Dataset Title

Data associated with: Fine-Scale Population Structure and Relatedness of Argali (Ovis ammon) in Kyrgyzstan Revealed by High-Density SNP Data

Dataset DOI: 10.5061/dryad.76hdr7t7t

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1. General Description

This dataset contains genetic and associated metadata used to examine fine-scale population structure and relatedness of Argali wild sheep (Ovis ammon) in Kyrgyzstan using high-density single nucleotide polymorphism (SNP) genotyping.

The dataset includes:

• Sample-level metadata (sample identifiers and geographic coordinates)
• Raw SNP genotype data generated using the Illumina HD Ovine SNP array
• SNP mapping information aligned to the Ovis aries reference genome

The data are intended for reuse in population genetics, conservation biology, and spatial or landscape genetic analyses. This README is written to support users who may be new to SNP array data formats or Argali biology.

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2. File List and Organization

2.1 Metadata File

File: Argali_DNA.xlsx

Description

This file contains sample‑level metadata and DNA quality metrics for Argali (Ovis ammon) samples used in this study. The file includes two sample sets corresponding to two separate mailings of biological samples to the laboratory. The sample sets differ only by shipment timing and handling logistics; all samples were processed using the same laboratory protocols and quality control procedures.

Sample Sets

• Argali DNA Sample Set One: First shipment of samples received and processed.

• Argali DNA Sample Set Two: Second shipment of samples received and processed.

Sample set designation reflects mailing batches only and does not indicate biological, geographic, or analytical differences.

Variable Definitions

Mapping ID

• Description: Internal identifier used to link samples in this metadata file to corresponding genotype files (.dsf).

• Format: Numeric (integer or decimal for replicate extractions; e.g., 14.1, 14.2).

• Notes: Decimal values indicate replicate DNA extractions or repeated measurements from the same biological sample.

Sample ID

• Description: Field‑assigned sample identifier.

• Format: Numeric.

• Notes: Sample IDs may repeat across sample sets; the combination of Sample ID and Sample Set uniquely identifies each record.

Species

• Description: Species identification.

• Format: Text.

• Values: Ovis ammon (abbreviated as O. ammon).

Notes: Blank or NA values indicate species was assumed based on collection context but not explicitly recorded in the original metadata.

Sample Type

• Description: Biological material used for DNA extraction.

• Format: Text.

• Values include: skin, hair, skin + hair, skin + hide, blood + bone, meal/fur.

• Notes: “NA” indicates sample type was not recorded.

Sex

• Description: Sex of the sampled individual.

• Format: Text.

• Values: M (male), F (female), Unknown, NA.

Age

• Description: Estimated age of the individual at the time of sampling.

• Format: Numeric (years).

• Notes: “NA” indicates age was not available or could not be reliably estimated.

GPS

• Description: Geographic coordinates of sample collection location.

• Format: Text.

• Values: Coordinates recorded either in degrees/minutes/seconds (DMS) or projected coordinate format, depending on field conditions.

• Notes: Coordinate format varies among records due to multiple field teams and collection periods.

Place of Collection

• Description: Text description of the collection location.

• Format: Text.

• Notes: Includes region, area, and local geographic feature names.

Conc. (ng/µL) Test 1, 2

• Description: DNA concentration measured during quality control.

• Format: Numeric.

• Units: nanograms per microliter (ng/µL).

• Notes: When multiple measurements were taken, values represent replicate tests from the same extraction or replicate extractions.

Quality (260/280) Test 1, 2

• Description: DNA purity ratio measured as absorbance at 260 nm divided by 280 nm.

• Format: Numeric.

• Notes: Values near ~1.8 indicate high‑quality DNA; lower values may indicate protein or reagent contamination.

Date Tested

• Description: Date DNA concentration and quality were measured.

• Format: Date (DD/MM/YYYY)

Relationship to Genotype Files

Records in Argali_DNA.xlsx correspond to genotype data stored in proprietary .dsf / .dsm / .cache files. The Mapping ID column provides the link between metadata records and genotype files. Replicate Mapping IDs (e.g., 32.1 and 32.2) indicate multiple extractions or measurements from the same biological sample.

Missing Values

• NA or n/a indicates information that was not available, not recorded, or not applicable at the time of data collection or processing.

• For some records in Sample Set One, Species or Mapping ID values are missing due to incomplete metadata received with the original biological samples or clerical omissions during early data intake.

• Mapping ID entries with decimal values (e.g., 73.1) denote replicate DNA extractions or repeated measurements from the same biological sample. If a Mapping ID cell is blank, the corresponding sample did not receive a unique mapping identifier at the time of genotyping.

• Missing values do not imply exclusion from analysis unless explicitly stated in downstream analytical workflows.

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2.2 Genotype Data Files

Files: data2.dsf – data100.dsf (30 files total; non-consecutive numbering)
Format: Illumina Data Storage Format (.dsf)

Description:
Each .dsf file contains raw SNP genotype data produced by the Illumina HD Ovine SNP array. These files store genotype calls and associated signal intensity information for one or more Argali samples.

Associated auxiliary files:
Each .dsf file has a corresponding .dsf.cache file that contains indexing and cache information required by Illumina software. The .cachefiles do not contain independent biological data but are necessary for efficient file access and interpretation.

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2.3 SNP Map Files

File: map20.dsm
Format: Illumina SNP map (.dsm)

Description:
Provides SNP mapping information, including chromosomal positions of SNPs aligned to the Ovis aries reference genome assembly. This file is required to associate genotype calls with genomic coordinates.

Associated auxiliary file:

• map20.dsm.cache: Cache file required by Illumina software.

  2.4 Genotype Data File List

  The following Illumina genotype data files are included in this dataset. Each .dsf file contains SNP genotype data generated using the Illumina HD Ovine SNP array. Each .dsf file has a corresponding .dsf.cache file that contains auxiliary indexing information required by Illumina software.

  2.4.1 Genotype Data Files (.dsf)

  data2.dsf
  data5.dsf
  data8.dsf
  data11.dsf
  data14.dsf
  data17.dsf
  data23.dsf
  data27.dsf
  data30.dsf
  data34.dsf
  data38.dsf
  data41.dsf
  data46.dsf
  data49.dsf
  data52.dsf
  data55.dsf
  data58.dsf
  data67.dsf
  data70.dsf
  data74.dsf
  data78.dsf
  data81.dsf
  data87.dsf
  data91.dsf
  data94.dsf
  data97.dsf
  data100.dsf
  
  

  Description:
  Each .dsf file stores raw SNP genotype calls and associated signal intensity data for one or more Argali (Ovis ammon) samples. Sample identifiers embedded within these files correspond to entries in Argali_DNA.xlsx.

  2.4.2 Auxiliary Cache Files (.dsf.cache)

  data2.dsf.cache
  data5.dsf.cache
  data11.dsf.cache
  data14.dsf.cache
  data17.dsf.cache
  data23.dsf.cache
  data27.dsf.cache
  data30.dsf.cache
  data34.dsf.cache
  data38.dsf.cache
  data41.dsf.cache
  data46.dsf.cache
  data49.dsf.cache
  data52.dsf.cache
  data55.dsf.cache
  data58.dsf.cache
  data67.dsf.cache
  data70.dsf.cache
  data74.dsf.cache
  data78.dsf.cache
  data81.dsf.cache
  data87.dsf.cache
  data91.dsf.cache
  data94.dsf.cache
  
  

  Description:
  These files are automatically generated cache and index files associated with each .dsf genotype file. They are required for efficient data access by Illumina software but do not contain independent biological or metadata information.

  2.4.3 SNP Mapping Files

  map20.dsm
  map20.dsm.cache
  
  

  Description:
  The map20.dsm file contains SNP identifiers and genomic positions aligned to the Ovis aries reference genome. The corresponding .cache file is required by Illumina software.

  4. Relationship Between Files (Clarification for Reuse)

  • The list of .dsf files above constitutes the full set of genotype data used in this study.
  • Sample identifiers embedded within these .dsf files correspond directly to the Sample_ID column in Argali_DNA.xlsx.
  • The .cache files are auxiliary and should be retained with their corresponding primary files.
  • The map20.dsm file provides the genomic coordinate reference required to interpret SNP locations.

  5. Data Formats and Software Requirements

  The genotype and SNP mapping files included in this dataset are provided in proprietary Illumina formats generated by the Illumina HD Ovine SNP array platform.

  5.1 Genotype Data Files (.dsf and .dsf.cache)

  • .dsf files contain raw SNP genotype calls and associated signal intensity data.
  • .dsf.cache files are auxiliary cache and index files automatically generated by Illumina software and are required for efficient file access.
    These files are not readable using standard spreadsheet or text-based software. They are intended to be accessed using Illumina-compatible genotyping and analysis software, including but not limited to:
  • Illumina GenomeStudio (Illumina, Inc.)
  • Other bioinformatics tools or pipelines capable of importing Illumina SNP array data after appropriate format conversion

  5.2 SNP Mapping Files (.dsm and .dsm.cache)

  • The .dsm file contains SNP identifiers and genomic positions aligned to the Ovis aries reference genome.
  • The accompanying .cache file is required by Illumina software.
    These files are used in conjunction with genotype data to assign genomic coordinates to SNPs and are accessed through the same Illumina-compatible software environments.

  5.3 Metadata File (Argali_DNA.xlsx)

  The metadata file is provided in Microsoft Excel format and can be opened using standard spreadsheet software or imported into statistical environments such as R or Python. This file enables users to link genotype data to sample identifiers and geographic metadata.

  5.4 Notes for Data Reuse

  Users unfamiliar with Illumina SNP array formats are encouraged to consult Illumina documentation or population genetics resources describing SNP array data workflows prior to reanalysis. No data files in this repository are corrupted; inability to open .dsf, .dsm, or .cache files using general-purpose software reflects expected behavior for these proprietary formats.

  5.5 Conversion to Analysis‑Ready Formats

  While the genotype data are provided in Illumina proprietary formats (.dsf and .dsm), these files can be converted to commonly used population genetics formats (e.g., PLINK or text‑based genotype matrices) using Illumina-compatible software or downstream bioinformatics workflows.

  Such conversions are typically performed after importing the data into Illumina-supported environments (e.g., GenomeStudio), followed by export to analysis-ready formats supported by population genetics software. Users interested in reanalysis are encouraged to consult documentation for their preferred analysis tools to determine appropriate conversion workflows.

  No converted or derived genotype files are included in this repository; the raw data are provided to maximize flexibility for reuse.

  6. Reuse Notes

  This dataset supports analyses including:

  • Population structure and clustering
  • Relatedness and kinship estimation
  • Conservation and landscape genetics
    Because Ovis ammon is a conservation-relevant species, results should be interpreted within appropriate ecological and management contexts.

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  7. Citation and Contact

  Please cite this dataset using the DOI listed above, along with the associated publication.

  Questions regarding data structure or interpretation should be directed to the corresponding author of the associated manuscript.