malballinger / ballingermack_pnas_2023

Data, code, and analyses associated with Ballinger, Mack et al. (2023)

Environmentally robust cis-regulatory changes underlie rapid climatic adaptation

Link to our open access paper published in PNAS:

All sequence data have been deposited to the National Center for Biotechnology Information Sequence Read Archive:

Data and code have been deposited on Zenodo:

See our bioRxiv preprint here:

Abstract:

Changes in gene expression are thought to play a major role in adaptive evolution. While it is known that gene expression is highly sensitive to the environment, very few studies have determined the influence of genetic and environmental effects on adaptive gene expression differences in natural populations. Here, we utilize allele-specific expression to characterize cis and trans gene regulatory divergence in temperate and tropical house mice in two metabolic tissues under two thermal conditions. First, we show that gene expression divergence is pervasive between populations and across thermal conditions, with roughly 5 to 10% of genes exhibiting genotype-by-environment interactions. Second, we found that most expression divergence was due to cis-regulatory changes that were stable across temperatures. In contrast, patterns of expression plasticity were largely attributable to trans-effects, which showed greater sensitivity to temperature. Nonetheless, we found a small subset of temperature-dependent cis-regulatory changes, thereby identifying loci underlying expression plasticity. Finally, we performed scans for selection in wild house mice to identify genomic signatures of rapid adaptation. Genomic outliers were enriched in genes with evidence for cis-regulatory divergence. Notably, these genes were associated with phenotypes that affected body weight and metabolism, suggesting that cis-regulatory changes are a possible mechanism for adaptive body size evolution between populations. Our results show that gene expression plasticity, largely controlled in trans, may facilitate the colonization of new environments, but that evolved changes in gene expression are largely controlled in cis, illustrating the genetic and nongenetic mechanisms underlying the establishment of populations in new environments.

Overview:

BallingerMack_NYBZase_2023
|- README          # top level description of content
|
|- data            # raw and processed data, are not changed once created
|  |- raw/         # raw data, will not be altered
|  |- processed/   # cleaned data, will not be altered once created
|
|- code/           # programmatic code for processing, analyzing, and plotting
|
|- results/        # all output from workflows and analyses
|  |- tables/      # tables, designated for supplementary material
|  |- figures/     # graphs, designated for manuscript figures
|
|- submission      # files for manuscript

ballingermack_pnas_2023's Issues

Ask for help

Hi Mallory,

Thank you for your scripts. I want to perform allele-specific expression between two species.
When i run your code in
grep \"vW:i:1\" ${Sample}.STAR_ASEAligned.sortedByCoord.out.sam | grep \"vA:B:c,1\" \ | awk -F' ' '{if(\$18 ~ /2/){}else{print}}' > ${Sample}.geno1.sam
and
grep \"vW:i:1\" ${Sample}.STAR_ASEAligned.sortedByCoord.out.sam | grep \"vA:B:c,2\" \ | awk -F' ' '{if(\$18 ~ /1/){}else{print}}' > ${Sample}.geno2.sam

I find this two sam files size are very different. geno1.sam is very larger than geno2.sam. Do you know why that？

Best,

Guo-Cheng