Genomics‐informed delineation of conservation units in a desert amphibian

Dryad file "README_Forester_RALU.txt" (pasted in below) includes information on this Dryad submission:

This README file was generated on 2022-08-25 by Brenna R. Forester

GENERAL INFORMATION

1. Title of Dataset: Data from: Genomics-informed delineation of conservation units in a desert amphibian

2. Recommended citation for this dataset: Forester BR, Murphy M, Mellison C, Petersen J, Pilliod DS, Van Horne R, Harvey J, Funk WC (2022) Data from: Genomics-informed delineation of conservation units in a desert amphibian, Dryad, Dataset, https://doi.org/10.5061/dryad.w6m905qqn

3. Associated paper: Forester BR, Murphy M, Mellison C, Petersen J, Pilliod DS, Van Horne R, Harvey J, Funk WC (2022) Genomics-informed delineation of conservation units in a desert amphibian. Molecular Ecology. https://doi.org/10.1111/mec.16660

4. Corresponding Author Information
    Name: Brenna R. Forester
    ORCID: 0000-0002-1608-1904
    Institution: Colorado State University / U.S. Fish & Wildlife Service
    Email: brenna.forester@colostate.edu / brenna_forester@fws.gov

    Author/Alternate Contact Information
    Name: W. Chris Funk
    ORCID: 0000-0002-6466-3618
    Institution: Colorado State University
    Email: chris.funk@colostate.edu

DATA & FILE OVERVIEW

1. File list:

    File 1 Name: 01.0-RALU_snps_360.vcf.gz
    File 1 Description: 360 individuals genotyped at 438,848 SNPs; produced using Stacks v. 2.4.1 by applying the following filters in the "populations" module: -p 1, -R 0.3, --min_mac 2.
    
    File 2 Name: 01.1-RALU_strata_360.txt
    File 2 Description: Individual, site, and HUC metadata for the 360 individuals in 01.0-RALU_snps_360.vcf.gz.
    
    File 3 Name: 02.0-populations.full.snps.vcf.gz
    File 3 Description: Final filtered vcf for 357 individuals genotyped at 39,914 SNPs.
    
    File 4 Name: 02.1-stacks.full.whitelist.tsv
    File 4 Description: Final filtered Stacks whitelist of 39,914 SNPs.
    
    File 5 Name: 02.2-full_imputed_39914.csv
    File 5 Description: Final filtered and imputed dataset for 357 individuals genotyped at 39,914 SNPs.
    
    File 6 Name: 03.0-populations.neutral.snps.vcf.gz
    File 6 Description: Final neutral vcf for 357 individuals genotyped at 39,225 SNPs.
    
    File 7 Name: 03.1-stacks.neutral.whitelist.tsv
    File 7 Description: Final neutral Stacks whitelist of 39,225 SNPs.
    
    File 8 Name: 04.0-populations.adaptive.snps.vcf.gz
    File 8 Description: Final candidate adaptive vcf for 357 individuals genotyped at 689 SNPs.
    
    File 9 Name: 04.1-stacks.adaptive.whitelist.tsv
    File 9 Description: Final adaptive Stacks whitelist of 689 SNPs.
    
    File 10 Name: 05.0-RALU_ind_357.csv
    File 10 Description: Metadata for final 357 retained individuals including sample IDs, site IDs, HUCs, library, coordinates, environmental data, and assignments for ANOVA tests.


DATA-SPECIFIC INFORMATION FOR: 01.1-RALU_strata_360.txt

1. Number of variables: 3

2. Number of cases/rows: 360

3. Variable List:
    INDIVIDUALS: Individual frog ID
    STRATA: Population ID
    HUC: Watershed ID

4. Missing data codes:
    None


DATA-SPECIFIC INFORMATION FOR: 02.1-stacks.full.whitelist.tsv

1. Number of variables: 2

2. Number of cases/rows: 39,914

3. Variable List:
    COLUMN 1: Stacks catalog locus
    COLUMN 2: Column within the locus with the selected SNP

4. Missing data codes:
    None


DATA-SPECIFIC INFORMATION FOR: 02.2-full_imputed_39914.csv

1. Number of variables: 39,914

2. Number of cases/rows: 357

3. Variable List:
    EACH COLUMN: Genotypes coded as 0/1/2 for 39,914 SNP loci

4. Missing data codes:
    None


DATA-SPECIFIC INFORMATION FOR: 03.1-stacks.neutral.whitelist.tsv

1. Number of variables: 2

2. Number of cases/rows: 39,225

3. Variable List:
    COLUMN 1: Stacks catalog locus
    COLUMN 2: Column within the locus with the selected SNP

4. Missing data codes:
    None


DATA-SPECIFIC INFORMATION FOR: 04.1-stacks.adaptive.whitelist.tsv

1. Number of variables: 2

2. Number of cases/rows: 689

3. Variable List:
    COLUMN 1: Stacks catalog locus
    COLUMN 2: Column within the locus with the selected SNP

4. Missing data codes:
    None


DATA-SPECIFIC INFORMATION FOR: 05.0-RALU_ind_357.csv

1. Number of variables: 26

2. Number of cases/rows: 357

3. Variable List:
    INDIVIDUALS: Individual frog ID
    STRATA: Population ID
    basin: Watershed ID
    library: Sequencing library of individual
    Northing: UTM coordinate (Zone 11)
    Easting: UTM coordinate (Zone 11)
    ppt.JJA: Average summer precipitation in mm (June-August) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)
    ppt.SON: Average fall precipitation in mm (September-November) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)
    tmin.DJF: Average winter minimum temperature in degrees C (December-Februrary) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)
    elevation: Elevation in meters
    HUC2: Individual assignment into groups for AMOVA testing based on HUC2 watershed delineations
    HUC6: Individual assignment into groups for AMOVA testing based on HUC6 watershed delineations
    HUC8: Individual assignment into groups for AMOVA testing based on HUC8 watershed delineations
    HUC10: Individual assignment into groups for AMOVA testing based on HUC10 watershed delineations
    FWS_MUs: Individual assignment into groups for AMOVA testing based on current U.S. Fish and Wildlife Service Management Units
    admixture7: Individual assignment into groups for AMOVA testing based on Admixture results for K=7
    admixture8: Individual assignment into groups for AMOVA testing based on Admixture results for K=8
    admixture9: Individual assignment into groups for AMOVA testing based on Admixture results for K=9
    admixture10: Individual assignment into groups for AMOVA testing based on Admixture results for K=10
    admixture11: Individual assignment into groups for AMOVA testing based on Admixture results for K=11
    admixture12: Individual assignment into groups for AMOVA testing based on Admixture results for K=12
    admixture13: Individual assignment into groups for AMOVA testing based on Admixture results for K=13
    MU_11_sfowyhee: Individual assignment into 11 Management Units for AMOVA testing based on combined results from Admixture, PCA, and flow predictions; this assignment does not place Winters Creek in a separate Management Unit relative to MU_12
    MU_11_northfork: Individual assignment into 11 Management Units for AMOVA testing based on combined results from Admixture, PCA, and flow predictions; this assignment does not split the North Fork Management Unit into two separate units relative to MU_12
    MU_11_salmon-mary: Individual assignment into 11 Management Units for AMOVA testing based on combined results from Admixture, PCA, and flow predictions; this assignment combines Salmon and Marys watersheds into a single Management Unit relative to MU_12
    MU_12: Individual assignment into 12 Management Units for AMOVA testing based on combined results from Admixture, PCA, and flow predictions

4. Missing data codes:
    None

Funding provided by: David H. Smith Conservation Research Fellowship*
Crossref Funder Registry ID:
Award Number:

Funding provided by: U.S. Fish and Wildlife Service
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000202
Award Number:

Funding provided by: U.S. Bureau of Land Management
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100007149
Award Number:

Funding provided by: Nevada Department of Wildlife
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100010427
Award Number:

Funding provided by: University of Wyoming
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100008106
Award Number: WYO-5360-14