I am very happy to wait for your comments on the PSMC method and why you believe that it would detect a sudden sharp bottleneck of two. Please don’t feel under any pressure; I appreciate your attempts to make all this accessible to non-specialist audiences. That is not always an easy task.
Regarding the passage from chapter 3 of Adam and the Genome that I am asking you for citations to support. You have responded in your comment above:
What I'm talking about there is a summary of the field as a whole - and the PSMC analyses in the 1,000 genomes paper is certainly one of the relevant experiments. So are LD studies. So are the Li and Durban PSMC results.I am sorry, I am struggling to follow you here. I'm afraid I can't see how that passage is a summary of the field as a whole, and therefore I don't understand how citations of the PSMC and LD studies support it.
Here is the passage that we are discussing in its context in Adam and the Genome: I have placed it in italics, and also added some emphases in bold.
...given the importance of this question for many Christians— and the strong insistence of many apologists that the science is completely wrong— it is worth at least sketching out a few of the methods geneticists use that support the conclusion that we descend from a population that has never dipped below about 10,000 individuals. While the story of the beleaguered Tasmanian devil provides a nice way to “see” the sort of thing we would expect if in fact the human race began with just two individuals, scientists have many other methods at their disposal to measure just how large our population has been over time. One simple way is to select a few genes and measure how many alleles of that gene are present in present-day humans. Now that the Human Genome Project has been completed and we have sequenced the DNA of thousands of humans, this sort of study can be done simply using a computer. Taking into account the human mutation rate, and the mathematical probability of new mutations spreading in a population or being lost, these methods indicate an ancestral population size for humans right around that 10,000 figure. In fact, to generate the number of alleles we see in the present day from a starting point of just two individuals, one would have to postulate mutation rates far in excess of what we observe for any animal. Ah, you might say, these studies require an estimate of mutation frequencies from the distant past. What if the mutation frequency once was much higher than it is now? Couldn’t that explain the data we see now and still preserve an original founding couple? Aside from the problems this sort of mutation rate would present to any species, we have other ways of measuring ancestral population sizes that do not depend on mutation frequency. These methods thus provide an independent way to check our results using allele diversity alone. Let’s tackle one of these methods next: estimating ancestral population sizes using something known as “linkage disequilibrium.”Then, after describing the LD study you write:
The results indicate that we come from an ancestral population of about 10,000 individuals— the same result we obtained when using allele diversity alone.A little later you write
A more recent and sophisticated model that uses a similar approach but also incorporates mutation frequency has recently been published. This paper was significant because the model allows for determining ancestral population sizes over time using the genome of only one individual. [You then describe the PSMC method.]
I am therefore struggling to understand how the passage we are discussing - the one in italics above - could be a “summary of the field as a whole” including linkage disequilibrium and PSMC methods. It seems to just be about the allele frequency method. You clearly distinguish the allele frequency method from the other methods. You say that the linkage disequilibrium method is “an independent way to check our results using allele diversity alone.” You say it gives “the same result we obtained when using allele diversity alone”. You describe the PSMC methods as “A more recent and sophisticated model”.
I am sorry that I am spending so long on this point - this really is not where I had expected our discussion to go. I thought I was making a very straightforward request when I asked for a citation for the calculations in this passage. I am still hoping that you may be able to, now I have reminded you of the context of the passage. I appreciate that it may be a while since you re-read the chapter for yourself, and your recollection of what you wrote could be different from the text of the book. I know that I am sometimes surprised when I re-read something that I wrote myself after several months away from it.