Mate choice in the brain: Species differ in how male traits ‘turn on’ gene expression in female brains

Mate choice plays a fundamental role in speciation, yet we know little about the molecular mechanisms that underpin this crucial decision-making process. Stickleback fish differentially adapted to limnetic and benthic habitats are reproductively isolated and females of each species use different male traits to evaluate prospective partners and reject heterospecific males. Here, we integrate behavioral data from a mate choice experiment with gene expression profiles from the brains of females actively deciding whether to mate. We find substantial gene expression variation between limnetic and benthic females, regardless of behavioral context, suggesting general divergence in constitutive gene expression patterns, corresponding to their genetic differentiation. Intriguingly, female gene co-expression modules covary with male display traits but in opposing directions for sympatric populations of the two species, suggesting male displays elicit a dynamic genomic response that reflects known..., , , # Mate choice in the brain: Species differ in how male traits ‘turn on’ gene expression in female brains

[https://doi.org/10.5061/dryad.ncjsxkt3g](https://doi.org/10.5061/dryad.ncjsxkt3g)

## Description of the data and file structure

We include in this submission all data required to run included code (see below for which order to run scripts):

1. bedtools_gene_counts.gff

Tab delimited text file with rows corresponding to counts of genes for each sample. The first column is the Ensembl gene name.
2. design.csv

Comma delimited text file with information for each female for which we have a transcriptome. It contains the following columns:
1. female - female ID
2. spawn - whether a female laid eggs (TRUE or FALSE)
3. lake - female lake of origin (Paxton or Priest)
4. species - female species (Limnetic or Benthic)
5. treatment - experimental treatment (Het = heterospecific courtship, Con = conspecific courtship, Fem = social control)
6. preferen...,