Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought

While we know that climate change can potentially cause rapid phenotypic evolution, our understanding of the genetic basis and degree of genetic parallelism of rapid evolutionary responses to climate change is limited. In this study, we combined the resurrection approach with an evolve and resequence design to examine genome-wide evolutionary changes following drought. We exposed genetically similar replicate populations of the annual plant Brassica rapa derived from a field population in southern California to four generations of experimental drought or watered conditions in a greenhouse. Genome-wide sequencing of ancestral and descendant population pools identified hundreds of SNPs that showed evidence of rapidly evolving in response to drought. Several of these were in stress response genes, and two were identified in a prior study of drought response in this species. However, almost all genetic changes were unique among experimental populations, indicating that the evolutionary chan..., We combined experimental evolution with the resurrection approach to explore adaptation to experimental drought in Brassica rapa (field mustard).
We founded 24 experimental populations from lines which originated from a natural population and randomly assigned each experimental population to a watering regime. We assigned 8 populations for storage as ancestors, 8 to receive four generations of experimental drought, and 8 to receive four generations of experimental well-watered conditions. During these four generations of experimental evolution, drought regime populations received a draw-drown drought treatment aimed to mimic Mediterranean drought while well-watered regime populations were watered every other day. We collected data (flowering time, survival, and seed mass) on a subset of individuals each generation to explore trends in fitness and selection during experimental evolution.
After experimental evolution, we grew all experimental populations (ancestors included) under unstres..., Our data submission includes Python and R scripts., # README file for Johnson et al. 2023 manuscript published in Journal of Evolutionary Biology

## Article Citation:

Johnson, S. E., Tittes, S., & Franks, S. J. (2023). Rapid, nonparallel genomic evolution of Brassica rapa (field mustard) under experimental drought. Journal of Evolutionary Biology, 36(3), 550-562.

## Repository location:

DOI: 10.5061/dryad.n5tb2rbzx

## Note:

Files are named as 2022 because that is when the final analyses and submission were prepared, but the manuscript was published in 2023.

## Data files:

\"Truseq3-PE-2.fa\" contains adapters used to trim reads with trimmomatic software.
\"bam.txt\" is a list of bam file names used in the fais_baypass.py script.
\"brassica.poolsize\" is a list of the ploidy number of each population used when running the core and axillary models in BayPass.
\"brassica.covariates\" is a file that encodes whether each population is ancestor or descendant for the first covariate (row 1) and, if descendant, drought or watered for the sec...