Smith, Matthew M. (ORCID: 0000-0002-2259-5135) Van Hemert, Caroline (ORCID: 0000-0002-6858-7165) 20190617 tabular digital data Anchorage, Alaska U.S. Geological Survey, Alaska Science Center Smith, M.M., Van Hemert, C. 2019. Blood parasite infection data from Northwestern Crows (Corvus caurinus), Alaska, 2007-2008: U.S. Geological Survey Data Release, https://doi.org/10.5066/P9EBB1LG https://doi.org/10.5066/P9EBB1LG This data set consists of two tables associated with a study of Haemosporidian parasite infection in Northwestern Crows (Corvus caurinus) sampled at six locations throughout southcentral and southeast Alaska in 2007-2008. The first table contains species, location, banding, and morphometric data for all samples. The second table contains results from heamosporidian parasite screening of crow blood samples using molecular techniques. Genomic DNA was extracted from blood samples and screened for the presence of Haemoproteus, Plasmodium, and Leucocytozoon blood parasites using a nested-PCR method. Parasite genetic data is provided as GenBank accession numbers for any samples that tested positive for haemosporidian infection These data provide a basis for the study of: 1) the detection, prevalence, and diversity of avian haemosporidian parasites in northwestern crows sampled in southeast and southcentral Alaska, and 2) the effects of location, year, and other climatic and host variables on parasite prevalence. 20070320 20080417 observed Complete None planned Northwestern Crows were sampled from six sites in southcentral and southeastern Alaska from 2007-2008. Birds were sampled at Seward (60.11°N, 149.44°W), Kenai (60.55°N, 151.23°W), and Homer (59.64°N, 151.54°W) in 2007-2008 and at Valdez (61.12°N, 146.35°W), Haines (59.23°N, 135.44°W), and Juneau (58.38°N, 134.64°W) in 2008. -151.54 -134.64 58.38 61.12 USGS Metadata Identifier USGS:ASC213 ISO 19115 Topic Category Biota Environment NASA GCMD Earth Science Thesaurus Animals/Vertebrates Birds Perching birds Biosphere Ecological dynamics Species/Population interactions Parasitism USGS CSA Biocomplexity Thesaurus Birds Avian physiology Genetic diversity Genetic variance Parasitic diseases Vector borne diseases USGS Thesaurus Sciences Life sciences Zoology Wildlife biology Parasitology Disease vectors Genetics Polymerase chain reaction DNA Sequencing NIH MeSH Thesaurus Natural science disciplines Biological science disciplines Biology Genetics Parasitology Pathologic processes Disease None Blood parasites Hematozoa Haemosporidians USGS Geographic Names Information System Alaska Kenai Homer Seward Valdez Haines Juneau None Corvus caurinus ITIS Integrated Taxonomic Information System Unknown database Taxonomic Serial Number TSN 179736 online ITIS-North America Taxonomy details for Corvus caurinus were retrieved April 16, 2019, from the Integrated Taxonomic Information System on-line database: http://www.itis.gov http://www.itis.gov/ None NCBI Taxonomy database Unknown database online National Center for Biotechnology Information Taxonomy details for Hematozoa were retrieved April 16, 2019, from the National Center for Biotechnology Information (NCBI) Taxonomy database on-line https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi None Bird species were identified by skilled observers in the field based on general appearance of plumage and behavior. Haemoproteus, Plasmodium, and Leucocytozoon parasites were identified by nested-PCR. No vouchers were collected. Taxonomy is complete for all samples. No vouchers were collected. Life Life Kingdom Animalia Subkingdom Bilateria Infrakingdom Deuterostomia Phylum Chordata Subphylum Vertebrata Infraphylum Gnathostomata Superclass Tetrapoda Class Aves Order Passeriformes Family Corvidae Genus Corvus Species Corvus caurinus Northwestern Crow TSN: 179736 no rank Alveolata Phylum Apicomplexa Class Aconoidasida Order Haemosporida hematozoa avian blood parasites Family Leucocytozoidae Genus Leucocytozoon Family Haemoproteidae Genus Haemoproteus Family Plasmodiidae Genus Plasmodium 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 All DNA sequencing was performed by: Functional Biosciences Inc. (MGE Innovation Center, Madison, WI, USA). https://functionalbio.com/web/ Van Hemert, C. Meixell, B.W. Smith, M.M. Handel, C.M. 2019 journal article Parasites & Vectors 12:292 Online Biomed Central Ltd Van Hemert, C., Meixell, B.W., Smith, M.M., Handel, C.M., 2019. Prevalence and diversity of avian blood parasites in a resident northern passerine. Parasites & Vectors 12:292 doi:10.1186/s13071-019-3545-1 https://doi.org/10.1186/s13071-019-3545-1 Sampling dates, and location and morphological data were all cross-checked and verified to match field data. Individual extraction numbers and parasite screening results were verified to be correct according to laboratory notes. Sterile technique was used throughout all molecular protocols, including positive controls for DNA extractions and negative controls included in all nested-PCR reactions. All assigned GenBank accession numbers were cross-checked for accuracy. Attribute values fall within expected ranges and data were proofed for the presence of duplication and omission. No data were omitted and there are no missing data. Blank cells indicate that no haemosporidian mtDNA was detected in any replicate screenings and thus no GenBank accession numbers were assigned. Positions collected with Garmin hand held GPS with average accuracy to within 3 m. Field Northwestern Crows were sampled at six locations throughout southcentral (Seward, Kenai, Homer, and Valdez, AK) and southeastern (Haines, AK and Juneau, AK) Alaska during February-April of 2007 and 2008. Birds were captured using modified drop-net traps and bungee-loaded whoosh nets and classified as juvenlies (< 1 year of age) or adults (>1 year of age) based on molt limits, rectrix shape, and mouth color) Pyle, P 1997 Book Bolinas, California Slate Creek Press Pyle, P. 1997. Identification Guide to North American Birds. Part 1. Columbidae through Ploceidae. Slate Creek Press, Bolinas, CA 732pp. ISBN 13:9780961894047 Field Birds were weighed to the nearest gram using a digital scale, and tarsus, culmen, and wing length were measured using digital calipers and a metal ruler. Whole blood (0.5-1.0 mL) was collected from the brachial vein of each bird and preserved in longmire buffer. Birds were classified as affected or unaffected by avian keratin disorder (AKD) based on the presence or absence of beak deformities per critieria described in Van Hemert and Handel (2010). Van Hemert, C. Handel, C.M. 2010 journal article The Auk 127(4):746-751 Online Oxford University Press Van Hemert C., Handel C.M. 2010 Beak deformities in Northwestern Crows: evidence of a multispecies epizootic. Auk 127(4):746-751 doi:10.1525/auk.2010.10132 https://doi.org/10.1525/auk.2010.10132 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 journal article Genomics 2(1):14–24 Online Elsevier Inc. 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. doi:10.1016/0888-7543(88)90104-8 https://doi.org/10.1016/0888-7543(88)90104-8 Lab Blood parasites were detected using molecular methods. Genomic DNA was extracted from blood samples using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Two replicate screenings of DNA extracionst were conducted using a nested-PCR protocol (Hellgren et al 2004). Amplicons were visualized on 0.8% agarose gels stained with Gel Red Nucleic Acid Gel Stain (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. Hellgren, O. Waldenstrom, J. Bensch, S. 2004 journal article Journal of Parasitology 90(4):797-802 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. doi:10.1645/GE-184R1 https://doi.org/10.1645/GE-184R1 Lab Samples that produced amplicons when visualized on agarose gels were subsequently sequenced to verify the presence of Plasmodium DNA. Products were treated with Exo-SapIT (USB Inc., Cleveland, OH, U.S.A.) at a 3:7 dilution and sent to Functional Biosciences (MGE Innovation Center, Madison, WI, USA) for sequencing. A 479 bp fragment of Plasmodium mitochondrial DNA cytochrome b gene was bidirectionally sequenced using Big Dye Terminator v3.1 mix and analyzed on an ABI 3730xl automated DNA sequencer (Applied Biosystems, Foster City, CA, U.S.A.) National Center for Biotechnology Information (NCBI) Unknown application/service https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome digital database file 20161114 observed NCBI nucleotide BLAST DNA sequences obtained in the current study were queried against all known hematozoa sequences in GenBank using the Basic Local Alignment Search Tool (BLAST) and determined to be positive if there was >90% consensus with one or more entries in GenBank Altschul, S.F. Gish, W. Miller, W. Myers, E.W. Lipman, D.J. 1990 journal article Journal of Molecular Biology 215(3):403-410 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. doi:10.1016/S0022-2836(05)80360-2 https://doi.org/10.1016/S0022-2836(05)80360-2 journal article 1990 publication date Altschul et al 1990 Reference for the use of the BLAST (Basic local alignment search tool) function in searching alignment of nucleotide sequences. Hellgren, O. Waldenstrom, J. Bensch, S. 2004 journal article Journal of Parasitology 90(4):797-802 online American Society of Parasitologists Hellgren, O., J. Waldenstrom, S. Bensch. 2004. A new PCR assay for simultaneous studies of Leucocytozoon, Plasmodium, and Haemoproteus from avian blood. Journal of Parasitology 90(4):797-802. doi:10.1645/GE-184R1 https://doi.org/10.1645/GE-184R1 journal article 2004 publication date Hellgren et al. 2004 Reference for detecting haemosporidian mtDNA in Northwestern Crow blood samples Pyle, P. 1997 Book Bolina, CA Slate Creek Press Pyle P. Identification guide to North American birds. Bolinas, CA: Slate Creek Press; 1997 Book 1997 publication date Pyle 1997 Reference for species and age identification Van Hemert, C. Handel, C.M. 2010 journal article The Auk 127(4):746-751 Online Oxford University Press Van Hemert C., Handel C.M. 2010. Beak deformities in Northwestern Crows: evidence of a multispecies epizootic. Auk 127(4):746-751 doi:10.1525/auk.2010.10132 https://doi.org/10.1525/auk.2010.10132 Journal article 2010 publication date Van Hemert and Handel Source for classifying beak deformities of Northwestern Crows Handel, Colleen M. Pajot, Lisa M. Talbot, Sandra L. Sage, George K. Unknown journal article Wildlife Society Bulletin 4 Online The Wildlife Society Handel, C.M., L.M. Pajot, S.L. Talbot, and G.K. Sage, 2006. Use of buccal swabs for sampling DNA from nestling and adult birds. Wildlife Society Bulletin 34:1094-1100 https://doi.org/10.2193/0091-7648(2006)34[1094:UOBSFS]2.0.CO;2 journal article 2006 publication date Handel et al. 2006 Source for using molecular methods to sex individual Northwestern Crows Field notes were transcribed into electronic spreadsheets. 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. Unknown Genetic sequences were assigned to genera (Leucocytozoon, Haemoproteus, or Plasmodium) using the nucleotide BLAST (Basic Local Alignment Search Tool) function available through the National Center for Biotechnology Information (NCBI). Assignment was based on the top NCBI BLAST result with a minimum identity score of at least 90%. Unknown Blood parasite infections were confirmed when the genetic sequencing resulted in a bi-directionally aligned consensus sequence of target mtDNA that was successfully assigned to one of three parasite genera using the nucleotide BLAST (Basic Local Alignment Search Tool) function. Sequences that were not bi-directionally aligned and sequences with <90% identity were considered negative to reduce the possible occurrence of false positives. Unknown Site names indicate a representative local geographic name. Each site has a representative coordinate. Point 0.01 0.01 Decimal degrees World Geodetic System of 1984 World Geodetic System of 1984 6378137 298.257223563 nwCrow_sampling_alaska_smith_2007_2008.csv Sampling and morphological data from Northwestern Crows captured in Southcentral and Southeast of Alaska, 2007-2008. Presented in a Comma Separated Value (CSV) formatted table. Author defined Field ID Unique identification code used to mark individual birds in the field Author defined 06101 86718 DATE Date that captured Northwestern Crow was sampled Author defined 2007-03-20 2008-04-17 Date (YYYY-MM-DD) LOC Four letter abbreviation for any of six locations where Northwestern Crows were captured USGS Geographic Names Information System SEWA Seward, Alaska, USA USGS Geographic Names Information System KENA Kenai, Alaska, USA USGS Geographic Names Information System HOME Homer, Alaska, USA USGS Geographic Names Information System HAIN Haines, Alaska, USA USGS Geographic Names Information System VALD Valdez, Alaska, USA USGS Geographic Names Information System JUNE Juneau, Alaska, USA USGS Geographic Names Information System LAT Latitude of location where associated Northwestern Crow was captured Author defined 58.38 61.12 Decimal degrees (WGS84) LONG Longitude of location where associated Northwestern Crow was captured Author defined -151.54 -134.64 Decimal degrees (WGS84) SEX Sex of sampled Northwestern as determined by molecular methods Handel et al. 2006 1 Male Author defined 2 Female Author defined AGE Age of sampled Northwestern Crows as determined by molt limits, rectrix shape, and mouth color Pyle 1997 1 Adult Author defined 2 Juvenile Author defined AKD Designation given to sampled Northwestern crows based on presence or absence of clinical signs of Avian Keratin Disorder. Van Hemert and Handel 2010 1 Clinical signs of Avian Keratin Disorder absent Author defined 0 Clinical signs of Avian Keratin Disorder present Author defined TARSUS Diagonal tarsus length (mm) of sampled Northwestern crows Author defined 42.3 55.8 Millimeters WING Unflattened wing chord length (mm) of sampled Northwestern crows Author defined 246 303 Millimeters MASS Mass (g) of sampled Northwestern crows. Blank cells indicate that mass was not measured for that individual Author defined 295 495 Grams nwCrow_bloodParasites_alaska_smith_2007_2008.csv Blood parasite infection data and GenBank accession numbers from Northwestern Crows, Alaska, 2007-2008 Producer defined Extraction # Unique number assigned to each individual DNA extraction from blood samples collected from Northwestern crows captured in Southcentral and Southeast of Alaska, 2007-2008. Presented in a Comma Separated Value (CSV) formatted table. Author defined Unique sample identifier: Four letter code (NOCR) indicating host species followed by a sequential extraction number (001-186) LEUC1 Result from the first replicate of the nested-PCR test for Leucocytozoon parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST Author defined LEUC2 Result from the second replicate of the nested-PCR test for Leucocytozoon parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST Author defined HAEM1 Result from the first replicate of the nested-PCR test for Haemoproteus parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Haemoproteus parasite genera via NCBI nucleotide BLAST Author defined HAEM2 Result from the second replicate of the nested-PCR test for Haemoproteus parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Haemoproteus parasite genera via NCBI nucleotide BLAST Author defined PLAS1 Result from the first replicate of the nested-PCR test for Plasmodium parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Plasmodium parasite genera via NCBI nucleotide BLAST Author defined PLAS2 Result from the second replicate of the nested-PCR test for Plasmodium parasite infection Author defined 0 Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST Author defined 1 Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Plasmodium parasite genera via NCBI nucleotide BLAST Author defined Leuc_GenBank_Accession GenBank accession number for Leucocytozoon cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from any of two replicates of the nested-PCR. Blank cells signify negative results from all replicates of the nested-PCR Author defined Unique identifier: GenBank accession number assigned by National Center for Biotechnology Information. This number may be used to retrieve detailed sample and sequence information from https://www.ncbi.nlm.nih.gov/ Haem_GenBank_Accession GenBank accession number for Haemoproteus cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from any of two replicates of the nested-PCR. Blank cells signify negative results from all replicates of the nested-PCR Authorr defined Unique identifier: GenBank accession number assigned by National Center for Biotechnology Information. This number may be used to retrieve detailed sample and sequence information from https://www.ncbi.nlm.nih.gov/ Plas_GenBank_Accession GenBank accession number for Plasmodium cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from any of two replicates of the nested-PCR. Blank cells signify negative results from all replicates of the nested-PCR Author defined Unique identifier: GenBank accession number assigned by National Center for Biotechnology Information. This number may be used to retrieve detailed sample and sequence information from https://www.ncbi.nlm.nih.gov/ 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/P9EBB1LG None 20240822 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