Reed, John A. (ORCID: 0000-0002-3239-6909) Buchheit, R.M. Schmutz, Joel A. (ORCID: 0000-0002-6516-0836) Uher-Koch, Brian D. (ORCID: 0000-0002-1885-0260) Ramey, Andrew M. (ORCID: 0000-0002-3601-8400) 20210310 tabular digital data Anchorage, Alaska U.S. Geological Survey, Alaska Science Center Suggested Citation: Reed, J.A., Buchheit, R.M., Schmutz, J.A., Uher-Koch, B.D., Ramey, A.M., 2021, Blood parasite infection data from Emperor geese (Anser canagicus) and Cackling geese (Branta hutchinsii minima), Yukon-Kuskokwim Delta, Alaska, 1998-2014: U.S. Geological Survey data release, https://doi.org/10.5066/P9F7LD2I https://doi.org/10.5066/P9F7LD2I This dataset includes one table of blood parasite (hematozoa) infection data from 197 Emperor Geese (Anser canagicus) and 110 Cackling Geese (Branta hutchinsii minima) sampled on the Yukon-Kuskokwim Delta, Alaska, in 1998 and 2014. Three genera of blood parasites (Leucocytozoon, Haemoproteus, Plasmodium) were detected by molecular sequencing of a 479 bp fragment of the Cytochrome-b gene. The table provides age, sex, infection status, and NCBI GenBank accession numbers of the DNA sequences obtained from infected samples. These data provided the basis for a study of detection, prevalence, and transmission of avian hematozoa (blood parasites) in Emperor Geese and Cackling Geese in western Alaska breeding areas. 1998 2014 observed Complete None planned Manokinak River in the Yukon-Kuskokwim Delta National Wildlife Refuge, Alaska, USA -165.2 -165.1 61.2 61.1 USGS Metadata Identifier USGS:ASC357 ISO 19115 Topic Category Biota Environment Health NASA GCMD Earth Science Keyword Thesaurus Animals/vertebrates Birds Ducks/geese/swans Protists Parasitism Species life history USGS CSA Biocomplexity Thesaurus Migratory birds Waterfowl Parasitic diseases Vector borne diseases USGS Thesaurus Wildlife Tundra ecosystems Wetland ecosystems Wildlife disease Parasitology Genetics Polymerase chain reaction DNA sequencing NIH MeSH Thesaurus Parasitology None Emperor goose Anser canigicus Cackling goose Branta canadensis minima Blood parasites Haematozoa Leucocytozoon Haemoproteus Plasmodium USGS Geographic Names Information System (GNIS) Alaska Manokinak River Protected Areas Database of the United States (PAD-US) Yukon Delta National Wildlife Refuge None Emperor Goose Anser canagicus Cackling Goose Branta hutchinsii Branta hutchinsii minima ITIS Integrated Taxonomic Information System Unknown online database online ITIS-North America Taxonomic details retrieved April 2, 2025 from the Integrated Taxonomic Information System online database https://www.itis.gov https://doi.org/10.5066/F7KH0KBK Bird species were identified by skilled observers in the field based on general appearance of feathers and plumage, behavior, and vocalization. Taxonomy is complete for all samples. No voucher specimens were collected. Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Anseriformes Family Anatidae Genus Anser Species Anser canagicus TSN: 175031 Genus Branta Species Branta hutchinsii TSN: 714068 Subspecies Branta hutchinsii minima TSN: 714727 No access constraints. No use constraints. These data are marked with a Creative Common CC0 1.0 Universal License and are in the public domain. It is requested that this USGS data release be cited for any subsequent publications that reference or utilize these data. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. U.S. Geological Survey, Alaska Science Center Mailing and Physical

4210 University Drive

Anchorage Alaska 99508 USA 907-786-7000 gs-ak_asc_datamanagers@usgs.gov All DNA sequencing was performed by the: University of Wisconsin-Madison Biotechnology Center – DNA Sequencing Facility; 425 Henry Mall; Madison WI 53706. https://www.biotech.wisc.edu/services/dnaseq Buchheit, R.M. Schmutz, J.A. Reed, J.A. Uher-Koch, B.D. Ramey, A.M. 2021 journal article Journal of Wildlife Diseases 57(4):799-807 online Wildlife Disease Association Buchheit, R.M., Schmutz, J.A., Reed, J.A., Uher-Koch, B.D., Ramey, A.M., 2021. Assessment of variation in the detection and prevalence of blood parasites among sympatrically breeding geese in western Alaska, USA. Journal of Wildlife Diseases 54(4):799-807. https://doi.org/10.7589/JWD-D-20-00159 https://doi.org/10.7589/JWD-D-20-00159 Individual sample ID's, species, age, sex, and breeding status, were cross-checked and verified to match field data. We observed sterile techniques in the handling of all DNA. All nested-PCR procedures included negative controls to check for contamination. Infection data uncertainty is related to the detection limitation of the nested-PCR procedure described in Lab Methodology. GenBank accession numbers were cross-checked to the appropriate individual samples. Attribute values fall within expected ranges. Blank cells indicate that no parasite haplotype was identified for the specific nested-PCR procedure. No data were omitted and there are no missing data. FIELD: During the summers 1998 and 2014, we live-captured geese near the Manokinak River during incubation and brood rearing. Nesting females were captured with mist nets and bow nests. Flightless hatch year and adult geese were captured during brood rearing by herding birds into corrals. Whole blood was collected via jugular venipuncture, stored in Longmire buffer (Longmire et al 1988), and frozen for long-term preservation. Unknown LAB: Blood parasites were detected using molecular methods. DNA was extracted from samples using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Three replicate aliquots of DNA extract were screened for hematozoa using a nested-PCR protocol (Hellgren et al 2004). A minimum of one negative control was incorporated into PCR reactions for every 24 wells. Reactions were conducted in eight-well strip tubes with individual caps that remained closed, except while loading template and reagents, to prevent cross contamination. Amplicons were visualized on 0.8% agarose gels stained with Gel Red Nucleic Acid Gel Stain 10,000× in DMSO (Biotium, Hayward, CA). All samples that had amplicons present on agarose gels, were further tested for infection by sequencing a 479-base pair target fragment of cytochrome-b mitochondrial DNA. All samples that tested positive for hematozoa infection by nested-PCR, were sent for sequencing of the Cytochrome-b gene at the University of Wisconsin-Madison Biotechnology Center – DNA Sequencing Facility. PCR products were treated with ExoSap-IT (USB Inc., Cleveland, OH) per manufacturer instructions and not otherwise purified prior to sequencing. Amplified DNA was sequenced with the same genus-specific primers from the second stage of the nested-PCR and with BigDye Terminator version 3.1 mix (Applied Biosystems, Foster City, CA) on an Applied Biosystems 3730xl automated DNA sequencer (Applied Biosystems, Foster City, CA). Unknown Sequencher version 5.1 (Gene Codes Corp., Ann Arbor, MI) was used to examine and align all sequence data. International Union of Pure and Applied Chemistry (IUPAC) ambiguity codes were assigned to base pairs with uncertain or multiple nucleic acid identity. Blood parasite infections were confirmed and assigned to a genus (Leucocytozoon, Haemoproteus, or Plasmodium) when a bi-directional consensus sequence of target mtDNA was matched to one of the three parasite genera with >90% identity. Sequences were matched using the nucleotide BLAST function (Altschul et al 1990) for comparison with sequences on NCBI GenBank. Sequences that were not bi-directionally aligned and sequences with <90% identity were considered negative to reduce the possible occurrence of false positives. Unknown Each unique DNA sequence (haplotype) isolated in this study has been submitted to NCBI GenBank and assigned a GenBank Accession Number which may be used to retrieve detailed sequence information from the NCBI GenBank database https://www.ncbi.nlm.nih.gov/genbank Unknown LITERATURE CITED: Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., 1990. Basic local alignment search tool. Journal of Molecular Biology. 215(3):403-410. https://doi.org/10.1016/S0022-2836(05)80360-2 Hellgren, O., Waldenstrom, J., Bensch, S., 2004. A new PCR assay for simultaneous studies of Leucocytozoon, Plasmodium, and Haemoproteus from avian blood. Journal of Parasitology 90(4):797-802. https://doi.org/10.1645/GE-184R1 Longmire, J.L., Lewis, A.K., Brown, N.C., Buckingham, J.M., Clark, L.M., Jones, M.D., Meincke, L.J., Meyne, J., Ratliff, R.L., Ray, F.A., Wagner, R.P., Moyzis, R.K., 1988. Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae. Genomics 2(1):14–24. https://doi.org/10.1016/0888-7543(88)90104-8 Unknown Blood samples were collected from geese near the mouth of the Manokinak River in the Yukon-Kuskokwim Delta National Wildlife Refuge (approximately 61.15 N 165.15 W). goose_bloodParasites_YKD_reed_1998_2014.csv Table with sample and blood parasite infection data from Emperor geese and Cackling geese in western Alaska, 1998-2014. Presented in a Comma Separated Value (CSV) formatted table. Author defined Sample_ID Unique identifier of each blood sample included in the analysis. Author defined Unique identifier composed of: species code (EMGO = Emperor goose CACG = Cackling goose), location code (AK = Alaska), two-digit year (1998, 2014), and a sequential sample number. Band_ID Unique field identification code, used to mark individual birds in the field such as a coded plastic neck collar, tarsal flag, or the final 5 digits of the metal leg band issued by the USGS Bird Banding Lab. Blank cells indicate the individual did not have a band. Author defined Unique field identification code for each bird. Species Bird species. Taxonomic details (including scientific names) are provided in the Taxonomy section of this metadata record. American Ornithological Society Common name of bird species AgeClass Age class of sampled goose. Author defined AHY After hatch year; a bird known to have hatched before the calendar year of banding; year of hatch otherwise unknown. Author defined HY Hatch year; a bird known to have hatched during the calendar year in which it was banded. Author defined Sex Sex of the sampled goose. Author defined F Female Author defined M Male Author defined BreedingStage Breeding stage of goose when captured. Author defined Nesting Adult female captured while nesting. Author defined Brood Drives Adult or hatch year goose captured during brood drive. Author defined L1 through P3 These 9 columns present infection results for three replicate tests (indicated by the number) for three blood parasite genera (L = Leucocytozoon, H = Haemoproteus, P = Plasmodium). Author defined 0 Negative result: nested-PCR test that resulted in no product, single-stranded sequences, or products that could not be assigned to blood parasite genera via nucleotide BLAST. Author defined 1 Positive result: nested-PCR resulted in double-stranded target mitochondrial DNA (mtDNA) that was verified through genetic sequencing and assigned to a blood parasite genus (with an identity >90%) by nucleotide BLAST. Author defined L1_GenBank through P3_GenBank These 9 columns present the GenBank Accession Numbers of the cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment isolated from infected samples (see the corresponding infection results attributes). Blank cells indicate negative results from the nested-PCR. The accession number is a unique identifier assigned by the National Center for Biotechnology Information (NCBI) for nucleotide sequences. Each unique DNA sequence (haplotype) isolated in this study has been assigned an accession number which may be used to retrieve detailed sequence information from the NCBI GenBank database https://www.ncbi.nlm.nih.gov/genbank Author defined GenBank Accession Number. A unique identifier assigned by NCBI U.S. Geological Survey USGS ScienceBase Team Mailing and Physical

Denver Federal Center, Building 810, Mail Stop 302

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/P9F7LD2I None 20250410 U.S. Geological Survey, Alaska Science Center Mailing and Physical

4210 University Drive

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