Dataset DOI: [10.5061/dryad.mpg4f4rgg] (https://doi.org/10.5061/dryad.mpg4f4rgg)

Description of the data and file structure

Files and variables

File: Metadata_RAD_samples.xlsx

Description: The metadata of the samples that were rad-sequenced to find SNP markers for the panel.

Any empty cells in this data should be interpreted as missing data. Some dates are missing because of different lab workflow between labs.

Variables

• Sample_ID: Unique identifier for each sample given in the lab at SLU.
• SeqID: Unique identifier for each sample given at NGI for sequencing
• Region: Classifier representing the region of origin of the sample.
  • 1 = Denmark + Skåne (southernmost Sweden)
  • 2 = Finland
  • 3 = Finnmark (Northernmost Norway)
  • 4 = Gotland (Swedish Island)
  • 5 = Central Sweden
  • 6 = Central Norway + Central Swedish mountains
  • 7 = Northern Sweden
• Age: Age of individual when sampled.
  • Juv = Juvenile
  • Ad = Adult
  • UNK = Unknown age when sampled
• Sex: Sex of sampled individual from genetic analysis.
  • m = Male
  • f = Female
• lab date: Date of DNA extraction (yymmdd)
• sample type: Sample material that DNA was extracted from
  • Blood FTA = Blood on FTA card
  • Tissue = Tissue sample from dead bird
  • Blood wet = Blood in ethanol

File: golden_eagle_SNPdata_assay-test.xlsx

Description: The SNP genotypes of the validation samples

Variables

• SampleID: Unique identifier for each sample. Sample doublets are identified with ",2" after the ID.
• species: Common name for the species sampled.
  • Golden eagle = Aquila chrysaetos
  • White-tailed eagle = Haliaeetus albicilla
• individual: Unique identifier for each sampled individual.
• sexSTRs: Sex as identified with established microsatellites.
  • Male
  • Female
  • NA = Missing data. Where the marker either failed to amplify (Norway sample) or no sex marker has been used in the protocol (Finland samples)
• sexSNP: Sex as identified with the SNP sex marker.
  •  Male
  • Female
  • NA = Missing data. Where the marker failed to amplify.
• country.sample.origin: Country of sample origin.
• sample.material: Material the DNA was extracted from.
  • Eggshell
  • Footpad
  • Moulted feather = Naturally molted feathers found in the environment
  • Pulled feathers = feathers pulled directly from the bird while handling.
  • Blood
  • Claw
  • Bone
• callrate: The fraction of successfully genotyped markers.

The following columns are the SNP markers. Each marker is represented in 2 columns each with representative genotyping letters "X", or "Y". The first column title holds the marker name and the second is empty to avoid double name of the markers.

• CHD1ZW: The sex SNP marker. Genotypes represented with the letters "X" and "Y"
  • XX = Female
  • YY = Male
  • -99 = missing data. In these cases the marker failed to amplify.

The remaining columns are all autosomal SNP markers represented with 2 columns each (the second column of each marker is empty). Genotypes represented with the letters "X" and "Y" and missing data represented as "-99" where the markers failed to amplify.

File: Golden_eagle_Assay_Design_v4_(003).xlsx

Description: The assay designs for the 96 SNP markers in our panel

Variables

• POSITION ASSAY VER4: Position of the assay in our plate.
• ASSAY_ID: Unique assay identifier.
• SNP_NAME: SNP marker name.
• ALLELE: The SNP alleles.
• ASP1_NAME: Allele-Specific Primer name for allele 1
• ASP2_NAME: Allele-Specific Primer name for allele 2
• SNP_SEQ: SNP sequence.
• ASP1_SEQ: ASP sequence for allele 1
• ASP2_SEQ: ASP sequence for allele 2
• LSP_SEQ: Locus specific primer sequence
• STA_SEQ: Specific target amplification sequence
• amp_GC: GC fraction of the amplified target/amplicon

File: Golde_Eagle_Genotypes.xlsx

Description: The SNP genotypes of the RAD-sequenced samples used for discovery of the SNP markers in our panel

Variables

• Sample_ID: Unique identifier for each sample
• SNP_Calls: Sample position in the chip when run.
• zzs: Number of missing data markers in the sample.
• Sex: Sex as identified with the SNP sex marker.

The remaining columns are the SNP markers used in this study. Note: that in this data file each marker use only one column, with genotypes represented as "XX", "XY", and "YY", plus the missing data represented by "ZZ" unlike "golden_eagle_SNPdata_assay-test.xlsx" dataset where each marker is using 2 columns.

• CHD1ZW: Genotypes of the SNP sex marker.
  • YY = male
  • XY = female
  • ZZ = missing data. Where the marker failed to amplify

Note: There is a difference in sex genotype representation between "Golde_Eagle_Genotypes.xlsx" (here XY = Female) and "golden_eagle_SNPdata_assay-test.xlsx" (where XX = Female). This is simply a difference in how different labs are reading the sex marker.

File: R_code_SNP_manuscript.R

Description: The R code that was used for analyses in the paper, including stats on sample material, PID and exclusion probability and data formatting.

Code/software

The analyses were done in R. All data are in Excel format and should be transformed to a .csv file before reading into R. Any R packages that are needed for the code can be found in the code.

Any empty cells are kept empty to avoid confusion when analysing the data using our code.