Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.)

Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly-evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defense cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find..., Sample Collection, DNA Extraction, and GBS Library Preparation
Using a nationwide network of K-12 science teachers, citizen scientists and colleagues, we obtained mature seeds or stolon cuttings for 419 wild white clover accessions across 43 locations in North America during the growing seasons of 2014-2017. Each location was represented by 6 to 11 accessions (individual genotypes), and latitude and longitude were recorded for each sample. Seeds and stolon cuttings were cultivated in the greenhouse at Washington University in St. Louis under standard greenhouse conditions (see Wright et al. 2022). Genomic DNA was extracted from young leaves using a standard DNA extraction protocol (Whitlock et al., 2008). Extraction quantity and quality were assessed using a NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer, and Qubit™ dsDNA HS Assay Kits.
Genotyping-by-sequencing (GBS) libraries were prepared following Elshire et al. (2011) with ApeKI methylation sensitive restriction enzyme. Bar..., , # Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (*Trifolium repens* L.)

[https://doi.org/10.5061/dryad.s7h44j1fd](https://doi.org/10.5061/dryad.s7h44j1fd)

The dataset includes the vcf files using in this study, which are the documentations of the genetic polymorphism of the 415 genotypes from the 43 locations.

## Description of the data and file structure

bwa_wild_DP0_diploid_hardfilter_miss0.25_maf0.05_GT.vcf.gz - A vcf file including all the polymorphic sites after filtering. See methods for detailed filtering conditions.

bwa_wild_DP0_diploid_hardfilter_miss0.25_maf0.05_GT_imputed.vcf.gz - A vcf file with imputations for the missing data in bwa_wild_DP0_diploid_hardfilter_miss0.25_maf0.05_GT.vcf.gz.

All the vcf files have not been subjected to LD pruning.

LFMM_output_20230606.txt - LFMM result output.