Non-synonymous base substitutions

The Precocious Llama had the idea to keep track of some thoughts for journal club, and I'm joining in because I thought it was a good idea.

The paper was Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato by Koenig et al. (2013).

I thought the paper was a fun introduction to quite a few analyses I hadn't encountered before, including the models the Precocious Llama discusses in her post. I can't speak to their technical merits since I know very little about them, but it didn't seem like terribly many actionable conclusions were drawn. The Llama pointed out these examples of vague conclusions: "Enrichment for these categories indicates that abiotic and biotic stresses have played a major role driving transcriptional variation among these species" (do any stresses exist outside of these two categories?), and "Taken together, our studies highlight both parallels and contrasts between natural and artificial selection and their effects on genome evolution".

My specific comment for journal club:
  • At least in the mammalian and yeast literature, there is evidence that some synonymous base substitutions (which the authors call neutral divergence) are actually under selection, especially in regions of condensed chromatin structure. I think this provides an alternate explanation for what the authors say is a reduction in neutral divergence near the centromere shown in Figure 1. 
References for my comment:


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