Blood Parasite Infection Data from Northwestern Crows (Corvus caurinus), Alaska, 2007-2008

Identification_Information:

Citation:

Citation_Information:

Originator: Smith, M.M. (ORCID: 0000-0002-2259-5135)
Originator: Van Hemert, C. (ORCID: 0000-0002-6858-7165)
Publication_Date: 20190617
Title:

Geospatial_Data_Presentation_Form: tabular digital data
Publication_Information:

Publication_Place: Anchorage, Alaska
Publisher: U.S. Geological Survey, Alaska Science Center

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.5066/P9EBB1LG
Larger_Work_Citation:

Citation_Information:

Originator: U.S. Geological Survey, Alaska Science Center
Publication_Date: 2005
Title:

Epidemic of Beak Deformities (Avian Keratin Disorder) among Wild Bird Populations

Geospatial_Data_Presentation_Form: website
Series_Information:

Series_Name: Alaska Science Portal
Issue_Identification: 107

Publication_Information:

Publication_Place: Anchorage, AK
Publisher: U.S. Geological Survey, Alaska Science Center

Other_Citation_Details:

This is a link to the broader USGS Alaska Science Center research project supported by these data. Users will find a description of the research project and links to associated reports, publications, and data products.

Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=107

Description:

Abstract:

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

Purpose:

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.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 20070320
Ending_Date: 20080417

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

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.

Bounding_Coordinates:

West_Bounding_Coordinate: -151.54
East_Bounding_Coordinate: -134.64
North_Bounding_Coordinate: 58.38
South_Bounding_Coordinate: 61.12

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC213

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota

Theme:

Theme_Keyword_Thesaurus: NASA GCMD Earth Science Thesaurus
Theme_Keyword: Biological Classification
Theme_Keyword: Animals/Vertebrates
Theme_Keyword: Birds
Theme_Keyword: Perching Birds
Theme_Keyword: Biosphere
Theme_Keyword: Ecological Dynamics
Theme_Keyword: Species/Population Interactions
Theme_Keyword: Parasitism

Theme:

Theme_Keyword_Thesaurus: USGS CSA Biocomplexity Thesaurus
Theme_Keyword: Birds
Theme_Keyword: Avian physiology
Theme_Keyword: Genetic diversity
Theme_Keyword: Genetic variance
Theme_Keyword: Parasitic diseases
Theme_Keyword: Vector borne diseases

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: Sciences
Theme_Keyword: Life sciences
Theme_Keyword: Zoology
Theme_Keyword: Wildlife biology
Theme_Keyword: Parasitology
Theme_Keyword: Disease vectors
Theme_Keyword: Genetics
Theme_Keyword: Polymerase chain reaction
Theme_Keyword: DNA Sequencing

Theme:

Theme_Keyword_Thesaurus: NIH MeSH Thesaurus
Theme_Keyword: Natural Science Disciplines
Theme_Keyword: Biological Science Disciplines
Theme_Keyword: Biology
Theme_Keyword: Genetics
Theme_Keyword: Parasitology
Theme_Keyword: Pathologic Processes
Theme_Keyword: Disease

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: Blood Parasites
Theme_Keyword: Hematozoa
Theme_Keyword: Haemosporidians

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: State of Alaska
Place_Keyword: Kenai
Place_Keyword: Homer
Place_Keyword: Seward
Place_Keyword: Valdez
Place_Keyword: Haines
Place_Keyword: Juneau

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Corvus caurinus

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: ITIS Integrated Taxonomic Information System
Publication_Date: Unknown
Title: ITIS Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Series_Information:

Series_Name: Taxonomic Serial Number
Issue_Identification: TSN 179736

Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomy details for Corvus caurinus were retrieved April 16, 2019, from the Integrated Taxonomic Information System on-line database: http://www.itis.gov

Online_Linkage: http://www.itis.gov/

Classification_System_Modifications: None

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: NCBI Taxonomy database
Publication_Date: Unknown
Title: National Center for Biotechnology Information Taxonomy Database
Geospatial_Data_Presentation_Form: database
Publication_Information:

Publication_Place: online
Publisher: National Center for Biotechnology Information

Other_Citation_Details:

Taxonomy details for Hematozoa were retrieved April 16, 2019, from the National Center for Biotechnology Information (NCBI) Taxonomy database on-line

Online_Linkage: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

Classification_System_Modifications: None

Taxonomic_Procedures:

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.

Taxonomic_Completeness:

Taxonomy is complete for all samples. No vouchers were collected.

Taxonomic_Classification:

Taxon_Rank_Name: Life
Taxon_Rank_Value: Life
Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Taxonomic_Classification:

Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:

Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:

Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Taxonomic_Classification:

Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:

Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Aves
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Passeriformes
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Corvidae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Corvus
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Corvus caurinus
Applicable_Common_Name: Northwestern Crow
Applicable_Common_Name: TSN: 179736

Taxonomic_Classification:

Taxon_Rank_Name: no rank
Taxon_Rank_Value: Alveolata
Taxonomic_Classification:

Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Apicomplexa
Taxonomic_Classification:

Taxon_Rank_Name: Class
Taxon_Rank_Value: Aconoidasida
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Haemosporida
Applicable_Common_Name: hematozoa
Applicable_Common_Name: avian blood parasites
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Leucocytozoidae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Leucocytozoon

Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Haemoproteidae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Haemoproteus

Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Plasmodiidae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Plasmodium

Access_Constraints: None
Use_Constraints:

It is requested that the authors and the USGS Alaska Science Center be cited for any subsequent publications referenced to this dataset.

Point_of_Contact:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization: U.S. Geological Survey, Alaska Science Center

Contact_Address:

Address_Type: mailing and physical
Address: 4210 University Drive
City: Anchorage
State_or_Province: Alaska
Postal_Code: 99508
Country: USA

Contact_Voice_Telephone: 907-786-7000
Contact_Electronic_Mail_Address: ascweb@usgs.gov

Data_Set_Credit:

All DNA sequencing was performed by: Functional Biosciences Inc. (MGE Innovation Center, Madison, WI, USA). https://functionalbio.com/web/

Cross_Reference:

Citation_Information:

Originator: Van Hemert, C. (ORCID: 0000-0002-6858-7165)
Originator: Meixell, B. W. (ORCID: 0000-0002-6738-0349)
Originator: Smith, M.M. (ORCID: 0000-0002-2259-5135)
Originator: Handel, C.M. (ORCID: 0000-0002-0267-7408)
Publication_Date: 2019
Title:

Prevalence and diversity of avian blood parasites in a resident northern passerine

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Parasites & Vectors
Issue_Identification: 12:292

Publication_Information:

Publication_Place: Online
Publisher: Biomed Central

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1186/s13071-019-3545-1

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Band numbers, 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.

Logical_Consistency_Report:

Attribute values fall within expected ranges and data were proofed for the presence of duplication and omission.

Completeness_Report:

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.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:

Positions collected with Garmin hand held GPS with average accuracy to within 3 m.

Lineage:

Methodology:

Methodology_Type: Field
Methodology_Description:

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)

Methodology_Citation:

Citation_Information:

Originator: Pyle, P
Publication_Date: 1997
Title: Identification guide to North American birds
Geospatial_Data_Presentation_Form: Book
Publication_Information:

Publication_Place: Bolinas, California
Publisher: Slate Creek Press

Other_Citation_Details:

Pyle, P. 1997. Identification Guide to North American Birds. Part 1. Columbidae through Ploceidae. Slate Creek Press, Bolinas, CA 732pp. ISBN 13:9780961894047

Methodology:

Methodology_Type: Field
Methodology_Description:

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).

Methodology_Citation:

Citation_Information:

Originator: Van Hemert, C.
Originator: Handel, C.M.
Publication_Date: 2010
Title:

Beak deformities in Northwestern Crows: evidence of a multispecies epizootic

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: The Auk
Issue_Identification: 127(4):746-751

Publication_Information:

Publication_Place: Online
Publisher: Oxford University Press

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1525/auk.2010.10132

Methodology_Citation:

Citation_Information:

Originator: Longmire, J.L.
Originator: Lewis, A.K.
Originator: Brown, N.C.
Originator: Buckingham J.M.
Originator: Clark, L.M.
Originator: Jones, M.D.
Originator: Meincke, L.J.
Originator: Meyne, J.
Originator: Ratliff, R.L.
Originator: Ray, F.A.
Originator: Wagner, R.P.
Originator: Moyzis, R.K.
Publication_Date: 1988
Title:

Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Genomics
Issue_Identification: 2(1):14–24

Publication_Information:

Publication_Place: Online
Publisher: Elsevier Inc.

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1016/0888-7543(88)90104-8

Methodology:

Methodology_Type: Lab
Methodology_Description:

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.

Methodology_Citation:

Citation_Information:

Originator: Hellgren, O.
Originator: Waldenstrom, J.
Originator: Bensch, S.
Publication_Date: 2004
Title:

A new PCR assay for simultaneous studies of Leucocytozoon, Plasmodium, and Haemoproteus from avian blood

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Journal of Parasitology
Issue_Identification: 90(4):797-802

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1645/GE-184R1

Methodology:

Methodology_Type: Lab
Methodology_Description:

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.)

Source_Information:

Source_Citation:

Citation_Information:

Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: Reference database of known Hematozoa DNA sequences, NCBI
Geospatial_Data_Presentation_Form: application/service
Online_Linkage:

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 20161114

Source_Currentness_Reference: observed

Source_Citation_Abbreviation: NCBI nucleotide BLAST
Source_Contribution:

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

Source_Information:

Source_Citation:

Citation_Information:

Originator: Altschul, S.F.
Originator: Gish, W.
Originator: Miller, W.
Originator: Myers, E.W.
Originator: Lipman, D.J.
Publication_Date: 1990
Title: Basic local alignment search tool
Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Journal of Molecular Biology
Issue_Identification: 215(3):403-410

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1016/S0022-2836(05)80360-2

Type_of_Source_Media: journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1990

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Altschul et al 1990
Source_Contribution:

Reference for the use of the BLAST (Basic local alignment search tool) function in searching alignment of nucleotide sequences.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Hellgren, O.
Originator: Waldenstrom, J.
Originator: Bensch, S.
Publication_Date: 2004
Title:

A new PCR assay for simultaneous studies of Leucocytozoon, Plasmodium, and Haemoproteus from avian blood

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Journal of Parasitology
Issue_Identification: 90(4):797-802

Publication_Information:

Publication_Place: online
Publisher: American Society of Parasitologists

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1645/GE-184R1

Type_of_Source_Media: journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2004

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Hellgren et al. 2004
Source_Contribution:

Reference for detecting haemosporidian mtDNA in Northwestern Crow blood samples

Source_Information:

Source_Citation:

Citation_Information:

Originator: Pyle, P.
Publication_Date: 1997
Title: Identification guide to North American birds
Geospatial_Data_Presentation_Form: Book
Publication_Information:

Publication_Place: Bolina, CA
Publisher: Slate Creek Press

Other_Citation_Details:

Pyle P. Identification guide to North American birds. Bolinas, CA: Slate Creek Press; 1997

Type_of_Source_Media: Book
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1997

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Pyle 1997
Source_Contribution: Reference for species and age identification

Source_Information:

Source_Citation:

Citation_Information:

Originator: Van Hemert, C.
Originator: Handel, C.M.
Publication_Date: 2010
Title:

Beak deformities in Northwestern Crows: evidence of a multispecies epizootic

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: The Auk
Issue_Identification: 127(4):746-751

Publication_Information:

Publication_Place: Online
Publisher: Oxford University Press

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.1525/auk.2010.10132

Type_of_Source_Media: Journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2010

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Van Hemert and Handel
Source_Contribution: Source for classifying beak deformities of Northwestern Crows

Source_Information:

Source_Citation:

Citation_Information:

Originator: Handel, Colleen M.
Originator: Pajot, Lisa M.
Originator: Talbot, Sandra L.
Originator: Sage, George K.
Publication_Date: Unknown
Title:

Use of Buccal Swabs for Sampling DNA from Nestling and Adult Birds

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Wildlife Society Bulletin
Issue_Identification: 4

Publication_Information:

Publication_Place: Online
Publisher: The Wildlife Society

Other_Citation_Details:

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

Online_Linkage: https://doi.org/10.2193/0091-7648(2006)34[1094:UOBSFS]2.0.CO;2

Type_of_Source_Media: journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2006

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Handel et al 2006
Source_Contribution:

Source for using molecular methods to sex individual Northwestern Crows

Process_Step:

Process_Description: Field notes were transcribed into electronic spreadsheets.
Process_Date: Unknown

Process_Step:

Process_Description:

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.

Process_Date: Unknown

Process_Step:

Process_Description:

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%.

Process_Date: Unknown

Process_Step:

Process_Description:

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.

Process_Date: Unknown

Spatial_Data_Organization_Information:

Indirect_Spatial_Reference:

Site names indicate a representative local geographic name. Each site has a representative coordinate.

Direct_Spatial_Reference_Method: Point

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Geographic:

Latitude_Resolution: 0.01
Longitude_Resolution: 0.01
Geographic_Coordinate_Units: Decimal degrees

Geodetic_Model:

Horizontal_Datum_Name: World Geodetic System of 1984
Ellipsoid_Name: World Geodetic System of 1984
Semi-major_Axis: 6378137
Denominator_of_Flattening_Ratio: 298.257223563

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: nwCrow_sampling_alaska_smith_2007_2008
Entity_Type_Definition:

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.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: Field ID
Attribute_Definition:

Unique identification code used to mark individual birds in the field

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 06101
Range_Domain_Maximum: 86718

Attribute:

Attribute_Label: DATE
Attribute_Definition: Date that captured Northwestern Crow was sampled
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 03/20/2007
Range_Domain_Maximum: 04/17/2008
Attribute_Units_of_Measure: Date (MM/DD/YYYY)

Attribute:

Attribute_Label: LOC
Attribute_Definition:

Four letter abbreviation for any of six locations where Northwestern Crows were captured

Attribute_Definition_Source: USGS Geographic Names Information System
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: SEWA
Enumerated_Domain_Value_Definition: Seward, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: KENA
Enumerated_Domain_Value_Definition: Kenai, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: HOME
Enumerated_Domain_Value_Definition: Homer, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: HAIN
Enumerated_Domain_Value_Definition: Haines, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: VALD
Enumerated_Domain_Value_Definition: Valdez, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: JUNE
Enumerated_Domain_Value_Definition: Juneau, Alaska, USA
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System

Attribute:

Attribute_Label: LAT
Attribute_Definition:

Latitude of location where associated Northwestern Crow was captured

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 58.38
Range_Domain_Maximum: 61.12
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Attribute:

Attribute_Label: LONG
Attribute_Definition:

Longitude of location where associated Northwestern Crow was captured

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -151.54
Range_Domain_Maximum: -134.64
Attribute_Units_of_Measure: Decimal degrees (WGS84)

Attribute:

Attribute_Label: SEX
Attribute_Definition: Sex of sampled Northwestern as determined by molecular methods
Attribute_Definition_Source: Handel et al. 2006
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 2
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: AGE
Attribute_Definition:

Age of sampled Northwestern Crows as determined by molt limits, rectrix shape, and mouth color

Attribute_Definition_Source: Pyle 1997
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition: Adult
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 2
Enumerated_Domain_Value_Definition: Juvenile
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: AKD
Attribute_Definition:

Designation given to sampled Northwestern crows based on presence or absence of clinical signs of Avian Keratin Disorder.

Attribute_Definition_Source: Van Hemert and Handel 2010
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition: Clinical signs of Avian Keratin Disorder absent
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition: Clinical signs of Avian Keratin Disorder present
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: TARSUS
Attribute_Definition: Diagonal tarsus length (mm) of sampled Northwestern crows
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 42.3
Range_Domain_Maximum: 55.8
Attribute_Units_of_Measure: Millimeters

Attribute:

Attribute_Label: WING
Attribute_Definition:

Unflattened wing chord length (mm) of sampled Northwestern crows

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 246
Range_Domain_Maximum: 303
Attribute_Units_of_Measure: Millimeters

Attribute:

Attribute_Label: MASS
Attribute_Definition:

Mass (g) of sampled Northwestern crows. Blank cells indicate that mass was not measured for that individual

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 295
Range_Domain_Maximum: 495
Attribute_Units_of_Measure: Grams

Detailed_Description:

Entity_Type:

Entity_Type_Label: nwCrow_bloodParasites_alaska_smith_2007_2008
Entity_Type_Definition:

Blood parasite infection data and GenBank accession numbers from Northwestern Crows, Alaska, 2007-2008

Entity_Type_Definition_Source: Producer defined

Attribute:

Attribute_Label: Extraction #
Attribute_Definition:

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.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique sample identifier: Four letter code (NOCR) indicating host species followed by a sequential extraction number (001-186)

Attribute:

Attribute_Label: LEUC1
Attribute_Definition:

Result from the first replicate of the nested-PCR test for Leucocytozoon parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: LEUC2
Attribute_Definition:

Result from the second replicate of the nested-PCR test for Leucocytozoon parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: HAEM1
Attribute_Definition:

Result from the first replicate of the nested-PCR test for Haemoproteus parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Haemoproteus parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: HAEM2
Attribute_Definition:

Result from the second replicate of the nested-PCR test for Haemoproteus parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Haemoproteus parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: PLAS1
Attribute_Definition:

Result from the first replicate of the nested-PCR test for Plasmodium parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Plasmodium parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: PLAS2
Attribute_Definition:

Result from the second replicate of the nested-PCR test for Plasmodium parasite infection

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test resulted in no product, single-stranded sequences, or products that could not be assigned via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 1
Enumerated_Domain_Value_Definition:

Positive result: nested-PCR resulted in double-stranded, target mtDNA sequence that was successfully assigned to Plasmodium parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Leuc_GenBank_Accession
Attribute_Definition:

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

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

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/

Attribute:

Attribute_Label: Haem_GenBank_Accession
Attribute_Definition:

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

Attribute_Definition_Source: Authorr defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: Plas_GenBank_Accession
Attribute_Definition:

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

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Blood Parasite Infection Data from Northwestern Crows (Corvus caurinus), Alaska, 2007-2008

Metadata: