Testing Jeanson's Model: Y Chromosome Mutation Rates

That’s true.

Going by the most recent quote I have, 10x coverage (60 Gb of data, 150 bp reads) would cost just under $2,000. 20x would be twice that. This is assuming 150 bp reads would be sufficient for this purpose.

True. The free stuff tends to be less user friendly, so newbs like me prefer the paid software. We have to put up with the computer nerds looking down on us for our lack of Linux skills. :wink:

Indeed. The ingenuity among biotech companies continues to amaze me, with nanopore sequencing being one of the more recent advances.

You usually need paired ends, longer reads (to disambiguate CNVs), and more than 100x coverage to get error rates low enough. It isn’t trivial, except that it’s done all the time.

20x coverage is not sufficient for this analysis.

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Thanks for the info (and @swamidass)!


What if his prediction had somehow been confirmed? Would that support YEC? Clearly not, as a 6000-year-old universe, or earth, or life, or even Homo sapiens, is contradicted by much more than human genetic diversity. What we would have had would be a strange mystery, but YEC would not be a possible solution to that mystery. You can’t just ignore the evidence against your hypothesis, even if it comes from a different field from the one you happen to be looking at right now.

It would be epic, New-York-Times-front-page-level misconduct.

Lesser misconduct, more relevant in this discussion perhaps, is selective citation (aka cherry picking). I say “lesser” because some kinds of selective citation are mostly obnoxious (citing friends, failing to cite competitors) while not usually rising to the level of “misconduct.” At our journal and our sister journals, we very rarely (as a matter of policy) require correction when the authors should have cited particular papers but didn’t. More serious misconduct would be selective citation that amounts to misrepresentation of the literature. For example, an author who cited only a single paper in 2004, since shown to be incorrect about X, in support of a claim of X, is not merely omitting citations–they are misrepresenting the literature. Such things are rare at our journal and very few can make it through peer review uncorrected, but that is actual misconduct IMO, subject to correction or retraction.

So, if this author has misrepresented the literature, making it appear to support a claim that is known to be false, they are obligated to correct the error once it has been pointed out. I am not taking a position on whether this has happened.

What is much more of a concern to me is that the author has engaged in public accusation while not engaging in professional correspondence about the science. If that is the case, then the author has, IMO, left scientific discourse and should not be given a prominent platform among scientists. This can of course be fixed, by engaging in professional correspondence, correcting errors, and seeking the company of more-qualified colleagues.


OK - I’m a little slow to understanding what you meant and what he’s referring to. He is referring to just the Y-chromosome mutations and you say he’s ignoring the whole genome, which fits with what you said. The links you provide are sequencing the entire genome.

However, for what he’s saying, do we need the entire genome? Why run into all these complicated mathematical problems when we know Y chromosome is inherited from a father who passes it down to his son and so on? Wouldn’t that yield a more accurate pedigree rate for each generation of males rather than sequencing the entire genome?

The entire genome includes the Y chromosome. The authors would be trumpeting it from the rooftops if they found that the Y mutation rate was 50x higher than the rest of the genome. That is not what they found.


Why would it be expected to be the same? I don’t see a reason that it has to be…

And maybe as creationist we would expect that they should be different. We could share similar genetic makeup as animals but X, Y chromosomes would be different.

AND…in the middle of typing I decided to do a quick Google search. First hit :wink: do chimpanzees have y chromosomes - Google Search

I have to read the paper through later.


Great questions!

Turns out that evolutionary science predicts that X and Y have different rates than the rest of the genome. We expect Y chromosome to have a bit higher mutation rate (not 50x higher, but maybe 1.5x) and X chromosome to have a bit lower mutation rate.

So here is the thing, by measuring the mutation rate across the whole genome, they also measured the rate of mutation in the X and Y chromosome. They include a table of data in (if I remember correctly) 10,000 bp blocks showing the mutation rate for each block across the genome. So we can directly look at the Y Chromosome mutation rate specifically, what Nathaniel needs to test his hypothesis, and it is exactly what evolutionary science predicts. It does not confirm the YEC hypothesis he puts forward.

This, also, is why the paper is a higher quality than those he cites. The best technology works in such a way that it makes little sense to measure Y-chromosome mutation rates in isolation. I just makes most sense to measure the mutation rate across the whole genome (including Y Chromosome), but in a way that we can measure it specifically in Y Chromosome if we want to. That’s what they did here.


6 posts were split to a new topic: Scientific Ethics, Enculturation, and Policy

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.


3 posts were merged into an existing topic: Scientific Ethics, Enculturation, and Policy

We expect Y chromosome to have a bit higher mutation rate (not 50x higher, but maybe 1.5x) and X chromosome to have a bit lower mutation rate.

Can you explain why this is? Is it because the Y chromosome doesn’t contain genes necessary for survival? After all, women get along just fine without one.

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Thank you for providing this argument. I give you lots of credit for reading this book. I am very interested to see how the mutation rate argument shakes out.


Well, in fact the Y mutation rate is higher than that in most of the genome, and the X rate is a bit slower. But the difference isn’t nearly as high as Jeanson needs. You can google “male-driven evolution” for information.

Oops, I see @swamidass has already answered this.

Not sure why you would expect such a thing. But again the X is a little less different than autosomes. So the prediction, whatever the reason for it, is wrong. And yes, chimps have Y chromosomes.


How does 275,000 years line up with evolutionary timescales? You would have the invent the other million+ years needed to satisfy evolutionary requirements. What if someone claimed, based on your statement, that mankind simply began 275,000 years ago? That would leave you far short of evolution. And with such a recent number as 275,000 years, still another could claim that external factors may have affected internal genomic results such that hundreds of thousands of years may have been reduced to mere thousands years. How do you guarantee uniformity of mutation rates such that a range of 275,000 to 588,000 years becomes infallible science?


That’s not true @r_speir. Mt-Eve and Y-Adam are expected to be a few hundred thousand years in the past. We get the mutation rate, however, this way:

The formula is pretty simple: Rate x Time = Distance.


You should mention that the observed distance needs to be corrected for multiple hits, site-to-site rate variation, and different probabilities of different mutations. Though not so much within the human population.


I believe that very few creationists have any notion of coalescence, and suppose that mt Eve and Y Adam must be placed at the beginning of the species at least, and likely at the start of the lineage. You should remind @r_speir that there is no correlation.