Alaska Science Center
NPPSD Taxonomic Code List for Pelagic Bird and Mammal Surveys, Version 2.1 READ ME
NPPSD Taxonomic Code List for Pelagic Bird and Mammal Surveys, Version 2.1
While compiling the North Pacific Pelagic Seabird Database (NPPSD) we found that there was significant variation in the codes used to identify species. We recognized the need for a cross-walk that would allow us to integrate various data sets into a single database and develop a standard set of codes. The U.S. Bird Banding Laboratory (BBL) was one of the first groups to establish a standard set of four-letter alpha codes. These codes simplified data transcription and have become standard shorthand for various ornithological programs in North America. Unfortunately, the BBL list contains a limited number of species and there are some inconsistencies with the American Ornithological Union (AOU) taxonomy. A new set of four-letter codes, hereafter referred to as the AOU code list, was developed by Pyle and DeSante (2012) to reconcile the BBL list with the current AOU taxonomy. The AOU list has been updated seven times, most recently in 2012 (http://www.birdpop.org/alphacodes.htm).
Unfortunately, even the AOU code list does not include every species observed in the North Pacific, marine mammal species, or account for many birds not identifiable to species, e.g. Unidentified Tern. These limitations have led the assignment of numerous codes assigned on an ad hoc basis. To create NPPSD code list, we used a combination of codes including the most recent AOU list and those used historically by the U.S. Fish and Wildlife Service, U.S. Geological Services, and various University based investigators working in the North Pacific. Where possible we followed the naming conventions used to create the AOU code list. Marine mammal codes generally followed the same naming conventions as the bird codes; commonly, the first two letters of each word in common name, e.g. Common Murre = COMU.
When dealing with historical data researchers are faced with the problem of reconciling codes due to changes in both common names and scientific names. We only list the most current taxonomic information in the NPPSD code list. For taxonomic purposes we relied on the Integrated Taxonomic Information System (ITIS; (http://www.itis.gov/), which is now the standard reference used by federal and state governments as well as non-government organizations. Additionally, for birds we used the AOU Checklist (http://www.aou.org/checklist/north/print.php) to assure that the common names and scientific names used were up to date. The current data list is current as of September 2012. One limitation of the ITIS codes is that they are not in phylogenetic order. To resolve this problem we also included the older National Oceanographic Data Center (NODC) numeric codes (up to 12 characters). The NODC codes were developed during the Outer Continental Shelf Environmental Assessment Program (OCSEAP), and adopted widely by other organizations working in the North Pacific. Although NODC codes are no longer assigned, they are still useful, both for reference to historical data, and because this code provides a sort by taxonomic order (class, order, family, genus, species, and subspecies). Note, we included hybrids and groups that are not in standard phylogenetic groups, e.g. “Unidentified Petrel,” in the NPPSD ver. 2.1. There are no ITIS or NODC codes for these birds, so, for hybrids we added “99” to the NODC code of the species that is listed last in the NODC list. For example, the Glaucous-winged Gull has a NODC code of 9128020103 and the Western Gull has code of 9128020106. The Western Gull is listed last, so the hybrid Western x Glaucous-winged Gull was given a NODC code of 912802010699. For species not listed in the NODC code list or other non-listed taxonomic groups we added 99 to the lowest common level, usually genus. This preserves the phylogenetic order when sorting, but is not a historical NODC code. Note, this field must be treated as text to sort correctly.
Because of the history of NPPSD data collection and organization, we have used North American taxonomic classifications in accordance with the American Ornithological Union nomenclature. Naming conventions and taxonomy differ somewhat with recent international checklists of birds of the world (e.g., Gill and Wright 2006; Clements 2007). It must also be noted that owing to advances in genetic methods and sampling, taxonomic classifications proposed by the International Ornithological Congress (IOC) have changed yet again in recent years (Gill and Donsker 2014), resulting in significant changes at the order and family levels, and leading to a major difference in the "taxonomic order" by which species should be itemized in lists or databases. These higher order changes in classifications do not impact our designations at the genus, species and subspecies level. We plan to reorganize our taxonomy to reflect the IOC classification scheme in the next version of the NPPSD.
The current version of the NPPSD code list contains 332 unique 4-letter codes and common names for all marine bird taxa (n=283) and marine mammal taxa (n=49) encountered on surveys found in the NPPSD database. This list is provided to further the goal of standardizing pelagic seabird data. Researchers are encouraged to use this list for marine bird and mammal surveys in the North Pacific, particularly if you will be providing data to the NPPSD.
Version 2.1 of the NPPSD taxonomic code list was prepared by USGS personnel at the Alaska Science Center, 4210 University Dr., Anchorage, Alaska 99508. Please direct any questions about, or corrections to, the code list to Gary Drew (email@example.com) or John Piatt (firstname.lastname@example.org).
Clements, J.F. 2007. The Clements Checklist of Birds of the World (Sixth Edition). Cornell University Press, Ithaca, NY. 843 pp.
Gill, F., and M. Wright. 2006. Birds of the World: Recommended English Names. Princeton University Press, Princeton, NJ. 259 pp.
Pyle, P., and D. DeSante. 2012. List of North American birds and alpha codes according to American Ornithologists' Union taxonomy through the 53rd AOU Supplement [Downloaded 5/1/2013]. [Full Publication]