Natural selection drives emergent genetic homogeneity in a century-scale experiment with barley

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 stabiliz..., , , # 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.v...