If you have been following this discussion then it should be clear this trend in SIE is unrelated to sequence information, including Genetic Entropy as proposed by Sanford. Thermodynamic bias in the third codon mutations might have some effect on SIE, but depending on initial conditions this could also cause SIE to increase towards the theoretical maximum.
More importantly, there is no useful biological interpretation of SIE in this context, and no reason to think it is anything more than a statistical oddity of a random walk.
Then why is there a non-random distribution of mutations across the genome? When you look at any current SARS-CoV-2 genome it will have more mutations in the S gene than in other genes on a per nucleotide basis.
It will have more variation. Mutations are occurring throughout the genome. When we sequence genomes, we’re seeing the mutations filtered by drift and selection, not mutation frequencies themselves.
That’s the point I was making to @Giltil. The increased number of mutations in the S gene compared to the reference sequence is evidence for stronger selection in the S gene. That’s before we even factor in negative selection. @Giltil was trying to claim that the differences were due to thermodynamics instead of selection, which really doesn’t make sense in itself unless you parse it through a creationist interpreter.
When you use “mutations,” it leads those who don’t understand evolution to the false impression that the mutations are occurring more often there. We see more*** variation*** in the spike gene because of selection.
That would be more accurate, thanks for the clarification. We don’t expect there to be a higher mutation rate in the S gene compared to the rest of the genome. At the same time, it might be worthwhile to see if there are any trends for GC content across the genome. I wouldn’t expect there to be any big departures.
Mutations are more clearly thought of as events. What we’re seeing has already been filtered by selection and drift.
It’s also why “The virus is mutating” is misleading in the lay press, when “The virus is evolving” is the actual subject.
You’re welcome. I often think that everything would be more clear to laypeople if we all followed the practice of clinical geneticists, who avoid “mutant” and “mutation” for a different reason–to avoid objectification of patients.
