DOI: 10.5061/dryad.31zcrjdz1
title: Museum genomics of reveals temporal genetic stasis and global genetic diversity in Arabidopsis thaliana

description: Global patterns of genetic diversity through time offer a window into
 evolutionary processes that maintain diversity. Over time, lineages may
 expand or contract their distribution, causing turnover in population
 genetic composition. At individual loci, drift, environmental changes, and
 purifying selection may affect allele frequencies. Museum specimens of
 widely distributed species offer a unique window into genetic composition
 of understudied populations and changes over time. Here, we sequenced
 genomes of 130 herbarium specimens and 91 new field collections of
 Arabidopsis thaliana and combined these with published genomes. We sought
 a broader view of genomic diversity across the species, and to test if
 population genomic composition is changing through time. Using herbarium
 specimen sequences, we documented extensive and previously uncharacterized
 diversity in a range of populations in Africa, populations that are under
 threat from anthropogenic climate change. Through time, we did not find
 dramatic changes in population genomic composition of populations.
 Instead, we found a pattern of genetic change every 100 years of the same
 magnitude seen when comparing Eurasian populations that are 185 km apart,
 potentially due to a combination of drift and changing selection. However,
 we found only mixed signals of polygenic adaptation at phenology and
 physiology QTL. We did find that genes conserved across eudicots show
 altered levels of directional allele frequency change, potentially due to
 variable purifying and background selection. Our study highlights how
 museum specimens can reveal new dimensions of population diversity and
 show how wild populations are evolving in recent history.
description: # Museum genomics of reveals temporal genetic stasis and global genetic
 diversity in Arabidopsis thaliana
 [https://doi.org/10.5061/dryad.31zcrjdz1](https://doi.org/10.5061/dryad.31zcrjdz1) ## Description of the data and file structure This contains SNP data for the project. One file contains SNPs filtered for missingness used for population structure and another contains those used for temporal allele frequency change (using essentially a GWAS with year of collection as the 'phenotype'. ### Files and variables #### File: stem_out_GWAS.zip **Description:**  SNPs filtered for missingness used for temporal allele frequency change analysis. Includes the three standard PLINK type formatted files, stem_out_GWAS.bed, stem_out_GWAS.bim, and stem_out_GWAS.fam. These can be read in using the PLINK software. #### File: stem_outLowMiss_allrange.zip **Description:** SNPs filtered for missingness used for population structure. Includes the three standard PLINK type formatted files, stem_outLowMiss_allrange.bed, stem_outLowMiss_allrange.bim, and stem_outLowMiss_allrange.fam. These can be read in using the PLINK software. ## Code/software Scripts for PLINK and R found here [https://github.com/jesserlasky/Arabidopsis_herbarium](https://github.com/jesserlasky/Arabidopsis_herbarium) Also, scripts are archived in this Dryad submission, in this file **Arabidopsis_herbarium-main.zip** This directory contains aDNA_bionf_Lua.sh - a shell script for bioinformatics of the herbarium specimen sequencing. PLINKcode.4.sh - a shell script for running PLINK analyses. PLINK_assist.3_S.R - an R script for analyzing population structure. TimeGWAS5_QTL.R - an R script for testing for allele frequency change over time and enrichment in putative QTL. regGWAS_conserved_splineFig2.R - an R script testing global and regional patterns of allele frequency change in conserved genes and making a figure. bgs_lasky2_stepping_flex.slim - a SLiM simulation script to test how background selection affects allele frequency change over time.