NOAA Technical Memorandum NMFS-AFSC-209
 

Results from the April 2009 Gulf of 

Alaska Line Transect Survey (GOALS) 

in the Navy Training Exercise Area 

by 

B. K. Rone, A. B. Douglas, A. N. Zerbini, L. Morse, 

A. Martinez, P. J. Clapham, and J. Calambokidis 

U.S. DEPARTMENT OF COMMERCE 

National Oceanic and Atmospheric Administration
 

National Marine Fisheries Service
 

Alaska Fisheries Science Center
 

May 2010 
NOAA Technical Memorandum NMFS 

The National Marine Fisheries Service's Alaska Fisheries Science Center 

uses the NOAA Technical Memorandum series to issue informal scientific and 

technical publications when complete formal review and editorial processing 

are not appropriate or feasible. Documents within this series reflect sound 

professional work and may be referenced in the formal scientific and technical 

literature. 

The NMFS-AFSC Technical Memorandum series of the Alaska Fisheries 

Science Center continues the NMFS-F/NWC series established in 1970 by the 

Northwest Fisheries Center. The NMFS-NWFSC series is currently used by 

the Northwest Fisheries Science Center. 

This document should be cited as follows: 

Rone, B. K., A. B. Douglas, A. N. Zerbini, L. Morse, A. Martinez, P. J. 

Clapham, and J. Calambokidis. 2010. Results from the April 2009 Gulf 

of Alaska line transect survey (GOALS) in the Navy training exercise 

area. U.S. Dep. Commer., NOAA Tech. Memo. NMFS-AFSC-209, 39 p. 

Reference in this document to trade names does not imply endorsement by 

the National Marine Fisheries Service, NOAA. 
NOAA Technical Memorandum NMFS-AFSC-209
 

Results from the April 2009 Gulf of
 

Alaska Line Transect Survey (GOALS)
 

in the Navy Training Exercise Area
 

by 

1 2 1,2 1 B. K. Rone, A. B. Douglas, A. N. Zerbini, L. Morse, 

3 1 2 A. Martinez, P. J. Clapham, and J. Calambokidis 

1

Alaska Fisheries Science Center 

7600 Sand Point Way N.E. 

Seattle, WA 98115 

www.afsc.noaa.gov

2 Cascadia Research Collective
 

218 1⁄2 W Fourth Ave.

 Olympia, WA 98501
 

3

Southeast Fisheries Science Center
 

75 Virginia Beach Drive
 

Miami, FL 33149
 

U.S. DEPARTMENT OF COMMERCE 

Gary F. Locke, Secretary 

National Oceanic and Atmospheric Administration

 Jane Lubchenco, Under Secretary and Administrator 

National Marine Fisheries Service 

Eric C. Schwaab, Assistant Administrator for Fisheries 

May 2010 
This document is available to the public through: 

National Technical Information Service 

U.S. Department of Commerce 

5285 Port Royal Road 

Springfield, VA 22161 

www.ntis.gov 
iii 

                                                                   ABSTRACT 

 Little is known about the present-day occurrence of cetaceans found in offshore waters in 

the Gulf of Alaska; however, whaling records and a few recent surveys have shown this area to 

be important habitat. The U.S. Navy maintains a maritime training area in the central Gulf of 

Alaska, east of Kodiak Island, and has requested additional information on marine mammal 

presence and use of this area. To describe the occurrence and distribution of marine mammals in 

and around the U.S. Navy training area, a line transect visual and acoustic survey was conducted 

10-20 April 2009 from the NOAA ship Oscar Dyson. The primary survey area encompassed 

nearshore and offshore pelagic waters of the central Gulf of Alaska. Survey lines were designed 

to provide equal coverage of the nearshore and offshore habitat. 

During this project, the visual survey covered a total of 760 km (410 nautical miles, nmi) 

on-effort (visible horizon, Beaufort sea state 5 or less, and survey speed of 10 knots through the 

water) while transit (visible horizon, Beaufort sea state 5 or less, and survey speed of 12 knots) 

and fog effort (no horizon, Beaufort sea state 5 or less) legs accounted for 553 km (298 nmi). 

There were a total of 96 sightings (453 individuals) of 11 confirmed marine mammal species; 

these included fin (Balaenoptera physalus), humpback (Megaptera novaeangliae), gray 

(Eschrichtius robustus), minke (B. acutorostrata) whales, and killer whales (Orcinus orca), 

Dall’s (Phocoenoides dalli) and harbor (Phocoena phocoena) porpoise, Pacific white-sided 

dolphins (Lagenorhynchus obliquidens), Steller sea lions (Eumetopias jubatus), harbor seals 

(Phoca vitulina), and sea otters (Enhydra lutris). Additionally, there were 36 sightings (46 

individuals) of unidentified large whales, dolphins, and pinnipeds. Passive acoustic operations 

were conducted 24 hours/day surveying a total of 3,519 km (1,900 nmi) and recorded 49 acoustic 
iv 

detections of sperm whales (Physeter macrocephalus) and killer whales. Photographs of 19 

individual killer whales and 4 fin whales were obtained on this cruise and compared to existing 

photo-identification catalogs. 

Density and abundance estimates were calculated for fin and humpback whales by 

stratum using line transect methods with and without covariates in detection probability models. 

Additional sightings from a previous cruise on a comparable vessel were used for improving 

estimation of detection probability. All results were fairly similar given the constraints of the 

sample sizes involved. Estimates of abundance in the inshore and offshore strata were 594 (CV 

= 0.29) and 889 (CV = 0.57) for fin whales, and 219 (CV = 0.57) and 56 (CV = 0.57) for 

humpback whales, respectively. A small proportion of large whales were not identified to species 

but were probable fin or humpback whales based on observations, and estimates of these 

unidentified whales were assigned to these species based on the proportion of fin and humpback 

whales identified in each stratum. This raised fin whale estimates of abundance to 666 (CV = 

0.3) and 938 (CV = 0.57) and humpback whale estimates to 265 (CV = 0.48) and 63 (CV = 0.51, 

inshore and offshore strata, respectively). 

Despite a number of logistical and time limitations, the survey provided new information 

on the occurrence and abundance of marine mammals in the region. Sighting sample sizes were 

adequate to provide density and abundance estimates for fin and humpback whales. 

Identification photographs obtained on this cruise also verify the seasonal presence of individual 

fin and killer whales in a study area that is rarely surveyed. 
v 

 CONTENTS

ABSTRACT...................................................................................................................................iii 

INTRODUCTION .......................................................................................................................... 1

METHODS ..................................................................................................................................... 3

 Survey Design and Visual Survey Methods................................................................ 3

 Ship-based Passive Acoustics ..................................................................................... 4

 Photo-identification..................................................................................................... 6

 Line Transect Analysis of Large Whale Data ............................................................. 7

RESULTS ..................................................................................................................................... 9

 Visual Survey Effort and Sightings............................................................................. 9 

 Ship-based Passive Acoustics ..................................................................................... 9

 Photo-identification................................................................................................... 10

 Line Transect Analysis of Large Whale Data ........................................................... 11 

GOALS 2009 Data Only....................................................................................... 11 

GOALS 2009 and Miller Freeman 2003 Data .................................................... 12 

DISCUSSION............................................................................................................................... 13

ACKNOWLEDGMENTS ............................................................................................................ 17

CITATIONS ................................................................................................................................. 19 

APPENDIX................................................................................................................................... 35 

INTRODUCTION 

 The U. S. Navy uses a maritime training area (144,560 km2) in the Gulf of Alaska located 

south of Prince William Sound and east of Kodiak Island. The training area encompasses various 

marine habitats, both shelf and pelagic, that support most species of marine mammals found in 

the Gulf of Alaska. Twenty-six species of marine mammals are known to reside in or seasonally 

frequent the Gulf of Alaska. Although marine mammals are present year-round in the Gulf of 

Alaska, the greatest number of animals occurs during the spring and summer. Three of the whale 

species present in the Gulf of Alaska, humpback (Megaptera novaeangliae), fin (Balaenoptera 

physalus) and right (Eubalaena japonica) whales, feed in the outer continental shelf and slope 

waters during the summer into early fall, while blue (B. musculus), sei (B. borealis), and sperm 

(Physeter macrocephalus) whale species are thought to be more pelagic (Berzin and Rovnin 

1966, Rice 1974). Gray whales (Eschrichtius robustus) are thought to migrate along the shore of 

the Gulf of Alaska (Rice and Wolman 1982) as well as maintain a summer-long presence off 

Kodiak Island (Moore et al. 2007). From sea otters (Enhydra lutris) to blue whales, some species 

of marine mammals found in the Gulf of Alaska were aggressively hunted from land and/or 

vessel until the passage of the Marine Mammal Protection Act of 1972 and the U.S. Endangered 

Species Act of 1973 (Rice and Wolman 1982, Scheffer 1972). In 1980, a survey conducted and 

described by Rice and Wolman (1982) determined that the populations of all great whales in the 

Gulf of Alaska had been severely depleted. Since that time some of these species have shown 

signs of recovery; however, only the eastern North Pacific gray whale has experienced a 

seemingly complete population recovery (Rugh et al. 2005). Historically, distribution of 

cetaceans in the Gulf of Alaska has been based on commercial catch records (Nishiwaki 1966, 
2

Townsend 1935) and whaling-related scouting vessel data (Berzin and Rovnin 1966, Wada 

1979). For pinnipeds and sea otter, species that are found seasonally close to shore, current 

abundance and distribution estimates are available (Angliss and Allen 2009); however, for most 

cetacean species in the Gulf of Alaska, marine mammal survey effort has not generated sufficient 

sighting data to create abundance estimates. Absence/presence data is available from the 2004 

Southwest Fisheries Science Center vessel-based marine mammal survey for humpback whales 

that crossed through the U.S. Navy’s Gulf of Alaska training area (Barlow and Henry 2005). In 

addition, bottom-mounted hydrophones in the offshore Gulf of Alaska have been used to record 

calls from blue, humpback and fin whales throughout the year (Stafford et al. 2007). 

Despite the challenges of studying marine mammals in the Gulf of Alaska, information 

on these populations is necessary for management, particularly for populations that inhabit 

pelagic waters where minimal survey effort has occurred. To determine marine mammal 

distribution and abundance in the Gulf of Alaska training area, the U.S. Navy provided funds for 

a vessel-based line transect survey in the Gulf of Alaska during April 2009.

 The Gulf of Alaska Line Transect Survey (GOALS) had three main objectives: (1) to 

visually assess the distribution and occurrence of marine mammals in the Gulf of Alaska with 

specific focus on the U.S. Navy maritime exercise area, (2) to conduct 24-hour acoustic 

operations to record the presence of marine mammals in the U.S. Navy training area in 

coordination with and in addition to visual operations, and (3) to document individual animals 

through photo-identification and biopsy sampling.
3

METHODS 

Survey Design and Visual Survey Methods 

The survey was conducted from 10 to 20 April 2009 aboard the NOAA ship Oscar 

Dyson, a 63 m fisheries research vessel. Two strata, inshore and offshore, were proposed and 

tracklines were designed to provide a uniform spatial coverage of the study area (Table 1, 

Fig. 1). The inshore stratum encompassed the continental shelf/slope region of the training area 

and the offshore stratum contained the pelagic zone. This proposed design allowed for the 

computation of abundance estimates. 

Rotating teams of three scientists collected sighting data using standard line transect 

methods during on-effort status. Operations began at 07:20 and ceased at 20:00, or as long as 

conditions would allow. A full observation period lasted 2 hours (40 minutes in each position) 

and was followed by a 2 hour rest period. All three observers (starboard and port observers and 

data recorder) were stationed on the ship’s flying bridge. Starboard and port observers used 25× 

‘big-eye’ binoculars with reticles to scan from 10° on the opposite side to 90° abeam. The data 

recorder surveyed the trackline with 7 × 50 binoculars while scanning through the viewing areas 

of the two primary observers. In addition, an independent observer positioned on the flying 

bridge scanned for animals using 7 × 50 binoculars and recorded marine mammal sightings in a 

notebook, silently providing the information to the recorder if it was not detected by the primary 

observers. When a sighting was made, the primary observer conveyed to the recorder the 

horizontal angle and number of reticles from the horizon to the initial sighting. Additional 

information collected was sighting cue, course and speed, species identity, and best, low, and 
4

high estimates of group size. The computer program WINCRUZ (available at 

http://swfsc.nmfs.noaa.gov/PRD/softwares/software.html) was used to record all sighting and 

environmental data (e.g., cloud cover, wind speed and direction, and sea conditions). 

On-effort status was defined as a visible horizon, Beaufort sea state 5 or lower, and 

survey speed of 10 knots through the water. Lines connecting the end/start points of designated 

tracklines as well as lines to and from the survey area were classified as ‘transit lines’ and were 

surveyed using on-effort protocols whenever possible; however, typically they were conducted at 

a speed of 12 knots. Fog effort corresponded to observations conducted under poor visibility (no 

horizon) but with a Beaufort sea state 5 or less and was conducted on both designated tracklines 

and transit lines. Under unacceptable weather conditions (visibility ≤ 0.5 nautical miles (nmi) 

and/or sea state ≥ 6), off-effort watches on the bridge were conducted. Two observers were 

positioned on the bridge to record off-effort sightings and environmental data. At the cruise 

leader’s discretion, line transect survey effort was temporarily suspended to allow closer 

approaches to sightings for photo-identification. Although a biopsy sampling plan was 

established, no sampling occurred due to the limited survey time and opportunities. Given the 

limited time to cover the tracklines and because acoustic operations could be conducted despite 

weather conditions, the ship continued along the transect lines and visual operations were 

conducted when possible. 

Ship-based Passive Acoustics 

Passive acoustic operations were conducted continuously throughout the survey area. 

During periods of favorable daytime conditions, the passive acoustic survey was conducted in 
5

concert with the visual survey effort. The towed acoustic array was used to collect high quality 

examples of vocalizations and to determine the presence of acoustically active cetaceans at times 

when no visual survey effort was possible due to high sea states or darkness. 

Passive acoustic data were monitored using a two-element towed hydrophone array. This 

towed array was a 400 m long, Kevlar reinforced, multi-conductor armored cable assembly with 

an oil-filled tow section at the end of the cable. The array could be towed at any speed up to 

12 knots. For this survey, the array was deployed 200 m astern of the vessel. The tow section 

contained two Teledyne Benthos AQ-4 high-gain hydrophones with a designed frequency 

response of 10 Hz to 15 kHz. These hydrophones, along with their associated signal conditioning 

and line drive electronics, were separated by 3 m within the oil-filled tow section. 

The analog acoustic signal was passed into the acoustics lab for filtering, amplification, 

recording and monitoring. These acoustic signals were continuously monitored in real-time by an 

acoustics operator. The analog signal was digitized via a National Instruments DAQCard-6062E 

at a sample rate of 96 kHz. Continuous recordings were copied to hard disk in real time as .WAV 

files 10 minute in duration. The software package Ishmael, a program designed to analyze 

acoustic data sets (Mellinger 2001), was used to monitor signals and make high bandwidth 

recordings. The relative bearing of manually selected signals of interest could be calculated by 

Ishmael utilizing the difference in the time of arrival of a signal at each hydrophone. These 

relative bearings could then be sent to a second computer for display. This computer was 

connected to a GPS receiver and loaded with the WhalTrak2 software package (created by Glen 

Gailey at Texas A&M University). WhalTrak2 displayed the ship’s current position and track in 

a graphic display window, overlaying lines of bearings as instructed by the operators. This 

provided the acoustics team with a picture of how acoustic detections related to visual sightings 
6

of cetaceans and other possible sources of sound, such as ship traffic. WhalTrak2 was also 

programmed to record ship position, effort, weather, and general comments to a Microsoft 

Access data file. 

 Due to flow noise, we expected to lose an approximate range of 0-1,000 Hz, resulting in 

the loss of low frequency calls (i.e., baleen whales). A cursory review of acoustic recordings for 

low frequency baleen whales was conducted at the start of the cruise, particularly when fin 

whales were sighted, and confirmed the absence of these calls. As a result, real-time monitoring 

on Ishmael occurred only for upper frequency, audible calls. 

Photo-identification 

Identification photographs of target species were obtained to allow evaluation of 

movements of animals during the survey and comparison to existing catalogs. Highest priority 

species for photo-identification on the Gulf of Alaska survey were North Pacific right, blue, and 

fin whales. Other high priority species were humpback, killer, sperm, minke (Balaenoptera 

acutorostrata), Baird’s beaked whale (Berardius bairdii) and Stejneger’s beaked whale 

(Mesoplodon stejnegeri). When the observers located a target species, the visual survey effort 

was suspended and the primary survey vessel was directed to obtain photographs of the animals. 

The vessel was positioned for the best lighting and angle so that photographs could be obtained 

of the dorsal fin as well as the chevron on fin whales, flukes of humpback whales and saddle 

patches of killer whales. Photographs were taken using Nikon D-200 and Canon 20D autofocus 

digital cameras equipped with a 70-300 mm or a 100-400 mm zoom lens. All photographs were 

reviewed, and the highest quality identification photograph(s) of each animal were selected to be 
7

compared to existing photo-identification catalogs from the northeastern Pacific and the Gulf of 

Alaska. 

Line Transect Analysis of Large Whale Data 

 Line transect analysis (Buckland et al. 2001, 2004) was conducted to estimate density and 

abundance of fin, humpback, and unidentified large whales only. Detection functions were fit 

using data from all three species categories. Line transect analysis combined effort conducted 

under appropriate survey conditions in on-effort, on-transect, and transit lines with good 

visibility and sea conditions. Sighting data collected during transect and transit lines were used to 

estimate detection probability, but only data from transect lines were used in estimation of 

density and abundance. We also evaluated whether acoustic detections of sperm whales could be 

used to estimate a line transect density, but this did not appear possible because many acoustic 

detections could not be localized. 

 Initially, estimation of detection probability was conducted using only sighting data from 

GOALS 2009. Due to the relatively small sample size (Table 2), perpendicular distance data 

were left untruncated and only two conventional distance sampling (CDS, Buckland et al. 2001) 

models were used for fitting a detection function: the hazard rate and the half normal. 

 In order to increase sample size to estimate detection probability, fin (n = 57), humpback 

(42), and unidentified large whale (1) sightings collected during a research cruise conducted by 

the National Marine Mammal Laboratory (NMML) in the Gulf of Alaska from 26 June to 15 

July 2003 aboard the NOAA ship Miller Freeman (Fig. 2) were included in the analysis (Table 

2). This cruise was carried out on a similar platform within the general area and followed similar 
8

searching methodology employed during GOALS 2009; therefore, sighting data were expected 

to be comparable. The addition of such sightings not only provided additional data for estimating 

detection probability with better precision, but also allowed the use of multiple covariate distance 

sampling methods (MCDS, Marques and Buckland 2003). Exploratory analysis indicated that 

truncation at 5 km was the most appropriate for estimation of detection probability as it provided 

relatively good model fits and allowed for most of the sighting data (94%, n = 138) to be used in 

the analysis. 

Five covariates (Table 3) were proposed to estimate detection probability with MCDS 

methods. Only single covariate models were used in the estimation of detection probability and 

those that did not conform to this detection probability hypothesis were excluded from the 

analysis. For example, detection probability is expected to increase as group size increases; 

models that indicated otherwise were excluded. 

Encounter rate and its variance were empirically estimated from the data 

(Buckland et al. 2001). For CDS models, size bias regressions were computed to investigate 

whether group size was influencing detection probability (Buckland et al. 2001). If the regression 

was significant to an α = 0.15 level, then the size bias regression coefficients were used to 

estimate average group size. Otherwise, a simple mean was computed. For MCDS models, group 

sizes were estimated by dividing the estimated density of individuals by the estimated density of 

groups in the study area (Marques and Buckland 2003). 

For density estimation, stratum-specific abundance estimates were calculated using the 

detection probability model that received most support from the data (the “best” model) 

according to the Akaike Information Criterion (AIC). For the purpose of this analysis, detection 
9

probability on the trackline was assumed to be (g[0] = 1). All parameter estimates were 

computed using the software Distance 5.0, release 2 (Thomas et al. 2006). 

RESULTS 

Visual Survey Effort and Sightings 

The survey covered a total of 760 km (410 nmi) on-effort while transit and fog effort legs 

accounted for 553 km (298 nmi) (Table 4, Fig. 3). The offshore stratum was not surveyed in its 

entirety due to limited survey time resulting from delayed departure. 

 There were a total of 96 sightings (453 individuals) of 11 confirmed marine mammal 

species; these included fin, humpback, gray, and minke whales, as well as killer whales, Dall’s 

and harbor porpoise, Pacific white-sided dolphins, Steller sea lions, harbor seals and sea otters. 

Additionally, there were 36 sightings (46 individuals) of unidentified large whales, dolphins, and 

pinnipeds (Table 5, Figs. 4-7). 

Ship-based Passive Acoustics 

Acoustic effort covered approximately 3,519 km (1,900 nmi) with 760 km (410 nmi) 

conducted during full visual effort (Fig. 8). 

There were a total of 49 acoustic detections, 9 during full visual effort, and 40 during 

“acoustics only” effort periods (Table 6, Fig. 8). Of these detections, eight were localized to a 

position located equidistant right or left of the trackline. This towed array configuration and 

methodology did not allow for resolution of the right/left ambiguity of relative bearings without 
10

purposely altering the ship’s heading during the detection period. Constraints on survey time did 

not allow for this resolution throughout the survey. Three detections were matched to visual 

sightings of killer whales. 

Killer whales (16) and sperm whales (28) were the only identified species acoustically 

detected. The unidentified odontocetes (5) are likely killer whales but the calls were too weak or 

indistinct to classify with certainty. Acoustic identification was based on published call type 

descriptions. Due to limitations of available sound processing software, group size estimates 

were not possible for the killer whale detections. 

As expected, low frequency baleen whale calls were not detected due to the masking 

effect of flow noise as the array was towed through the water. 

Photo-identification 

Photographs for photo-identification purposes were collected on three separate days 

(Table 7). There were a total of 721 photographs collected during encounters with fin whales and 

killer whales. See Appendix for photo-analysis results. 

The four fin whale identification photographs (left sides) were compared to photographs 

of approximately 100 fin whales from the Gulf of Alaska (catalog maintained by Bree 

Whitteveen; University of Alaska Fairbanks), 79 fin whales from Southern California (catalog 

maintained by Cascadia Research Collective) and an additional 25 animals from the Gulf of 

Alaska (collected by NMML). Many photographs from existing catalogs showed only right 

sides. No matches were made between the fin whale photographs collected on this survey and the 

two collections. The 19 individual killer whales were compared to photographs from a catalog 
11

maintained by NMML that contains 1,237 western Alaska resident killer whales from the Gulf of 

Alaska, Aleutian Islands and Bering Sea as well as 400 transient killer whales collected from 

those same areas. No matches were found between individuals identified on this survey and the 

existing catalogs. 

Line Transect Analysis of Large Whale Data 

Line transect analysis was conducted using the two strata, an inshore (area = 47,411 km2

) 

and an offshore stratum (area = 98,253 km2

) (Fig. 1). On-effort visual survey included six lines 

totaling 460 km in the inshore stratum, and three full or partial lines totaling 300 km in the 

offshore stratum (other sections of lines were completed in either limited visibility or with 

acoustics only). In addition, 384 km were surveyed in transit and 169 km under foggy conditions. 

A total of 19 fin whale sightings were observed on-effort within the survey area. Eleven were 

documented in transects on the inshore stratum and seven on the offshore stratum. One sighting 

was recorded during transit. Eight humpback whale sightings were recorded on-effort, seven in 

the inshore and one in the offshore stratum. Six sightings were made of unidentified large 

whales, five in the inshore and one in the offshore, and these most likely represented fin or 

humpback whales based on the identified sightings. 

GOALS 2009 Data Only

For the dataset using only the GOALS 2009 data for the detection probability, only CDS 

models with or without series expansions were fit to these data because of the relatively small 
12

sample size of sightings. Model 1 had the lowest AIC value. Model parameter and density 

estimates for this model is summarized in Tables 8 and 9, respectively. 

GOALS 2009 and Miller Freeman 2003 Data

For the combined detection function (GOALS 2009 and Miller Freeman 2003 data), 

results from best CDS and MCDS models (those within ∆ AICs = 3) are summarized in Table 

10. Overall the best model (Model 3) was the half normal with Method as covariate (Table 10). 

The combined detection function resulted in a slightly lower (but not statistically different) 

calculation of effective search half-width than that using the GOALS 2009 data alone and a 

slightly lower CV (0.08 for Model 3 versus 0.15 for Model 1, Tables 8, 10). Estimates of density 

and abundance for the best model (Model 3) are shown in Table 11. Density and abundance 

estimates were approximately 15% higher (but not statistically different) for detection 

probability Model 3 when compared to estimates with Model 1. Density and abundance CVs 

were slightly lower due to the larger sample size used in the estimation of Model 3. 

All results are fairly similar given the constraints of the sample sizes involved. Because 

the results of Model 3 have the lower CV and the lowest AIC scores, we recommend them as the 

best estimates of density and abundance. Resulting estimates are 594 (CV = 0.29) and 889 (CV = 

0.57) fin whales for the inshore and offshore strata, respectively, and 219 (CV = 0.57) and 56 

(CV = 0.57) humpback whales in the inshore and offshore strata, respectively. 

 Unidentified large whales were most likely fin or humpback whales and estimates of 

 unidentified large whales1

 could be assigned to these species based on the proportion of fin and 

___________________ 

1 CVs of pooled (fin/humpback + unidentified large whales) estimates of abundance were computed assuming 

species-specific estimates were independent. 
13

humpback whales identified in each stratum. This would raise fin whale estimates of abundance 

to 666 (CV = 0.3) and 938 (CV = 0.57) and humpback whale estimates to 265 (CV = 0.48) and 

63 (CV = 0.51, inshore and offshore strata respectively).

DISCUSSION 

This survey faced several challenges including limited survey time, a large survey area, 

and inclement weather. Despite these limitations, the survey was successful and provided an 

unexpectedly large number of visual sightings and acoustic detections. The visual sightings 

generated density and abundance for fin, humpback, and unidentified large whales. Although a 

density estimate may be produced for harbor and Dall’s porpoise in the future, both these species 

are known to have reactive movement to ships that will need to be considered in the analysis. 

Although this survey produced the highest number of acoustic detections and localizations of 

sperm whales in comparison with previous surveys, there were not enough positive range and 

bearings to provide a density estimate at this time. Acoustic detection of baleen whales was not 

possible with the towed array because their lower frequency calls cannot be detected due to flow 

noise and sonobuoys were not available for this cruise. This did not alter our ability to estimate 

density and abundance since these were based on visual sighting rates. 

Fin whales were the most common large cetacean sighted visually on this cruise. Fin 

whales are encountered seasonally off the coast of North America and in the Bering Sea. Based 

on data from bottom-mounted offshore hydrophone arrays, there were peaks in call rates 

occurring during fall and winter in the central North Pacific and the Aleutian Islands. Fewer calls 

were recorded during the summer months (Moore et al. 1998, Stafford et al. 2007, Watkins et al. 
14

2000). Presence or absence of recorded calls may not reflect the actual presence or absence of fin 

whales since there may be a seasonal pattern to their call rates or difference in oceanographic 

properties. Current reliable estimates for fin whales do not exist for the entire Gulf of Alaska; 

however, sighting data from coastal surveys between the Kenai Peninsula and Amchitka Pass 

conducted July-August 2001-2003 have generated a population estimate of 1,652 (95% CI: 1,142 

- 2,389) (Zerbini et al. 2006). Density estimates of fin whales vary in the Pacific Ocean off the 

California coast. Fin whales are observed year-round with an estimated 1.1 fin whales per 

1,000 km2

 (Barlow 1995, Forney et al. 1995). In Hawaiian waters where sightings of fin whales 

are extremely rare, passive acoustic monitoring has been used to estimate a density of 0.081 fin 

whales per 1,000 km2 (McDonald and Fox 1999). 

Sperm whales are distributed widely throughout the North Pacific. Although the visual 

observers never sighted sperm whales, they were the most common acoustically detected species 

during the survey. High acoustic detections of this species and absence of visual sightings can 

be explained by their long dive times and loud, expansive echolocation clicks. While sperm 

whale females and young generally remain in the tropical and temperate waters year-round, 

males are thought to move north in the summers to feed in the Gulf of Alaska and Bering Sea 

(Kasuya and Miyashita 1988), and sperm whales have been acoustically detected year-round in 

the Gulf of Alaska (Mellinger et al. 2004). Although a minimum population estimate is not 

available for sperm whales in the Gulf of Alaska, results from data collected during visual 

surveys conducted by NMML during summer months between 2001 and 2006 have shown that 

sperm whales were the most frequently sighted large cetacean (NMML unpublished data in 

Angliss and Allen 2009). 
15

Sightings of humpback whales on GOALS 2009 provide important data on spring-time 

distribution in the Gulf of Alaska. Humpback whales were the second most common whale 

encountered on the survey. Other than a single sighting in the offshore stratum, humpback 

whales were found exclusively within the inshore stratum and this is reflected in the higher 

density and abundance estimates for the inshore stratum. Our findings of higher humpback whale 

abundance in the inshore stratum coincides with past line transect surveys of the area that found 

93% of humpback whale groups were observed in water depths between 46 and 183 m 

(Brueggeman et al. 1988). Humpback whales encountered during the summer along southeast 

Alaska and the northern Gulf of Alaska migrate primarily to the Hawaiian Islands and Mexico 

(Calambokidis et al. 2008). Current estimates of abundance for humpback whales based on 

photo-identification and line transect surveys in the western and northern Gulf of Alaska during 

summers 2004, 2005 and 2006 is 3,000-5,000 animals (Calambokidis et al. 2008). Because 

humpback whales generally spend the winter months in lower latitudes and would just be 

returning to their feeding grounds in early spring when the GOALS cruise occurred, our 

estimates represent only a portion of the summer abundance in the study area. 

Gray whales were the third most common large whale sighted on the GOALS 2009 cruise 

and while this provides important data on spring-time distribution, it is not adequate for an 

abundance or density estimate. Gray whales pass through the Gulf of Alaska twice each year as 

they migrate to feed in the northern Bering and Chukchi seas and migrate back down to calving 

and breeding lagoons along Baja California (Braham 1984). In recent years, a large aggregation 

of gray whales has inhabited the Kodiak Island area throughout the entire summer (Moore et al. 

2007). Reflecting their more inshore distribution, gray whales were only sighted in the inshore 

stratum. 
16

Although small boat operations were not possible during this cruise, we were able to 

obtain photographic identifications of fin and killer whales from the ship (see Appendix). 

Photographs obtained on this cruise provide seasonal identifications of fin and killer whales in a 

difficult study area. Due to survey limitation, we were unable to document both sides of the fin 

whales. Therefore, matching to existing catalogs was limited to the one available side of the 

animal. However, due to the distinct dorsal fins of these four whales, there is a high probability 

that each animal could be matched if it existed in the catalogs. The 19 killer whales identified 

from two encounters on the GOALS cruise did not match the available catalog of photographs 

managed by NMML; however, in the months to come there may be an opportunity to compare 

these photographs to the catalog managed by Graeme Ellis at Canada’s Pacific Biological 

Station, British Columbia. Research (including collection of identification photographs) on 

resident and transient killer whales commenced in Prince William Sound in the 1970s (Hall 

1981), and is ongoing in the southeastern Bering Sea, the eastern/central Aleutian Islands region, 

and the western and central Gulf of Alaska (Dahlheim 1997; Ellis 1984, 1987; Leatherwood 

et al. 1984). 

Overall the cruise provided valuable new data about the presence of marine mammals in 

the Gulf of Alaska during the spring in relation to the U.S. Navy training area and surrounding 

areas. Analyses of the visual data provided abundance and density estimates for fin and 

humpback whales in a region where scant data on these species exist. Although limitations on 

acoustic software prevented obtaining group size estimates, results provided information on the 

presence of killer and sperm whales in the study area, valuable information given that the latter 

was never sighted by the visual team. 
17

ACKNOWLEDGMENTS 

We would like to thank the Pacific Fleet Commander (CPF) and the Chief of Naval 

Operations Environmental Readiness (OPNAV N45) for supporting this cruise. Robin Brake 

(CAPT OASN) and Frank Stone (CIV) helped arrange for funding. The Naval Postgraduate 

School made contractual arrangements on short notice thanks to the efforts of Curt Collins 

(CIV). George Hart (CIV CNRNW, N40BA) pushed for and helped design the survey. Jeff 

Leonard (CTR NSWC Crane) worked on sonobuoy supplies. Commander Chief Pittman and the 

U.S. Coast Guard Kodiak assisted with sonobuoy receiving logistics. Thank you to the officers 

and crew of the NOAA ship Oscar Dyson and the visual and acoustic observers who participated 

on this cruise: Suzanne Yin, Ernesto Vázquez Morquecho, Greg Fulling, Carol Keiper, Cynthia 

Christman, Kelly Cunningham and Sean Suk. Thank you to Holly Fearnbach and Dave Ellifrit 

for conducting the killer whale photo-identification analysis. Tarry Rago provided helpful 

suggestions on the report. Special thanks to Catherine Berchok, Tom Norris, and Greg Falxa who 

advised and helped with the set-up and design of the cruise. Thank you to the Southeast Fisheries 

Science Center for the use of their towed array. Many thanks for the thoughtful reviews by 

Janice M. Waite (NMML) and Kathleen M. Stafford (Applied Physics Lab, University of 

Washington). Technical edits were provided by Gary Duker and James Lee of the Alaska 

Fisheries Science Center’s Publications Unit. This survey was conducted under MMPA 

Scientific Research Permit No. 782-1719. 

19

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22

Table 1. -- Strata and proposed effort allocation in the study area. 

Stratum Area 

(km2

) 

Number of 

tracklines Total effort (km) 

Inshore 47,411 12 1,905 

Offshore 98,253 10 1,944 

Total 22 3,849 

Table 2. -- Sample sizes for estimation of detection probability using the GOALS 2009 and 

Miller Freeman 2003 sighting data. 

Species GOALS 2009 Miller Freeman 2003 

Fin whale 19 57 

Humpback whale 9 42 

Unidentified large whale 10 1 

Total 38 100 

Table 3. -- Covariates used in the multiple covariate distance sampling (MCDS) models using 

GOALS 2009 and Miller Freeman 2003 sighting data. 

Covariate Type Levels 

Method Factor Naked eye, Big eye binoculars 

Ship Factor Oscar Dyson (2009), Miller Freeman (2003) 

Group size Factor Group size estimate for each sighting 

Beaufort scale Factor 0, 1, 2, 3, 4, and 5 

Species Factor Fin, humpback and unidentified large whale 
23

Table 4. -- Completed visual effort for the GOALS 2009 research cruise. 

Stratum Effort 

(km) 

Inshore 460 

Offshore 300 

Total on-effort 760 

Transit 384 

Fog effort 169 

Total 1,313 

Table 5. -- Marine mammal sightings (individuals) from the GOALS 2009 research cruise. 

Species On-effort Off-effort Total 

Cetaceans 

Fin whale 20(56) 4(8) 24(64) 

Humpback whale 10(19) 1(1) 11(20) 

Gray whale 1(2) 2(6) 3(8) 

Minke whale 2(3) 0 2(3) 

Killer whale 6(119) 0 6(119) 

Dall’s porpoise 10(59) 0 10(59) 

Harbor porpoise 30(89) 0 30(89) 

Pacific white-sided dolphin 1(60) 0 1(60) 

Unid large whale 22(31) 6(7) 28(38) 

Unid. small whale 2(2) 0 2(2) 

Unid. dolphin/porpoise 2(2) 0 2(2) 

Total cetacean 106(442) 13(22) 119(464) 

Pinnipeds and Otters 

Steller sea lion 6(28) 0 6(28) 

Harbor seal 2(2) 0 2(2) 

Sea otter 1(1) 0 1(1) 

Unid. pinniped 4(4) 0 4(4) 

Total pinniped 13(35) 0 13(35) 

Total 119(477) 13(22) 132(499) 
24

Table 6. -- Acoustic detections from the GOALS 2009 research cruise using two-element towed 

 array. 

Species Detections during 

visual effort 

Detections during 

acoustic only effort Total 

Killer whale 8(3*) 8 16 

Sperm whale 1 27 28 

Unidentified odontocete 0 5 5 

Total 9 40 49 

 * Acoustic detections matched to visual sightings. 

Table 7. -- Number of photo-identified individuals collected during the GOALS 2009 research 

 cruise. 

Species 11 April 09 12 April 09 18 April 09 Total 

Fin whale 4 0 0 4 

Killer whale 0 5 14 19 

Total 23 

Table 8. -- Model parameter of detection probability estimation for the GOALS 2009 large whale 

sighting data only. 

Model No. Model No. 

par 

∆ AIC ESW 

(km) 

ESW 

CV 

1 Half normal without series expansions 1 0.00 2.91 0.15 

2 Hazard rate without series expansions 2 1.54 3.17 0.17 

No. par – number of parameters, AIC – Akaike Information Criterion, ESW – effective search half-width, 

CV – coefficient of variation 
25

Table 9. -- Estimation of density and abundance of fin, humpback, and unidentified large whales 

in inshore (area = 47,411 km2) and offshore (area = 98,253 km2) strata using the 

GOALS 2009 data only. 

Fin whale Humpback whale Unidentified large whale 

Inshore Offshore Inshore Offshore Inshore Offshore 

No. sightings 11 7 7 1 5 1 

Encounter rate 0.067 0.050 0.024 0.003 0.013 0.003 

Encounter rate CV 0.29 0.57 0.61 0.56 0.50 0.57 

Group Size 2.81 2.14 1.57 1 1.2 1 

Group Size CV 0.23 0.07 0.12 0 0.17 0 

Model 1 

Density (ind/km2) 0.011 0.009 0.004 0.0005 0.002 0.0005 

Density 95% CI (0.005, 0.024) (0.001, 0.068) (0.000, 0.017) (0.000, 0.005) (0.000, 0.008) (0.000, 0.005) 

Abundance 548 843 194 56 106 56 

CV 0.33 0.59 0.63 0.59 0.53 0.59 

Table 10. -- Model parameter of detection probability estimation for the GOALS 2009 and 

 Miller Freeman 2003 large whale sighting data. 

Model No. Model No. 

par 

∆ AIC ESW (km) ESW CV 

3 Half normal with Method covariate 2 0.00 2.69 0.08 

4 Half normal without covariate 1 0.38 2.72 0.07 

5 Half normal with Ship covariate 2 2.03 2.71 0.07 

6 Half normal with Species covariate 3 2.57 2.70 0.08 

No. par – number of parameters, AIC – Akaike Information Criterion, ESW – effective search half-width, 

CV – coefficient of variation. 
26

Table 11. -- Estimation of density and abundance of fin, humpback and unidentified large whales 

 in inshore (area = 47,411 km2) and offshore (area = 98,253 km2) using the 

 GOALS 2009 and Miller Freeman 2003 data. 

Fin whale Humpback whale Unidentified large whale 

Inshore Offshore Inshore Offshore Inshore Offshore 

No. sightings 11 7 7 1 5 1 

Encounter rate 0.067 0.050 0.024 0.003 0.013 0.003 

Encounter rate CV 0.29 0.57 0.61 0.56 0.50 0.57 

Group Size 2.81 2.14 1.57 1 1.2 1 

Group Size CV 0.23 0.07 0.12 0 0.17 0 

Model 3 

Density (ind/km2

) 0.012 0.009 0.004 0.0005 0.003 0.0005 

Density 95% CI (0.006, 0.025) (0.000, 0.083) (0.001, 0.017) (0.000, 0.005) (0.000, 0.009) (0.000, 0.005) 

Abundance 594 889 219 56 118 56 

CV 0.29 0.57 0.57 0.57 0.52 0.57 

Figure 1. -- Tracklines for the GOALS 2009 research cruise. 
27

Figure 2. -- Completed visual effort and baleen whale sightings from the NOAA ship Miller 

Freeman 2003 research cruise used in combination with the GOALS 2009 data for 

analysis (circle = fin whale; star = humpback whale, square = unidentified large 

whale). Inshore and offshore strata for the 2009 GOALS survey (gray) are shown 

here for geographic reference. 
28

Figure 3. -- Completed visual and acoustic effort for the GOALS 2009 research cruise (visual 

and acoustic on-effort – bold black; transit and acoustic effort – dark gray; fog and 

acoustic effort – light gray; acoustic effort only – thin black). 
29

Figure 4. -- Baleen whale sightings from the GOALS 2009 research cruise (circle = fin whales, 

square = gray whale, star = humpback whale, diamond = minke whale; open 

 symbol = on-effort sightings, dotted symbol = off-effort sightings). 
30

Figure 5. -- Toothed whale sightings from the GOALS 2009 research cruise (star = harbor 

porpoise, square = Dall’s porpoise, circle = killer whale, diamond = Pacific whitesided dolphin; open symbol = on-effort sightings). 
31

Figure 6. -- Unidentified cetacean sightings from the GOALS 2009 research cruise (square = 

 large whale, star = dolphin/porpoise, circle = small whale; open symbol = on-effort 

 sightings, dotted symbol = off-effort sightings). 
32

Figure 7. -- Pinniped and otter sightings from the GOALS 2009 research cruise (circle = Steller 

sea lion, star = sea otter, square = harbor seal, diamond = unidentified pinniped; 

open symbol = on-effort sightings). 
33

Figure 8. -- Acoustic effort and detections from the GOALS 2009 research cruise (light, dotted 

 triangle = killer whale, dark, open triangle = sperm whale). 

35

APPENDIX 

 Catalog of photo-identified individuals during the GOALS 2009 research cruise. 

Fin Whales 

CRC-BP-temporary-001-20090411-D6-0011edit; Cascadia Research Collective, Annie B. Douglas 

CRC-BP-temporary-002-20090411-D6-0019edit; NMML, Brenda K. Rone 

CRC-BP-temporary-003-20090411-D6-0027edit; Cascadia Research Collective, Annie B. Douglas 
36

CRC-BP-temporary-004-20090411-D6-0037edit; Cascadia Research Collective, Annie B. Douglas 

Killer Whales

 

CRC-OO-temporary-001-20090412-30D-0164edit-OOh 

(r); Cascadia Research Collective, Annie B. Douglas 

CRC-OO-temporary-001-20090412-30D-0184edit 

OOh(l); Cascadia Research Collective, Suzanne Yin

 

CRC-OO-temporary-002-20090412-30D-0181edit OOg; 

Cascadia Research Collective, Annie B. Douglas 

CRC-OO-temporary 003-20090418-30D-0066edit OOc; 

Cascadia Research Collective, Annie B. Douglas
37

 

 

 

 

CRC-OO-temporary 005-20090418-30D-0066edit OOd; 

Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary 007-20090418-30D-0073edit OOk; 

(right) Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary-004-20090412-30D-178edit OOc; 

Cascadia Research Collective, Suzanne Yin 

\ CRC-OO-temporary 006-20090418-30D-0060edit OOg; 

Cascadia Research Collective, Annie B. Douglas

 

 

 

CRC-OO-temporary 008-20090418-30D-0060edit Ooh; 

Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary 009-20090418-30D-0076edit OOl; 

Cascadia Research Collective, Annie B. Douglas
38

 

CRC-OO-temporary-010-20090412-30D-0172edit OOa; 

Cascadia Research Collective, Suzanne Yin

CRC-OO-temporary 011-20090418-30D-0071edit OOe; 

Cascadia Research Collective, Annie B. Douglas

 

 CRC-OO-temporary 012-20090418-30D-0080edit(l) 

OOm; Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary 012-20090418-30D-0089edit OOm(r); 

Cascadia Research Collective, Annie B. Douglas

 

 CRCRC-OO-temporary 013-20090418-30D 0120edit 

OOn; Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary 014-20090418-30D-0127edit OOp; 

Cascadia Research Collective, Annie B. Douglas 
39

 

CRC-OO-temporary 016-DY0905_18-Apr-09_S57 60 

63_BKR_8441 OOa; NMML, Brenda K. Rone

CRC-OO-temporary 015-20090418-30D- 0083edit OOq(r) 

Cascadia Research Collective, Annie B. Douglas

 

 

CRC-OO-temporary -017-20090418R-30D-0069edit OOb; 

Cascadia Research Collective, Annie B. Douglas

CRC-OO-temporary-018-20090418-D6-0086edit OOs; 

Cascadia Research Collective, Suzanne Yin

 

CRC-OO-temporary-019-20090412-D6-0048 OO1; 

Cascadia Research Collective, Annie B. Douglas
RECENT TECHNICAL MEMORANDUMS
 

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