Review for "The rate and effect of de novo mutations in natural populations of Arabidopsis thaliana"

Completed on 18 May 2016 by Remco Stam. Sourced from

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The paper shows some great work and making use of recent and herbarium
samples is really interesting and overall, we were impressed by the analysis and also the amount of data that has been analysed. It is a shame that the diversity in this arabidopsis lineage is so low that one can not really draw firm conclusions, but the paper does, as stated in the conclusions, indeed show the potential of herbarium sequencing for analysis of evolutionary trajectories.

We discussed this paper in our Journal Club recently. Unfortunately, I
didn't take notes of all things that were said. From the top of my head,
this is what we discussed. If some things don't make sense, just get in

- We wondered if there would be a way to show what the effect of linkages is on the presented results? In E.g. in Fig. S4, it would be informative to know which sites are linked in this population. One could plot locations of recombination events or LD
- Figure 3D,E shows transitions vs transversions, but these are not very informative in terms of the expected effect. A way to get some more information from these data is to show synonymous vs nonsynonymous mutations or to check per gene or per window SFS or DFE.
s- Someone in our group even mentioned that there is coalescent software available that could theoretically be used to sample and reconstruct the SFS in time, since there appears to be some decent historic data available.
- With Figure 5 it was not quite clear for us if/how the phenotypes of the herbarium samples were included.
- We also wondered if some of the observed effects are Background selection, rather than Positive selection See e.g.