'I think most of the differences between father-son pairs in this study are errors."
As with radiocarbon dating and ancient carbon, in the pursuit of reality denial, YEC rejects the signal and embraces the noise.
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These results were also plotted by Jobling and Tyler-Smith (2017), with the exception of Karmin et al 2015 and Petr et al 2020.
(I’m not quite sure why Karmin isn’t included in the graph, as it’s cited elsewhere in the paper.)
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Why isn’t he testing his hypothesis and generating those data?
What makes you think that AiG is the problem?
You haven’t addressed Jeanson’s lack of curiosity at all.
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None of the “families” studies in that figure include y-chromosome father-son differences except the two low-coverage studies Jeanson cited.
Mendez is based on an autosomal rate, which is then odd to include it (When I googled it I came across a paper critical of that method.) Petr is using ancient DNA.
So thanks to @Herman_Mays emailing someone who would be aware of the literature, I think we can call it definitive there aren’t any others.
Why should they have to include father-son differences though? Looking at differences accumulated over a larger number of generations is likely to give a less noisy estimate just in principle, don’t you think?
Balanovsky et al. (2015) should be Jeanson’s dream: very high-coverage sequencing AND directly relating the Y chromosome phylogeny to known genealogical history! Shame the result doesn’t agree with him though…
The genetic tree based on high-throughput sequencing of the Kazakh G1 chromosomes (Fig 6A) perfectly fits the genealogical tree: representatives of Argyn clans who originated from Karakhoja (from Kazakh1 to Kazakh6) form a single and young subcluster and all are equidistant from the MRCA, as predicted by the genealogy (Fig 6B). Thus, the de jure ancestor known from genealogical tradition and historical records was likely to be also the de facto biological ancestor of most present-day male members of the Argyn tribe. Considering the time span of 606 years between Karakhoja (who was around 50 years old in 1405 and then likely fathered his sons on average around 1385) and average date of birth of the 6 present-day Kazakhs sampled (1991), the total length of Y-chromosomal segments sequenced in each of these 6 Kazakh samples (10,005,352 bp), and the average number of accumulated mutations 4.67 (S2 Fig), we obtained the mutation rate for Y-chromosomal sequences 0.77×10-9 per bp per year.
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So to put it another way none of these studies give you the answer you want so you are just going to ignore them and go with Jeanson’s estimate even though the author says that information simply isn’t in their study.
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Wouldn’t multiple generations give you better data, less likely to be swamped by noise?
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Including, to the best of my knowledge, one from Jeanson. I’ve tried, without success, to find his x.x e-x SNP rate, and would appreciate a reference to a definite value. Do you happen to know?
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Right smack in the middle of all the other estimates Skov shared with me across a diversity of different studies and approaches. Hmmmm….
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Why would they need to be “father-son difference” studies to provide a check on Jeanson’s work when Jeanson himself is not using them to estimate changes over a single generation, but over hundreds (YEC timeframes) or thousands (consensus science timeframes) of years? This makes multi-generational studies a better check on his work that father-son studies.
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I was skimming through that study earlier to find out how they calculated their rate and their methods. Really cool they ended up confirming family history.
I don’t know if you noticed my hypothesis earlier about the same mutations occuring in different lineages (I guess that’s called parallel mutations?). So this caught my attention.
To estimate the potential sequencing error rate, we applied a phylogenetic approach. We checked whether we found all SNPs in the BigY captured region which are known to be phylogenetically located between haplogroups A0 and G (www.isogg.org) and thus should be present in our samples. The proportion of missed SNPs was the false negative rate. We also checked whether we see SNPs known to define other haplogroups, which are therefore not expected to be present in our haplogroup G samples. The proportion of these unexpected SNPs was considered as the false positive rate. We note that this approach overestimates the error rate, because it considers parallel mutations as errors and ignores potential inaccuracies in identifying the SNP ancestral states in ISOGG database. The (over)estimated rates were 0.008 for false negatives and 0.005 for false positives. (See details in S2 Table
That is quite the error rate compared to Lauritz Skov. Maybe the methods are different enough, but it makes me wonder about back mutations. So yes, I still want more father-son studies specifically.
Uh, what? 
Was that reaction the point? If so, point made. 
If not, please explain.
I wrote the above and then went back to look at Balanovsky because I was curious how they described filtering before I finished my post. I clicked on Supplementary Table 2 and then was looking at the number of false negative and false positive SNPs and then…I saw what they wrote behind the asterisks at the bottom. I thought my hypothesis about parallel mutations occuring often was a pretty good idea, but when I looked at the error rate listed there compared to what’s in the main text of the paper…I haven’t picked my jaw up off the floor yet.
Im sharing a screenshot but it’s probably tiny so you’ll have to go look for yourselves.
In this case, I’m really just asking a genuine question. These other studies put out actual Y chromosome SNP mutation rates stated in terms of substitutions per some power of ten per year. Jeanson maintains these are flawed, but I have not found a reference where he specifically stipulates the rate he thinks is valid. The paper I have seen, Evidence for a Human Y Chromosome Molecular Clock: Pedigree-Based Mutation Rates Suggest a 4,500-Year History for Human Paternal Inheritance, has much discussion about coverage and filters, and makes qualitative statements such as:
This suggested that the real per-generation Y chromosome single nucleotide mutation rate was much higher than previously determined.
I may be blind, but I could not find the bottom line plug and chug number Jeanson ended up with. Is it tucked away in a supplementary table somewhere or what?
He certainly has published his rate, several times. He has published several papers on this topic. It is approx 50x higher than the rate everyone else is computing.
He is far more vague as to why these other studies are flawed.
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Table 1
This is not true. 10-17x in the paper above.
That’s not true either. He gives low coverage as the reason the other father-son studies are giving a low rate and there aren’t any others than don’t use an evolutionary timeline (ancient DNA, etc).
That’s a nonsensical reason. Do you see why?
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Nope. Why?
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It seems to me that you are here making an exact argument that the fixation rate should be markedly lower than the mutation rate.
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I’m not seeing any such curiosity.
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I don’t think so?.. you’ll still lose one or both of most of those parallel mutations to drift over time
In case anyone missed what I was suggesting earlier, it’s that the mutation rate is still high in that paper with high coverage. It looks to me like Balanovsky ignored 5+16+17+10 mutations to get his rate, unless I’m not understanding something.
With so many back mutations as then I’m also suggesting, I don’t know if that changes how the rate of fixation is understood?
The other thing that I noticed is all of the “false positives”/back mutations are in what Jeanson identifies as the Hammitic line and all the “false negatives”/parallel mutations are not in those particular lineages. That makes me wonder if the majority of y-chromosome mutations are not deleterious, or the mutation rate introduces beneficial variety.
Rather impossible? On the contrary, ancient DNA constitutes direct evidence. Do not let the tail wag the dog, phylogenetic inference for the Y-chromosome tree and human dispersal must take account of the archeology and radiometric dating associated with human remains. Science is not perturbed or threatened by this, and both population densities of haplogroups and paleo genetics are utilized and synthesized. If Jeanson cannot accommodate the totality of evidence, that is so much the worse for his narrative.
Interestingly, for r1b haplogroup, we actually can attach names from the 18th dynasty of new kingdom Egypt - 3 kya - Akhenaten, Amenhotep, and Tutankhamun:
Maternal and paternal lineages in King Tutankhamun’s family
Insights from ancient DNA analysis of Egyptian human mummies: clues to disease and kinship
A 4-generation pedigree of Tutankhamun’s immediate lineage and the identity of his ancestors were established. The Royal male lineage was the Y-chromosome haplogroup R1b that was passed from the grandparent (Amenhotep III) to the father (KV55, Akhenaten) to the grandchild (Tutankhamen).
We have the recent analysis of the 14 kya Villabruna individual from Italy identified as R1b1
The genetic history of Ice Age Europe
7500 kya - Samara hunter-gatherer, Sok River, Russia
Massive migration from the steppe was a source for Indo-European languages in Europe
Two hunter-gatherers from Russia included in our study belonged to R1a (Karelia) and R1b (Samara)
The following quotes are from the supplementary material pdf which is linked at the bottom of the paper:
The individual we refer to as ‘Samara hunter-gatherer’ I0124/SVP44 (5640-5555 calBCE, Beta-392490) is an adult male from grave 1 in a Neolithic-Eneolithic settlement producing artifacts from the Elshanka, Samara, and Repin cultures. The specific site is Lebyazhinka IV, on the Sok River, Samara oblast, Russia. (‘Neolithic’ here refers to the presence of ceramics, not to domesticated animals or plants.) The radiocarbon date of this individual, based on a femur, is centuries before the appearance of domesticated animals in the middle Volga region.
I0806 (Bell_Beaker_LN)
The individual was assigned to haplogroup R1b1a2a1a2 based on mutation P312:22157311C→A. Two Bell Beaker individuals from Kromsdorf, Germany were previously determined to belong to haplogroup R1b. The individual also has upstream mutations for R1 (P236:17782178C→G), R1b1 (L278:18914441C→T), R1b1a2 (F1794:14522828G→A), and R1b1a2a1 (L51:8502236G→A).
I0410 (Spain_EN)
We determined that this individual belonged to haplogroup R1b1 (M415:9170545C→A), with
upstream haplogroup R1b (M343:2887824C→A) also supported. […] The occurrence of a basal form of haplogroup R1b1 in both western Europe and R1b1a in eastern Europe (I0124 hunter-gatherer from Samara) complicates the interpretation of the origin of this lineage.
I0231 (Yamnaya)
This individuals was assigned to haplogroup R1b1a2a2 (CTS1078:7186135G→C,
Z2105:15747432C→A) with upstream haplogroups R1b1a2a (L23:6753511G→A), and R1b1a2
(PF6399:2668456C→T, L265:8149348A→G, PF6434:8411202A→G, L150.1:10008791C→T,
PF6482:18381735A→G, M269:22739367T→C) also supported.
I0370 (Yamnaya) This individual was assigned to haplogroup R1b1a2a2 S1078/Z2103:7186135G→C), with upstream haplogroups R1b1a2 (M269:22739367T→C, L150.1:10008791C→T), R1b1a (L320:4357591C→T) also supported.
[…] Summarizing the results from the Yamnaya males, all seven belonged to haplogroup R1b1a. Six of these could be further assigned to haplogroup R1b1a2a, and five of these to haplogroup R1b1a2a2. The uniformity of R1b Y-chromosomes in this sample suggests a patrilineal organization of the Yamnaya, or at least of the people who were given expensive Kurgan burials.
Wikipedia has a listing of several ancient specimens of R1b in addition to the above, found in the Balkans, Latvia, Ukraine, Romania, Serbia, Bulgaria, Russia, and Spain, all 5 kya or greater.
The extent of ancient R1b discredits any idea that parallel mutation is at work, but were this not sufficient in itself, several of these remains present mutations which identify downstream sub-types up to three nodes deep. That all these samples would represent dead ends, and the same mutation patterns would independently re-emerge, cannot be seriously entertained. It is apparent that R1b, and many of its sub-clades, has been with us continuously from prehistory through history.
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