DOI: 10.5061/dryad.z34tmpgm8
title: Data from: Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley

description: Direct observation is central to our understanding of the process of
 adaptation, but evolution is rarely documented in a large, multicellular
 organism for more than a few generations. Here, we observe genetic and
 phenotypic evolution across a century-scale competition experiment, barley
 composite cross II (CCII). CCII was founded in 1929 with tens of thousands
 of unique genotypes and has been adapted to local conditions in Davis, CA,
 USA for 58 generations. We find that natural selection has massively
 reduced genetic diversity leading to a single clonal lineage constituting
 most of the population by generation F50. Selection favored alleles
 originating from similar climates to that of Davis, and targeted genes
 regulating reproductive development, including some of the most
 well-characterized barley diversification loci, Vrs1, HvCEN, and Ppd-H1.
 We chronicle the dynamic evolution of reproductive timing in the
 population and uncover how parallel molecular pathways are targeted by
 stabilizing selection to optimize this trait. Our findings point to
 selection as the predominant force shaping genomic variation in one of the
 world’s oldest ongoing biological experiments.
description: # Data From "Natural selection drives emergent genetic homogeneity in
 a century-scale experiment with barley"
 [https://doi.org/10.5061/dryad.z34tmpgm8](https://doi.org/10.5061/dryad.z34tmpgm8) Genetic datasets from the sequencing of composite cross II ## Description of the data and file structure -Genotype datasets **CCII_PARENTS_AND_EXOME.vcf.gz** Genotype file for the merged CCII parents and Exome sequencing panel (Russell et al. 2016, Nature Genetics) **FILTERED_PARENTAL_SNPS.vcf** CCII parent SNP calls **FINAL_AFS.txt.gz** Allele counts in CCII progeny pools for each SNP. Columns are in the following order. Chromosome Position Reference_allele Alternate_allele Reference_allele_count_Parents Alternate_allele_count_Parents Reference_allele_count_F18 Alternate_allele_count_F18 Reference_allele_count_F28 Alternate_allele_count_F28 Reference_allele_count_F58 Alternate_allele_count_F58 SNP_EFF_ANNOTATION SNP_EFF_EFFECT SNP_EFF_NEAREST_GENE **GBS_PARENTS_PROGENY.vcf.gz** Inidividual GBS genotype calls for parents and progeny. Pedigree numbers are as follows. Generation numbers of the CCII are indicated as F** F18: 1_#### F28: 2_#### F58: 7_#### -Phenotypic datasets for the CCIIselect Columns are as follows: Genotype name rows (Count of seed rows) tiller_number (Count) spikes mature_spikes (Count) immature_spikes (Count) X100_seed_mass (g) seed_mass (g) seed_estimate (Count) days_to_awn_emergence (Count) days_to_heading (Count) plant_height (cm) spike_length (cm) spike_width (cm) awn_length (cm) days_to_heading_2017 (Count) **Parents_pheno.txt.gz** Trait measurements from greenhouse grow outs of the parents of CCII **Prog_pheno.txt.gz** Trait measurements from greenhouse grow outs of progeny selections of CCII. Pedigree numbers are the same as in the GBS dataset. -The following datasets are derived from the whole genome datasets above and were the specific input files for the whole genome simulations. **afs_for_sim.txt.gz** Allele frequency data used for input for the simulations **parents_for_sim.txt.gz** Input data for sites with no missing data to simulate the CCII