It was recently pointed out to me that a RNA-seq dataset I've been working on could have interesting implications for evaluating the evolution of traits in a species related to my species of interest. Both species have well described reference genomes and I'm considering incorporating some comparative work to the project.
The formal question I'm interested in is: Are genes which see significantly increased expression in my species of interest more likely to have increased homologs in the more derived species (and the opposite case for the decreased genes)?
Does anyone have any experience applying RNA-seq data sets to these sorts of questions? My initial searches haven't turned up much, and this is outside what we normally work on, so any pointing to potentially useful seminal publications/software would be greatly appreciated.