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Haplogroup R Private SNPs, Notes and Papers - 2012
SNP SYMBOLS:
Private
Investigation
NOTE: Corrections/Additions made to this page are shown at the bottom of the main Haplogroup R page.
Private SNPs are being removed from the tree and placed in the Private categories.
R1a Private SNPs - After having been investigated, these SNPs have not met the population distribution
criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple
confirmed testers were confined to either a single surname or to a small group of related males.
- M56, M64.2/Page44.2, M87, M157.1, M204, M434, P98 and
PK5 are downstream of M417. Listed 19 July 2012.
- M334 is downstream of M458. Listed 19 July 2012.
- L175/S467 is downstream of L176.1/S179.1. Listed 19 July 2012.
R1a SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L12, L235, L399, L450, L451, L458, L579
and Page68 are located at approximately R-M417. Listed 24 Jun 2011.
- L291 is located at approximately R-M458. Listed 24 Jun 2011.
- L457 is located at approximately R-M417. Listed 19 July 2012.
R1b Private SNPs - After having been investigated, these SNPs have not met the population distribution
criteria for placement on the tree. Either too few confirmed positive testers have been found OR multiple
confirmed testers were confined to either a single surname or to a small group of related males.
- L5 is located downstream of R-U106. Listed 6 Apr 2006.
- S50 is located at approximately R-M269. Listed 6 Apr 2006.
- L50/S136 is located at approximately R-L23.
Listed 28 Oct 2010.
- L179 and L180
are located downstream of Z6. L179 and L180 were found in a single individual, and are likely phylogenetically
equivalent. Listed 21 Mar 2011.
- L3/S216 is located at approximately R-L562. Listed 10 Jul 2011.
- L147.5 is downstream of Z14. Listed 21 March 2011.
- L135, L209 and S42 are
located at approximately R-L2. Listed 21 Mar 2011.
- L7, L95, L171, L173
and L194 are located at approximately R-P312. Listed 21 Mar 2011.
- L141.2 and S44 are located at approximately R-U152.
Listed 6 Aug 2011.
- L626 is located under L627. Listed 6 Aug 2011.
- L625 is located under R-L626. Listed 6 Aug 2011.
- M65 is located downstream of R-P312/S116. The position of private SNP
M65 is uncertain with respect to the positions of Z196, L238/S182, DF19 and DF27.
Listed 26 June 2012.
- M126 and M160 are located downstream R-S28/U152.
The positions of M126 and M160 are uncertain with respect to
the positions of L2, Z36, and Z56. Listed 26 June 2012.
- M228.2 is located downstream of R-L21/M529/S145. Listed 26 June 2012.
- M37 is located downstream of R-L21/M529/S145. The position of private SNP M37 is uncertain with respect to the positions
DF23/S193, DF1/L513, L96, L144/S175, L195, L159.2/S169.2, Z253, DF21/S192, L371, and DF41. Listed 26 June 2012.
- L319.1 is located under R-DF13. Listed 8 July 2012.
- L302/S464 is located under R-DF49. Listed 8 July 2012.
- L9, L10 and L130 are located under
R-L513. Listed 8 July 2012.
- L894 and L895 are located downstream of R-L1066.
Listed 8 July 2012.
- L696 is downstream of Z326. Listed 18 July 2012.
- L653 is downstream of Z18. Listed 18 July 2012.
- L129 is downstream of U198. Listed 18 July 2012.
- L217.2 is downstream of Z7. Listed 18 July 2012.
- P107 is downstream from U106. Listed 9 August 2012.
- L6 is is downstream from U106. Listed 9 August 2012.
- L325 is downstream from Z18. Listed 9 August 2012.
- L188 is downstream from Z326. Listed 9 August 2012.
- V8 is downstream from V88 and parallel to M18. Listed 9 August 2012.
- V7 is downstream from V35. Listed 9 August 2012.
- L127.2 is located downstream from L128. Listed 18 August 2012.
- L199 is located downstream from U106. Listed 18 August 2012.
- L259/S266 is located downstream from Z301. Listed 18 August 2012.
- M157.2 is located downstream from Z6. Listed 18 August 2012.
- L693 is located downstream from L48. Listed 19 August 2012.
- S420 is located downstream from S190. Listed 13 September 2012.
- L1308 is located downstream of R-Z253, parallel to L277, L554, L643, and Z2185.
Listed 1 December 2012.
R1b SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L100 is located at approximately R-S47. Listed 21 Mar 2011.
- L216 is located at approximately R-L23. Listed 22 Mar 2011.
- L86.2, L220.1, L221, L253, L289, L326
and M228.1 are located at approximately R-P312. Listed 6 Aug 2011.
- L192.1 is located at approximately R-L21. Listed 26 June 2012.
- L408, L409, L443, L552, L553 and L594 are
located at approximately R-L2. Listed 6 Aug 2011.
- L654.1 is located at approximately R-U152.
Listed 6 Aug 2011.
- L276, L628 and L659 are located downstream of R-M167.
Listed 6 Aug 2011.
- L629 is located at approximately R-Z196. Listed 6 Aug 2011.
- L641 and L642 are located at approximately R-DF21/S192.
Listed 6 Aug 2011.
- L671 is located at approximately R-Z36. Listed 4 Sep 2011.
- S281/Z248 is being investigated to determine its exact position with respect to DF5. Listed 10 Aug 2011.
- L132.2 is located downstream of R-L1. Listed 22 Dec 2011.
- L343 and L356 are located at approximately R-U152. Listed
26 June 2012.
- Z258 and S492/Z384 are located at approximately R-Z367.
Listed 26 June 2012.
- Z276 is located at approximately R-Z34. Listed 26 June 2012.
- L737, L738, L739, Z383 and Z291 are located at
approximately R-L20/S144. Listed 26 June 2012
- Z245 is approximately equivalent to R-L21/M529/S145, L459. Listed 26 June 2012.
- L159.3/S169.3 is located downstream of R-L21/M529/S145, L459, and parallel to S219/Z255.
Listed 26 June 2012.
- S450/Z268 is approximately equivalent to Z209. Listed 8 July 2012.
- L643 and L743 are located at approximately R-L21. Listed
8 July 2012.
- L1231 is located at approximately R-DF27. Listed 8 July 2012.
- L1199 and L1200 are located at approximately R-DF19.
Listed 8 July 2012.
- L526, L564, L580, L583 and L679 are located at approximately R-DF13.
Listed 8 July 2012.
- L577, L908 and L909 are located at approximately
R-L513. Listed 8 July 2012.
- L557/S394 and L561 are located at approximately R-L555.
Listed 8 July 2012.
- S261/Z16 is approximate with Z18. Listed 18 July 2012.
- Z15 is approximate with L257. Listed 18 July 2012.
- S500/Z153, Z154 and Z155 are downstream of Z301. Listed
18 July 2012.
- L782 is downstream of Z156. Listed 18 July 2012.
- L292 is downstream of L45. Listed 18 July 2012.
- S269/Z328, S380/Z329, S505/Z330, Z327, Z331, Z332, Z333, Z334, Z335 and
Z336 are approximate with Z326. Listed 18 July 2012.
- S381/Z81, S506/Z82, Z80 and Z83 are downstream of
Z326. Listed 18 July 2012.
- S279/Z249 is located at approximately R-DF1. Listed 9 August 2012.
- S473/Z261 is located downstream of L21. Listed 9 August 2012.
- S471/Z252 is located at approximately L21. Listed 9 August 2012.
- S227/Z195 appears to be equivalent with S355/Z196. Z195 is not yet testable at FTDNA.
Listed 17 August 2012.
- S225/Z225 does not yet have a derived sample at FTDNA to check. Listed 17 August 2012.
- S359/Z229 is expected to be at the same node as S225/Z225. Both Z225 and Z229 were initially observed in
two Peruvian samples. Listed 17 August 2012.
- DF73 is located downstream of R-Z253 and Z2545, parallel to Z2185. Listed 1 December 2012.
- S302, S303, S421, and S422 are downtream from S190. Listed
13 September 2012.
- Z198 is potentially equivalent to L176.2/S179.2. M167/SRY2627, L165/S68, Z262 and
L147.3 are all derived below R-Z198 as well as L176.2/S179.2. Listed 13 September 2012.
- L147.3 is derived below R-Z198 as well as L176.2/S179.2, and parallel to R-Z262
and R-L165/68. Listed 13 September 2012.
- Z2184 is located at approximately Z2185 and is downstream of Z253 and upstream of L1066 and Z2183.
Listed 8 November 2012.
- Z2183 is located at approximately L1066 and is downstream of Z2184 and Z2185. Listed 8 November 2012.
- Z2534 is located downstream of R-Z253, and upstream of Z2185 and DF73. Listed 1 December 2012.
- L147.7 is located downstream of R-DF13. Listed 1 December 2012.
- L147.8 is located downstream of R-Z253. Listed 1 December 2012.
- Z275 is located at approximately R-U152. Listed 5 December 2012.
R2 SNPs under Investigation - Additional testing is needed to confirm adequate positive samples
and/or correct placement on the tree.
- L261, L288, L381, M367.2 and
M368.2 are located at approximately R2-M124. Listed 17 Mar 2011.
- L384 and L385 are located under R2-L294. Listed 17 Mar 2011.
- Page4 is located at approximately R2-M479. Listed 17 Mar 2011.
- L722 and L726 are located at approximately R2-M124.
Listed 18 July 2012.
NOTES:
- Identical SNPs that were discovered separately are listed in alphabetical order, not necessarily in
the order of discovery, and separated by "/". Examples: M207/UTY2, M306/S1, M173/P241, SRY1532.2/SRY10831.2,
L23/S141, L48/S162, L11/S127, P310/S129, P311/S128, M405/S21/U106, M467/S29/U198, DYS439/L1/S26, P312/S116,
M167/SRY2627, S28/U152, L2/S139, L20/S144, L21/S145, M222/USP9Y+3636.
- The position of L196 is undertain with respect to the position of Z49
- L405/L584 (ChrY:27141305) is a triallelic SNP with allele values "A", "C", and "T". A value of "A" indicates haplogroup Y(xP)
and is referred to as L405-. A value of "C" indicates haplogroup P and is referred to as L405+ and a value of "T" indicates
haplogroup R1b1a2a1c and is referred to as L584+.
- L342.2 is known to co-mutate with L319.4, L348.3 and
L349.2 in haplogroup R1a; all should be derived if any one of them is.
Listed 7 Aug 2011.
- Due to lack of positive control samples for M56, M157.1, M64.2, M87, M204, P98, PK5, and M434, the positions of those
private or uncommon SNPs in the haplotree are uncertain with respect to the positions of Z93, Z280, and L176.1/S179.1.
- P25 is an unreliable SNP with a 2% reversion rate within R1b1. It should not be used by
itself to classify individuals. For further details see Adams et al (2006) and
Discussion of P25
- L49 is a recurrent mutation in Haplogroup R and may be generally unstable in Haplogroup R. In haplogroup
R1b1a2a, L49.1 is phylogenetically equivalent to L23. In haplogroup R1a1a1, L49.2 is located under M417.
In haplogroup R2a, L49.3 is located at or near P267.
- L150 data from 23andME is either inconsistent/incorrect, or if correct, reflects multiple parallel/back
mutations. A single kit at FTDNA is M269+, L49+, L23+, L150-, L51-; all other known L23+ samples at FTDNA are
also L150+. It is also possible there is some kind of deletion or recombination effect that is causing issues
with the L150 results.
- SNP L277.1 may form a distinct clade at a peer level to L51, underneath L23 and L150. It was initially placed
on the haplogroup R tree at that location in January 2011. It was withdrawn from the tree in September 2011, due
to issues with testing the SNP. Genotyping results from 23andME include at least eight results that are L23+ L277+
L51-. Sequencing tests at FTDNA have been unable to replicate these results, and all tests at FTDNA have either
failed to yield a sequencing trace, or yielded a L277- result. This may be due to a null allele or deletion in
that region, or the 23andME results may be incorrect due to false hybridization on the X chromosome. In addition,
one sample that was found L277+ at 23andME was found to be L277- by FTDNA, further confusing the issue. The placement
of L277.1 will be re-evaluated once a consistent and reliable sequencing test is available for it.
- SNP SRY1532/SRY10831 appears twice on the Y-DNA Haplogroup tree. It is first seen as a mutation
SRY1532.1/SRY10831.1 which is reported as a positive in BT and then reappears as a back mutation
SRY1532.2/SRY10831.2 which is reported as a negative in R1a.
- Thomas Krahn has developed a new primer for DYS439-Null (aka L1, S26) that gives a score of 12 rather than null.
- Thanks to Jim Wilson and Thomas Krahn for their consultation on Haplogroup R.
- Data from the 1000 Genomes Project suggests that Z220 is downstream from Z209 and Z278 is downstream of Z216.
Listed 26 June 2012.
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