The Y-chromosome tree bursts into leaf

[1798]

http://mbe.oxfordjournals.org/content/early/2014/11/26/molbev.msu327.abstract

Abstract

"Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51 ×, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analysing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of non-synonymous variants in 15 MSY single-copy genes."


This new paper will need to go to the shredder.
M207 19 KYA and M269 4,9 KYA.

[PNGarrison]

Why bother with science when you have determined in advance what the answer has to be?

[1798]

Why bother with science when you have determined in advance what the answer has to be?

I read the paper, how could M269 be 4,900 years old? There are 90 SNPs from M269 to the present.
Mal'ta boy's remains R* was radio carbon dated to 24,000 ybp so how could M207 be 19,000 ybp?
U106 is at least 6000 years old.

[T E Peterman]

There is a +- around the estimated dates.

I use to think that M269 came about in maybe 7500 BC. With the passage of time, including new & better information, I have acknowledged that M269 has an origin more recent. I am more inclined today to say that M269 dates back to maybe 4000 BC; maybe 3500 BC. This would mean that L23, L51, L11, & P311 happened in rapid fire succession, with maybe a couple hundred years between each. P312 probably dates to 2500 BC+-. Ditto U106. Several years ago, estimates were that the MRCA of all extant U106 was maybe 1000 BC; I suspect the date is closer to 2000 BC to 2500 BC.

Timothy Peterman

[1798]

There is a +- around the estimated dates.

I use to think that M269 came about in maybe 7500 BC. With the passage of time, including new & better information, I have acknowledged that M269 has an origin more recent. I am more inclined today to say that M269 dates back to maybe 4000 BC; maybe 3500 BC. This would mean that L23, L51, L11, & P311 happened in rapid fire succession, with maybe a couple hundred years between each. P312 probably dates to 2500 BC+-. Ditto U106. Several years ago, estimates were that the MRCA of all extant U106 was maybe 1000 BC; I suspect the date is closer to 2000 BC to 2500 BC.

Timothy Peterman

So you are saying that 90 SNPs happened in 6000 years. Dr. Iain McDonald thinks that there are 135 years per SNP.

[T E Peterman]

How many of the 90 SNPs that you talk about happened at the same time in the same generation? Does each represent the establishment of a new branch (ie, line of descent)? Or are several of them shared by several lines of descent?

Timothy Peterman

[1798]

How many of the 90 SNPs that you talk about happened at the same time in the same generation? Does each represent the establishment of a new branch (ie, line of descent)? Or are several of them shared by several lines of descent?

Timothy Peterman

I didn't know that a child could have more than one new YSNP when he is born. So why do people write that there are 3-5 generations between YSNPs? I thought that the 90 SNPs were single events.

[1798]

Timothy
On another note, I noticed that my son and I match you on chromosome 17. When I saw the colour codes matching in the same place I knew that you have relatives tested as well.I am having my wife tested so that I can find out which side of the family the cousins are on.I also want to see how well our SNPs line up.

[T E Peterman]

Cool. The relevant side of the family is only 1/16 Irish. Another 7/16 is English or Scottish. The other 8/16 is Swiss.

Do you get this 90 SNP count from novel variants on the Big Y?

I have 96 "so called" novel variants. They aren't that novel because there are 41 Big Y participants who differ by 4 or less known SNPs from me & this covers a lot of the R1b U152 crowd. Of my 96 "novel" variants, over 30 are shared with all 41 of the matched participants. This tells me that, although not previously detected, a full 1/3 of the novel variants are higher on the tree than R1b U152.

I just bought a Big Y for my maternal uncle. He is R1b L23+ L11-. His surname is Robinson. I suspect that a soldier from Thrace may have been brought by the Romans to Britain. Will be interesting to see how many novel variants he has.

Timothy Peterman

[T E Peterman]

My uncle is R1b CTS7822.

Timothy Peterman

[1798]

Cool. The relevant side of the family is only 1/16 Irish. Another 7/16 is English or Scottish. The other 8/16 is Swiss.

Do you get this 90 SNP count from novel variants on the Big Y?

I have 96 "so called" novel variants. They aren't that novel because there are 41 Big Y participants who differ by 4 or less known SNPs from me & this covers a lot of the R1b U152 crowd. Of my 96 "novel" variants, over 30 are shared with all 41 of the matched participants. This tells me that, although not previously detected, a full 1/3 of the novel variants are higher on the tree than R1b U152.

I just bought a Big Y for my maternal uncle. He is R1b L23+ L11-. His surname is Robinson. I suspect that a soldier from Thrace may have been brought by the Romans to Britain. Will be interesting to see how many novel variants he has.

Timothy Peterman

Most of the SNPs are in the FTDNA R tree on our homepage from the Geno 2 results. I added on the average number of SNPs under U106 from the Big-Y tests.There are possibly more SNPs to be added to the Y-tree. When that will take place is anyone's guess.

[T E Peterman]

I just looked at the R1b U106+ SNPs at the ISOGG website. I don't see any place where there are 90 columns going across. Each column indicates a nested SNP. If you see two SNPs seprated by a / mark, this indicates that they are the same, but have been given different names by different labs. If you see two SNPs, separated by a , mark, it means there are two different SNPs, but they are always found together, which means they could have happened at the same generation.

If you were to find 90 nested SNPs, this would indicate that there had been 90 SNP mutations since the beginning of the haplogroup. The deepest I see for U106 at ISOGG is 12 nested SNPs. I wouldn't factor in any Big Y data or Geno 2.0 until ISOGG concurs and a tree structure ascertained.

Assuming 135 years on average per nested SNP, I see a minimum average age for U106 of 1,620 years. It's probably at least 4,000 years, since most nested SNPs more recent than 1,500 years old are limited to so few lineages, they just haven't been discovered yet.

Timothy Peterman

[PNGarrison]

"I didn't know that a child could have more than one new YSNP when he is born. So why do people write that there are 3-5 generations between YSNPs? I thought that the 90 SNPs were single events."

It could occasionally happen that more than one SNP could happen in a generation. I can't remember that anyone has looked specifically at the Y, but multi-mutation events (within 10,000 bp or so) occur more frequently than one would calculate by multiplication of rates. I would guess that this is the result of the individual having sub-optimal DNA repair gene(s), or even a DNA replication complex or DNA repair complex being temporarily out of whack (possibly lacking a subunit or containing a protein with a translation error.) From what I've read, I wouldn't expect it to be a very common event, though.

As to the mutation rate they used in this paper, I think Iain had some question about it - he thought there was a better one available that would result in somewhat older dates.

[PNGarrison]

Another interesting tidbit from this paper is that they found a SNP recurrence rate (the same SNP appearing at different points in the tree) of about 1%. That's higher than I would have expected, especially since they didn't use any of the palindromic regions.

[1798]

I just looked at the R1b U106+ SNPs at the ISOGG website. I don't see any place where there are 90 columns going across. Each column indicates a nested SNP. If you see two SNPs seprated by a / mark, this indicates that they are the same, but have been given different names by different labs. If you see two SNPs, separated by a , mark, it means there are two different SNPs, but they are always found together, which means they could have happened at the same generation.

If you were to find 90 nested SNPs, this would indicate that there had been 90 SNP mutations since the beginning of the haplogroup. The deepest I see for U106 at ISOGG is 12 nested SNPs. I wouldn't factor in any Big Y data or Geno 2.0 until ISOGG concurs and a tree structure ascertained.

Assuming 135 years on average per nested SNP, I see a minimum average age for U106 of 1,620 years. It's probably at least 4,000 years, since most nested SNPs more recent than 1,500 years old are limited to so few lineages, they just haven't been discovered yet.

Timothy Peterman

I don't understand this bit.How did you come up with this figure? You are stating that we are all descended from one man 1620 years ago.
The Issog tree is light years behind.Some of the group I belong to have 40 SNPs downstream of Z156 from the Big-Y.