Vessel surveys for marine birds in the Gulf of America (Gulf of Mexico): Protocol manual (2017–2025)

This manual provides contextual background and detailed instructions for survey procedures that were used to collect, enter, archive, and analyze digitally-entered field data collected for marine birds during three large-vessel survey projects in the northern Gulf of America (also Gulf of Mexico, hereafter “Gulf”). Projects using this protocol included the Gulf of Mexico Marine Assessment Program for Protected Species (GoMMAPPS: 2017-2018), the Vessel Surveys for Abundance and Distribution of Marine Mammals and Seabirds (VSAD: 2023-2024), and certain repositioning legs of the Atlantic Marine Assessment Program for Protected Species (AMAPPS: 2021, 2023). Based substantially on Ballance and Force (2011), the protocol used in the Gulf is based on a standardized 300 m wide strip transect using software architecture available in program SeeBird (v.4.3.7), a data collection program developed by Robert Holland at the National Oceanic and Atmospheric Administration (NOAA) Southwest Fisheries Science Center, La Jolla, CA. Survey protocols relied on the digital entering of standardized metadata linked to sightings of seabirds (e.g., species, number, location, distance bin, association[s], behavior, flight direction, flight height, angle from ship, age, sex, plumage, and optional comments) as well as other protected species. SeeBird has additional modules that may be used to input data on mixed-species seabird flocks and flying fish (only the latter was used in the Gulf). SeeBird includes “user-driven” commands issued through the keyboard, touch screen, and/or mouse, many of which are aided by drop-down menus that prompt the user options that are available for input. In addition, the program features “event–driven” inputs updated at intervals selected by the user, and that also record exact time and location of such edits. We describe how SeeBird was adapted in the Gulf both to run directly via serial connections from the ship’s navigation system and to operate independently from the ship through a satellite-derived GPS feed. This user manual also gives information about: procedures used to document flying fish abundance on Gulf surveys; how to use the Beaufort scale for standardizing wind force and sea state environmental conditions; how to make and use a hand-held rangefinder for delimiting strip transect bin distances; additional functionalities in SeeBird for which user guides are not available; file-naming, file-archiving, and file location conventions used on Gulf marine bird surveys; protocols used in the Gulf for describing relative abundance of the macro-alga Sargassum as an environmental covariate; the standardized four-letter taxa codes (summarized in a SpeciesCode.txt file) used in the Gulf for denoting species, other taxonomic, and event categories as inputs to SeeBird; an Excel example spreadsheet that has successfully imported SeeBird’s ASCII text file; procedural steps to import, edit, and archive into Excel ASCII text files from SeeBird; initialization instructions for starting up program SeeBird on a Panasonic ToughBook™ that relies on integrated, satellite-derived GPS, and for writing “S” (seabirds + other taxa) and “E” (flying fish) ASCII files to a folder or subfolder other than the default root location on the laptop that contains program SeeBird; how to trouble-shoot miscellaneous start-up problems with program SeeBird; how to add new four-letter codes (into a SpeciesCode.txt file) when additional taxa or objects of interest are encountered. The primary objective of this manual is to archive a permanent, replicable history of survey methodology to facilitate continuity with comparable future projects that may be conducted in the Gulf. A secondary objective is to describe why and how program SeeBird was applied and adapted specifically for operating in Gulf survey conditions. As of late 2025, user guides for software program SeeBird were no longer readily accessible, so this manual serves also to address that gap.