DOI: 10.5061/dryad.w6m905qqn
title: Genomics‐informed delineation of conservation units in a desert amphibian

description: 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.
description: See manuscript for full details on data processing.
description: 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<br><br>GENERAL INFORMATION<br><br>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<br>    Name: Brenna R. Forester<br>    ORCID: 0000-0002-1608-1904<br>    Institution: Colorado State University / U.S. Fish & Wildlife Service<br>    Email: brenna.forester@colostate.edu / brenna_forester@fws.gov<br><br>    Author/Alternate Contact Information<br>    Name: W. Chris Funk<br>    ORCID: 0000-0002-6466-3618<br>    Institution: Colorado State University<br>    Email: chris.funk@colostate.edu<br><br>DATA & FILE OVERVIEW<br><br>1. File list:<br><br>    File 1 Name: 01.0-RALU_snps_360.vcf.gz<br>    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. <br>    <br>    File 2 Name: 01.1-RALU_strata_360.txt<br>    File 2 Description: Individual, site, and HUC metadata for the 360 individuals in 01.0-RALU_snps_360.vcf.gz.<br>    <br>    File 3 Name: 02.0-populations.full.snps.vcf.gz<br>    File 3 Description: Final filtered vcf for 357 individuals genotyped at 39,914 SNPs.<br>    <br>    File 4 Name: 02.1-stacks.full.whitelist.tsv<br>    File 4 Description: Final filtered Stacks whitelist of 39,914 SNPs.<br>    <br>    File 5 Name: 02.2-full_imputed_39914.csv<br>    File 5 Description: Final filtered and imputed dataset for 357 individuals genotyped at 39,914 SNPs.<br>    <br>    File 6 Name: 03.0-populations.neutral.snps.vcf.gz<br>    File 6 Description: Final neutral vcf for 357 individuals genotyped at 39,225 SNPs.<br>    <br>    File 7 Name: 03.1-stacks.neutral.whitelist.tsv<br>    File 7 Description: Final neutral Stacks whitelist of 39,225 SNPs.<br>    <br>    File 8 Name: 04.0-populations.adaptive.snps.vcf.gz<br>    File 8 Description: Final candidate adaptive vcf for 357 individuals genotyped at 689 SNPs.<br>    <br>    File 9 Name: 04.1-stacks.adaptive.whitelist.tsv<br>    File 9 Description: Final adaptive Stacks whitelist of 689 SNPs.<br>    <br>    File 10 Name: 05.0-RALU_ind_357.csv<br>    File 10 Description: Metadata for final 357 retained individuals including sample IDs, site IDs, HUCs, library, coordinates, environmental data, and assignments for ANOVA tests.<br><br><br>DATA-SPECIFIC INFORMATION FOR: 01.1-RALU_strata_360.txt<br><br>1. Number of variables: 3<br><br>2. Number of cases/rows: 360<br><br>3. Variable List: <br>    INDIVIDUALS: Individual frog ID <br>    STRATA: Population ID<br>    HUC: Watershed ID<br><br>4. Missing data codes: <br>    None<br><br><br>DATA-SPECIFIC INFORMATION FOR: 02.1-stacks.full.whitelist.tsv<br><br>1. Number of variables: 2<br><br>2. Number of cases/rows: 39,914<br><br>3. Variable List: <br>    COLUMN 1: Stacks catalog locus <br>    COLUMN 2: Column within the locus with the selected SNP<br><br>4. Missing data codes: <br>    None<br><br><br>DATA-SPECIFIC INFORMATION FOR: 02.2-full_imputed_39914.csv<br><br>1. Number of variables: 39,914<br><br>2. Number of cases/rows: 357<br><br>3. Variable List: <br>    EACH COLUMN: Genotypes coded as 0/1/2 for 39,914 SNP loci<br><br>4. Missing data codes: <br>    None<br><br><br>DATA-SPECIFIC INFORMATION FOR: 03.1-stacks.neutral.whitelist.tsv<br><br>1. Number of variables: 2<br><br>2. Number of cases/rows: 39,225<br><br>3. Variable List: <br>    COLUMN 1: Stacks catalog locus <br>    COLUMN 2: Column within the locus with the selected SNP<br><br>4. Missing data codes: <br>    None<br><br><br>DATA-SPECIFIC INFORMATION FOR: 04.1-stacks.adaptive.whitelist.tsv<br><br>1. Number of variables: 2<br><br>2. Number of cases/rows: 689<br><br>3. Variable List: <br>    COLUMN 1: Stacks catalog locus <br>    COLUMN 2: Column within the locus with the selected SNP<br><br>4. Missing data codes: <br>    None<br><br><br>DATA-SPECIFIC INFORMATION FOR: 05.0-RALU_ind_357.csv<br><br>1. Number of variables: 26<br><br>2. Number of cases/rows: 357<br><br>3. Variable List: <br>    INDIVIDUALS: Individual frog ID <br>    STRATA: Population ID<br>    basin: Watershed ID<br>    library: Sequencing library of individual<br>    Northing: UTM coordinate (Zone 11)<br>    Easting: UTM coordinate (Zone 11)<br>    ppt.JJA: Average summer precipitation in mm (June-August) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)<br>    ppt.SON: Average fall precipitation in mm (September-November) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)<br>    tmin.DJF: Average winter minimum temperature in degrees C (December-Februrary) from the 800m PRISM climate normal (1981-2010, Daly et al., 2008)<br>    elevation: Elevation in meters<br>    HUC2: Individual assignment into groups for AMOVA testing based on HUC2 watershed delineations<br>    HUC6: Individual assignment into groups for AMOVA testing based on HUC6 watershed delineations<br>    HUC8: Individual assignment into groups for AMOVA testing based on HUC8 watershed delineations<br>    HUC10: Individual assignment into groups for AMOVA testing based on HUC10 watershed delineations<br>    FWS_MUs: Individual assignment into groups for AMOVA testing based on current U.S. Fish and Wildlife Service Management Units<br>    admixture7: Individual assignment into groups for AMOVA testing based on Admixture results for K=7<br>    admixture8: Individual assignment into groups for AMOVA testing based on Admixture results for K=8<br>    admixture9: Individual assignment into groups for AMOVA testing based on Admixture results for K=9<br>    admixture10: Individual assignment into groups for AMOVA testing based on Admixture results for K=10<br>    admixture11: Individual assignment into groups for AMOVA testing based on Admixture results for K=11<br>    admixture12: Individual assignment into groups for AMOVA testing based on Admixture results for K=12<br>    admixture13: Individual assignment into groups for AMOVA testing based on Admixture results for K=13<br>    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<br>    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<br>    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<br>    MU_12: Individual assignment into 12 Management Units for AMOVA testing based on combined results from Admixture, PCA, and flow predictions<br><br>4. Missing data codes: <br>    None