DOI: 10.5061/dryad.2280gb638
title: Population genomics reveals local adaptation related to temperature variation in two stream frog species: Implications for vulnerability to climate warming

description: Identifying populations at highest risk from climate change is a critical
 component of conservation efforts. However, vulnerability assessments are
 usually applied at the species level, even though intraspecific variation
 in exposure, sensitivity, and adaptive capacity play a crucial role in
 determining vulnerability. Genomic data can inform intraspecific
 vulnerability by identifying signatures of local adaptation that reflect
 population-level variation in sensitivity and adaptive capacity. Here, we
 address the question of local adaptation to temperature and the genetic
 basis of thermal tolerance in two stream frogs (Ascaphus truei and A.
 montanus). Building on previous physiological and temperature data, we
 used whole genome resequencing of tadpoles from four sites spanning
 temperature gradients in each species to test for signatures of local
 adaptation. To support these analyses, we developed the first annotated
 reference genome for A. truei. We then expanded the geographic scope of
 our analysis using targeted capture at an additional 11 sites per species.
 We found evidence of local adaptation to temperature based on
 physiological and genomic data in A. montanus and genomic data in A.
 truei, suggesting similar levels of sensitivity (i.e., susceptibility)
 among populations regardless of stream temperature. However, invariant
 thermal tolerances across temperatures in A. truei suggests that
 populations occupying warmer streams may be most sensitive. We identified
 high levels of evolutionary potential in both species based on genomic and
 physiological data. While further integration of these data is needed to
 comprehensively evaluate spatial variation in vulnerability, this work
 illustrates the value of genomics in identifying spatial patterns of
 climate change vulnerability.
description: # Population genomics reveals local adaptation related to temperature
 variation in two stream frog species: Implications for vulnerability to
 climate warming
 [https://doi.org/10.5061/dryad.2280gb638](https://doi.org/10.5061/dryad.2280gb638) ## Description of the data and file structure **1. Title of dataset:** Data from: Population genomics reveals local adaptation related to temperature variation in two stream frog species: implications for vulnerability to climate warming **2. Recommended citation for this dataset:** Forester BR, Cicchino AS, Shah AA, Mudd AB, Anderson EC, Bredeson JV, Crawford AJ, Dunham JB, Ghalambor CK, Landguth EL, Murray BW, Rokhsar D, Funk WC (2025) Data from: Population genomics reveals local adaptation related to temperature variation in two stream frog species: implications for vulnerability to climate warming, Dryad, Dataset, [https://doi.org/10.5061/dryad.2280gb638](https://doi.org/10.5061/dryad.2280gb638) **3. Associated paper:** Forester BR, Cicchino AS, Shah AA, Mudd AB, Anderson EC, Bredeson JV, Crawford AJ, Dunham JB, Ghalambor CK, Landguth EL, Murray BW, Rokhsar D, Funk WC (2025) Population genomics reveals local adaptation related to temperature variation in two stream frog species: implications for vulnerability to climate warming. Molecular Ecology. [https://doi.org/10.1111/mec.17651](https://doi.org/) **4. Corresponding author information:** Brenna R. Forester * ORCID: 0000-0002-1608-1904 - Institution: Colorado State University / U.S. Fish & Wildlife Service * Email: [brenna.forester@colostate.edu](mailto:brenna.forester@colostate.edu) / [brenna_forester@fws.gov](mailto:brenna_forester@fws.gov) **5. Alternate contact information:** W. Chris Funk * ORCID: 0000-0002-6466-3618 * Institution: Colorado State University * Email: [chris.funk@colostate.edu](mailto:chris.funk@colostate.edu) ### Files and variables #### File: MT\_strata.csv **Description:** Metadata for the 40 *Ascaphus montanus* tadpoles genotyped in imp_full_annotated_filtered_MT.vcf.gz. ##### Variables * INDIVIDUALS: Individual *Ascaphus montanus* tadpole name * STRATA: WGR lane (1 or 2) * Pop: Population/site * ID: Individual tadpole ID number * Elevation: Site elevation (m) * LengthAvg: Averaged tadpole length (cm) * CTmax: Critical thermal maximum temperature (degrees C) * AugMeanTemp: Site August mean temperature (degrees C) * PC1: Individual coordinates from PC1 (derived from the LD-pruned genotype matrix) #### File: OR\_strata.csv **Description:** Metadata for the 40 *Ascaphus truei* tadpoles genotyped in imp_full_annotated_filtered_OR.vcf.gz. ##### Variables * INDIVIDUALS: Individual *Ascaphus truei* tadpole name * STRATA: WGR lane (1 or 2) * Pop: Population/site * ID: Individual tadpole ID number * Elevation: Site elevation (m) * LengthAvg: Averaged tadpole length (cm) * CTmax: Critical thermal maximum temperature (degrees C) * AugMeanTemp: Site August mean temperature (degrees C) * PC1: Individual coordinates from PC1 (derived from the LD-pruned genotype matrix) #### File: imp\_full\_annotated\_filtered\_MT.vcf.gz **Description:** 40 *Ascaphus montanus* tadpoles genotyped at 33,709,071 filtered and imputed variants; derived from whole genome resequencing data. #### File: imp\_full\_annotated\_filtered\_OR.vcf.gz **Description:** 40 *Ascaphus truei* tadpoles genotyped at 39,825,878 filtered and imputed variants; derived from whole genome resequencing data. #### File: MT\_strata\_Capture.csv **Description:** Metadata for the 108 *Ascaphus montanus* tadpoles genotyped in adaptive_imp_annotated_MT_filtered.vcf.gz. ##### Variables * INDIVIDUALS: Individual *Ascaphus montanus* tadpole name * STRATA: Population/site * State: State where tadpoles were sampled (MT for *Ascaphus montanus*) * ID: Individual tadpole ID number * Year: Year of collection * WCF: Alternative ID number * Elevation: Site elevation (m) * Length_Avg_cm: Averaged tadpole length (cm) * CTmax: Critical thermal maximum temperature (degrees C) * AugMeanTemp: Site August mean temperature (degrees C) #### File: adaptive\_imp\_annotated\_MT\_filtered.vcf.gz **Description:** 108 *Ascaphus montanus* tadpoles genotyped at 1,269 filtered and imputed variants; derived from targeted capture data. #### File: adaptive\_imp\_annotated\_OR\_filtered.vcf.gz **Description:** 101 A*scaphus truei* tadpoles genotyped at 1,052 filtered and imputed variants; derived from targeted capture data. #### File: OR\_strata\_Capture.csv **Description:** Metadata for the 101 *Ascaphus truei* tadpoles genotyped in adaptive_imp_annotated_OR_filtered.vcf.gz. ##### Variables * INDIVIDUALS: Individual *Ascaphus truei *tadpole name * STRATA: Population/site * State: State where tadpoles were sampled (MT for *Ascaphus montanus*) * ID: Individual tadpole ID number * Year: Year of collection * WCF: Alternative ID number * Elevation: Site elevation (m) * Length_Avg_cm: Averaged tadpole length (cm) * CTmax: Critical thermal maximum temperature (degrees C) * AugMeanTemp: Site August mean temperature (degrees C)