SNPs

General discussions regarding DNA and its uses in genealogy research

Posts: 2277
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Thu May 03, 2012 6:41 pm
There are only 12 principle SNPs between M207 and M405 that I can see at Isogg for R1b. R1b is said to be 18,500 years old. That means there are more than 1000 years between each of these SNPs. Is that correct?
User avatar
Posts: 202
Joined: Sun Apr 01, 2012 5:38 am

YDNA:
R-L21+, L226+
PostPosted: Thu May 03, 2012 10:42 pm
The time between each SNP could vary dramatically. There are many statistical methods for estimating the TMRCA for each and these estimates are highly controversial but yield pretty good estimates if the sample sizes are large enough. Here is an example of the TMRCAs for R-L21 SNPs

http://eng.molgen.org/viewtopic.php?f=122&t=306

Posts: 2277
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Sat May 12, 2012 10:01 am
He gives a TMRCA of 1700 years for M222 which is only half of what some other people give.
I think SNPs are more reliable than YSTRs.The same way that we know that there are 30 years per generation there is an average rate for SNPs.When some Scientist figures that out then we will get a realistic age for some of these Haplogroups and Subclades.
User avatar
Posts: 202
Joined: Sun Apr 01, 2012 5:38 am

YDNA:
R-L21+, L226+
PostPosted: Sat May 12, 2012 6:37 pm
dartraighe wrote:He gives a TMRCA of 1700 years for M222 which is only half of what some other people give.
I think SNPs are more reliable than YSTRs.The same way that we know that there are 30 years per generation there is an average rate for SNPs.When some Scientist figures that out then we will get a realistic age for some of these Haplogroups and Subclades.


Unfortunately, TMRCA is primarily based on the Y-STR MRCA of the SNPs. These are controversial since Y-STRs are not the reliable after 800 to 1,200 years since most scientists think that is the limit of use of Y-STRs - due to numerous undetectable backwards and parallel mutations. L226 was originally estimated to be 1,300 years of age. However, the discovery of Z253 in between L21 and L226 has changed that estimate to 2,800 years. DF23 has now been discovered between L21 and M222. The combined DF23/M222 estimate may radically different than previous M222 only TMRCA estimates. It is unfortunate the M222 only TMRCA was not included.

With the DF13 Y-SNP coming online soon, all L21 TMRCAs will probably change as DF13 is suppose to be around 90 % of all L21s. The more intermediate Y-SNPs that become available and tested, the more accurate TMRCA calculations will become. Y-SNPs will become much more useful over time as many more are discovered. However, at this point in time, there are too few of them to help genealogists who fund 90 % of consumer DNA testing. As Y-SNPs get closer together in the timeframe - Y-STR mutations between Y-SNP events will become much more reliable.
Last edited by Robert Casey on Sun May 13, 2012 2:54 am, edited 2 times in total.
User avatar
Posts: 34
Joined: Thu Mar 15, 2012 4:03 am

MtDNA:
V9
PostPosted: Sun May 13, 2012 2:05 am
Robert, does DF19 replace DF13, or was that a typo?

I wonder about the TRMCA given to L144, it only used 5 results to calculalte, propbably including Kendall whos haplotype is completly different to other L144, may that is why it comes out older than other groups.
L144 30.0 N=5 GA coal= 83.5 2,506.3 GA= 107.7 3,231.5
User avatar
Posts: 202
Joined: Sun Apr 01, 2012 5:38 am

YDNA:
R-L21+, L226+
PostPosted: Sun May 13, 2012 2:53 am
frances wrote:Robert, does DF19 replace DF13, or was that a typo?

I wonder about the TRMCA given to L144, it only used 5 results to calculate, probably including Kendall whose haplotype is completely different to other L144, may that is why it comes out older than other groups.
L144 30.0 N=5 GA coal= 83.5 2,506.3 GA= 107.7 3,231.5


DF19 was a typo for DF13 which I corrected in purple. I agree with you that there are two very different fingerprints for L144. However, there are only two explanations: 1) the Y-SNP is much older than expected and there are two very different surviving Y-STR fingerprints; 2) It could be parallel mutations of the same Y-SNP (L144.1 and L144.2) which seems unlikely. If scenario 1) is correct, the TMRCA would be much older with the two different fingerprints. Here is my analysis of L144:

http://www.rcasey.net/DNA/R_L21/Analysis/R_L21_Analysis_L144&L195.html
User avatar
Posts: 34
Joined: Thu Mar 15, 2012 4:03 am

MtDNA:
V9
PostPosted: Sun May 13, 2012 7:26 am
Thanks for claifying Robert.

I think I go with the 2nd explanation for two L144 groups.
Kendall have a very tight group of family, (Group 1 Virginia) in their project, with three testing L144+ and 4 testing L144-.
It would seem that within that particular family L144 is quite recent and so far particular to the Stafford County Virgina line.
User avatar
Posts: 202
Joined: Sun Apr 01, 2012 5:38 am

YDNA:
R-L21+, L226+
PostPosted: Sun May 13, 2012 3:29 pm
frances wrote:I think I go with the 2nd explanation for two L144 groups.
Kendall have a very tight group of family, (Group 1 Virginia) in their project, with three testing L144+ and 4 testing L144-.
It would seem that within that particular family L144 is quite recent and so far particular to the Stafford County Virgina line.


That makes sense. Since R-L21 is the only broader Y-SNP that has multiple fingerprints matching L144, it may be hard to convince
the scientific community that the only two independent mutations of L144 are under L21 - specially since L144 has been part of the
deep clade test for while. But I doubt if the deep clade tests for L144 until P312 or L21 are verified first. Not sure how you can
distinguish between the two scenarios until L144 tests positive somewhere outside of L21. WTY tests could reveal that since
the WTY tests all known Y-SNPs for each WTY test. It is really sad that data mining that very valuable resource is so manual in nature.

The other sticky point is the duplicate Y-SNP L195. If these are truly independent Y-SNPs, they should test different for L144.1 and
L144.2 - unless they are close to each on the Y chromosome. I just verified that L144 and L195 are adjacent to each other on
the Y-chromosome - L144 at 21,120,848 (A to T) and L195 at 21,120,849 (+string). So these two Y-SNPs are probably truly track
each other. The Y chromosome browser shows L144 - 16 positive and 1,856 tested and L195 - 11 positive and 1,654 tested. Wish
we could drill down to see which submissions were involved - specially the WTY tests.

Also, the TMRCA estimates are based on all 111 marker submissions found that test positive for any Y-SNP. So if both groups have
111 marker submissions, the TMRCA estimate for L144 would come out very old.

Posts: 2277
Joined: Fri Mar 16, 2012 5:43 pm

MtDNA:
U5b2b
PostPosted: Tue May 15, 2012 3:24 pm
Robert Casey wrote:
dartraighe wrote:He gives a TMRCA of 1700 years for M222 which is only half of what some other people give.
I think SNPs are more reliable than YSTRs.The same way that we know that there are 30 years per generation there is an average rate for SNPs.When some Scientist figures that out then we will get a realistic age for some of these Haplogroups and Subclades.


Unfortunately, TMRCA is primarily based on the Y-STR MRCA of the SNPs. These are controversial since Y-STRs are not the reliable after 800 to 1,200 years since most scientists think that is the limit of use of Y-STRs - due to numerous undetectable backwards and parallel mutations. L226 was originally estimated to be 1,300 years of age. However, the discovery of Z253 in between L21 and L226 has changed that estimate to 2,800 years. DF23 has now been discovered between L21 and M222. The combined DF23/M222 estimate may radically different than previous M222 only TMRCA estimates. It is unfortunate the M222 only TMRCA was not included.

With the DF13 Y-SNP coming online soon, all L21 TMRCAs will probably change as DF13 is suppose to be around 90 % of all L21s. The more intermediate Y-SNPs that become available and tested, the more accurate TMRCA calculations will become. Y-SNPs will become much more useful over time as many more are discovered. However, at this point in time, there are too few of them to help genealogists who fund 90 % of consumer DNA testing. As Y-SNPs get closer together in the timeframe - Y-STR mutations between Y-SNP events will become much more reliable.


Robert
How is that Thomas Krahn's SNP tree shows all the SNPs from L11 back to Africa and why is it he cant fill in the SNPs from L11 to the present? There are thousands of R1b people tested.I had my first test eight years ago and I'm still in Limbo.
User avatar
Posts: 202
Joined: Sun Apr 01, 2012 5:38 am

YDNA:
R-L21+, L226+
PostPosted: Tue May 15, 2012 6:22 pm
dartraighe wrote:Robert
How is that Thomas Krahn's SNP tree shows all the SNPs from L11 back to Africa and why is it he cant fill in the SNPs from L11 to the present? There are thousands of R1b people tested.I had my first test eight years ago and I'm still in Limbo.


L11 is currently the grandfather of L21:


R1b1a2a1a1_____L11
R1b1a2a1a1b____P312
R1b1a2a1a1b4___L21

Are you confirmed L11* - tested negative for all downstream SNPs: L11+, U106- and P312- ?

If you are not U106- and P312-, you have options to test for around 100 downstream Y-SNPs. This can be accomplished in one of three ways:

1) Order the the deep clade test for $139 - which will continue to test under it tests negative for all Y-SNPs in the FTDNA haplotree.
2) Order P312 and U106 separately for $58 - but if one tests positive - you have to continue to test for each level until all sons of the
most recent Y-SNP returns negative.
3) Order a WTY test for $750 to discover new Y-SNPs more recent than L11 (if U106 and P312 tests negative).

What is your FTDNA kit number and what project do you belong to so that people can look at your Y-STR and Y-SNP testing to date ?

If you test both negative for U106 and P312, somebody will have to test via "Walk the Y" test to discover a new Y-SNP that would
cover your genetic line or you have to passively wait for 1000 genomes or other groups to discover a new Y-SNP. Where your most
recent Y-SNP terminates is pretty random. My father's all male Y-DNA line stops at L226 (son of L21) but my mother's all male line
stops at P312. It is just somewhat chance as well as support for WTY testing that reveals how recent any branch of the haplotree
will be found.
Next

Return to General DNA Discussion

Who is online

Users browsing this forum: No registered users and 2 guests