Range-wide climate risk and adaptive potential in a cold-water fish species (Part 1/2)
Data files
Oct 21, 2025 version files 104.38 GB
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7116_9173_35601_HG23CBGXY_all_R1.fastq.gz
31.04 GB
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7116_9173_35601_HG23CBGXY_all_R2.fastq.gz
29.34 GB
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7117_9173_35602_HL2K7BGXY_BT_2_R1.fastq.gz
21.87 GB
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7117_9173_35602_HL2K7BGXY_BT_2_R2.fastq.gz
22.13 GB
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RADseq_Brook_Trout_Barcode_Information.csv
8.80 KB
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README.md
2.10 KB
Abstract
Predicting extinction risk from climate change requires understanding adaptive variation and local adaptation across species’ ranges. We combine experimental and -omics approaches with climate change modeling to identify molecular mechanisms of local adaptation to heat stress in brook trout, a coldwater species experiencing extirpations due to warming temperatures. We identify genomic variation corresponding with thermal conditions across the native range, suggesting local adaptation, and experimentally identify variants linked with gene expression responses to thermal stress. Using climate projections, we find that southern brook trout populations are the most vulnerable to extirpation from climate warming and mid-range populations are the most promising candidates for receiving assisted gene flow to improve climate resilience. Together, this work highlights the importance of genomic information in managing populations threatened by climate change. This is Part 1 of the full dataset, containing the RADseq dataset.
https://doi.org/10.5061/dryad.sj3tx96fs
This is one of two datasets related to the same study:
- Part 1 (this dataset) contains all the RADseq data, https://doi.org/10.5061/dryad.sj3tx96fs
- Part 2 contains all of the RNAseq data, https://doi.org/10.5061/dryad.nk98sf84m
Description of the data and file structure
The code and RADseq data associated with Meek et al. Nature Communications 2025 manuscript.
RADseq data are contained in:
- 7116_9173_35601_HG23CBGXY_all_R1.fastq.gz 31.04 GB - Forward reads Plate 1
- 7116_9173_35601_HG23CBGXY_all_R2.fastq.gz 29.34 GB - Reverse reads Plate 1
- 7117_9173_35602_HL2K7BGXY_BT_2_R1.fastq.gz 21.87 GB - Forward reads Plate 2
- 7117_9173_35602_HL2K7BGXY_BT_2_R2.fastq.gz 22.13 GB - Reverse reads Plate 2
Files and variables
Description: All RADseq data generated on individuals used in the brook trout common garden experiment in Meek et al. Nature Communications 2025.
File: RADseq_Brook_Trout_Barcode_Information.csv
Metadata for samples: "RADseq Brook Trout Barcode Information"
Column descriptions:
| Variable | Description |
|---|---|
| Library Index | NEBNext Library index used |
| Library Index Sequence | Library index genetic sequence |
| Individual Index | Individual barcode sequence |
| Plate ID | Name of 96 well plate |
| DNA well | Well in 96 well plate |
| SampleID | Individual sample ID |
| Date sampled | Date of individual sampling |
| Location | Tank number individual was in |
blank cells = NA
Code/software
"BrookTroutCommonGardenExperimentScripts.zip" contains the scripts to process the RNAseq data and do the eQTL analysis for the common garden experiment as described in Meek et al. Nature Communications 2025.