (Semicossyphus
pulcher), yellowtail (Seriola dorsalis), and many others. Marine mammals around the islands
include the pinnipeds listed above and many cetacean species such as blue whales (Balaenoptera
musculus), gray whales (Eschrichtius robustus), humpback whales (Megaptera novaeangliae),
bottlenose dolphin (Tursiops truncates), long-beaked and short-beaked common dolphins
(Delphinus capensis and D. delphis), and many others (NCCOS 2005).

We recognize that many of the resources that are the focus of our inquiry here are linked in
complex ways to the natural and cultural resources found in the terrestrial realm of the islands.
Similar inquiries as ours were directed to terrestrial flora and fauna and cultural resources of
Santa Cruz Island (Boser et al. in review; Morrison et al. in revision; Randall et al. in review;
Rick et al. in review.) We encourage readers to review those assessments for a multidisciplinary
overview of the study area, as there were many overlapping interests and complementary sets of
recommendations.

DOCUMENTATION OF THE PAST

Historical ecology approaches have been used to understand long-term change in marine systems
(Jackson et al. 2001; Pandolfi et al. 2003; McClenachan 2009) with goals of informing
restoration, conservation and management (Pesch and Garber 2001; VanDyke and Wasson
2005). For example, in California, museum seabird specimens have played a key role in
documenting historic population size, changes in diet, community structure, ocean conditions, or
pollutants over time (Beissinger and Peery 2007; Osterback et al. 2015). While some of the
methods and data sources for historical ecology are similar between terrestrial and coastal or
marine systems, there are important differences. For example, often specialized tools are
required for accessing underwater environments, so research in marine systems has lagged far
behind terrestrial systems. Relatively recent advances in SCUBA, remotely operated vehicles
(ROV), autonomous underwater vehicles (AUV) and submarines have made more habitats
accessible and some monitoring now occurs in most marine ecosystems. However,
reconstructions of the past in marine systems tend not to be as ‘deep in time’ as terrestrial
examples.

Examples of use of historical ecology from the Channel Islands

The Channel Islands and broader Santa Barbara Channel have a long history of environmental
change and human occupation and exploitation of resources, including 13,000 years of maritime
Chumash presence and hundreds of years of Spanish, Asian, and Euro American presence. The
archeological record reflects that history and documents significant changes in flora and fauna in
the region that can inform modern day management (Rick et al. 2008). In the Channel Islands,
two case studies using very different types of data provide examples of how historical
information could be used in modern-day management and conservation. Bellquist and Semmens
(2016) used fishing records compiled from a regional fishing newspaper (Western Outdoor
News) to reconstruct changes in size structure of recreationally-fished species throughout coastal
California, but with an emphasis on the northern Channel Islands. The work followed from
previous studies from Florida that utilized old photographs from fishing piers (McClenachan et
al. 2009) and a long-time series of fishing records from the International Game Fishing
Association (Roberts et al. 2001; Bohnsack 2011) to document temporal declines in fish size and
changes in fish community structure, and to assess benefits of MPAs to recreational fishing,
respectively. Bellquist and Semmens (2016) showed that since 1966, 12 out of 16 species
analyzed showed declines in trophy size (size of the largest individuals in a population). Of those
12 species, nine showed very recent stabilization or increases in trophy size. Importantly, the

creation of this database from an untraditional source overcame current limitations in temporal-
and spatial-resolution with traditional fisheries-dependent and fisheries-independent data
collected in California.

A second study (Braje et al. 2017) measured very long-term changes (over 10,000 years) to
population abundance and size structure of an ecologically and commercially important fish
species, California sheephead. Comparing zooarchaeological records from the Channel Islands
with contemporary samples, and using stable isotope analysis to measure food habits, these
authors provide a more accurate baseline of the size and diet of California sheephead, prior to the
development of a fishery in the early 20th century. They found that the average size of sheephead
along the northern Channel Islands today is significantly smaller than in the deep past. This may
be due to the targeting of large sheephead by modern commercial and recreational anglers, which
has culled many of the largest fish from the modern population. However, the authors also
provide evidence for the long-term continuity and stability of sheephead populations in the
northern Channel Islands, both in terms of relative abundances and average sizes with
fluctuations in time in both metrics, suggesting hope for the restoration of this fishery in the
Channel Islands region. This research is a rare example of long-term historical analysis
attempting to provide actionable data for modern fisheries management.

Despite a growing interest in historical information, and increasing discovery of a variety of non-
traditional data types, historical data are still not commonly utilized in marine management or

conservation decisions (McClenachan et al. 2012). These authors note several obstacles ranging
from funding limitations on gathering historical data in the first place to challenges of
incorporating non-traditional data into existing quantitative frameworks. Yet, when historical
long-term data are incorporated into marine population assessments (e.g., for fisheries or
extinction risk assessments), they often point to more severe population declines than in
assessments without long-term data (McClenachan et al. 2012). In fact, this problem of shifting

baselines in marine ecosystems and populations has been described by many authors (Pauly
1995; Dayton et al. 1998; Jackson et al. 2001; Pinnegar and Engelhard 2007) and has potentially
limited management and restoration efforts by identifying rebuilding targets that may be
dangerously low or simply underestimating the magnitude of declines. As we move forward
collecting and archiving data on marine and coastal ecosystems of the present, attention to the
current challenges of incorporating these data into conservation and decision-making may help to
overcome these limitations in the future. For example, accessibility and documentation (via
archiving and good metadata practices) might make data more discoverable to future historical
ecologists.

Importance of historical information in context of ocean change

The importance of taking a longer view of our coastal and marine ecosystems, especially in a
dynamic area like the northern Channel Islands cannot be overstated. Recent human-induced
climate fluctuations are layered on decadal (e.g., Pacific Decadal Oscillation) and shorter-term
(e.g., El Nino Southern Oscillation) timeframes. Anthropogenic activities have increased
dramatically in the region since the early 19th and 20th centuries with increases in fishing pressure
brought by the Chinese and Euro-American fisheries as the native Chumash populations were
reduced (Braje et al. 2017). More recently, commercial shipping, invasive species, pollution,
disease outbreaks and tourism have all increased, with largely unstudied impacts on the marine
and coastal systems. Several well-documented extirpations of marine species have occurred in
the Channel Islands region with varying effects on present day marine communities. One of the
best-documented examples involved the loss of a keystone predator in the system, the southern
sea otter (Enhydra lutris nereis), due to intensive hunting associated with the fur trade beginning

in the early-1800s (Braje et al. 2013). By 1830, southern sea otters were functionally extinct
throughout California. After protection in 1911 by the International Fur Seal Treaty, southern sea
otter populations have increased, albeit very slowly (USFWS 2015). Current community
structure of rocky reefs and kelp forests (essentially encompassing all modern kelp forest
monitoring time series) almost certainly reflects the loss of this top, keystone predator. However,
it has been suggested that southern California kelp forests may be more resilient to change than
other kelp forests in the range of the sea otter due to high levels of functional redundancy in
predators, including sheephead and spiny lobster (Steneck et al. 2002; Graham et al. 2008).

Should the sea otter expand its current range to the northern Channel Islands (a small re-
introduced population lives at San Nicolas Island), we might expect to see dramatic changes to

the kelp forest systems, perhaps a reflection of the historical state.

Another dramatic loss of a suite of species involved a combination of overfishing and disease.
Red and black abalone (Haliotis rufescens and H. cracherodii, respectively) were important food
sources for the Chumash Indians on Santa Cruz Island (Braje et al. 2009). With the loss of sea
otters described above, and declines in the Chumash population, two main predators on these
species, abalone experienced population explosions in the early 1800’s (Braje et al. 2009), with
black abalone reported to be stacked five deep in the intertidal on Santa Cruz Island. Beginning
in the 1960s, five species of abalone suffered serial depletion in the Channel Islands, attributed to
a combination of overharvest, disease, and a long-term warming trend leading to poor
recruitment (Leet et al. 1992; Engle 1994). One species of abalone, the white abalone was the
first marine invertebrate on the federal endangered species list. Very recent, anecdotal reports of
recovery of some species of abalone are encouraging but to date, the fishery for abalone south of

Point Conception remains closed. Conservation and management today, and into the future,
could benefit from a better understanding of the longer-term context of the region, including both
natural and human-induced fluctuations in populations and how marine communities were
structured. This does not mean that restoration to some previous state is either possible or even
desirable. However, knowing the bounds of fluctuations and their relationships to abiotic and
biotic factors over long time scales can guide restoration towards realistic endpoints.

Potential sources of historical data for northern Channel Islands

The northern Channel Islands provide rich opportunities for exploration and ‘rediscovery’.
Workshop participants identified many potential sources of information that could allow for
reconstruction of past environmental conditions and human uses of coastal and marine systems.
We grouped these potential sources into seven categories that span from ‘deep time, such as
information potentially obtained from reconstructed environmental records and archeological
surveys, to the more recent past, as potentially obtained from historical records, oral histories,
scientific surveys, imagery, and fishing data (Table 1). With these types of information sources,
it is then often possible to reconstruct historic baselines though temporal comparisons, time
series analysis, hindcasting, and space-for-time comparisons (Lotze and Worm 2009).

Some of these historic data sources are highly vulnerable to loss. For example, many of the
coastal archeological sites around the northern Channel Islands – sites that contain a rich archive
of data regarding both marine and terrestrial ecosystems – are experiencing ongoing destruction
due to storm surge and sea level rise (Reeder et al. 2012). The knowledge of many late-career
scientists who spent decades conducting research in the study area could be lost unless

investments are made in interviewing them as part of an “oral history” project and facilitating the
archiving of their field notes. We urge managers and scientists to prioritize data collection from
ephemeral sources that are susceptible to degradation or loss.

C. Minto, S.R. Palumbi, A.M. Parma, D. Ricard, A.A. Rosenberg, R. Watson, and D. Zeller.
2009. Rebuilding global fisheries. Science 325:578-585.

DOCUMENTATION OF THE PRESENT

Investment in long-term ecological studies and monitoring can have significant benefits in
tracking ecosystem changes through time, as well as informing environmental policy (Hughes et
al. 2017). Probably one of the most important actions we can take today to help the
conservationist or manager of the future is to comprehensively inventory and document today’s
marine and coastal ecosystems and make sure those data are archived well into the future. As we
considered how we could improve data collection and archiving in the present and for historical
ecologists’ use in the future, there was broad agreement among workshop participants that
completing a baseline on ocean conditions and ensuring stable support for long-term monitoring
are critical.

Completing ocean baseline and supporting long-term monitoring

There is a high density of academic institutions, state and federal agencies, and non-profits
located on the adjacent mainland who have conducted research or monitoring of coastal and
marine resources in the northern Channel Islands. In fact, a variety of long-term monitoring
programs are already in place (Table 2). Some of the best examples come from the multiple
programs that survey kelp forests and rocky intertidal areas. The implementation of MPAs
throughout California has provided impetus and funding for continuing and expanding many
existing long-term monitoring programs, as well as developing new monitoring in habitats where

programs did not already exist (e.g., deep-water, sandy beach), or adding alternative types of
data to assessments (e.g., social and economic data). In addition to the ‘benthic’ ecological
monitoring programs mentioned above, the region hosts some very comprehensive seabird and
marine mammal monitoring programs (Table 2). Finally, the area is also well studied from an
oceanographic perspective with many of the programs mentioned above also maintaining
instrumentation to measure, for example, temperature, wave exposure, salinity, oxygen and
currents.

Despite a relative wealth of existing data and monitoring programs in the coastal and marine
environment, workshop participants identified areas where present day monitoring or assessment
could be added or enhanced. When asked what data the marine scientist or manager of the future
would like to see collected now, several areas of inquiry emerged. First, measures of abiotic
habitat (e.g., extent, type, quality) are fundamental to understanding variation in biotic
communities over space and time. California has made substantial progress in completing

benthic habitat maps for the majority of the state using technology such as side-scan and multi-
beam sonar. Side scan and multi-beam sonar can provide important information on benthic

structure, erosion, geomorphological change, and patterns of island subsidence over time.
Unfortunately, one of the primary gaps in the statewide mapping process is in the area around the
northern Channel Islands. While substantial progress has been made recently and 70% of the
Sanctuary seafloor has been surveyed by high-resolution sonar, only 20% of the area contains an
actual habitat map developed by post-processing those data. The majority of the remaining
seafloor mapping gaps occur in shallower areas that are home to some of the most productive
and healthy kelp forest and rocky reef communities in the region. Completion of benthic habitat

mapping in this area would provide critical information to aid incident response and restoration
activities, inform protected resources and fishery management, and improve navigational safety.
These core products are building blocks for informed survey design and fundamental to
understanding species/habitat presence, abundance, and vulnerability.

Similarly, when investigating the drivers of change or spatial variation in biotic communities,
understanding anthropogenic activities at relevant spatial and temporal scales is critical. For
example, the widespread implementation of MPAs, a spatial management tool, should be
accompanied by data on fishing effort at similar spatial scales. Similar arguments can be made
for spatial data on other human uses including recreational activities, military actions, and energy
development. Expansion of long-term monitoring programs into new habitats (e.g., deep water)
initiated during the MPA baseline monitoring period should be continued. New technology is
continually advancing and one technique in particular, the use of soundscapes and audio
recordings, was identified by the group as having potential for use in the Channel Islands. Audio
has been used successfully for some time to assess marine cetaceans, but increasingly, sound is
being used to document seabird populations and the ‘health’ of whole ecosystems such as reefs or
estuaries (Buxton and Jones 2012; Lillis et al. 2014; Oppel et.al. 2014; Harris et al. 2016).

Prioritizing what needs to be done now to guide future management

Ecologists, conservation practitioners and natural resource managers agree that long-term
monitoring of the environment is critical for understanding and making decisions in complex
ecological systems (Lindenmayer and Likens 2009). Increasingly, the linkages between humans

and ecosystems are also recognized as important aspects to monitor (i.e., Social-Ecological
Systems (SES); Folke 2006; Ostrom 2009). However, resources to do long-term monitoring are
limited. Virtually all long-term, environmental or social monitoring programs face funding
challenges and as such, must evaluate where and when to allocate limited resources for
maximum benefit. The benefits of long-term monitoring programs and the value of the data
might not be realized until well into the future. Building monitoring programs that can address
both present day and future needs is a difficult, but important, undertaking. As a general rule,
developing criteria for data collection investments can help to clarify needs and increase the
future utility of monitoring programs.

Given the many ongoing monitoring programs in existence in the Channel Islands region,
potential criteria could be established to help guide and prioritize monitoring investments. These
criteria should include: 1) the length of existing time series; 2) filling key gaps, both disciplinary
and geographic (e.g., nearshore benthic habitat mapping, human use patterns, deep water
habitats); 3) monitoring of new stressors and emerging issues (e.g., climate change, ocean
acidification, plastic pollution, marine diseases, invasive species); and 4) incorporation of new
and cost-effective technologies (e.g., monitoring soundscapes with autonomous recording units;
eDNA for biodiversity monitoring; satellite imagery; new underwater visual technologies; drones
and UAVs; and the use of citizen science).

Other general features of successful monitoring programs include the ability to adapt. Long-term
monitoring programs are often plagued by poor planning from the outset and a lack of tractable
questions. Lindenmayer and Likens (2009) suggest a framework for adaptive monitoring that

stresses asking clear, tractable questions, developing solid, defensible statistical and data
collection methodologies, and most importantly, iterating the process, thereby allowing for
learning and adaptation. In the context of the northern Channel Islands, with its large number of
ongoing monitoring programs, consistency in methods but also foresight and flexibility to react
to changing conditions will be critical to gathering useful information.

In addition to monitoring programs, it is also critically important that individual scientists and
managers take responsibility for and take every opportunity to document their work, archive their
data, and preserve specimens in museums and institutions. If this were a regular practice and
expectation for all scientists, over time we would do a better job of accumulating information
about the systems of today. Some key institutions that currently house coastal and marine
specimens from the Channel Islands include the Santa Barbara Museum of Natural History, Los
Angeles County Museum, University of California (e.g., Jepson Herbaria), California Academy
of Sciences, San Francisco Maritime Museum, Western Foundation of Vertebrate Zoology,
Smithsonian Institution, NOAA National Centers for Coastal Ocean Science, and others.
Reviewing the myriad data archiving resources available to marine scientists is beyond the scope
of this paper but funding agencies and foundations as well as scientific publishing enterprises are
increasingly requiring data to be made discoverable and accessible through links to data
repositories when available (Table 2).

COORDINATION AND COLLABORATION

Two important themes that emerged from the workshop were: a) the need for increased
coordination and collaboration among groups doing ocean related work and b) the importance of

building and maintaining public support for research and monitoring. As mentioned above, the
Santa Barbara Channel region is relatively data rich compared to many marine regions of the
world, and while efforts have been made to coordinate research capacity and emerging data
streams, more can be done. Currently, the Sanctuary’s Research Activities Panel acts as an
informal clearinghouse for marine research in the Sanctuary, meeting at least once per year and
gathering many local researchers for roundtable discussions of findings. Data documentation and
discovery has also improved substantially over the past decade with most long-term monitoring
programs hosting and serving data via internet accessible portals (see links in Table 2). Next
steps might include the development of joint databases or repositories such as the Sanctuary
Integrated Monitoring Network (SiMON) portal or the inclusion of more disparate types of data
into Southern California Ocean Observing System (SCOOS).

While data availability into the future is key to guiding conservation and management, the idea
of having informed and invested stakeholders who support continued conservation and science
was viewed as equally important. The public has already invested in the Channel Islands, via
managing agencies such as the Sanctuary, National Park Service, U.S. Fish and Wildlife Service,
and the California Department of Fish and Wildlife; what is needed is to ensure those
investments last into the future. The northern Channel Islands are a special place to many
generations of stakeholders in that they are so close to such large population centers, they present
iconic land and seascapes, and have a rich cultural and natural history. Suggestions for building
public support for research and monitoring include durable outreach that tells compelling stories
of how research has contributed to ecosystem improvement, especially stories that can counter
the narrative that monitoring is boring and expensive (Suarez and Tsutsui 2004). Involvement of

citizens in research and monitoring programs can also help to build a strong and educated
constituency (Bonney et al. 2009). Citizen science is a growing enterprise and several existing
programs operate in the Channel Islands including Reef Check California which utilizes
recreational scuba divers to monitor kelp forests (Friewald et al. in review). Coordination at all
levels, from data collection, archiving and analysis, to outreach and public involvement will
increase the effectiveness of management and conservation in the region.

CONCLUDING REMARKS

Scientists and managers of today have an opportunity and a responsibility of leaving a legacy of
solid information, data, and collections to inform coastal and marine conservation and
management into the future. The workshop participants had many ideas for how to help the
scientist or manager of the future who will be looking back at our time and trying to understand
the ecosystems, culture, management context and decisions of our day. A handful of ‘no-regrets’
strategies surfaced that, if implemented, would provide a strong foundation upon which
scientists, conservationists, and managers of the future could use to understand the ecosystems of
our time. These recommendations include:
(1) Use hindcasting, modeling, and historic data to better understand the past coastal and
marine conditions and ecosystems around the northern Channel Islands, how those
ecosystems have changed over time, and how resilient they were in the past to climate
change, harvest, and species introductions or removals.
(2) Complete and archive today’s “baseline” information including filling key gaps like
seafloor mapping, surveying deeper unexplored sites, mapping human uses around the
islands, interviewing key stakeholders, and preserving specimens to leave future
scientists a thorough and useful record. We also need to make sure that we are adaptively
managing our monitoring programs and using the data to help drive management and
resource protection as new threats arise (e.g., invasive species, plastics, ocean
acidification).
(3) Promote a sense of individual scientist’s responsibility to document, archive, and
preserve data and specimens to make sure our colleagues in the future will be able to
locate and capitalize on collections, materials, and data from our time. By working with
oral historians and museum curators, we could collect and preserve the scientific stories
and specimens of our time. Such an archiving system can also help to connect researchers
and resource managers via joint data needs.
(4) Document today’s management decisions and their rationale, so that future generations
understand the management context of our time and why we made the management
decisions we did. This includes documenting smaller decisions (not necessarily captured
in the public record) and even when we decided not to take an action (e.g., to reduce
populations or remove an invasive species).
(5) Break down silos across disciplines (terrestrial/marine, benthic/pelagic,
ecology/archeology, etc.) to ensure that we are telling the whole story and able to
understand complex dynamics in our changing world. Particularly as ocean temperatures,
chemistry, currents, and species distributions change, we will need to understand the
impacts of those changes across many systems and over time.
(6) Build a constituency of public support for and investment in scientific monitoring,
research, and data collection through education, citizen science, and outreach to the many
people who have enjoyed the northern Channel Islands for generations. There are limited

funds for data collection and archiving and we need to identify new ways to engage the
public in this important work.

ACKNOWLEDGEMENTS

We thank the participants of the 2016 Island Rediscovery Workshop held January 28-29, 2016 at
the Santa Barbara Museum of Natural History and sponsored by The Nature Conservancy and
the Smithsonian Institution, as well as the participants at the Marine Rediscovery session held on
October 3, 2016 as part of the 9th Channel Islands Symposium. S. Ostermann helped with Table
2 and M. Cajandig helped with Figure 1. S. Morrison and two anonymous reviewers kindly
reviewed the draft manuscript.

FIGURE LEGEND

Figure 1. Map of study region showing the northern Channel Islands with state marine reserves
and conservation areas shown in outlines. Dotted line and dark shading delineates the Channel
Islands National Marine Sanctuary boundaries.

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deepdirk2021-03-10T21:17:37-08:00August 24th, 2017|research|

June 2017 – Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017

Coastal Impact Assistance Program CIAP 2016 Survey 5 Final Technical Report

Visual Surveys of Fish, Macro-invertebrates and Associated Habitats Using a Remotely Operated Vehicle: Soquel Canyon to Point Buchon, September – October 2016
Coastal Impact Assistance Program
CIAP 2016 Survey 5 Final Technical Report
CDFW Contract # P1370005
Report Prepared by
Andrew Lauermann
& Heidi Lovig
June 22, 2017
Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.

Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.org

TABLE OF CONTENTS
LIST OF FIGURES ………………………………………………………………………………………………………………………….. 3
LIST OF TABLES ……………………………………………………………………………………………………………………………. 4
INTRODUCTION …………………………………………………………………………………………………………………………… 6
OBJECTIVES….. …………………………………………………………………………………………………………………………….. 6
PURPOSE…… ………………………………………………………………………………………………………………………………… 6
DATA COLLECTION METHODS ……………………………………………………………………………………………………… 8
ROV EQUIPMENT ………………………………………………………………………………………………………………………….. 8
ROV SAMPLING OPERATIONS ………………………………………………………………………………………………………. 9
SITE AND SURVEY LINE SELECTION ……………………………………………………………………………………………. 10
POST-PROCESSING METHODS …………………………………………………………………………………………………….. 12
ROV POSITIONAL DATA ……………………………………………………………………………………………………………….. 12
SUBSTRATE AND HABITAT …………………………………………………………………………………………………………… 12
FINFISH ENUMERATION ………………………………………………………………………………………………………………. 13
INVERTEBRATE ENUMERATION ………………………………………………………………………………………………….. 14
RESULTS ……………………………………………………………………………………………………………………………………….. 16
SURVEY TOTALS…………………………………………………………………………………………………………………………….. 16
SUBSTRATE AND HABITAT ……………………………………………………………………………………………………………. 16
FINFISH AND MACRO-INVERTEBRATE SUMMARIES ……………………………………………………………………. 19
FISH COUNTS ………………………………………………………………………………………………………………………………… 21
INVERTEBRATE COUNTS……………………………………………………………………………………………………………….. 25
INVERTEBRATE PATCH COVER …………………………………………………………………………………………………….. 29
PROJECT DELIVERABLES ……………………………………………………………………………………………………………… 32
MAPS …………………………………………………………………………………………………………………………………………….. 33
REFERENCES ………………………………………………………………………………………………………………………………… 40

“LIST OF FIGURES”

“Figure 1. Study locations (blue boxes) from Soquel Canyon to Point Buchon and the sites (red boxes) surveyed within each…………………………………………………….33
“Figure 2. ROV survey lines within the Soquel Canyon (SQ3) and Portuguese Ledge (PRL1, PRL2, PRL3) site boundaries………………………………………………………..34
Figure 3. ROV survey lines within the Pacific Grove (PG1, PG2), Asilomar (AS1, AS2, AS4), Point Lobos (PL1, PL4, PL7, PL11) and Carmel Bay (CB1) site boundaries…….35
Figure 4. ROV survey lines within the Point Sur (PS2, PS3, PS5) and Big Creek (BC7) site boundaries…………………………………………………………………………………….36
Figure 5. ROV survey lines within the Big Creek (BC1, BC2, BC3, BC4, BC5, BC6) site boundaries…………………………………………………………………………………………..37
Figure 6. ROV survey lines within the Piedras Blancas (PIE1, PIE2) site boundaries………………………………………………………………………………………………………………38
Figure 7. ROV survey lines within the Morro Bay (MB1, MB2, MB3, MB4), Church Rock (CR) and Point Buchon (PB2, PB5) site boundaries…………………………….39

“LIST OF TABLES”
“Table 1. Total distance of hard and/or mixed habitat, with min and max depth, from completed survey lines and the total number of fish and invertebrate transects generated from video collected at sites sampled in September and October, 2016……17”

“Table 2. Percentages of substrates and habitats for all survey lines completed and post processed at each of the sites sampled in September and October, 2016……………..18

Table 3. Total kilometers and total counts for finfish and invertebrates (inverts) and the average count per kilometer for fish and invertebrates at sites sampled in September and October, 2016……………………………………………………………………………..20”

“Table 4. Common and taxonomic names, course size (see methods) and depth range of quantified finfish (list sorted by count). Description of criteria used for complexes or unidentified groupings is included with database metadata provided to CDFW………..23

Table 5. Common and taxonomic names and depth range of quantified invertebrates (list sorted by count). Description of criteria used for complexes or unidentified groupings is included with database metadata provided to CDFW………………………27

Table 6. Invertebrate patch cover by site and species/groupings (see methods for a complete list). Total area of site is the sum total of the area (m2) surveyed and total area with invertebrate is the total area (m2) of the site that the invertebrate was present. Percent cover code is the average of all the cover codes for each patch by site and species………………………………………………………………………………………….30”

INTRODUCTION

The California Department of Fish and Wildlife (CDFW) and its partners have conducted video surveys using remotely operated vehicles (ROVs) in MPAs statewide since 2002. Utilizing Coastal Impact Assistance Program (CIAP) funding, CDFW has initiated a three year project to support ROV surveys within the state. The goal of this project is to complete quantitative baseline surveys of commercially and recreationally important fish and macro-invertebrate species in three regions: Southern California, Northern California, and North Central California. Data from completed surveys will be used to examine the condition of habitats important to managed species inside and outside of selected MPAs in each study region, as well as informing fishery and MPA management. Specifically, at-sea ROV surveys will target MPA and reference site (fished area) site pairs and other sites designated by CDFW. Survey data will be collected, post-processed, and summarized by Marine Applied Research and Exploration (MARE) and provided to CDFW to complete the following project objectives:

OBJECTIVES
1) Estimate fish and macro-invertebrate species density and relative abundance inside and outside of MPAs.
2) Determine size frequency distributions of ecologically important commercial and recreational species to one centimeter resolution using stereo cameras.
3) Provide spatial data to allow examination of the distribution of observed species in relation to other spatial datasets such as high resolution bathymetry, spatially derived habitat classification, and fishery dependent data.
4) Provide an archive of high quality video transects that capture the baseline ecological conditions for California’s MPAs
PURPOSE
The purpose of this report is to present detailed data collection and post-processing methods, and summarized post-processing results of data collected from Soquel Canyon to Point Buchon, surveyed in September and October 2016. Results focus on basic data summaries that are simply a starting point for further analysis, therefore no detailed comparison or statistical analyses are presented.

DATA COLLECTION METHODS

ROV EQUIPMENT

The ROV used in this study was a Deep Ocean Engineering Vector M4, named ROV Beagle, owned and operated by Marine Applied Research and Exploration. The ROV was equipped with a three-axis autopilot including a rate gyro-damped compass and altimeter. Together, these allowed the pilot to maintain a constant heading (± 1 degree) and constant altitude (± 0.3 m) with minimal corrections. In addition, a forward speed June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 19 control was used to help the pilot maintain a consistent forward velocity between 0.25 and 0.5 m/sec. A pair of Tritech® 500 kHz ranging sonars, which measure distance across a range of 0.1–10 m using a 6° conical transducer, were used as the primary method for measuring transect width for both the forward an downward facing video. Each transducer was pointed at the center of view in each camera and was used to calculate the distance to middle of screen, which was subsequently converted to width using the known properties of each cameras field of view. Readings from these sonars were averaged five times per second and recorded at a one-second interval with all other sensor data. Measurements of transect width using a ranging sonar are accurate to ± 0.1 m (Karpov et al. 2006).

An ORE Offshore Trackpoint III® ultra-short baseline acoustic positioning system with ORE Offshore Motion Reference Unit (MRU) pitch and roll sensor was used to reference the ROV position relative to the ship’s Wide Area Augmentation System Global Positioning System (WAAS GPS). The ship’s heading was determined using a KVH magnetic compass. The Trackpoint III® positioning system calculated the XY position of the ROV relative to the ship at approximately two-second intervals. The ship-relative position was corrected to real world position and recorded in meters as X and Y using the World Geodetic System (WGS)1984 Universal Transverse Mercator (UTM) coordinate system using HYPACK® 6.2 hydrographic survey and navigation software. Measurements of ROV heading, depth, altitude, water temperature, camera tilt and ranging sonar distance both forward and downward to the substrate, were averaged over a one-second period and recorded along with the position data.

The ROV was equipped with three standard resolution and one high definition (HD) video color cameras: two locally recorded stereo cameras for highly accurate measurements of size and two primary data collections cameras; one facing forward (HD) and set approximately 30o below the horizon and the other pointing downwards. The two-camera system provided a continuous, slightly overlapping view. Video for both cameras was captured using vMix® recording software (codec H.264, 50 Mbps, 30fps, 1920 x 1080) and Pioneer DVR510 digital video disc recorders. In addition to capturing biological and habitat observations, the forward video was overlaid with an on screen display of text characters representing real time sensor data (time, depth, temperature, range, altitude, forward camera angle and heading). The ROV was also equipped with an HD still camera and strobe, which was locally were locally recorded on the vehicle. At the end of each survey day, imagery was downloaded and saved to a porTable hard drive.

GPS time was used to provide a basis for relating position, field data and video observations (Veisze and Karpov 2002). A Horita® GPS3 and WG-50 were used to generate on screen displays of GPS time, as well as output Society of Motion Picture and Television Engineers (SMPTE) linear time-code (LTC) for capture on SONY® DSR audio tracks at an interval of 1/30th of a second. This method was improved by customizing HYPACK® navigational software to link all data collected in the field to the GPS time. ROV tracked position and sensor data were recorded directly by HYPACK® as a time-linked text file. A redundant one-second time code file of sensor data was also collected in the field using a custom built on-screen display and operating system software with time code extracted from the system’s internal clock which was synced to GPS time.

All data collected by the ROV, along with subsequent observations extracted during post-processing of the video, was linked in a Microsoft Access® database using GPS time. Data management software, developed by MARE, was used to expand all data records to one second of Greenwich Mean Time (GMT) time code. During video post-processing, a Horita® Time Code Wedge (model number TCW50) was used in conjunction with a customized computer keyboard to record the audio time code in a Microsoft Access® database.

ROV SAMPLING OPERATIONS

ROV operations were conducted off the F/V Donna Kathleen, a 19 m research vessel owned and operated by Captain Robert Pedro. Surveys were conducted between the hours of 0800 and 1700 PST to avoid the low light conditions of dawn and dusk that might affect finfish abundance measurements and underwater visibility.

June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 20
The ROV was flown off the vessel’s port side using a “live boat” technique that employed a 317.5 kg (700 lb.) clump weight. Using this method, all but 45 m of the ROV umbilical was isolated from current-induced drag by coupling it with the clump weight cable and suspending the clump weight at least 10 m off the seafloor. The 45 m tether allowed the ROV pilot sufficient maneuverability to maintain a constant speed (0.5 to 0.75 m/sec) and a straight course down the planned survey line.

In addition, the ROV pilot and ship’s helm used real-time video displays of the location of the ship and the ROV, relative to the planned survey line, to navigate along the 500 m line. The ship’s captain used the displays to follow and maintain the position of the ship within 35 m of the ROV.

At each site, the ROV was flown along pre-planned survey lines. The ROV pilot maintained forward direction within ± 10 m of the planned line. The ranging sonars were fixed below and parallel to the camera between two forward-facing red lasers spaced 100 mm apart. The ROV pilot used the sonar readings to sustain a consistent transect width by maintaining the distance from the camera to the substrate (at the screen horizontal mid-point) between 1.5 and 3 m.

SITE AND SURVEY LINE SELECTION
Survey site selection was made by the CDFW lead scientist to collect baseline data on both soft and hard bottom habitats within select MPAs and outside fished reference areas from Soquel Canyon to Point Buchon (Figure 1). Prior to at-sea operations, planned survey lines within each site were selected and placed across the width of the site parallel to the prevailing depth contour and bathymetry. The locations of the survey lines were chosen by selecting the desired number of planned lines and then using a systematic random approach, distributing them across the site. Survey lines were numbered according to the distance along the site boundary running from shallow to deep. The number of survey lines planned at each site was determined by the CDFW lead scientist.

POST-PROCESSING METHODS

ROV POSITIONAL DATA
Acoustic tracking systems generate numerous erroneous positional fixes due to acoustic noise and other errors caused by vessel movement. For this reason positional data was post-processed to remove outliers. Positional information, in the form of XY metric coordinates, was filtered for outliers and smoothed using a 21-point running mean (Karpov et al. 2006). Planar length of positions tracked was calculated for each second and combined with width to calculate area surveyed per second. Gaps in the positional data that occurred due to deviations from quantitative protocols, such as pulls (ROV pulled back by ship induced tension on the 45 m tether), stops (ROV stops to let the ship catch up) or loss of target altitude caused by traveling over backsides of high relief structures (visual loss of 4 m target distance for more than 6 seconds which typically occurs on the downward slope of high relief habitat) were removed from the data to be used to generate quantitative transects along each survey line. The remaining usable portions of each survey line were then divided into two different transect types; fish density transects and invertebrate density transects. Details on each transect type are described later in the post-processing methods.

SUBSTRATE AND HABITAT
A protocol to characterize substrate observed in video along survey lines was developed to be compatible to a hierarchical classification system developed by Green June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 21 et al. (1999). The video record was reviewed and substrate types were classified independently as rock, boulder, cobble, sand or mud. Rock was defined as any igneous, metamorphic or sedimentary substrate; boulder as rounded rock material that is between 0.25 and 3.0 m in diameter and clearly detached from the base substrate; cobble as broken or rounded rock material that is between 6 and 25 cm in diameter and clearly detached; sand as any granular material with a diameter less than 6 cm (may include organic debris such as shell or bone, gravel or pebble); and mud as fine silt like material.
During review of the video record, a transparency film overlay with guidelines approximating a 1.5 m wide swath was placed over a video monitor screen. Each of the substrate types are identified by the processor independently and were recorded as discrete segments of the transect by noting where it was present with a beginning and ending time code. Thus, the segments of substrate types may overlap each other along the survey line, creating areas of mixed substrate combinations (e.g. rock/sand, sand/cobble) along the transect.

A substrate segment was considered continuous until a break of two meters or greater occurred along the survey line or the substrate dropped below 20% of the total combined substrates for a distance of at least three meters. After the review process, the substrates were combined to create three independent habitat types: hard (rock and/or boulder), mixed (rock and/or boulder with cobble and/or sand and/or mud) or soft (cobble and/or sand and/or mud).

FINFISH ENUMERATION
Fish density transects used the entire forward cameras horizontal field of at the mid-screen and were calculated using a two-step approach. First, the usable portions of each survey line were divided into 25 m2 segments (subunits). Each subunit’s total percent hard and/or mixed habitat was then calculated and those with percentages below 50% hard or mixed were removed. Next, the remaining subunits were concatenated into 100 m2 transects (four sequential useable 25 m2 subunits) for use in density calculations. One spacer subunit was discarded between each transect to minimize bias of contiguous transects (spatial autocorrelation). Using this method of post-stratification generates hard substrate transects without the loss of rock/sand interface habitat which may be important to some species. All subunits and final transects are created using a labeling scheme that preserves the original data, thus future data analysis can stratify using other parameters or transect sizes.

Finfish video review and enumeration classified finfish to the lowest taxonomic level possible. Finfish that were not able to be classified to the species level were grouped into a complex of species, or recorded as unidentified. All finfish species and groupings were selected after a preliminary review of video prior to the formal enumeration processing. Several fish species were only enumerated as a complex due to visual characteristics and sizes that are difficult to discern from video and include: olive rockfish (Sebastes serranoides) and yellowtail rockfish (Sebastes flavidus), which were grouped together into the olive/yellowtail rockfish complex. Rosy rockfish (S. rosaceus) and starry rockfish (S. constellatus) were grouped into the Sebastomus rockfish complex. All combfish and eelpout species were enumerated using the combfish complex and eelpout complex respectively.

A screen overlay representing a diminishing perspective was used during fish review to approximate the transect width across the vertical viewing screen, calculated by the ranging sonar, at mid-screen (Karpov et al. 2006). The overlay served as a guide for determining if a fish was in or out of the ROV transect. Finfish enumeration was limited to a maximum distance of four meters. Using the sonar range value depicted on the screen as a gauge, the processor determined if a fish was within four meters as it entered the viewing area. Fish that entered the viewing area were only counted if more than half the fish crossed the overlay guidelines.

In order to accurately correlate the location of the fish with habitat, time code entry was made when the fish crossed the mid-screen line. For finfish that were within four meters, but swam away before they crossed the mid-screen line, time code entry was made when the location where the finfish had been observed reached the mid-screen point. All data entries were recorded in a Microsoft Access® database linked with the time code.
Fish size (total length) was estimated by the video observer with the use of two parallel lasers placed 10 cm apart aimed to hit the seafloor in the center of the video viewing screen of the forward facing camera. Fish sizes were estimated to the nearest cm and when possible tagged for future stereo sizing. Criteria for stereo sizing included fish orientation (almost perpendicular) and distance (within 2 meters) to the cameras. Only fish that were close to perpendicular and within the center of the viewing area were tagged for future stereo sizing.

INVERTEBRATE ENUMERATION
Invertebrate transects used only the field of view at the bottom of the viewing monitor, which was calculated using paired lasers as 45% of the mid screen width. Each transect was calculated by dividing the usable portions of each survey line into 30 m2 transects. The total percent hard and/or mixed habitat was then calculated. No transects were removed from the summaries based on habitat criteria.

Invertebrate video review and enumeration identified macro-invertebrates to the lowest taxonomic classification level possible, or grouped them into a complex of species. All invertebrate species and groupings were based on review of video prior to enumeration. Only macro-invertebrates with body forms and colors that were uniformly identifiable on video were selected to be enumerated (Gotshall 2005). Invertebrate species that form large colonial mats or cover large areas, were not enumerated as individuals, but rather identified as patches with discrete start and stop points along the transect and given a coverage code to quantify the total coverage within the viewing area of the patch. Patches were coded for percent cover using four groupings: 1) less than 25% cover, 2) between 25% and 50% cover, 3) between 50% and 75% cover, and 4) greater than 75% cover. Six species/groupings were quantified using these methods: Unidentified brachiopod species, mat-forming brittle star species, club-tipped anemone (Corynactus californica), market squid eggs, unidentified zoanthid species, and feather stars (class Crinoidea). All identifications to species level were based on visual attributes and should be considered the best possible identification based on appearance only.

A screen overlay was also used during invertebrate review and enumeration to approximate the transect width, calculated by the ranging sonar, at the bottom of the screen. The diminishing perspective overlay lines served as a guide for determining if an invertebrate was in or out of the ROV transect. The overlay used for invertebrate enumeration was the same as the overlay used in habitat classification, allowing for direct correlation of habitat to each invertebrate observation. In order to accurately correlate the location of the invertebrate with the habitat, time code entry was made when the invertebrate crossed the bottom of the screen line. All data entries were recorded in a Microsoft Access® database linked with the time code. Invertebrates that entered the viewing area were only counted if more than half the animal crossed the overlay guidelines at the bottom of the screen.

RESULTS

SURVEY TOTALS
ROV surveys were conducted from September 16, to October 14, 2016. A total of 97.4 km were surveyed and post-processed across 33 sites, distributed over 12 study locations (Table 1). A total of 68% of the area surveyed was made up of hard and/or mixed habitat types (66.4 km).
The number of transects (both fish and invertebrate) varied by site and was dependent on the number of survey lines planned, and the amount of available rocky habitat (fish transects only) at each site. A total of 1,023 post-stratified fish transects (100 m2) and 4,346 invertebrate transects (30 m2) were generated from the 146 survey lines sampled (Table 1).

SUBSTRATE AND HABITAT
Substrate and habitat composition for all study sites and survey lines processed are given in Table 2. The ‘Percent by substrate’ represents the ratio of the survey line that has a given substrate compared to the total line. Each substrate type (i.e. Rock, boulder, cobble, etc.) are not relative percentages to other substrate categories. Habitat percentages derived from substrate types and are presented as the proportion of the survey line that contained that specific habitat type.
Rock was the dominant substrate observed, accounting for an average of 67% of the total substrate coverage at each site. Sand and mud were observed next most commonly observed substrate types, accounting for 27% and 26% of the average total substrate coverage at each site, respectively. Boulder and cobble were the least observed substrates, accounting for an average of only 3% and 8% of the observed substrate at each site, respectively.
Hard habitat was the dominant habitat observed over all study sites, accounting for an average of 43% of the habitat surveyed at each site. Soft and mixed habitats were less common, accounting for an average of 33% and 24% of the habitat observed at each site, respectively.

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June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 23

FINFISH AND MACRO-INVERTEBRATE SUMMARIES

Total counts for fish and invertebrates, as well as counts per kilometer of transect surveyed by site, are given in Table 3.
More fish were counted at Point Sur, than any other study location. A total of 83,618 individuals were enumerated at all of the Point Sur sites combined, which represented 26% of the total number of fish counted at all survey locations. Point Sur also had a high average count of fish per km, with 6,709 fish per km at all sites combined. Point Lobos had the highest average counts of fish per km, just slightly more than Point Sur, with 6,993 fish counted per km. Soquel Canyon had the lowest number of fish enumerated, with a total count of only 1,330 fish at the SQ3 site.

Approximately two times more macro-invertebrates were counted at Portuguese Ledge, than at any other study location. A total of 21,072 individuals were enumerated (not including invertebrate patch cover) at all of the Portuguese Ledge sites combined, which represented approximately 24% of the total number of invertebrates counted at all survey locations. Over half of those were counted at just one site, PLR1. Big Creek study location had the second highest number of invertebrates, with a total of 17,168 counted at all sites combined.

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FISH COUNTS
A complete list of total counts for all 101 finfish species and groupings June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 25 identified from video collected at all sites combined in September and October of 2016 are shown in Table 4. Of the 320,152 total finfish observed at all sites, the majority (95.5%) were identified as a rockfish species or grouping. Of the smaller rockfish species/groupings, YOY were the most commonly observed, accounting for over 80.5% of all fish observations.

June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 26 While, the small schooling rockfish species/groupings (typically <15 cm), which included Shortbelly, Halfbanded, Squarespot, Pygmy and other unidentified small schooling rockfishes, were less common, accounting for 7.3% of all fish observations. Larger rockfish species (>15 cm) were also less commonly observed, accounting for 7.7% of all fish observations. Larger epi-benthic schooling rockfish (such as Blue, Black, Olive/Yellowtail and Widow rockfishes) represented the largest proportion of the large rockfish observations, accounting for 62.2% of the total large rockfish observations. Benthic and demersal rockfish (such as Vermilion, Gopher, Canary and Copper rockfishes) accounted for 25.6% of the total large rockfish observations. Due to the low visibility conditions of the North Coast, the remaining 12.2% of the large rockfish observed were classified as unidentified rockfish.

Non-rockfish species represented a substantially smaller proportion of the total June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 27 fish observations, accounting for a combined total of just 4.5% of the total fish counts. Unrecognized and unidentified fish accounted for a substantial number (57.8%) of the non-rockfish species observations. Kelp and Painted Greenling, Lingcod, flatfish and surfperch made up approximately 23% of the total non-rockfish counts, or just 1% of the total fish observations.

Due to poor water visibility and video resolution limitations, positive identifications were not always possible and a proportion of the fish observations were classified as “unidentified”. In addition, smaller fish were more difficult to recognize than larger ones. When possible, unidentified observations were placed into groupings such as unidentified rockfish or unidentified flatfish. The unidentified categories of fish only accounted for a little over 4% of the total finfish observations

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June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 29

INVERTEBRATE COUNTS
A complete list, including total counts of all 103 macro-invertebrate species and June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 30 groupings (not including invertebrate patches) identified from video collected from September and October of 2016, is given in Table 5.
Of the 88,236 individual invertebrates observed at all sites, sea stars (from 25 species/groupings) were the most abundant, accounting for 25.4% of all invertebrates enumerated. Two species, the bat star and the red sea star, accounted for nearly 80% of the total sea star observations (47.6% and 31.4% respectively). Other commonly observed sea stars included: the long legged sunflower star, the Henricia star complex, cookie star and fish eating star, which combined accounted for 15.4% of the total sea star observations. The remaining 19 species/groupings accounted for the other ~5.6% of sea star observations.

June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 31 Urchins represented 19.8% of the total invertebrate observations, with 17,449 individuals enumerated from six species/groupings. White urchins were the most abundant, accounting for over 60% of the total urchin observations. The red sea urchin, purple sea urchin and fragile pink urchin were also frequently observed, accounting for 20.8%, 10.3% and 8.2% of the total urchin observations, respectively.
Corals and gorgonians represented 12.7% of the total invertebrate observations, with 11,191 individuals enumerated from 12 species/groupings. Red gorgonians were the most abundant, accounting for nearly 43% of all coral and gorgonian observations. The white sea pen, UI dead gorgonians, UI sea pens, and sea whips were also frequently observed, accounting for 22.2%, 18.3%, 7.9% and 6.3% of the total coral and gorgonian observations, respectively.

Other invertebrates that were commonly observed included anemones June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 32 (from 10 species/groupings), crabs (7 species/ groupings), sea cucumbers (7 species/ groupings) and sponges (9 species groupings) which combined accounted for nearly 30% of the total invertebrate observations. The most abundant species from each were the white-plumed anemone, pelagic red crab, California sea cucumber and UI nipple sponge, which combined accounted for 20.3% of the total invertebrate observations.

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June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 34

INVERTEBRATE PATCH COVER
Invertebrate patch cover for four quantified species/groupings is given in Table 6. June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 35 The club-tipped anemone was the most commonly observed invertebrate patch, observed on over 1,993 m2 and occurring at 25 of the 30 sites surveyed in September and October of 2016. The percent of total area containing club-tipped anemones was highest at Church Rock, where club-tipped anemones were present on over 12% of the total area surveyed there. They were also commonly observed at four of the Point Lobos sites covering 3.6% of the total area surveyed at all four sites combined.

Feather stars (Crinoidea) were observed at fewer sites (13) than club-tipped anemones, but covered just slightly less area, 1,701 m2. They were most abundant at June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 36 the Portuguese Ledge study location, where they were observed at all 3 sites, covering 3.4% of the total area surveyed at all three sites combined.

Other patch-cover invertebrates observed include: brittle stars, UI zoanthids, UI brachiopoda, market squid eggs and Lophelia complex. Brittle stars covered a total of 546 m2 and were only observed at three sites, June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 37 one in Point Lobos (PL4) and two at Big Creek (BC2 and BC3). UI zoanthids covered a total of 98 m2, and were only observed at three of the southern study locations, Big Creek (site BC6), Morro Bay (site MB3) and Church Rock (site CR). UI brachiopoda, market squid eggs and Lophelia complex were each present at only one site, and covered only 44 m2, 2 m2 and 25 m2, respectively.

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June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 39

PROJECT DELIVERABLES
MARE has delivered to the CDFW lead scientist six copies of the primary video (forward and downward facing) for the entire survey on DVD. Each copy has been provided in individual binders with a corresponding look-up catalog that provides survey location, date, dive number and DVD disc number. Each DVD has an accompanying storyboard detailing the ROV name, date, dive number, location, and transect ID number. In addition to the six DVD copies of the survey, MARE has also delivered a full copy of the master HD forward video on a portable hard. All video recordings contain a timecode audio track that can be used to automatically extract GPS time from the video.

In addition to the primary video record, MARE has also provided a complete hard drive copy of all high definition (HD) still photos, including the standard resolution stereographic video, collected during the survey. Stereographic video was recorded continuously during ROV dives, capturing more than 30 individual fish/km (for abundant fish species) with accuracy to 0.5 cm. All imagery has been provided on a PC based hard drive and each file has been labeled using a naming scheme that provides date and GPS timecode.

A copy of the master Microsoft Access database, which contains all the raw and post-processed data has also been provided to the CDFW lead scientist. These data will include ROV position (raw and cleaned), ROV sensor (depth, temperature, salinity, dissolved oxygen, forward and downward range, heading, pitch and roll), calculated transect width and area, substrate and habitat, fish and invertebrate identifications and invertebrate patch location and percent cover. Included in the processed position table are the computed transect identifications for both fish and invertebrate transects (see methods). Also provided to the CDFW lead scientist were the GIS shapefiles for all survey lines and site boundaries sampled.

MAPS
Maps of all study locations and sites surveyed within each location are given in Figures 1 – 6. All sites were surveyed in September and October 2016.

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Figure 1. Study locations (blue boxes) from Soquel Canyon to Point Buchon and the sites (red boxes) surveyed within each location.

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Figure 2. ROV survey lines within the Soquel Canyon (SQ3) and Portuguese Ledge (PRL1, PRL2, PRL3) site boundaries.

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Figure 3. ROV survey lines within the Pacific Grove (PG1, PG2), Asilomar (AS1, AS2, AS4), Point Lobos (PL1, PL4, PL7, PL11) and Carmel Bay (CB1) site boundaries.

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Figure 4. ROV survey lines within the Point Sur (PS2, PS3, PS5) and Big Creek (BC7) site boundaries.

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Figure 5. ROV survey lines within the Big Creek (BC1, BC2, BC3, BC4, BC5, BC6) site boundaries.

June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 45

Figure 6. ROV survey lines within the Piedras Blancas (PIE1, PIE2) site boundaries.

June 2017 - Coastal Impact Assistance Program-E Soquel Canyon to Point Buchon 2017 46

Figure 7. ROV survey lines within the Morro Bay (MB1, MB2, MB3, MB4), Church Rock (CR) and Point Buchon (PB2, PB5) site boundaries.

REFERENCES

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. Cailliet. 1999. A classification scheme for deep
seafloor habitats: Oceanologica Acta 22(6):663–678.

Gotshall, D.W. 2005. Guide to marine invertebrates – Alaska to Baja California,
second edition (revised). Sea Challengers, Monterey, California, USA.

Karpov, K., A. Lauermann, M. Bergen, and M. Prall. 2006. Accuracy and
Precision of Measurements of Transect Length and Width Made with a
Remotely Operated Vehicle. Marine Technical Science Journal 40(3):79–85.

Veisze, P. and K. Karpov. 2002. Geopositioning a Remotely Operated Vehicle for
Marine Species and Habitat Analysis. Pages 105–115 in Undersea with GIS. Dawn J.
Wright, Editor. ESRI Press.

deepdirk2021-07-21T18:49:17-08:00June 22nd, 2017|research|

June 2017 – Oceana Deep sea Coral and Sponge 2017 Final Report

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Oceana Deepsea Coral and Sponge 2017 Final Report

June 5, 2017

Andrew R. Lauermann, Heidi M. Lovig, Yuko Yokozawa, Johnathan Centoni, Greta Goshorn

Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.org

TABLE OF CONTENTS

INTRODUCTION 4

METHODS 5

DATA COLLECTION 5

ROV Equipment 5

ROV Sampling Operations 6

POST-PROCESSING 6

Substrate and Habitat 7

Finfish and Invertebrate Enumeration 7

RESULTS 9

SURVEY TOTALS 9

SUBSTRTATE AND HABITAT 11

Substrate 11

Habitat 11

FISH AND INVERTEBRATE TOTAL COUNTS 11

Fish 11

Invertebrates 11

FISH AND INVERTEBRATE DENSITY 16

Fish 16

Invertebrates 16

MAPS OF TRANSECTS 20

Southeast Santa Rosa Island 21

Footprint Deep Ridge 22

West Santa Barbara Island 23

West Santa Barbara Island 24

West Santa Barbara Island 25

South Santa Barbara Island 26

West Butterfly Bank 27

UNIDENTIFIED SPECIES LIST 28

Anemones 28

Boot Sponges 28

UI Lobed Sponge 29

Other Sponges Observed 30

UI Bubblegum Coral 31

REFERENCES 32

INTRODUCTION

From August 7th through 11th of 2016, four study locations were surveyed using a remotely operated vehicle (ROV) within the Sothern California Bight. The goal of this Oceana lead expedition was to collect high definition video and still imagery within unique deep-water sponge and coral habitats. Study areas and dive locations were based on bathymetry mapping data and/or data from NOAA’s Deep Sea Coral National Observation Database. The data collection protocols used for this project were similar to those used inside the Channel Islands National Marine Sanctuary, Monterey Bay National Marine Sanctuary, Farallon Islands National Marine Sanctuary, Cordell Bank National Marine Sanctuary and at over 175 sites in and adjacent to California’s marine protected areas network.

During the 5-day expedition, deep-water ROV surveys were conducted near Santa Rosa Island, Footprint MPA, Santa Barbara Island and Butterfly Bank. During each dive, ROV survey lines were broken into 15-minute transects at the discretion of Oceana scientists onboard. Each 15-minute transect and the corresponding positional data were subsequently post-processed in the lab by Marine Applied Research and Exploration (MARE) using standardized methods that were developed in partnership by the California Department of Fish and Wildlife and MARE. These methods have been used since 2003 to process over 2,000 km of ROV video.

The following report describes the data collection and post-processing methods used for the survey. Data summaries are provided which highlight post-processing results and a complete database of all data collected will be provided to Oceana.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 49

METHODS

DATA COLLECTION

ROV Equipment

An observation class ROV, the Beagle, was used to complete benthic surveys of select Southern California Bight study locations. The ROV was equipped with a three-axis autopilot including a rate gyro- damped compass and altimeter. Together, these allowed the pilot to maintain a constant heading (± 1 degree) and constant altitude (± 0.3 m) with minimal corrections. In addition, a forward speed control was used to help the pilot maintain a consistent forward velocity between 0.25 and 0.5 m/sec while on transect. A Tritech® 500 kHz ranging sonar, which measure distance across a

range of 0.1–10 m using a 6° conical transducer, was used as the primary method for measuring transect width from the forward facing HD video. The transducer was pointed at the center of the camera’s viewing area and was used to calculate the distance to middle of screen, which was subsequently converted to width using the known properties of the cameras field of view. Readings from the sonar were averaged five times per second and recorded at a one-second interval with all other sensor data. Measurements of transect width using a ranging sonar are accurate to ± 0.1 m (Karpov et al. 2006). ROV Beagle was also equipped with parallel lasers set with a 10 cm spread and positioned to be visible in the field of view of the primary forward camera. These lasers provided a scalable reference of size when reviewing video.

An ORE Offshore Trackpoint III® ultra-short baseline acoustic positioning system with ORE Offshore Motion Reference Unit (MRU) pitch and roll sensor was used to reference the ROV position relative to the ship’s Wide Area Augmentation System Global Positioning System (WAAS GPS). The ship’s heading was determined using a KVH magnetic compass. The Trackpoint III® positioning system calculated the XY position of the ROV relative to the ship at approximately two-second intervals. The ship-relative position was corrected to real world position and recorded in meters as X and Y using the World Geodetic System (WGS)1984 Universal Transverse Mercator (UTM) coordinate system using HYPACK® 2013 hydrographic survey and navigation software. Measurements of ROV heading, depth, altitude, water temperature, camera tilt and ranging sonar distance were averaged over a one-second period and recorded along with the position data.

The ROV was equipped with four cameras, including one forward facing high definition (HD) camera, two standard definition cameras and one HD still camera. The primary

data collection camera (HD video camera) and HD still camera were oriented obliquely forward. All video and still images were linked using UTC timecode recorded as a video overlay or using the camera’s built-in time stamp which was set to UTC time each day.

All data collected by the ROV, along with subsequent observations extracted during post-processing of the video, was linked in a Microsoft Access® database using GPS time. GPS time was used to provide a basis for relating position, field data and video observations (Veisze and Karpov 2002). Data management software was used to expand all data records to one second of Greenwich Mean Time (GMT) time code. During video post-processing, a Horita® Time Code Wedge (model number TCW50) was used in conjunction with a customized computer keyboard to record the audio time code in a Microsoft Access® database.

ROV Sampling Operations

R/V Shearwater, a 22 m NOAA research vessel, was used to complete the 2016 survey. At each site, the ROV was piloted along 15-minute transect lines (determined during dive) and was flown off the vessel’s stern using a “live boat” technique that employed a 317.5 kg (700 lb) clump weight. Using this method, all but 50 m of the ROV umbilical was isolated from current-induced drag by coupling it with the clump weight cable and suspending the clump weight at least 10 m off the seafloor. The 45 m tether allowed the ROV pilot sufficient

maneuverability to maintain a constant speed (0.5 to 0.75 m/sec) and a straight course down the planned survey line, while on transect.

POST-PROCESSING

Following data collection, the ROV position data was processed to remove outliers and data anomalies caused by acoustic noise and vessel movement, which are inherent in these systems (Karpov et al. 2006). In addition, deviations from sampling protocols

such as pulls (ROV pulled by the ship), stops (ROV stops to let the ship catch up), or loss of target altitude caused by traveling over backsides of high relief structures, were identified in the data and not used in calculations of density for fish and invertebrate species.

Substrate and Habitat

For each study area, all video collected was reviewed for up to six different substrate types: rock, boulder, cobble, gravel, sand and mud (Green et al. 1999). Each substrate was recorded as discrete segments by entering the beginning and ending UTC timecode. Substrate annotation was completed in a multi-viewing approach, in which each substrate type was recorded independently, enabling us to capture the often overlapping segments of substrates (Figure 1). These overlapping substrate segments allowed identification of mixed substrate areas along the transect line.

After the video review process, the substrate data was combined to create three independent habitat types: hard, soft, and mixed habitats (Figure 1). Rock and boulder were categorized as hard substrate types, while cobble, gravel, sand, and mud were all considered to be unconsolidated substrates and categorized as soft. Hard habitat was defined as any combination of the hard substrates, soft habitat as any combination of soft substrates, and mixed habitat as any combination of hard and soft substrates.

Finfish and Invertebrate Enumeration

After completion of habitat and substrate review, video was processed to collect data for use in estimating finfish and macro-invertebrate distribution, relative abundance and density. During the review process, both the forward and down video files were simultaneously reviewed, yielding a continuous and slightly overlapping view of what was present in front of and below the ROV. This approach effectively increased the resolution of the visual survey, by identifying animals that were difficult to recognize in the forward camera, but were clearly visible and identifiable in the down camera.

During multiple subsequent viewings, finfish and macro-invertebrates were classified to the lowest taxonomic level possible. Observations that could not be classified to species level were identified to a taxonomic complex, or recorded as unidentified (UI). During video review, both the HD video and HD still imagery were used to aid in species identification. Each fish or invertebrate observation was entered into a Microsoft Access® database along with UTC timecode, taxonomic name/grouping, sex/developmental stage (when applicable), and count. Fish, were sized using the two sets of parallel lasers to estimate total length. Not all fish were sizeable due to their position within the field of view of the ROV.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 53

Figure 1. (a) Basic ROV strip transect methodology used to collect video data along the sea floor, (b) overlapping base substrate layers produced during video processing and (c) habitat types (hard, mixed soft) derived from the overlapping base substrate layers after video processing is completed.

All clearly visible finfish and macro-invertebrates were enumerated from the video record. Invertebrate species that typically form large colonial mats or cover large areas and could not be counted individually were instead recorded as invertebrate layers (with discrete start and stop points and percent cover estimates for each segment). Invertebrate patch segments were coded for percent cover using four groupings: 1) less than 25% cover, 2) 25% to 50% cover, 3) 50% to 75% cover and 4) greater than 75% cover. Only data on individual invertebrate observations are presented in this report. Invertebrate patch data are provided as part of the final data submission for use in future analysis.

RESULTS

Due to technical difficulties with the ROV’s USBL tracking system, several ROV dives surveyed during the 2016 expedition do not have positional data. These dives include, dive #8 at East Butterfly Bank and dive #11 at South Santa Rosa Island. Because there was no base data to correlate video observations, dive #8 at East Butterfly Bank was not video post-processed. However, video collect on dive #11 at South Santa Rosa Island had already been processed when it was discovered that the positional files were corrupted. Therefore, fish and invertebrate observational data at South Santa Rosa Island will be included in the data package, but those observations are not presented in the results section of this report.

In addition, dive #6 at West Butterfly Bank was aborted before completing the transect; and no transects were defined during dive #10 at Footprint Ridge.

SURVEY TOTALS

Total number of fish and macro-invertebrates observed and sampling effort and are given in Table 1. Over 18,000 fish and macro-invertebrates were observed at depths ranging from 126 m to 379 m, and a total of 10.8 kilometers of seafloor was surveyed during the completion of 23 transects at all five study areas combined (Figure 2).

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 54

Table 1. Total sampling effort at five Southern California study areas, showing total distance, area, fish and macro-invertebrate counts and depth range.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 55

Figure 2. ROV dive locations for the five study areas video post-processed.

SUBSTARTATE AND HABITAT

Substrate

Substrate types observed on transects are not mutually exclusive and represent the proportion of the total surveyed transect distance that has a given substrate present (see methods for full description). Overall, mud, cobble and rock substrates were the most common (Table 2). Sand was only observed at Southeast Santa Rosa Island (the shallowest area surveyed).

Habitat

Habitat types derived from substrate data show that across all sites, soft and mixed habitats were the most common, combined accounting for between 81% – 100% of the habitat observed across all sites (Table 2). Hard habitats were the least common accounting for only 0% to 19 % of the available habitat across all sites.

Table 2. Percent substate and habitat types encountered at the five study areas.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 56

FISH AND INVERTEBRATE TOTAL COUNTS
Fish
Rockfish were the most commonly observed fish accounting for 92.7% of the total fish count at all study areas combined (Table 3). Halfbanded rockfish were the most abundant rockfish species, accounting for nearly 40% of all of the fish observations. The next most abundant species were the following rockfish: YOY, Swordspine rockfish, Sebastomus rockfish, UI rockfish and Pygmy rockfish which combined accounted for another 44% of all fish observations. Cowcod, a currently listed overfished species, was observed, representing 0.3% of the total count. The most abundant non-rockfish grouping was the combfish complex, accounting for 2.4% of the fish observations.

Invertebrates
Four species/groupings of macro-invertebrates accounted for approximately 65% of the total invertebrate counts (Table 4). The most abundant species observed was the fragile pink urchin, which accounted for approximately 26% of the overall count; followed by the squat lobster, UI lobed sponge and white slipper sea cucumber which accounted for the remaining 39%.

Over 3,400 structure forming sponges from 11 species/groupings were observed, accounting for 26% of the total invertebrate observations. Corals were commonly observed and represented 9% of the observations (11 species/groupings). Gorgonians were the most commonly observed coral type, with 3 species/groupings representing the majority of the observations: gray, red swiftia and yellow gorgonians. Fifteen species/groupings of sea stars were also observed, but represented less than 5% of the total macro-invertebrate observations.

Table 3. Overall fish counts are presented in order from highest to lowest abundance.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 57

Table 4. Overall macro-invertebrate counts are presented in order from highest to lowest abundance.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 58

Table 4. Continued.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 59

FISH AND INVERTEBRATE DENSITY

Fish

At Southeast Santa Rosa Island, fish densities were higher than any other study area, with 53 fish/100 m2 (Table 5). Halfbanded rockfish represented the majority of the density, accounting for over 45 fish/100 m2. When Halfbanded rockfish are not included in the overall densities of each study area, West Santa Barbara Island has the highest overall density at almost 12 fish/100 m2. At West Butterfly Bank, the lowest overall fish density was observed with just over 2 fish per 100 m2.

Halfbanded rockfish

After Halfbanded rockfish, the next most abundant species/groupings were YOY and swordspine rockfish at West Santa Barbara Island. Sebastomus rockfish, unidentified rockfish and small benthic fish were also common across all sites. Bank rockfish were observed at all sites except at Southeast Santa Rosa Island. Cowcod were only observed at South Santa Barbara Island.

The number of species observed at each study location varied greatly. June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 61 Of the 46 species/groupings observed, 30 were observed at West Santa Barbara Island, the highest of all study areas. In contrast, the lowest number of fish species observed was at West Butterfly Bank, with only 11 species/groupings observed.

Invertebrates

Cowcod

The Footprint Deep Ridge study area had the highest overall macro-invertebrate density, with over 196 invertebrates/100 m2 (Table 6). At Footprint Deep Ridge, fragile pink urchin densities were the highest observed, with densities over 7 times higher than the next most abundant species/grouping, which was the squat lobster at West Butterfly Bank. West Santa Barbara Island had the most species/groupings of any study area surveyed with a total of 52 species/groupings (Table 6).

In contrast, Southeast Santa Rosa Island had the lowest number of invertebrate species/groupings observed and lowest total invertebrate density. At Southeast Santa Rosa Island, a total of 20 invertebrate species/groupings produced a total density of just over 8 invertebrates/100 m2. All other sites overall densities exceeded 33 invertebrates/100 m2.

Coral and sponge species were observed at all study areas, with some notable differences at each location. The gray gorgonian was only observed at West Santa

Barbara Island and Footprint Deep Ridge. Densities of the gray corals were almost 16 times June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 62 higher at West Santa Barbara Island than at Footprint Deep Ridge. Black corals were found at both the Footprint Deep Ridge and Santa Barbara Island sites, though black corals were over four times denser at Footprint Deep Ridge.

Other corals observed included: an unidentified small orange gorgonian (UI orange gorgonian) at Footprint Deep Ridge and West Butterfly Bank, a yellow gorgonian observed at all locations except Footprint Deep Ridge, and the red swiftia gorgonian found at all study areas.

Gray gorgonian

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 63 Structure forming sponges were observed at all study areas, with the highest density observed at West Butterfly Bank. At this site, three sponge types: the hairy boot sponge, UI laced sponge and UI lobed sponge accounted for over 38 sponges per 100m2. Trumpet sponges were unique to only West Butterfly Bank, while the UI large yellow sponge was only observed at West Santa Barbara Island.

UI hairy boot sponge

Sponge identification was based on morphology, which created June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 64
a particular issue for one morphotype: the UI lobed sponge. UI lobed sponges were observed at all study areas, but the type of lobed sponge varied (see unidentified species list). Lobed sponges at West Butterfly Bank were almost entirely ‘Type 3’ lobed sponge, while at both Santa Barbara Island study areasthe lobed sponges were predominantly ‘Type 1’. At Southeast Santa Rosa Island, lobed sponges were entirely ‘Type 1’, while Footprint Deep Ridge was 50% ‘Type 1’ and 50% ‘Type 2’.

MAPS OF TRANSECTS

Maps of ROV transects for all four study areas surveyed are shown in Figures 3 – 9. Each set of maps shows select invertebrates that were of species interest during the survey, and substrate types encountered along each transect.

Select invertebrates include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

Southeast Santa Rosa Island

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 68

Figure 3. ROV transects at Southeast Santa Rosa Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

Footprint Deep Ridge

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 69

Figure 4. ROV transects at Footprint Deep Ridge Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

West Santa Barbara Island

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 70

Figure 5. ROV transects at West Santa Barbara Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

West Santa Barbara Island

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 71

Figure 6. ROV transects at West Santa Barbara Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

West Santa Barbara Island

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 72

Figure 7. ROV transects at West Santa Barbara Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

South Santa Barbara Island

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 73

Figure 8. ROV transects at South Santa Barbara Island showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 74

Figure 9. ROV transects at West Butterfly Bank showing select invertebrates (top) and substrates encountered (bottom). Invertebrate grouping include: black corals, gorgonians (UI orange, red, yellow, gray, red swiftia and unidentified gorgonians), other corals (bubblegum and mushroom corals), basket stars and sponges (laced, large yellow, boot, hairy boot, branched, lobed, vase and trumpet sponges).

UNIDENTIFIED SPECIES LIST

Anemones

The three Unidentified anemone species were observed:

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 75

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 76

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 77

UI anemone 1 UI anemone 2 UI anemone 4

Boot Sponges

Two boot sponges were observed, one ‘hairy’ type and the more typically seen boot sponge:

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 78

UI hairy boot sponge UI boot sponge

UI Lobed Sponge

Three UI lobed sponges were observed. The visually estimated percent of UI lobed sponges for each type by location are given in Table 7.

Type 1: Forms a thicker, softer, more variable mat. It is variable color, and may have darker margins.

Type 2: Forms thin, rigid, sheet-like structures, and is off-white in color.

Type 3: Ossicles are large and clearly visible, and is bright white in color.

Other Sponges Observed

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 82

UI Bubblegum Coral

Of the 24 UI bubblegum coral observed, only one large, highly branched individual was enumerated across all sites (upper right photo). All other bubblegum coral observed resembled the other three photos shown here.

June 2017 - Oceana Deep sea Coral and Sponge 2017 Final Report 83

REFERENCES

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. Cailliet. 1999. A classification scheme for deep seafloor habitats: Oceanologica Acta 22(6):663–678.

Karpov, K., A. Lauermann, M. Bergen, and M. Prall. 2006. Accuracy and Precision of Measurements of Transect Length and Width Made with a Remotely Operated Vehicle. Marine Technical Science Journal 40(3):79–85.

Veisze, P. and K. Karpov. 2002. Geopositioning a Remotely Operated Vehicle for Marine Species and Habitat Analysis. Pages 105–115 in Undersea with GIS. Dawn J. Wright, Editor. ESRI Press.

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deepdirk2021-03-10T21:21:07-08:00June 1st, 2017|research|

May 2017 – North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems

North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems

Lead PI: Andrew R. Lauermann
Co-PI: Dirk Rosen
Contributors:
Kelsey Martin-Harbick and Heidi Lovig – Marine Applied Research
and Exploration
Donna Kline and Rick Starr – Moss Landing Marine Laboratories
Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.

Final Report: Mid-depth and Deep Subtidal Ecosystems – 2017
Baseline Characterization and Monitoring of the MPAs along
the North Coast: ROV Surveys of the Subtidal (20-500 m)

Marine Applied Research and Exploration
320 2nd Street, Suite 1C, Eureka, CA 95501 (707) 269-0800
www.maregroup.org

Final Report: Mid-depth and Deep Subtidal Ecosystems – 2017

ACKNOWLEDGEMENTS

Generous Funding Support Provided by:

California Ocean Protection Council
California Ocean Science Trust
California Sea Grant (Project #R/MPA-41A; Grant Number 12-029)
Campbell Foundation
J.W. and H.M. Goodman Family Charitable Foundation
The Seed Fund

Key Office and Field Support:

Yuko Yokozawa – MARE GIS and Data Management Specialist
Steve Holtz – MARE ROV Operations Deck Officer
Johnathan Centoni – MARE Senior Video Analyst
Megan Nativo – MARE Data Management Specialist
Andrea Jolley – MARE Senior Video Analyst
Allison Lui – MARE Video Analyst
Portia Saucedo – MARE Video Analyst
Jessica Coming – MARE Office Technician
Daniel Troxel – MARE Video Analyst
Samuel Parker – MARE Video Analyst

Key Partnerships:

Mike Prall – California Department of Fish and Wildlife
Robert Pedro – Captain R/V Miss Linda
Garry Taylor – First Mate R/V Miss Linda
Jerry Evans – Deck crew R/V Miss Linda
Mark Burnap – Deck crew R/V Miss Linda

“LIST OF FIGURES”

TABLE OF CONTENTS
LIST OF FIGURES …………………………………………………………………………………………………….. 9
LIST OF TABLES……………………………………………………………………………………………………….14
EXECUTIVE SUMMARY …………………………………………………………………………………………….15
INTRODUCTION ……………………………………………………………………………………………………….20
Background ……………………………………………………………………………………………………………20
Study Region………………………………………………………………………………………………………….20
Goals and Objectives ………………………………………………………………………………………………21
METHODS………………………………………………………………………………………………………………..22
Study Design………………………………………………………………………………………………………….22
Study Locations …………………………………………………………………………………………………..22
Transect Selection ……………………………………………………………………………………………….22
Data Collection……………………………………………………………………………………………………….24
ROV Equipment…………………………………………………………………………………………………..24
ROV Applications…………………………………………………………………………………………………25
ROV Sampling Operations…………………………………………………………………………………….26
Post-Processing ……………………………………………………………………………………………………..26
Substrate and Habitat …………………………………………………………………………………………..27
Finfish and Invertebrate Enumeration ……………………………………………………………………..28
Analysis…………………………………………………………………………………………………………………29
Characterization of MPAs and Reference Areas ……………………………………………………….29
Analysis of Index Sites………………………………………………………………………………………….30
Fish Depth Distribution………………………………………………………………………………………….31
Regional Fish Size Distribution ………………………………………………………………………………32
Between Year Comparison ……………………………………………………………………………………33
RESULTS AND DISCUSSION……………………………………………………………………………………..35
Baseline Survey Totals…………………………………………………………………………………………….35
Fish Totals ………………………………………………………………………………………………………….37
Invertebrate Totals ……………………………………………………………………………………………….40
BASELINE CHARACTERIZATION OF STUDY AREAS……………………………………………………43
Point St. George Reef Offshore SMCA and Reference Area ………………………………………….43
Substrate ……………………………………………………………………………………………………………44
Habitat ……………………………………………………………………………………………………………….45
Fish……………………………………………………………………………………………………………………46
Invertebrates……………………………………………………………………………………………………….47
Reading Rock SMR and Reference Area ……………………………………………………………………48
Substrate ……………………………………………………………………………………………………………49
Habitat ……………………………………………………………………………………………………………….50
Fish……………………………………………………………………………………………………………………51
Invertebrates……………………………………………………………………………………………………….52
Mattole Canyon SMR and Reference Area………………………………………………………………….53
Substrate ……………………………………………………………………………………………………………54
Habitat ……………………………………………………………………………………………………………….55
Fish……………………………………………………………………………………………………………………56
Invertebrates……………………………………………………………………………………………………….57
Ten Mile State Marine Reserve and Reference Area…………………………………………………….58
Substrate ……………………………………………………………………………………………………………59
Habitat ……………………………………………………………………………………………………………….60
Fish……………………………………………………………………………………………………………………61
Invertebrates……………………………………………………………………………………………………….62
ANALYSIS OF INDEX SITES ………………………………………………………………………………………63
Fish Densities ……………………………………………………………………………………………………..63
Similarity Test ……………………………………………………………………………………………………..64
Point St. George Index Sites………………………………………………………………………………….65
Reading Rock Index Sites……………………………………………………………………………………..66
Mattole Canyon Index Sites …………………………………………………………………………………..66
Ten Mile Index Sites …………………………………………………………………………………………….66
FISH DEPTH DISTRIBUTION………………………………………………………………………………………68
Rocky Reef Transects ……………………………………………………………………………………………..69
Point St. George – Rocky Reef ……………………………………………………………………………….69
Reading Rock – Rocky Reef…………………………………………………………………………………..70
Mattole Canyon – Rocky Reef ………………………………………………………………………………..71
Ten Mile – Rocky Reef…………………………………………………………………………………………..72
Canyon Transects …………………………………………………………………………………………………..74
Mattole Canyon – Canyon ……………………………………………………………………………………..74
FISH SIZE DISTRIBUTION………………………………………………………………………………………….77
Laser-based Size Estimates…………………………………………………………………………………..77
Black Rockfish …………………………………………………………………………………………………….78
Blue Rockfish………………………………………………………………………………………………………79
Canary Rockfish…………………………………………………………………………………………………..80
Copper Rockfish ………………………………………………………………………………………………….81
Olive/Yellowtail Rockfish……………………………………………………………………………………….82
Quillback Rockfish ……………………………………………………………………………………………….83
Vermillion Rockfish ………………………………………………………………………………………………84
Yelloweye Rockfish………………………………………………………………………………………………85
Lingcod………………………………………………………………………………………………………………86
Kelp Greenling …………………………………………………………………………………………………….87
Analysis of Laser-based Sizing Technique……………………………………………………………….89
BETWEEN YEAR COMPARISON ………………………………………………………………………………..91
Rocky Reef Index Sites ……………………………………………………………………………………………91
Fish……………………………………………………………………………………………………………………91
Invertebrates……………………………………………………………………………………………………….91
Soft Bottom Transects ……………………………………………………………………………………………..93
MONITORING RECOMMENDATIONS………………………………………………………………………….94
FINANCIAL REPORT …………………………………………………………………………………………………97
LITERATURE CITED………………………………………………………………………………………………….98
APPENDIX 1. NCSR Fish Mean Densities (100 m2) by Transect Type for 2014 and 2015….100
APPENDIX 2. NCSR Invertebrate Mean Densities (100 m2) by Transect Type for 2014 and
2015……………………………………………………………………………………………………………………….102
APPENDIX 3. Full Baseline Characterizations by Study Location. ……………………………………104
Point St. George Reef Offshore SMCA and Reference Area ………………………………………..104
Survey Totals…………………………………………………………………………………………………….105
Substrate ………………………………………………………………………………………………………….105
Habitat ……………………………………………………………………………………………………………..106
Fish………………………………………………………………………………………………………………….108
Rocky Reef Fish…………………………………………………………………………………………………111
Soft Bottom Fish ………………………………………………………………………………………………..111
Invertebrates……………………………………………………………………………………………………..112
Rocky Reef Invertebrates…………………………………………………………………………………….115
Soft Bottom Invertebrates ……………………………………………………………………………………115
Reading Rock SMR and Reference Area ………………………………………………………………….116
Survey Totals…………………………………………………………………………………………………….117
Substrate ………………………………………………………………………………………………………….117
Habitat ……………………………………………………………………………………………………………..118
Fish………………………………………………………………………………………………………………….120
Rocky Reef Fish…………………………………………………………………………………………………123
Soft Bottom Fish ………………………………………………………………………………………………..123
Invertebrates……………………………………………………………………………………………………..124
Rocky Reef Invertebrates…………………………………………………………………………………….127
Soft Bottom Invertebrates ……………………………………………………………………………………127
Mattole Canyon SMR and Reference Area………………………………………………………………..129
Survey Totals…………………………………………………………………………………………………….130
Substrate ………………………………………………………………………………………………………….130
Habitat ……………………………………………………………………………………………………………..131
Fish………………………………………………………………………………………………………………….134
Rocky Reef Fish…………………………………………………………………………………………………137
Soft Bottom Fish ………………………………………………………………………………………………..137
Canyon Fish………………………………………………………………………………………………………137
Invertebrates……………………………………………………………………………………………………..139
Rocky Reef Invertebrates…………………………………………………………………………………….142
Soft Bottom Invertebrates ……………………………………………………………………………………142
Canyon Invertebrates………………………………………………………………………………………….143
Ten Mile State Marine Reserve and Reference Area…………………………………………………..144
Survey Totals…………………………………………………………………………………………………….145
Substrate ………………………………………………………………………………………………………….145
Habitat ……………………………………………………………………………………………………………..146
Fish………………………………………………………………………………………………………………….148
Rocky Reef Fish…………………………………………………………………………………………………151
Soft Bottom Fish ………………………………………………………………………………………………..151
Invertebrates……………………………………………………………………………………………………..152
Rocky Reef Invertebrates…………………………………………………………………………………….155
Soft Bottom Invertebrates ……………………………………………………………………………………155
APPENDIX 4. Rocky Reef Fish Communities and Analysis of Index Sites. ……………………….156
APPENDIX 5. Rock Reef Fish – Between Year Comparisons by Study Location………………..183
APPENDIX 6. Rocky Reef Invertebrates – Between Year Comparisons by Study Location….187
APPENDIX 7. Soft Bottom Fish – Between Year Comparisons by Study Location………………191
APPENDIX 8. Soft Bottom Invertebrates – Between Year Comparisons by Study Location….195

LIST OF FIGURES

Figure E1. Mean densities per 100m2 of selected rocky reef rockfish, Kelp Greenling and Lingcod for regional averages for the NCSR (white) compared to Point St. George SMCA (blue), Reading Rock SMR (red), Mattole Canyon SMR (red) and Ten Mile SMR (red) and their respective reference areas (gray)……………………………………………..17

Figure E2. Mean densities per 100m2 of selected rocky reef invertebrate species for regional averages for the NCSR (white) compared to Point St. George SMCA (blue), Reading Rock SMR (red), Mattole Canyon SMR (red) and Ten Mile SMR (red) and their respective reference areas (gray)……………………………………………………………18

Figure 1. Example of transect allocation within soft bottom and rocky reef habitats (including index sites) inside and outside the Reading Rock SMR………………………23

Figure 2. (a) Basic ROV strip transect methodology used to collect video data along the sea floor, (b) overlapping base substrate layers produced during video processing and (c) habitat types (hard, mixed soft) derived from the overlapping base substrate layers after video processing is completed. ………………………………………………..27

Figure 3. ROV transect lines completed in 2014 and 2015 at (a) Point St. George Reef Offshore SMCA and reference area, (b) Reading Rock SMR and reference area (c) Mattole Canyon SMR and reference area and (d) Ten Mile SMR and reference area………………………………………………………………………………………………36

Figure 4. Point St. George study area showing the rocky reef and surrounding soft bottom habitats in (a) the SMCA and (b) reference area………………………………….43

Figure 5. Percent substrate (rock, boulder, cobble, gravel sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the (a) Point St. George SMCA and (b) reference area……………………………………………………………………………………….44

Figure 6. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Point St. George Reef Offshore SMCA and (b) reference area for transect lines targeting: (I) the rocky reef and (II) the soft bottom habitats…….45

Figure 7. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a) Point St. George SMCA and (b) reference area for 2014 and 2015. For a breakdown of the taxonomic composition of subgroups, see Appendix 4…………….46

Figure 8. Mobile and sessile invertebrate mean densities for rocky reef and soft bottom transects inside (a) Point St. George SMCA and (b) reference area. For a breakdown of the taxonomic composition of subgroups, see Appendix 4………………………………..47

Figure 9. Reading Rock study location showing rocky reef and soft bottom habitats in (a) the reference area and (b) SMR. ………………………………………………………..48

Figure 10. Percent substrate (rock, boulder, cobble, gravel sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the Reading Rock SMR and (b) reference area. ………………………………………………………………………………..49

Figure 11. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Reading Rock SMR and (b) reference area, for transect lines targeting (I) rocky reef and (II) soft bottom habitats. ………………………………..50

Figure 12. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a) Reading Rock SMR and (b) reference area in survey years 2014 and 2015 combined. For a breakdown of the taxonomic composition of subgroups, see Appendix 5. …………………………………………………………………………………….51

Figure 13. Mobile and sessile invertebrate mean densities for rocky reef and soft bottom transects inside (a) Reading Rock SMR and (b) reference area. For a breakdown of the taxonomic composition of subgroups, see Appendix 5……………….52

Figure 14. Mattole Canyon study area showing the rocky reef and surrounding soft bottom habitats in (a) the SMR and (b) reference area……………………………………53

Figure 15. Percent substrate (rock, boulder, cobble, gravel sand and mud) by transect type (rocky reef, soft bottom and canyon) for survey lines inside (a) Mattole Canyon SMR and (b) reference area………………………………………………………………….54

Figure 16. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Mattole Canyon SMR (b) reference area for transect lines targeting: (I) the rocky reef, (II) soft bottom and (III) canyon habitats……………………55

Figure 17. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a) Mattole Canyon SMR and (b) reference area for 2014 and 2015. For a breakdown of the taxonomic composition of subgroups, see Appendix 6……….56

Figure 18. Mobile and sessile invertebrate mean densities for rocky reef and soft bottom transects inside the (a) Mattole Canyon SMR and (b) reference area. For a breakdown of the taxonomic composition of subgroups, see Appendix 6……………….57

Figure 19. Ten Mile study location showing rocky and soft bottom habitats in (a) the SMR and (b) reference area………………………………………………………………….58

Figure 20. Percent substrate (rock, boulder, cobble, gravel sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the (a) Ten Mile SMR and (b) reference area………………………………………………………………………………………………59

Figure 21. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Ten Mile SMR and (b) reference area, for transect lines targeting (I) the rocky reef and (II) the soft bottom habitats………………………………60

Figure 22. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a) Ten Mile SMR and (b) reference area for 2014 and 2015. For a breakdown of the taxonomic composition of subgroups, see Appendix 7……………….61

Figure 23. Mobile and sessile invertebrate mean densities for rocky reef and soft bottom transects inside the (a) Ten Mile SMR and (b) reference area. For a breakdown of the taxonomic composition of subgroups, see Appendix 7…………………………….62

Figure 24. Density per 100 m2 of select rocky reef fishes at each MPA (SMR or SMCA) and reference area index site pair at Point St. George, Reading Rock, Mattole Canyon and Ten Mile……………………………………………………………………………………64

Figure 25. Similarity (group average agglomerative clustering) among index site fish assemblages in MPA and reference area pairs, for Point St. George, Reading Rock, Mattole Canyon and Ten Mile. Analyses are based on densities for individual species and taxonomic groups (see methods for full list of taxonomic groups). Data were combined for observations over all substrates……………………………………………..65

Figure 26. The total area of rocky reef transects surveyed per depth bin for each MPA: Point St. George SMCA (blue), and Reading Rock SMR, Mattole Canyon SMR and Ten Mile SMR (all SMRs in red) and their reference areas (gray)…………………………………..69

Figure 27. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Point St. George SMCA and reference area………………………………………………………………………………………………70

Figure 28. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Reading Rock SMR and reference area…………71

Figure 29. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Mattole Canyon SMR and reference area………..72

Figure 30. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Ten Mile SMR and reference area……………….73

Figure 31. The total area surveyed per depth bin for canyon transects at Mattole Canyon SMR……………………………………………………………………………………74

Figure 32. The density of each fish species per depth stratified bin, with bubble size as the relative density of fish in that depth bin. There was insufficient data (less than 200 m) for the 140-149 meter depth bin (indicated by the gray line). The shelf/canyon break occurred at about the 100 m mark (indicated by the red line)…………………………….76

Figure 33. Percent (%) size frequency of Black Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 41 cm (—) for females (Love et al 2002)……………………………………….78

Figure 34. Percent (%) size frequency of Blue Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 29 cm (—) for females (CDFW 2016f)………………………………………….79

Figure 35. Percent (%) size frequency of Canary Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 44.5 cm (—) for females (Stock assessment, Thorson and Wetzel 2016)…………………………………………………………………………………………….80

Figure 36. The percent (%) frequency of size (cm) of Copper Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 31.4 cm (—) for females (Love et al 2002)………………………81

Figure 37. Percent (%) size frequency of Olive/Yellowtail Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 33-35 cm (—) for female Olive Rockfish and 36-45 cm (—) for female Yellowtail Rockfish (Love et al 2002)………………………………………………………..82

Figure 38. Percent (%) size frequency of Quillback Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 28 cm for females (—) (Love et al 2002)……………………………….83

Figure 39. Percent (%) size frequency of Vermillion Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity (—) is 38.2 cm for females (Stock assessment, MacCall 2005)……….84

Figure 40. Percent (%) size frequency of Yelloweye Rockfish at Point St. George (PSG), Reading Rock (RR) and Mattole Canyon (MC). Size at 50% sexual maturity is 39.6 cm (—) for females (Stock assessment, Stewart et al. 2009)……………………….85

Figure 41. Percent (%) size frequency of Lingcod at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 57.1 cm (—) for females (Stock assessment, Hamel et al. 2009). The recreational minimum size is 55.88 cm (CDFW 2016e)……………………………………………………………86

Figure 42. Percent (%) size frequency of Kelp Greenling at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 29.5 cm for females (—) (CDFW 2016f). The recreational minimum size is 30.48 cm (CDFW 2016f)………………………………………………………………………87

Figure 43. Comparisons of healthy (left photo) and wasting (right photo) sea stars including: (a) Stimpson’s sun star, (b) sunflower star and (c) the short spined sea star………………………………………………………………………………………………92

Figure 44. Comparison of slipper sea cucumbers in (a) 2014 with their tentacles exposed, and (b) 2015 with their tentacles retracted………………………………………93

LIST OF TABLES

Table 1. Survey totals for ROV dives at Point St. George, Reading Rock, Mattole Canyon, Sea Lion Gulch and Ten Mile MPAs and paired reference areas for the 2014 and 2015 sampling years combined…………………………………………………………35

Table 2. Total count, estimated size and depth of all fish observed from video collected in 2014 and 2015 within the NCSR………………………………………………………….38

Table 3. Total count and depth range of all invertebrates observed from video collected in 2014 and 2015 within the NCSR………………………………………………………….41

Table 4. Number of observations and mean density in all index sites per 100 m2 (+SE) for ten fish species selected for statistical comparisons among MPAs and their respective reference areas. Proportion of obs. is the proportion of non-YOY observations in the index sites only. Frequency of observation (FO) is the proportion of ROV transects in index sites in which the species occurred at least once………………63

Table 5. The total area and depth range surveyed from rocky reef and canyon transects inside MPAs (SMCA or SMR) and their associated reference areas for Point St. George, Reading Rock, Mattole Canyon and Ten Mile………………………………………68

Table 6. The mean total length of select fish species within each MPA (SMCA & SMR) and reference (Ref.) area for Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Dash marks indicate no individuals were counted at that study area. ‘N/A’ indicates too few fish were counted to report a mean……………77

Table 7. Mean length comparison between laser-length-estimates and stereo-video measurements. P-value refers to the probability that the two methods were the same (Ho: μ1=μ2) using two-tailed paired-sample t-tests. Measurements are all in centimeters. Bolded numbers indicate significant differences at a probability of 0.05. Difference shows the difference between the means and the signs indicate direction of the laser-length-estimate difference relative to stereo-measurements…………………..89

Table 8. Mean proportional difference in total length for laser-estimates from stereo- estimates by species for all analysts combined…………………………………………….90

EXECUTIVE SUMMARY

California’s network of Marine Protected Areas makes up 16% of the states coastal waters. May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 87 This network was implemented in four uniquely distinct coastal regions. The final region to be implemented, the North Coast Study Region (NCSR), extends from the California-Oregon border to Alder Creek, Mendocino County. The NCSR has some of the least developed coastal areas in the state due to the remote, rugged coastline and frequently unfavorable ocean conditions, which limit access to much of the coastal and offshore waters. The NCSR lies within one of only four major temperate upwelling systems in the world, making it one of the most highly productive ecosystems that supports diverse and abundant assemblages of fish and invertebrate species.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 88 Marine Applied Research and Exploration (MARE) preformed quantitative baseline surveys within the NCSR in 2014 and 2015 with the overall goal to describe the condition of three distinctive priority ecosystem features within four MPAs and their adjacent reference study areas: a) mid-depth rock ecosystems, b) soft- bottom subtidal ecosystems, and c) deep ecosystems (including canyons). Long-term monitoring trends within these habitats will be compared to baseline conditions, assisting in evaluating MPA effectiveness. The four MPAs chosen for evaluation include: Point St. George Reef Offshore SMCA, Reading Rock State Marine Reserve, Mattole Canyon State Marine Reserve and Ten Mile State Marine Reserve. Outside reference areas with similar habitats and depths were also surveyed for comparison.

During the first two years following implementation, benthic visual surveys May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 89 were conducted using a remotely operated vehicle (ROV) to assess initial changes in fishes, macro-invertebrates and associated seafloor habitats. The ROV collected video and still imagery while moving along a fixed path (transect) along the sea floor. Video imagery collected was analyzed to characterize substrate, habitat types, habitat complexity (rugosity), and estimate finfish and macro-invertebrate distribution, relative abundance and density. In total, 60 ROV dives were completed surveying more than 106 km (19 ha) between 13 and 421 m deep. In addition, over 16,500 still photos were taken.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 90 Of the 101,666 fish observed over both years, over 85% were rockfish. Young of year rockfish (YOY) were the most numerous rockfish grouping observed; with over 61,000 recorded individuals, accounting for 60% of all of the fish observations. Larger rockfish represented only 14% of the rockfish identified, with four species/groupings accounting for 80% of the observations: Blue, Olive/Yellowtail, unidentified and Canary Rockfishes. Non-rockfish species represented 15% of the fish identifications, with two groupings accounting for 71% of the total observations: unidentified smelt and May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 91 flatfish. Overall, fish species composition and density was similar between all MPA and reference area pairs within rocky reef and soft bottom habitats. One exception was documented at Point St. George Reef Offshore SMCA within rocky reef habitats, where rockfish densities were significantly lower in the reference area than the MPA (Figure E1). In addition, Point St. George Reef Offshore SMCA had the highest density of Yelloweye Rockfish, over two times more than any other study area (Figure E1).

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 92 Of the 124,064 individual invertebrates enumerated, seven species/groupings represented the majority of the observations (approximately 89%) within the NCSR: white- plumed anemones, slipper and California sea cucumbers, short red gorgonians, California hydrocoral, sea stars, sea whips and sea pens. Overall, invertebrate species composition and density was similar between all MPA and reference pairs within rocky reef habitats (Figure E2). However, within soft-bottom habitats species composition and abundance varied greatly across study locations.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 93

Figure E1. Mean densities per 100 m2 of selected rocky reef rockfish, Kelp Greenling and Lingcod for regional averages for the NCSR (white) compared to Point St. George Reef Offshore SMCA (blue), Reading Rock SMR (red), Mattole Canyon SMR (red) and Ten Mile SMR (red), and their respective reference areas (gray). Error bars represent ± 1 standard error.

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Figure E2. Mean densities per 100 m2 of selected rocky reef invertebrate species for regional averages for the NCSR (white) compared to Point St. George Reef Offshore SMCA (blue), Reading Rock SMR (red), Mattole Canyon SMR (red) and Ten Mile SMR (red), and their respective reference areas (gray). Error bars represent ± 1 standard error.

Initial changes between sampling years were May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 95
compared for fish and invertebrate species
abundance and distribution. Overall, there were
few significant differences for either fish or
invertebrate species, with most having low initial
variability. One of the exceptions was a
considerable decline in sea star species across
all sites within the NCSR from 2014 to 2015.
During the 2014 survey, active signs of sea star
wasting disease were observed in several
species of sea stars. When we returned to the
same locations in 2015, these same species
were observed in very low numbers, or not at
all.

Based on survey results in the NCSR, candidate indicators were identified based on
their abundance, ease of identification and management concern for inclusion in a
video-based surveying program for future monitoring and management efforts in the
region. They are listed by ecosystem type below:

Mid-depth Rock Ecosystems
Canary Rockfish
Copper Rockfish
Quillback Rockfish
Vermillion Rockfish
Yelloweye Rockfish
Lingcod Soft-bottom
Kelp Greenling
Soft-bottom Subtidal Ecosystems
Flatfish Sea whip
Deep Canyon Ecosystems
Greenstriped Rockfish
Shortspine Thornyheads
Longspine Thornyheads
Sablefish
Flatfish

Mid-depth Rock Ecosystems
White-plumed anemones
CA sea cucumbers
Short red gorgonians
Sea stars (all species)
Basket stars
Subtidal Ecosystems
White sea pen
Orange sea pen
Sea whip
Red octopus
Dungeness crabs
Deep Canyon Ecosystems
White-plumed anemones
Short red gorgonians
Mushroom soft coral

While a set of indicator species was given, due to the limited knowledge we have about mid-depth and deep ecosystems it is highly recommended that long-term sampling continue to identify all fish and macro-invertebrate species and physical habitat characteristics as completed during the baseline assessment.

INTRODUCTION

Background

California’s diverse marine territory stretches 13,688 square kilometers, with over 70% of the state’s marine seafloor habitats exceeding depths of 30 m. Vast stretches of unconsolidated sediment give way to patches of rocky outcroppings, pinnacles and steep walled canyons. More than 550 marine fish species and thousands of marine invertebrate species are found in California’s territorial waters (Froese 2016). Many of these species are only found within deep subtidal ecosystems, extending well beyond the reach of conventional SCUBA surveys.

These deep marine ecosystems are only effectively accessible via manned or unmanned submersibles. Although less is known about California’s deep ecosystems than kelp forest ecosystems, they have been long targeted by commercial and recreational fisheries. Due to historic commercial fishing effort, many species were overfished, including Cowcod (Sebastes levis), Canary Rockfish (Sebastes pinniger), and Yelloweye Rockfish (Sebastes ruberrimus). The impacts on these fisheries were further exacerbated by California’s growing recreational fleet (Schroeder and Love 2002).

Federal regulations now prohibit bottom fishing within certain depths. In response to critically low population sizes of seven overfished rockfish species, the Pacific Fishery Management Council enacted area closures in September of 2002. These areas, called the Rockfish Conservation Areas (RCAs), prohibit the take of groundfish across vast stretches of the west coast continental shelf. Within Northern California, RCA closures limit bottom fishing to waters shallower than 20 fathoms (~37 m). While current regulations protect much of Northern California’s deepwater fish populations, they still remain poorly studied.

Recognizing the lack of visual data available on deep subtidal habitats, Marine Applied Research and Exploration (MARE) was founded in 2003 to explore and document deepwater ecosystems to assist in their conservation and management. MARE works collaboratively with state and federal agencies, academic institutions, and other non- governmental organizations. To date, MARE has documented over 2,700 kilometers of seafloor off California’s coast alone—much of which had never been viewed before.

Study Region

In December 2012, the fourth California Marine Protected Area (MPA) region was implemented along the North coast of California. The North Coast Study Region (NCSR) extends from the California-Oregon border to Alder Creek, Mendocino County, encompassing 2,660 square kilometers of coastal waters (CMLPAI 2010). The remote coastal areas of the NCSR are some of the least populated in the state, with vast stretches of coastal mountains having little to no development, reducing access to much of the regions shoreline. Three major river systems discharge into the northern half of the NCSR: the Smith, Klamath, and Eel rivers. The Eel River has an average annual sediment discharge greater than any other river of its size in the contiguous United States (Wolman et al. 1990), impacting nearshore marine ecosystems of the NCSR.

Soft-bottom habitats are the most common within the study region, while hard-bottom and deep submarine canyon habitats add relief and structural complexity. Strong onshore winds drive nutrient rich upwelling that combines with the California Current Large Marine Ecosystem to support an abundance of marine life. These oceanographic conditions of the NCSR support highly productive and diverse marine ecosystems.

The remote, rugged coastline and frequently unfavorable ocean conditions limit access to much of the region. Historical data for deep subtidal ecosystems within the NCSR are primarily limited to fisheries-dependent data from the commercial and recreational sectors. Very few fisheries-independent surveys have been conducted within the NCSR prior to MPA implementation.

Goals and Objectives

This report presents findings from visual surveys conducted as part of a two-year baseline study of selected MPAs within the NCSR. The data collected during this study has been integrated into a statewide dataset to provide a benchmark for evaluating the effectiveness of MPAs. The overall goal of this project is to describe the condition of three priority ecosystems within MPAs and adjacent reference study areas: mid-depth rock ecosystems, soft-bottom subtidal ecosystems, and deep ecosystems (including canyons). The specific objectives of this project include:

1) Produce a quantitative baseline characterization of selected MPAs across the

NCSR.

2) Assess initial changes in fishes, macro-invertebrates and associated seafloor

habitats in select MPAs during the first two years following implementation.

3) Identify candidate system indicators for the NCSR.

4) Inform future monitoring and management efforts in the region.

Study Design

Benthic visual surveys of North coast MPAs were conducted using a remotely operated May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 96 vehicle (ROV) that is owned and operated by MARE. The ROV configuration and sampling protocols for this project were based on those developed by the project’s principal investigators in partnership with the California Department of Fish and Wildlife. The baseline assessment protocols have been used to survey MPAs of the northern Channel Islands as well as North central coast, Central coast, and South coast MPA study regions. To date, over 1,800 km of seafloor have been surveyed statewide using similar survey design and data collection protocols.

Study Locations For this baseline assessment, four MPAs were selected to cover both the northern and southern bioregions of the NCSR: Point St. George Reef Offshore State Marine Conservation Area, Reading Rock State Marine Reserve, Mattole Canyon State Marine Reserve and Ten Mile State Marine Reserve. Outside reference areas with similar habitats and depths were also surveyed for comparison.

Transect Selection Two different sampling techniques were used to capture video imagery, characterization transects and index site transects. At each location we collected video across two different habitat types (rocky reef and soft bottom) for use in developing a basic characterization of the benthic habitat structures and species assemblages present. We also captured additional video data within defined rocky habitat sites (index sites) to increase the statistical power specifically for monitoring changes in species density at those sites.

At each location, long characterization transect lines (~1 km) were planned both inside and outside of the MPA, to transverse rocky reef and soft bottom habitats. Within the rocky reef, transects were distributed to cover both the interior reef, as well as the transitional habitats found on the edges of the rocky reef (Figure 1). Transects were chosen based on the distribution of habitat types within each MPA and reference area. When possible, transects were placed near each other to maximize ROV bottom time. This sampling approach provided information that was used in the descriptive characterization of each MPA and reference area.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 97

Figure 1. Example of transect allocation within soft bottom and rocky reef habitats (including index sites) inside and outside the Reading Rock SMR.

At each study location, a 500 m wide by 1,000 m long index site was placed over selected rocky habitat (Figure 1). Six 500 m long transects stretching across the width of the site were selected each sampling year using a systematic random approach, in which the start location of the shallowest line was selected randomly and the remaining transects were equally spaced thereafter. This survey design has been used to monitor changes in species density for use in evaluation of MPA effectiveness and fisheries management throughout California’s MPA network. To date, 178 index sites have been established and surveyed statewide, some having been resurveyed up to seven times.

Data Collection

ROV Equipment MARE’s observation class ROV, Beagle, was used to complete May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 98 benthic surveys of select North coast MPAs. The ROV was equipped with a three-axis autopilot including a rate gyro-damped compass and altimeter. Together, these allowed the pilot to maintain a constant heading (± 1 degree) and constant altitude (± 0.3 m) with minimal corrections. In addition, a forward speed control was used to help the pilot maintain a consistent forward velocity between 0.25 and 0.5 m/sec. A pair of Tritech® 500 kHz ranging sonars, which measure distance across a range of 0.1–10 m using a 6° conical transducer, were used as the primary method for measuring transect width for both the forward and downward facing video. Each transducer was pointed at the center of the viewing area in each camera and was used to calculate the distance to middle of screen, which was subsequently converted to width using the known properties of each cameras field of view. Readings from these sonars were averaged five times per second and recorded at a one-second interval with all other sensor data. Measurements of transect width using a ranging sonar are accurate to ± 0.1 m (Karpov et al. 2006).

The ROV was equipped with six cameras, including two standard definition primary cameras, two standard definition stereo sizing cameras, one high definition (HD) video camera and one HD still camera. The primary data collection cameras were oriented forward and down, with slightly overlapping fields of view. Both still and video HD cameras were oriented forward. Video for both cameras was captured on SONY® DSR 45 digital video tape recorders and Pioneer DVR510 digital video disc recorders. The two stereo sizing cameras were oriented forward facing with overlap for use in standardizing size measurements of fishes. All video and still images were linked using UTC timecode recorded as a video overlay or using the camera’s built-in time stamp which was set to UTC time each day.

GPS time was used to provide a basis for relating position, sensor data and video observations (Veisze and Karpov 2002). A Horita® GPS3 and WG-50 were used to generate on screen displays of GPS time, as well as output Society of Motion Picture and Television Engineers (SMPTE) linear time-code (LTC) for capture on SONY® DSR audio tracks at an interval of 1/30th of a second. This method was improved by customizing HYPACK® navigational software to link all data collected in the field to the GPS time. ROV tracked position and sensor data were recorded directly by HYPACK® as a time-linked text file. A redundant one-second time code file of sensor data was also collected in the field using a custom built on-screen display and operating system software with time code extracted from the system’s internal clock which was synced to GPS time.

All data collected by the ROV, along with subsequent observations extracted during post-processing of the video, was linked in a Microsoft Access® database using GPS time. Data management software was used to expand all data records to one second of Greenwich Mean Time (GMT) time code. During video post-processing, a Horita® Time Code Wedge (model number TCW50) was used in conjunction with a customized computer keyboard to record the audio time code in a Microsoft Access® database.

ROV Beagle was also equipped with two sets of parallel lasers, three sonar units, and a Sea-Bird CTD with dissolved oxygen sensor. The parallel lasers were set with a 10 cm spread and positioned to be visible in the field of view of the primary forward and down facing cameras. These lasers provided a scalable reference of size when reviewing the video. The two ranging sonars also aligned with the forward and down facing cameras, allowed the ROV pilot to maintain a constant height off the bottom; they were also used to calculate the area covered (Karpov et al. 2006).

ROV Applications ROVs are a non-obtrusive monitoring tool that can be used to collect detailed information on the entire benthic ecosystem, rather than just select metrics or indicators. ROVs can be equipped with not only cameras, but also monitoring probes such as oxygen and salinity sensors. This enables them to collect additional information from the surrounding environment beyond video. Additionally, ROVs can be equipped with manipulating arms that can be used to collect samples from the environment. These features make ROVs an all-around good choice for monitoring benthic ecosystems.

ROVs however are not currently very effective at collecting video data on fishes that school off the bottom. Therefore, data collected using the ROVs may not provide an accurate measure of biomass on epibenthic schooling fish species like Blue, Black and Olive/Yellowtail Rockfishes that tend to school around tall rock outcroppings

ROV Sampling Operations R/V Miss Linda, a 24 m research vessel owned and May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 99 operated by Captain Robert Pedro, was used to complete both the 2014 and 2015 surveys. Surveys were conducted between the hours of 0800 and 1700 PST to avoid the low light conditions of dawn and dusk that might affect finfish abundance measurements and underwater visibility. At each site, the ROV was piloted along pre-planned transect lines and was flown off the vessel’s port side using a “live boat” technique that employed a 317.5 kg (700 lb) clump weight. Using this method, all but 45 m of the ROV umbilical was isolated from current-induced drag by coupling it with the clump weight cable and suspending the clump weight at least 10 m off the seafloor. The 45 m tether allowed the ROV pilot sufficient maneuverability to maintain a constant speed (0.5 to 0.75 m/sec) and a straight course down the planned survey line.

The ship remained within 35 m of the ROV position at all times. To achieve this, an acoustic tracking system was used to calculate the position of the ROV relative to the ship. ROV position was calculated every two seconds and recorded along with UTC timecode using navigational software. Additionally, the ROV pilot and ship captain utilized real-time video displays of the location of the ship and the ROV, in relation to the planned transect line. A consistent transect width, from the forward camera’s field of view, was achieved using the ranging sonars to maintain a constant distance and altitude from the substrate. The ranging sonars were fixed below and parallel to the camera between two forward-facing red lasers spaced 100 mm apart. The ROV pilot used the sonar readings to sustain a consistent transect width by maintaining the distance from the camera to the substrate (at the screen horizontal mid-point) between 1.5 and 3 m. In areas with low visibility, a BlueView multibeam sonar was used to navigate hazardous terrain. All sonar and CTD data were recorded at one second intervals along with UTC timecode.

Post-Processing Following the survey, the ROV position data was processed to remove outliers and data anomalies caused by acoustic noise and vessel movement, which are inherent in these systems (Karpov et al. 2006). In addition, deviations from sampling protocols such as pulls (ROV pulled by the ship), stops (ROV stops to let the ship catch up), or loss of target altitude caused by traveling over backsides of high relief structures, were identified in the data and not used in calculations of density for fish and invertebrate species.

Substrate and Habitat For each study area, all video collected was reviewed for up to six different substrate types: rock, boulder, cobble, gravel, sand and mud (Green et al. 1999). Each substrate patch was recorded as discrete segments by entering the beginning and ending UTC timecode. Substrate annotation was completed in a multi-viewing approach, in which each substrate type was recorded independently, enabling us to capture the often overlapping segments of substrates (Figure 2). These overlapping substrate segments allowed identification of mixed substrate areas along the transect line.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 100

After the video review process, the substrate data was combined to create three May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 101 independent habitat types: hard, soft, and mixed habitats (Figure 2). Rock and boulder were categorized as hard substrate types, while cobble, gravel, sand, and mud were all considered to be unconsolidated substrates and categorized as soft. Hard habitat was defined as any combination of the hard substrates, soft habitat as any combination of soft substrates, and mixed habitat as any combination of hard and soft substrates.

The video record was then reviewed two more times to identify the primary and secondary substrates along the survey line, and to capture the habitat complexity (rugosity). The video was also reviewed to classify the complexity of the habitat as it relates to fish and their ability to find refuge. Four levels of rugosity were used, and include: no rugosity (no refuge), low rugosity (refuge for 5-15 cm fish), medium rugosity (refuge for 15-25 cm fish), and high rugosity (refuge for >25 cm fish). Only base substrate, habitat, and rugosity data are presented in this report. Primary/secondary substrate data are provided as part of the final data submission for use in future analysis.

Finfish and Invertebrate Enumeration After completion of habitat and substrate review, video was processed to collect data for use in estimating finfish and macro-invertebrate distribution, relative abundance and density. During the review process, both the forward and down video files were simultaneously reviewed, yielding a continuous and slightly overlapping view of what was present in front of and below the ROV. This approach effectively increased the resolution of the visual survey, by identifying animals that were difficult to recognize in the forward camera, but were clearly visible and identifiable in the down camera.

During multiple subsequent viewings, finfish and macro-invertebrates were classified to the lowest taxonomic level possible. Observations that could not be classified to species level were identified to a taxonomic complex, or recorded as unidentified (UI). During video review, both the HD video and HD still imagery were used to aid in species identification. Each fish or invertebrate observation was entered into a Microsoft Access database along with UTC timecode, taxonomic name/grouping, sex/developmental stage (when applicable), and count. Fish, were sized using the two sets of parallel lasers to estimate total length. Not all fish were sizeable due to their position within the field of view of the ROV.

Invertebrate patch segments were coded for percent cover using four groupings: 1) less than 25% cover, 2) 25% to 50% cover, 3) 50% to 75% cover and 4) greater than 75% cover. Only data on individual invertebrate observations are presented in this report. Invertebrate patch data are provided as part of the final data submission for use in future analysis.

Analysis

Characterization of MPAs and Reference Areas For each MPA and paired reference area, baseline data collected over the 2014 and 2015 sampling years were combined to describe the physical and biological characteristics of three ecosystem features: mid-depth rock and soft bottom habitats, and deep canyon habitats. Data were summarized to highlight the profundity of information generated from this baseline project. Characterizations are restricted to describing species composition and abundance within each study area, as well as the similarities and differences between MPA pairs, and not to compare regional MPAs to each other. Abbreviated descriptions highlighting key findings at each study location are given in the main body of this report. Detailed characterizations are also provided in Appendix 3, which include fish and invertebrate species counts and mean densities for each MPA and reference area.

Derived habitats are summarized by transect type (rocky reef, soft bottom and canyon) and presented as a percentage of the total transect distance for all transects combined. Fish and invertebrate mean densities for each habitat type (presented in Appendix 1 for fish and Appendix 2 for invertebrates) were calculated for each transect as: total individuals / total area of transect and expressed as individuals/100 m2.

For each study area, fish and invertebrate densities were summarized into subgroupings. Each fish and invertebrate subgroup was selected for the purposes of displaying all fish and invertebrate density data and were not based on management importance. All fish observed were summarized into one of seven subgroups that include rockfish (schooling and non-schooling larger species), small schooling rockfish (dwarf type species), young of year rockfish (YOY), Lingcod (Ophiodon elongatus), Kelp Greenling (Hexagrammos decagrammus), flatfish (Pleuronectidae) and ‘all other fish’.

Invertebrates were grouped into seven mobile and seven sessile macro-invertebrate subgroupings. Mobile subgroups include California sea cucumbers (Parastichopus californicus), octopuses, sea stars, urchins, Dungeness crabs (Cancer magister), basket stars (Gorgonocephalus eucnemis), and ‘other mobile invertebrates’. Sessile subgroups include white-plumed anemones (Metridum farcimen), branched sea cucumbers, whips and pens, gorgonians, sponges, and ‘other sessile invertebrates’. For breakdown of taxonomic composition of subgroups see Table 2 for fish and Table 3 for invertebrates.

Analysis of Index Sites To assess the relationship between occupancy and abundance of fishes across the NCMPA region, and within each of the selected MPAs and their outside reference areas, analyses were conducted on the combined 2014-2015 dataset at three different levels of ecological organization: 1) all fishes combined to represent the entire assemblage (multivariate analyses), 2) fishes separated into taxonomic or functional groups (multivariate analyses) and 3) individual species analyses for the 10 most abundant, reliably identifiable fish species. Additionally these groups were evaluated at three levels: regional (MPA location), treatment (inside/outside of MPA pairs), and habitat (rock, soft and canyon). The canyon habitat was considered unique, and was evaluated separately as the depth range and topography were significantly different from rock and soft shelf habitats.

Multivariate analyses – The initial objective was to characterize the overall similarity of MPA locations and their paired reference site in the NCSR. Average agglomerative clustering of taxa densities at the transect level was used to determine how overall assemblage structure varied by MPA (regional), treatments (inside and outside reference) and habitats (rock, soft and canyon); and to evaluate the similarity of assemblages among MPA locations. We did this by grouping all ROV transect data in two ways. Mean densities for each group or species observed were calculated for soft, rock and canyon habitat transects, inside and outside each MPA. Densities were calculated by dividing the number of individuals observed by the area covered for each transect, creating a density matrix. Square root transformed densities were used to calculate a Bray-Curtis Similarity (Krebs 1999) matrix, used for average agglomerative clustering.

A number of individual taxa had very low numbers of observations, or were difficult to identify to species level. Therefore, we completed the same analysis for taxa densities after grouping all species into higher level taxa such as genus, family, or functional group, including: Chondrichthyans (sharks, rays and ratfish), flatfishes, young of the year rockfish (YOY), Sebastomus Rockfish, small schooling rockfish (Pygmy, Halfbanded, Squarespot, Shortbelly, and unidentified small schooling), demersal non- aggregating rockfishes (Aurora, Brown, China, Copper, Darkblotched, Gopher, Greenspotted, Greenstriped, Quillback, Redbanded, Sharpchin, Stripetail, Tiger, and Yelloweye), epibenthic aggregating rockfishes (Black, Blue, Bocaccio, Canary, Chilipepper, Olive/Yellowtail, Vermilion and Widow), seaperches, combfishes, small benthic fishes (eelpouts, gobies, sculpins, and poachers), other benthic fishes (Sablefish, hagfishes, thornyheads and sand lance), and other fishes (Pacific Tomcod, Pacific Hake, salmonids, smelts, sunfish, and cods).

Similar analyses were completed using only index site species occurrence data. Mean densities and frequency of occurrence were calculated for each species or taxon within each of the index sites. Similarity analyses and statistical comparisons were restricted to species or species groups that occurred on ROV transects within the index sites, and those species considered resident or semi-resident. Migratory or highly mobile species such as Ocean Sunfish, Sixgill Shark, Sablefish, smelts, Shortbelly Rockfish, and other schooling pelagics were removed. Individual species or taxa were grouped as previously described either taxonomically or functionally when observations were low. Similarly, small schooling rockfishes, other than Shortbelly Rockfish, were grouped for analyses as they have similar appearance and they occupy similar habitat in loosely aggregated schools. Kelp Greenling and Lingcod were analyzed as individual taxa due to occupying different ecological niches. At the depths in which the index sites were located (20-70 m), two Sebastomus species were expected to be observed – Starry and Rosy Rockfishes. These two species were combined with the Sebastomus Rockfish complex (hereafter referred to as Sebastomus Rockfish) to reduce ambiguity in calculations. Unidentified taxa were either eliminated or incorporated into appropriate higher level taxonomic groups. Analyses were conducted for transect-level densities, as well as individually for each substrate type.

Individual species analyses – General linear modeling (GLM) was used with analysis of variance (ANOVA) and post-hoc multiple comparisons to investigate the relationships among square root transformed densities of individual fish species by treatment, MPA and between the two sample years. Species were selected based on abundance and frequency of observation in index sites and restricted to resident or semi-resident species.

ODDS Analyses – We used odds-ratio analysis to determine if individual species were using hard substrates similarly among the four MPAs in the paired Index sites. This analysis is used to measure the odds of an outcome (yes or no) given a two-way treatment. We used number of observations over hard substrate (number of yes’s) or not (number of no’s) in Index sites as the outcomes in each treatment – inside and outside the MPAs. The resulting number is calculated: Odds ratio = A*D/B*C. A result near 1 would indicate that a species is observed over substrates similarly both inside and outside the MPA. Greater than 1 would indicate that the species is more likely to use hard substrates inside than outside and less than one more likely to use hard substrates in the outside treatment. The results of this analysis are not included in the main body of this report.

A full report on analyses conducted in the evaluation of index sites can be found in Appendix 4.

Fish Depth Distribution The depth distribution of selected fish species across all rocky reef transects (characterization and index site transects combined) was assessed for all MPA and reference areas in the NCSR. Depth distribution of select fish species across the Mattole Canyon SMR was assessed using only those transects that targeted the canyon.

Fishes that were relatively high in abundance, and were of management concern, were selected for enumeration. Fish assessed from rocky reef transects include: Black Rockfish, Canary Rockfish, Copper Rockfish, Quillback Rockfish, Sebastomus Rockfish, Vermilion Rockfish, Yelloweye Rockfish, Lingcod, and Kelp Greenling. Fish assessed in canyon transects include all of the aforementioned species, as well as the following abundant, relatively deep water species: Greenstriped Rockfish, thornyhead complex (which includes Shortspine Thornyheads, and Longspine Thornyheads), and flatfish (including, Rock Sole, Slender Sole, Curlfin Turbot, Spotted Turbot, Pacific Halibut, Dover Sole, unidentified sanddabs, English Sole, Petrale Sole, and Rex Sole, as well as unidentified flatfish). Additionally, five flatfish species/groupings that had a higher identification rate were shown and include: Dover Sole, unidentified sanddabs, English Sole, Petrale Sole, and Rex Sole.

To account for differences in density of fish along a depth gradient, transects in rocky reefs were stratified into 10 m depth bins. Transects targeting canyons were stratified into either 10 or 50 m bins. For the shallower portion of the canyon (50 to 149 m), depth was broken into 10 m bins; for the deeper portions of the canyon (150 to 450 m), 50 m depth bins were used. The total usable transect area was summarized within each depth bin (see ROV Positional Data methods section). Only those depth bins in which at least 200 m2 was surveyed were used for density calculations. Density was calculated as: total fish observed/total area surveyed and was expressed as fish/100 m2, for each depth bin.

Regional Fish Size Distribution Fish size (total length) was approximated using two parallel lasers mounted to the ROV’s forward and down facing cameras. The lasers were placed 10 cm apart in the center of the video-viewing screen providing a scalable reference size. Estimates of fish total length were made using the lasers as a guide (laser-based size estimate) when the lasers made contact with the fish or when the lasers were visible on adjacent substrate or other fish. Length measurements were made to the nearest 1 cm and applied to all fish deemed sizeable by the trained video analysts.

Ten species were selected for analysis: Black Rockfish, Blue Rockfish, Canary Rockfish, Copper Rockfish, Olive/Yellowtail Rockfish, Quillback Rockfish, Vermilion Rockfish, Yelloweye Rockfish, Lingcod, and Kelp Greenling (see table 2 for species names). Mean laser-based size estimates for these species were calculated for each MPA and reference area. Because there was little difference overall in mean total length between MPA and reference areas for the ten fish species presented, length data for MPA and reference area pairs were combined to show the size frequency for each of the four study locations in the NCSR. Percent size frequency is presented in 5 cm bins, and size at which 50% of the females of the population reach sexual maturity, is referenced for each species/grouping presented (Love et al. 2002; Thorson and Wetzel 2016; MacCall 2005; Stewart 2009; CDFW 2016f).

To test the accuracy of the laser-based sizing technique used in this report, stereo video that was collected concurrently with the primary forward facing video was compared by independent analysts. Fish size (total length) was measured using commercially available SeaGIS EventMeasure® software (www.seagis.com.au/event). Eleven fish species were selected for comparison and include: Lingcod, Kelp Greenling, and the following rockfishes: Black, Blue, Canary, Copper, Olive/Yellowtail, Quillback, Rosy, Vermillion, and Yelloweye Rockfish.

Video collected using the ROV Beagle’s stereo-video cameras was provided to Moss Landing Marine Lab (MLML) analysts for processing. Fish that were previously given a laser-based size estimate were located in the stereo-video files using the same timecode that was recorded in the primary forward-facing camera. Using EventMeasure® software, fish that appeared to be the same individual as previously sized using the laser-based method were measured. Only fish that met the software requirement of head and tail being visible in both cameras simultaneously were sized. To assess potential differences between the two techniques:

1) Mean total lengths of fish species measured using both methods were compared

using two-tailed paired-sample t-tests.

2) Laser-estimated total lengths were subtracted from stereo-estimates of fish species measured using both methods. Then we looked at the mean proportional differences, using the equation:

Proportional difference = (difference / stereo measurement) * 100

Between Year Comparison The differences between 2014 and 2015 baseline survey years were compared for select MPAs and their respective reference areas. Two types of transects were analyzed for the between year comparisons: transects surveyed in the rocky reef index sites and transects surveyed in soft bottom habitats. Fish and macro-invertebrate species abundance were analyzed for between year differences at each survey location. As there were no substantial differences in habitat composition between 2014 and 2015 for any of the survey locations, habitat will not be compared between years.

To show the percentage difference between the two sampling years for both rocky reef index and soft bottom transects, Initial Variability was calculated with the equation:

Absolute value of ((mean density 2015 – mean density 2014) / mean density 2014)

For rocky reef index sites only, we tested for differences in density between years inside the MPAs and their reference sites using t-tests for select fish and invertebrate species (soft bottom sample sizes were insufficient). Tables with initial variability and t-test results are in Appendices 5-8.

Fish species/groupings were chosen for between year comparison totaling the counts of all fish species for all sites and looking at species that were relatively high in abundance and of management concern. Fish species chosen for between year comparisons in rocky reef index sites include the following rockfish species: Black, Blue, Brown, Canary, Copper, Olive/Yellowtail, Quillback, Sebastomus, Shortbelly, small schooling, Vermilion, Yelloweye, unidentified (UI), young of year (YOY); and the following non- rockfish species: Kelp Greenling, Lingcod, and flatfish. Fish species chosen for between year comparisons in soft bottom transects include: combfish complex, Dover Sole, English Sole, Lingcod, Pacific Hake, Petrale Sole, Rex Sole, UI cod, UI eel pout,

UI flatfish, UI sanddab, UI small benthic fish and UI smelt (see table 2 for scientific names).

Select macro-invertebrate species that were relatively high in abundance were also chosen for comparison. Macro-invertebrate species selected for between year comparisons in rocky reef index sites include the following: basket star, California hydrocoral, California sea cucumber, cushion star, fish eating star, Henricia complex, leather star, rainbow star, red sea star, red sea urchin, short red gorgonian, short spined sea star, slipper sea cucumber, spiny/thorny star complex, Stimson’s sun star, sunflower star, white branched cucumber, and white-plumed anemone. Macro- invertebrate species chosen for between year comparisons in soft bottom transects include: Dungeness crab, orange sea pen, Pleurobranchaea californica, red octopus, sand star, sand-rose anemone, sea whip, white sea pen and white-plumed anemone (see table 3 for scientific names).

RESULTS AND DISCUSSION

Baseline Survey Totals The baseline assessment of deep subtidal ecosystems within the North Coast Study Region was conducted between September 12 and October 9 2014, and October 6 to October 18 2015. Surveys were completed over a total of 24 operational days at sea (excluding weather and travel days) and covered nine different study areas: Point St. George SMCA and reference area, Reading Rock SMR and reference area, Mattole Canyon SMR and reference area, Sea Lion Gulch SMR, and Ten Mile SMR and reference area (Figure 3). In 2014, 31 ROV dives were completed, surveying over 59 km of benthic habitats between 13 and 421 meters in depth. In 2015 we returned to the same sites and completed 29 dives, surveying 47 km of transects between 24 and 364 meters in depth.

Poor weather conditions and reduced visibility did not allow subsequent surveys of the 2015 planned transects within the Point St. George SMCA reference area. Therefore, two dives inside the Sea Lion Gulch SMR were re-surveyed within a site previously surveyed in 2014 as part of a CDFW statewide survey contract. Sea Lion Gulch SMR results are presented in this section only.

In total, 60 ROV dives were completed covering more than 106 km (19 ha) of sea floor (Table 1). Over 101,000 fish and 124,000 invertebrates were enumerated from the videos. In addition, over 16,500 HD still photos were taken during 2014-2015 survey.

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Table 1. Survey totals for ROV dives at Point St. George, Reading Rock, Mattole Canyon, Sea Lion Gulch and Ten Mile MPAs and paired reference areas for the 2014 and 2015 sampling years combined.

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Figure 3. ROV transect lines completed in 2014 and 2015 at (a) Point St. George Reef Offshore SMCA and reference area, (b) Reading Rock SMR and reference area, (c) Mattole Canyon SMR and reference area and (d) Ten Mile SMR and reference area.

Fish Totals For a full list of scientific names, see Table 2; fish will be referred to by common name throughout this report. For all sites and survey years combined, a total of 66 individual fish species and another 26 groupings were identified (Table 2). Of the 101,666 fish observed over both years, over 85% were rockfish. Young of year rockfish (YOY) were the most numerous fish observed; with over 61,000 recorded individuals, they accounted for 60% of all of the fish observations, and 71% of all rockfish observations. Small schooling rockfish were also abundant and with over 14,500 observed across both years, accounted for 17% of the rockfish observations. Small schooling rockfish include Shortbelly, Halfbanded, Squarespot, and Pygmy Rockfishes, as well as those fish that could only be classified as unidentified small schooling rockfish.

Observations of larger rockfish (both aggregating and non-aggregating species/groupings) represented only 14% of the total rockfish observations, with four species/groupings accounting for 80% of the observations: Blue, Olive/Yellowtail, unidentified and Canary Rockfishes. Canary Rockfish, a species that was listed as overfished until the end of 2016, was one of the more abundant species identified, with almost 1,600 individuals observed over the length of the survey. Yelloweye Rockfish, a currently listed overfished species, accounted for 220 individuals.

Non-rockfish species represented 15% of the total fish identified, with two groupings accounting for 71% of the total observations: unidentified smelt and flatfish (all species/groupings combined). Unidentified smelt had the highest count within the non- rockfish grouping, with just under 7,000 observed individuals. A total of 14 species/groupings of flatfish were observed with combined total counts equaling 4,171 fish.

For a full list of fish species and their overall densities by study site (MPA or reference) and transect type (rocky reef, soft bottom, or canyon), see Appendix 3.

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Table 2. Total count, estimated size and depth of all fish observed from video collected in 2014 and 2015 within the NCSR.

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Invertebrate Totals For a full list of scientific names, see Table 3; invertebrates will be referred to by common name throughout this report. For all sites and survey years combined, a total of 70 individual macro-invertebrate species and another 29 groupings were identified (Table 3). Of the 124,064 individual invertebrates enumerated, seven species/groupings represented the majority of the observations (approximately 89%). Over 27% of the invertebrates identified were white-plumed anemones, which accounted for 86% of all anemone observations. The next most abundant invertebrates were slipper and California sea cucumbers, which combined, accounted for 40% of the total invertebrate observations. Two rocky reef coral species were also commonly observed: the short red gorgonian and California hydrocoral. Combined, these two species accounted for 11% of the total invertebrate observations. Sea stars represented 8% of the total invertebrate observations, with two species/groupings accounting for 61% of the total sea star observations: red sea stars and the Henricia complex. Lastly, two soft bottom coral species, sea whips and sea pens, accounted for 3% of the total invertebrate observations.

For a full list of macro-invertebrate species and their overall densities by study area (MPA or reference) and transect type (rocky reef, soft bottom, or canyon), see Appendix 3.

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Table 3. Total count and depth range of all invertebrates observed from video collected in 2014 and 2015 within the NCSR.

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BASELINE CHARACTERIZATION OF STUDY AREAS

The following MPA and reference area characterizations are abbreviated descriptions which include key findings for both the 2014 and 2015 survey years combined. In-depth characterizations for each MPA and reference pair are presented in Appendix 3.

Point St. George Reef Offshore SMCA and Reference Area Located northeast of Crescent City, California, the Point St. George Reef Offshore State Marine Conservation Area (PSG SMCA) protects 24.7 square kilometers of marine habitats with depths ranging from 55 to 125 m (CDFW 2016b). The MPA is predominantly soft habitat (96%), but also protects the tip of a large offshore rocky reef (Figure 4). All fishing is prohibited within the SMCA with the exceptions of salmon by trolling and Dungeness crab by trapping. In addition to these exceptions, two federally recognized tribes, Elk Valley Rancheria and Tolowa Dee-ni’ Nation, are exempt from the area and take regulations of the PSG SMCA, but still must comply with all other existing regulations, including the Rockfish Conservation Areas, which have prohibited the take of groundfish in depths exceeding 20 fathoms (~37 m) since 2002.

Located 6.3 km southeast of the PSG SMCA, a rocky reef and the surrounding soft bottom habitats were selected as a reference area for comparison (Figure 4). The reference area was selected based on similar habitats and depths (determined from multibeam mapping imagery) as inside its corresponding MPA. There are no state regulations specific to the reference area, but federal regulations prohibit the take of groundfish as part of the Rockfish Conservation Areas. Annual sampling within the reference area was planned to mirror survey efforts inside the SMCA.

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Figure 4. Point St. George study area showing the rocky reef and surrounding soft bottom habitats in (a) the SMCA and (b) reference area.

Substrate Inside the SMCA and reference area, transects that targeted the rocky reef were primarily composed of rock and mud, while soft bottom transects were mainly composed of mud (Figure 5). Rocky reef habitats within both study areas were heavily influenced by sedimentation. Fine particulate material was suspended a few meters off the sea floor, and covered both rock and soft bottom surfaces in a thick layer of fine sediment and detritus. Only the vertical surfaces or tops of the highest relief rock outcroppings were free of these deposits. The density of suspended material was dependent on ocean conditions. Sampling at the reference site in 2015 was halted when large ocean swells moved into the study location causing visibility to decrease from a few meters to zero overnight. Future monitoring of the Point St. George study areas may encounter similar conditions.

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Figure 5. Percent substrate (rock, boulder, cobble, gravel, sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the (a) Point St. George SMCA and (b) reference area

Habitat Overall, inside the SMCA and reference area, the habitat and rugosity within both rocky reef and soft bottom transects were comparable (Figure 6). Within the rocky reef, both study areas were mainly composed of hard and soft habitats, which combined represented 89% of the habitat at the SMR and 86% at the reference area. Outside the rocky reef transects targeting soft bottom habitats within the SMR and reference area were classified as 100% soft habitat.

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Figure 6. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Point St. George Reef Offshore SMCA and (b) reference area for transect lines targeting: (I) the rocky reef and (II) the soft bottom habitats.

Fish The rocky reef of both study areas was characterized by rockfish species, Lingcod and Kelp Greenling (Figure 7). Rockfish densities were approximately three times lower in the rocky reef of the reference area, when compared to the SMCA. In addition, observed rockfish species richness was lower inside the reference area. The majority of rockfish identified within both study areas were epibenthic aggregating species such as Black, Blue and Olive/Yellowtail Rockfish, which were observed in large numbers near the tops of high relief rocky outcroppings. Canary Rockfish, a semi-aggregating species, were observed in high densities near the bottom, especially around sand channels within the rocky reef. Yelloweye and Quillback Rockfish were also common, with the highest regional rocky reef density of both species occurring at these two study areas. Yelloweye Rockfish densities within the SMCA were two times higher than observed anywhere else during this project. Soft bottom habitats were dominated by few species compared to rocky habitats, with flatfish and unidentified eel pouts being characteristic of both areas.

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Invertebrates Invertebrate species composition within rocky reef habitats of both May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 112 study areas was similar (Figure 8). Five macro-invertebrate species dominated observations within the rocky reef of both the SMCA and reference area: white-plumed anemones, slipper sea cucumbers, California sea cucumbers, short red gorgonians and red sea stars. While not characteristic of both study areas, basket stars were also common within the rocky reef of the SMCA.

Soft bottom habitats were dominated by few species compared to rocky habitats (Figure 8). Dungeness crabs and red octopus were characteristic of both study areas accounting for over 80% of the total mobile invertebrate density. While, two groups, sea whips and pens, and white-plumed anemones accounted for 97% of the total sessile invertebrate density.

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Reading Rock SMR and Reference Area Reading Rock State Marine Reserve (SMR) is located just south of Reading Rock approximately 8 kilometers off the coast of Prairie Creek Redwoods State Park, in Humboldt County, CA (Figure 9). The SMR encompasses approximately 25 square kilometers of sea floor with depths ranging from 44 m to 77 m. It is mainly comprised of soft bottom habitats (98%), but also includes a small portion of rocky reef habitat (2%) that encompasses Reading Rock, but does not include the above-surface visible portion of the rock (CDFW 2016c).

The Reading Rock reference area is located 0.95 kilometers north of the Reading Rock SMR. The reference area was selected to encompass similar habitats and depths (determined from multibeam mapping imagery) as those found within the MPA. There are no state regulations specific to the reference area, but federal regulations prohibit commercial or recreational the take of groundfish as part of the Rockfish Conservation Areas. Annual sampling within the reference area was planned to mirror survey efforts inside the SMR.

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Figure 9. Reading Rock study location showing rocky reef and soft bottom habitats in (a) the reference area and (b) SMR

Substrate Inside the SMR and reference area, transects that targeted the May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 115 rocky reef were composed of all 6 substrate types (Figure 10). However, the reference area contained greater amounts of boulder, cobble and gravel at the transitional portions of the rocky reef than the SMR. Transects targeting soft bottom habitats within the SMR and reference area were entirely composed of mud substrate.

During both survey years, there was better visibility at the reference area than inside the SMR. Visibility at the SMR ranged from 1 to 1.5 m, while at the reference area it ranged from 2 to 2.5 m. In addition, rocky substrates observed within the reference area were less sediment impacted than those within the SMR. These observations may indicate that the reference area, located on the north side of the rocky reef, may be subject to heavy currents and/or storm surges that carry away loose sediment and detritus which is deposited on the southern side of the reef in the SMR.

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Figure 10. Percent substrate (rock, boulder, cobble, gravel, sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the Reading Rock SMR and (b) reference area.

Habitat Overall, inside the SMCA and reference area, the habitat and rugosity within both rocky reef and soft bottom transects were comparable (Figure 11). Rocky reef transects within the SMR and reference areas were predominantly hard and mixed habitat combined, while soft bottom transects within the SMR and reference area were classified as 100% soft habitat.

Figure 11. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Reading Rock SMR and (b) reference area, for transect lines targeting (I) rocky reef and (II) soft bottom habitats

Fish Fish species composition between the two study areas was similar. May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 118 Rockfish species, Lingcod and Kelp Greenling characterized the rocky reef, even though their densities were quite low (Figure 12). Five species/groupings of rockfish accounted for 76% of the overall rockfish subgrouping density in the SMR, and over 65% in the reference area: unidentified rockfish, Olive/Yellowtail, Black, Blue, and Canary Rockfish. The epibenthic aggregating species including Blue Rockfish and Olive/Yellowtail Rockfish were commonly observed schooling around the tops of larger rock outcroppings. Another semi-aggregating species, the Canary Rockfish, was observed schooling near the sea floor close to the transition from soft bottom to rocky reef. Canary Rockfish were also observed within the rocky reef itself, but in lower numbers. Additional benthic rockfish species, such as Yelloweye Rockfish, Quillback Rockfish, Vermilion Rockfish and Rosy Rockfish, were observed intermixed throughout the rocky reef in both study areas.

Surveys of soft bottom habitat were primarily dominated by flatfish and the ‘all other fish’ subgroup, of which unidentified smelt represented over 98% of the observations within both study areas. Smelt may be characteristic of the soft bottom habitats surrounding Reading Rock and are known to spawn on the nearby beaches.

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Figure 12. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a) Reading Rock SMR and (b) reference area for 2014 and 2015. For a breakdown of the taxonomic composition of subgroups, see Appendix 3.

Invertebrates There were approximately 2.7 times as many invertebrates enumerated at the reference area as the SMR, however species composition was similar within both study areas (Figure 13). Within both areas, five macro-invertebrate species/groupings characterized the rocky reef: slipper sea cucumber, white-plumed anemone, California sea cucumber, red sea star and the Henricia sea star complex.

Soft bottom habitats at the SMR and reference area were also characterized by few species. Sea whips and pens, and white-plumed anemones were the dominant sessile invertebrates, accounting for over 99% of the total sessile invertebrate density in soft bottom habitats at both areas. While no rocky substrates were observed on soft bottom transects, it is possible that cobble or large shell debris are buried just beneath the surface of the mud, providing attachment structure for the white-plumed anemones. The dominant mobile invertebrates included red octopus and Pleurobranchaea californica, which occurred in similar densities at both study areas. Sand stars were also common, but were three times as numerous at the reference area as the SMR.

Mattole Canyon SMR and Reference Area Mattole Canyon State Marine Reserve is located offshore of the Mattole River estuary and California’s Lost Coast region, a portion of California’s North Coast that is sparsely populated with limited coastal access (Figure 14). Mattole Canyon SMR protects 25.4 square kilometers of marine habitats ranges in depth from 25 m to 502 m (CDFW 2016a). The SMR is predominately soft habitat (94%), but it also includes several rocky habitats (6%). Approximately 14% of the area of the SMR is deep submarine canyons, which makes it unlike any other MPA we surveyed within the NCSR.

The Mattole Canyon reference area is located just 0.3 kilometers south of Mattole Canyon SMR and includes a portion of the same rocky reef structure (Figure 14). The reference area was selected to encompass similar habitats and depths (determined from multibeam mapping imagery) as those found within the MPA. There are no state regulations specific to the reference area, but federal regulations prohibit the take of groundfish as part of the Rock Fish Conservation Areas. Annual sampling within the reference area was planned to mirror survey efforts inside the SMR.

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Figure 14. Mattole Canyon study area showing the rocky reef and surrounding soft bottom habitats in (a) the SMR and (b) reference area.

Substrate Within both study areas, transects targeting the rocky reef were similar, and were primarily composed of rock with sand and mud (Figure 15). Transects that targeted the canyon were also similar, and were mainly composed of mud with smaller amounts of rock and cobble depending on the study area. In contrast, soft bottom habitats in the two areas were distinctly different. The SMR had large amounts of scattered exposed rocky patches, creating mixed habitats unlike any other soft bottom area we surveyed regionally, including the reference area which was mainly composed of sand.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 121 Strong currents and large swells were common during our surveys of this location, along with strong afternoon winds and seas. These currents appeared to be characteristic of the area, as evident by the large, deep scour depressions around rock outcroppings and near the transitions between soft bottom and rocky reef. Dives targeting the canyon wall were difficult to complete due to the strong currents that swept across the shelf and accelerated down into the canyon. On the canyon floor we observed currents flushing organic materials out into deeper waters. Weather conditions changed rapidly and were not always consistent with predicted weather reports, making it a difficult location to sample. The typical work day for Mattole Canyon was short, requiring additional days beyond what was planned for this study location.

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Figure 15. Percent substrate (rock, boulder, cobble, gravel, sand and mud) by transect type (rocky reef, soft bottom and canyon) for survey lines inside (a) Mattole Canyon SMR and (b) reference area.

Habitat Inside the SMR and reference area, transects targeting the rocky reef were composed of nearly equal parts of hard, mixed and soft habitats and were similar in rugosity (Figure 16). However, transects targeting soft bottom and canyon transects at the two study areas were not similar. In the SMR, both transect types were mainly composed of soft habitats with smaller amounts of mixed and hard habitats. Whereas, at the reference area, both transect types were almost exclusively soft only habitat.

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Figure 16. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Mattole Canyon SMR (b) reference area for transects lines targeting: (I) the rocky reef, (II) soft bottom and (III) canyon habitats.

Fish Fish species composition on rocky reef transects was similar in both study areas (Figure 17). YOY was the most abundant subgrouping and accounting for half of the total fish density at both areas. While, the same species of aggregating rockfish: Blue, Black, Canary, Widow and Olive/Yellowtail Rockfishes accounted for 75% and 85% of the rockfish observations in the reference area and SMR respectively.

Transects targeting soft bottom habitats inside the SMR had the highest observed densities of rockfish, compared to all other study areas and habitat types. YOY rockfish densities were also 1.7 times higher than any other study area surveyed. Shortbelly Rockfish accounted for the majority of the small schooling rockfish observations in both study areas, but were twice as abundant in the reference area than the SMR.

At the SMR, Sablefish and skates were commonly observed on dives that targeted the canyon floor. Moving up the sides of the canyon, rock outcroppings and compacted sediment shelves broke up the otherwise steep walls of the canyon where thornyheads, Greenstriped Rockfish and flatfish species were common. Just below the transitional point between the flat shelf and canyon, Canary, Olive/Yellowtail and Yelloweye Rockfishes were found sheltering from stronger currents above. Only one canyon dive was completed in the reference area. The slope of the canyon wall was considerably less steep, and currents there were greatly reduced. Spiny Dogfish, flatfish and Pacific Hake were the most abundant fish.

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Invertebrates Invertebrate species composition within transects targeting the rocky reef of both study areas was similar (Figure 18). White-plumed anemones, California sea cucumbers, short red gorgonians and California hydrocorals were among the most abundant species observed at both areas. Sea star species and sponges were also common.

Species composition on transects targeting soft bottom habitats within the SMR and reference area were fairly different. This was likely due to the differences in substrate composition between the two areas, with the SMR having many scattered rocky patches that hosted a greater abundance and diversity of sea stars, anemones, sponges and other invertebrates than the reference area that was composed of only soft habitats. May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 125

The same was true for transect targeting the canyon, with the SMR having a greater number and abundance of species than the reference area. However, anemones, white plumed anemones and red octopus were common in both study areas.

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Ten Mile State Marine Reserve and Reference Area The Ten Mile State Marine Reserve (TM SMR) is located approximately 14.5 kilometers north of Fort Bragg, California, and encompasses 31 square kilometers of marine habitats (CDFW 2016d). The SMR spans 5 km of shoreline and shares its southern border with Ten Mile Beach State Marine Conservation Area. With depths ranging from 0 to 105 meters, the SMR is comprised of approximately 86% soft habitat, 8% rocky habitat and 6% unidentified habitat (Figure 19). The Ten Mile SMR was the only MPA we surveyed as part of the baseline program that previously was open to bottom fishing in its shallower waters prior to MPA implementation in 2014. Fishing deeper than 37 m was prohibited in 2002 through implementation of the Rockfish Conservation Areas by Pacific States Marine Fisheries Council.

Located 2.2 kilometers south of TM SMR, a rocky reef and surrounding soft bottom habitats were selected as the Ten Mile reference area for comparison (Figure 19). The reference area was selected based on similar habitats and depths (determined from multibeam mapping imagery) as inside its corresponding SMR. There are no state regulations specific to the reference area, but federal regulations prohibit the take of groundfish deeper than 37 m as part of the Rock Fish Conservation Areas. Annual sampling within the reference area was planned to mirror survey efforts inside the SMR.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 127

Figure 19. Ten Mile study location showing rocky and soft bottom habitats in (a) the SMR and (b) reference area.

Substrate Overall, substrate composition at the SMR and reference area May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 128 was similar (Figure 20). At both areas, transects that targeted the rocky reef were mainly composed of rock with smaller amounts of sand and mud. Rock surfaces had less sedimentation and detritus buildup than the two northernmost study locations. These cleaner rocky surfaces hosted encrusting coralline algae in the shallower portions of the rocky reef, which was not observed at any of the other study locations. We also observed less suspended fine particulate material, which may have accounted for the better water visibility, that was typically 4 to 6 m, compared to 1 to 3 m observed at other locations such as Point St. George. Transects that targeted the soft bottom were composed exclusively of sand or mud at both study areas.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 129

Figure 20. Percent substrate (rock, boulder, cobble, gravel, sand and mud) by transect type (rocky reef and soft bottom) for survey lines inside the (a) Ten Mile SMR and (b) reference area.

Habitat Overall, inside the SMR and reference area, transects that targeted the rocky reef and soft bottom habitats and rugosity were comparible (Figure 21). Rocky reef transects within the SMR and reference areas were mainly composed of hard and soft habitats, which combined represented, 84% of the habitat at the SMR and 88% at the reference area. While soft bottom transects within the SMR and reference area were classified as 100% soft habitat.

Figure 21. Percent habitat type (hard, mixed and soft) and percent rugosity (high, medium, low and flat) at (a) Ten Mile SMR and (b) reference area, for transect lines targeting (I) the rocky reef and (II) the soft bottom habitats.

Fish Fish species composition and abundance were similar within the SMR and reference area (Figure 22). Rockfish were common and, along with Lingcod and Kelp Greenling, characterized the rocky reef. Epibenthic aggregating rockfish species were the most abundant rockfish, with Blue, Canary and unidentified rockfish being the most common species at both study locations. YOY were also very common within the rocky reef, with densities higher than at any other study are pair.

Fish observed in the soft bottom habitats were similar within both study areas, May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 131 and were mainly composed of flatfish and ‘all other fish’. The ‘all other fish’ subgroup was most notably different between the two areas. Unidentified smelt were observed in large numbers at the reference area accounting for 90% of the ‘all other fish’ density, compared to only 18% within the SMCA.

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Figure 22. Mean density of fish subgroupings observed within rocky reef and soft bottom transects at (a)
Ten Mile SMR and (b) reference area for 2014 and 2015. For a breakdown of the taxonomic composition
of subgroups, see Appendix 3.

Invertebrates Invertebrate species composition within both the rocky reef and May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 133 soft bottom habitats was similar between the two study areas (Figure 23). Within the rocky reef, like the northernmost two MPAs we studied, white-plumed anemones and slipper sea cucumbers were the characteristic sessile macro-invertebrates, while California sea cucumbers were the characteristic mobile invertebrate. However, unlike the northernmost MPAs, sponges and other anemones were also abundant in the rocky reef at the Ten Mile study location.

Within the SMR, red sea urchins were also observed in much higher densities than compared to the reference area. The higher urchin observations are likely a result of the shallower depths surveyed at the SMR, compared to the reference area, where very few red urchins were observed.

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ANALYSIS OF INDEX SITES

Fish species distribution and abundance are important considerations for MPA placement; they influence their effectiveness and are characteristics used to assess MPA performance. We used visual species observations directed at paired index sites to establish nearshore rocky reef fish assemblage metrics. These metrics can be monitored over time to inform performance assessment and adaptive management. The paired index sites where chosen to be representative of the general rocky reef habitat at each of the four locations (Point St. George, Reading Rock, Mattole Canyon and Ten Mile), inside the MPAs and outside of the MPAs in their respective reference areas. Ten rocky reef fish species/groupings were selected for in-depth density analyses to establish baseline metrics for future comparisons (Table 4).

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Table 4. Number of observations and mean density at all index sites per 100 m2 (+SE) for ten fish species selected for statistical comparisons among MPAs and their respective reference areas. Proportion of obs. is the proportion of non-YOY observations in the index sites only. Frequency of observation (FO) is the proportion of ROV transects in index sites in which the species occurred at least once.

Fish Densities Overall, individual species densities were low at all locations (<1 per 100 m2), with the highest densities occurring at Point St. George SMCA and Ten Mile SMR (Figure 24). While densities differed significantly for nearly all species among the MPA locations, they were the same inside each MPA and reference area pair except Point St. George. The Olive/Yellowtail Rockfish was common, and observed in the highest density at Point St. George.

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Figure 24. Density per 100 m2

of select rocky reef fishes at each MPA (SMR or SMCA) and reference

area index site pair at Point St. George, Reading Rock, Mattole Canyon and Ten Mile.

Similarity Test
Based on the results of the Bray-Curtis Similarity Test (group average agglomerative
clustering) among index site fish assemblages we found three of the four MPA and
reference area index site pairs were well placed, which will allow for robust comparisons
in long-term monitoring in the North Coast Study Region. However, assemblage
similarity was the lowest between the Point St. George SMCA and reference area index
sites.

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Figure 25. Similarity (group average agglomerative clustering) among index site fish assemblages in MPA and reference area pairs, for Point St. George, Reading Rock, Mattole Canyon and Ten Mile. Analyses are based on densities for individual species and taxonomic groups (see methods for full list of taxonomic groups). Data were combined for observations over all substrates.

Point St. George Index Sites The Point St. George SMCA index site spans the most exposed portion of the reef. The reference area index site is located approximately 16 km southeast along another strip of reef that is somewhat protected from the predominant northwest winds and currents. The two index sites both range from 50-70 m in depth.

The SMCA and reference area index sites showed the least similarity between fish species assemblages (60% overall and 40% over rock substrates) and the most significant differences in species densities of any other MPA/reference area index site pair. The highest densities of Canary, Blue and Olive/Yellowtail Rockfish were observed at the SMCA index site, while the lowest densities of Kelp Greenling and Lingcod were also observed there. Additionally, Copper and Widow Rockfish were observed at the SMCA index site but were absent at the reference site. Black Rockfish were also present at the reference site, but not at the SMCA site. While a greater percentage of hard rocky habitats were surveyed at the reference site, generally higher densities of most rockfishes, flatfishes, Lingcod, and Kelp Greenling were observed at the SMCA site. Only Tiger Rockfish, Quillback Rockfish, and small benthic fishes showed higher densities at the reference area index site.

Differences in geographical orientation and resulting physical conditions may have influenced the differences observed between the index sites at Point St. George. The SMCA’s position at the outer edge of the reef makes it difficult to find a reference site with similar habitat conditions. It is recommended that the Point St. George reference area be re-evaluated and potentially moved to a location closer to the MPA to increase comparability to the SMCA in both assemblage and species densities, but this may not be feasible. During the 2014 cruise, several other locations near the PSG SMCA were surveyed with the ROV as a part of a California Department of Fish and Wildlife survey of the North Coast Region. Two additional sites located off Point St. George SMCA and two sites just south of Crescent City were surveyed using the ROV. These locations were also considered as a possible reference area for the SMCA, though none of them were a suitable match. Even though there are differences in the fish species assemblages and habitat conditions, the baseline data collected at each site should still provide some metrics for monitoring change over time.

Reading Rock Index Sites Reading Rock’s SMR index site is positioned on the southern tip of a small offshore elliptical reef and the reference area index site is located on the northern edge of the same reef just 1,500 m from the SMR site. Species assemblages were more than 80% similar at the SMR and reference area index sites. All fish species densities were low at both Reading Rock index sites. Lingcod and Blue Rockfish exhibited the highest densities both at the SMR and reference site. Black Rockfish were more common at the SMR site, and Canary Rockfish were more common at the reference site. All ten species chosen for metric establishment were observed in small numbers at Reading Rock. Statistical differences in densities were observed for Vermilion Rockfish (none observed at the SMR site) and Black Rockfish; density for both species was higher at the SMR index site.

Mattole Canyon Index Sites Mattole Canyon’s two index sites were positioned less than 500 m apart on the southern side of the canyon head, with depths ranging from 20-60 m. Index site assemblages at this location were very similar overall, greater than 80%. Blue, Black, and Canary Rockfish, as well as Kelp Greenling and Lingcod, were observed in the highest densities at these sites. Kelp Greenling densities at Mattole Canyon were highest of all four MPA locations. There were no density differences between the SMR and reference area sites at this location for the ten selected species.

Ten Mile Index Sites Ten Mile’s SMR index site is located offshore of the Ten Mile estuary and contains a higher percentage of rocky reef than the other MPA’s surveyed. The SMR index site is located on the southern edge of the reef, while the reference site is located approximately 8 km south on the north edge of another reef in the same depth range (40-60 m). At Ten Mile, we found relatively high densities of Blue and Canary Rockfish in both index sites, many of which were juvenile and sub-adult fishes. A very large number of YOY and various small individuals were also observed at the Ten Mile location compared to the other three sites.

FISH DEPTH DISTRIBUTION

The depth distribution of select fish species/groupings across rocky reef transects are presented here for Point St. George, Reading Rock, Mattole Canyon and Ten Mile MPAs and their paired reference areas (see methods for a list of fish species). In addition, the depth distribution of select fish across canyon transects are shown for Mattole Canyon SMR. Only one exploratory canyon transect was surveyed in the Mattole Canyon reference area, therefore the depth distribution of fish within the canyon of the reference area are not presented. Due to an absence in species diversity, with 2 categories ‘unidentified flatfish’ and ‘all other fish’ accounting for 98% of the fish observed on soft bottom transects, results for soft bottom transects are not shown.

Depth distributions of select fish species are presented for all rocky reef transects surveyed (index sites and characterization transects combined) for each study area. During the planning phase, effort was made to place index sites in the most prominent rocky reef habitat within the 40-60 m depth range in each MPA. Index site placement was not intended to cover the full range of depths in which rocky habitat was predicted (using multibeam mapping) in each MPA, but to cover similar depth ranges at all study areas. Paired reference areas were subsequently selected to provide comparable rocky habitat within the same depth range as the MPA index site.

The total area and range of depths surveyed for each MPA and reference area pair, and the depth range of each index site is given in Table 5. Effort was made to survey a similar amount of area within each MPA and reference area pair and to survey, as much as possible, the full range of depths in which rocky habitat was predicted using characterization transects. Additionally, we attempted to survey similar depth ranges between each MPA pair, although this was not always possible as rocky reef and canyon habitat did not always occur within the same range of depths. For shallower rocky habitat, the ROV’s operational capacity was limited to approximately 15 m.

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 138

To show the density of fish along a vertical gradient, depth was stratified into 10 m bins for rocky reef transects and 10 and 50 m bins for canyon transects. The total area surveyed per depth bin at each site is shown in Figure 26 for rocky habitat transects and Figure 31 for canyon transects. The distribution and density of select fish species were plotted for each depth bin and are shown in Figures 27-30.

Rocky Reef Transects

May 2017 - North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems 139

Figure 26. The total area of rocky reef transects surveyed per depth bin for each MPA for Point St. George SMCA (blue), and Reading Rock SMR, Mattole Canyon SMR and Ten Mile SMR (all SMRs in red) and their reference areas (gray).

Depth distributions for select fish species are presented for all MPA and reference area pairs surveyed. Data is presented as a reference for the depths surveyed within the rocky habitat, and to show overall density by species/grouping across those depths. Additionally, the depth range for index sites within each study area are presented to show the expected distribution of select fish within each index site at paired MPA and reference areas.

Point St. George – Rocky Reef Rocky reef habitat at Point St. George SMCA and reference area encompass a limited range of depths (Figure 26). Less than 200 m2 was surveyed in the 40-49 m bin at both the SMCA and references areas, therefore, these data were not included in Figure 27. Depth bins ranged from 50-79 m at the SMCA and from 50-69 m at the reference area. The depth range of the Index site placed over rocky features within reference area overlap the depths surveyed within the SMCA and appear to be representative of the distribution of rocky habitats within both study areas.

Overall, the SMCA and reference area appeared to have similar distributions of fish in each of the depth stratified bins. The most notable difference was for Olive/Yellowtail Rockfish, where at the SMR densities are greater in the 50-59 m depth bin, while at the reference area they are greater in the 60-69 m depth bin.

Figure 27. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Point St. George SMCA and reference area.

Reading Rock – Rocky Reef Reading Rock SMR and reference area also encompass a limited range of depths (Figure 26). At these two study areas, less than 200 m2 were surveyed in the 30-39 m bin in the SMR, and in the 30-39 and 60-69 m depth bins in the reference area. Consequently, this data was not included in density calculations for Figure 28. Depth bins in the SMR ranged from 40-69 m, and 40-59 m in the reference area. The depth range of index sites placed over rocky features within the SMR and reference area overlapped much of the depths surveyed within the SMR and are more representative of the distribution of rocky habitats within both study areas. Again, the SMR and reference sites appeared to have similar distributions of fish in each of the depth stratified bins. The most notable differences are for Blue Rockfish, where densities appear to be higher in the 40-49 m depth bins and for Canary Rockfish and the Olive/Yellowtail Rockfish complex, where density appears to increase with depth. Also notable, there are no observations of Black, Blue, Copper, Quillback or Sebastomus Rockfish in the 60-69 m depth bin within the SMR.

Figure 28. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Reading Rock SMR and reference area.

Mattole Canyon – Rocky Reef Mattole Canyon rocky reef habitat encompassed a wider range of depths than the northern two sites (Figure 29). Less than 200 m2 was surveyed in the 20-29 m and 80- 89 m depth bins at the SMR site, and in the 60-69 m, 70-79 m and 80-89 m depth bins at the reference site; these data were not included in density calculations for Figure 29. Depth bins ranged from 30-79 m at the SMR and 20-59 m at the reference area.

Overall, the following notable trends were seen at Mattole Canyon SMR and reference sites: Sebastomus, Vermilion, and Yelloweye Rockfish were present at nearly all depths in the SMR site; however, they were not observed at the reference site, with the exception of Vermilion Rockfish being present in one depth bin (30-39 m). Olive/Yellowtail Rockfish density increased with depth at the SMR site, but at the reference site, density remained low across most depth bins. Kelp Greenling and Lingcod were present at all depths in both the SMR and reference sites with Lingcod density increasing with depth. Canary Rockfish were common at both the SMR and reference sites in all depth bins 30 m and deeper. Index sites placed in the Mattole Canyon SMR did not fully overlap the surveyed depth range, and are therefore not completely representative of the available rocky reef habitat within the SMR. Additionally, the index site placed at the reference area

covered a shallower range of depths than the index site within the SMR. Overall fish distribution also appears to be different within each site, with fewer species observed at the reference site. These differences are most notable for some of the non-aggregating rockfish species, such as Sebastomus, Vermilion, and Yelloweye Rockfish. Given these differences, future monitoring plans should consider expanding the range of depths surveyed beyond the index sites to capture the full distribution of species within the SMR and reference area at the Mattole Canyon study location.

Figure 29. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Mattole Canyon SMR and reference area.

Ten Mile – Rocky Reef Ten Mile’s rocky reef habitat encompassed a wider range of depths than the other sites surveyed (Figure 26). Less than 200 m2 were surveyed in the 70-79 m and 80-89 m depth bins in SMR, and 10-19 m and 20-29 m depth bins in the reference area; these data were not included in density calculations for Figure 30. Depth bins ranged from 10-69 m deep in the SMR and 30-89 m deep in the reference area.

For both the SMR and reference area, Blue Rockfish densities increased as depth decreased, while Canary Rockfish showed the opposite, and increased in density with depth. Black Rockfish were only observed in the SMR and only at depths shallower than 49 m, with the highest densities observed at the shallowest depth bin surveyed (10-19 m). The Sebastomus Rockfish complex was observed at both sites, but only at depths greater than 40 m.

The index site placed in the Ten Mile SMR did not fully overlap the surveyed depth range, and is therefore not representative of the available rocky reef habitat (for depths greater than 20 m) within the SMR. The index site placed within the reference area did fully overlap with the depth range of the SMR index site, as did the fish distributions observed within both sites. As currently situated, both index sites are a good match and will allow for monitoring long-term trends in both areas.

Within the SMR, available rocky reef habitats extend shallower than the range of depths at the index site. Therefore the index site may not be suitable for detecting the shallower range of species observed in the SMR. For example, Black Rockfish, which were more abundant in the shallow areas of the rocky reef, may not be observed within the index site. The opposite occurred at the reference area, where surveyed depths extended deeper than the index site. Given these differences, future monitoring plans should consider expanding the range of depths surveyed beyond the index site to capture the full distribution of species within the SMR and reference area.

Figure 30. Density of select fish species per depth stratified bin, with bubble size representing their relative density for Ten Mile SMR and reference area.

Canyon Transects

Figure 31. The total area surveyed per depth bin for canyon transects at Mattole Canyon SMR.

Mattole Canyon – Canyon Within the Mattole Canyon SMR transects, canyon habitat depths ranged from 52-420 m. Effort is shown in Figure 31 and surveyed depths are broken into 10 m bins from 50- 149 m, and into 50 m bins from 150-449 m in depth. Less than 200 m2 were surveyed in the 140-149 m bin. As a result, these data were not included in density calculations for Figure 32. Although index sites were not placed in the canyon, Figure 32 shows the distribution at which select species occur in the canyon, which may be used for future monitoring.

Overall, the occurrence and relative densities of several species showed marked differences between shallow (<100 m) and deep zones (>100 m) where the shelf/canyon interface occurs (indicated by a red line in Figure 32). The following notable trends were present in the rockfish species surveyed: Canary Rockfish are relatively high in density in the shallower depth bins surveyed and decrease in density until just after the shelf/canyon break at 110-119 m, where they were no longer present. Olive/Yellowtail Rockfish showed the highest density around the shelf/canyon interface, but were also observed in the shallowest depth bin (50-59 m). Yelloweye Rockfish were observed with similar densities around the shelf/canyon break from 80-119 m, while Greenstriped Rockfish occurred from just above the shelf break down to 249 m. Black, Blue, Copper, and Vermilion Rockfish were not present on any of the canyon transects.

Thornyheads occurred exclusively in the deeper ranges of the canyon, within the typical range expected. Lingcod occurred in a wide range of depths, but were observed in much higher densities in the shallower (50-89 m) depth bins. While Lingcod densities were lower around the shelf/canyon break, they were observed to a depth of 300 m. No Lingcod were observed between 120 m and 139 m. Kelp Greenling were only observed in the shallowest depth bins, from 50-89 m.

The ‘all flatfish’ grouping shown in Figure 32 includes all observations of unidentified flatfish plus all flatfish identified to species level (see Appendix 6 for a full list of species). Additionally, the five more commonly observed flatfish species that were identified to species level are also shown, although their densities only represent the proportion that was identified. Overall, flatfish were observed from 70-449 m, with the highest density of flatfish observed in the 150-199 m depth range. Dover Sole only occurred at the canyon-shelf interface and deeper, while sanddabs only occurred at the canyon-shelf interface, and shallower. English Sole and Petrale Sole were observed mainly in the mid-ranged depths, while the Rex Sole was observed exclusively in the deeper ranges of the canyon.

Overall, the interface between the shelf and canyon appears to be an important habitat feature for some of the species presented. Yelloweye Rockfish were only observed near the canyon-shelf interface, from 80 to 119 m. For other species, such as Canary and Olive/Yellowtail Rockfish, densities decrease with depth and eventually disappear at the canyon-shelf interface. The opposite was true for Greenstriped Rockfish and Dover Sole, which increased in density deeper than the canyon-shelf interface. Future monitoring plans for Mattole Canyon SMR should consider capturing the full extent of the canyon, with importance placed on capturing information on either side of the canyon-self interface.

Figure 32. The density of select fish species per depth stratified bin, with bubble size as the relative density of fish in that depth bin. There was insufficient data (less than 200 m surveyed) for the 140-149 meter depth bin (indicated by the gray line). The shelf/canyon break occurred at about the 100 m mark (indicated by the red line).

FISH SIZE DISTRIBUTION

Laser-based Size Estimates Mean visual size estimates for ten select species of fish (Black, Blue, Canary, Copper, Olive/Yellowtail, Quillback, Vermillion, and Yelloweye Rockfish, and Lingcod and Kelp Greenling) are presented in Table 7.

Table 6. The mean total length of select fish species within each MPA (SMCA & SMR) and reference (Ref.) area: Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). A dash mark indicates no individuals were counted at that study area. ‘N/A’ indicates too few fish were counted to report a mean.

Overall, the ten species show little difference in mean total length between MPA and reference area pairs. For the rockfish species, the largest mean size difference between a MPA and reference area was found at Mattole Canyon, where Blue Rockfish mean total lengths differed by 11.9 cm. Surveys at the Mattole Canyon reference area had a shallower depth range than Mattole Canyon SMR (see table 5 in the depth section). Since smaller juvenile Blue Rockfish were typically seen at shallower depths, this likely accounts for the large difference in the mean density between the two areas. All other rockfish mean differences ranged from 0.2 cm to 4.6 cm.

Lingcod showed a large difference in mean total length between study areas at Mattole Canyon, where the means differed by 10.6 cm. At all other study area pairs, the difference in the means was 2.3 cm or less. Kelp Greenling showed the smallest difference in mean total length between study areas, with a 1.4 cm difference at Point St. George, and a 0.1 cm to 0.6 cm difference at all other study areas.

Because there was little difference overall in mean total length between MPA and reference areas for the ten fish species presented, lengths for MPA and reference pairs were combined to show the size frequency for each of the 4 study locations: Point St. George, Reading Rock, Mattole Canyon and Ten Mile (Figures 33-42). Percent size frequency is presented in 5 cm bins and size at which 50% of the females of the population reach sexual maturity is referenced in each of the size frequency graphs with dashed lines (Love et al. 2002; Thorson and Wetzel 2016; MacCall 2005; Stewart 2009; CDFW 2016f). 77

Black Rockfish No smaller size classes (10-19 cm) of Black Rockfish were identified at any of the four study locations (Figure 33). Mature fish over 35 cm represented 72% to 100% of the population depending on the location. There were no Black Rockfish observations at the Ten Mile reference area, while Point St. George and Ten Mile SMR had relatively few observations of Black Rockfish at 20 and 22 fish respectively, when compared with Reading Rock and Mattole Canyon that had 97 and 138 fish respectively.

Figure33. Percent (%) size frequency of Black Rockfish at Point St. George (PSG), Reading

The above photo is a 44 cm Black Rockfish from Mattole Canyon.

Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 41 cm (—) for females (Love et al. 2002).

Blue Rockfish Mattole Canyon and Ten Mile locations had the highest proportion of smaller size classes (10 – 24 cm) of Blue Rockfish, representing 39% to 51% of the population at each site respectively (Figure 34). This result was expected, as Mattole Canyon and Ten Mile surveys encompassed a shallower range of depths, where smaller juvenile Blue Rockfish were typically observed. Mature fish over 29 cm represented 41% to 62% of the population depending on the site.

Juvenile Blue Rockfish, as seen in Photo A of a 13 cm Blue Rockfish from Ten Mile, were commonly observed at the two southern sites, Mattole Canyon and Ten Mile. Photo B is of a 33 cm Blue Rockfish from Ten Mile.

Figure 34. Percent (%) size frequency of Blue Rockfish at Point St. George (PSG), Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 29 cm (—) for females (CDFW 2016f).

Canary Rockfish The majority of Canary Rockfish seen, 90% to 97% depending on the site, were less than 39 cm in total length (Figure 35). Depending on the study location, only 3% to 11% of the population represented sexually mature fish over 40 cm. At the Reading Rock study location, the smaller size class (10-14 cm) represented nearly 20% of total observations, while they represented less than 10% of the observations at the other three study areas.

Juvenile Canary Rockfish exhibit a large black spot on the spiny dorsal fin as seen in Photo A of a 13 cm Canary Rockfish from Ten Mile. As Canary Rockfish mature they may retain

Figure 35. Percent (%) size frequency of remnants of the black spot as seen in Photo B of

Canary Rockfish at Point St. George (PSG), a 26 cm sub adult from Ten Mile. Photo C is a 45 cm adult, the size at which 50% of females are sexually mature.

Reading Rock (RR), Mattole Canyon (MC) and Ten Mile (TM). Size at 50% sexual maturity is 44.5 cm (—) for females (Stock assessment; Thorson and Wetzel 2016).

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March 2019- Assessment of Warty Sea Cucumber Abundance at Anacapa Island

Assessment of Warty Sea Cucumber Abundance at Anacapa Island

Final Report to: Resources Legacy Fund Foundation Grant #13319 March, 2019 Andrew Lauermann, Heidi Lovig, Greta Goshorn

March 2017 – Survey and Research Priorities for Coastal and Marine Systems of the Northern Channel Islands, CA

Western North American Naturalist HORIZON SCANNING: SURVEY AND RESEARCH PRIORITIES FOR COASTAL AND MARINE SYSTEMS OF THE NORTHERN CHANNEL ISLANDS, CALIFORNIA

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June 5, 2017 Andrew R. Lauermann, Heidi M. Lovig, Yuko Yokozawa, Johnathan Centoni, Greta Goshorn

INTRODUCTION

METHODS

DATA COLLECTION

ROV Equipment

ROV Sampling Operations

POST-PROCESSING

Substrate and Habitat

Finfish and Invertebrate Enumeration

RESULTS

SURVEY TOTALS

SUBSTARTATE AND HABITAT

Substrate

Habitat

FISH AND INVERTEBRATE DENSITY

Fish

Invertebrates

MAPS OF TRANSECTS

Southeast Santa Rosa Island

Footprint Deep Ridge

West Santa Barbara Island

West Santa Barbara Island

West Santa Barbara Island

South Santa Barbara Island

UNIDENTIFIED SPECIES LIST

Anemones

Boot Sponges

UI Lobed Sponge

Other Sponges Observed

UI Bubblegum Coral

REFERENCES

DOWNLOAD PDF

May 2017 – North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems

North Coast Baseline Program Final Report: Mid-depth and Deep Subtidal Ecosystems

INTRODUCTION

Final Report to:

Resources Legacy Fund Foundation

Grant #13319

March, 2019

Andrew Lauermann, Heidi Lovig, Greta Goshorn

Western North American Naturalist HORIZON SCANNING:

SURVEY AND RESEARCH PRIORITIES FOR COASTAL AND MARINE SYSTEMS

OF THE NORTHERN CHANNEL ISLANDS, CALIFORNIA

June 5, 2017

Andrew R. Lauermann, Heidi M. Lovig, Yuko Yokozawa, Johnathan Centoni, Greta Goshorn