Attribute_Accuracy_Report:
Identifying information about samples were cross-checked with original field data. Polymerase chain reaction (PCR) amplification and electrophoresis followed protocols described in Sonsthagen et al 2004. Quality control (QC) included a minimum of 20% re-extraction and PCR replication for each locus and all laboratory techniques were performed using sterile procedures. All duplicate characterizations of the same individual resulted in concordant data. NCBI BioSample numbers were cross-referenced to the appropriate samples in attributes.
For microsatellite loci, reported allele sizes were reviewed to confirm they conform to expected distributions (e.g. dinucleotide repeats with 1 base pair differences were reviewed on gel images by laboratory personnel, gaps in allele sizes were reviewed, and single occurrences of an allele size were scrutinized). No inconsistencies in genotype scores were observed between replicates. Tests for null alleles and allelic dropout were implemented in MicroChecker (van Oosterhout et al 2004).
Methodology:
Methodology_Type: Field
Methodology_Description:
Samples were assembled as part of other research efforts. Feathers, muscle, or blood were collected from Barrow’s Goldeneye in Alaska and British Columbia at winter or spring staging areas from 2009 to 2014. Common Goldeneye samples were collected opportunistically in Alaska, Canada, and Denmark, mainly during summer (breeding) periods, but also some samples from potential breeders (spring), and from wintering sites. Blood samples were collected from the jugular or brachial vein and stored in preservation buffer or Whatman FTA cards.
Methodology:
Methodology_Type: Lab
Methodology_Description:
DNA was extracted by a modified salt extraction technique (Medrano et al 1990; Sonsthagen et al 2004)) or using a Qiagen Dneasy Blood and Tissue extraction kit (QIAGEN, Düsseldorf, Germany) following manufacturer’s protocol.
Methodology:
Methodology_Type: Lab
Methodology_Description:
Polymerase chain reaction (PCR) amplification and scoring of microsatellites followed Sonsthagen et al 2004 except the thermocycler parameters consisted of a 2 min denaturation at 94°C, followed 40 cycles at 94°C for 15 seconds, 50°C for 15 seconds and 72°C for 30 seconds with a final extension at 72°C for 30 min. Microsatellite alleles were resolved on a 25 cm 6% polyacrylamide gel using a LI-COR (IR 4200) automated DNA sequencer. For quality control purposes, we extracted, amplified, and genotyped, 20% of the samples in duplicate.
Methodology:
Methodology_Type: Lab
Methodology_Description:
Double digest restriction-site associated DNA (ddRAD) library preparation, sequencing, assembly of reads, and alignment of loci followed DaCosta and Sorenson 2014. DNA was digested with two restriction enzymes SfbI and EcoRI and ligated adapters included dual indices. Libraries were size-selected (size range 300–450 base pairs), amplified for 20 cycles, and single-end sequenced (150 base pairs) on an Illumina HiSeq 2500 at the Tufts University Core Genomics Facility. Raw data were uploaded to NCBI Short Read Archive.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Medrano, J.F.
Originator: Aasen, E.
Originator: Sharrow, L.
Publication_Date: 1990
Title: DNA extraction from nucleated red blood cells
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Biotechniques
Issue_Identification: 8(1):43
Publication_Information:
Publication_Place: online
Publisher: Future Science, Ltd.
Other_Citation_Details:
Medrano, J.F., Aasen, E., Sharrow, L. 1990. DNA extraction from nucleated red blood cells. Biotechniques 8(1):43
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 1990
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Medrano et al 1990
Source_Contribution:
Laboratory Technique Citation: describes DNA extraction technique.
Source_Information:
Source_Citation:
Citation_Information:
Originator: Sonsthagen, S.A.
Originator: Talbot, S.L.
Originator: White, C.M.
Publication_Date: 2004
Title:
Gene flow and genetic characterization of Northern Goshawks breeding in Utah
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Condor
Issue_Identification: 106(4):826–836
Publication_Information:
Publication_Place: Oxford, UK
Publisher: Oxford University Press
Other_Citation_Details:
Sonsthagen, S.A., Talbot, S.L., White, C.M. 2004. Gene flow and genetic characterization of Northern Goshawks breeding in Utah. Condor 106(4):826–836
Online_Linkage: http://www.jstor.org/stable/3247787
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2004
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: Sonsthagen et al 2004
Source_Contribution:
Laboratory Technique Citation: describes DNA extraction, polymerase chain reaction (PCR) amplification and electrophoresis and microsatellite scoring protocols.
Source_Information:
Source_Citation:
Citation_Information:
Originator: van Oosterhout, C.
Originator: Hutchinson, W.F.
Originator: Wills, D.P.M.
Originator: Shipley, P.
Publication_Date: 2004
Title:
MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Molecular Ecology Notes
Issue_Identification: 4(3):535-538
Publication_Information:
Publication_Place: online
Publisher: Wiley Online Library
Other_Citation_Details:
van Oosterhout, C., Hutchinson, W.F., Wills, D.P.M., Shipley, P. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4(3):535-538 doi:10.1111/j.1471-8286.2004.00684.x
Online_Linkage: https://doi.org/10.1111/j.1471-8286.2004.00684.x
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2004
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: van Oosterhout et al 2004
Source_Contribution:
Laboratory Technique Citation: describes tool used to identify potential scoring errors and null alleles of microsatellite loci.
Source_Information:
Source_Citation:
Citation_Information:
Originator: DaCosta, J.M.
Originator: Sorenson, M.D.
Publication_Date: 2014
Title:
Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: PLoS ONE
Issue_Identification: 9(9):e106713
Publication_Information:
Publication_Place: online
Publisher: Public Library of Science (PLoS)
Other_Citation_Details:
DaCosta, J.M., Sorenson, M.D, 2014. Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol. PLoS ONE 9(9):e106713 doi:10.1371/journal.pone.0106713
Online_Linkage: https://doi.org/10.1371/journal.pone.0106713
Type_of_Source_Media: publication
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2014
Source_Currentness_Reference: publication date
Source_Citation_Abbreviation: DaCosta and Sorenson 2014
Source_Contribution:
Laboratory Technique Citation: describes double-digest restriction associated DNA sequence library preparation and read assembly protocol.
Source_Information:
Source_Citation:
Citation_Information:
Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: BioProject
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://www.ncbi.nlm.nih.gov/bioproject/
Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2020
Source_Currentness_Reference: observed
Source_Citation_Abbreviation: NCBI BioProject
Source_Contribution:
Information regarding sampling, biological source material, and sequences obtained in this study are publicly accessible in the NCBI BioProject database (BioProject accession number PRJNA649808).
Source_Information:
Source_Citation:
Citation_Information:
Originator: National Center for Biotechnology Information (NCBI)
Publication_Date: Unknown
Title: BioSample
Geospatial_Data_Presentation_Form: database
Online_Linkage: https://www.ncbi.nlm.nih.gov/biosample/
Type_of_Source_Media: digital database file
Source_Time_Period_of_Content:
Time_Period_Information:
Single_Date/Time:
Calendar_Date: 2020
Source_Currentness_Reference: observed
Source_Citation_Abbreviation: NCBI BioSample
Source_Contribution:
Information regarding sampling and the biological source material used in this study are publicly accessible in the NCBI BioSample database (accession numbers provided in this data package).
Process_Step:
Process_Description:
Initial microsatellite allele sizes were determined by scoring based on PCR product size relative to an M13 DNA sequence ladder using Gene Profiler 4.05 (Scanalytics, Inc., Fairfax, VA). Subsequent gels included these known size individuals from which relative sizes of unknown individuals were assigned using Gene Profiler 4.05. For this reason, these microsatellite data cannot be combined with data generated outside the USGS Alaska Science Center without molecular size calibration between laboratories. Tests for null alleles and allelic dropout were implemented in MicroChecker (van Oosterhout et al 2004).
Process_Date: Unknown
Process_Step:
Process_Description:
Raw Illumina reads were de-multiplexed and processed using DaCosta and Sorenson (2014) pipelines.
Process_Date: Unknown
Process_Step:
Process_Description:
Raw read data generated in this study were submitted to the NCBI short read archive publicly available high throughput sequence data database.
Process_Date: Unknown
Source_Produced_Citation_Abbreviation: NCBI SRA