Y-Chromosome Haplogroups Have Differing Mutation Rates

 An amazing study came out last fall claiming that different Y-Chromosomes have wildly different mutation rates. Y-haplopgroups are passed down from father to son. Y-haplpgroup B for example, the one found mostly in Baka, Mbuti (formerly Pygmies) and some Khosian, has a mutation rate 1.5 times greater than Y-haplogroups R and E, found in Europeans and most Africans. The longer the "branch", or time it branched off according to past calculations, the greater the mutation rate.

I'd like someone in the field to delve into this deeply, but this finding would appear to tighten the window of Y-haplogroup branching. That is, the ones that seem older may owe a part or even most, of their apparent age difference to the fact that they have higher mutation rates. The ones that seem younger may be a bit older than they seem because "age" is determined by the mutations they have accumulated. That is unless, as I suspect, the mutation rate assumed in the past were those of Europeans or African Haplogroup E. Both of those were slow to mutate according to this study. So maybe scientists have been using a low mutation rate to do these calculations. If that is the case then the older branches would move closer in time and the younger branches remain where they are. The study recommended using each Y-haplogroup's rate to measure branching dates. 

They did not test any of the "A" haplogroups such as A00, A0, or A1. They tested "B", thought to have branched off 100,000 years ago from the "A1b2" haplogroups. If one goes back and recalculates based on the idea that those mutations they were using to calculate time really happened 1.5 times faster than we thought, then you in effect take 1/3 of that time away. This would put the splitting of the "B" branch at roughly 67 kya. Surprisingly recent and close to the time for "E". That's just a napkin-figure of course.

Since I am going there, let's talk about "Y-haplogroup Adam". That is, the "common ancestor" of all of these groups. I have explained elsewhere that under the Christ-centered model the Adam in the bible came later, and that humanity started as a "host" or group, not a single couple. So then these very ancient dates for "Y-haplogroup Adam" are calculations of when an event that never happened might have occurred. They are meaningless if humanity started as a population with a set amount of diversity at the start rather than all came from a single pair. So in effect the diversity does not require an explanation, but I do wonder if the following occurred with the A groups:

Initial calculations of the origin date of A0 were only about 60,000 years ago but that figure was upped to 142,000 years ago (with a wide margin of error) in later studies. That haplogroup wasn't tested in this study, but the pattern of longer branching correlating with a higher mutation rate would indicate that the date should be recalibrated toward the more recent figure. We can't know how much toward it until we get more data, but if B mutates at roughly 1.5 times the rate of R1 and E then we might expect A0 to have an even higher value. If, for example, the mutation rate was twice as high (2.0), then if the more recent studies were otherwise properly done they would imply a branching date of 142.000/2 = 71,000 years ago. There are a lot of "ifs" there, but that is how we figure out what questions need to asked and what things need to be tested for.

All of the A Y-haplogroups, A00, A0, A1a, and A1b, are very distantly related, perhaps no closer to one another than they are to haplogroup BT from which the rest (and bulk) of mankind sprang. They are all defined by missing the mutation (M91) which defines BT and the stream which represents the bulk of humanity. But it seems odd to me that in this accounting, mutations are always added but never lost. We know that back-mutations happen in nature on a regular basis. Why couldn't each of these A haplogroups represent an instance when the defining mutation M91 was lost? This would only require a back mutation in that particular gene four times in all of human history. 

In this accounting, A00 would represent one event where M91 was lost, A0 another event in which M91 was lost, and this split would have yet another defining mutation which A00 lacks. So again, A0 did not really spring from A00. Nor did A1. Rather, they each represent independent events where the defining mutation of the real basal haplogroup for mankind, something like BT, was lost in a tiny sliver of the population due to mutations. In this scenario the A00 split from BT was not even necessarily prior to the A0 split from BT. It simply occurred in a part of the population which lacked the defining mutation for A0.

Under this scenario then, these various clades of  Y-haplogroup A don't represent relics that have been largely displaced by spin-offs of BT. Rather, they are also spin-offs of BT who happened to have lost M-91, the defining mutation of BT. It isn't that all of mankind started like them and the spin-offs from BT pushed them to the edge of extinction, rather they were just a few of the many groups which sprang from a humanity that started somewhere around, and something much like, BT. Pure BT hasn't been found anywhere yet, but that's probably just because "mutations happen". Mankind didn't stay still for long. 

On rare occasions we will find an "out-of-place" Y-haplogroup A. We chalk it up to say, unknown male African ancestry for someone in England. In most cases this is probably correct. But what if some of these are modern example of what I am talking about? I call for a study to look at out-of-place haplogroups and try to find one with the fingerprints of a 'recent' M91 deletion (for example one that contained many of the markers of downstream haplogroups but was just missing M91). I think we already have a good example of one something like that, we just didn't catch it "in the act". There is the case of A1b1b2b (A-M13), which though it seems very downstream on A branching, also has signs of a very deep divergence. 

There is simply a lot we still don't know about this subject. I urge everyone in the field to hold to their conclusions loosely, and keep asking questions. 

*****

PS- my best guess on an explanation for the study? If we are shooting in the dark here, what about the idea that the original population which became us was the product of some dramatic re-arrangements (a special creation, but you naturalists can think of it as a random act of nature if you wish)? The aftermath of this would be for a microevolutionary "settling effect" to occur. So then, what we see in these mutations that tend to stick (like the defining ones of Y haps for example) is that they might have a stabilizing effect on the Y chromosome. After all, once "nature" hits on a winning formula, too much re-arrangement is not good!

So for example, the route that led to Y-hap. E in Africa and R and all the other Eurasian Y haplogroups wound up increasing stability as they were acquired. The A haplogroups, along with B, probably still acquired increased stability over the original haplogroup(s) (which may be part of why we don't see BT "pure" anymore) but their chromosomes stumbled onto a less-efficient route of stabilization. This means they still have higher mutation rates. This would explain the data in the study showing that mutation rate is correlated to branch length.

I mean, as long as we are guessing....

*****

Hey my book isn't much about this, but rather theology and apologetics, but I will never write a more important book.....

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