Hi Dennis,
Thank you for such a quick response to my query, and thank you for the citation to Li and Durbin and to the 1000 genomes project.
I am saying this is my understanding of the published literature and the relevant publically-available databases.I had assumed that was the case as this is what one expects from a scientist. This is of course, why, as a fellow scientist, I am asking you - I hope courteously and professionally - to point me to the exact papers in the published literature, and to actual analyses of the public databases that support the claims you are making in Adam and the Genome.
Li and Durban would be one paper relevant hereThank you. As you know, this is the paper that presents the PSMC method. In my email to you and my blog I have explained why I do not think that the PSMC method is able to detect a short sharp population bottleneck. I assume that you are going to respond to my comments on PSMC in Part II of your response, so I will not press you further on this issue now.
moreover the 1,000 genomes consortium papers, papers that estimate the present-day human mutation rate, and so on. For example A global reference for human genetic variationI can see how the 1,000 genomes project can provide the raw data for an analysis such as the one I am asking you for clarification on - the one that you mention in the passage from your book that I quoted in my previous post (above).
However, as far as I can see, the 1,000 genomes paper does not do the calculations that you report in that passage. Unless I am missing something, the authors do not report a calculation of ancestral population sizes from the number of alleles found in present day populations. They do present several PSMC analyses (which are based on runs of heterozygosity within genomes) but they do not seem to present the calculation that you mention in the passage I quoted from Adam and the Genome. Is there another paper in which they conduct the calculations that you are telling your readers about? As I say, I am very keen to know what genes were used in these calculations and how they generated an ancestral population size of 10,000.