To give a little bit of background here, I’d recommend you read the latter part of this blog post (subtitled “Y no Y chromosome”), in which I was rebutting chapter 8 of Jeanson’s book:
In brief, chapter 7 of Jeanson’s book focused on mtDNA mutation rates, and then chapter 8 focused on nuclear genome mutation rates, but there was a conspicuous lack of any discussion on Y chromosome mutation rates specifically. I found this odd, because Jeanson himself said in the book that the Y chromosome could function as a clock in the same way as the mtDNA (passed down in a single sex).
I suspect he didn’t talk about because as I show in the blog post, the published literature on Y chromosome diversity and mutation rates lines up perfectly with evolutionary timescales. Multiple pedigree studies and ancient DNA studies consistently showed that the Y chromosome mutation rate in the commonly sequenced, non-recombining regions is around 0.80×10^-9 mutations per nucleotide per year, or roughly 1 mutation every 4 generations. Given the observed Y chromosome diversity in human populations today, it can be calculated that this diversity took about 275,000 years to accumulate. if we include Neanderthal diversity (that Jeanson rejects) that number rises to 588,000 years.
Jeanson doesn’t say a word about any of this in his book, but he does mention it in this more recent “paper”:
“To date, two published studies explicitly attempt to obtain the pedigree-based per-generation mutation rate for the Y chromosome (Helgason et al. 2015; Xue et al. 2009). Both studies have reported results to be consistent with the evolutionary timescale.”
The whole point of this recent “paper” is to argue that all these previous results are based on 1) low coverage sequencing studies that miss a lot of variants and 2) that these studies also use filters of variants that are far too stringent, leading to further loss of real variants. Jeanson is saying that when these factors are accounted for, the pedigree Y chromosomal mutation rate is actually about 50x higher than previously reported, and now its suddenly compatible with YECism after all.
This is quite a remarkable claim to make, especially given that Jeanson (and his coauthor Holland) have a grand total of zero background in any of this kind of genomic sequencing technology. It would be a remarkable thing indeed if they had spotted something missed by the hundreds of scientists involved in studying Y chromosome genomics over the past few decades. I can’t claim to understand this subject well enough to engage all the nitty-gritty technical details (at least not yet, maybe one day I’ll dedicate some time to it), but I can note at least one immediate problem.
One paper that Jeanson doesn’t touch on in this recent “paper” is Balanovsky et al (2015) who performed sequencing of 20 Y chromosomes to an average coverage of 67x, far higher than either of the “high-coverage” studies Jeanson cites, and yet they still arrive at a mutation rate consistent with the lower coverage sequencing - consistent with evolutionary timescales. Perhaps he would argue that they fiddled the numbers in the filtering step.