This README file was generated on 2023-10-03 by Asako Chaille.

GENERAL INFORMATION

1. Title of Dataset: Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer’s Pochard (Aythya baeri) in North America
2. Author Information First Author Contact Information Name: Asako Chaille San Diego Zoo Wildlife Alliance Address: San Diego, CA USA Email: achaille@sdzwa.org
3. Date of data collection (single date, range, approximate date): Birds were sampled for blood between 2017 and 2019. ddRAD data was generated and analyzed between 2019-2021
4. Geographic location of data collection: Birds were sampled across 21 participating North American facilities. The ddRAD library preparation and sequencing was done at the Genomic and bioinformatics Service, Texas A&M AgriLife Research laboratory.
5. Information about funding sources that supported the collection of the data: This work was funded by Akron Zoo, Buttonwood Park Zoo, Minnesota Zoo, Pinola Conservancy, and San Diego Zoo Wildlife Alliance.

SHARING/ACCESS INFORMATION

1. Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
2. Links to publications that cite or use the data:

Chaille, A. Y., Lacy, R. C., Putnam, A. S., Toste, J. L., & Ivy, J. A. (2023). Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer’s Pochard (Aythya baeri) in North America. Journal of Heredity.

1. Links to other publicly accessible locations of the data: None
2. Links/relationships to ancillary data sets: None
3. Was data derived from another source? No A. If yes, list source(s): NA
4. Recommended citation for this dataset:

Chaille, A. Y., Lacy, R. C., Putnam, A. S., Toste, J. L., & Ivy, J. A. (2023). Data from: Implications of methodologies for integrating empirical kinships into ex situ population management using PMx: A case study of Baer’s Pochard (Aythya baeri) in North America. Dryad Digital Repository. https://doi.org/10.5061/dryad.6t1g1jx3m

DATA & FILE OVERVIEW

1. File List:

A) Individuals_1_20.zip
B) Individuals_21_38.zip
C) Individuals_39_55.zip
D) Individuals_56_72.zip
E) Individuals_73_89.zip
F) Individuals_90_107.zip
G) Individuals_108_123.zip
H) Individuals_124_141.zip
I) PopulationMap.txt
J) populations.snps.vcf
K) KinshipMatrix_N56_Scenario2.txt
L) KinshipMatrix_N141_Scenario3.txt
M) KinshipMatrix_N141_OriginalWithNegativeValues.txt
N) BaersPochard_Scenario1.pmxproj
O) BaersPochard_Scenario2.pmxproj
P) BaersPochard_Scenario3.pmxproj

1. Relationship between files, if important: Files A-H are raw ddRAD sequence data (paired-end) for 141 sampled Baer's pochard.
2. Additional related data collected that was not included in the current data package: None
3. Are there multiple versions of the dataset? No A. If yes, name of file(s) that was updated: NA i. Why was the file updated? NA ii. When was the file updated? NA

#########################################################################

DATA-SPECIFIC INFORMATION FOR:

Individuals_21_38.zip
Individuals_39_55.zip
Individuals_56_72.zip
Individuals_73_89.zip
Individuals_90_107.zip
Individuals_108_123.zip
Individuals_124_141.zip

These files contain raw ddRAD sequence data (paired-end) for 141 sampled Baer's pochard in FASTQ format.
Data are divided into multiple zipped folders by sample number 1-141, and not by individual ID.

#########################################################################

DATA-SPECIFIC INFORMATION FOR: PopulationMap.txt

This is the population map input file used for the STACKS analysis.

1. Number of variables: 2
2. Number of cases/rows: 141
3. Variable List:
   • 1st column: studbook number (individual identifier) for all 141 birds sampled for the study
   • 2nd column: population assignment - all given 1
4. Missing data codes: None
5. Specialized formats or other abbreviations used: None

#########################################################################

DATA-SPECIFIC INFORMATION FOR: populations.snps.vcf

Output of SNPs and haplotypes from STACKS containing 26,454 filtered SNPs for 141 individuals.

1. Number of variables: 149 (16 variables and 141 birds sampled for the study)
2. Number of cases/rows: 26,454 polymorphic SNPs
3. Variable List:
   • CHROM: Catalog locus
   • POS: SNP location
   • ID: Locus number not applicable (.)
   • REF: Primary SNP allele
   • ALT: Alternative SNP allele
   • QUAL: Not applicable '.'
   • FILTER: Passed the filtering steps
   • INFO: NS = number of samples with data; AF = allele frequency
   • FORMAT: The format used in the VCF file to describe haplotypes for each individual (GT:DP:AD:GQ:GL)
   • COLUMNS '024'through to'285': 141 birds' studbook identifiers
4. Missing data codes: not applicable '.'
5. Specialized formats or other abbreviations used: Variant Call Format (VCF)

#########################################################################

DATA-SPECIFIC INFORMATION FOR: KinshipMatrix_N56_Scenario2.txt

Empirical kinship text file for 56 pedigree terminals integrated into the PMx project for Scenario 2.

The first 56 rows list the 56 pedigree terminals by studbook identifier.
This is followed by a full matrix of the pairwise empirical kinships (KING-robust) between a pair of individuals in the order listed in the rows above.

Missing data codes: '-1'

#########################################################################

DATA-SPECIFIC INFORMATION FOR: KinshipMatrix_N141_Scenario3.txt

Empirical kinship text file for all 141 birds in the population integrated into the PMx project for Scenario 3.

The first 141 rows list the 141 pedigree terminals by studbook identifier.
This is followed by a full matrix of the pairwise empirical kinships (KING-robust) between a pair of individuals in the order listed in the rows above.

Missing data codes: '-1'

#########################################################################

DATA-SPECIFIC INFORMATION FOR: KinshipMatrix_N141_OriginalWithNegativeValues.txt

The original empirical kinship text file for all 141 birds in the population prior to truncating negative values to '0'.

The first 141 rows list the 141 pedigree terminals by studbook identifier.
This is followed by a full matrix of the pairwise empirical kinships (KING-robust) between a pair of individuals in the order listed in the rows above.

Missing data codes: '-1'

#########################################################################

DATA-SPECIFIC INFORMATION FOR:

BaersPochard_Scenario1.pmxproj
BaersPochard_Scenario2.pmxproj
BaersPochard_Scenario3.pmxproj

PMx project files for Scenario 1 in which no empirical kinships were applied, Scenario 2 in which empirical kinships are applied to pedigree terminals, and Scenario 3 in which empirical kinships are applied for the entire population.

The PMx (scti.tools/pmx/) software is required to open the PMx project files. The files themselves are compressed (zipped) file that uses the standard file compression format.

For the manuscript, PMx version 1.6.20200804 was used to run those files.

#########################################################################

CODE/SOFTWARE

A custom bioinformatics pipeline (available at https://github.com/apwilder/StacksParameterSelection) was used to select optimal parameters (m, M, n) for STACKS based on the guidelines of Paris et al. (2017).