Evaluating the roles of drift and selection in trait loss along an elevational gradient
Data files
Apr 16, 2025 version files 552.75 MB
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GWAS.zip
552.61 MB
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README.md
4.68 KB
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RelatednessMatrices.zip
140.65 KB
Abstract
Traits that have lost function sometimes persist through evolutionary time. Persistence may occur if there is not enough standing genetic variation for the trait to allow a response to selection, if selection against the trait is weak relative to drift, or if the trait has a residual function. To determine the evolutionary processes shaping whether nonfunctional traits are retained or lost, we investigated short stamens in 16 populations of Arabidopsis thaliana along an elevational cline in northeast Spain. A. thaliana is highly self-pollinating and prior work suggests short stamens do not contribute to self-pollination. We found a cline in short stamen number from retention of short stamens in high elevation populations to incomplete loss in low elevation populations. We did not find evidence that limited genetic variation constrains short stamen loss at high elevations, nor evidence for divergent selection on short stamens between high and low elevations. Finally, we identified loci associated with short stamens in northeast Spain that are different from loci associated with variation in short stamens across latitudes from a previous study. Overall, we did not identify the evolutionary mechanisms contributing to an elevational cline in short stamen number so further research is clearly warranted.
This dryad dataset includes the GWAS output results. See the github for phenotypic data and SRA for genotypic data.
Dataset DOI: 10.5061/dryad.8sf7m0d0z
Description of the data and file structure
These files are the relatedness matrices and GWAS output files for a GWAS on short stamen number in A. thaliana from an elevation gradient across the Pyrenees. The associated paper is "Evaluating the Roles of Drift and Selection in Trait Loss along an Elevational Gradient" by Buysse et al. The code used to generate the files can be found on github: https://github.com/sfbuysse/A_thaliana_StamenLoss_2025.
The input data is SNP information for 61 genotypes from 16 native populations of A. thaliana.
Files and variables
File: RelatednessMatrices.zip
Description: RelatednessMatrices.zip contains centered Relatedness Matrices made with GEMMA v0.98.4. Relatedness matrices are *.cXX.txt and *.log.txt show the code and run log information.
allSNPs.PlinkFiltering_Asin, allSNPs.PlinkFiltering_Binary, allSNPs.PlinkFiltering_raw : identical relatedness matrices made using all SNPs in the dataset after filtering with Plink. Names were changed to match the phenotype files to run the GWAS.
allSNPs.PlinkFiltering*_*raw_subset : centered relatedness matrix made with all SNPs after plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2).
NoCent.PlinkFiltering_Asin, NoCent.PlinkFiltering_Binary, NoCent.PlinkFiltering_raw : identical relatedness matrices made after excluding the centromere region and filtering with Plink. Names were changed to match the phenotype files to run the GWAS.
NoCent.PlinkFiltering_raw_subset. : centered relatedness matrix made after excluding the centromere and plink filtering but only the individuals with some short stamen loss (mean short stamen number < 2).
File: GWAS.zip
Description: GWAS.zip contains GWAS output files. The GWAS output files are *.assoc.txt and the code information is *.log.txt. GWAS were run in GEMMA v0.98.4. Within each .assoc.txt file the columns are as follows:
- chr = chromosome
- rs = snp id (chromosome:base pair position)
- ps = base pair position
- n_miss = number of genotypes missing genetic information at that SNP
- allele1 = minor allele
- allele2 = major allele
- af = minor allele frequency
- beta = affect size
- se = standard error for beta
- log_lH1 = log liklihood of alternative hypothesis that beta does not equal 0 (H0 is that beta =0)
- l_remle = restricted maximum liklihood estimates for lambda
- l_mle = maximum liklihood estimates for lambda
- p_wald = p value from the Wald test
- p_lrt = p value from liiklihood ratio test
- p_score = p value from score test
allSNPs.PlinkFiltering_Asin.c : include allSNPs after filtering with plink. phenotypes were arcsine transformed before GWAS. Centered relatedness matrix used.
allSNPs.PlinkFiltering_Binary.c : include allSNPs after filtering with plink. phenotypes were transformed to a binary trait before GWAS - no short stamen loss = 0, any short stamen loss = 1. Centered relatedness matrix used.
allSNPs.PlinkFiltering_raw.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS. Centered relatedness matrix used.
allSNPs.PlinkFiltering*_*raw_subset.c : include allSNPs after filtering with plink. phenotypes were not transformed before GWAS but the individuals used were subset down to only those that had some short stamen loss (mean short stamen number < 2). Centered relatedness matrix used.
NoCent.PlinkFiltering_Asin.c : Centromere excluded. Plink Filtering as before. Arcsine transformed phenotypes. Centered relatedness matrix.
NoCent.PlinkFiltering_Binary.c : Centromere excluded. Plink Filtering as before. Phenotypes converted to a binary trait. Centered relatedness matrix.
NoCent.PlinkFiltering_raw.c : Centromere excluded. Plink Filtering as before. Phenotypes not transformed. Centered relatedness matrix.
NoCent.PlinkFiltering_raw_subset.c : Centromere excluded. Plink Filtering as before. Individuals subset to only those that had some short stamen loss. Centered relatedness matrix.
Code/software
We used GEMMA v0.98.4 to create the files.
Access information
Other publicly accessible locations of the data:
- https://github.com/sfbuysse/A_thaliana_StamenLoss_2025 : scripts and information for creation of input files and use of output files after generation.
- Genotypic data used is submitted to NCBI SRA as accession PRJNA1246133.