MAY 2013

 by

The Southwest Fisheries

Science Center

ADMINISTRATIVE REPORT LJ-14-03

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 

2013 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-14-03

MAY 2013

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 2013 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. This section includes brief descriptions of some of the contributions and activities 

during the past year, May 2012–April 2013.

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. Information on 

vessels, gears, effort, catch, bycatch, protected species interactions, landings, biological 

sampling, and observer data are compiled and managed by the fisheries monitoring group under 

the Fisheries Resources Division (FRD). 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 

these eight monitored HMS fisheries. The fishery harvests over 200,000 metric tons (t) of 

tropical tunas each year, generating millions of dollars in ex-vessel revenue. SWFSC staff 

manage the data from the WCPO purse-seine fleet 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 and Oregon, and albacore, 

bluefin, and yellowfin tunas in southern California waters. The 2012 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 2012 CATCH IN 

METRIC TONS

NUMBER OF 

VESSELS

Central Western Pacific Ocean 

(WCPO) Purse Seine 259,760 39

North Pacific Albacore Troll 

and Pole-and-line 14,137 816

South Pacific Albacore Troll 198 7

Eastern Tropical Pacific (ETP) 

Purse seine < 3

California Large-mesh Drift 

Gillnet 97 17

California Harpoon 21 9

Longline (California-based) < 3

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

albacore troll and pole-and-line fishery (a.k.a. albacore surface fishery) in 2012 totaled 14,137 t,

an increase of 28% from 11,037 t in 2011. The number of vessels also increased from 641 

vessels in 2011 to 816 vessels in 2012. The average weight of retained albacore in 2012 is 15.4 

pounds compared to 16.3 pounds average weight in 2011. 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 Fishery Management Council in 2005. An electronic logbook 

computer application was made available to fishermen in this fishery in 2006. Each year between 

five and ten vessels utilize this electronic logbook program and submit their logbook data 

electronically. Efforts to update and improve this reporting option have been in progress for 

several years.

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. Seven vessels participated in the 2012 fishery,

compared to six vessels in 2011. Total catch in 2012 was 198 t, a decrease of 51% from the 402 t 

landed in 2011. 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 and Canada.

Purse-seine Fisheries (EPO and WCPO)– 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, sardines, anchovies, and 

other coastal pelagic species and occasionally 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 2012, 39 vessels caught 259,760 t of 

all species combined (yellowfin, bigeye (Thunnus obesus), and skipjack (Katsuwonus pelamis)

tunas) in the WCPO purse-seine fishery. In recent years very few of these vessels fished in the 
3

EPO.

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

decreased from 23 vessels in 2011 to 17 vessels in 2012. These vessels landed 121 t of swordfish 

caught in 2011 compared to 97 t of swordfish in 2012. FRD staff manage the gillnet logbook 

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

Fish and Wildlife (CDFW). Data editing and data entry are done by staff from both offices. The 

NOAA Southwest Regional office (SWR) runs a fishery observer program to monitor ~20% of 

the fishery effort and conducts on-board size sampling.

California Harpoon– The California harpoon fishery decreased from 17 vessels in 2011 to 9 

vessels in 2012. These vessels caught 21 t in 2011 of swordfish compared to 5 t in 2012. No size 

sampling information is collected from this fishery. The logbook data from this fishery are also 

managed by SWFSC 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 based out of 

Hawaii. Logbook data from the west coast are submitted to the SWR and maintained at SWFSC. 

Data from this fishery are combined 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 increased from 415 t in 2011 to 902 t in 2012. Estimates for recreational 

catches of bluefin tuna are not available yet for 2012, but estimates for 2011 are 499 t.

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 are 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). SWFSC staff compile and summarize a wide variety of fisheries statistics and 

group these summaries by various time and space resolutions for submission to these RFMOs 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 (Sarah Shoffler) –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
4

members and to RFMOs of the Pacific Ocean.

Albacore Stock Assessment and Research –The commercial surface albacore fishery is the 

most important fishery for HMS on the U.S. West Coast. In preparation for the upcoming stock 

assessment due in April 2014, SWFSC researchers attended an intercessional workshop of the 

ISC Albacore Working Group (ALBWG) in Shanghai, China, from 19-26 March 2013. The 

goals of this workshop were: (1) to review results of high priority research and develop proposals 

for incorporation into stock assessment process/model; (2) to discuss information and advice on 

biological reference points requested by the Northern Committee of the Western and Central 

Pacific Fisheries Commission (Northern Committee, 2012) and develop work plans and 

assignments to prepare WG responses for ISC Plenary review in July 2013; and (3) to discuss 

Chinese fishery data for north Pacific albacore with Chinese scientists. Matters related to the 

future work plans for the WG and the next stock assessment cycle, beginning in the fall of 2013, 

were also included on the agenda for this workshop. During the workshop, SWFSC researchers 

presented their work on understanding the influences on the observed population scaling of the 

previous north Pacific albacore stock assessment model.

Bluefin Tuna Stock Assessment and Research – Pacific bluefin tuna was historically 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. Nevertheless, there remains an important commercial fishery for Pacific 

bluefin tuna in Mexican waters. In November 2012, SWFSC researchers participated in the stock 

assessment of Pacific bluefin tuna as members of the ISC Pacific Bluefin Tuna Working Group 

(PBFWG).The assessment was conducted using fishery data through 2011 and a seasonal, 

length-based, age-structured Stock Synthesis (SS3) model. Based on this assessment, the Pacific 

bluefin tuna stock is considered to be overfished and overfishing continues to occur. 

A total of 14 fisheries were defined for use in the stock assessment model based on country/gear 

stratification. Quarterly observations of catch and size composition (when available) were input 

into the model to describe the removal processes. Annual estimates of standardized catch per unit 

effort (CPUE) from the Japanese distant water and coastal longline, Taiwanese longline, and 

Japanese troll fleets were used as measures of the population’s relative abundance. Life history 

parameters included a length-at-age relationship from otolith-derived ages and natural mortality 

estimates from a tag-recapture study. The assessment model was fit to the input data in a 

likelihood-based statistical framework. 

The working group recognized uncertainties in the standardized CPUE series, weighting of data, 

and the methods used to estimate selectivity patterns. The influences of these uncertainties on 

stock dynamics were considered using alternative models and characterized by 20 trial runs. 

Extensive model runs were conducted using alternative data weightings and structural 

assumptions. While no single model provided a good fit to all sources of data that were 

considered reliable, the key model results from each model generally agreed. All plausible 

models depicted large long-term fluctuations in spawning stock biomass (SSB) and an 

overexploited stock that has been declining for over a decade. Model estimates of current 

biomass are at or near the lowest level; however, there is no evidence of reduced recruitment.

The WG agreed to use a representative run (Run 2) to determine stock status and provide 
5

management advice, acknowledging that while it represents the general conclusions above, the 

model was unable to reconcile all key data sources.

The representative run indicated that the 2010 levels (most current) of stock biomass (age 0+) as 

well as SSB were 53,216 mt and 22,606 mt, respectively. The recent 5-year average level of 

recruitment (calendar years 2006-2010) was 15.6 million fish. Estimated age-specific fishing 

mortalities on the stock in the recent period (2007-2009) relative to 2002-2004 (the base period 

for the current WCPFC conservation and management measure 2010-04) show 4%,17%, 8%, 

41% and 10% increases for ages 0, 1, 2, 3 and 4+, respectively. Although no target or limit 

reference points have been established for the Pacific bluefin tuna stock under the auspices of the 

WCPFC and IATTC, the current F (average 2007-2009) is above all reasonable target and limit 

biological reference points (BRPs), indicating overfishing of the population.

Shark Stock Assessments– SWSFC staff provide scientific advice on the stock status of pelagic 

sharks to domestic and international (RFMOs) fishery management organizations. 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 SWR began a multiyear effort 

with collaborators at Centro de Investigación Científica y de Educación Superior de Ensenada 

(CICESE), led by Dr. Oscar Sosa-Nishizaki, to coordinate artisanal fish camp monitoring and 

sampling in Baja California, Mexico, and help advance cooperative stock assessment efforts with 

Mexico, U.S., and IATTC scientists. CICESE scientists are conducting data collection for 

common thresher, blue, and shortfin mako sharks at fish camps throughout Baja California. The 

2012 sampling effort was completed in early 2013.The 2012 sampling was extensive and now 

supplements a time series begun as part of an earlier collaboration with investigators at Scripps 

Institution of Oceanography (SIO) and CICESE. As a result of the new sampling program, 

fishery data for pelagic sharks now includes some size and sex sampling as well as several years 

of species-specific catch information. The data collected thus far have already been used to 

develop historic and recent time series catch information for common thresher, blue, and shortfin 

mako sharks.

In 2012, shark assessment effort was focused on conducting the first ISC SHARKWG stock 

assessment of north Pacific blue shark. The assessment is on track to be completed in time for 

review by the ISC Plenary in July. The assessment is being conducted with a Bayesian Surplus 

Production model using compiled estimated catch data for most North Pacific nations including 

Canada, China, Chinese Taipei, Japan, Korea, Mexico, and the U.S., as well as some estimated 

catch contributed by IATTC for purse-seine vessels operating in the IATTC Convention area, 

and non-ISC member longline catch in the WCPFC Convention area contributed by SPC.

Preliminary modeling with an age-structured model will also be conducted. For Mexico catch, 
6

the species composition data collected through the sampling program described above 

contributed to an analysis of estimated blue shark catch for use in the assessment (SosaNishizaki, 2013).

II. SUPPORTING PACIFIC FISHERY MANAGEMENT COUNCIL ACTIVITIES

SWFSC scientists Stephen Stohs and Suzanne Kohin continued serving on the Highly Migratory 

Species Management Team (HMSMT) of the Pacific Fishery Management Council (PFMC) over 

the past year. Stohs continued to serve as vice chair after having served as chair of the HMSMT 

from April 2009 through January 2012. Center scientist Tim Sippel is scheduled to replace 

Kohin on the HMSMT beginning with the June 2013 Council meeting.

The team met several times in 2012 and early 2013 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 

recommendations on international HMS fishery management issues to the U.S. delegations of the 

WCPFC and IATTC, including Council recommendations to the WCPFC Northern Committee 

(NC) delegation on the adoption of biological reference points under the proposed management 

framework for North Pacific albacore tuna; (2) presenting a proposal to the Highly Migratory 

Species Advisory Subpanel (HMSAS) to develop a decision template for managing the U.S. west 

coast commercial albacore fishery in case a future international RFMO management measure 

requires a domestic management response; (3) reporting at the March 2013 Council meeting on 

potential changes to the closure dates for, and/or the southern boundary of, the Pacific 

Leatherback Conservation Area (PLCA) and the next steps for establishing hard take caps for 

Endangered Species Act-listed sea turtles in the large-mesh drift gillnet fishery to mitigate 

bycatch impacts; and (4) preparing the 2012 Stock Assessment and Fishery Evaluation (SAFE) 

Report and planning for the 2013 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 

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 the biological data 
7

from albacore fishing vessels when they unload their catches in coastal ports. In recent years, 

with AFRF support, fishermen onboard two to five vessels have also collected biological data 

during selected fishing trips, which augment the size data collected through the port sampling 

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

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 801 archival tags and 43 dummy tags were

deployed. Two tagging trips were conducted during 2012 aboard the chartered F/V Royal Dawn.

The first trip occurred off Oregon, 5-12 October, during which 56 tags were deployed, and the 

second was off central California, 1-7 November, when an additional 25 tags were deployed.

Plans are being made to similarly deploy over 100 tags during the 2013 season.

During 2012, one recapture was reported by an angler on a recreational trip out of Astoria, 

Oregon. The recaptured fish was at liberty just over one year. All the detailed tag data were 

recovered. The juvenile albacore was tagged in August 2011 off Oregon. Over the following 

year, the fish migrated out into the central-north Pacific transition zone reaching roughly 180° in 

late April before turning back toward the North America coast. The movement pattern and 

timing were similar to several other recovered juvenile albacore tagged on the U.S. commercial 

troll fishing grounds off Oregon. This is one of 5 migration patterns described so far from 23 

albacore tagged and recaptured in the eastern Pacific waters off the U.S and Mexico.

Because of the broad range of movement patterns and behaviors recorded by the first 23 

recoveries, 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. In 2010, 

the SWFSC purchased four mini pop-off satellite archival (mini-PSAT) tags to launch a pilot 

project to deploy tags on adult albacore that are caught near Hawaii in an artisanal handline 

fishery. The group is collaborating with researchers from the SPC who have contributed two

mini-PSATs in order to help test the use of the new attachment anchors on albacore for potential 

use on south Pacific albacore. Albacore are some of the smaller tunas and their flesh and skin is 

soft relative to other tuna species that have carried these types of tags for up to one year.

During August 2012, a cooperating fisherman deployed three of the mini-PSATs on handlinecaught albacore ranging from 102 to 114 cm FL. They were all rigged with a standard dart 

anchor, and two of the tags popped off prematurely after only two weeks. The third tag has not 

yet reported, but was programmed for 350 days. Plans have been made to continue the effort 

during the 2013 season in hopes of getting longer deployments with a newly designed loop type 

of attachment. 

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 

collecting biological samples of otoliths, muscle, liver DNA fin biopsies, and stomachs through a 

cooperative biological sampling program along the U.S. West Coast. In addition, otoliths have 

been acquired from the central and western Pacific, in collaboration with Japanese scientists.
8

Sample collection is ongoing and supports the ISC’s recent 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.

Tunas in the EPO, including the waters off the U.S. and Mexico, support substantial commercial 

and recreational fisheries and are also important components of the local food web. To better 

understand their basic biology and ecological role in the EPO, the SWFSC and the Sportfishing 

Association of California initiated a biological sampling program in 2007 to collect data on tuna 

and other HMS. While initially the program was focused in the Southern California Bight (SCB), 

the program was expanded in 2009 to the northeast Pacific Ocean where commercial fishermen 

collected 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, samples 

from albacore, Pacific bluefin tuna, yellowfin tuna (Thunnus albacares), skipjack (Katsuwonus 

pelamis), yellowtail (Seriola lalandi), opah (Lampris guttatas) and dorado (Coryphaena 

hippurus) were collected (Table 2) from collaborative efforts with the commercial passenger 

fishing vessels (CPFV), the commercial albacore troll and pole-and-line fleet, recreational 

anglers based out of San Diego, along with SWFSC research cruises. 

Table 2. 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 to provide an integrated picture of foraging and migration 

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

(3) radioanalysis of radiocesium found in the muscle tissue of Pacific bluefin tuna exposed to 

waters containing radionuclides discharged from the failed Fukushima nuclear power plant in 

Japan, (4) using otolith microchemistry to determine the dynamics and stock structure of 

albacore and bluefin 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 and other mesopelagic predators. 
9

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 in who is eating whom is critical to 

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

California Current, SWFSC scientists have been investigating the foraging ecology of a range of 

species since 1999.

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

species and years. Preliminary analysis of stomach contents shows that tunas forage almost 

exclusively on juvenile fish and squid. For albacore, the average standard length of fish prey was 

5.3 cm, and for the squid, lower rostral length was 0.34 cm. A comparison across years for 

albacore reveals some interesting differences in the percentage of stomachs in which prey are 

found. In 2007, small epipelagic teleosts comprised the dominant prey category by frequency of 

occurrence (89%), followed by cephalopods (18%) and crustaceans (16%). In 2008, a shift in 

prey composition occurred with cephalopods (Abraliopsis felis), California market squid (Loligo 

opalescens), and jumbo squid (Dosidicus gigas) playing a more important role by frequency of 

occurrence (86%), followed by teleosts (84%), and crustaceans (56%). The composition of the 

teleosts also shifted between years. In 2007, 80% of the stomachs contained northern anchovies 

(Engraulis mordax), whereas in 2008 this dropped to only 2%. Juvenile Sebastes spp., 

myctophids, and jack mackerel (Trachurus symmetricus) made up the majority of teleost prey in 

2008. Further analysis is needed to determine the potential reasons for the shift in prey between 

years. During the period fish were sampled, anecdotal data from the commercial fishery for 

California market squid corroborates that squid availability has been increasing since 2008. 

Results from 2009 appear to be similar to 2008, with much of the diet comprised by crustaceans, 

teleosts, and cephalopod typically associated with the deep scattering layer (DSL). In 2010, 

epipelagic teleosts dominated the diet of albacore in the SCB with Pacific mackerel and saury 

making up 50% of the diet by frequency of occurrence. Samples collected during 2011 and 2012 

are currently being analyzed. Overall, analysis shows that prey composition can vary 

dramatically and will likely be linked to oceanographic conditions. 

Regional diet differences between albacore caught off Washington, Oregon, and southern 

California are also being explored. Crustaceans and cephalopods comprise a larger portion of the 

diet for albacore caught in Washington and Oregon. Results will be used to explore differences 

in migration patterns and growth rates between the two different regions to assist with stock 

structure analysis and management. Diet analysis of Pacific bluefin and yellowfin is currently 

under way and will be compared to albacore. Preliminary results suggest tunas in the SCB 

exhibit different foraging strategies with yellowfin and albacore foraging on epipelagic prey in 

larger numbers than bluefin. 

Stable isotope analyses of muscle tissues are currently being used to help characterize trophic 

relationships between prey and predators in the SCB. The California Current is known as a 

highly productive eastern boundary current, and researchers have suggested that these are waspwaist systems with low diversity at mid-trophic levels. This low diversity of prey for top 

predators has been linked to dramatic bottom-up effects associated with variability in mid-level 

prey species. Estimates of trophic level are being used to evaluate links between prey and 
10

predators in regards to wasp-waist dynamics. Results suggest predator-prey relationships in the 

SCB are more complex than would be predicted in a wasp-waist system, with a high degree of 

diversity and omnivory in predator diets. Consequently, predators in the SCB should be more 

resilient to prey variability than would be suggested under a wasp-waist model. 

In addition to studying the highly migratory large pelagic fish themselves, the predators can be 

used as biological samplers and provide a snapshot of the forage base. Linking changes to 

environmental factors that influence the recruitment, distribution, and resulting availability of 

forage prey types may reveal insight about habitat quality and migration patterns of HMS in the 

California Current. The result of sampling over multiple years gives scientists insight into the 

impacts of climate variability on local prey and predators, which will help predict the impacts of 

climate change in the California Current ecosystem.

Albacore Age and Growth –During 2012, a manuscript was finalized describing the results of 

ageing 486 albacore of a wide size range collected throughout the North Pacific Ocean. The 

growth model is considered an improvement over models previously published and used in stock 

assessments of north Pacific albacore. Simulations demonstrated that use of the otolith data and 

the fitted revised growth curve had a dramatic result on the 2011 stock assessment. Of particular 

importance is the L∞ parameter, which can be thought of as representing the average size of the 

oldest fish in the population. The growth model used in previous stock assessments had a 

significantly larger L∞, which implied that fish of a larger size should be present in the 

population. Since these large fish were not present in the catch, the assessment results showed 

that the stock experienced high fishing mortality such that the fish did not survive long enough to 

reach these large sizes.

One of the other findings of the albacore age and growth study was that albacore of the same age 

had slightly different lengths depending upon where they were collected, suggesting that there 

may be regional differences in growth. The next phase of the collaborative work is to try to 

further examine this pattern in addition to studying the difference in growth rates between sexes.

Collaboration under the ISC will continue during a winter 2013/2014 ISC-sponsored albacore 

and bluefin tuna ageing workshop.

Radioanalysis of Radiocesium Found in the Muscle Tissue of Pacific Bluefin Tuna – The 

detection of Fukushima-derived radionuclides in Pacific bluefin tuna (PBF) that crossed the 

Pacific Ocean to the California Current Large Marine Ecosystem (CCLME) in 2011 presented 

the potential to use radiocesium as a tracer in highly migratory species. This tracer requires that 

all western Pacific Ocean emigrants acquire the Cs134 signal, a radioisotope undetectable in 

Pacific biota prior to the Fukushima accident in 2011. Working collaboratively with scientists at 

Stanford University and Stony Brook University, FRD scientists tested the efficacy of the 

radiocesium tracer by measuring Cs134 and Cs137 in Pacific bluefin tuna (n = 50) caught in the 

CCLME in 2012, more than a year after the Fukushima accident. All small Pacific bluefin tuna

(n = 28; recent migrants from Japan) had Cs134 (0.7 ± 0.2 Bq kg−1) and elevated Cs137 (2.0 ± 

0.5 Bq kg−1) in their white muscle tissue. Most larger, older fish, presumed to have remained in 

the CCLME since the prior summer (n = 22), had no Cs134 and only background levels of 

Cs137, showing that one year in the CCLME is sufficient for Cs134 and Cs137 values in Pacific 

bluefin tuna to reach pre-Fukushima levels. Radiocesium concentrations in 2012 Pacific bluefin 
11

tuna were less than half those from 2011, with levels during both years well below safety 

thresholds for public health. Detection of Cs134 in all recent migrant Pacific bluefin tuna

supports the use of radiocesium as a tracer in migratory animals in 2012. 

Microchemistry Analysis of Bluefin and Albacore Otoliths– Otolith chemistry is one approach

used 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 composition in whole otoliths collected in the WCPO and EPO over 

several age classes of fish. Comparison of young of the year, juvenile, and adult bluefin otoliths 

will be used to characterize the water chemistry for different collection regions and known 

spawning grounds. Results will help determine how many Pacific bluefin migrate to the 

California Current and to characterize the dynamics of movement in the Pacific Ocean, data 

which is critical to effective management. In 2012, researchers began collecting young of the 

year bluefin from spawning area waters near Japan. 

For albacore, the purpose of the study is to determine whether there are two substocks of 

albacore that utilize the waters of the California Current Large Marine Ecosystem. Based on 

differences in growth rates and movement patterns, it is hypothesized that albacore caught in 

southern California and Mexico waters comprise a separate substock from those caught on the 

commercial fishing grounds of Oregon and Washington with relatively little mixing during their 

sub-adult years. This study began in 2011 and is ongoing. Preliminary analyses show that 

significant differences exist in otolith chemistry from ages 2-4 fish collected between the two 

regions and overall cross-validated classification success was 100%, with age-specific 

comparisons exceeding 90% success. Otolith delta18O was significantly enriched in the southern 

region relative to the northern region, similar to reported seawater delta18O differences. In 

addition, significantly higher concentrations of sodium and magnesium, combined with lower 

phosphorus in otoliths from fish collected in the southern region, is consistent with regional 

physicochemical conditions (i.e., salinity, temperature, phosphate). These findings support 

previous studies that have shown limited regional mixing of albacore in the EPO and provide life 

history information useful for management of North Pacific albacore.

Albacore Distribution and Environmental Effects– SWFSC scientists, in collaboration with 

Canada’s Department of Fisheries and Oceans (DFO) scientists, received funding last year 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”. Some preliminary results were recently presented at the ISC Albacore 

Working Group meeting in Shanghai (19-25 March 2013) and published in a working paper 

titled "Environmental influences on albacore tuna (Thunnus alalunga) distribution in the coastal 

and open oceans of the Northeast Pacific: preliminary results from boosted regression trees 

models". Boosted regression trees models were used to examine the link between albacore 

distribution and a range of environmental variables, such as temperature, sea surface heights, 

chlorophyll-a, etc. Once the study is more comprehensive, the analyses may be integrated into 

population dynamics models to help improve albacore management in the face of environmental 

changes.
12

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 2012 

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

International Billfish Angler Survey– In 2012, SWFSC researchers summarized the results from 

the 2011 Billfish Angler Survey. Initiated in 1969, the survey now provides a 43-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 survey covering the 

entire Pacific. The CPUE, measured in number of billfish caught per angler fishing day, was 0.44 

across all reporting areas, in 2011. This was slightly lower than that reported in 2010 (0.46) and 

well below the most recent 5-year average (2007-2011; 0.58 CPUE). The CPUEs reported from 

most individual locations did not fluctuate much from the previous year; however, an increase 

was reported from off the coasts of both Hawaii and Baja California, Mexico. Conversely, the 

billfish CPUE reported off Southern California decreased and remains at a historic low.

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 1). Blue marlin CPUE off Hawaii was 0.28, which 

was above the annual average, however off Baja California, Mexico, it dropped to 0.03, the 

lowest reported value since 1981. Striped marlin CPUE off Southern California was the lowest 

on record (0.02). Striped marlin CPUE did, however, increase in all areas reported throughout 

Mexico. Not shown was an increase in striped marlin CPUE off Baja California from 0.45 in 

2010 to 0.54 in 2011. Despite this increase, 0.54 is slightly below the annual average reported 

from this area (0.59). Sailfish CPUE reported throughout Mexico was 0.18, the second lowest 

value in more than a decade.
13

Figure 1. CPUE as catch-per-angler-day is shown from 1969 through 2011 for Pacific blue 

marlin, striped marlin, Pacific sailfish, and black marlin. 
14

Recreational Billfish Tagging Program–2012 marks the 50th 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 CDFW, over 76,000 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 902 tags were released on billfish in 2011 through the efforts of a combination of over 700 

anglers and 127 captains. This was an increase of over 100% in the number of tags released in 

2010. A total of 846 tags were deployed on billfish off Hawaii, representing over 90% of the total 

tagging effort. The majority of these tags (596) were released on blue marlin. Nearly all billfish 

species were tagged in greater percentages compared to the previous year. The most substantial 

difference was a 300% increase in the number of striped marlin tagged. Table 3 shows the 

tagging effort for 2011 and tag recoveries throughout the program’s history. The data include 

releases made by SWFSC scientists during research cruises.
15

Table 3.Summary of fish tagged through the Billfish Tagging Program in 2011 with releases and 

recoveries for 1963–2011, including SWFSC’s ongoing research tagging.

SPECIES NAME RELEASE 

2011

RELEASE 

TOTAL

RETURN 

TOTAL

RETURN 

RATE (%)

Striped Marlin 178 23112 347 1.50

Pacific Blue Marlin 608 11382 93 0.82

Sailfish 21 9222 49 0.53

Billfish, unidentified 0 4386 6 0.14

Black Marlin 3 3390 69 2.04

Shortfin Mako Shark 64 5486 313 5.71

Shortbill Spearfish 91 2236 2 0.09

Common Thresher Shark 407 1872 90 4.81

Blue Shark 301 9609 171 1.78

Albacore Tuna 90 849 29 3.42

Broadbill Swordfish 1 522 17 3.26

Yellowfin Tuna 0 349 25 7.16

Skipjack Tuna 0 100 2 2.00

Bigeye Tuna 0 79 2 2.53

Bluefin Tuna 0 58 8 13.79

Hammerhead Shark 0 62 2 3.23

Bronze Whaler Shark 0 52 3 5.77

Leopard Shark 1 224 12 5.36

Whitetip Shark 0 44 1 2.27

Atlantic Blue Marlin 0 43 0 0.00

Soupfin Shark 0 40 1 2.50

Salmon Shark 0 36 3 8.33

Silky Shark 0 24 1 4.17

White Marlin 0 13 1 7.69

Basking Shark 0 65 0 0.00

Longbill Spearfish 0 3 0 0.00

Other Tunas 0 21 1 4.76

All Others 4 2832 124 4.38

TOTAL 1,769 76,111 1372 1.80

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 Protected Resources Division (PRD) and the NOAA SWR 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. The first step in this 
16

process was a stakeholder workshop conducted in May 2008. A report detailing the content and 

discussions of the workshop was published as an Administrative Report in 2009 (Benson et al., 

2009). While a large organized initiative has yet to be established, FRD and PRD 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 Use of the PLCA – To investigate the 

possibility of predicting occurrence and behavior of leatherback turtles in the PLCA using 

satellite telemetry data, SWFSC scientists have been modeling the assumed behavior and 

occurrence of the tagged turtles in the PLCA using a suite of oceanographic and environmental 

variables. Satellite telemetry data of leatherback turtles in the PLCA were compiled from 41 

individuals. Daily locations of these turtles were estimated using a statistical movement model.

The movement model also provided the probability of foraging/transit behavior for each 

estimated location. Based on the results of a previous study, seven environmental variables were 

selected to model turtles’ behavior using the statistical method of random forests and boosted 

regression trees. The variables in the model are sea-surface temperature, chlorophyll 

concentrations, latitude, longitude, day-of-the-year, eddy kinetic energy, and depth. Boosted 

regression trees and random forests are non-parametric regression/categorization analytical tools 

that use multiple predictor variables to build mathematical prediction models for a response 

variable.

A preliminary analysis indicated that all seven variables were useful in predicting the probability 

of foraging and that more than 70% of the variability in the dependent variable (probability of 

possible foraging) can be explained by the models. Seasonality of their behavior was indicated 

by the importance of the day-of-the-year variable in the prediction model. The output of the 

models will be used to develop probability surfaces of turtles’ behavior for given environmental 

conditions and to identify the temporal and spatial use of the PLCA by leatherback turtles. This 

information can be used to identify the sites of greatest leatherback bycatch vulnerability.

Deep-set Longline Survey to Investigate Swordfish-Sea Turtle Habitat Separation – In the fall 

of 2011 and 2012, using NOAA cooperative research funds and funds awarded by Collaborative 

Fisheries Research (CFR) West, SWFSC scientists conducted 10-day and 16-day deep-set 

pelagic longline cruises off Central and Southern California. The 2012 research cruise was 

conducted between 23 October and 7 November, 2012. The objectives of the cruises were 1) to 

experiment with targeting swordfish deep during the day below the epipelagic waters where sea 

turtles live, and 2) to deploy electronic tags on swordfish to examine their fine scale behavior in 

an area where they overlap with turtles .In collaboration with the fishermen aboard the F/V

Ventura II, the team worked on methods for setting gear deep during the day. A total of 28 sets 

were made during the two cruises. For each set, approximately 12 miles of monofilament 

mainline was set with an average of 288 branchlines, 36 feet in length. 18/0 C style hooks were 

baited with whole mackerel or sardine. Time-depth recorders were used to document hook depth 

across all sets and hook numbers. Fishing depth was determined by the maximum depth recorded 

per deployment. In 2012, fishing depths ranged from 107 m to 460 m. The average minimum 

depth per set was 139 m (± 19 m SD); average max depth per set was 350 m (± 55 m).
17

A range of marketable species were caught including swordfish, tunas and opah, and satellite 

tags were deployed on swordfish and opah. One common mola (Mola mola) and a number of 

blue sharks were also caught, nearly all of which were released alive. Unfortunately, in 2011, 

weather restricted most effort to more southern waters, south of Point Conception. In 2012, 

waters shifted to winter conditions earlier than usual and overall fishing was very poor at that 

time for the drift gillnet fleet and the experiment. Some funding has been received to continue 

the experiments during 2013 with the goals of 1) further developing the deep-set fishing 

approach, 2) better characterizing the potential catch composition, 3) characterizing catch in 

relation to depth and oceanography including the deep scattering layer, 4) deploying electronic 

tags on swordfish and other potential target species, and 5) assessing the economic value of the 

catch. Based on the results to date, the fishing technique shows promise for catching swordfish 

and other marketable species at depths below the turtle habitat.

Swordfish Deep-Set Buoy Gear Research – The SWR and Pfleger Institute of Environmental 

Research (PIER) are conducting research using a deep-set vertical line configuration to target 

swordfish within the California exclusive economic zone. To minimize interactions with species 

of concern, the deep-set gear was designed to fish below the thermocline (270 to 350m) during 

daylight hours. Gear specifications include the use of ten individual sets of deep-set gear which 

consist of two-8m gangions with 18/0 circle hooks. All ten sets are soaked for four consecutive 

hours and baited with both mackerel and squid. Gear trials were conducted during the 2011 and 

2012 swordfish seasons off the coast of southern California using both research and cooperative 

fisher vessels. A total of 54 sets were completed resulting in the capture of 15 swordfish. No 

interactions with species of concern were recorded across all 4,320 hook-hours. Additional nontarget catch included: bigeye thresher sharks, Alopias superciliosus (7), opah (2), blue sharks (2), 

and common thresher shark, Alopias vulpinus (1).These data suggest that deep-set buoy gear can 

selectively be used to target swordfish in deep waters during the day off southern California.

Additional trials that investigate alternative configurations (i.e., gear modification, bait 

presentation) and reduce the probability of lost gear are currently underway.

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

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

with other pelagic predators. Over the past year, 53 swordfish stomachs from the 2011 and 2012 

seasons were analyzed. The stomachs were predominantly provided through the CADGN 

observer program. The results of these analyzed stomachs show that the most frequently 

encountered prey species (F=Frequency of prey occurrence) were: Gonatopsis borealis squid 

(F=32), market squid (F=27), duckbill barracudina (Magnisudis atlantica) (F=27), and Pacific 

hake (Merluccius productus) (F=24). These very preliminary results show a possible shift in 

feeding trends. In past seasons, jumbo squid was frequently found in the stomachs of swordfish, 

while current data indicates a decrease in the importance of jumbo squid.

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 has 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 

conducted, especially in the SCB. For example, there is little data on foraging ecology, size 
18

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 2012 a total of 67 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. Thirty-nine opah were caught during the 2012 cruise, 

14 opah were caught in 2011, 16 in 2010, and 8 in 2009. Prior to 2009, only one other opah had 

been recorded during a longline survey cruise, in June 2000. The apparent increase in opah 

availability provided an opportunity to begin collecting biological samples and data for a species 

which little is known about. This apparent increase is likely influenced by many factors 

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

conduct the survey, the 171-foot-long NOAA ship 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 may have impacted catch 

rates. Further analyses of the variability in survey catch as well as examining opah catch using 

logbooks from the CADGN and recreational sport fishing 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 68 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 (L. opalescens, Gonatus spp., 

D. gigas) making up the most important prey items 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 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 diets between 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 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 in 

the SCB (n=4) and off central California (n=4). All tags were deployed during research longline 

cruises conducted by SWFSC scientists. The PAT tags were programed to collect light level, 

depth, and temperature data for 240 days. Four tags popped off prematurely. Preliminary analysis 

suggests opah in the California Current exhibit similar behavior as those observed near Hawaii, 

with diel patterns moving between depths of ~ 250 m during the day to ~50 m at night. Unlike 
19

most diel vertical migrators, opah appear to remain below the mixed layer. 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 in 

March off Mexico. One tag deployed off central California in late October 2011 popped up 

northeast of Hawaii in June.

Gill Morphology and Regional Heterothermy – In 2011, three sets of opah gills were preserved 

in 10% formalin and transported to the SWFSC for examination and comparison to other pelagic 

fishes. Determination of gill surface area and associated dimensions allows for insights into both 

the metabolic requirements and dissolved oxygen concentrations experienced by this species. In 

addition to a number of morphometric similarities with other pelagic fishes, opah gills show 

extensive fusion of the gill filaments, a characteristic previously documented only in highperformance teleosts (tunas of the genus Thunnus, the wahoo, Acanthocybium solandri, and 

billfishes). The occurrence of filament fusions in opah suggests a role other than that proposed 

for the high-performance fishes, which use gill fusions to maintain optimal gill orientation and 

reduce branchial flow rates during ram ventilation. Opah are not thought to be obligate ram 

ventilators, but like tunas are active predators.

A number of opah were collected on the 2012 shark cruise and deep-set long line cruise for 

determination of blood properties, gill 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. Researchers 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.

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 (A. 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 through various surveys and tagging studies. This information is provided to 

international, national, and regional fisheries conservation and management bodies having 
20

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. Although the blue shark is targeted in Mexico, it has little market importance in the 

U.S. but 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 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.

Efforts to determine abundance trends from commercial fishery data have been complicated by 

changes in regulations, targeted areas, and fishing methods over time. These changes have 

resulted in inconsistent capture rates and catch distributions that are difficult to interpret.

Therefore, fishery-independent sampling was initiated, with slightly different survey strategies 

required depending upon the species. 

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.

For mako sharks, the surveys have enabled SWFSC researchers to obtain a valuable abundance 

index, which can be linked to a historical time series of logbook and landings data from a former 

experimental shortfin mako longline fishery in the SCB that occurred during 1988-1991.

Abundance trend information was also obtained for the blue shark, which is compared to that 

obtained by observers of the CADGN and U.S. and Japanese high-seas longline fisheries.

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

Initial studies demonstrated that neonate threshers are rarely encountered in waters deeper than 

about 90 m. Therefore, surveys are conducted in the shallower nearshore waters between Point 

Conception, California and the U.S.-Mexico border. The primary purpose of the surveys is to 

produce a relative abundance index for the West Coast population by periodically sampling 0-

year pups (neonates) in their nursery grounds off Southern California. Representative areas were 

initially identified and are now sampled annually. The resulting neonate index of abundance 

should mirror adult abundance due to the tight relationship between the adult population and 

recruitment in K-selected species such as sharks. This study complements the fishery-dependent 

data available through the nearshore small mesh net fisheries and offshore CADGN fishery to 

provide measures of relative abundance of common thresher sharks for stock assessment models. 

Juvenile Mako and Blue Shark Survey– In 2012, the SWFSC researchers conducted the

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

survey was completed between 20 June and 19 July 2012. Working aboard F/V Ventura II, a 

team of scientists and volunteers fished a total of 5,592 hooks during 28 daytime sets within 

seven focal areas of the SCB. The survey catch totaled 151 shortfin makos, 26 blue sharks, 16 

pelagic rays (Pteroplatytrygon violacea), and 4 opah. The preliminary data indicate that the 

nominal survey catch rate was 0.53 per 100 hook-hours for shortfin mako and 0.15 per 100 hookhours for blue sharks. The mako shark nominal CPUE was slightly higher than the previous year.
21

However, there is a declining trend in nominal CPUE for both species over the time series of the 

survey.

Additional research projects were also conducted during the shark survey research cruise. Six 

deep sets were completed targeting opah and swordfish during daytime hours. A longline shooter 

was used to deploy the gear between 200 and 300 meters depth over a horizontal distance 

ranging from five to ten miles. An average 170 branchlines, each 38 feet in length, were 

deployed during these sets. Four surface sets were also conducted targeting opah. Additionally, a 

total of 18 sets were conducted as part of an experiment to examine differences in catch rate, 

catch composition, and survivability between circle-type hooks and J-type hooks. Preliminary 

results indicated no differences.

In total, 56 longline sets including survey sets were completed. A total of 423 animals were 

caught; ancillary sampling resulted in 262 captures. Most animals were brought onboard, 

measured, tagged, and sampled for DNA biopsies before they were released. Spaghetti tags were 

released on 338 sharks to allow for movement and stock structure data. A total of 387 DNA 

samples were collected, including samples from 254 shortfin mako, 92 blue shark, 29 opah, 9 

pelagic rays and 3 common thresher.

Neonate Common Thresher Shark Survey – In 2012, the SWFSC team conducted the survey 

aboard the F/V Outer Banks. Fifty longline sets were made in relatively shallow, nearshore 

waters and a total of 5,000 hooks were fished during the 18-day cruise. A total of 367 fish 

including a range of species were sampled during the survey, 282 were common thresher sharks.

Most of these sharks were tagged with a combination of conventional tags for movement and 

stock structure data and oxytetracycline (OTC) paired with plastic dorsal tags with information 

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

growth studies. In addition, a pop-off archival GPS tag was released on a 151-cm female 

common thresher. 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.

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

common thresher sharks per 100 hook-hours. This is a drop in CPUE from 2011 when the 

nominal catch rate was 5.57. 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 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 fish, primarily blue, shortfin 

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

years, shark tag deployments have been carried out in collaboration with Mexican colleagues at 

CICESE, Canadian colleagues at the Department of Fisheries and Oceans (DFO) Pacific 

Biological Station in Nanaimo, British Columbia, and the TOPP program (www.topp.org). The 

goals of the projects are to document and compare the movements and behaviors of these species 
22

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 subsequently to better 

understand how populations might shift in response to changes in environmental conditions on 

short or long time scales. 

In 2012, a number of large pelagic fish were deployed with electronic tags in support of several 

collaborative projects. Five (5) shortfin mako sharks, 5 blue sharks, and 1 common thresher were 

tagged with either SPOT tags or towed GPS tags. Three (3) mako sharks, 2 blue sharks, and 6 

opah were released with pop-off archival tags. In addition, 5 mako sharks were released with 

acoustic tracking tags. 

SPOT tags continue to provide excellent information on the movements of blue and mako 

sharks. Data have been collected data for a decade for both species, which allows continued 

monitoring of the horizontal movement patterns on many different time scales. More recently, 

the focus is tagging of larger animals, for which there is less information. Historical data shows 

that the larger animals retain the tag longer and provide us with longer tracks. The average size 

of blue sharks (n=5) tagged with a SPOT in 2012 was 229 cm. Two of the five blue sharks were 

tracked for close to 200 days (Figure 2). Combined data from many years suggest that both sexes 

spend considerable time in the California Current, with the females possibly extending farther 

north and south. When offshore, generally, the females move south into the subtropical 

convergence zone, whereas the males make more westerly migrations. These patterns do vary 

though, and the two male blue sharks illustrated in Figure 2 demonstrated behavior more 

common to what has been observed for females. The track of the larger shark looks as though he 

may have been heading back to the California Current, which has been documented for many of 

the longer blue shark tracks. Both habitat separation by sex, and site fidelity have implications 

for the management of blue shark populations. For example, fidelity to specific areas is 

increasingly recognized in fish from swordfish to salmon sharks (Lamna ditropis) and raises the 

potential for local depletion where fisheries exist. 
23

Figure 2.Tracks from two blue sharks spanning seven months and showing similar movement 

patterns into subtropical waters (left 221 cm FL male, right 241 cm FL male).

For mako sharks, three tags were still transmitting in early 2013 (Figure 3).All three sharks were 

deployed with SPOT tags in July, 2012. Tracking success has been very good for mako sharks, 

as they generally provide longer duration tracks than blue sharks, allowing the opportunity to 

examine seasonal movement patterns and regional fidelity. The smallest shark of the three, the 

male, traveled the greatest distance latitudinally, ranging from 14 to 38o N.. The females both 

spent some time migrating south-westward, terminating near 120o W before returning to the 

coast on a similar path. All three sharks spent some time near or in San Sebastian Vizcaino Bay 

off Baja California, Mexico, which is an area of high use for makos based on combined data 

from several years. Additional analyses are needed to determine (1) how patterns link to sex and 

size, (2) what triggers the onset of migration, and (3) what characterizes the ultimate 

destinations. As with blue sharks, this type of regional site fidelity has important implications for 

management.
24

Figure 3.Tracks from three shortfin mako sharks showing nearly nine months of data for each and 

some similarities in movement patterns (left 167 cm FL male, center 173 cm FL female, right 241 

cm FL female).

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 aging methods for these three species based on band deposition periodicity determined 

using OTC. Our 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, 3,183 OTC-marked individuals have been released during 

juvenile shark surveys. Sharks tagged include 1,221 shortfin mako, 1,187 common thresher, 757 

blue, 15 silky (Carcharhinus falciformis), and 3 pelagic thresher sharks.

Oxytetracycline Age Validation of Juvenile Shortfin Makos –The results of OTC age validation 

of 29 juvenile shortfin mako sharks tagged with OTC in the Southern California Bight were 

recently published (Wells et al., 2013) and showed vertebral band pair deposition rates of two 

per year. The results of this study differ from two other studies on shortfin makos that used a 

direct age validation technique: one study validated a single band pair deposition rate in an 

estimated 18 year old shortfin mako shark tagged with OTC and recaptured in the Atlantic after 

one year at liberty; and the second used a bomb radiocarbon signal as a marker in 37 sharks 

collected in the Northwest Atlantic between 1950 and 1984 ranging in estimated ages of 1 to 31 

years. Age and growth in shortfin mako sharks continues to be uncertain because growth curves 

estimated from length-frequency analysis and tag-recapture methods tend to show faster growth 

rates than obtained from vertebral counts based on deposition of a single band pair per year.

Furthermore, this validation study applies to juvenile sharks in the northeast Pacific. This study 

raises questions about potential regional differences in band pair deposition rates or the 

possibility of an ontogenetic shift from a period of more rapid growth with two band pair 

deposition per year to slower growth and a switch to a band pair deposition rate of one per year.

In winter 2013-2014, the ISC plans to convene its second Shark Age and Growth Workshop 

during which participants hope to resolve some of the uncertainties regarding shortfin mako age 

and growth.

Oxytetracycline Age Validation of Juvenile Blue Sharks – The purpose of this study is to 
25

validate vertebral band counts of blue sharks tagged and recaptured in the northeast Pacific 

Ocean. OTC-labeled vertebrae of 13 blue sharks have been obtained from tag-recapture activities 

and processed to determine timing of centrum growth band deposition. Several methodologies 

were used to examine blue shark vertebrae and digital images of the whole vertebrae centrum 

were determined to be the best. OTC-tagging of the recaptured sharks occurred off southern 

California from 2007 to 2009, with time at liberty ranging from 22 to 473 days. For vertebrae 

samples used in this study, shark size at release ranged from 90 to 276 cm total length (TL).

OTC-marked vertebrae from at least 20 more sharks have been returned and will be processed to 

build upon this study. Results thus far from band counts of vertebrae distal to OTC marks 

indicate that a single band pair (one translucent and one opaque) is formed per year for blue 

sharks of the size range examined. These preliminary results corroborate annual deposition rates 

found in the only other OTC validation study for blue sharks and should aid in future blue shark 

age and growth studies in the Pacific Ocean.

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 these spatially 

overlapping species, stomach content analyses have been ongoing at the SWFSC 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. 

From March 2012-March 2013 a total of 91 stomachs of several species of pelagic sharks have 

been analyzed from fishing seasons 2011 and 2012. Current levels of analysis have allowed us to 

identify some of the most frequently encountered prey species. Shortfin mako stomachs (n=30) 

contained market squid (F=8), Pacific saury (F=8), and Pacific sardine (Sardinops sagax) (F=7).

Blue shark stomachs (n=7) contained Octopus squid (Octopoteuthis spp.) (F=4), market squid 

(F=4), and Gonatus spp. squid (F=4). Common thresher shark stomachs (n=44) contained market 

squid (F=21), Pacific mackerel (Scomber japonicus) (F=11), and Pacific sardine (F=11). Salmon 

shark stomachs (n=6) contained Pacific mackerel, duckbill barracudina, striped mullet (Mugil 

cephalus), unidentified rockfish, and market squid. Bigeye thresher stomachs (n=4) contained 

Pacific mackerel, market squid, and tunicates.

These very preliminary results already show a possible shift in feeding trends. In past seasons, 

jumbo squid were frequently found in the stomachs of examined predators, especially shortfin 

mako and blue shark (Preti et al. 2012), whereas current data indicate a decrease in the 

importance of jumbo squid to the diets of these species.

Data on shark foraging ecology were also used to develop a new approach for characterizing 

habitat use and improving understanding of ecological interactions. FRD scientists introduced a 

resampling method to indirectly estimate foraging habitat based on diet data and knowledge of 

prey habitat use. The method is unique in that, (1) it is based on resampling by bootstrapping, 

and (2) it does not require quantitative prey distribution information. For this study, scientists

combined diet data with qualitative prey distribution information for six different habitats 

segregated by depth and distance from shore. The combined data were organized into various 

matrices and resampled by bootstrapping to create an estimate of predator distribution based on 

prey habitat occupancy. This method indicates a significant difference in foraging habitat 
26

between predator species. Generally, blue sharks foraged more frequently in offshore habitats, 

threshers foraged mostly in nearshore epipelagic habitats, and shortfin makos foraged both nearand offshore in epi- and mesopelagic habitats. The flexibility of the new method should allow for 

wide application, adding to the suite of possible indirect techniques available to infer foraging 

habitat use. The results of this research are now under internal review. 

Algal Toxins in the Forage of Pelagic Sharks – In 2011, FRD scientists began to sample the 

stomach contents of several species to study algal toxins (domoic acid) in sharks. A blue shark 

contained 4172 ng/g of domoic acid in its stomach juices and its prey, a paper nautilus 

(Argonauta sp.), contained over 2000 ng/g. Three thresher shark stomachs with juices and prey 

also had high levels of the toxin, the highest being 1708 ng/g found in one thresher stomach with 

its prey of squid having a level exceeding 2000 ng/g.

These results confirm that the toxin is present in the food chain and can be transferred from the 

bottom up. Further studies are needed to document domoic acid in muscle and the potential 

implications of measured concentrations for shark and human health.

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 commercial fishery that catches the greatest number of each of these species. While 

thresher and mako sharks are landed, almost all blue sharks are discarded. Thresher and mako 

sharks are growing in popularity in regional recreational fisheries. 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 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 SWR 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 a 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 2011-2012 season, 12 blue sharks (100 to 200 cm FL, median 149 cm) had been 

tagged by fishery observers. Three of the 12 sharks were released in “good” condition while the 

remaining 9 were released in “fair” condition. Satellite tag records suggest that all animals 

survived the acute effects of capture in the CADGN fishery.

During the 2011-2012 season, fishery observers deployed three survivorship PAT (sPAT) tags, 

which are new, more economical tags, that record daily minimum and maximum depths and 
27

temperatures and are programmed to pop off if the tag exceeds a certain depth or remains at a 

constant depth for several days. These tags are effective for determining the fate of tagged fish.

Of the three sharks tagged (2 females of 134 and 162 cm FL, and one 161 cm FL male), two 

were in “poor” condition when released and one was considered in “fair” condition. Two of the

three sharks died immediately and the third one died after eight days. These results, combined 

with the results from the prior years, suggest that sharks that are released in “good” condition are 

likely to survive, whereas those released in “poor” condition are likely to die. The study will 

continue during the 2012 season when the final three tags are deployed on sharks in “fair” or 

“poor” condition. Work will continue on compiling the data on the condition of all sharks 

released in order to be able to apply the survivorship estimates to the discarded population more 

accurately. 

Thresher Sharks Released from the Recreational Fishery – Researchers from the SWFSC, 

SWR, and PIER are conducting a three-phase study to assess the post-release survival of thresher 

sharks caught by recreational anglers. During the first phase of the study, sharks were released 

after being 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, seven sharks died shortly after release 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). The results from all phases of 

this study will be used to estimate the survival rates and incorporate best fishing practices into 

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. A brochure on 

best practices for thresher shark fishing and handling was developed 

(http://www.pier.org/userdocs/images/images/flyers/BREP_thresher_brochure.pdf). 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 Gallery 

(http://www.nmfs.noaa.gov/gallery/videos/). A second video, highlighting phases two and three 

of the research effort, is currently under development by OMC and will be available for outreach 

events in the summer of 2013 and will be posted on the NOAA Fisheries website. 

Basking Shark Research Program– 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 individuals were observed off the U.S. West Coast in the early to mid1900s, sighting even a few individuals is now rare. Due to concern over basking shark 

populations along the West Coast, the basking shark was listed as endangered in Canada and as a 

Species of Concern in the United States in 2010. Given severe data gaps for this population, 

SWFSC scientists initiated a basking shark research program in 2010 to (1) mine existing data 

for additional biological information, (2) conduct an electronic tagging study, (3) improve 
28

international data collection, and (4) improve national sightings information by developing a 

sightings website and an education and outreach program centered around Monterey Bay, 

California.

This research program has progressed at a number of different levels. A dedicated website 

(http://swfsc.noaa.gov/baskingshark/), email (basking.shark@noaa.gov), and hotline (858-334-

2884) have been established as a part of a sightings network. A tri-national team was developed 

with colleagues in Canada and Mexico to coordinate research efforts.

During the past year, SWFSC scientists continued to monitor basking shark sightings in order to 

collect and analyze data on patterns of occurrence and potentially deploy more satellite tags. A

few constituents reported basking shark sightings in the SCB during the spring and early summer 

of 2012, although reports were sparse and sporadic. A couple of failed attempts were made to 

find sharks for tagging based on some of the reports. Significant progress has been made on the 

quantitative modeling of historical basking shark records with environmental variables. 

Data from the three sharks tagged with satellite tags in 2010 and 2011 have been analyzed and 

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.

Dramatic shifts in behavior make estimating abundance based on aerial surveys and predicting 

overlap with fisheries challenging. Additional information on the patterns in vertical and 

horizontal movements is needed.

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 species range, distribution, and life history into account. Various genetic 

analyses are useful to help identify differentiation between and within presumed stocks.

Shortfin Mako Shark –As part of his Ph.D. work at University of California Davis and San 

Diego State University and in collaboration with the SWFSC, Dovi Kacev has developed a suite 

of 11 nuclear microsatellite markers and optimized an additional 5 to further refine the spatial 

and temporal resolution of shortfin mako stocks within the Pacific. In addition to studies of stock 

structure, these markers are being used to develop estimates of effective population size within 

the California Current region. Data analyses are ongoing and a manuscript is being drafted.

These markers have also been shared with international collaborators and are currently being 

applied to global studies of shortfin makos.

Common Thresher Shark – Common threshers are regularly encountered in temperate coastal 

marine fisheries but little is known about regional connectivity. In recent years, threshers have 

become part of an increasingly important recreational fishery in Southern California in addition 

to being a major component of local gillnet fisheries. In order to better understand population 

connectivity, Dovi Kacev has developed eight nuclear microsatellite markers for this species and 

successfully cross amplified three of the shortfin mako loci. These markers are being applied and 

data collection is ongoing.

Silky Shark – Silky sharks are the most abundant shark encountered by tropical tuna fisheries 

world-wide. In an effort to better inform the first stock assessment for this species in the EPO,
29

~450 samples were added to an earlier study to examine stock structure in the Pacific. These 

samples filled in areas of previous low sample size (i.e. western Pacific) and areas for which 

there is specific EPO management concern (i.e. southeastern equatorial Pacific). The current 

dataset includes nuclear (9 microsatellite loci) and mitochondrial data (control region sequence) 

for ~730 animals, predominantly from the Pacific. These new data continue to support stock 

structure generally north and south of the equator with animals south of the Galapagos Islands in 

the EPO more closely allied with the northern stock. This spillover of the northern stock south of 

the equator is likely seasonal and is concordant with regional oceanography and size composition 

data.

Pelagic Thresher Shark – Pelagic thresher sharks are landed in high numbers by artisanal 

fisheries throughout the tropical Pacific and Indian Oceans. Due to past misidentification with 

other thresher species there is little known regarding the biology and life history of this species.

Recent genetic work by scientists at SWFSC, using both nuclear (five microsatellite loci) and 

mitochondrial DNA data (cytochrome oxidase sequence), has revealed the presence of very 

strong stock structure between eastern and western Pacific populations. Interestingly, the central 

Pacific seems to be an area of overlap for these two populations. Additional samples and genetic 

data are being added this year in collaboration with colleagues in Columbia to better characterize 

the stock structure for this species.

V. IDCPA RESEARCH

The SWFSC research conducted under the International Dolphin Conservation Program Act 

(IDCPA) during 2012 was focused on evaluating line transect methodology 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) analysis of data collected during the 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. 

Ecosystem data collected on this same cruise (STAR-LITE 2007) have been analyzed. 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. Wind mixing decreased surface temperature and reduced fine-scale variability. The 

thermocline shoaled and stratification decreased. Chlorophyll in the surface layer increased, 

apparently due to both mixing of phytoplankton from depth and to enhance production. 

Macrozooplankton biomass increased slowly, perhaps in response to the increased phytoplankton 

production. These environmental changes had a variety of effects on mid-trophic and apex 
30

predator components of the ecosystem. Changes in the stomach fullness and diet composition of 

planktivorous flyingfish were consistent with the increase in zooplankton biomass. Changes in 

the abundance and community composition of both seabirds and cetaceans were observed, but 

are confounded by seasonal migration. Fiedler et al. (2013) describes these results. 

This is 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, 

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 

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, Stenella longirostris, and 

pantropical spotted, S. attenuata, dolphins) are conducted with an ecosystem approach. In 

addition to investigating the status and trends of these dolphin stocks, auxiliary projects are 

conducted to improve our understanding of their surrounding environment. Data analyses, 

processing, and publications included (1) investigations of cetacean biodiversity hotspots; (2) 

identifying critical habitat for large whales; (3) assessment of relative fishery exposure for ETP 

dolphins; (4) dolphin swimming kinematics research; (5) spotted dolphin form and function 

review; (6) investigations of dolphin reproductive biology; (7) ETP dolphin population genetic 

structure; (8) investigations of the ETP ecosystem and its change over time; (9) cephalopods as 

indicators of spatial variation in biochemical properties between marine systems; (10) seasonal 

and interannual patterns of ETP dolphin distributions from tuna vessel observer data (TVOD); 

and (11) conducting catch sampling to evaluate the impacts of smaller, unobserved purse-seine 

vessels on ETP dolphins.

Investigations of Cetacean Biodiversity Hotspots – The PRD continues to investigate species 

richness hotspots for 28 species of cetaceans in the ETP (ca. 20 million km2) based on data 

collected using line transect methods aboard NOAA research vessels, August–November, in 

each of the 10 years during a 21-year period (1986-2006). Density was calculated using speciesand area-specific published values of g(0) and f(0), and interpolated throughout a 1° x 1° grid of 

the study area using two smoothing algorithms and two resolutions. 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. These results were robust to smoothing algorithm 

and spatial resolution. These regions are highly variable in space and time with respect to 

physical oceanographic properties. Current analyses are focused on identifying the mechanisms 

underlying the hotspot patterns.
31

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. Mitigating these 

threats requires a transboundary, systematic planning approach. SWSFC scientists are using 

three species of baleen whales in the ETP to explore several components of the planning process.

The ETP is seasonally occupied by migratory blue and humpback whales from both northern and 

southern hemispheres; it also hosts important numbers of resident Bryde’s whales. Through 

collaborations with international colleagues, SWFSC scientists obtained 5,633 humpback whale 

sightings from breeding areas off Mexico, Columbia, Costa Rica, Panama, Ecuador, and the 

Galapagos Islands. Simple environmental envelope models are being used to describe the 

oceanographic conditions associated with these sightings. Scientists are also exploring the 

performance of MaxEnt, a more sophisticated presence-only modeling technique. SWFSC 

scientists have been systematically collecting data in the EPO for over twenty-five years; 

colleagues have collected additional cetacean sightings opportunistically or on non-systematic 

surveys. Habitat models have been successfully built for multiple species using the 

systematically collected SWFSC survey data (Forney et al., 2012). Following an approach 

similar to Forney et al. (2012), the systematically collected data will be used to develop 

generalized additive models (GAMs) of species density. The GAMs will be compared to MaxEnt 

models built with only the systematic data, a combination of systematic and opportunistic data, 

and only the opportunistic data.

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. Based on this movement model, the method weighs purse-seine sets given their distance 

from a particular school of dolphins sighted at sea and how long ago they occurred. The method 

also takes into account the species composition and school size in the set. As a demonstration, 

the authors use the method to examine the spatial and temporal distribution of this index over an 

11-year period for which there is detailed data on purse-seine sets. While the method was 

designed for examining exposure to the ETP purse-seine fishery, it is also applicable to studies of 

other anthropogenic effects where there is concern about exposure rates, such as underwater 

sound, pollution, or ship strikes. Planned studies for 2013 and beyond 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. Immediate next steps 

include working with colleagues in the IATTC Directorate to identify mutually agreeable data 

access to facilitate completion of these important analyses.

Dolphin Swimming Kinematics Research – Based on the results of a series of research papers 

on various aspects of dolphin hydrodynamics published between 2002 and 2012, development 

has begun on a hydrodynamics-based energetics model that will investigate the potential for 

dolphin mother-calf separation and subsequent calf mortality due to tuna purse-seine chase in the 

ETP. The model is still in development stages and is projected for completion during 2013.
32

Spotted Dolphin Form and Function Review – A comprehensive review of literature regarding 

form, function and pathology of spotted dolphins (Stenella attentuata) has been completed and is 

currently in review prior to publication as a NOAA Technical Memorandum. The review 

summarizes and synthesizes all available information on these topics published through 2012, 

and is intended to serve as a resource for researchers interested in this species, with particular 

emphasis on data collected from the ETP, which forms the basis of most of the available 

information. A publication is anticipated during 2013.

Investigations of Dolphin Reproductive Biology – A doctoral dissertation (Kellar et al., 2008) 

was completed examining the pregnancy patterns of spotted dolphins in the ETP. This work has 

been revised and submitted to Marine Biology for review. It states that one hypothesis for the 

lack of recovery of the spotted dolphin population in the ETP is that continued chase and 

encirclement by the tuna fishery negatively affects reproduction.

Insufficient life history sampling in this region over the last decade makes traditional estimation 

of population reproductive rates impossible. The current reproductive patterns of these dolphins 

were examined using a molecular method to assess pregnancy state from blubber progesterone 

concentrations in biopsy samples. Blubber progesterone was quantified in 212 biopsies from 

female offshore spotted dolphins sampled between 1998 and 2003 in the northeastern tropical 

Pacific. These concentrations were found to be sharply bimodal with no value observed between 

49 ng/g and 87 ng/g, a finding consistent with the concentration gap between known pregnant 

and non-pregnant dolphins. Given that high blubber progesterone (≥ 87 ng/g) indicates 

pregnancy, scientists found that 11.8% of the biopsied females were pregnant. This is 

substantially lower than an estimate of the proportion pregnant found in the fishery kill over the 

same region (22.3%) between 1973 and 1992. To try to ascertain the potential cause of this 

discrepancy, the relationship between pregnancy and fishery exposure was analyzed, and it was

found that pregnant females were exposed to significantly less fishery activity than non-pregnant 

ones (P < 0.046), suggesting that the fishery has an inhibitive effect on pregnancy. However, 

there are several caveats to this finding, and how this relationship might explain the discrepancy 

between these data sets is unclear. Scientists also examined and modeled spatial patterns of 

reproduction and found that pregnancy was more aggregated than random (P = 0.020), with the 

highest proportion pregnant in the mouth of the Gulf of California, an area with relatively low 

reported fishery activity.

In 2009, work began quantifying the levels of progesterone in spinner dolphins to replicate this 

study in another fishery-impacted species. To date, 189 animals have been processed; hormones 

have been measured and pregnancy determination is complete. The next step is to analyze and 

add a spinner dolphin-specific fishery exposure index to these data and assess the relationship 

between reproduction and exposure.

ETP Dolphin Population Genetic Structure – Research is underway to determine 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. Population structure information is needed to develop accurate stock 

abundance estimates for population-specific dolphin bycatch limits.
33

In 2011, work began quantifying the levels of genetic structure in spinner and spotted dolphin 

populations in the ETP. Using high-throughput DNA sequencing, Matthew S. Leslie (Ph.D. 

candidate at Scripps Institution of Oceanography) has collected DNA sequence data from 80 

nuclear loci (84Kbp) and entire mitochondrial genomes (16Kbp) for a subset of biopsy samples 

(n=250). The mitogenomic data were analyzed using an integrated phylogenetic and population 

genetic framework to characterize variability and structure. Little population genetic structure 

across the ETP was detected in the mitochondrial genomes. The nuclear data are currently being 

analyzed for population structure. 

Given the challenges in detecting genetic differences in dolphin populations with recent 

divergence, ongoing interbreeding and high variability, Leslie is now genotyping ETP spinner 

and spotted dolphins on a genome-wide scale. Using a method that targets restriction enzyme 

binding sites, he is sequencing millions of short portions of DNA dispersed throughout the 

genome in an effort to find tens-of-thousands of mutation sites for population structure analyses. 

This volume and type of data should have the power to detect genetic structure in these 

populations. These data will also be used to develop addition nuclear DNA assays to genotype 

additional modern and historical specimens. The goal of this integrative study is to provide a 

total-evidence, process-oriented analysis using morphology, genetics and environmental 

variables. Permission to sample and genotype museum specimens from the National Museum of 

Natural History has been requested.

The next steps are to: 1) publish the findings from the mitogenome analyses, 2) finish analyzing 

the 80 nuclear DNA loci, 3) finish collecting the genome-wide genotype data and 4) collect 

genetic material from museum specimens.

Investigations of the ETP Ecosystem and Its Change over Time – An analysis of variations in 

thermocline depth and stratification in the eastern tropical and North Pacific has been published 

(Fiedler et al., 2013).Time series from 1958-2008 were decomposed into seasonal, interannual 

cycle, and long-term trend components using state-space techniques. On shorter time scales, 

interannual variations related to the ENSO are seen. Long-term regional variability is observed, 

either a monotonic trend or with one or more change points resembling climate regime shifts.

Such changes in upper-ocean structure and associated ecosystem effects are well known in wellmonitored regions such as the California Current. In the eastern equatorial Pacific, the 

pycnocline has shoaled but become less stratified, while in the ETP warm pool, pycnocline depth 

and stratification has varied up and down with little overall change. The thermocline influences 

nutrient input to surface waters, which limits primary productivity throughout this region.

Potential ecosystem effects of the observed long-term trends are discussed. Further analysis will 

quantify the extent to which interannual cyclic variability observed at higher latitudes, for 

example in the California Current, is related to ENSO.

Cephalopods as Indicators of Spatial Variation in Biochemical Properties between Marine 

Systems – Ruiz-Cooley et al. (2013) investigated the ecology of the Humboldt (jumbo) squid (D. 

gigas) using specimens collected in the California Current during a cetacean and ecosystem 

assessment survey in 2008 to investigate their migration patterns and habitat use through 

biochemical analysis (stable isotopes from bulk and individual amino acids - Phenylalanine and 
34

Glutamic acid). Data indicate that large squid feed in California Current waters but migrated 

from at least three different geographic origins, including regions within the ETP. This analysis 

confirms that both physical and biological factors in the ETP influence adjacent ecosystems, with 

the potential to significantly alter them. In this case, because D. gigas is abundant, prey of many 

large-bodied marine vertebrates, and a voracious predator, migrants from the ETP have the 

potential to restructure food webs in an adjacent ecosystem. 

Seasonal and Inter-annual Patterns of ETP Dolphin Distributions from Tuna Vessel 

Observer Data (TVOD) – A study of the variability of spatial distributions of target stocks and

relationships to seasonal and inter-annual changes in habitat has been initiated in cooperation 

with IATTC scientists. Although sampling is not as rigorous as on research vessel surveys 

(RVOD), tuna vessel observer data has more much more sighting effort with fewer gaps within 

and between years. Therefore, it is likely that patterns of variability that cannot be resolved by 

RVOD can be detected and related to environmental variability from remote sensors and dataassimilation models. Both seasonal and ENSO-scale (El Niño/La Niña) variability are important 

in the ETP and likely affect the distribution of motile top predators like dolphins.

Conducting Catch Sampling to Evaluate the Impacts of Smaller, Unobserved Purse-seine 

Vessels on ETP Dolphins – Despite achievements in dolphin conservation for the tuna purseseine fishery of the EPO, debate continues about the magnitude and importance of dolphin 

mortality caused by small (unobserved) vessels. In-port sampling of tuna catch size composition 

is a potentially cost-effective means of identifying unobserved vessels that may be catching tunas 

associated with dolphins because yellowfin tuna caught in association with dolphins are larger, 

on average, than those caught in other types of purse-seine sets. A classification algorithm to 

predict purse-seine set type (“dolphin” vs. “non-dolphin”) was built from port-sampling data on 

yellowfin tuna length-frequencies and the date and location of fishing of large (observed) 

vessels. This classification algorithm was used to screen the port-sampling data of small vessels 

collected by IATTC and NMFS samplers during 2006-2009, assuming the fishing practices of 

the two groups resulted in similar catch characteristics. From these results, hypothetical time 

series of dolphin mortality for small vessels were constructed and incorporated into a population 

dynamics model, along with mortalities of large vessels. Results suggest that any dolphin 

mortality of small vessels is unlikely to be substantially affecting trends in dolphin abundance. 

These results underscore the importance of in-port sampling, in combination with at-sea 

observation and fishery-independent surveys, to effective management. Additional project 

findings can be found in a paper published by Lennert-Cody et al. (2012).

Challenge against the U.S. Dolphin-Safe Labeling Standard for Tuna – In 2008, Mexico 

initiated World Trade Organization (WTO) dispute proceedings to challenge the Department of 

Commerce “dolphin safe” tuna label scheme as a violation of provisions of the WTO’s General 

Agreement on Tariffs and Trade (GATT) and Agreement on Technical Barriers to Trade (TBT 

Agreement). A WTO dispute panel issued a mixed decision, finding in favor of the United States 

on most claims. In January 2012, the United States and Mexico cross-appealed to the WTO 

Appellate Body. The WTO Appellate Body issued its report on 16 May 2012, finding in favor of 

the United States in four out of five of Mexico’s claims, and finding in favor of Mexico on its 

claim that the labeling scheme afforded less favorable treatment to Mexican tuna products. In the 

less favorable treatment finding, the Appellate Body concluded that the current US “dolphin 
35

safe” labeling scheme does not set conditions for use of the label in a way that reflects risks 

faced by dolphins in fisheries outside the ETP. Under WTO rules, the United States must bring 

its non-conforming measure into compliance, and the deadline to do so will likely be in 2013.

VI. PUBLICATIONS

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Preti, A., C. U. Soykan, H. Dewar, R. J. D. Wells, N. Spear, and S. Kohin. 2012. Comparative 

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Jackson, A. R. 2012. A description of the tuna-porpoise observer data collected by the U.S. 

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Lee, H.H., K. Piner, and I. Taylor. 2012. Future Projections of Western and Central Pacific 

Striped Marlin. ISC//12/BILLWG-1/01. 16 p.

MacCall, A. D., and S. L. H. Teo.2011.Exploration of a hybrid Stock Synthesis-VPA model of 

Pacific bluefin tuna to distinguish between trends in recruitment and changes in fishing 

intensity on young fish. ISC/11-1/PBFWG/01. Working document submitted to the ISC 

Pacific Bluefin Tuna Working Group Meeting, 6-13 January 2011.Shimizu, Japan.

Michaud A., J. Hyde, S. Kohin, and R. Vetter.2011.Mitochondrial DNA sequence data reveals 

barriers to dispersal in the highly migratory shortfin mako shark (Isurus oxyrinchus). 

Working paper ISC/11/SHARKWG-2/03 submitted for the ISC Shark Working Group 

Meeting, 28 November–3 December 2011.La Jolla, Calif., USA.

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Approved by the Science Director

James, K., R. Lewison, P. Dillingham, K. A. Curtis, and J. Moore. Patterns of retention and 

discards of elasmobranch bycatch. For consideration for publication in Canadian Journal 

of Fisheries and Aquatic Sciences. 

Martin, S.L, S. Stohs and J.E. Moore. (Under review). A Bayesian approach to improve 

prediction and management of rare-event bycatch. 

Moore, J. E. A cautionary note about assessing human impacts on age-structured populations: 

recent examples from sea turtles and fisheries. For consideration for publication in 

Biological Conservation.