Ramey, Andrew M. (ORCID: 0000-0002-3601-8400) 20170331 tabular digital data Anchorage, AK U.S. Geological Survey, Alaska Science Center Suggested Citation: Ramey, A., 2017, Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America, 1986-2014: U.S. Geological Survey data release, https://doi.org/10.5066/F7MP51GP https://doi.org/10.5066/F7MP51GP Data set pertaining to avian paramyxovirus (APMV-1) sequences used in phylogenetic analyses. Data contains GenBank Accession numbers, host species common name and taxonomic order, collection year, and collection location. The purpose of this data set is to support analysis of contemporary genetic diversity and evidence for inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. 1986 2014 observed Complete None planned The study area is worldwide, as virus sequences from around the globe are used in phylogenetic analyses. Further analyses restricted data to only viruses collected from North America. -180.00000 -45.00000 75.00000 15.00000 USGS Metadata Identifier USGS:ASC91 ISO 19115 Biota Environment NASA GCMD Earth Science Keyword Thesaurus Animals/vertebrates Birds USGS CSA Biocomplexity Thesaurus Aquatic birds Waterfowl Genetic diversity Phylogeny None Shorebird Duck Goose Swan Gull Seabird NIH MeSH Thesaurus Natural science disciplines Biological science disciplines Biology Genetics Disease USGS Geographic Names Information System (GNIS) United States NGA GEOnet Names Server Canada None bird ITIS Integrated Taxonomic Information System Unknown online database online ITIS-North America Taxonomic details retrieved April 27, 2016 from the Integrated Taxonomic Information System online database https://www.itis.gov https://doi.org/10.5066/F7KH0KBK Avian species sampled were identified by common name of host species as reported by original virus sequence author within the National Center for Biotechnology Information's GenBank database. Taxonomy is complete for all samples. No vouchers were collected. Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Anseriformes Order Charadriiformes Order Pelecaniformes Order Suliformes No access constraints. No use constraints. We request that the suggested citation of this USGS data release be included in any publications that reference or utilize these data. U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov Ramey, A.M. Goraichuk, I.V. Hicks, J.T. Dimitrov, K.M. Poulson, R.L. Stallknecht, D.E. Bahl, J. Afonso, C.L. 20170303 journal article Virology Journal 14:43 Online Springer Nature Ramey, A. M., I. V. Goraichuk, J. T. Hicks, K. M. Dimitrov, R. L. Poulson, D. E. Stallknecht, J. Bahl, and C. L. Afonso. 2017. Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America. Virology Journal 14:43. https://doi.org/10.1186/s12985-017-0714-8 https://doi.org/10.1186/s12985-017-0714-8 All data were sorted in Microsoft Excel and outliers were checked for accuracy. Data were peer-reviewed for accuracy. No inconsistencies were found in the attribute data acquired from GenBank. Duplicate and recombinant sequences, sequences of man-made clonal viruses, and sequences that were obtained from vaccine-like viruses were removed from the dataset in order to analyze only viruses representing natural circulation and evolution in reservoir and spill-over hosts. Sequences were cropped to the complete coding region of the fusion gene. Avian paramyxovirus serotype 1 (APMV-1) sequences were queried for completeness of the gene of interest and downloaded for use on 26 August 2016. A total of 1835 sequences were algined and cropped to create a phylogenetic tree of AMPV-1. Unknown LITERATURE CITED: Clark, K., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W., 2015. GenBank. Nucleic Acids Research 44(D1):D67–D72, https://doi.org/10.1093/nar/gkv1276 Unknown Indirect spatial references, country and/or state/province, were described by original data producers/contributors for sequences submitted to GenBank database. ampv_1_genBankAssessionNo_migratoryBirds_northAmerica_ramey_1986_2014.csv Table of GenBank Accession Numbers and their corresponding sequences used for the classification of avian paramyxoviruses serotype 1 (APMV-1). Presented in a Comma Separated Value (CSV) formatted table. Author defined and Clark et al. 2015 GenBank accession A unique identifier given to a nucleotide sequence or other biological polymer sequence (DNA, protein) when it is submitted to National Center for Biotechnology Information NCBI GenBank database. Clark et al. 2015 A unique identifier given to a nucleotide sequence or other biological polymer sequence (DNA, protein) when it is submitted to National Center for Biotechnology Information NCBI GenBank database. ampv_1_assessingExchange_migratoryBirds_northAmerica_ramey_1986_2014.csv Table of GenBank accession numbers of the sequences used. Associated data on host species and geographic location of virus sample collection is included. Presented in a Comma Separated Value (CSV) formatted table. Author defined and Clark et al. 2015 GenBank_accession A unique identifier given to a nucleotide sequence or other biological polymer sequence (DNA, protein) when it is submitted to National Center for Biotechnology Information NCBI GenBank database. Clark et al. 2015 A unique identifier given to a nucleotide sequence or other biological polymer sequence (DNA, protein) when it is submitted to National Center for Biotechnology Information NCBI GenBank database. Host_species Common name provided by original sequence data producer reported within the National Center for Biotechnology Information's GenBank database. See table "ampv_1_taxonomy_migratoryBirds_northAmerica_ramey_1986_2014.csv" for additional species information. Author defined. Species common name, are given, except for some cormorant species (sp.) that were not identified to species in the original studies. For Latin names, see table "ampv_1_taxonomy_migratoryBirds_northAmerica_ramey_1986_2014.csv". Host_order Avian taxonomic order to which the virus host belongs based on common names provided by original sequence producer, and uploaded to the Integrated Taxonomic Information System (ITIS). ITIS Integrated Taxonomic Information System Anseriformes Ducks, geese and swans ITIS Integrated Taxonomic Information System Suliformes Frigatebirds, boobies, cormorants and anhingas ITIS Integrated Taxonomic Information System Charadriformes Gulls and shorebirds ITIS Integrated Taxonomic Information System Pelicaniformes Pelicans ITIS Integrated Taxonomic Information System Location Location of host (wild bird) sampling.Code is made up of country (USA or Canada) and U.S. state and Canadian province abbreviation (e.g., USA/MN for USA Minnesota). Canada provinces unknown. Author defined Canada Canada Author defined USA/AK USA Alaska Author defined USA/CA USA California Author defined USA/CT USA Connecticut Author defined USA/DE USA Deleware Author defined USA/FL USA Florida Author defined USA/ID USA Idaho Author defined USA/LA USA Louisiana Author defined USA/MA USA Massachusettes Author defined USA/MD USA Maryland Author defined USA/ME USA Maine Author defined USA/MI USA Michigan Author defined USA/MN USA Minnesota Author defined USA/ND USA North Dakota Author defined USA/NH USA New Hampshire Author defined USA/NJ USA New Jersey Author defined USA/NV USA Nevada Author defined USA/NY USA New York Author defined USA/OH USA Ohio Author defined USA/OR USA Oregon Author defined USA/TX USA Texas Author defined USA/WI USA Wisconsin Author defined NAmerican_region Six broad geographic regions made up of different states in those regions from which samples were collected: Alaska, Canada, the Western USA (California, Idaho, Nevada, Oregon), the Midwestern USA (Michigan, Minnesota, North Dakota, Ohio, Wisconsin), the Gulf Coast USA (Florida, Louisiana, Texas), and the Eastern USA (Connecticut, Delaware, Massachusetts, Maryland, Maine, New Hampshire, New Jersey, New York, Pennsylvania). Canada provinces were not recorded. Author defined Alaska Alaska Author defined West Western USA (California, Idaho, Nevada, Oregon) Author defined Midwest Midwestern USA (Michigan, Minnesota, North Dakota, Ohio, Wisconsin) Author defined Gulf Coast Gulf Coast USA (Florida, Louisiana, Texas) Author defined East Eastern USA (Connecticut, Delaware, Massachusetts, Maryland, Maine, New Hampshire, New Jersey, New York, Pennsylvania) Author defined Canada Canada Author defined Strain Unique identifier supplied by the original virus sequence producer as reported within the National Center for Biotechnology Information's GenBank database. See GenBank accession number of each strain for more information. Author defined Unique identifier supplied by the original virus sequence producer as reported within the National Center for Biotechnology Information's GenBank database. Year Year in which the virus sample was collected as noted in GenBank by individual studies. See GenBank accession numbers for more information. Author defined 1986 2014 ampv_1_taxonomy_migratoryBirds_northAmerica_ramey_1986_2014.csv Table providing the taxonomic classification of all species sampled in this study. Presented in a Comma Separated Value (CSV) formatted table. Author Defined Kingdom Taxonomic hierarchical level; Kingdom Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Kingdom Class Taxonomic hierarchical level; Class. Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Class Order Taxonomic hierarchical level; Order. Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Order Family Taxonomic hierarchical level; Family. Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Family Genus Taxonomic hierarchical level; Genus. Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Genus Species Taxonomic hierarchical level; Species. Integrated Taxonomic Information System (ITIS) Taxonomic hierarchical level; Species Common_name Common name of the species sampled. Corresponds to the "Host_species" attribute in table "ampv_1_assessingExchange_migratoryBirds_northAmerica_ramey_1986_2014.csv" included with this data package. Author defined Common name of the species sampled. ITIS_TSN The identification number of the prey in the Integrated Taxonomic Information System (ITIS) database. Integrated Taxonomic Information System (ITIS) Integrated Taxonomic Information System (ITIS) identification number U.S. Geological Survey USGS ScienceBase Team Mailing and Physical

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Denver Colorado 80225 USA 1-888-275-8747 sciencebase@usgs.gov The U.S. Geological Survey, Alaska Science Center is the authoritative source of these data, distributed by ScienceBase (a USGS Trusted Digital Repository). Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data for other purposes or on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. CSV Tabular data in CSV format; FGDC metadata in XML and HTML formats. https://doi.org/10.5066/F7MP51GP None 20250220 U.S. Geological Survey, Alaska Science Center Mailing and Physical

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Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (CSDGM) FGDC-STD-001.1-1999