Population genomics reveals local adaptation related to temperature variation in two stream frog species: Implications for vulnerability to climate warming
Data files
Jan 08, 2025 version files 7.71 GB
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adaptive_imp_annotated_MT_filtered.vcf.gz
657.84 KB
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adaptive_imp_annotated_OR_filtered.vcf.gz
568.02 KB
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imp_full_annotated_filtered_MT.vcf.gz
3.62 GB
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imp_full_annotated_filtered_OR.vcf.gz
4.10 GB
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MT_strata_Capture.csv
7.74 KB
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MT_strata.csv
2.53 KB
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OR_strata_Capture.csv
6.92 KB
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OR_strata.csv
2.48 KB
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README.md
5.08 KB
Abstract
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.
README: 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
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
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
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 / 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
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)