MAY 2014

 by

The Southwest Fisheries

Science Center

ADMINISTRATIVE REPORT LJ-14-04

FISH ERI E S

FISH ERI E S

FISH ERI E S

S O U T HWE ST

S O U T HWE ST

S O U T HWE ST

S C I E N C E C E N T ER

S C I E N C E C E N T ER

S C I E N C E C E N T ER

THE SWFSC DIRECTOR’S 

2014 REPORT ON RESEARCH 

REGARDING HIGHLY MIGRATORY

SPECIES (HMS) AND THEIR FISHERIES 

IN THE NORTH PACIFIC OCEAN

NOAA FISHERIES - 

NATIONAL MARINE FISHERIES SERVICE - 

SOUTHWEST FISHERIES SCIENCE CENTER
“This report is used to ensure prompt dissemination of preliminary results, interim 

reports, and special studies to the scientific community. The material is not ready for 

formal publication since the paper may later be published in a modified form to 

include more recent information or research results. Abstracting, citing, or 

reproduction of this information is not allowed. Contact the author if additional 

information is required.”
ADMINISTRATIVE REPORT LJ-14-04

MAY 2014

by

The Southwest Fisheries

Science Center

Southwest Fisheries Science Center

National Marine Fisheries Service

National Oceanic & Atmospheric Administration

8901 La Jolla Shores Drive

La Jolla, California 92037-1509

THE SWFSC DIRECTOR’S 2014 REPORT ON RESEARCH 

REGARDING HIGHLY MIGRATORY SPECIES (HMS) AND THEIR 

FISHERIES IN THE NORTH PACIFIC OCEAN 
1

I. SUPPORTING U.S. OBLIGATIONS OF INTERNATIONAL AGREEMENTS 

The United States is party to a number of international agreements for the conservation of highly 

migratory species (HMS) in the Pacific Ocean. As such, it is obligated to collect fishery statistics 

from U.S. HMS fisheries and to participate in advancing fishery science for species of interest.

Scientists at the Southwest Fisheries Science Center (SWFSC) have been tasked to fulfill this 

obligation. In this section, some of the contributions and activities during the past year, May 

2013–April 2014, are briefly described.

Monitoring U.S. HMS Fisheries – SWFSC scientists monitor eight U.S. HMS fisheries in the 

Pacific, providing information from these fisheries to HMS researchers and fisheries managers in 

support of the conservation and management of HMS stocks in the Pacific .The fisheries 

monitoring group under the Fisheries Resources Division (FRD) compiles and manages 

information on vessels, gears, effort, catch, bycatch, protected species interactions, landings, 

biological sampling, and observer data. This information is routinely summarized and data 

products are provided to researchers and fisheries management organizations, as well as other 

customers. Fisheries monitoring staff collaborate with staff from other National Marine Fisheries 

Service (NMFS) regional science centers, regional offices, headquarters, fisheries councils, 

commissions, and others to collect and share information from HMS fisheries in the Pacific.

The purse-seine fishery, operating in the western-central Pacific Ocean (WCPO), is the largest of 

the eight HMS fisheries that the SWFSC monitors. The fishery harvests over 200,000 metric tons 

(t) of tropical tunas each year, generating millions of dollars in ex-vessel revenue. The data from 

the WCPO purse-seine fleet are managed as part of U.S. obligations under the South Pacific 

Tuna Treaty (SPTT). The purse-seine fishery in the eastern Pacific Ocean (EPO), which was 

historically a large vessel fleet fishing throughout the tropics, has dwindled to a few smaller 

coastal purse-seine vessels that occasionally target albacore (Thunnus alalunga) and bluefin tuna 

(Thunnus orientalis) in southern California waters. The north Pacific albacore surface (troll/pole 

and line) fishery is the largest HMS fishery based on the west coast. This fishery began in the 

1940s and has expanded and contracted over the decades from southern California and Baja 

waters to the international dateline, to the southern Pacific Ocean in the austral summer months 

(creating an entirely new fishery in 1986) and most recently back to the coastal waters off 

Washington and Oregon. The large-mesh drift gillnet fishery off of California targets swordfish 

and thresher sharks. The California harpoon fishery targets swordfish. The longline fishery that 

targets swordfish and tunas used to be based out of California, but most vessels have since 

relocated to Hawaii. The recreational fisheries that target HMS are composed of private and 

commercial passenger vessels that target albacore off of Washington, Oregon and central 

California, and albacore, bluefin, and yellowfin tunas (Thunnus albacares) in southern California 

and Mexican waters. The 2013 total landed catch for the HMS fisheries that the SWFSC FRD 

staff monitors is shown in Table 1 below.
2

Table 1: Landed catch in the U.S. HMS fisheries. Catches cannot be reported for fisheries for 

which fewer than 3 vessels participated.

FISHERY 2013 CATCH IN 

METRIC TONS

NUMBER OF 

VESSELS

Central Western Pacific Ocean 

Purse Seine 254,348 40

North Pacific Albacore Troll 

and Pole-and-line 12,325 702

South Pacific Albacore Troll 390 6

Eastern Pacific Ocean Purse 

Seine 0

California Large-mesh Drift 

Gillnet 89 18

California Harpoon

Longline (California-based) < 3

North Pacific Albacore Troll and Pole-and-line - Total annual catch of albacore from the North 

Pacific albacore troll and pole-and-line fishery (a.k.a. albacore surface fishery) in 2013 totaled 

12,325 t, a decrease of 13% from 14,149 t in 2012. The number of vessels also decreased from 

840 vessels in 2012 to 702 vessels in 2013. The average weight of retained albacore in 2013 was 

17.5 pounds compared to 15.4 pounds in 2012. Logbook data from this and other HMS fisheries 

are required to be submitted to SWFSC under the HMS Fisheries Management Plan enacted by 

the Pacific Fisheries Management Council in 2005.

South Pacific Albacore Troll - Participation in the South Pacific albacore troll fishery has 

decreased substantially in recent years relative to the 1980s and early 1990s when greater than 50 

vessels typically participated annually. Six vessels participated in the 2013 fishery, compared to 

nine vessels in 2012. Total catch of albacore in 2013 was 390 t, an increase of 44% from the 270 

t landed in 2012. No size sampling has been done in this fishery since 2007. In recent years, 

vessels from this fishery have sold their catches in French Polynesia, Canada and U.S. West 

Coast ports.

Purse-seine Fisheries (WCPO and EPO) - The U.S. has purse-seine vessels fishing in the EPO 

and WCPO .In the EPO, the purse-seine fishery has two components. Smaller coastal purse-seine 

vessels based out of southern California ports normally target mackerel, sardine, anchovy, and 

other coastal pelagic species and opportunistically target albacore or bluefin tuna when schools 

are available during summer months. In recent years less than three of these vessels have fished 

for tuna. Larger purse-seine vessels based out of American Samoa target tropical tunas and fish 

mostly in the WCPO, but occasionally fish in the EPO. In recent years very few of these vessels 

fished in the EPO. In 2013, 40 vessels caught 254,348 t of all species combined (yellowfin, 

bigeye (Thunnus obesus), and skipjack (Katsuwonus pelamis) tunas) in the WCPO purse-seine 

fishery. No vessels fished for tuna in the small vessel EPO purse-seine fishery in 2013.
3

California Large-mesh Drift Gillnet - The California large-mesh drift gillnet (CADGN) fleet 

increased from 17 vessels in 2012 to 18 vessels in 2013. These vessels landed 89 t of swordfish 

in 2013 compared to 118 t of swordfish caught in 2012. The FRD staff manages the gillnet 

logbook database (including set net and small-mesh drift gillnet) on behalf of California 

Department of Fish and Wildlife (CDFW), and data editing and data entry are done by staff from 

both offices. The NOAA West Coast Regional office (WCR) runs a fishery observer program to 

monitor ~20% of the fishery effort and conducts on-board size sampling.

California Harpoon - The California harpoon fishery increased from 9 vessels in 2012 to 13 

vessels in 2013. There was also a slight increase in swordfish caught, from 5 t in 2012 to 6 t of in 

2013. No size sampling information is collected from this fishery. The logbook data from this 

fishery are also managed by FRD staff in cooperation with CDFW.

Longline (California-based) - In recent years less than three longline vessels have operated out 

of Southern California. Most longline vessels targeting tunas and swordfish are currently based 

out of Hawaii .Logbook data from the West Coast are submitted to the West Coast Regional 

office in Long Beach, California (WCR) and maintained at SWFSC. During 2013, there was one 

California-based longline vessel targeting HMS. Data from this fishery are combined with the 

Hawaii longline data by the Pacific Islands Fisheries Science Center (PIFSC) for reporting.

Recreational HMS Fisheries - The recreational catch of albacore by vessels that target albacore 

off the West Coast decreased from 1,212 t in 2012 to 839 t in 2013. The recreational catch of 

bluefin tuna by U.S. recreational boaters increased from 615 t in 2012 to 984 t in 2013.

Miscellaneous Fisheries - HMS caught incidentally in other fisheries are summarized from the 

PacFIN database where state landings data from marine fisheries are maintained. The major 

customers that require detailed information on U.S. HMS fisheries in the Pacific Ocean include 

three Regional Fisheries Management Organizations (RFMOs): the Western and Central Pacific 

Fisheries Commission (WCPFC), the Inter-American Tropical Tuna Commission (IATTC); and 

the International Scientific Committee for Tuna and Tuna-like Species in the North Pacific 

Ocean (ISC). FRD staff compile and summarize a wide variety of fisheries statistics and group 

these summaries by various time and space resolutions for submission to the RFMOs and the 

ISC in order to fulfill the U.S. membership obligations. Statistics range from annual catch and 

bycatch estimates to size composition of the catches and estimations of fishing effort.

Contributing to the Work of the ISC – The United States is a member of the ISC. Other 

members include Canada, China, Chinese Taipei, Japan, Korea, the North Pacific Marine 

Science Organization, the Secretariat of the Pacific Community, and the Food and Agriculture 

Organization. The purpose of the ISC is to enhance scientific research and cooperation for 

conservation and rational utilization of species of tuna and tuna-like fishes which inhabit the 

North Pacific Ocean, and to establish the scientific groundwork for the conservation and rational 

utilization of these species in the region through a multilateral regime. The ISC is organized into 

five Working Groups—statistics, Pacific bluefin tuna, albacore, billfish, and sharks—that meet 

intercessionally and report to a Plenary body. The overall chairman of the ISC is Gerard DiNardo 

of the NMFS PIFSC. Results of the ISC are made available to participating members and to 

RFMOs of the Pacific Ocean.
4

Key Results of the 13th Meeting – The13

th ISC Plenary was held in Busan, Republic of Korea,

from 17-22 July 2013. The meeting was attended by members from Canada, Chinese Taipei,

Japan, Korea, Mexico, and the United States as well as the WCPFC. The Plenary reviewed

results, conclusions, new data and updated analyses of the Billfish, Shark, and Pacific Bluefin 

Tuna working groups. The Plenary endorsed the findings that the Pacific blue marlin and North 

Pacific blue shark stocks are not overfished nor experiencing overfishing, and reiterated that

Pacific bluefin tuna are overfished and experiencing overfishing. It further provided projections

for managers to consider in crafting management measures for North Pacific albacore tuna,

swordfish, and striped marlin, and updated the conservation advice of ISC12 based on these 

projections. A special seminar on Pacific Ocean ecosystem and tuna dynamics was held. The 

Plenary discussed formalizing the ISC structure and administration and began researching means 

of doing both. The Plenary also noted the strides Working Groups had made in incorporating best 

available scientific information (BASI) into stock assessment work, enhanced stock assessment

reports, and the increased transparency in Working Group efforts. Observers from the Pew 

Charitable Trust, International Seafood Sustainability Foundation, and World Wildlife Fund 

attended. The ISC work plan for 2013-2014 includes completing new albacore tuna and 

swordfish stock assessments, and an updated Pacific bluefin tuna assessment in time for ISC14, 

completing a shortfin mako shark stock assessment in 2014, enhancing database and website 

management, and a tuna ageing workshop scheduled for November 2014 in Shimizu, Japan. The

Plenary re-elected Gerard DiNardo for a second term as ISC Chair and welcomed Ziro Suzuki as

the newly elected Pacific Bluefin Tuna Working Group Chair. The next Plenary will be held in

Chinese Taipei in July 2014.

North Pacific Albacore Stock Assessment and Research – North Pacific albacore tuna 

supports the most important HMS commercial fishery on the U.S. West Coast and is an essential 

stock for recreational fisheries. In preparation for the stock assessment in April 2014, SWFSC 

researchers attended a data preparation workshop of the ISC Albacore Working Group 

(ALBWG), in Shizuoka, Japan, from 5-12 November, 2013. At the workshop, the ALBWG 

examined critical time series for the stock assessment including catch, abundance indices, size 

composition, and conditional age-at-length data. During the workshop, SWFSC scientists 

presented an analysis of the catch-per-unit-effort data (CPUE) of the U.S. and Canadian surface 

fleets, which led to improved abundance indices for these fisheries. After examining the data and 

preliminary model runs, the ALBWG agreed upon tentative fishery definitions, primary data 

sources, and important biological parameters.

A full stock assessment of North Pacific albacore tuna was completed by the ALBWG during a 

meeting at the SWFSC, La Jolla, from 14-28 April, 2014. Participants included scientists from 

SWFSC, IATTC, International Pacific Halibut Commission, National Research Institute of FarSeas Fisheries, and National Kaoshiung Marine University. One of the key improvements to this 

stock assessment is the use of sex-specific growth models as recently published studies have 

shown strong evidence of sex-specific growth, with adult males growing to a larger size. The 

stock assessment was conducted using fishery data through 2012 and a seasonal, length-based, 

age- and sex-structured Stock Synthesis model (v3.24f). The stock assessment will have to be 

reviewed and endorsed by the ISC Plenary at the ISC Plenary meeting in July 2014 before being 

released.
5

In addition to the stock assessment, SWFSC scientists were involved in several studies that will 

improve the understanding of the population dynamics and biology of North Pacific albacore.

SWFSC published a study (Wells et al., 2013) in Fisheries Research titled “Age and growth of 

North Pacific albacore (Thunnus alalunga): Implications for stock assessment,” which provides a 

new growth curve for North Pacific albacore and examines the implications for future stock 

assessments. SWFSC scientists also participated in a tuna age determination workshop sponsored 

by the ISC in November 2013.

Bluefin Tuna Stock Assessment and Research – Pacific bluefin tuna historically supported an 

important commercial fishery for HMS on the U.S. West Coast. In recent years, however, the 

primary U.S. fishery targeting this species has been the U.S. sport fishery operating out of San 

Diego, California. There remains an important commercial fishery for Pacific bluefin tuna in 

Mexican waters. In February 2014, SWFSC hosted a meeting of the ISC Pacific Bluefin Tuna 

Working Group (PBFWG) to update the stock assessment of Pacific bluefin tuna. Participants 

included scientists from SWFSC, IATTC, Chinese-Taipei, Japan, Korea, and Mexico. The 

assessment was conducted using fishery data through June 2013 and a seasonal, length-based, 

age-structured Stock Synthesis (SS3) model. Results from this update assessment were highly 

similar to the full assessment conducted in November 2012.

Population dynamics were estimated using a fully integrated age-structured model (Stock 

Synthesis v3.23b) fitted to catch, size composition and CPUE data from 1952 to 2013, provided 

by ISC PBFWG members. Life history parameters included a length-at-age relationship from 

otolith-derived ages, and natural mortality estimates from a tag-recapture study and empiricallife history methods. A total of 14 fisheries were defined for use in the stock assessment model 

based on country and gear type stratification. Quarterly observations of catch and size 

compositions, when available, were used as inputs to the model to describe the removal 

processes. Annual estimates of standardized CPUE from the Japanese distant water and coastal 

longline fleets, the Taiwanese longline fleet, and the Japanese troll fleet were used as measures 

of the relative abundance of the population. The assessment model was fitted to the input data in 

a likelihood-based statistical framework. Maximum likelihood estimates of model parameters, 

derived outputs, and their variances, were used to characterize stock status and to develop stock 

projections.

While no single model run provided a good fit to all sources of data that were deemed reliable 

and estimates of current spawning stock biomass (SSB) varied, there was general agreement on 

the depleted state of the stock among all scenarios. Long-term fluctuations in SSB occurred 

throughout the assessment period (1952-2012) and in the most recent period SSB was found to 

have been declining for over a decade. The recruitment level in 2012 was estimated to be 

relatively low (the 8th lowest in 61 years), and the average recruitment level for the last five

years may have been below the historical average level.

The updated stock assessment model was unable to adequately represent much of the updated 

data .Poor fit to the two adult indices of abundance and their associated size compositions in the 

last two years indicate results are highly uncertain. Improvements to the model are advisable 

before re-assessing, and the current results with regard to the recent trends in SSB should be 
6

interpreted with caution. Using the updated stock assessment, the current (2012) SSB of 26,324 t 

is slightly higher than that estimated for 2010 (25,476 t). Across sensitivity runs in the updated

stock assessment, it was considered that the estimates of recruitment were robust. Estimated agespecific fishing mortalities on the stock in the recent period (2009-2011) relative to 2002-2004 

(the base period for the current WCPFC Conservation and Management Measure 2010-04) show 

19%, 4%, 12%, 31%, 60%, 51%, and 21% increases for ages 0-6, respectively, and a 35% 

decrease for age 7+. Although no target or limit reference points have been established for the 

Pacific bluefin stock under the auspices of the WCPFC and IATTC, the current F (average 2009-

2011) exceeds all target and limit biological reference points (BRPs) except for Floss, and the 

ratio of SSB in 2012 relative to unfished SSB (depletion ratio) is less than 6%. In summary, 

based on reference point ratios, overfishing is occurring and the stock is overfished.

Historically, the Western Pacific Ocean (WPO) coastal fishery group has had the greatest impact 

on the Pacific bluefin stock, but since about the early 1990s the WPO Japanese purse-seine fleet 

has increased its impact, and the effect of this fleet is currently greater than any of the other 

fishery groups. The impact of the U.S. purse-seine fishery in the EPO was large before the mid1980s, but decreased after the 1990s until the mid-2000s. The WPO longline fleets (Japan and 

Chinese-Taipei) has had a limited effect on the stock throughout the analysis period. The impact 

of a fishery on a stock depends on both the number and size of the fish caught by each fleet; i.e., 

catching a high number of smaller juvenile fish can have a greater impact on future spawning

stock.

The current (2012) Pacific bluefin biomass level is near historically low levels and experiencing 

high exploitation rates above all biological reference points except for Floss. Based on projection 

results, the recently adopted WCPFC Conservation and Management Measures (CMMs) and 

IATTC resolutions for 2014, if continued into the future, are not expected to increase SSB if 

recent low recruitment continues. Further substantial reduction of fishing mortality and juvenile 

catch over the whole range of juvenile ages should be considered to reduce the risk of SSB 

falling below its historically lowest level. If the low recruitment of recent years continues, the 

risk of SSB falling below the historically lowest level observed increases. This risk can be 

reduced with implementation of more conservative management measures.

Shark Stock Assessments - The SWSFC staff provide scientific advice on stock status of 

pelagic sharks to international and domestic RFMOs. Collaborative stock assessment work on 

pelagic sharks is organized through the Shark Working Group (SHARKWG) of the ISC (chaired 

by Dr. Suzanne Kohin – SWFSC), and through other multinational efforts. In 2010, the 

SHARKWG, in collaboration with scientists in member nations of the ISC, the IATTC, Mexico, 

and the Secretariat of the Pacific Community (SPC), began the first formal assessments of 

common thresher, blue, and shortfin mako sharks in the eastern Pacific and north Pacific basins. 

These sharks are both targeted and caught incidentally as bycatch in numerous fisheries 

throughout their range and their status requires long-term monitoring.

In order to promote data collection in Mexico, the SWFSC and WCR are collaborating on

multiyear efforts with Centro de Investigación Científica y de Educación Superior de Ensenada

(CICESE), led by Dr. Oscar Sosa-Nishizaki. This collaboration is intended to coordinate 

artisanal fish camp monitoring and sampling in Baja California, Mexico, and help advance 
7

cooperative stock assessment efforts with Mexico, U.S., and IATTC scientists. Sampling has 

provided valuable data for international assessment efforts through the ISC as well as for a USAMexico partnership to assess the status of common thresher sharks. As a result of the sampling 

program, fishery data for pelagic sharks now includes some size and sex sampling as well as 

several years of species-specific catch information.

In 2013, the ISC produced its first assessment of blue sharks (Prionace glauca) in the North 

Pacific Ocean. Two assessment models, including a surplus production model and an agestructured model, were used to investigate stock status. The ISC accepted the assessments at its 

July 2013 Plenary meeting in Busan, South Korea. The assessments were subsequently submitted 

to the Scientific Committee (SC) of the WCPFC. The SC recognized these efforts, but requested 

further analyses to explore key aspects of uncertainty, including changes in targeting practices 

through time, the effect on estimated abundance indices, as well as additional exploration of the 

model process. The ISC SHARKWG is working to reassess the stock for a resubmission to the 

2014 ISC Plenary and the WCPFC SC.

During the second half of 2014, the ISC SHARKWG will begin an assessment of shortfin mako 

sharks in the North Pacific. The first meeting focused on the shortfin mako assessment is 

scheduled to be held in Mexico, with participation from ISC members and observers from 

Canada, China, Chinese Taipei, Japan, Korea, Mexico, the U.S., IATTC, and potentially SPC.

Time permitting, a collaborative assessment of common thresher sharks will be conducted with 

Mexican colleagues in 2014 since much of the data needed for the assessment has been 

compiled.

II. SUPPORTING PACIFIC FISHERY MANAGEMENT COUNCIL ACTIVITIES

Center scientist Stephen Stohs continued serving on the Highly Migratory Species Management 

Team (HMSMT) of the Pacific Fishery Management Council (PFMC) over the past year. 

Suzanne Kohin completed her term of service on the HMSMT and was replaced by fellow 

Center biologist, Tim Sippel, after the June 2013 Council meeting.

The team met several times in 2013 and early 2014 to review fishery information, complete 

assignments from the Council, and evaluate provisions of the Fishery Management Plan for U.S. 

West Coast Fisheries for Highly Migratory Species. The main HMS issues facing the team and 

the Council over the past year have been: (1) assisting the Council with developing a response to 

Pacific bluefin tuna overfished status; (2) continuing with work to develop a precautionary 

management framework for north Pacific albacore; (3) analysis of a proposed modification to the 

drift gillnet fishery Pacific Leatherback Conservation Area (PLCA) closure policy; and (4) 

preparing the 2013 Stock Assessment and Fishery Evaluation (SAFE) Report and planning for 

the 2014 SAFE Report.

III. ADVANCING RESEARCH ON TUNAS, BILLFISH, AND OPAH

SWFSC scientists have focused on improving the biological and ecological understanding of 

tunas and billfishes in the Pacific Ocean to better assess the effects of fishing and the 
8

environment on their populations or stocks. Described here are studies that have been recently 

completed or are ongoing by Center staff. These studies are carried out largely in cooperation 

with stakeholders and in collaboration with colleagues both in the U.S. and abroad.

Cooperative Research with the U.S. Surface Albacore Fishery – SWFSC scientists are 

working with the American Fishermen’s Research Foundation (AFRF) and the American 

Albacore Fishing Association (AAFA) on monitoring programs and other research efforts to 

improve knowledge of the biology and migration of North Pacific albacore in the waters off the

U.S. Pacific coast.

North Pacific Albacore Size Data Sampling Program – Since 1961, size data have been 

collected from albacore landings made by the U.S. and Canadian troll fleets at ports along the 

U.S. Pacific coast. SWFSC staff work with state fishery personnel to collect biological data from 

albacore fishing vessels when they unload their catches in coastal ports. During 2012, 82,807

fish averaging 69.9 cm fork length (FL) were measured at various west coast ports. Two distinct

size modes represent approximately 2.5 and 3.5 year old fish.

In recent years, with AFRF support, fishermen have also collected biological data during 

selected fishing trips. Following procedures established by SWFSC scientists in 2012, size data 

were collected from two cooperating vessels in 2012 and 2013, with 1422 and 736 fish 

measured, respectively. These onboard samples augment the size data collected through the port 

sampling program. These data are all sent to SWFSC for processing.

North Pacific Albacore Electronic Logbook Project – In 2005, a computer program was 

developed to allow albacore troll fishermen to enter their logbook data directly into a digital 

worksheet rather than completing the traditional paper forms. The advantages of recording the 

data through a computer program include implementing validation rules at the point of entry thus 

limiting data entry errors, saving time and money on data entry costs, and making the data 

available in a timelier manner. Since 2006, the program has been used by 5-10 fishermen 

annually and has received positive feedback on its functionalities and ease of use. During the 

2013 season, logs for 63 trips were submitted electronically, representing 4.6% of all trips 

reported. In 2013, FRD staff developed a new, alternative electronic logbook in PDF format. The 

format mimics the current paper form and provides simpler computer installation, data entry 

functionality, and submission processes. The goal is to increase the use of electronic logbooks.

Testing should be completed during the 2014 season.

North Pacific Albacore Archival Tagging Project – Staff from SWFSC and AFRF initiated an 

archival tagging program in 2001 to study the migration patterns and stock structure of juvenile 

albacore in the North Pacific. Since 2001, a total of 878 archival tags have been deployed. One 

archival tagging trip was conducted during 2013 aboard the chartered F/V Royal Dawn, during 

which 74 tags were deployed. The trip started in Westport, Washington, on 23 October and made 

its way south, ending in San Francisco, California, on 1 November. In addition, collaborators 

from the Pfleger Institute of Environmental Research (PIER) opportunistically released 3 

archival-tagged albacore off central California. Plans are being made to deploy over 100 tags 

during the 2014 season.
9

In 2013, three recaptured albacore all had tags that had been deployed during a single tagging 

trip in August 2011. Interestingly, a fourth fish from the same tagging trip was recaptured in 

2012. The three fish recaptured in 2013 were at liberty for 684, 693 and 753 days representing 

some of the longest tracks yet recorded during the study. Of the three fish, two were recaptured

by Japanese pole-and-line fishermen very close to the coast of Japan. The third was recaptured 

very close to where it was released, off the coast of Oregon. Although the sensors of one tag 

malfunctioned partway through its deployment, these recoveries provide remarkable multi-year 

data on juvenile albacore behavior and movement patterns throughout the Pacific Ocean.

Because of the broad range of movement patterns and behaviors recorded by juvenile albacore so 

far, a greater number of tag returns from fish that have been at liberty for several years will be 

needed in order to fully understand the dynamics and structure of the North Pacific albacore 

stock. Information on the distribution and migrations of adults is also needed. During 2013, in 

collaboration with scientists of the SPC and a cooperating artisanal handline fisherman in 

Hawaii, SWFSC researchers continued a pilot study to test the use of the new attachment anchors 

for mini pop-off satellite archival (mini-PSAT) tags and began to collect information on the 

movements and behaviors of adult albacore. One albacore (106.5 cm FL) was tagged off Kona, 

HI, in October with a novel monofilament loop attachment. This tag remained on the fish and 

collected good data for 13 days before releasing prematurely 41 miles from the tagging location.

The behavior of the albacore was consistent throughout the track, descending below the 

thermocline to greater than 400 m during the day, while remaining in the upper 150 m in warmer 

water at night. The swimming behavior of this fish differed from that of most of the tagged 

juveniles, but juveniles display a very broad range of behaviors depending upon the region and 

season. More data will be needed to fully compare the behavior patterns of adults and juveniles.

Collection and Analysis of Biological Samples to Support Stock Assessments – Given the 

uncertainty surrounding current growth models, stock structure, and ecosystem interactions of 

several tuna and tuna-like species in the North Pacific, scientists at the SWFSC have been 

working with a range of partners to collect biological samples of otoliths, muscle, liver, heart, fin 

spines, scales, vertebrae, DNA fin biopsies, and stomachs from a number of species along the 

U.S. West Coast. In 2007, the SWFSC and the Sportfishing Association of California initiated a 

sampling program to collect data on tuna and other HMS. While initially the program was 

focused in the Southern California Bight (SCB), the program was expanded to the northeast 

Pacific Ocean in 2009, working with commercial fishermen to collect samples from albacore off 

Oregon and Washington. In 2010, the program was expanded to central California (Monterey 

Bay and San Francisco) where albacore are commonly encountered from August through 

November in the California Current (CC). In 2012, sampling effort for swordfish expanded to 

include Hawaii and Mexico to examine the potential for mixing of two purported stocks off 

California. Japanese colleagues of the National Research Institute of Far Seas Fisheries 

(NRIFSF) have also been collaborating with SWFSC scientists and contributing otoliths for 

ageing and microchemistry studies. Sample collection is ongoing and supports the ISC’s 

proposal for a North Pacific-wide sampling program to address the uncertainties regarding 

biological information, notably growth models, maturity schedules, and stock structure of several 

tuna and tuna-like species.

Samples of albacore, Pacific bluefin, yellowfin, skipjack (Katsuwonus pelamis), yellowtail 
10

(Seriola lalandi), opah (Lampris guttatus) and dorado (Coryphaena hippurus) have been 

collected through working cooperatively with commercial passenger fishing vessels (CPFV), the 

commercial albacore troll and pole-and-line fleet, and recreational anglers (Table 1).

Table 1. Summary of all fish sampled by the biological sampling program for tuna and related 

species.

These biological samples are used to understand an array of questions. Initial efforts centered on

characterizing diets of tunas in the SCB using stomach contents and investigating inter-annual 

and interspecific differences. In the past few years, the research program expanded to include (1) 

stable isotope analysis of muscle tissue aimed at providing an integrated picture of foraging and 

migration patterns of tunas and swordfish in the CC, (2) using otoliths to better characterize age 

and growth of albacore, (3) radioanalysis of cesium-134 and 137 found in the muscle tissue of 

Pacific bluefin tuna exposed to waters containing radionuclides discharged from the failed 

Fukushima nuclear power plant in Japan, combined with stable isotope analysis to determine 

migration rates and stock structure of juvenile Pacific bluefin tuna in the CC, (4) using otolith 

microchemistry to determine the dynamics and stock structure of albacore, bluefin, and 

swordfish in the North Pacific, (5) characterizing the genetic diversity of California yellowtail in 

preparation for commercial aquaculture production off southern California, (6) comparing 

inshore- versus offshore-caught California yellowtail with respect to ontogeny and migration 

patterns using stable isotope analysis and lab derived trophic discrimination factors, and (7) 

characterizing the diet of opah.

Tuna Foraging Ecology –With the reauthorization of the Magnuson-Stevens Fishery 

Conservation and Management Act in 2006, there is a move towards ecosystem-based 

management. Understanding temporal and spatial patterns of who is eating whom is critical to 

this approach. To determine the trophic relationships of highly migratory species in the CC, 

SWFSC scientists have been investigating the foraging ecology of a range of species since 1999.

Species 2007 2008 2009 2010 2011 2012 2013

Pacific Bluefin 0 75 78 54 189 294 171

Albacore: Washington/ Oregon 0 0 42 191 49 60 60

Albacore: Central California 0 0 0 0 27 31 43

Albacore: Southern California 116 35 93 118 7 62 3

Yellowfin 15 45 95 71 128 132 112

Skipjack 0 5 9 8 15 16 25

Yellowtail 0 0 7 30 190 186 90

Opah 0 0 1 11 16 64 30

Dorado 0 43 39 0 40 18 0
11

Figure 1. Pie charts showing the 

relative importance of squid 

(dark blue), crustaceans (green) 

and fish (light blue) in the diets 

of albacore from three regions in 

the California Current.

Fish

Squid

Crust

%GII WA/OR

n=46

Fish

Squid Crust

%GII Central CA

n=45

Fish

Squid

Crust

%GII Southern CA

n=3

Analyses of stomach contents of tunas conducted to date reveal a number of interesting patterns 

across species, regions and years. Looking across regions, a comparison of the top diet items of 

albacore collected in 2013 off Oregon/Washington, central California, and southern California

show a clear difference in diet from north to south (Figure 1). Off Oregon/Washington, stomach 

contents were dominated by crustaceans, primarily krill that composed 43.5% of the Geometric 

Index of Importance (GII). Squid was only a minor component of the diet (5.8%). Off Central 

California, squid comprised 5 of the 7 top diet items 

making up a total of 48% of the dietary GII. Interestingly, 

although the sample number was low, the diet of albacore 

off southern California shows a similar degree of 

importance of squid as off central California, but 

crustaceans are slightly more important and fish less 

important farther south. This information is useful for 

pinpointing differences in habitat use and energetics 

across regions. 

Given the long-term data series on stomach contents, is it 

also possible to examine diet shifts over time. By

comparing these results to other studies across the years, 

it is apparent that over the last decade, tuna in the 

Southern California Bight show an increase in diet 

diversity, a reduced reliance on anchovies and sardines,

and an increased reliance on squid and other fish species. 

This likely relates to shifts in prey availability associated 

with changes in oceanography that has also been reflected 

in other biological indices.

Albacore Age and Growth –A number of lines of 

evidence support the hypothesis that there are two 

different substocks of albacore in the California Current, 

divided at 40°N. A study recently published by SWFSC 

scientists in collaboration with the University of San 

Diego and Texas A&M University examined the daily 

rings in otoliths of 126 albacore from both regions to 

determine, age, growth rates, and hatching dates. Overall, 

fish from the southern region were larger than those in the 

north, concurring with other studies. Calculated age data 

reveal that although the size differences were primarily 

due to differences in age, the presence of significantly 

larger albacore in the southern population indicates a

faster growth rate over some time period. Results showed 

that fish from both regions had protracted hatch dates 

from February-September with a peak from April-July 

and no significant difference between the two purported 

substocks. Additional research is needed to address the 

important questions: (1) why are the growth rates 
12

different, (2) what are the mixing rates between the two regions, and (3) are there two distinct 

substocks or just differences in the locations to which the fish recruit into the California Current 

waters from spawning grounds to the western Pacific?

Radioanalysis of cesium-134 found in the muscle tissue of Pacific bluefin tuna–Understanding 

movement patterns of migratory marine animals is critical for effective management, but often 

challenging due to the cryptic habitat of pelagic migrators and the difficulty of assessing past 

movements. Chemical tracers can partially circumvent these challenges by reconstructing recent 

migration patterns. Radionucleotides released into the ocean off Japan provide a unique chemical 

tracer for animals occupying these waters including Pacific bluefin tuna. Pacific bluefin tuna 

inhabit the WPO and EPO, and current stock assessments indicate that they are overfished.

Understanding age-specific eastward trans-Pacific migration patterns can improve management 

practices, but these migratory dynamics remain largely unquantified. A collaborative study with 

the State University of New York (SUNY) combined a Fukushima-derived radiotracer (134Cs) 

with bulk tissue and amino acid stable isotope analyses of Pacific bluefin to distinguish recent 

migrants from residents of the EPO, and to time the migrations of juvenile bluefin as they cross 

the Pacific Ocean. The proportion of recent migrants to residents decreased in older year classes, 

though the proportion of older Pacific bluefin that recently migrated across the Pacific was 

greater than previous estimates. Using radioactive decay and bioenergetic turnover rates, it was 

possible to estimate the time when fish left Japan for their trans-Pacific migration. Of 33 fish 

samples, 25 are estimated to have left the waters off Japan in June. This novel toolbox of 

biogeochemical tracers can provide new insights into the dynamics of migration and can be 

applied to any species that crosses the North Pacific Ocean.

Microchemistry Analysis of Otoliths– Otolith chemistry is one approach to investigate 

population structure of tunas and other fish. The principal assumption is that the otolith acts as a 

natural tag because the chemical composition of the otolith is related to the physicochemical 

conditions of the ambient water. For Pacific bluefin, the purpose of the study is to examine stable 

isotope and trace element composition in both whole otoliths and serial samples collected in the 

WPO and EPO over several age classes of fish. Comparisons of otoliths from young of the year, 

juvenile, and adult bluefin will be used to characterize the dynamics of movement across the 

Pacific. Results will help determine how many Pacific bluefin migrate to the California Current, 

what proportion of the spawning stock biomass are California Current migrants and whether 

these California Current migrants come from one or both spawning grounds. Efforts to collect 

samples from the WPO spawning grounds were started in 2012 and are ongoing. Otoliths from 

the EPO have been collected since 2008. Efforts are part of a collaboration between U.S., 

Japanese, and Taiwanese scientists.

Stable Isotope Analysis of Muscle Tissue in Albacore and California Yellowtail – Stable 

isotope analysis (SIA) is another tool used by scientists at the SWFSC to examine both 

migrations and foraging ecology of HMS. SIA measures the amounts of isotopes of carbon 

(δ13C) and nitrogen (δ15N) in tissues. The approach is based on the principle that “you are what 

you eat” and the stable isotope signatures in predators will reflect that of their prey. The 

signature depends both on the predator’s trophic level and on the isotope ratios of the primary 

producers in the region. Given information on regional differences at the base of the foodweb, it 

is possible, using both δ13C and δ15N, to get a sense for both where geographically fish are 
13

Figure 2: Mean (±SD) δ13C and δ15N values for 

albacore caught between 2008-2013.

foraging and at what trophic level. SIA is being conducted on a number of different species to 

answer a range of questions.

SWFSC scientists are using SIA to 

complement the work on age and growth 

and otolith microchemistry in the 

examination of the difference between 

albacore north and south of 40°N. The 

signatures of tissue compared between the 

two regions will provide insight into the 

potential separation between the two 

groups and help determine in what water 

masses they typically forage, onshore 

versus offshore. By also conducting SIA 

analyses on regional prey species, it will 

be possible to examine potential 

differences in foraging ecology and 

trophic level over longer time periods 

than is possible using stomach contents 

alone.

An initial run of 66 muscle samples (33 

northern, 33 southern) collected in 2012, was completed in September 2013, to examine the

initial hypothesis of discernible separation between the two potential substocks. Data from the 

initial samples were also supplemented with samples collected from the SCB between 2008 and 

2013 (n=159), as described in the Albacore Age and Growth section. These preliminary data 

support separation between the northern and southern albacore, with mean δ13C and δ15N values 

from the south showing enrichment compared to northern samples (Figure 2). The δ13C values 

show distinct carbon sources being utilized by two potentially separate substocks with limited 

mixing, while δ15N values are different but fall short of indicating distinct trophic levels.

The California yellowtail is found in both coastal and pelagic regions of the southern California 

Current Large Marine Ecosystem. Historical tagging data suggest that yellowtail migrate 

seasonally; they travel north from Baja California, Mexico into southern California during spring 

and summer months, spawn in pelagic waters, and return south during fall and winter. These 

migrations may reflect an ontogenetic shift in habitat use, with smaller individuals traveling long 

distances in pelagic water offshore before settling into nearshore coastal regions. SWFSC 

scientists used stable isotope analysis of carbon and nitrogen (δ13C and δ15N) to determine the 

extent to which offshore- and inshore-caught yellowtail resemble their environment of capture, 

and to ascertain the size(s) over which the potential shift from pelagic to coastal waters takes 

place. δ

13C and δ15N values were used to group yellowtail into ‘inshore’ or ‘offshore’ using 

discriminant analysis, with δ13C and δ15N values of a pelagic predator, yellowfin tuna, and a 

coastal predator, white sea bass (Atractoscion nobilis), serving as training data. SWFSC

scientists also used two separate Bayesian mixing model approaches to determine the extent to 

which inshore- and offshore-yellowtail reflect; (1) pelagic and offshore prey inputs, and (2) their 

similarity to the predators above. Results show a shift in habitat use, based on changes in δ13C 
14

and δ15N, between 81 and 96 cm (strait FL). Mixing models confirmed that smaller, offshore 

yellowtail largely reflected pelagic prey resources and SIA values were similar to yellowfin tuna.

In contrast, larger, inshore yellowtail reflected higher input from inshore resources and were 

similar to white sea bass, though there was significant contribution (25-45%) of offshore prey to 

diet of inshore yellowtail. Future work on muscle tissue turn-over rates of captive yellowtail will 

help discern how changes in food sources could reflect the shift from offshore to inshore habitat 

use as yellowtail grow larger.

In addition to the work on albacore and yellowtail, a number of other projects are ongoing using 

SIA to examine migrations and foraging ecology. Two new projects were started in 2013. The 

first will expand the use of SIA to broadbill swordfish, shortfin mako, blue sharks, and thresher 

sharks. Like the above studies, tissue samples will be collected from both the predators 

themselves as well as prey found in their stomachs. This work seeks to strengthen results from 

traditional stomach content analysis on these species which has been ongoing at the SWFSC 

since 1999. In the second project, the stable isotopes of both the fin spines and muscles of 

swordfish will be used to examine stock structure. Currently it is thought that there are two 

stocks of swordfish in the North Pacific with the dividing line between the two of them starting 

off the Baja Peninsula, Mexico at 30°N and extending to the southwest reaching the equator at 

170°W. Swordfish in the northwestern area support the second largest HMS fishery off the U.S. 

West Coast. Important management related questions are; (1) whether the two-stock hypothesis 

is supported by complementary datasets and, (2) if there are two stocks, what are the dynamics of 

mixing between the two stocks on eastern Pacific fishing grounds. Preliminary results reveal 

distinct differences in the isotope signatures between the “Hawaii fish” (i.e. from the 

northwestern area) and the “Mexican fish” providing a proof of concept for differentiating 

between the two in samples collected off California if they mix. 

Albacore distribution and environmental effects - SWFSC scientists, in collaboration with 

scientists of Canada’s Department of Fisheries and Oceans (DFO), received funding in 2012 

from NOAA's Fisheries and the Environment (FATE) program to study the “Influence of the 

North Pacific Current on the spatial distribution and availability of North Pacific albacore in the 

northeast Pacific Ocean.” As a result of this collaborative study, SWFSC scientists have 

submitted two manuscripts for review and publication in a special issue of Progress in 

Oceanography. These studies have improved the development of abundance indices for albacore 

in the Northeast Pacific.

Xu et al. (In review) examines the influence of subtropical fronts on the spatial distribution of 

albacore in the Northeast Pacific over the past 30 years by relating albacore CPUE from U.S. and 

Canadian logbooks with subtropical fronts derived from an analysis of sea surface temperature 

(SST) gradients using an improved version of the Cayula-Cornillion frontal detection algorithm

(Nieto et al., 2012). Results suggest that areas with high albacore CPUE tend to occur in regions 

with high SST gradients, such as the North Pacific Transition Zone (NPTZ) and the North 

American coast. Approaching the North American coast along the NPTZ, SST gradients drop off 

substantially around 130°W before increasing rapidly near the coast, which corresponded to a 

similar pattern in albacore CPUE. In the NPTZ, the centroid of albacore CPUE showed a 

seasonal shift northwards in summer and southwards in fall, which coincided with seasonal 

spatial shifts of areas with high SST gradients. A similar pattern was found on an inter-annual 
15

scale, with the exception of several years with limited fishery data in the NPTZ due to changes in 

fishery operations.

Nieto et al. (In review) examines coastal upwelling fronts as key habitat for albacore tuna in the

Northeast Pacific Ocean. The study uses satellite-derived SST data to characterize coastal fronts 

in an automatic way and boosted regression trees (BRTs) to relate the effects of these fronts on 

albacore distribution. The results suggest that albacore CPUE distribution is strongly influenced 

by SST and chlorophyll at fishing locations, albeit with substantial seasonal and inter-annual 

variation. Albacore CPUEs were higher near warm, low chlorophyll oceanic waters, and near 

SST fronts. Sequential leave-one-year-out cross-validations were performed for all years and it 

was found that the relationships in the BRT models were robust for the entire study period. 

Spatial distributions of model-predicted albacore CPUE were similar to observations, but the 

model was unable to predict very high CPUEs in some areas.

Cooperative Research with Billfish Anglers – SWFSC researchers have been working with the 

billfish angling community since 1963, to study various aspects of billfish biology and to obtain an 

index of angler success in the Pacific Ocean This collaboration has resulted in one of the longest 

CPUE time-series available for the recreational fishing of billfishes. The research has also included 

recreational and commercial fishery monitoring, stock assessment efforts, biological research 

into the life history and ecology of specific billfish species, and determining the economic 

importance of billfish resources. Two major components of the cooperative research for 2013 

were the International Billfish Angler Survey and the Billfish Tagging Program.

International Billfish Angler Survey– In 2013, SWFSC researchers summarized the results from 

the 2012 Billfish Angler Survey. Initiated in 1969, the survey now provides a 44-year time series 

of billfish angling effort and catch in the Pacific Ocean. The time series of angler success 

provides a measure of relative abundance and is the only fisheries-independent index for billfish 

covering the entire Pacific. The CPUE, measured in number of billfish caught per angler fishing 

day, was 0.48 across all reporting areas in 2013. This was a slight improvement from the 2012 

CPUE of 0.44, but below the five year average (2007-2011; 0.58 CPUE). Over 90% of survey 

angler fishing days during 2012 were spent at three locations: Hawaii, Southern California, and 

Baja California, Mexico. The greatest effort from survey respondents was off the coast of 

Hawaii. Over 3,500 fishing days were reported from the Hawaiian Islands. The 2012 Hawaii 

CPUE was 0.39 compared to the previous five-year average (2007-2011; 0.42 CPUE). Similarly, 

success off the coast of Southern California during 2012 was down from recent years with 

anglers reporting the second lowest CPUE (0.03) on record. Conversely, 2012 was a good 

fishing year off the coast of Baja California, Mexico. During 2012, anglers caught 0.82 billfish 

per fishing day, which was the sixth highest CPUE reported for this location in 29 years.

However, compared to the previous 5 years, this CPUE was still below average (2007-2011; 1.08 

CPUE). This five-year average was influenced by great results in 2007 and 2008 which were by far

the two highest CPUEs on record.

The CPUE time series were examined individually for the main species caught (Pacific blue 

marlin, striped marlin, Pacific sailfish (Istiophorus platypterus), and black marlin (Makaira 

indica)), in the main fishing areas (Hawaii; Baja California, Mexico; Southern California; Costa 

Rica; Panama; Tahiti; and Australia; Figure 3). Blue marlin CPUE off Hawaii and Tahiti was 
16

down from the previous year and has trended down at each location over the last five years.

However, the blue marlin CPUE reported from Baja California, Mexico, was up after a very slow 

2011. Striped marlin CPUE was up from the previous year at two of the three highlighted 

locations. The slight increase in catch per fishing day off Southern California was not necessarily 

something to celebrate. This increase was following the lowest CPUE on record (0.02). The 

striped marlin CPUE throughout Mexico also increased in 2012 and appears to be trending in the 

right direction. Not shown was an increase in striped marlin CPUE off Baja California, Mexico,

from 0.54 in 2011 to 0.69 in 2012. The 2012 result was above the five most recent year average 

(0.60). Sailfish CPUE reported throughout Mexico (0.15) was the lowest it has been in over 20 

years.
17

Figure 3. CPUE as catch-per-angler-day is shown from 1969 through 2012 for Pacific blue 

marlin, striped marlin, Pacific sailfish, and black marlin.
18

Recreational Billfish Tagging Program–The year 2012 marked the 51st year that the SWFSC’s 

Billfish Tagging Program has provided tagging supplies to recreational billfish anglers. Tag 

release and recapture data are used to determine movement and migration patterns, species 

distribution, and age and growth patterns. This volunteer tagging program depends on the 

participation and cooperation of recreational anglers, sportfishing organizations, and commercial 

fishers. In collaboration with California Department of Fish and Wildlife, over 77,000 fish have 

been tagged and released since the inception of the tagging program. Emphasis continues to be 

on the skillful tag and release of billfish.

A total of 575 tags were released on billfish in 2012 through the efforts of captains and anglers.

Most billfish were tagged and released in U.S. or Mexican waters; however, billfish were also 

tagged and released by anglers in many locations across the Pacific. Most tag releases occurred 

off the coast of Hawaii, the majority of these on blue marlin. The number of sailfish tag releases 

during 2012 (67) is worth highlighting because this was more than three times the number of 

sailfish releases in 2011.In fact, the number of sailfish tag releases had been on the decline for 

several years until 2012.The focus of this effort was centered along the central coast of Mexico 

where a group of dedicated anglers has made a big contribution by working with local charter 

operations out of Zihuatanejo. Table 2 shows the tagging effort for 2012 and tag recoveries 

throughout the program’s history. The data include releases made by SWFSC scientists during 

research cruises.

Table 2.Summary of fish tagged through the Billfish Tagging Program in 2012 with releases and 

recoveries for 1963–2012, including SWFSC’s ongoing research tagging.

SPECIES NAME RELEASE 

2012

RELEASE 

TOTAL

RETURN 

TOTAL

RETURN 

RATE 

(%) 

Striped Marlin 123 23,235 348 1.5

Pacific Blue Marlin 328 11,718 94 0.8

Blue Shark 225 9,834 193 2.0

Sailfish 67 9,292 49 0.5

Shortfin Mako Shark 253 5,739 338 5.9

Billfish, unidentified 0 4,386 6 0.1

Black Marlin 0 3,392 69 2.0

Shortbill Spearfish 57 2,294 3 0.1

Common Thresher 

Shark 265 2,137 98 4.6

Albacore Tuna 81 930 30 3.2

Broadbill Swordfish 0 522 17 3.3

Yellowfin Tuna 0 349 25 7.2

Leopard Shark 1 225 12 5.3

Skipjack Tuna 0 100 2 2.0

Bigeye Tuna 0 79 2 2.5

Basking Shark 0 65 0 0.0
19

Hammerhead Shark 0 62 2 3.2

Bluefin Tuna 0 58 8 13.8

Bronze Whaler Shark 0 52 3 5.8

Whitetip Shark 0 44 1 2.3

Atlantic Blue Marlin 0 43 0 0.0

Soupfin Shark 1 41 1 2.4

Salmon Shark 0 36 3 8.3

Silky Shark 0 24 1 4.2

White Marlin 0 13 1 7.7

Longbill Spearfish 0 3 0 0.0

Other Tunas 0 21 1 4.8

All Others 6 2,803 125 4.5

TOTAL 1,407 77,497 1,432 1.8

Swordfish Research and SLUTH –Since 2006, SWFSC researchers have been studying 

swordfish in the SCB to examine migratory patterns, foraging ecology, and local stock structure.

In 2008, FRD teamed up with the Marine Mammal and Turtle Division (MMTD) and the NOAA 

WCR to launch a new initiative, Swordfish and Leatherback Use of Temperate Habitat 

(SLUTH). The overarching objective of SLUTH is to integrate studies of swordfish and 

leatherback sea turtles to inform management and conservation efforts. The endangered 

leatherback is taken incidentally in swordfish fisheries, and concerns about leatherback 

populations are currently shaping the management of swordfish fisheries along the U.S. West 

Coast. While a large organized initiative has yet to be established, FRD and MMTD have a 

number of ongoing research projects to characterize the habitat of swordfish and leatherback sea 

turtles to identify where habitat separation is maximized in time and space. Information on 

habitat separation can be used to increase the selectivity of fisheries and to reduce bycatch.

Modeling leatherback turtle temporal and spatial habitat use patterns– Further progress has 

been made on characterizing the geographic habitat use patterns and behavior of leatherback sea 

turtles along the U.S. West Coast based on electronic tagging data. Satellite telemetry position 

data collected from leatherback turtles tagged at nesting beaches in the western Pacific and along 

the central coast of California between 2003 and 2011 were used to predict the foraging habitat 

in the California Current ecosystem. Environmental data (sea surface temperature, upwelling 

indices, chlorophyll concentration, etc.) were associated with each location. All observed 

locations in the PLCA were assumed to be associated with foraging .A predictive model was 

developed to infer foraging by leatherbacks at areas and times lacking turtle telemetry data. A 

high probability of foraging behavior occurred within the PLCA from August through 

November, but varied among years according to the annual variability in the environmental 

conditions. This telemetry research has helped understand leatherback turtle habitat and 

important behavioral patterns along the U.S. West Coast.

Combined with the geographic analyses, SWFSC scientists have been looking at vertical habitat 

use of leatherbacks along the U.S. West Coast and comparing it to that of swordfish. Based on 

preliminary data it appears there may be considerable vertical habitat separation between the two 

species that could be exploited to reduce bycatch. Swordfish make diel migrations between the 
20

Figure 4. Histogram showing the depth distribution across all 

locations in the shaded green area. Inset map shows the 

locations of all associated dives. The area is red is the 

leatherback critical habitat.

0.00

0.05

0.10

0.15

0.20

0.25

0.30

10 20 30 40 50 60 70 80 90 100110120

Relative time spent

depth (m) Unpublished data: J. Okuyama, S. Benson, J. 

Seminoff, T. Eguchi, P. Dutton

7605 dives

surface at night and deep 

waters during the day 

whereas preliminary data 

indicate that leatherbacks

remain in near-surface waters 

both day and night. The dive 

data initially examined for 

leatherbacks was very 

limited and in other areas 

leatherbacks have been 

shown to dive to 1000m. To 

better quantify the vertical 

distribution of leatherbacks,

MMTD researchers 

examined all dive data from 

satellite tagging efforts 

where locations were outside 

of critical habitat but inside 

the U.S. EEZ. Analyses of 

over 7,000 dives reveal that 

the majority of time is spent above 50 m with no dives below 100 m (Figure 4). In contrast, 

daytime depths of swordfish in the same region are expected to be from 250 to 500 m (when not 

basking). This indicates that targeting swordfish deep during the day may be a valid approach to 

reducing interactions with leatherbacks.

Deep-set Longline Survey to Investigate Swordfish-Sea Turtle Habitat Separation– Heightened 

focus on minimizing bycatch of protected species has lead U.S. fisheries managers to implement 

combinations of gear restrictions and time-area closures. For example in 2001, to reduce sea 

turtle bycatch in swordfish fisheries, shallow-set longline (SSLL) fisheries were closed in the 

Atlantic and Central Pacific and a time-area closure was imposed on the CADGN fisheries. In 

response to the SSLL closures, fishers and scientists collaborated to develop gear modifications 

that reduced loggerhead and leatherback bycatch by 90% and 65%, respectively, leading to MSC 

certification of the Atlantic SSLL fishery. In contrast, the CADGN fishery has declined 

dramatically since implementing a large time-area closure in 2001. The goal of this project was 

to explore potential gear alternatives for targeting swordfish off California, building on previous 

efforts to reduce turtle bycatch in longline fisheries. The idea was to shift the longline gear to 

deeper water to capitalize on the difference is daytime depths; swordfish typically spend the 

daylight hours in waters deeper than 200 m whereas leatherbacks remain above 120 m. 

On three cruises from 2011-2013, NOAA collaborated with longline fishers aboard the chartered 

F/V Ventura II off central and southern California to investigate the efficacy of targeting 

swordfish during the day using a deep-set longline (DSLL). During 47 sets, with average hook 

depths of 230-247 m and soak times of 2.7-4 hours, 111 marketable fish (including 8 swordfish, 

67 opah, and 23 pomfret) and 352 non-marketable fish (including 328 blue sharks and 17 kingof-the-salmon) were caught. Short soak times were used to maximize fish condition for tagging; 

two swordfish, five opah and five blue sharks were released with satellite tags and the majority 
21

of the remaining blue sharks were tagged with conventional tags and released. Based on previous 

research on blue shark post-release mortality, 81%-91% of blue sharks would be expected to 

survive after release. This study concluded that it is possible to catch swordfish and other 

marketable species below turtle habitat with a DSLL however, swordfish catch was low. Fishing 

conditions during these cruises were probably impacted by anomalous oceanographic conditions; 

swordfish catch for the CADGN fleet was very low over the same time periods. Efforts to collect 

additional data under more realistic fishing operations (i.e. fishing when and where conditions 

are best, over longer time periods) would provide a further test of the gear’s potential. Given the 

experimental and small-scale nature of this research, these results are promising, but should not 

be projected beyond the study and warrant more research.

Swordfish Deep-Set Buoy Gear (DSBG) Research– The WCR Long Beach Sustainable 

Fisheries Division and PIER researchers are conducting research using a deep-set vertical hook 

and line configuration (buoy gear) to target swordfish within the exclusive economic zone off the 

coast of California. To minimize interactions with species of concern, the deep-set gear was 

designed to fish below the thermocline (270 to 350 m) during daylight hours. Gear trials were 

conducted during the 2011 and 2012 swordfish seasons off the coast of southern California using 

both research and cooperative fisher vessels. There were no interactions with species of concern, 

minimal interaction with non-target species (i.e., sharks), and swordfish were the primary catch.

This work has been submitted for publication in 2013. Additional DSBG field experiments in 

2013 focused on improving the test configuration, enhancing deployment and retrieval efficiency 

and preparing for cooperative trials in 2014. These data will be used in 2014 to trial DSBG from 

cooperative fisher platforms and to assess the domestic market niche for buoy-caught swordfish.

Additional collaborative efforts of the WCR, SWFSC, and PIER in 2013 focused on 

documenting the depth distribution for swordfish in the PLCA. Scientists deployed 13 pop-off 

satellite archival tags and provided the first movement data for swordfish within the study 

region. These data will be analyzed and submitted for publication in 2014. Preliminary research 

results were presented at the March 2014 meeting of the Pacific Fishery Management Council.

Foraging Ecology of Swordfish in the SCB– In support of ecosystem based studies, the foraging 

ecology of swordfish is being investigated to examine predator-prey interactions and niche 

overlap with other pelagic predators. Stomach contents for this work have been predominantly 

provided through the CADGN observer program. Since 2012, 59 stomachs have been analyzed 

(35 from 2012 and 24 from 2013). Current levels of analysis have allowed SWFSC researchers 

to identify some of the most frequently encountered prey species (F=Frequency of prey 

occurrence). Broadbill swordfish stomachs in season 2012-13 contained jumbo squid (Dosidicus 

gigas) (F=48), Gonatopsis borealis squid (F=34), Abraliopsis sp. squid (F=32), Gonatus spp. 

squid (F=18). These preliminary results show a possible shift in feeding trends. In 2012-13 

jumbo squid showed a resurgence in dietary importance for swordfish compared to the previous 

season.

Opah Research in the Eastern Pacific Ocean–The opah is a large, mid-water pelagic fish that 

occurs seasonally in the SCB. While they are not targeted, they are taken incidentally in both 

local recreational fisheries for tuna and the CADGN fishery targeting swordfish. In recent years,

opah have become increasingly popular in seafood markets. Despite their value to commercial 

and recreational fishermen, little research on the basic biology and ecology of opah has been 
22

conducted, especially in the SCB. For example, there is little data on foraging ecology, size 

composition in fisheries, essential habitat, and stock structure. To begin to fill some of the data 

gaps, SWFSC scientists began collecting biological samples from opah caught in 2009 and 

initiated an electronic tagging program in 2011.

Incidental Catch of Opah during Juvenile Shark Abundance Surveys conducted by the 

SWFSC– From 2009 to 2013 a total of 80 opah were caught during the cruises associated with 

the SWFSC’s annual Juvenile Shark Abundance Survey. In contrast, only one opah was caught 

in the 19 years of the survey prior to 2009. The increase in opah availability has provided an 

opportunity to begin collecting biological samples and data for a species about which little is 

known. The apparent increase in opah catch starting in 2009 is likely influenced by many factors 

including fishing methods and environmental variability. The research vessel historically used to 

conduct the survey, the 171 foot R/V David Starr Jordan (DSJ), was no longer available after 

2007. To continue the shark survey, in the absence of the DSJ, the SWFSC began chartering 

smaller commercial longline fishing vessels in 2008 which could have impacted catch rates, 

although the gear was configured to match that used on the DSJ in an effort to not change the 

survey methodologies. Further analyses of the variability in survey catch as well as examining 

opah catch using logbooks from the CADGN fishery and recreational sportfishing efforts are 

underway. Additional efforts will focus on the impacts of environmental variability, and how 

opah catch rates are influenced by El Niño Southern Oscillation (ENSO) events.

Opah Foraging Ecology– To characterize the foraging ecology of opah in the California Current 

SWFSC researchers began collecting opah stomachs in 2009. A total of 94 stomachs have been 

collected to date. Sampled fish ranged from 72 cm to 126 cm FL with a mean of 98 cm FL.

Stomach contents included species of squid and fish typically associated with mesopelagic 

waters. Thirteen species of cephalopods were identified with three making up the most important 

prey items (Loligo opalescens, Gonatus spp., Dosidicus gigas) based on the IRI (index of 

relative importance). Squid ranged from 30 mm (Gonatus spp.) to over 266 mm mantle length 

(D. gigas). In addition, a few stomachs were dominated by epipelagic fish including Pacific 

saury (Cololabis saira). Interestingly, 30% of stomachs contained either small pieces of kelp or 

plastic. Regional diet differences comparing central and southern California are also being 

examined. Based on the data collected to date, opah appear to feed primarily on species 

associated with the deep scattering layer (DSL). This is consistent with their diel migrations that 

are similar to those of swordfish that also feed on the DSL. A previous study in the central North 

Pacific also found that mesopelagic prey species dominated opah diet. A comparison of the diets 

of opah, tunas, and swordfish from the SCB suggests greater niche overlap between opah and 

swordfish than between opah and tunas. Considering opah are often caught in association with 

tunas, differences in their diets could reflect some habitat partitioning.

Opah Electronic Tagging– To help characterize the vertical and horizontal movements of opah 

in the California Current, eight Wildlife Computers PSAT-Mk10 tags were deployed on opah off 

southern California prior to 2013. During 2013, an additional 6 tags were deployed on opah. All 

tagging was done during research longline cruises conducted by SWFSC scientists. The PSAT 

tags were programed to collect light level, depth, and temperature data for 240 days. Of the 

original eight tags for which the data have been analyzed, four tags popped off prematurely.

Preliminary analysis suggests opah in the California Current exhibit similar behavior as those 
23

observed near Hawaii, with diel patterns moving between depths of ~ 250 m during the day to 

~50 m at night. Unlike most diel vertical migrators, opah appear to remain below the mixed 

layer. Opah also appear to switch their diving behavior after leaving the SCB, staying further 

below the sea surface and making deeper dives into cooler water. Light level and temperature 

data recorded from one tag indicated it was possibly predated upon by an endothermic shark. The 

four fish with full 240-day deployments traveled distances ranging from 589 to 1,404 nautical 

miles. Of these, three fish released off southern California popped up off Mexico the following 

March .One tag, deployed north of Point Conception in late October 2011, popped up northeast 

of Hawaii the following June.

Opah Physiology– Opah were collected on the 2013 shark cruise and DSLL cruise for 

determination of blood properties, examination of gill and cardiovascular structure, and the 

assessment of the ability to retain internal body heat. Because opah live in a relatively deep 

habitat where both low temperatures and low dissolved oxygen concentrations can limit 

physiological processes, understanding opah adaptations to withstand these conditions can 

provide insight into their thermal and dissolved oxygen tolerances. Unlike most pelagic fish, the 

opah uses its pectoral fins for continuous swimming. The insulation of the large, red (aerobic) 

pectoral muscles by a thick layer of fat and connective tissue appears to allow for the 

conservation of internal heat. SWFSC scientists recorded pectoral muscle temperatures that are 

significantly elevated above ambient for freshly decked opah and for fish outfitted with 

intramuscular temperature loggers swimming at depth. The morphological work revealed retia 

mirabilia in the gills of the opah that appear to function as countercurrent heat exchangers to 

conserve heat derived from the pectoral muscles. The unique placement of these countercurrent 

exchangers potentially allows for warm blood to be distributed throughout the body. In addition 

to the pectoral muscle, temperatures in the heart, gut, and cranial region are all significantly 

elevated above ambient allowing for increased function at cold temperatures. Along with their 

large gill surface area these adaptations allow opah to maintain warm body temperatures and 

survive in low dissolved oxygen environments. A manuscript describing these results is currently 

being drafted.

IV. ADVANCING PELAGIC SHARK RESEARCH

The SWFSC’s shark research program focuses on pelagic sharks that occur along the U.S. 

Pacific coast, including shortfin mako, blue sharks, basking sharks (Cetorhinus maximus), and 

three species of thresher sharks: common thresher (Alopias vulpinus), bigeye thresher (A. 

superciliosus), and pelagic thresher (A. pelagicus). Center scientists are studying the sharks’ 

biology, distribution, movements, stock structure, population status, and potential vulnerability 

to fishing pressure. This information is provided to international, national, and regional fisheries 

conservation and management bodies having stewardship for sharks.

Abundance Surveys– Blue, shortfin mako, and thresher sharks are all taken in regional 

commercial and recreational fisheries. Common thresher and mako sharks have the greatest 

commercial value and are also specifically targeted by sport fishers, especially off Southern 

California. While blue shark has little market importance in the U.S., it is a leading bycatch 

species in the CADGN fishery and high-seas longline fisheries. Although catches of adult blue, 

thresher, and shortfin mako sharks do occur, the commercial and sport catch of these species off 
24

Southern California consists largely of juvenile sharks. 

To track trends in the abundance of juvenile and sub-adult blue and shortfin mako sharks and 

neonate (0-1 year old) common thresher sharks, surveys are carried out in the SCB each summer.

Offshore longline surveys from relatively large research vessels have proved most effective for 

sampling and estimating abundance trends of the more oceanic shortfin mako and blue sharks.

Surveys for neonate thresher sharks are conducted using a small commercial longline vessel in 

near shore waters.

Juvenile Mako and Blue Shark Survey– In 2013, SWFSC researchers conducted the twentieth 

juvenile shark survey for mako and blue sharks since 1994. The annual abundance survey was 

completed between 3 July and 26 July. Working aboard F/V Ventura II, a team of scientists and 

volunteers fished a total of 5,946 hooks during 28 daytime sets within seven focal areas of the 

SCB. The survey catch totaled 257 shortfin makos, 14 blue sharks, 11 pelagic rays 

(Pteroplatytrygon violacea), 8 opah, and 1 ocean sunfish (Mola mola). The preliminary data 

indicate that the nominal survey catch rate was 1.08 sharks per 100 hook-hours for shortfin mako 

and 0.06 sharks per 100 hook-hours for blue sharks. The mako shark nominal CPUE was higher 

than the previous year. However, there is a declining trend in nominal CPUE for both species 

over the time series of the survey.

In addition to survey longline sets, other fishing methods were used to maximize time on the 

water and increase the opportunity for catching other large HMS. Longline gear was modified 

for ancillary sets in an effort to cover a greater vertical distribution of the water column by using 

longer branchlines and more hooks per basket.

In all, 35 longline sets were completed. A total of 317 animals were caught. Most animals were 

brought onboard, measured, tagged, and sampled for DNA biopsies before they were released.

Conventional spaghetti tags were released on 267 sharks to collect data on movement and stock 

structure. In addition, sharks tagged with conventional tags were also injected with 

oxytetracycline (OTC) and tagged with plastic dorsal tags containing information for fishers 

upon recapture of the animal to retain a portion of the vertebrae for ongoing age and growth 

studies. Biological collections included DNA samples from most sharks captured, as well as 

stomachs, digestive tracts, and blood from a small number of sharks that did not survive.

Neonate Thresher Shark Survey– In 2013, SWFSC scientists and volunteers conducted the 

survey aboard the F/V Outer Banks. Forty-nine longline sets were made in relatively shallow, 

nearshore waters and a total of 4,916 hooks were fished during the 18-day cruise. A total of 336 

fish across a range of species were sampled during the survey. Two hundred and eighty-five 

thresher sharks were captured. Most of these sharks were injected with OTC and tagged with a 

combination of conventional tags for movement and stock structure, and plastic dorsal tags 

containing return information for the age and growth study.

The preliminary survey data indicate that the average nominal catch rate by set was 2.49 thresher 

sharks per 100 hook-hours, equivalent to the CPUE from 2012. The overall average trend since 

the start of the survey is increasing. However, the distribution of common threshers is very patchy 

and areas of high abundance are not consistent across years. In all years, a large percentage of the 
25

catch has been neonates, which were found in all areas surveyed. In addition to providing important 

information on abundance and distributions, the thresher shark pre-recruit survey enhances other 

ongoing research at the SWFSC, including age and growth, feeding, and habitat utilization studies.

Electronic Tagging Studies– Since 1999, SWFSC scientists have been using satellite 

technology to study the movements and behaviors of large pelagic sharks; primarily blue, 

shortfin mako, and common thresher sharks, while other species are tagged opportunistically.

Shark tag deployments have been carried out in collaboration with a number of partners in the 

U.S., Mexico, and Canada. The goals of the projects are to document and compare the 

movements and behaviors of these species in the California Current and to link these data to 

physical and biological oceanography. This approach will allow characterization of the essential 

habitats of sharks and a better understanding of how populations might shift in response to 

changes in environmental conditions over short or long time scales. SWFSC scientists have been 

collecting data on shortfin mako and blue sharks for over a decade and continue to look at 

horizontal and vertical movement patterns on many different time scales. In 2013, a number of 

sharks and other large pelagic fish were deployed with electronic tags in support of several 

collaborative projects. Four shortfin mako sharks and two blue sharks were tagged with satellitelinked radio position tags (SPOTs). Three mako sharks, three swordfish, one common thresher, 

one opah, and one albacore tuna were released with pop-off archival tags (PSATs).

Shortfin Mako Sharks– In 2012 the SWFSC began a collaboration with Fishtrack to deploy 

SPOT tags on larger makos during the longline survey. Four makos have been released with tags 

sponsored by Fishtrack. The tracking data are posted in near-real-time on their website 

(http://www.fishtrack.com/live-track/). Tags of two sharks tagged in 2012 and one tagged in 

2013 were still reporting as of April 2014 (Figure 5).
26

Figure 5. Tracks of three shortfin mako sharks tagged in collaboration with Fishtrack in 

2012 and 2013.The tracks show two months of data representing movements during March 

and April 2014.

In 2013, the SWFSC began a collaboration with recreational anglers to deploy PSATs on very 

large shortfin mako sharks that are typically not caught in commercial fisheries nor on the 

SWFSC’s fishery-independent shark survey. Three makos estimated at 250 kg or larger were 

tagged with PSATs in September and October 2013. SWFSC scientists are hoping to hear from 

the tags in May 2014.

SWFSC scientists have been synthesizing all the electronic tagging data for mako sharks.

Tracking success has been very good for makos as they generally provide long duration tracks 

allowing an incredible opportunity to examine seasonal movement patterns and regional fidelity.

Data from 85 SPOTs with deployment durations of 3 to 1025 days and 56 PSATs with durations 

of 18 to 227 days, including data from 40 double tagged sharks, have been analyzed. The sharks 

ranged from the surface to more than 600 m depth, with the majority of time spent in the top 100 

m. The range of horizontal movements of tagged sharks spanned along the coast of North 

America, from the northern coast of Washington to just south of Puerto Vallarta, Mexico, and 

out to the Hawaiian Islands. Two sharks travelled as far south as 4 ̊ N but did not cross the 

equator. Sharks showed seasonal movements travelling out of the SCB in the fall and winter and 

returning in the spring and summer. A manuscript is currently being drafted.

Basking Shark–The eastern North Pacific basking shark population appears to have declined 

dramatically in the last 50 years with no evidence of recovery. Where hundreds to thousands of 
27

individuals were observed off the U.S. West Coast in the early to mid-1900s, sighting even a few 

individuals is now rare. Due to concern over basking shark populations along the west coast of 

North America, the basking shark was listed as endangered in Canada and as a Species of 

Concern in the U.S. in 2010. Given severe data gaps for this population, SWFSC scientists

initiated a basking shark research program in 2010 that includes an electronic tagging study.

During 2013, data from the three sharks tagged with satellite tags in 2010 and 2011 were 

analyzed and the results are being prepared for publication. The three sharks showed impressive 

plasticity in vertical behaviors depending upon the region and distance from shore, as has been 

shown in the Atlantic. Figure 6 shows the track and vertical movements from one shark that 

moved to just north of Hawaii after 240 days. As it moved offshore, swimming depths increased 

and the shark avoided surface waters. While at depth, a distinct diel pattern was apparent with 

the shark remaining at shallower depths at night than during the day. These data support the 

hypothesis that when offshore, basking sharks forage on the deep scattering layer and not on 

aggregations of copepods in surface waters as seen near-shore.

Figure 6. (Left) The track of a basking shark tagged on 6/7/2011 off San Diego. The tag 

released as programmed on 2/2/2012. (Right) The vertical movements of the same shark 

showing the shift in habitat use as it moved offshore. 

Age Validation Studies– Age and growth of mako, common thresher, and blue sharks are being 

estimated from band formation in vertebrae. In addition to being important for studying basic 

biology, accurate age and growth curves are needed in stock assessments. SWFSC scientists are 

validating ageing methods for these three species based on band deposition periodicity 

determined using OTC. Annual research surveys provide an opportunity to tag animals with 

OTC. When the shark is recaptured and the vertebrae recovered, the number of bands laid down 

since the known date of OTC injection can be used to determine band deposition periodicity.

Since the beginning of the program in 1997, 3,718 individuals have been injected with OTC.

During the 2013 SWFSC shark surveys, 243 shortfin mako, 259 thresher, and 68 blue sharks 

were injected with OTC and released.

The ISC SHARKWG has developed a collaborative research plan to address uncertainties about 

age and growth of pelagic sharks. As part of the plan, participating national scientists are 

collecting samples from blue and shortfin mako sharks for a reference collection. Band 

enhancement methods vary between labs and the reference collection will be used to corroborate 
28

age reading across labs and ultimately develop improved growth models for these two species.

SWFSC scientists collected samples during research cruises and through the fishery observer 

program during 2013 and has contributed those samples to the ISC SHARKWG age and growth 

specialists. In January 2014, the ISC convened its second Shark Age and Growth Workshop 

during which participants progressed on their work plan. The group hopes to provide the 

SHARKWG updated information on shortfin mako shark growth for use in their upcoming stock 

assessment. 

Oxytetracycline Age Validation of Juvenile Shortfin Makos– Wells et al. (2013) recently 

published the results of OTC age validation of 29 juvenile shortfin mako sharks tagged in the 

SCB. The study showed vertebral band pair deposition rates of two per year for sharks up to 

about 4-5 years old in the northeast Pacific.

Oxytetracycline Age Validation of Blue Sharks– Vertebrae of 26 blue sharks marked with 

OTC were obtained from tag-recapture activities to determine timing of centrum growth band 

deposition. Length-frequency modal analysis was also used to obtain growth estimates from a 

22-year data set of research and commercial catch data. Tagging occurred off southern California 

with time at liberty ranging from 22 days to 1.61 years including six returns at liberty over one 

year (390-587 days). For recaptured blue sharks used for age validation, shark size at initial 

capture ranged from 73 to 231 cm FL consisting of nine females and 17 males. Results from 

band counts distal to the OTC mark on each vertebrae indicate a single band pair (one translucent 

and one opaque) is formed per year for blue sharks ranging from one to eight years of age.

Length-frequency analysis identified three age-class modes at 79, 108, and 133 cm FL with 

estimated growth rates of 29 and 25 cm FL for the first two years, respectively. Results provide 

support for annual vertebral band pair deposition in blue sharks in the northeast Pacific Ocean.

Oxytetracycline Age Validation of Common Thresher Sharks– A total of 1,454 common 

thresher sharks ranging in size from 45 to 230 cm FL have been injected with OTC. Vertebrae 

from 54 of these sharks (size range at tagging: 63-145 cm FL) have been returned with an 

average time-at-liberty of 342 days. Sample processing is underway and the preliminary results 

suggest an annual deposition rate for the size classes studied.

Record Shortfin Mako Shark Studied– Predatory sharks can be difficult to study, especially 

for the larger size classes which are infrequently encountered and rarely landed in commercial 

and recreational fisheries. In the Northeastern Pacific Ocean, shortfin mako sharks are important 

predators, and while data are increasing for smaller size classes, there is a paucity of data 

regarding large adults. On 3 June 2013, a record-breaking female shortfin mako shark (total 

length = 373 cm, mass = 600.1 kg) was captured by a recreational angler off Huntington Beach, 

California, and was subsequently donated to the SWFSC and California State University Long 

Beach for research. Samples of various tissue types were collected and analyzed to gain more 

information about the shark’s anatomy, physiology, ecology, and life history. The shark was 

found to have an approximately three-year old female sea lion carcass in its stomach. This 

confirms the presence of pinnipeds in the diet of larger shortfin makos, which are available prey 

items year round in southern California. The spiral valve contents included two species of 

cestode parasite including 20 specimens of a tetraphyllidea tapeworm and two of a 

trypanorhyncha tapeworm. Two damaged specimens of a capillaria nematode were also found, 
29

but as this genus is not known to parasitize sharks, it is likely that they were ingested along with 

their teleost hosts. Two ageing methods, thin sectioning with microscopy and x-ray imaging, 

were used to age the vertebrae of this mako, producing counts of 26 and 27 band pairs, 

respectively. Given that shortfin mako sharks in the northeast Pacific deposit two band pairs in 

vertebrae per year through age 5 (Wells et al., 2013) and the uncertainty regarding band pair 

deposition rates in older specimens, the estimated age range of this shark was 13-22 years old.

Organic contaminants and total mercury were measured in the liver and muscle tissue of the 

shark and were found to be substantially greater than most animals previously measured in 

southern California (total DDTs: 0.2 mg/g wet weight; total PCBs: 0.03 mg/g wet weight); 

however, the potential implications of this contaminant burden are unknown. Mercury levels 

were much higher than FDA recommendations for human consumption. This rare opportunity 

allowed for the collection of important data and contributes to the knowledge about the life 

history characteristics of large shortfin mako sharks.

Foraging Ecology of Pelagic Sharks– The California Current is a productive eastern boundary 

current that is an important nursery and foraging ground for a number of highly migratory 

predator species. To better understand niche separation and the ecological role of spatially 

overlapping species, SWFSC researchers have been analyzing the stomach contents of pelagic 

sharks since 1999. Stomachs are obtained primarily from the CADGN observer program.

Stomach content analysis work has continued since the publication of Preti et al. (2012).

The stomachs of several species of pelagic sharks caught during the 2012 and 2013 fishing 

seasons have been analyzed. Current levels of analysis have allowed SWFSC scientists to 

identify some of the most frequently encountered prey species. For the 2012 and 2013 seasons, 

shortfin mako stomachs (n=39) contained Pacific saury (F=23; F=Frequency of prey 

occurrence), jumbo squid (F=7), market squid (F=6), and octopus squid (Octopoteuthis spp.) 

(F=4). Blue shark stomachs (n=13) contained Gonatus spp. squid (F=11), octopus squid (F=5), 

and paper nautilus. Common prey in thresher shark stomachs (n=12) was market squid (F=6) and 

Pacific saury (F=4). Jumbo squid was found in mako stomachs for the 2012 season only. Not all 

stomachs for the 2013 season have been analyzed, however, and the absence of jumbo squid in 

mako stomachs is preliminary pending completion of all the analyses.

Survival after Capture and Release – Common thresher, shortfin mako, and blue sharks are 

captured in both commercial and recreational fisheries in the California Current. The CADGN 

fishery is the west coast commercial fishery which catches the greatest number of each of these 

species. While thresher and mako sharks are landed, almost all blue sharks are discarded.

Regional recreational fisheries have also seen a rise in the popularity of thresher and mako 

sharks. Recreational fishers are often only interested in the challenge of the fight and will 

frequently release their catch. The survival rate of sharks released both from the CADGN fishery 

and by recreational anglers is unknown. Reliable estimates of removals (i.e., mortality) are 

necessary in order to adequately assess the status of the stocks and determine the effects of the 

fisheries on their abundance.

Blue Sharks Released from the California Drift Gillnet Fishery – The CADGN fishery 

targets swordfish in the California Current. With the exception of ocean sunfish, blue sharks are 

caught in greater numbers than any other fish species taken in this fishery. Nearly all blue sharks
30

are discarded at sea due to lack of market value. A 2009 analysis of the 1990-2008 observer data 

reveals that 32% of blue sharks captured were released alive, and an additional 5% were 

discarded with their disposition unknown. The remaining 63% were discarded dead. In 2007, 

researchers from the SWFSC and the WCR began deploying PSAT tags on sharks released from 

the CADGN fishery to assess survivorship in order to determine more accurate estimates of 

fishery mortality for use in a blue shark stock assessment. As part of the study, a set of criteria 

was developed to document the condition of all live blue sharks released: “good”, “fair” or 

“poor”.

Prior to the 2012-2013 season, 15 blue sharks (100 to 200 cm FL) had been tagged by fishery 

observers. Three of the 15 sharks were released in “good” condition, 10 were released in “fair” 

condition, and 2 in “poor” condition. The two sharks that were released in “poor” condition as 

well as one released in “fair” condition did not survive the acute effects of capture in the 

CADGN fishery. These results, suggest that sharks that are released in “good” condition are 

likely to survive, whereas those released in “poor” condition are likely to die. No tags were 

released during the 2013-2014 season due to low effort and few blue sharks caught during the 

time the tags were available to observers, but SWFSC scientists hope to complete the study 

during the 2014-2015 season.

Thresher Sharks Released from the Recreational Fishery – Researchers from the SWFSC, 

WCR, and PIER have conducted a three-phase study to assess the post-release survival of 

thresher sharks caught by recreational anglers. The first phase of the study, which was completed 

in 2010, involved releasing sharks which had been captured using tail-hooking techniques 

(common practice in the southern California fishery). The results from this work revealed that 

survivorship is low for large sharks (>185 cm FL) that endure fight times that exceed 85 minutes 

(Heberer et al., 2010). The second and third phases of the research effort focused on assessing 

post-release survival in two modes of capture routinely observed in the southern California 

recreational fishery: (1) sharks that are caught using caudal-based angling techniques and 

unintentionally released with trailing gear left embedded, and (2) sharks that are caught and 

released using mouth-based angling techniques. Post-release survivorship was assessed using 

pop-up satellite archival tags. For the trailing gear investigation, six sharks died shortly after 

release, one died after several weeks, and two sharks survived the deployment period for an 

overall survivorship rate of 22%. For the mouth-based trials, all common thresher sharks 

survived the acute effects of capture (100% survivorship). These results indicate that trailing gear 

left embedded in sharks can negatively affect post-release survivorship, while mouth-based 

angling, when performed properly, can result in high survivorship of released sharks. The second 

publication for this project, based on results from phases two and three, has been submitted and 

is currently undergoing peer review in the journal Fisheries Research. Overall, the results from 

all phases of this study indicate that methods which maximize mouth-based capture and reduced 

fight times should be adopted as best fishing practices by the fishery to reduce the mortality of 

released thresher sharks.

A major component of this project is to promote fishing practices that enhance thresher shark 

catch and release survival by developing education and outreach tools for the recreational fishing 

community. An outreach video highlighting phase one of the research was produced by the 

Ocean Media Center (OMC) and posted on the NOAA Fisheries Home Page under the Video 
31

Gallery (http://www.nmfs.noaa.gov/gallery/videos/) in 2012. A second video, highlighting 

phases two and three of the research effort, is still under development by OMC.

Genetic Analysis of Pelagic Sharks– An understanding of stock structure is important in order 

to make accurate assumptions for stock assessments and to develop effective management 

objectives that take the population range, distribution, and life history into account. Various 

genetic analyses are useful to help identify differentiation between and within presumed stocks.

During 2013, sample collection and processing continued to examine stock structure for a 

number of shark species including shortfin mako, common thresher, silky, and pelagic thresher 

sharks. In addition, samples of blue shark tissue have been sent to colleagues in Japan as part of a 

Pacific-wide collaboration. DNA samples were collected during research cruises in 2013 from 

263 shortfin makos, 72 blue sharks, 262 common threshers, 6 leopard sharks (Triakis

semifasciata), and 1 brown smoothhound (Mustelus henlei). Additional samples were obtained 

by fishery observers on CADGN trips.

V. IDCPA RESEARCH

The SWFSC research conducted under the International Dolphin Conservation Program Act 

(IDCPA) during 2013 was focused on evaluating assumptions in line-transect methods used to 

estimate marine mammal abundance at sea and the potential roles of the fishery and ecosystem in 

the apparent lack of recovery of depleted dolphin stocks in the eastern tropical Pacific Ocean 

(ETP). This lack of recovery follows a period of significant reductions in observed dolphin 

mortality in the ETP tuna purse-seine fishery. Research activities included (1) continued analysis 

of data collected during a 2007 survey designed to collect fine-scale ecosystem data and assess 

standard methods for collecting dolphin sighting data, and (2) other data analyses, processing, 

and publications.

Analysis of Stenella Abundance Research Line Transect and Ecosystem Survey Data– In 

2007, SWFSC conducted a Stenella Abundance Research Line Transect and Ecosystem (STARLITE) cruise to survey marine mammals and their habitat in the ETP. The primary objective of 

the STAR-LITE cruise was to investigate line transect methods used on surveys in the ETP and 

to explore fine-scale spatial and temporal variability in the ecosystem using a multidisciplinary 

approach. A study of changes in regional ecosystem structure induced by a tropical storm was 

published (Fiedler et al., 2013a). 

Ecosystem data were collected during STAR-LITE 2007. As expected, environmental variability 

within days and day-to-day was relatively small. However, the passage of tropical storm Kiko 

through the study area caused persistent changes in the entire ecosystem. Kiko mixed water from 

beneath the strong, shallow thermocline to the surface. As a result, surface temperature decreased 

by 0.6°C, the thermocline and chlorophyll maximum layer shoaled by 10-20 m, stratification 

decreased by 27%, and chlorophyll increased by 33% at the surface and 35% over the euphotic 

zone. These changes persisted for at least four weeks. Zooplankton biomass increased by 59% 

about three weeks after the phytoplankton increase. Changes in the stomach fullness and diet 

composition of planktivorous flyingfish were consistent with the increase in zooplankton 

biomass. Among top predators, the sighting rate of dolphins declined, while the response of 

seabirds varied by species and was confounded by seasonal migration patterns. Tropical cyclones 
32

are a recurrent disturbance in this region. They initiate a bottom-up forcing of the ecosystem, 

creating persistent patches of higher primary and secondary production, and may be regarded as 

a disturbance regime.

Research conducted in 2007 represented the eleventh year of similar investigations conducted 

during the past 20 years, with previous cruises in 1986-1990, 1998-2000, 2003, and 2006. Using 

an ecosystem approach, SWFSC scientists conducted research on physical and biological 

oceanography (dolphin habitat); midtrophic-level fishes and squids (dolphin prey); and seabirds, 

marine turtles and other cetaceans (dolphin commensals, competitors, and predators). Data and 

analyses resulting from Stenella Abundance Research (STAR) surveys form the basis for many 

international measures adopted to conserve dolphin stocks and manage the tuna purse-seine 

fishery in the ETP. The next full STAR survey, scheduled to occur in the fall of 2009, was 

postponed by one year due to ship time constraints. On 6 April 2010, STAR 2010 was again 

postponed due to the same constraints. And in January 2010, plans for conducting STAR in the 

fall of 2011 were canceled indefinitely. At this time, the future of these cetacean and ecosystem 

assessment cruises is uncertain.

Data Analyses, Processing, and Publication– The SWFSC’s investigations of dolphin stocks 

historically depleted by the ETP tuna purse-seine fishery (spinner and pantropical spotted 

dolphins, Stenella longirostris and S. attenuata, respectively) are conducted with an ecosystem 

approach. In addition to investigating the status and trends of these dolphin stocks, auxiliary 

projects are conducted to improve the understanding of their surrounding environment. Recent 

data analyses, processing, and publications included: (1) investigations of cetacean biodiversity 

hotspots; (2) identifying critical habitat for large whales; (3) ecosystem modeling; (4) assessment 

of relative fishery exposure for ETP dolphins; (5) dolphin swimming kinematics research; (6) 

investigations of dolphin reproductive biology; (7) ETP dolphin population genetic structure; (8) 

investigations of the ETP ecosystem and its change over time; (9) metrics of ecosystem impact 

of the ETP purse-seine fishery; (10) cephalopods as indicators of spatial variation in biochemical 

properties between marine systems, and (11) comparative analysis of ETP ecosystem services.

Investigations of Cetacean Biodiversity Hotspots– Kaschner et al. (2011) uses a model to 

predict cetacean species richness patterns, and validates the model with empirical data, including 

data collected during SWFSC research surveys in the ETP. SWFSC scientists also investigated

species richness hotspots for 28 species of cetaceans in the ETP (ca. 20 million km2) based on 

data collected aboard NOAA research vessels, August–November, in each of 10 years during a 

21-year period (1986-2006). Density was converted to presence/absence on a species-specific 

basis, and species richness (number of species recorded in a particular grid cell) was mapped for 

all years combined. Richness hotspots were defined as any grid cell that contained greater than 

40% of the total species pool (≥ 11 species) and were clearly evident in three distinct regions: the 

Equatorial Front, the Costa Rica Dome, and waters to the southwest of the Baja California 

peninsula. Although these hotspots encompassed areas of highest density for a few species, the 

correlation between richness and density for any given species was generally low (mean 0.25, 

range 0.03 to 0.44), as was the proportion of cells where a particular species was present and 

encompassed by a hotspot (mean 0.20, range 0.04 to 0.56). A manuscript on this topic is in 

preparation.
33

Identifying Critical Habitat for Large Whales– Many species of baleen whales migrate long 

distances between breeding and feeding areas. These species are exposed to anthropogenic 

threats in their feeding and breeding areas and along their migration routes; threats include 

entanglement in fishing gear, ship strikes, ocean noise, contaminants, and climate change.

Mitigating these threats requires a transboundary, systematic planning approach. To facilitate 

planning efforts in the EPO, the SWFSC partnered with the Permanent Commission for the 

South Pacific (CPPS) to host an international workshop. The workshop was attended by 

participants from Chile, Colombia, Ecuador, Panama, Costa Rica, the United States’ National 

Oceanic and Atmospheric Administration, and CPPS. Scientific presentations were given 

summarizing the state of risk assessment in EPO waters. For example, representatives from the 

SWFSC gave presentations on assessing the risk of ships striking large whales in marine spatial 

planning and tools to develop species distribution models. These presentations used over 20 

years of large-scale survey effort conducted by SWFSC researchers in offshore waters and over 

1,000 opportunistic sightings held by CPPS in their Regional Information System on 

Biodiversity and Protected Areas. Participants, particularly those representing government 

agencies from the various countries, also addressed the following questions:

 How can you help to improve species distribution and threat data?

 How can you contribute to marine spatial planning efforts for the eastern Pacific?

 What are the institutional opportunities and barriers for resource protections in your 

country?

 How can you help move large whale conservation forward during the coming year?

Ecosystem Modeling– Development of an ecosystem model to explore patterns of cetacean 

distribution, migration, feeding, and breeding is underway. In the future, SWFSC scientists will 

use these ecosystem variables and models to help explain current cetacean ecological patterns 

and predict future changes.

Assessment of Relative Fishery Exposure for ETP Dolphins – For the past half century, the 

purse-seine fishery for yellowfin tuna has been a significant factor in the lives of dolphins in the 

ETP. However, little is known about how frequently an individual dolphin is exposed to the 

fishery, and no methods are available for accurately assessing the prior exposure of dolphins 

encountered at sea. Archer et al. (2010) developed a method to estimate an index of exposure 

based on a model of dolphin movement derived from data collected from multiple tracking 

studies. Planned studies for this index include examining its relationship to evasive behavior, calf 

production as assessed from aerial photographs, and reproductive rates as measured from skin 

biopsies.

Dolphin Swimming Kinematics Research– The results from a series of nine publications 

investigating various aspects of swimming kinematics of mother and calf dolphins between 2004 

and 2011 are being integrated into a hydrodynamics-based energetics model to investigate the 

potential for dolphin mother-calf separation and subsequent calf mortality due to tuna purseseine chase in the ETP. The model will contribute to understanding of indirect fishery effects on 

populations of dolphins targeted by the ETP tuna purse-seine fishery. In addition to progress on 

model development during 2013, a comprehensive review was published of form, function, and 

physiology in the most-often targeted species in the ETP, the pantropical spotted dolphin
34

(Stenella attenuata), by Edwards, E.F, N.M. Kellar, and W.F. Perrin in 2013. 

Investigations of Dolphin Reproductive Biology– Kellar et al. (2013) published Pregnancy 

patterns of pantropical spotted dolphins (Stenella attenuata) in the eastern tropical Pacific 

determined from hormonal analysis of blubber biopsies and correlations with the purse-seine 

tuna fishery. This paper examined reproductive patterns of these dolphins by measuring blubber 

progesterone (BP) concentrations in biopsy samples to assess pregnancy state. Blubber 

progesterone was quantified in 212 biopsies from female offshore dolphins sampled between 

1998 and 2003 in the northeastern tropical Pacific, and SWFSC scientists found that 11.5% of 

biopsied females were pregnant. The relationship between pregnancy and fishing effort was 

analyzed using the relative exposure index developed in Archer et al. (2010), and SWFSC 

scientists found that pregnant females were exposed to significantly less activity than nonpregnant ones (p=0.022), suggesting that the fishery may have an inhibitive effect on pregnancy. 

Additional spatial analysis indicated that pregnancy was more aggregated than random (p<0.05) 

at a scale up to 180-nmi, with the highest proportion pregnant in the mouth of the Gulf of 

California, an area with relatively low reported activity. 

ETP Dolphin Population Genetic Structure– Research is underway to examine population 

genetic structure for spotted and spinner dolphins in the ETP. Cranial and external morphology, 

as well as reproductive strategies, differ across the range of these animals; thus, genetic 

differences are expected. Updated population structure information is needed to ensure stock 

boundaries and abundance estimates remain accurate, as they are necessary to calculate dolphin 

stock mortality limits.

In 2011, work began quantifying the levels of genetic structure in spinner and spotted dolphin 

populations in the ETP. A Ph.D. student at Scripps Institution of Oceanography working in 

collaboration with SWFSC, has collected mitochondrial genomes (mtDNA) and nuclear SNPs 

from 111 spinner and 89 spotted dolphins to test for genetic structure using DNA capture arrays 

and next-generation sequencing. MtDNA shows differences between whitebelly and both eastern 

and Central American spinners, but not between the latter two (accepted subspecies). SNP 

analyses show differences between all three forms. Structure was not detected between spotted 

dolphin subspecies in the mtDNA; nuclear SNP analyses are ongoing. Results support current 

management boundaries for spinners, but were limited in the ability to detect substructure below 

the level of subspecies due to limited samples and power to detect genetic structure. The results 

suggest the need for additional data to determine the accuracy of stocks of spotted dolphins. Matt 

is currently writing this work for publication and now collecting restriction site associated 

(RAD) markers to test subspecies hypotheses in spotted dolphins and structure with the 

subspecies of spinner dolphins. Additional samples are being sequenced from throughout the 

spinner and spotted dolphin distributions in order to place these populations within a global 

phylogeographic context. 

Investigations of the ETP Ecosystem and Its Change over Time– Fiedler et al. (2013b) 

published an analysis of variations in thermocline depth and stratification in the ETP and North 

Pacific. Time series from 1958-2008 were decomposed into seasonal, inter-annual cycle, and 

long-term trend components using state-space techniques. The thermocline influences nutrient 

input to surface waters, which limits primary productivity throughout this region. Potential 
35

ecosystem effects of the observed long-term trends are discussed. Further analyses will 

investigate seasonal and inter-annual variability of the thermocline in this region.

SWFSC scientists completed a retrospective study analyzing trophic level of seabirds in the 

eastern Pacific warm pool during the past 50 years in order to gauge effects of the 1976-77 

regime shift of the Pacific Ocean in a tropical and pelagic community of seabirds. Using study 

skins of historical specimens from museum collections, stable carbon (δ13C) and nitrogen (δ15N) 

isotopes were retrospectively (1960-2006) measured for a suite of ecologically and 

phyolgenetically diverse seabirds from the eastern Pacific warm pool. In this region, seabirds 

generally forage by depending on subsurface predators to drive prey to the surface or by 

associating with oceanographic features that increase productivity or aggregate prey in space or 

time. Community-wide changes in response to the 1976-77 regime shift were not found. Instead, 

evidence was found suggesting a trophic shift and or change in foraging area for sooty terns 

(Onychoprion fuscatus) and a long-term decrease in feather δ13C for the eastern Pacific warm 

pool seabird community. This long-term decrease in feather δ13C can be accounted for by the 

Suess effect and not a decline in primary productivity of the system. This may be due to a

deepening trend in thermocline depth in the eastern Pacific warm pool affecting sooty terns more 

so than other species in the subsurface predator-dependent guild which depend less on smaller 

subsurface predators like skipjack tuna.

Metrics of Ecosystem Impact of the ETP Purse-Seine Fishery– Gerrodette et al. (2012)

summarizes the ecological effects of the ETP purse-seine tuna fishery by measuring the total 

removals (target catch and bycatch) using a variety of metrics. They found that floating-object 

sets removed two to three times as much biomass per set as dolphin or unassociated sets.

However, the three types of purse-seine fishing differed in the composition and amount of both 

target catch and bycatch. Metrics of ecosystem removal which measured diversity, trophic level,

and replacement time were more informative than metrics of biomass or numbers of individuals 

in assessing ecosystem impacts.

Cephalopods as indicators of spatial variation in biochemical properties between marine 

systems– Ruiz-Cooley et al. (2010) and Ruiz-Cooley and Gerrodette (2012) quantified two 

biochemical tracers (d13C and d15N) from epi-mesopelagic squid tissues, the jumbo squid (D.

gigas) and purple back squid (Stenotheuthis oualaniensis), to investigate ontogenetic shifts in 

diet, habitat use and differentiate distinct groups or subpopulations based on the unique 

biochemical properties of their habitat along the eastern Pacific. These two squid species are key 

components in food webs from the ETP and potential prey of tuna and dolphins as well as other 

pelagic fish and odontocetes. For the first time, Ruiz-Cooley and Gerrodette revealed that d13C 

and d15N measured from tissues of these squid species can serve to track large-scale latitudinal, 

longitudinal, and geographic variability in the biochemical distribution of carbon and nitrogen 

along the eastern Pacific. Furthermore, the results from this study can serve for future studies 

investigating pelagic food web dynamics using stable isotope analysis.

Ruiz-Cooley et al. (2013) built on this research by using stable isotopes to track origin of jumbo 

squid captured in the California Current ecosystem. Coincident with climate shifts and 

anthropogenic perturbations, the highly voracious jumbo squid reached unprecedented northern 

latitudes along the Northeast Pacific margin post 1997–98. The physical or biological drivers of 
36

this expansion, as well as its ecological consequences remain unknown. Novel analysis from 

both bulk tissues and individual amino acids (Phenylalanine; Phe and Glutamic acid; Glu) in 

both gladii and muscle of jumbo squid captured in the Northern California Current System 

(NCCS) documents for the first time multiple geographic origins and migration. Phe d15N 

values, a proxy for habitat baseline d15N values, confirm at least three different geographic 

origins that were initially detected by highly variable bulk d15N values in gladii for squid at small 

sizes (.30 cm gladii length). In contrast, bulk d15N values from gladii of large squid (.60 cm) 

converged, indicating feeding in a common ecosystem. The strong latitudinal gradient in Phe 

d

15N values from composite muscle samples further confirmed residency at a point in time for 

large squid in the NCCS. These results contrast with previous ideas, and indicate that small squid 

are highly migratory, move into the NCCS from two or more distinct geographic origins, and use 

this ecosystem mainly for feeding. These results represent the first direct information on the 

origins, immigration and habitat use of this key ‘‘invasive’’ predator in the NCCS, with

implications for understanding both the mechanisms of periodic jumbo squid population range 

expansions, and effects on ecosystem trophic structure.

Seasonal and inter-annual variability of dolphin distributions– An analysis of tuna-vessel 

observer data is underway in collaboration with the IATTC. These data, collected by observers 

aboard tuna purse seiners that fish tunas associated with dolphins, can be processed to yield 

sightings and effort data. While of lower quality than data collected on research vessel surveys, 

the data are continuous from 1980 to the present and thus can much more effectively resolve 

seasonal and inter-annual changes. These changes will be related to environmental variability. 

Comparative analysis of ETP ecosystem services– Beginning in 2011, research conducted by a 

Ph.D. student at Scripps Institution of Oceanography and SWFSC provides a case study in the 

analysis and valuation of open ocean ecosystem services, with a view toward evaluating 

tradeoffs among commercial fisheries, biodiversity conservation, and carbon storage and 

sequestration. Until recently, many ecosystem services were assumed to hold no economic value 

because they were not traditionally traded in markets. Society has made decisions to maximize 

economic value by choosing something that has monetary value (e.g., commercial fisheries) over 

something that has no monetary value (e.g., biodiversity). Ecosystem service valuation for the 

ocean has primarily focused on coastal systems, such as coral reefs, mangroves and estuaries, 

with much less emphasis on open ocean ecosystems. However, as management for open ocean 

ecosystems moves toward more holistic approaches, efforts to value their services will need to 

progress. Making use of extensive historical datasets from the SWFSC, the IATTC, and NMFS 

Office of Science and Technology (economic data on fisheries imports), they are documenting

and quantifying the major ecosystem services provided by the ETP, identifying the major user 

groups of these services, and quantifying some economic values of these services using existing 

data from commercial fisheries and biodiversity conservation efforts in the region, as well as 

global carbon markets. Results will contribute to the challenging but critical movement toward 

ecosystem-based management for the open ocean.

VI. PUBLICATIONS CITED

Archer, F. I., J. V. Redfern, T. Gerrodette, S.J. Chivers, and W. Perrin. 2010. Estimation of 

relative exposure of dolphins to fishery activity. Mar Ecol-Prog Ser.410:245-
37

255. doi:10.3354/meps08641.

Gerrodette, T., R. Olson, S. Reilly, G. Watters, and W. Perrin. 2012. Ecological metrics of 

biomass removed by three methods of purse-seine fishing for tunas in the eastern tropical 

Pacific Ocean. Conserv Biol. 26(2): 248–256.doi: 10.1111/j.1523-1739.2011.01817.x.

Heberer, C., S.A. Aalbers, D. Bernal, S. Kohin, B. DiFiore, and C.A. Sepulveda.2010.Insights 

into catch-and-release survivorship and stress-induced blood biochemistry of common 

thresher sharks (Alopias vulpinus) captured in the southern California recreational 

fishery.Fish Res.106:495-500. doi:10.1016/j.fishres.2010.09.024.

Kaschner, K., D. Tittensor, J. Ready, T. Gerrodette and B. Worm. 2011. Current and future 

patterns of global marine mammal biodiversity. PLoS ONE. 6(5): e19653. doi: 

10.1371/journal.pone.0019653.

Nieto, K., H. Demarcq, and S. McClatchie. 2012. Mesoscale frontal structures in the Canary 

Upwelling System: New front and filament detection algorithms applied to spatial and 

temporal patterns. Remote Sens Environ. 123:339–346. doi10.1016/j.rse.2012.03.028.

NOAA Technical Memorandum NMFS, NOAA-TM-NMFS-SWFSC-516. 76 p.

Preti, A., C.U. Soykan, H. Dewar, R.J.D.Wells, N. Spear, and S. Kohin. 2012. Comparative 

feeding ecology of shortfin mako, blue and thresher sharks in the California 

Current.EnvironBiolFish.95:127–146. doi: 10.1007/s10641-012-9980-x.

Ruiz-Cooley, R. I., E. C. Villa and W. R. Gould. 2010. Ontogenetic variation of δ13C and δ15N 

recorded in the gladius of the jumbo squid Dosidicus gigas: geographic differences. Mar 

Ecol-Prog Ser. 399: 187-198.doi:10.3354/meps08383.

Ruiz-Cooley, R. I. and T. Gerrodette. 2012. Tracking large-scale latitudinal patterns of δ13C and 

δ

15N along the E Pacific using epi-mesopelagic squid as indicators. Ecosphere. 3:art63. 

doi: 10.1890/ES12-00094.1.

VII.SWFSC PUBLICATIONS 

Published

Evans K., F. Abascal, D. Kolody, T. Sippel, J. Holdsworth, and P. Maru.2014. The horizontal 

and vertical dynamics of swordfish in the South Pacific Ocean. J Exp Mar Biol Ecol.

450:55–67. doi: 10.1016/j.jembe.2013.10.025.

Fiedler, P. C., J. V. Redfern, J. Van Noord, C. Hall, R. L. Pitman, and L. T. Ballance. 2013a. 

Effects of a tropical cyclone on a pelagic ecosystem from the physical environment to top 

predators. Mar Ecol-Prog Ser. 484:1-16.doi:10.3354/meps10378.

Fiedler, P. C., R. Mendelssohn, D. M. Palacios, and S. J. Bograd. 2013b. Pycnocline variations in 
38

the eastern tropical and North Pacific, 1958-2008. J Climate. 26:583-599. doi: 

10.1175/JCLI-D-11-00728.1.

Haltuch, M., O. Hamel, K. Piner, P. McDonald, C. R. Kastelle, and J.Field.2013. A California 

current bomb radiocarbon reference chronology and petrale sole age validation. 

CanJFishAquatSci. 70(1):22-31. doi: 10.1139/cjfas-2011-0504.

Hazen, E. L., S. Jorgensen, R. R. Rykaczewski, S. J. Bograd, D. G. Foley, I. D. Jonsen, S. A. 

Shaffer, J. P. Dunne, D. P. Costa, L. B. Crowder, and B. A. Block. 2013. Predicted 

habitat shifts of Pacific top predators in a changing climate. NatClimChange. 3(3):234–

238.doi:10.1038/nclimate1686.

Kellar, N. M., M. L. Trego, S. J. Chivers, and F. I. Archer. 2013. Pregnancy patterns of spotted 

dolphins in the eastern tropical Pacific determined from hormonal analysis of biopsies 

and their correlation with the purse-seine tuna fishery. Mar Biol. doi: 10.1007/s00227-

013-2299-0.

Kvamsdal, S. F. andS. M. Stohs. 2014. Estimating endangered species interaction risk with the 

Kalman filter. Am J Agr Econ. 96 (2): 458-468.doi: 10.1093/ajae/aat092.

Lewison, R., B. Wallace, J. Alfaro-Shigueto, J. C. Mangel, S. M. Maxwell, and E. L. Hazen. 

2013. Fisheries bycatch of marine turtles: lessons learned from decades of research and 

conservation. In J. Wyneken, K. J. Lohmann, and J. A. Musick (eds.), The biology of sea 

turtles, Vol. III, p. 329–352. CRC Press.

MacCall, A. D. and S. L.H. Teo. 2013. A hybrid stock synthesis - Virtual population analysis 

model of Pacific bluefin tuna. FishRes. 142:22–26.doi:10.1016/j.fishres.2012.05.001.

Madigan, D. J., Z. Baumann, A. B. Carlisle, D. K. Hoen, B. N. Popp, H. Dewar, O. E. Snodgrass, 

B. A. Block, and N. S. Fisher. 2014. Reconstructing trans-oceanic migration patterns of 

Pacific bluefin tuna using a chemical tracer toolbox. Ecology. 95:1674–1683. doi: 

10.1890/13-1467.1.

Madigan, D. J., Z. Baumann, O. E. Snodgrass, H. A. Ergül, H. Dewar, and N. S. Fisher. 2013. 

Radiocesium in Pacific bluefin tuna Thunnus orientalis in 2012 validates new tracer 

technique. EnvironSciTechnol. 47 (5), 2287–2294.doi: 10.1021/es4002423.

Maunder, M. N. and K. R. Piner. 2014. Contemporary fisheries stock assessment: many issues 

still remain. ICES J Mar Sci.doi:10.1093/icesjms/fsu015.

Nosal, A.P., D.P. Cartamil, J.W. Long, M. Lührmann, N.C. Wegner, and J.B. Graham. 2013. 

Demography and movement patterns of leopard sharks (Triakis semifasciata) aggregating 

near the head of a submarine canyon along the open coast of southern California, USA. 

EnvironBiolFish. 96: 865-878.doi: 10.1007/s10641-012-0083-5.

Nosal, A.P., S. Cailliet, E. K. Kisfaludy, M.A. Royer, and N.C. Wegner. 2014. Aggregation 
39

behavior and seasonal philopatry in male and female leopard sharks (Triakis 

semifasciata) along the open coast of southern California, USA. MarEcol-ProgSer.499: 

157-175.doi: 10.3354/meps10632.

Piner, K. R., H.H. Lee, I. G. Taylor, M. Kanaiwa, and C.L. Sun. 2013. Population dynamics and 

status of striped marlin in the western and central North Pacific Ocean. Mar Freshwater

Res. 64 (2), 108-118.doi: 10.1071/MF12302.

Renck, C. L., D.M. Talley, R. J. D. Wells, and H. Dewar. 2014. Regional growth patterns of 

juvenile albacore (Thunnus alalunga) in the eastern North Pacific. Cal Coop Ocean Fish. 

Vol. 55.

Ruiz-Cooley, R. I., L. T. Ballance, and M. D. McCarthy. 2013. Range Expansion of the Jumbo 

Squid in the NE Pacific: d15N Decrypts Multiple Origins, Migration and Habitat Use. 

PLoS ONE 8(3): e59651. doi:10.1371/journal.pone.0059651.

Sepulveda, C.A., C. Heberer, S. A. Aalbers, N. Spear, M. J. Kinney, D. Bernal, and S. Kohin. 

2015. Post-release survivorship studies on common thresher sharks (Alopias vulpinus) 

captured in the southern California recreational fishery. Fish Res. 161: 102-108. 

doi:10.1016/j.fishres.2014.06.014

Sippel T., J. Eveson, B. Galuardi, C. Lam, S. Hoyle, M. Maunder, P. Kleiber, F. Carvalho, V. 

Tsontos, S. L. H. Teo, A. Aires-da-Silva, and S. Nicol. 2014. Using movement data from 

electronic tags in fisheries stock assessment: A review of models, technology and 

experimental design. Fish. Res. 163: 152-160. doi: 10.1016/j.fishres.2014.04.006

Soykan, C. U., T. Eguchi, S. Kohin, and H. Dewar. 2014. Prediction of fishing effort 

distributions using boosted regression trees. Ecol Appl. 24(1), 71-83.doi: 10.1890/12-

0826.1.

Thomas, L.R., G. DiNardo, H. H. Lee, K. R. Piner, and S.E. Kahng. In Press. Factors influencing 

the catch rates of Kona crabs Ranina ranina (Brachyura: Raninidae) in the Main 

Hawaiian Islands. JCrustaceanBiol. 33(5).doi: 10.1163/1937240X-00002171.

Wegner, N. C., C. A. Sepulveda, S. A. Aalbers, and J. B. Graham. 2013. Structural adaptations 

for ram ventilation: Gill fusions in scombrids and billfishes. JMorphol. 274:108–120.doi: 

10.1002/jmor.20082.

Wells, R. J., S. Kohin, S.L. Teo, O. E. Snodgrass, and K. Uosaki. 2013. Age and growth of North 

Pacific albacore (Thunnus alalunga): Implications for stock assessment. Fish Res. 147, 

55-62.doi:10.1016/j.fishres.2013.05.001.

Wells, R. J. D., S. E. Smith, S. Kohin, E. Freund, N. Spear, and D. A. Ramon. 2013. Age 

validation of juvenile shortfin mako (Isurus oxyrinchus) tagged and marked with 

oxytetracycline off southern California. Fish B-NOAA. 111:147-160.doi 

10.7755/FB.111.2.3.
40

Technical Reports, Administrative Reports, and Working Papers

Dewar, H., T. Eguchi, J. Hyde, D. Kinzey, S. Kohin, J. Moore, B. L. Taylor, and R. Vetter. 2013. 

Status Review of the Northeastern Pacific Population of White Sharks (Carcharodon 

carcharias) Under the Endangered Species Act. NMFS, NOAA, Southwest Fisheries 

Science Center. La Jolla, CA.

Xu, Y., S.L.H. Teo, and J. Holmes. 2013. An update of the standardized abundance index of U.S. 

and Canadian albacore troll fisheries in the North pacific (1966-2012). Working Paper to 

the International Scientific Committee Albacore Working Group. ISC/13/ALBWG03/06.

Xu, Y., S.L.H. Teo, and J. Holmes. 2013. An update of the standardized abundance index of U.S. 

and Canadian albacore troll fisheries in the North pacific (1966-2011). Working Paper to 

the International Scientific Committee Albacore Working Group. ISC/14/ALBWG/03.

Xu, Y., T. Sippel, S.L.H. Teo, K. Piner, K. S. Chen, and R. J. D. Wells. 2013. A comparison 

study of North Pacific albacore (Thunnus alalunga) age and growth among various 

sources. Working Paper to the International Scientific Committee Albacore Working 

Group. ISC/14/ALBWG/04.

Approved by the Science Director

Nieto, K., Y. Xu, S. L. H. Teo, S. McClatchie, and J. Holmes. In review. Coastal upwelling 

fronts: a key habitat for albacore tuna (Thunnus alalunga) in the Northeast Pacific Ocean. 

Prog Oceanogr.

Xu, Y., K. Nieto, S. L. H. Teo, S. McClatchie, and J. Holmes. In review. Influence of subtropical 

fronts on the spatial distribution of albacore tuna (Thunnus alalunga) in the Northeast 

Pacific over the past 30 years (1982-2011). Prog Oceanogr.