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> Irish Haplotypes And Haplogroups, (in inglish)
Павел Шварев
сообщение 11.9.2010, 18:20
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Irish Haplotypes and Haplogroups

Anatole A. Klyosov
Newton, Massachusetts 02459, aklyosov@comcast.net


The following letter has recently appeared in one on the international Forums on DNA genealogy:

Subject: May, 11, 2010
Subject: [DNA] Comparing Irish Clades

Has anyone compared any of the recognized Irish clades - NWI, South Irish,
Type III, to see how long ago they would have had a common ancestor?? I
know these three are not the only ones, but they may be the largest.

What would be an appropriate methodology - would you use the modal haplotype for each or take a selection of members of the clades. Would you compare each to the other separately or all three together?


I know choice of mutation rates and years per generation and which loci are
chosen will make a difference - perhaps a considerable one - but even the
relativity of age would be interesting. Which is the youngest, I wonder?

Thanks for any advice.



In two days a new letter appeared:

Sent: May 13, 2010

Subject: Re: [DNA] Comparing Irish Clades


I've received no response to my note below, which I gather means no one
thinks my idea is a good one. Can someone perhaps explain the folly of my
approach and suggest some other way to investigate the concept?



Thank you.



A few rather passive comments have appeared since then, with no any really positive information.

Here it is.

-- North Western Irish, aka R1b1b2-M222, aka R1b1b2-a1a2f2,


base (ancestral) haplotype


13 25 14 11 11 13 12 12 12 13 14 29 – 17 9 10 11 11 25 15 18 30 15 16 16 17 –

11 11 19 23 17 16 18 17 38 39 12 12 – 11 9 15 16 8 10 10 8 10 10 12 21 23 16 10 12 12 16 8 12 25 20 13 12 11 13 11 11 12 12

The common ancestor lived 1450±160 years before present.

-- Irish Type III, aka R1b1b2-L226, aka R1b1b2-a1a2f4,

base (ancestral) haplotype

13 24 14 11 11 14 12 12 11 13 13 29 – 17 8 9 11 11 25 15 19 29 13 13 15 17 –

11 11 19 23 15 15 18 17 36 38 12 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 15 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12

The common ancestor lived 1325±225 years before present.

-- South Irish, base (ancestral) haplotype

13 24 14 10 11 15 12 12 11 13 13 29 – 17 9 10 11 11 24 15 19 29 15 15 17 17 –

11 11 19 23 15 15 18 17 36 37 13 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 11

The common ancestor lived 1400±190 years before present.

There is one more distinct branch in the Ireland Heritage haplotype tree (see below), of 13 haplotypes, with the base haplotype

13 24 14 11 11 14 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 30 15 15 17 17 –

11 11 19 23 16 15 18 17 38 39 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 14 8 12 22 20 13 13 11 13 11 12 12 12

with a timespan to a common ancestor of 1325±275 years (it looks like it is the Northern Irish branch, though it has to be verified).

It is of a certain interest that all four branches each has a common ancestor of around 1400 years before present, that is in the middle of the 1st millennium AD. Something has happened there. Was it the fall of the Roman Empire which had caused it? They split and moved around to new territories? As it is shown below, all these four lineages, or branches on a haplotype tree, or subclades (though two of them, South Irish and North Irish, have not any certain SNP assigned to them), descended directly from an R1b1b2 common ancestor who lived around 4000 years before present. It was, apparently, R1b1b2-L21, for which 3725±380 and 4200±350 years before present have been determined earlier (Klyosov, 2010a, )

Since we know the TMRCA values for all four "clades", or branches, we can determine a timespan to THEIR common ancestor. The rules of calculations are essentially the same as those published earlier (Klyosov, 2009). For this, we should write down all the four base haplotypes (in this particular case) and summarily count mutations either between them, keeping a number of mutations minimized for each allele, or, if a base haplotype of their common ancestor is known (or deduced), mutations should be counted summarily from it. Then a timespan to THEIR common ancestor should be calculated as it was described in (Klyosov, 2009), however, it this case an average TMRCA for all the four base haplotypes should be added to the calculated value. This operation is not needed when we consider contemporary haplotypes (in this case the average timespan to the contemporary haplotypes is zero, hence, we add zero, if we follow the procedure; for base haplotypes a timespan is not zero, but equals to hundreds and thousands of years). For the R1b1b2 base haplotypes, shown above, the average TMRCA is equal to (1450+1450+1400+1325)/4 = 1406 years, or approximately 1400 years.

Compared to the "R1b1b2 European Base Haplotype"

13 24 14 11 11 14 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 29 15 15 17 17 –

11 11 19 23 15 15 18 17 36 38 12 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12

(which is loosely called "Atlantic Modal Haplotype", though typically for its 12-marker variant), all four base haplotypes have accumulated 7 mutations in the first 12 marker panel, 21 mutations in the 25 marker panel, 33 mutations in the 37 marker panel, and 45 mutations in all 67 markers (mutations are marked)

13 25 14 11 11 13 12 12 12 13 14 29 – 17 9 10 11 11 25 15 18 30 15 16 16 17 –

11 11 19 23 17 16 18 17 38 39 12 12 – 11 9 15 16 8 10 10 8 10 10 12 21 23 16 10 12 12 16 8 12 25 20 13 12 11 13 11 11 12 12

13 24 14 11 11 14 12 12 11 13 13 29 – 17 8 9 11 11 25 15 19 29 13 13 15 17 –

11 11 19 23 15 15 18 17 36 38 12 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 15 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12

13 24 14 10 11 15 12 12 11 13 13 29 – 17 9 10 11 11 24 15 19 29 15 15 17 17 –

11 11 19 23 15 15 18 17 36 37 13 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 11

13 24 14 11 11 14 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 30 15 15 17 17 –

11 11 19 23 16 15 18 17 38 39 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 14 8 12 22 20 13 13 11 13 11 12 12 12

This gives 3575 years from their common ancestor calculated per 12-markers, 4650 years (per 25-markers), 3950 years (per 37 markers) and 3525 years (per 67 markers), 3925±400 years on average. As it was mentioned above, TMRCA of R1b1b2-L21 in Europe is in the range of 3725±380 and 4200±350 years before present (Klyosov, 2010a, ) , hence, a good fit.

If we count mutations between the above four haplotypes, without comparing them to the base European R1b1b2 haplotype, the number of "minimized" mutations are 7 mutations in the first 12 marker panel, 21 mutations in the 25 marker panel, 33 mutations in the 37 marker panel, and 45 mutations in all 67 markers, that is exactly the same mutational differences as above.

Now, let us consider how we obtained those base haplotypes for four clades (branches) and a number of mutations for each of them. There are two principal ways to go – either to have a list of haplotypes typed for the respective SNPs, or to identify the respective branches on a haplotype tree. We have explored both of those methodologies.

Fig. 1 shows the Irish Heritage 67 marker haplotype tree (1036 haplotypes) in which said four subclades were located.

The location has been done by consideration of distinct branches of the tree. For example, the very upper left-hand side part of the tree contains a branch shown in Fig. 2. This branch can be tentatively assigned to Northern Ireland, based on some information presented in the Project

http://www.familytreedna.com/public/IrelandHeritage/default.aspx

The branch is obviously "young". All 13 haplotypes contain 30 mutations in the first 25 markers from their base haplotype (shown above), which gives 30/13/0.046 = 50 generations without correction for back mutations, or 53 generations with the correction (Klyosov, 2009), that is 1325±275 years to their common ancestor. The branch is also small, 13 out of 1036 Irish haplotypes is merely 1.25%.


Fig. 1. A 67-marker haplotype tree for 1036 haplotypes (mainly subclades of R1b1b2) of the Ireland Heritage project http://www.familytreedna.com/public/IrelandHeritage/default.aspx

The outlier 796 belongs to R1b1 haplogroup. Branches for four clades described in the text are indicated.

The next, very small branch consists of only seven haplotypes, as can be clearly seen in Fig. 2 (between haplotypes 3019 and 1521), however, according to the Heritage Project data, the outlying 3019 was typed as R1b1b2-SRY2627, that is M167, R1b1b2-a1a2c, a downstream of P312, while the remaining six haplotypes were either L21 (3083, 3212, and, presumably, 2381), or undertyped, being assigned to


Fig. 2. A fragment of the 67-marker haplotype tree in Fig. 1, showing a distinct branch of 13 haplotypes, between haplotypes 3148 and 1626. Most of the 13 haplotypes in the Project are not assigned to a certain territory, however, some of them point at Northern Ireland.

R1b1b2 only (1521, 1522, 2823), and might have been L21 judging from their positions in the small branch. Those six remaining haplotypes have the following base haplotype:

13 24 14 11 11 13 12 12 11 13 13 29 – 16/17 9 10 11 11 25 15 19 29/30 15 15 17 17 –

11 11 19 23 15 15 19 17 37/38 38 12 12 – 11 9 15 16 8 10 10 8 10 10 12 22/23 23 15/16 10 12 12 16 8 12/13 22 20 12 12 11 13 11 11 12 12

Due to a small number of haplotypes in the branch, some base alleles are unresolved, when they contain, say, three alleles of 16 and three 17, as in DYS458. All 67x6 = 402 markers contained 69 mutations from the above base haplotype, which gives 69/402/0.00216 = 79 generations without a correction for back mutations, or 86 generations with the correction (Klyosov, 2009), that is 2150±340 years from a common ancestor. It is likely a descending branch from (or within) the L21 subclade, which itself is 3725±380 years "old". Mutational differences in the base haplotype of the branch compared to the European R1b1b2 Base Haplotype are marked in bold. There are 9 of them. Since the L21 subclade has exactly the same 67 marker base haplotype (Klyosov, 2010b), those nine mutations place a common ancestor of L21 and this small branch of 6 haplotypes to 3760 years before present, that is practically exactly 3725±380 years, the "age" of L21. This means that this small branch very likely descended from the L21 common ancestor with the branch's common ancestor having 9 mutations in its haplotype. His six likely descendants either do not have territories assigned or have US-based data, which is of little help with assigning the branch origin to a certain territory. It might have its own subclade, not yet identified.

Let us consider a large branch of the tree in Fig. 1, marked as M222. It contains 257 haplotypes, that is 25% of the all 1036 Irish haplotypes of the tree, and has the following base haplotype:

13 25 14 11 11 13 12 12 12 13 14 29 – 17 9 10 11 11 25 15 18 30 15 16 16 17 –

11 11 19 23 17 16 18 17 38 39 12 12 – 11 9 15 16 8 10 10 8 10 10 12 21 23 16 10 12 12 16 8 12 25 20 13 12 11 13 11 11 12 12

Its mutational differences with that of the European R1b1b2 Base Haplotype (aka R-L21, R-P312, and R-U152 with only one mutation on 67 markers) are marked, there are 19 of them in all 67 markers. The size and shape of the M222 branch can be seen in Fig. 3. It shows how the branch stems from the "trunk" of the tree and expands to more and more mutation haplotypes with time. The branch contains 89 base (that is identical) 12-marker haplotypes and 18 base 25-marker haplotypes. This gives [ln(257/89)]/0.022 = 48 generations without a correction, or 51 generations with the correction for back mutations, that is 1275±185 years to a common ancestor of the branch. Based on 25-marker haplotypes, without mutation counting, it gives [ln(257/18)]/0.046 = 58 62 generations, that is 1550±400 years from the common ancestor, which is within the margins of error.

Fig. 3. M222 67 marker haplotype branch (257 haplotypes) from the Irish Heritage tree, shown in Fig. 1.

In order to verify the obtained figures, we have considered an independent list of 67 marker haplotypes, typed for the M222 subclade. In fact, I have considered first a list containing 18 of 25-marker M222 haplotypes (Fig. 4) [only 13 of 67-marker haplotypes were available that time], and then lists of 155, 172, and 266 of 67-market haplotypes. Data obtained show a power of calculations of timespans for series of haplotypes even in rather small datasets. The 67-marker lists were provided by Michael Walsh, administrator of R-L21Plus Project

http://www.familytreedna.com/public/R-L21/default.aspx
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Павел Шварев
сообщение 11.9.2010, 18:46
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Fig. 4. A 25-marker haplotype tree for 18 of M222 haplotypes, the source of haplotypes was http://www.familytreedna.com/public/R-L21/default.aspx.

All 18 of 25-marker haplotypes contain 47 mutations from the M222 base haplotype in the dataset (see above the 67 marker base haplotype)

13 25 14 11 11 13 12 12 12 13 14 29 – 17 9 10 11 11 25 15 18 30 15 16 16 17

(the base haplotype is number 495 in the Fig. 4, on the top of the tree)
which gives 47/18/0.046 = 57 61 generations (with a correction for back mutations), that is 1525±270 years to a common ancestor of those 18 individuals. If there was indeed one common ancestor for the whole 18-haplotype dataset, the tree should contain x base haplotypes, where x can be determined from the formula [ln(18/x)]/0.046 = 57, and x here is 1.3. Indeed, there is only one base haplotype on the tree.

Fig. 5. A 67-marker haplotype tree for 155 of M222 haplotypes, the source of haplotypes was
http://www.familytreedna.com/public/R-L21/default.aspx, provided by the Project administrator Michael Walsh.

The next step was a consideration of 155 of M222 haplotypes from L21Plus Project (see above), in October 2009. The tree is shown in Fig. 5. All 155 haplotypes contained 432 mutations in the first 25 markers, which corresponds to 1625±180 years to a common ancestor. As one can see, it is practically the same 1525±270 years, obtained with only 18 haplotypes. The whole 155 haplotype set contains 48 base 12-marker haplotypes, which gives [ln(155/48)]/0.022 = 53 56 generations to a common ancestor, that is 1400±245 years. Again, it is within margin of error, which shows that the whole 155-haplotype set descended from one common ancestor. It does not matter one counts mutations or base haplotypes, they both accumulate (mutations) or disappear (base haplotypes) following the same rules of chemical kinetics. There are 14 base 25-marker haplotypes in the 155-haplotype series, which gives [ln(155/14)]/0.046 = 52 55 generations, that is 1375±390 years to the common ancestor. Again, it is the same figure withing margin of error.

Fig. 6. A 67-marker haplotype tree for 172 of M222 haplotypes, the source of haplotypes was http://www.familytreedna.com/public/R-L21/default.aspx, provided by the Project administrator Michael Walsh.

Recently, in April of 2010, a list of 172 of M222 67-marker haplotypes became available (Fig. 6), and immediately after it a new updated version of 266 M222 haplotypes has appeared (Fig. 7).


Fig. 7. A 67-marker haplotype tree for 266 of M222 haplotypes, the source of haplotypes was http://www.familytreedna.com/public/R-L21/default.aspx, provided by the Project administrator Michael Walsh.

Base 67 marker haplotypes for all these series were identical, and shown above.

All 172 haplotypes contained 462 mutations in their first 25 markers, which corresponded to 1575±170 years to a common ancestor of M222.
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Павел Шварев
сообщение 11.9.2010, 19:02
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Finally, with 266 of M222 67-marker haplotypes, the whole dataset contained 80 of 12-marker base haplotypes and 22 of 25-marker base haplotypes, and the 266 of 25-marker panels contained 667 mutations. This all gives:

[ln(266/80)]/0.022= 55 58 generations, that is 1450±220 years, [ln(266/22)]/0.046 = 54 57 generations, that is 1425±340 years, 667/266/0.046 = 55 58 generations, that is 1450±160 years

As one can see, this is practically absolute reproducibility for the "age" of M222 common ancestor. The data are summed up in Table 1, to illustrate a reproducibility of calculations in a rather wide range of haplotype datasets and employing the logarithmic and the linear methods of calculations.

Table 1.

Results of calculations of a timespan to a common ancestor for different datasets of R1b1b2-M222 haplotypes.


The average of these ten figures equals to 1465 years, which is practically equal to the most reliable figure of 1450±160 years before present, obtained with the largest dataset (266 haplotypes of M222 subclade).

Let us move to Irish III haplotypes, which belong to subclade L226, that is R1b1b2-a1a2f4, a downstream from L21. Michael Walsh has kindly provided me with a list of 22 haplotypes all of which were typed for L226. The respective haplotype tree is shown in Fig. 8.


Fig. 8. A 67-marker haplotype tree for 22 of L226 haplotypes ("Irish III"), the source of haplotypes was
http://www.familytreedna.com/public/R-L21/default.aspx, provided by the Project administrator Michael Walsh (April, 2010).

All the 22 haplotypes collectively deviated by 52 mutations in the first 25 markers from the following base L226 haplotype:

13 24 14 11 11 14 12 12 11 13 13 29 – 17 8 9 11 11 25 15 19 29 13 13 15 17 –

11 11 19 23 15 15 18 17 36 38 12 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 15 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 12

This results in 1325±225 years to a common ancestor of the sampled population.

At the same time, in April 2010, Dennis Wright,
www.irishtype3dna.org,

has kindly provided me with a list of 146 of 67-marker haplotypes assigned to Irish III series. The tree is shown in Fig. 9.



Fig. 9. A 67-marker haplotype tree for 146 of L226 haplotypes ("Irish III"), the source of haplotypes was http://www. Irishtype3dna.org, provided by Dennis Wright (April, 2010).

A 67-marker base haplotype of the tree was exactly as the L226 base haplotype shown above. There were 301 mutations in the first 25 markers in all 146 haplotypes, which placed the common ancestor of the population at 1175±135 years before present. It is withing margin of error with 1325±225 years before present for the above 22 haplotypes typed for L226 in the cited Project.

One more approach employed the Ireland Heritage haplotype tree, shown in Fig.1. Using the base haplotype of L226 subclade as a "probe", the respective branch was identified on the tree (Fig. 10), and the calculations have shown that the base haplotype of the branch was identical to the 67 marker base haplotype of Irish III clade (L226), see above. The respective tree is shown in Fig. 11.

All 27 haplotypes of the branch contained 67 mutations from the base haplotype, shown above, which resulted in 1425±225 years to a common ancestor. The data are summarized in Table 2.

Table 2.

Results of calculations of a timespan to a common ancestor for different datasets of R1b1b2-L226 haplotypes (Irish III).


The fact that the common ancestor came as "younger" by logarithmic method compared with the linear method likely means that the 146 haplotype dataset contains a rather significant admixture of related haplotypes of a younger "age", that is from a rather recent common ancestor. This is obviously a separate branch in the lower part of the tree, with identical last names of the haplotype bearers.
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Павел Шварев
сообщение 11.9.2010, 20:48
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Fig. 10. A fragment of the 67-marker haplotype tree in Fig. 1, showing a distinct Irish III (presumably L226) branch of 28 haplotypes, between haplotypes 1598 and 2878.


Fig. 11. A 67-marker haplotype tree for 27 of "Irish III" haplotypes (presumably L226) forming a distinct branch on the Ireland Heritage haplotype tree (see Fig. 1 and 10). The tree consists of 27 haplotypes, since haplotype 3234 was incomplete (some alleles were missing), and it was removed from further considerations.

Using the same methodology, the "South Irish" branch was identified in the Ireland Heritage haplogroup tree (Fig. 1, 12). The base haplotype of the branch was as follows:

13 24 14 10 11 15 12 12 11 13 13 29 – 17 9 10 11 11 24 15 19 29 15 15 17 17 –

11 11 19 23 15 15 18 17 36 37 13 12 – 11 9 15 16 8 10 10 8 10 10 12 23 23 16 10 12 12 15 8 12 22 20 13 12 11 13 11 11 12 11

Fig. 12. A fragment of the 67-marker haplotype Ireland Heritage tree in Fig. 1, showing a distinct "South Irish" branch of 48 haplotypes, between haplotypes 2318 and 3114.

All 48 haplotypes contained 118 mutations from the base haplotypes in the first 25 markers, which resulted in 1400±190 years to a common ancestor of the population. There are five of 25-marker base haplotypes in the dataset, which gives [ln(48/5)]/0.046 = 49 à 52 generations to the common ancestor, that is approximately 1300 years. This again is within margin of error with 1400±190 calculated by counting mutations in haplotypes.


Fig. 13. A 67-marker haplotype tree for 48 of "South Irish" haplotypes forming a distinct branch on the Ireland Heritage haplotype tree (see Fig. 1 and 12).

I also have received from Michael Walsh an interesting dataset of "Scottish Borders A-1", or "R-L21-1113-A-1", as he tentatively coined them, based on their STR patterns. Michael believed that the majority of the
individuals bearing the haplotypes claimed ancestry back to the Scottish Borders Reivers, and that the identifying STR signature for those haplotypes is "within R-L21* and it is 617>=13, 406s1>=11, 640=12, and usually 607>=16, 534<=14", as least with those 108 haplotypes of the 184 which were tested
to 67 markers. The whole group of 184 haplotypes (some of them were 12-marker ones) is positive for L21. Their carriers lived in Ireland, Scotland, England.

Fig. 14. A 67-marker haplotype tree for 108 of "Scottish Border" R1b1b2-L21 haplotypes, kindly provided by Michael Walsh. A 7-haplotype branch on the left containing DYS385=11,11 is marked (between haplotypes f125935 and f125241).

Fir. 14 shows a haplotype tree of 67-marker haplotypes of the "Scottish Borders" series. It is obvious that the tree is rather complicated and reflects a number of lineages (branches). For example, a left-hand branch containing DTS385=11,11 has the following base haplotype

13 24 14 11 11 11 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 30 14 15 17 17 –

11 11 19 23 16 16 17 17 38 39 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 14 8 12 22 20 13 13 8 13 12 12 12 12

(in which deviations from L21 and P312 are marked, amounted to as many as 19 mutations in 67-marker base haplotypes [equivalent to the total of 3750 years between their common ancestors]), which the rest of the tree has mainly DYS385=11,14 (one 11,13, one 11,15 and 99 of 11,14, that is 98% of the total in the rest of the tree), with a base haplotype

13 24 14 11 11 14 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 29 15 15 17 17 –

11 11 19 23 16 16 18 17 38 40 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 14 8 12 22 20 13 13 11 13 12 12 12 12

Since there was no any DYS385=11,12 and very few 11,13, these two datasets (11,11 and 11,14) represent two different lineages, which were split some time back, went through a population bottleneck, largely (or completely) lost a population of DYS385=11,12, and became two separate (in terms of their alleles) populations. Time, when their common ancestor lived, is calculated below. Since the both "Scottish Borders" datasets (with DYS385 11,11 and 11,14) include L193+ SNPs, the split between the 11,11 and 11,14 lineages occurred within R1b1b2-L193 subclade.

The second base haplotype (DYS385=11,14) is closer to the base L21/P312 haplotype, with 11 mutations in 67-marker haplotype (equivalent to the total of 2075 years between their common ancestors), and the two "Scottish Borders" base haplotypes have 10 mutations between each other (equivalent to the total of 1850 years between their common ancestors).

All available 27 of 25-marker haplotypes of the DYS11,11 lineage contained only 38 mutations from their base haplotype, which gives 800±150 years to their common ancestor. In the 67-marker format only 7 haplotypes are available, with only 25 mutations per 469 alleles, which gives 650±145 years to a common ancestor, which is within the margin of error of the calculations.

The separate dataset of 145 of 25-marker haplotypes, with 142 of DYS385=11,14 haplotypes two DYS385=11,13 and one DYS385=11,15, contains 305 mutations from the base haplotype, shown above, which gives 305/145/0.046 = 46 à 48 generations (with correction for back mutations), that is 1200±140 years to a common ancestor. Since the two lineages, DYS385 = 11,11 and 11,14, are separated by 1850 years between their common ancestors, THEIR common ancestor lived approximately (1850+800+1200)/2 = 1925 years before present, at the beginning of AD. Regarding their position with respect to a common ancestor of the L21 subclade, THEIR common ancestor lived (3750+3725+800)/2 = 4100 (for L21 and the lineage of DYS385=11,11 of "Scottish Borders"), and (2075+3725+1200)/2 = 3500 years (for L21 and the lineage of DYS385=11,14 of "Scottish Borders") before present. This is actually the L21 common ancestor himself, since he lived 3725±380 years before present (Klyosov, 2010b, see also Table 3 below).

In conclusion, Table 3 contains the most reliable timespans to common ancestors of several Irish R1b1b2 clades/branches, along with their 67 marker base haplotypes.



Table 3

A summary of data on several Irish R1b1b2 clades/branches of a haplotype tree, and their ancestral haplotype (the European R1b1b2 Base Haplotype)


Percentage of the branches/clades was calculated with respect to the total 1036 haplotypes in the Ireland Heritage haplotype tree (Fig. 1).
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Павел Шварев
сообщение 11.9.2010, 20:50
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References

Klyosov, A.A. (2009). DNA Genealogy, mutation rates, and some historical evidences written in Y-chromosome. I. Basic principles and the method. J Genetic Genealogy 5, 186-216.

Klyosov, A.A. (2010a) Mapping of Europe by R1b1b2-L21 migration times. Proc. Russian Academy of DNA Genealogy (ISSN 1942-7484), 3, No.2, 191-201

Klyosov, A.A. (2010b) Haplogroup R1b. Proc. Russian Academy of DNA Genealogy (ISSN 1942-7484), 3, No.2, 249-299.

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Павел Шварев
сообщение 11.9.2010, 20:54
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LETTER SIXTY-FIVE




Цитата
In your article "Irish Haplotypes and Haplotypes" published in the Proceedings, No. 6, June 2010, pp. 1029-1053, you have analyzed the principal Irish DNA-lineages M222 (25%of total), L226 ("Irish III", 2.6% of total), "South Irish" (4.6% of total), "North Irish" (1.25% of total), along with some other smaller lineages. I am sending you a dataset of apparently what can be called "Irish Group IV"lineage. They have two distinct and identical tetra-local signatures – 10-12-15-13 in DYS391-385a-385b-426, and 15-15-16-18 in DYS464a-d. Some of my work in identifying origins of those seen to conform can be seen on http://sites.google.com/site/irishtype4/

The lineage was first mentioned by Ken Nordtvedt in June 2006 as per the Roots list
http://archiver.rootsweb.ancestry.com/th/read/GENEALOGY-DNA/2006-06/1151028429 who called it the 'Irish Continental'. It was later expanded by other authors such as Jim Cullen on whose predictor it appears. It subsequently became re-named the 'Irish Group IV'. I'm not qualified to say if the identification of the sub-clade via the stated 'signature' markers is valid, but it now appears accepted as a legitimate grouping. Any thoughs?
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Павел Шварев
сообщение 11.9.2010, 20:59
Сообщение #7


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MY RESPONSE:

I suggest you to double check principles based on which you pick haplotypes which supposed to be "Irish IV". A 67-marker haplotype tree for 44 haplotypes from your list showed that it is very unlikely that the dataset belongs to any "family" of haplotypes. The dataset is VERY heterogeneous.

If the basic principle of haplotype selection was some kind of a "signature", it is not a good principle. Silly statistics can make any "signature" in quite unrelated haplotypes. It is quite clear that your "Irish IV" belong to different subclades and lineages.


CONTINUATION:

Yes, indeed, the spread sheet I sent you included a lot of raw data. I am forwarding you an edited list.


MY RESPONSE:

The haplotype tree for all 22 of 67-marker haplotypes from your list is shown below.


As you can see, it is very "heterogeneous" and contains two rather distant branches, a couple of stray haplotypes, and a couple of small branches or sub-branches. It shows that the selection of those haplotypes in the dataset suffered from some inconsistencies.

It fact, I am always dubious regarding hand-picking of haplotypes based on some "signatures". Haplotypes mutate, and some of those hand-picked haplotypes can belong to some other "family" with just an accidental "match" in them, or, on the contrary, some haplotypes can be lost because of some mutations.

There are two more objective ways to select haplotypes, as you well know – either based on SNPs, or let computer do it. When the SNP is identified, you cannot pick haplotypes based on your "taste" and judgment, you have to follow the SNP, you do like the haplotype or not. Unfortunately, in this particular case the SNP was not identified as yes, hence, it is a job for computer (see below).

In other words, hand-picking ALWAYS leads to a more narrow selection of haplotypes. You pick just a "tip of the iceberg", and miss more mutated haplotypes. As a result, TMRCA is always more recent than it should be. You arbitrarily chose a more recent common ancestor.

What is worse, as the tree shows, you have mixed two different DNA-lineages. Of course, eventually they have the same, more distant common ancestor, since they are within the same haplogroup anyway, however, you in fact picked two "tips of icebergs", from two different lineages.

Let's see what you have got, and then I will try to correct the situation, at some extent. I will run some rough calculations, just to show you an overall picture.

The right-hand side branch contains seven "clean" haplotypes or eight, if to add BCHT9. Let's see, it is stray haplotype or it belongs to the branch.

The base (ancestral) haplotype of the branch is as follows:

13 24 14 10 12 15 13 12 12 13 13 29 – 17 9 10 11 11 25 15 19 29 15 15 16 18 –

10 10 19 23 16 15 17 17 36 39 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 15 8 13 22 21 13 12 11 13 11 11 12 12

The seven haplotypes have collectively 37 mutations from the base haplotype. It gives 37/7/0.145 = 36.5 generations without correction for back mutations, or 37.5 generations with the correction, that is 940±180 years to a common ancestor.

If we consider all eight haplotypes of the branch, there are 43 mutations, hence, 43/8/0.145 = 37 generations à 38 generations, that is 950±170 years to a common ancestor. It is practically the same thing.

The base haplotype of the left-hand side branch of 8 haplotypes is as follows:

13 25 14 10 12 15 13 12 13 13 13 29 – 17 9 10 11 11 25 15 19 28 15 15 16 18 –

10 10 19 23 15 15 17 17 35/36 37 12 12 – 11 9 15 16 8 10 10 8 12 10 12 21 23 16 10 12 12 15 8 14 22 21 13 12 11 13 11 11 12 12/13

As you see, the both branches have the two "signatures" which you have outlined, however, they represent two difffernt lineages with two different common ancestors.

There are 11 mutations between these two base haplotypes, if to consider the rounded alleles. In fact there are 9.625 mutations. However, as you will see below, there is not a big difference between the two values. There are only 26 mutations in all 8 haplotypes of the branch from the above base haplotype, therefore: 26/8/0.145 = 22 generations, that is 550±120 years to a common ancestor (there is no correction for back mutations for 22 generations).

When two base haplotypes are separated by 9.625 mutations, and the respective common ancestors lived 950 and 550 years ago, then THEIR common ancestor lived 1650 years ago, in the middle of the 1st millennium AD. If we would have taken 11 mutations (between the rounded up alleles), there would be 1800 years to THEIR common ancestor. It is within margin of error of the calculations.


A 67-marker haplotype tree for 1036 haplotypes (mainly subclades of R1b1b2) of the Ireland Heritage project

http://www.familytreedna.com/public/IrelandHeritage/default.aspx

The outlier 796 belongs to R1b1 haplogroup. Branches for five clades (or branches) are indicated.

A tentative conclusion: for those hand-picked haplotypes of Irish IV series, there are two lineages, with 550±120 and 950±170 years to their common ancestors, and THEIR common ancestor lived close to the beginning of the AD.



In order to see the actual branch of Irish IV haplotypes, not a hand-picked one, I took the Irish Heritage Project database

http://www.familytreedna.com/public/IrelandHeritage/default.aspx

with its 1036 of 67-marker Irish R1b1b2 haplotypes, and composed a 67-marker haplotype tree. There are five "families" of haplotypes identified on the tree by their position, including Irish IV. I will now described how I did it.

I took a list of all 1036 haplotypes and found a few haplotypes which look similar to the base haplotypes of Irish IV family, identified above. It turned out that all of them were located within one particular branch of 21 haplotypes. The branch is shown in the next figure, between haplotypes 2857 and 1581. In fact, the closest branch contained only 6 haplotypes (1480, 1482, 1491, 2857, 3126, and 3185), however, it was clear that this 6-haplotype sub-branch is a part of a very distinct branch of 21 haplotypes. This Irish IV branch is tiny, and contain only 21/1036 = 2%of all Irish R1b1b2 haplotypes in the Project.

This 6-haplotype branch has the following base haplotype:

13 24 14 10 12 14/15 13 12 12 13 13 29 – 17 9 10 11 11 25 15 19 29 15 15 16 18 –

10 10 19 23 15 15 17 17 36 39 12 12 – 11 9 15 16 8 10 10 8 11 10 12 23 23 16 10 12 12 15 8 13 22 21 13 12 11 13 11 11 12 12

It differed only by ½ mutation per all 67 markers from the above "Irish IV" haplotypes you sent me. Besides, there were both 14 and 15 alleles in the sixths marker from the left. In other words, both the "signatures" you have indicated are there, in the above base haplotype. However, in the "real life" the 10-12-15-13 sequence can equally be 10-12-14-13. Apparently, a larger dataset should be considered in order to identify the "true" base haplotype.

These 6 haplotypes contained 40 mutations from the above base haplotype, that is 40/6/0.145 = 46 generation à 48 generations (after the correction for back mutations), that is 1200±225 years to a common ancestor.

The adjacent small branch of 4 haplotypes contained 45 mutations from the following base haplotype:

13 24 14 10 11/12 15 12 12 12 13/14 13/14 29/3016 9 9/10 11 11 25 15 19 30 15 15 17 18 – 10 11 19 22/23 16 15 18/19 17 36 37 12 12 – 11 9 15 16 8 11 10 8 11 10 12 21/23 23 16 10 12 12 15/17 8 12 22/25 21 13/14 12 11 13 11 11 12 12

It gives 45/4/0.145 = 78 generations à 85 generations, that is 2125±380 years to a common ancestor.

The last two base haplotypes differed by 15.66 mutations (marked above) , which gives ~ 3175 years to THEIR common ancestor.

Finally, if to consider all 21 haplotypes in the branch in Figure above, their 25-marker base haplotype is as follows

13 24 14 10 11 14 12 12 12 13 13 29 – 17 9 10 11 11 25 15 19 30 15 15 16 18

all 21 haplotypes contain 107 mutations from this base haplotypes, which gives 107/21/0.046 = 111 generations à 124 generations, that is 3100±430 years to a common ancestor, who has the base haplotype shown above. This is presumably a more realistic common ancestor of Irish IV family. What you hand-picked, it was apparently some more recent branch of Irish IV family. As you see, its "signature" are not 10-12-15-13 in DYS391-385a-385b-426, but 10-11-14-12. The "signature" 15-15-16-18 in DYS464a-d is indeed as one you have suggested.

For the record, the "signatures" in other subclades and groups of Irish haplotypes are as follows:

11-11-13-12 M222 and a small unassigned branch
11-11-14-12 L226, "North Irish" and "Scottish Borders 1" (and also P312)
10-11-15-12 "South Irish"
11-11-11-12 "Scottish Borders 2"
10-11-14-12 Alleged Irish IV
10-12-15-13 A branch of alleged Irish IV

15-16-16-17 M222
13-13-15-17 L226 ("Irish III")
15-15-17-17 "South Irish", "North Irish", "Scottish Borders 1", a small unassigned branch (and also P312 and L21)
14-15-17-17 "Scottish Borders 2"
15-15-16-18 Alleged Irish IV




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