Blood Parasite Infection Data from Spectacled Eiders (Somateria fischeri), Alaska, 2008-2012

Identification_Information:

Citation:

Citation_Information:

Originator: Reed, John A. (ORCID: 0000-0002-3239-6909)
Publication_Date: 201806
Title:

Geospatial_Data_Presentation_Form: spreadsheet
Publication_Information:

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

Other_Citation_Details:

Reed, J.A., 2018, Blood Parasite Infection Data from Spectacled Eiders (Somateria fischeri), Alaska, 2008-2012: U.S. Geological Survey data release, https://doi.org/10.5066/P9CDBRDC

Online_Linkage: https://doi.org/10.5066/P9CDBRDC
Larger_Work_Citation:

Citation_Information:

Originator: Flint, P.L. (ORCID: 0000-0002-8758-6993)
Originator: Meixell, B.W. (ORCID: 0000-0002-6738-0349)
Originator: Pearce, J.M. (ORCID: 0000-0002-8503-5485)
Originator: Ramey, A.M. (ORCID: 0000-0002-3601-8400)
Originator: Reeves, A. (ORCID: 0000-0002-7526-072)
Originator: Van Hemert, C.R. (ORCID: 0000-0002-6858-7165)
Publication_Date: 2011
Title:

Examining the role of migratory birds the movement of avian pathogens between and within continents

Geospatial_Data_Presentation_Form: website
Publication_Information:

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

Online_Linkage: https://alaska.usgs.gov/portal/project.php?project_id=321

Description:

Abstract:

This dataset includes two spreadsheets associated with a study of three genera of blood parasites (Leucocytozoon, Haemoproteus, Plasmodium) in 185 Spectacled Eiders (Somateria fischeri) sampled in Alaska, 2008-2012. The first spreadsheet provides age, sex, location, and blood parasite (hematozoa) infection data for three different genera of blood parasites. Hematozoa DNA, from eider blood samples, was detected by amplifying a 479bp fragment of the Cytochrome-b gene using a nested PCR technique with primers specific for the three target hematozoa genera. Amplicons were sequenced and assigned to genera by the nucleotide BLAST function of the NCBI GenBank database. Infection data are provided as NCBI GenBank accession numbers for DNA sequences obtained from samples that tested positive for infection. The second spreadsheet provides the geographic coordinates of the five sampling sites.

Purpose:

These data provided the basis for a study of detection, prevalence, and transmission of avian hematozoa (blood parasites) in Spectacled Eiders (Somateria fischeri) sampled in western and northern Alaskan breeding areas.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 200805
Ending_Date: 201208

Currentness_Reference: observed

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent:

Blood collections are from two sites on the Yukon-Kuskokwim Delta [Big Slough (61.23,-165.62) and Punoarat Point (61.31,-165.79)] and three sites on the Arctic Coastal Plain [Peard Bay (70.80,-158.25), Utqiagvik (formerly Barrow,71.28,-156.61), and Colville River Delta (70.43,-150.67)], Alaska, USA

Bounding_Coordinates:

West_Bounding_Coordinate: -165.79
East_Bounding_Coordinate: -150.67
North_Bounding_Coordinate: 71.28
South_Bounding_Coordinate: 61.23

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:ASC186

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: Ducks/Geese/Swans
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: Aquatic birds
Theme_Keyword: Waterfowl
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: Genetics
Theme_Keyword: Polymerase chain reaction
Theme_Keyword: DNA Sequencing
Theme_Keyword: Health and Disease
Theme_Keyword: Disease vectors

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

Place:

Place_Keyword_Thesaurus: USGS Geographic Names Information System
Place_Keyword: State of Alaska
Place_Keyword: Yukon Delta National Wildlife Refuge
Place_Keyword: Punoarat Point
Place_Keyword: Tutakoke River
Place_Keyword: Colville River Delta
Place_Keyword: Peard Bay
Place_Keyword: Barrow
Place_Keyword: Utqiagvik

Place:

Place_Keyword_Thesaurus: None
Place_Keyword: Big Slough
Place_Keyword: Arctic Coastal Plain
Place_Keyword: Yukon-Kuskokwim Delta

Taxonomy:

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Animals
Taxonomic_Keywords: Vertebrates
Taxonomic_Keywords: Birds
Taxonomic_Keywords: Spectacled Eider

Keywords/Taxon:

Taxonomic_Keyword_Thesaurus: None
Taxonomic_Keywords: Collection
Taxonomic_Keywords: Protists
Taxonomic_Keywords: Hematozoa
Taxonomic_Keywords: Leucocytozoon
Taxonomic_Keywords: simondi

Taxonomic_System:

Classification_System/Authority:

Classification_System_Citation:

Citation_Information:

Originator: Integrated Taxonomic Information System
Publication_Date: Unknown
Title: Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Publication_Information:

Publication_Place: online
Publisher: ITIS-North America

Other_Citation_Details:

Taxonomy details for Somateria fischeri were retrieved Mar 21, 2018, from the Integrated Taxonomic Information System on-line database

Online_Linkage:

https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=175161#null

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 Dec 13, 2017, from the National Center for Biotechnology Information (NCBI) Taxonomy database on-line

Online_Linkage:

https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=5819&lvl=3&lin=f&keep=1&srchmode=1&unlock

Classification_System_Modifications: None

Identification_Reference:

Citation_Information:

Originator: Valkiunas, G.
Publication_Date: 2004
Title: Avian malaria parasites and other haemosporidia
Geospatial_Data_Presentation_Form: book chapter
Publication_Information:

Publication_Place: Boca Raton, Florida (USA)
Publisher: CRC Press

Other_Citation_Details:

Valkiunas, G., 2004, Avian malaria parasites and other haemosporidia. CRC Press, Boca Raton, FL. 932pp.

Taxonomic_Procedures:

Bird species were identified by skilled observers in the field based on general appearance of feathers, plumage, behavior, and vocalization. No vouchers were collected. Hematozoa species were identified by trained observer who examined thin blood smears stained with Geimsa at 400x-1000x magnification. Six high quality voucher specimens of hematozoa (blood smears on glass slides) were selected to be accessioned with Smithsonian Institution, National Museum of Natural History (USNM)

Taxonomic_Completeness: Taxonomy is complete for all samples.
Vouchers:

Specimen:

Blood smear on glass slides (Catalog#: USNM1486967 - USNM1486972)

Repository:

Contact_Information:

Contact_Organization_Primary:

Contact_Organization:

Smithsonian Institution, National Museum of Natural History, Department of Invertebrate Zoology

Contact_Address:

Address_Type: Mailing and Physical
Address: Department of Invertebrate Zoology
Address: PO Box 37012
Address: MRC 163
City: Washington
State_or_Province: DC
Postal_Code: 20013
Country: USA

Contact_Voice_Telephone: (202) 633-1740

Taxonomic_Classification:

Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Applicable_Common_Name: Animal
Applicable_Common_Name: animaux
Applicable_Common_Name: animals
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
Applicable_Common_Name: cordés
Applicable_Common_Name: cordado
Applicable_Common_Name: chordates
Taxonomic_Classification:

Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Applicable_Common_Name: vertebrado
Applicable_Common_Name: vertébrés
Applicable_Common_Name: vertebrates
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
Applicable_Common_Name: Birds
Applicable_Common_Name: oiseaux
Taxonomic_Classification:

Taxon_Rank_Name: Order
Taxon_Rank_Value: Anseriformes
Applicable_Common_Name: Ducks
Applicable_Common_Name: Geese
Applicable_Common_Name: Screamers
Applicable_Common_Name: Swans
Applicable_Common_Name: Waterfowl
Applicable_Common_Name: canards
Applicable_Common_Name: cygnes
Applicable_Common_Name: oies
Applicable_Common_Name: sauvagine
Taxonomic_Classification:

Taxon_Rank_Name: Family
Taxon_Rank_Value: Anatidae
Applicable_Common_Name: Ducks
Applicable_Common_Name: Geese
Applicable_Common_Name: Swans
Applicable_Common_Name: canards
Applicable_Common_Name: cygnes
Applicable_Common_Name: oies
Taxonomic_Classification:

Taxon_Rank_Name: Subfamily
Taxon_Rank_Value: Anatinae
Taxonomic_Classification:

Taxon_Rank_Name: Genus
Taxon_Rank_Value: Somateria
Applicable_Common_Name: Greater Eiders
Applicable_Common_Name: Typical Eiders
Taxonomic_Classification:

Taxon_Rank_Name: Species
Taxon_Rank_Value: Somateria fischeri
Applicable_Common_Name: Spectacled Eider
Applicable_Common_Name: TSN: 175161

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: Species
Taxon_Rank_Value: Leucocytozoon simondi

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 Dr
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 the: University of Wisconsin-Madison Biotechnology Center – DNA Sequencing Facility; 425 Henry Mall; Madison WI 53706. https://www.biotech.wisc.edu/services/dnaseq

Cross_Reference:

Citation_Information:

Originator: Reed, J.A. (ORCID: 0000-0002-3239-6909)
Originator: Sexson, M.G. (ORCID: 0000-0002-1078-0835)
Originator: Smith, M.M. (ORCID: 0000-0002-2259-5135)
Originator: Schmutz, J.A. (ORCID: 0000-0002-6516-0836)
Originator: Ramey, A.M. (ORCID: 0000-0002-3601-8400)
Publication_Date: 2018
Title:

Evidence for haemosporidian parasite infections in Spectacled Eiders (Somateria fischeri) sampled in Alaska during the breeding season

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Journal of Wildlife Diseases
Issue_Identification: 54

Publication_Information:

Publication_Place: online
Publisher: Wildlife Disease Association

Other_Citation_Details:

Reed, J.A., M.G. Sexson, M.M. Smith, J.A. Schmutz, A.M. Ramey. 2018. Evidence for haemosporidian parasite infections in Spectacled Eiders (Somateria fischeri) sampled in Alaska during the breeding season, Journal of Wildlife Diseases. 54(4). doi/10.7589/2018-01-012

Online_Linkage: https://doi.org/10.7589/2018-01-012

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

Individual sample ID's, age, sex, collection dates, and sampling locations 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.

Logical_Consistency_Report:

Attribute values fall within expected ranges and data were checked for duplication and omission. Blank cells indicate that no parasite haplotype was identified for the specific nested-PCR procedure.

Completeness_Report:

No data were omitted and there are no missing data. Blank cells indicate that no parasite haplotype was identified for the specific nested-PCR procedure.

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:

During the summers 2008–2012, we live-captured (with mist nets and nest traps) spectacled eiders at two sites on the Yukon-Kuskokwim Delta (Big Slough and Punoarat Pt) and three sites on the Arctic Coastal Plain (Peard Bay, Utqiagvik (formerly Barrow), and Colville River Delta), Alaska, USA. After Hatch Year (AHY) and Hatch Year (HY) eiders were captured at three periods in the breeding cycle: pre-breeding, nesting, and brood rearing. HY were captured in tundra ponds within six weeks of hatch and prior to attainment of flight. HY were captured together with brood mates and their attending hen.

Methodology:

Methodology_Type: Field
Methodology_Description:

Blood samples (1-2 cc) were collected from each captured individual via jugular venipuncture and preserved in 2 cc vials with 0.75 cc Longmire Buffer (Longmire et al 1988) or BD Vacutainers with 7.2 mg K2 EDTA. We made thin blood smears on glass slides from 110 Arctic Coastal Plain samples.

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

Other_Citation_Details:

Longmire, J.L., A.K. Lewis, N.C. Brown, J.M. Buckingham, L.M. Clark, M.D. Jones, L.J. Meincke, J. Meyne, R.L. Ratliff, F.A. Ray, R.P. Wagner, R.K. Moyzis. 1988. Isolation and molecular characterization of a highly polymorphic centromeric tandem repeat in the family Falconidae. Genomics 2:14–24

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. DNA was extracted from samples using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA). Two replicate aliquots of DNA extract were screened for hematozoa using 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.

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

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.org/10.1645/GE-184R1

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

Methodology:

Methodology_Type: Lab
Methodology_Description:

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 (23Sep-6Oct 2016). 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).

Methodology:

Methodology_Type: Lab
Methodology_Description:

Samples which tested positive for infection via molecular screening were examined by microscopy to identify the morpho-species of hematozoa present. Blood smears were stained with Giemsa and examined at 400–1000x magnification. Six high quality slides were selected and archived at the Smithsonian Institution, National Museum of Natural History.

Source_Information:

Source_Citation:

Citation_Information:

Originator: Unknown
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: Hochbaum, H.A.
Publication_Date: 1942
Title: Sex and age determination of waterfowl by cloacal examination
Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: Transactions of the North American Wildlife Conference
Issue_Identification: 7

Other_Citation_Details:

Hochbaum, H.A. 1942. Sex and age determination of waterfowl by cloacal examination. Transactions of the North American Wildlife Conference. 7:299-307.

Type_of_Source_Media: journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1942

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Hochbaum 1942
Source_Contribution: Reference for sex and age determination in waterfowl

Source_Information:

Source_Citation:

Citation_Information:

Originator: Carney, S.M.
Publication_Date: 1992
Title: Species, age and sex identification of ducks using wing plumage
Geospatial_Data_Presentation_Form: book
Publication_Information:

Publication_Place: Washington, D.C.
Publisher: U.S. Department of the Interior, U.S. Fish and Wildlife Service

Other_Citation_Details:

Carney, S.M. 1992. Species, age and sex identification of ducks using wing plumage. U.S. Department of the Interior, U.S. Fish and Wildlife Service, Washington, D.C. 144pp.

Type_of_Source_Media: book
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 1992

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Carney 1992
Source_Contribution: Reference for sex and age determination in waterfowl

Source_Information:

Source_Citation:

Citation_Information:

Originator: Ramey, A.M.
Originator: Fleskes, J.P.
Originator: Schmutz, J.A.
Originator: Yabsley, M.J.
Publication_Date: 2013
Title:

Evaluation of blood and muscle tissues for molecular detection and characterization of haematozoa infections in Northern Pintails (Anas acuta) wintering in California

Geospatial_Data_Presentation_Form: journal article
Series_Information:

Series_Name: International Journal of Parasitology: Parasites and Wildlife
Issue_Identification: 2

Other_Citation_Details:

Ramey, A.M., J.P. Fleskes, J.A. Schmutz, M.J. Yabsley. 2013. Evaluation of blood and muscle tissues for molecular detection and characterization of haematozoa infections in Northern Pintails (Anas acuta) wintering in California. International Journal of Parasitology: Parasites and Wildlife 2:102-109. doi.org/10.1016/j.ijppaw.2013.02.001

Online_Linkage: https://doi.org/10.1016/j.ijppaw.2013.02.001

Type_of_Source_Media: journal article
Source_Time_Period_of_Content:

Time_Period_Information:

Single_Date/Time:

Calendar_Date: 2013

Source_Currentness_Reference: publication date

Source_Citation_Abbreviation: Ramey et al 2013
Source_Contribution:

Reference for determining presence or absence of hematozoa infection

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

Other_Citation_Details:

Altschul, S.F., W. Gish, W. Miller, E.W. Myers, D.J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology. 215:403-410. doi.org/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.

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: spectacledEider_bloodParasites_alaska_reed_2008_2012
Entity_Type_Definition:

Blood parasite infection data from Spectacled eiders sampled in Alaska, 2008-2012

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: Sample_ID
Attribute_Definition:

Individual identifier of each blood sample included in the analysis.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier: composed of species (SPEI for Spectacled Eider), a code for location (AK = Alaska), followed by a two digit code for year (08-12), and a sequential blood sample number (001-067).

Attribute:

Attribute_Label: Site
Attribute_Definition:

Name of capture site where blood sample was collected. Details of capture site locations are provided in a second table included with these data: spectacledEider_captureSites_alaska_reed_2008_2012

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Big Slough
Enumerated_Domain_Value_Definition: Capture site name
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Punoarat Point
Enumerated_Domain_Value_Definition: Capture site name
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Colville River Delta
Enumerated_Domain_Value_Definition: Capture site name
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Peard Bay
Enumerated_Domain_Value_Definition: Capture site name
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Utqiagvik
Enumerated_Domain_Value_Definition: Capture site name
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Age
Attribute_Definition:

Age (year Class) is represented as age (year) codes specified by the USGS - Bird Banding Laboratory. Age is determined by feather plumage coloration, pattern, or feather wear of specific feather tracks.

Attribute_Definition_Source: USGS Bird Banding Laboratory
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: AHY
Enumerated_Domain_Value_Definition:

After hatching year. A bird known to have hatched before the calendar year of banding; year of hatch otherwise unknown.

Enumerated_Domain_Value_Definition_Source: USGS Bird Banding Laboratory

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: HY
Enumerated_Domain_Value_Definition:

Hatching year. A bird capable of sustained flight and known to have hatched during the calendar year in which it was banded.

Enumerated_Domain_Value_Definition_Source: USGS Bird Banding Laboratory

Attribute:

Attribute_Label: Sex
Attribute_Definition:

Sex of the sampled Spectacled eider as determined by cloacal exam and plumage characteristics

Attribute_Definition_Source: Hochbaum 1942, Carney 1992
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: F
Enumerated_Domain_Value_Definition: Female
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: M
Enumerated_Domain_Value_Definition: Male
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Date
Attribute_Definition:

Date that a captured Spectacled Eider was sampled; Day Month Year (DD-MMM-YYYY).

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 13-May-2008
Range_Domain_Maximum: 19-Aug-2012
Attribute_Units_of_Measure: days

Attribute:

Attribute_Label: Leuc_1
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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 that was verified through genetic sequencing and successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Leuc_2
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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 that was verified through genetic sequencing and successfully assigned to Leucocytozoon parasite genera via NCBI nucleotide BLAST

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Haem_1
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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:

Attribute_Label: Haem_2
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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:

Attribute_Label: Plas_1
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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:

Attribute_Label: Plas_2
Attribute_Definition:

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

Attribute_Definition_Source: Ramey et al 2013, Altschul et al 1990
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 0
Enumerated_Domain_Value_Definition:

Negative result: nested-PCR test that 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:

Attribute_Label: Genbank_L1
Attribute_Definition:

GenBank accession number for Leucocytozoon cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the first replicate of the nested-PCR. Blank cells signify negative results from 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: Genbank_L2
Attribute_Definition:

GenBank accession number for Leucocytozoon cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the second replicate of the nested-PCR. Blank cells signify negative results from the nested-PCR.

Attribute_Definition_Source: author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: Genbank_H1
Attribute_Definition:

GenBank accession number for Haemoproteus cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the first replicate of the nested-PCR. Blank cells signify negative results from the nested-PCR. This attribute contains no data because the nested-PCR resulted in no Haemoproteus product.

Attribute_Definition_Source: author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: Genbank_H2
Attribute_Definition:

GenBank accession number for Haemoproteus cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the second replicate of the nested-PCR. Blank cells signify negative results from the nested-PCR. This attribute contains no data because the nested-PCR resulted in no Haemoproteus product.

Attribute_Definition_Source: author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: Genbank_P1
Attribute_Definition:

GenBank accession number for Plasmodium cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the first replicate of the nested-PCR. Blank cells signify negative results from the nested-PCR. This attribute contains no data because the nested-PCR resulted in no Plasmodium product.

Attribute_Definition_Source: author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: Genbank_P2
Attribute_Definition:

GenBank accession number for Plasmodium cytochrome b (cyt b) mitochondrial DNA (mtDNA) target fragment following a positive result from the second replicate of the nested-PCR. Blank cells signify negative results from the nested-PCR. This attribute contains no data because the nested-PCR resulted in no Plasmodium product.

Attribute_Definition_Source: author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Attribute:

Attribute_Label: USNM_ID
Attribute_Definition:

Catalog Number assigned to six hematozoa voucher specimens by the Smithsonian Institution, National Museum of Natural History (USNM), Department of Invertebrate Zoology. Blank cells indicate that no voucher slide is archived for this blood sample.

Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Unrepresentable_Domain:

Unique identifier: Catalog number for voucher blood smear slide assigned by the Smithsonian Institution, National Museum of Natural History (USNM), Department of Invertebrate Zoology, where the slide is archived.

Detailed_Description:

Entity_Type:

Entity_Type_Label: spectacledEider_captureSites_alaska_reed_2008_2012
Entity_Type_Definition:

The geographic coordinates of the five Spectacled Eider capture sites in Alaska associated with this data release.

Entity_Type_Definition_Source: Author defined

Attribute:

Attribute_Label: Site
Attribute_Definition: Name of capture site where blood sample was collected
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Big Slough
Enumerated_Domain_Value_Definition:

Informal place name used by local residents and found 5km south of the Tutakoke River.

Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Punoarat Point
Enumerated_Domain_Value_Definition: Punoarat Point, Alaska
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Colville River Delta
Enumerated_Domain_Value_Definition: Colville River Delta, Alaska
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Peard Bay
Enumerated_Domain_Value_Definition: Peard Bay, Alaska
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Utqiagvik
Enumerated_Domain_Value_Definition: Utqiagvik, Alaska
Enumerated_Domain_Value_Definition_Source: USGS Geographic Names Information System (GNIS)

Attribute:

Attribute_Label: Region
Attribute_Definition: Region of Alaska where blood samples were collected
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Yukon-Kuskokwim Delta
Enumerated_Domain_Value_Definition: Capture site located on the Yukon-Kuskokwim Delta
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Arctic Coastal Plain
Enumerated_Domain_Value_Definition: Capture site located on the Arctic Coastal Plain
Enumerated_Domain_Value_Definition_Source: Author defined

Attribute:

Attribute_Label: Lat
Attribute_Definition: Latitude of capture site
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 61.23
Range_Domain_Maximum: 71.28
Attribute_Units_of_Measure: Decimal Degrees
Attribute_Measurement_Resolution: 0.01

Attribute:

Attribute_Label: Long
Attribute_Definition: Longitude of capture site
Attribute_Definition_Source: Author defined
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: -165.79
Range_Domain_Maximum: -150.67
Attribute_Units_of_Measure: Decimal Degrees
Attribute_Measurement_Resolution: 0.01

Blood Parasite Infection Data from Spectacled Eiders (Somateria fischeri), Alaska, 2008-2012

Metadata: