Testing Jeanson's Model: Y Chromosome Mutation Rates

[swamidass (S. Joshua Swamidass)]

@thoughtful

I’f I’m understanding right, he’s saying that there’s only two studies determining pedigree rates, and he came up with a third one based on screenshots of some raw data from a few others that didn’t explicitly try to do so.

This review paper from 2016 alone has 11 pedigree studies. We can certainly be sure that many more studies have been done since then. Notice that the date on Jeanson’s study is 2019, which means there is just no excuse for not including the 11 papers in this review.

@swamidass

The mutation rate in human evolution and demographic inference , Aylwyn Scally, http://keinanlab.cb.bscb.cornell.edu/sites/default/files/papers/Scally_2016.pdf

The figure here shows mutation rate estimated in several ways:

You can see that the pedigree based methods (blue) produce results that are consistent with several other methods, not just pedigree. You can see that the variance of pedigree methods is high, but it is not that bad.

These are whole genome studies, which will also include Y-Chromosome. Even if they don’t state the Y-Chromosome rates directly, the supplementary information or a simple email to the authors will usually be enough to get that subset of the results/data.