The genetic architecture of repeated local adaptation to climate in distantly related plants

Closely related species often use the same genes to adapt to similar environments. However, we know little about why such genes possess increased adaptive potential, and whether this is conserved across deeper evolutionary lineages. Adaptation to climate presents a natural laboratory to test these ideas, as even distantly related species must contend with similar stresses. Here, we re-analyse genomic data from thousands of individuals from 25 plant species as diverged as lodgepole pine and Arabidopsis (~300 My). We test for genetic repeatability based on within-species associations between allele frequencies in genes and variation in 21 climate variables. Our results demonstrate significant statistical evidence for genetic repeatability across deep time that is not expected under randomness, identifying a suite of 108 gene families (orthogroups) and gene functions that repeatedly drive local adaptation to climate. This set includes many orthogroups with well-known functions in abiotic s..., Dataset selection criteria
We selected 29 datasets covering 25 species from 21 studies (see README) for which sequence data were available with either whole genome shotgun data (WGS), pooled sequencing data (POOL), or sequence capture data (CAPTURE) (Table S1). Such datasets provide broad genomic representation and maximise the resolution of the number of genes for each species. We limited our study to datasets with at least five populations distributed along latitudinal, longitudinal, and/or altitudinal gradients. Here, the minimum number of populations was set in order to allow for a minimum baseline of statistical power for Kendall’s τ correlations between environment and allele frequency (see below). The list of included datasets is not exhaustive but rather was selected to achieve a desired number of approximately 20-30 species for which power to detect repeated adaptation has been demonstrated for the methods used here. Datasets also had to provide locality information, either for..., , # The genetic architecture of repeated local adaptation to climate in distantly related plants

Dryad DOI: [https://doi.org/10.5061/dryad.15dv41p57](https://doi.org/10.5061/dryad.15dv41p57)

[![DOI](https://zenodo.org/badge/360660589.svg \"DOI\")](https://zenodo.org/doi/10.5281/zenodo.12680121)

### Author Contact Information

* Sam Yeaman - [[e-mail]](mailto:[e-mail])

## Dryad contents:

* 29 VCFs for SNP data across 25 species.
* Sampling location and climate change variables for each VCF.
* VCF metadata xlsx

### VCF formats

All capture and whole-genome sequencing data is in standard VCF format. The sampling location CSV for each VCF denotes where each sample was taken. For the sake of grouping individuals into 'populations' for analyses, these were grouped according to samples with the same lat/lon sampling locations.

Pool-sequencing data is in the format of simplified SNP tables, where the allele frequency for each SNP for each pool is given in a tabula...