Methods
I) Aerial Surveys

Aerial surveys were conducted from January through mid-May 2002 in the Cape Cod Bay Critical Habitat and adjacent waters (Figures 1a-e, Tables 1a-e). The aerial survey protocol for Cape Cod Bay, as described in Kraus et al (1997), was adopted with some modifications. Fifteen tracklines were flown latitudinally (east - west) at 1.5 nautical mile (nm) intervals from the mainland to the Cape Cod Bay shoreline (Figure 1a). An additional trackline, 25 nm in length, paralleled the outer coast of Cape Cod from east of Chatham to the eastern end of trackline one at a distance of about three nm from shore (Figure 1a, trackline number 16). The east-west flight pattern in Cape Cod Bay was chosen for scientific and safety reasons. In these latitudes, winter aerial surveys are hampered by low sun angles in the early and late hours of a survey day and glare is a significant factor in sightability of marine mammals. On east-west tracklines, although glare was a factor in one of the forward quadrants, there was always a section of the survey swath that could be observed without being compromised by glare. It was also safer to have the aerial survey tracklines begin and end near land. A total of 320 nm of 'on-trackline' miles were flown during each completed survey (Table 1a). "On-trackline" miles were those miles flown while surveying due east or due west in Cape Cod Bay and along the outer coast of Cape Cod, but excludes all miles flown between tracklines (cross legs) or while circling.

The surveys were flown under VFR (visual flight rules) conditions up to and including Beaufort sea state four. Surveys were aborted in Beaufort sea state five and/or when visibility decreased below two miles in fog, rain or snow. All aerial surveys originated at Chatham Airport, Chatham, MA. They were conducted in a Cessna 337 Skymaster (5382S), a twin engine, high-wing aircraft with retractable landing gear. The aircraft was equipped with two GPS (global positioning system) navigation systems, full IFR (instrument flight rules) instrumentation, marine VHF radio with external antenna, and wing-tip mounted VHF tracking antennas. Safety equipment included a life raft, four survival suits, signal flares, a medical kit, a waterproof VHF radio, a portable EPIRB, and an aircraft mounted ELT (emergency locator transmitter). All occupants wore aircraft approved PFDs (personal floatation device) during the entire flight.

Surveys were conducted at a standard altitude of 750 feet (229 meters) and a ground speed of approximately 100 knots, using methodology developed by CeTAP (Scott and Gilbert 1982, CeTAP 1982). The survey team consisted of a pilot, data recorder, and two observers positioned on each side of the aircraft in the rear seats. The two rear seat observers scanned the water surface from 0° - 90°, out to at least two nautical miles and reported sightings when they were abeam of the aircraft. In order to maintain a standardized sighting effort, the pilot and data recorder were instructed not to alert the observers to any sightings of marine mammals until after it had been passed by the aircraft and clearly missed by the observers. The turn at the end of each trackline was initiated and completed about 1.5 nm from shore in Cape Cod Bay to maximize the opportunity to observe any whales near shore.

All sightings of marine animals except birds were recorded. Sightings identified as species other than right whales were counted, logged and passed without breaking the trackline and circling in order to maximize flight time available for investigating right whale sightings. Sightings of all vessels in the area were recorded by location and type. At sightings identified as right whales, as well as sightings of large whales, which were not immediately identified by species, the aircraft broke track at right angles to the sighting and circled over the animal to obtain photographs. Photographs were obtained of as many individual right whales within a given aggregation as possible. For each right whale, behavior and interaction with other whales or any nearby vessels or fishing gear was noted. In a few instances, when right whales were spotted from the plane in close from the vessel so that the plane could devote more time to surveying. The right angle distance of each sighting from the flight track was determined from GPS positions.

At the conclusion of photographic effort at each sighting, the aircraft returned to the trackline at the point of departure using the GPS position recorded in the log. These methods conform to research protocols followed by the North Atlantic Right Whale Consortium (CCS, NEAq, URI, and WHOI) and approved by the US NMFS. Trackline and sighting data from the daily logs were entered into the Right Whale Initiative DBase program designed for compatibility with the Right Whale Consortium database. Copies of the daily logs from the aerial surveys are on file at CCS and URI.

Photographic Methods
i) Identification Photographs:
During aerial and shipboard surveys, photographs were taken on Kodak Kodachrome 200ASA color slide film, using hand-held 35-mm cameras equipped with 300-mm telephoto lenses and motor drives. From the air, photographers attempted to obtain good perpendicular photographs of the entire rostral callosity pattern and back of every right whale encountered as well as any other scars or markings. From the boat, photographers attempted to collect good oblique photographs of both sides of the head and chin, the body and the flukes. The data recorder on both platforms was responsible for keeping a written record of the roll and frame numbers shot by each photographer in the daily log.

ii) Photo-analysis and Matching:
Photographs of right whale callosity patterns are used as a basis for identification and cataloging of individuals, following methods developed by Payne et al (1983) and Kraus et al (1986). The cataloging of individually identified animals is based on using high quality photographs of distinctive callosity patterns (raised patches of roughened skin on the top and sides of the head), ventral pigmentation, lip ridges, and scars (Kraus et al 1986). New England Aquarium (NEAq) has curated the catalogue since 1980 and to the best of their knowledge, all photographs of right whales taken in the North Atlantic since 1935 have been included in NEAq's files. This catalogue allows scientists to enumerate the population, and, from resightings of known individuals, to monitor the animals' reproductive status, births, deaths, scarring, distribution and migrations. Since 1980, a total of 26,275 sightings of 436 individual right whales have been archived, of which 327 are thought to be alive, as of December 2001 (A. Knowlton, NEAq, pers. comm.)

The matching process consists of separating photographs of right whales into individuals and inter-matching between days within the season. To match different sightings of the same whale, composite drawings and photographs of the callosity patterns of individual right whales are compared to a limited subset of the catalogue that includes animals with a similar appearance. For whales that look alike in the first sort, the original photographs of all probable matches are examined for callosity similarities and supplementary features, including scars, pigmentation, lip crenulations, and morphometric ratios. A match between different sightings is considered positive when the callosity pattern and at least one other feature can be independently matched by at least two experienced researchers (Kraus et al 1986). Exceptions to this multiple identifying feature requirement include whales that have unusual callosity patterns, large scars or birthmarks, or deformities so unique that matches from clear photographs can be based on only one feature. Preliminary photo-analysis and inter-matching was carried out at CCS, with matches confirmed using original photographs cataloged and archived at NEAq.

iii) Photographic Data Archiving
Upon completion of the matching process, all original slides were returned to CCS and incorporated into the CCS catalogue of identified right whales to update existing files, using the same numbering system as NEAq, in archival quality slide sheets. New England Aquarium (NEAq) archives copies of photographs representing each sighting. Copies of photographs of individuals that are better than existing records, and photographs of newly identified whales, will be included in the NEAq master files as "type specimens" for future reference. The master files are maintained in fireproof safes at NEAq. All catalogue files are available for inspection and on-site use by contributors and collaborators.

whales_air_tracklines.csv