Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal, and occupancy data, to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog (Rana luteiventris). R. luteiventris occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change, and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (1) assessing support for ESUs within Nevada; (2) evaluating and revising, if warranted, the current delineation of MUs; and (3) evaluating genetic diversity, effective population size, adaptive differentiation, and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.

See manuscript for full details on data processing.

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