Large captivity effect based on gene expression comparisons between captive and wild shrew brains

Compared to their free-ranging counterparts, wild animals in captivity are subject to different conditions with lasting effects on their physiology and behavior. Alterations in gene expression in response to environmental changes occur upstream of physiological and behavioral phenotypes, but there are no experiments analyzing differential gene expression in captive vs. free-ranging mammals. We assessed gene expression profiles of three brain regions (cortex, olfactory bulb, and hippocampus) of wild juvenile shrews (Sorex araneus) in comparison to shrews kept in captivity for two months. We found hundreds of differentially expressed genes in all three brain regions, suggesting a large and widespread captivity effect. Many of the downregulated genes in captive shrews significantly enrich pathways associated with neurodegenerative disease (pcor<0.001, phip<0.001, polf<0.01), oxidative phosphorylation (pcor<0.001, phip<0.001, polf<0.001), and genes encoding ribosomal prote..., , , # Large captivity effect based on gene expression comparisons between captive and wild shrew brains

[https://doi.org/10.5061/dryad.qz612jmng](https://doi.org/10.5061/dryad.qz612jmng)

Scripts and code to reproduce RNAseq analysis for looking at changes in expression due to captivity effects in shrews; specifically in the cortex, hippocampus, and olfactory bulb. These regions will help to understand region specific changes to the brain, as well as impacts on the whole brain.

### Description of the data and file structure

First, we assess RNA-seq data quality, filtering low quality reads and trimming adapters in fastp. RNA-seq sample lists (samples_hippoc.txt, samples_olf_bulb.txt, samples_cortex.txt) are described below.

* Rows =Sample_ids. Note: Samples named HFS* correspond to wild shrews, and those named Eto* correspond to captive shrews as shown in the file.
* Columns = Organ, experimental group (wild or captive), sex, toothrow length (cm)

Then, we map reads pruned reads and...