DOI: 10.5061/dryad.7501v9s
title: Data from: Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopis lyrata

description: The process of ecotype formation has been invoked as an important driver
 of postglacial biodiversity, because many species colonized heterogeneous
 habitats and subsequently experienced divergent selection. Ecotype
 formation has been predominantly studied in outcrossing taxa, while far
 less attention has been paid to the implications of mating system shifts.
 Here we studied the genomic footprint of ecotype formation in Arabidopsis
 lyrata subsp. lyrata. The species colonized both rocky and sandy
 substrates during its postglacial range expansion, while it also shifted
 the mating system from predominantly outcrossing to predominantly selfing
 in a number of regions. We performed an association study on pooled
 whole-genome re-sequence data of 20 populations, which suggested genes and
 gene ontology terms related to substrate adaptation. We validated results
 by comparing root growth between plants from the two substrates in a
 common environment and found that plants originating from sand –
 independent of mating system – grew roots faster and produced more
 side-roots, potentially as a response to water limitation in the wild.
 Furthermore, we found single nucleotide polymorphisms associated with
 substrate-related ecotypes to be more clustered among selfing populations,
 presumably due to higher genome-wide linkage disequilibrium. Overall we
 show that a shift to selfing could initially facilitate ecotype formation
 linked to substrate, likely because selfing reduces effective
 recombination.
description: LD estimate per
 population using LDxLD estimates based on
 poolseq data for 20 populations using the program LDx
 https://sourceforge.net/p/ldx/wiki/Home/ The program is described here:
 Feder AF, Petrov DA, Bergland AO (2012) LDx: Estimation of Linkage
 Disequilibrium from High-Throughput Pooled Resequencing Data. PLOS ONE
 7(11): e48588. https://doi.org/10.1371/journal.pone.0048588 The output
 follows the data format of LDx and is for each column: 1) Location of SNP1
 2) Location of SNP2 3) Number of pairs observed with x_11 4) Number of
 pairs observed with x_12 5) Number of pairs observed with x_21 6) Number
 of pairs observed with x_22 7) Estimate for allele frequency of allele A
 8) Estimate for allele frequency of allele B 9) Read depth for SNP1 10)
 Read depth for SNP2 11) Intersecting read depth 12) Approx MLE R2 (low end
 of interval) 13) Approx MLE estimate 14) Approx MLE (high end of interval)
 15) Direction Computation R2 16) allele A 17) allele a 18) allele B 19)
 allele b LDx was run for each population separately with the following
 settings: perl lds.pl -l 100 -h 500 -q 28 -i 5 -a 0.15LD_estimates_per_population_using_ldx.zipSNP genotypes (VCF) filesContains three genotype files (VCF) using either all twelve outcrossing populations, all eight selfing populations or all twenty populations together. Each VCF file was filtered as described in the paper. All genotypes were used for the downstream GWAS analysis using the software BayPass.Genotypes_VCFs.zipLocation of outlier SNPs for each GWAS analysisContains the location of the top 1% outlier SNPs based on BaysFactors averaged across ten independent GWAS analyses in the program BayPass. Provided are five files: i) Outliers using only outcrossing populations (outcrossing_only_outliers.txt), ii) outliers using only selfing populations (selfing_only_outliers.txt), iii) outliers using all 20 populations together (selfing_and_outcrossing_combined_outliers_using_all_populations.txt), iv) outliers using the combined dataset but only analyzing outcrossing populations (selfing_and_outcrossing_combined_outliers_using_only_outcrossing_populations.txt), v) outliers using the combined dataset but only analyzing selfing populations (selfing_and_outcrossing_combined_outliers_using_only_selfing_populations.txt). Each file has two columns – the first is the scaffold, the second is the SNP position.Outlier_SNPs.zipRoot Morphology DataExcel sheet containing the experimental data from a growth experiment on agar plates using individuals that originate from a rock or sand substrate. For each individual root growth and the number of primary side roots were counted through time. The columns describe the following: 1. Substrate where wild type individuals were collected (rock or sand) 2. ID for the replicate run [1 or 2] 3. Agar plate ID [A = Replicate 1, B = Replicate B] 4. Seed Family 5. Population of origin 6. Relative position on agar plate [from left to right] 7. Consecutive number for each measurement for each individual 8. Individual seed ID [Population + Seed Family + Replicate] 9. Population & seed family 10. Mating system [O - Outcrossing, S - Selfing] 11. Phylogenetic Cluster [E - East; W - West] 12. Date measurement was taken in 2017 13. Days since germination 14. Days since germination 15. Number of primary site rootsRoot_morphology_data.xlsxPopulation IDsFile providing the population IDs used in the paper (ID) and the IDs used for the data files (Data ID). The Data ID is consistent with the one used for the genomic data (BioProject: PRJEB19338)population_IDs.txt