The survey was conducted on the NOAA Ship Delaware II from July 26^th to September 3^rd, 1999, beginning and ending in Woods Hole, Massachusetts. The study area encompassed the offshore waters from Georges Bank to the Bay of Fundy, and east along the Scotian Shelf to the Gully and French Bank. The cruise consisted of two legs, the first from 26^th July to 13^th August, and the second from 16^th August to 3^rd September. The in-port stop between the legs was in Woods Hole. Phil Clapham served as Chief Scientist for the first leg, Tim Cole for the second.

The intent of this cruise was to survey offshore waters, notably of the Scotian Shelf, for large whales. Objectives of the cruise were to: (i) assess the distribution of large whales in the study area; (ii) photographically identify large whales for the purpose of individual identification; (iii) obtain skin biopsy samples of large whales for genetic, toxicological and stable isotope analysis; and (iv) conduct intensive oceanographic sampling of present and historic large whale habitat. The priority species was the northern right whale (Eubalaena glacialis), but the cruise was also focused on other large baleen whales, including the humpback (Megaptera novaeangliae), blue (Balaenoptera musculus), sei (B. borealis) and fin (B. physalus). Skin biopsies were also taken on an opportunistic basis of several odontocete species.

Survey methods
On the first leg, Delaware II departed Woods Hole, Massachusetts on 26^th July 1999. The vessel steamed overnight to the Northeast Peak of Georges Bank, where she entered Canadian waters (report filed to DFO via email by the Master). She surveyed east along the 100-fathom isobath, and ran survey tracks through two areas of historically important right whale habitat: (i) Emerald and Western banks, and (ii) Emerald and Lahave Basins. Track lines were spaced approximately ten miles apart in these two survey blocks, with intensive CTD sampling at 5-nm intervals. Other portions of this region were surveyed in transit, or as determined by sightings. The vessel subsequently proceeded to a survey block north of Browns Bank (another area of historical importance for right whales), where oceanographic sampling was also conducted at predetermined stations. The vessel then proceeded into the Bay of Fundy, where the crew worked the large concentration of right whales found there and also conducted oceanographic sampling in the vicinity of whales. Delaware II left Canadian waters on 9^th August, stopping in Bar Harbor, Maine to shelter from bad weather and discharge an injured crew member. The vessel left again on 11^th August, proceeding to the Northeast Peak of Georges Bank, then along the Northern Edge and into Woods Hole, arriving early on the 13^th August.

On the second leg, the vessel departed Woods Hole on the 16^th August and proceeded directly to the Bay of Fundy. There, the crew conducted more oceanographic sampling around right whales before proceeding to search the banks of the Scotian Shelf. Delaware II ran as far east as the Gully, then northwest to French Bank before returning west to Roseway Basin. The vessel returned home on 3^rd September via the Northeast Peak, southern flank and Southeast Part of Georges Bank.

A sighting watch of four individuals, using both Big Eye and Little Eye binoculars, was maintained on the flying bridge during daylight hours (0700 to 1900 Eastern Daylight Time). All cetacean sightings were recorded, together with information on merchant ships. The vessel broke track for all right whale sightings, and opportunistically when other species were sighted. If weather conditions allowed, a 5.5 meter rigid-hulled inflatable boat was deployed to obtain photographs and skin biopsies.

Photographic and biopsy sampling methods
Photographs were taken with a 35 mm camera equipped with an autofocus zoom or telephoto lens, power winder and either 400 ASA black and white or 200 ASA color slide film. Individual identity was documented using the following natural or acquired characteristics: ventral fluke pattern and dorsal fin shape/scarring (humpback whales), callosity pattern and scarring (right whales), blaze and chevron pattern and dorsal fin shape (fin whales), mottling pattern on the body (blue whales).

Skin biopsies were taken with a 70-kg-draw crossbow or rolling block rifle and a specially designed sampling dart. Each biopsy was divided three ways: (i) central core into formalin for toxicological studies; (ii) part of the dermis and epidermis into DMSO for genetics; and (iii) remaining skin frozen for stable isotope analysis.

Oceanographic sampling methods
Oceanographic sampling involved CTD casts (including an optical plankton counter) as well as plankton sampling using bongo nets. Sampling was conducted at five-nm stations in survey blocks, and at other locations dictated by the presence of whales (notably right whales). The vessel's computer automatically recorded a variety of basic environmental data, together with position, every three minutes. An oceanographic sampling report is attached as Appendix I.
 
 

Area covered
This included the predetermined survey blocks on Emerald/Western Banks, in Emerald/Lahave Basins and an area around the shelf break south of Emerald Bank, as well as much of Western Gully and the 100 fathom isobath from Northeast Channel as far east as the Gully. Roseway Basin was also covered twice, as were various other banks as far east as French Bank. Occasional forays were made into deeper water on the shelf break to search for blue whales. Poor weather, especially dense fog on the first leg, made survey coverage difficult in some areas, but virtually all regions were covered at least once during the course of the entire study period.

Large whale sightings
Numbers of large whales observed are summarized in Table1. The situation on the Scotian Shelf was very different this year than in 1998 (see Cruise Report for DE-9808). Only a single right whale was observed in this area, while an unusually large concentration of this species was present in the Bay of Fundy. Humpbacks were less numerous on the Scotian Shelf than in 1998, although concentrations were found in various locations including the previously unstudied French Bank area. Fin whales were numerous throughout the study area (albeit somewhat less so than in the previous summer). A total of 180 right whales were observed, all but one in the Bay of Fundy. Four blue whales were recorded. A total of approximately 94 large whales were photographed for the purpose of individual identification; of these, most were humpback whales on the Scotian Shelf or right whales in the Bay of Fundy.

Other cetacean sightings
Numbers of other cetacean sightings are summarized by species in Table 2. Notable species included pilot whales (Globicephala melaena), offshore bottlenose dolphins (Tursiops truncatus), sperm whales (Physeter macrocephalus), striped dolphins (Stenella coeruleoalba), bottlenose whales (Hyperoodon ampullatus, all in the Gully), and common dolphins (Delphinus delphis).

Biopsy sampling
A total of 110 biopsy samples (and one sample of sloughed skin, from a blue whale) were taken during the cruise; these are summarized in Tables 1 (baleen whales) and Table 2 (other cetaceans). The final disposition of these samples is as follows: all toxicological subsamples to Woods Hole Oceanographic Institution (C. Godard and M. Moore); right whale genetic subsamples to McMaster University (B. White and M. Brown); all other large whale genetic samples to University of North Wales at Bangor (P. Palsbøll and M. Bérubé); all small cetacean samples to the Southeast Fisheries Science Center (P. Rosel); and all stable isotope subsamples to NEFSC (S. Wetmore).

Oceanographic sampling
Oceanographic sampling is summarized in Appendix I.
 
 

The data will be maintained by the Protected Species Branch of the Northeast Fisheries Science Center in Woods Hole, Massachusetts. All data are available on computer disk from the above.
 
 
 

Introduction
Oceanographic sampling was conducted aboard the Delaware II during the 1999 large whale assessment cruise from July 26 to September 3. The cruise was divided into two legs lasting from July 26 to August 13 and August 16 to September 3. The primary objective of the oceanographic sampling was to characterize the habitat of the North Atlantic right whale (Eubalaena glacialis) on the Scotian Shelf using both physical and biological oceanographic measurements. Although the primary species of interest was the North Atlantic right whale, the oceanographic data collected during this cruise will be useful in characterizing the habitat of other large whale species found on the Scotian Shelf (e.g., humpback, finback and minke whales).

Discrete vertical sampling was conducted with a caged instrument package that included a Seabird conductivity/temperature/depth (CTD) instrument (model SBE 19, serial number 853), a Focal Technologies optical plankton counter (OPC) (model OPC-1T, serial number TOW-015) and a Tracor acoustic profiling system (TAPS) (model III V6.041, serial number 4). Plankton tows were conducted periodically using a 61 cm double bongo frame and 333 µm mesh net with a Seabird CTD (model SBE 19, serial number 851) attached to the sea cable just above the bongo frame. Acoustic backscatter to 250 m depth was continuously recorded along survey transects at 38 and 120 kHz using a vessel-mounted Simrad EK 500 Scientific Echo Sounder (model EK5-082819, serial number 3115). Current profiles were measured in the upper 80 m using a vessel-mounted RD Instruments acoustic doppler current profiler (ADCP) (model VM-300S). Data from a variety of instruments, including a Seabird thermosalinograph (model SBE 21), a flow-through Turner Designs fluorometer (model 10-AU-005), a Young meteorological system, three Furuno hull-mounted, sea surface temperature sensors (model T-2000), a Sperry gyro compass (model MK 227) and the GPS navigational system, were logged continuously by the Delaware II Scientific Computer System (SCS).

Vertical Casts
The CTD/OPC/TAPS package was lowered at an average rate of 30 m min^-1 to within 5 m of the sea floor. The planned survey blocks consisted of 3 to 7 transects which ranged from 20 to 40 nm in length. Vertical casts were conducted at 5 nm station spacings along each survey transect. Because the time required to conduct oceanographic sampling had to be balanced with the time required to conduct the large whale assessment survey, not all transects were sampled. When possible, vertical casts and active surveying were conducted for entire transects or for station grids within survey blocks. Additional transects and survey blocks were added as time and sighting conditions warranted.

In total, 157 vertical casts were completed. Of these, 141 were planned stations along survey transects, 8 were in the vicinity of North Atlantic right whales (two casts were with the same group), 2 were in the vicinity of humpback whales, 1 was near a concentration of humpback, finback and minke whales and 5 were conducted for calibration purposes. The CTD and OPC performed very well while the TAPS was rendered useless because of a faulty pressure sensor. The TAPS is designed to begin transmitting sound when the pressure sensor indicates that the instrument has reached a specified depth. Since the pressure sensor was defective and measured zero pressure at all depths, the acoustics were never activated. The TAPS was removed from the instrument cage on August 17. Before permanent removal, the cage was lowered three times with the TAPS and three times without the TAPS at the same station to determine if the TAPS and its mounting plate interfered with water flow into the OPC. This experiment was repeated at a second station.

Plankton Tows
Zooplankton sampling was conducted with 61 cm side-by-side double bongos with 333 µm mesh nets. The nets were towed obliquely to 5 m off the sea floor or to the maximum depth allowed by the 500 m spool of sea cable available on the aft oceanographic winch. Pay-out and pay-in rates for the nets were approximately 35 and 20 m min^-1, respectively. The filtered volume for each net was estimated using a General Oceanics flowmeter. Samples from one of the bongos were preserved in 5% formalin (50 ml of 37% formaldehyde was added to a one quart jar of sample and seawater) for species identification and abundance estimation while a small portion of the opposite bongo was frozen for stable isotope analysis. Net deployment and sample processing were conducted in accordance with MARMAP protocols.

The bongo nets were deployed occasionally within a survey block to determine average species-specific abundance and species assemblage for comparison to the OPC data. Bongo tows were also conducted in the vicinity of all North Atlantic right whale sightings and in a few instances, near other large whale species. Two successive hauls were sometimes conducted at the same station but to different depths to resolve upper water column zooplankton assemblages from those occurring deeper or near the bottom. In total, 27 bongo tows were completed at 22 stations. Of those, 13 single hauls were conducted to calibrate the OPC, 5 double hauls and 2 single hauls were near right whales, 1 single haul was near a concentration of humpback, finback and minke whales and 1 single haul was near a blue whale. The CTD affixed to the bongo tow wire malfunctioned several times despite replacing the batteries, cleaning the battery contacts, cleaning the connector and tightening the on/off switch. Fortunately, the CTD tended to turn off on the upcast, so the nets were towed to an exact depth on all but three occasions. The left and right flow meters agreed to within 4.5% on all but one haul. At station 18, the flowmeters differed by 21% for unknown reasons.

Sonar
The EK 500 Scientific Echo Sounder recorded acoustic backscatter at two frequencies (38 and 120 kHz) at 2.0 and 2.5 second intervals during the first and second legs of the large whale assessment cruise, respectively. To reduce data volume, the instrument would typically be turned on before the beginning of the survey day and turned off at night. On several occasions, the EK 500 was left running continuously overnight to observe the timing of euphausiid vertical migration on the Scotian Shelf. The EK 500 was also turned off on several occasions when the ship was near bottlenose, humpback, minke and right whales. While in the Gully, it appeared that bottlenose whales readily approached to within 25 m of the ship while the sonar was turned off, but would stay outside of an approximate 500 m perimeter while the sonar was turned on. In contrast, humpback whales approached within 25 m of the ship many times while the sonar was actively pinging. It is unclear whether the sonar had an effect on right whales encountered in the Bay of Fundy and Roseway Basin. Animals frequently came within 100 m of the ship in the Bay of Fundy while the sonar was active. The sonar was immediately turned off during operations around the single right whale encountered in Roseway Basin, but the ship never came within 300 m of this animal.

Acoustic Doppler Current Profiler
The shipboard ADCP recorded vertical current profiles every 30 seconds over the upper 80 m in 2 m depth bins. The ADCP was only logged during leg 2 of the cruise. It was typically left on while the ship operated in a single survey block over several days. ADCP data were also collected while the ship was hove to at night to measure currents associated with the local tide.

SCS Data
The following data were logged continuously by the shipboard SCS at 15 second intervals: GPS latitude, GPS longitude, GPS speed over ground, GPS course over ground, Sperry gyro compass, ADCP speed over ground, water depth from the ADCP, water depth from the EK 500 38 kHz transducer, ADCP gyro compass, water depth from the bridge Furuno fathometer, surface temperature (4 measurements), surface salinity, surface chlorophyll, true wind speed and direction (port and starboard), air temperature, relative humidity and barometric pressure. During leg 2 of the large whale assessment cruise, the water depth measured by the EK 500 12 kHz transducer was included in the SCS data.

Remotely Sensed Data
Synoptic sea surface temperature (SST) data were collected during the cruise by the Advanced Very High Resolution Radiometer (AVHRR) carried aboard the NOAA-series polar-orbiting environmental satellites. Measurements of upwelling infrared radiation were telemetered via high resolution picture transmission (HRPT) to a ground station on Wallops Island, Virginia and post-processed into 1.1 km resolution sea surface temperature grids by the University of Rhode Island. Surface chlorophyll estimates were similarly derived from measurements of upwelling visible radiation made from the SeaWifs sensor carried aboard the polar-orbiting SeaStar satellite. Telemetered data were received by a HRPT receiving station in Nova Scotia and archived at NASA's Goddard Space Flight Center. These data will be post-processed into 1.1 km resolution surface chlorophyll grids in the near future.

Acknowledgments
Peter Ortner and Shailer Cummings (NOAA Atlantic Oceanographic and Meteorological Laboratory) provided the optical plankton counter, Mark Berman (NMFS Naragansett) provided the Tracor acoustic profiling system, Maureen Taylor (NMFS Woods Hole) provided the CTD instruments, Jerry Prezioso (NMFS Naragansett) provided the zooplankton sampling gear and Rick Trask (WHOI) provided the cage hardware. I am indebted to each for their generosity in loaning me their instruments and equipment. Bill Michaels (NMFS Woods Hole) donated his time and expertise in setting up and calibrating the EK 500 Scientific Echo Sounder. Peter Cornillon (URI) graciously agreed to acquire, process and archive the AVHRR-derived sea surface temperature data. The oceanographic sampling would not have been possible without the able assistance of the entire marine mammal survey team lead by chief scientists Phil Clapham (NMFS Woods Hole) (leg 1) and Tim Cole (NMFS Woods Hole) (leg 2) as well as the assistance of the officers and crew of the NOAA Ship Delaware II captained by Jack McAdam (leg 1) and Brian Lake (leg 2). Bruce Mate (OSU), Charlie Miller (OSU), Phil Clapham and Tim Cole all provided critical support and advice during the planning and execution of this study.