Rox2 SNPs: R1b-P312>DF27>ZZ12>ZZ19>Z34609>Z2571>(FGC11397 and a few dozen phylogenetic equivalents). YFull name: R-Y8397
A yDNA cluster is essentially a group of present-day people sharing similar Y-STR results - this indicates possible descent from the same earlier male common ancestor. SNP testing can confirm a STR cluster match to be a member of a SNP defined subclade (a related group). The Y chromosome is passed down virtually unchanged to all subsequent male descendants of a common ancestor from father to son, although small random differences accumulate over time. This is due to mutations/mistakes on the Y chromosome that occasionally occur when it is replicated. Those mutations form distinct patterns within the general population and can be used to identify clusters and also estimate age. The more recent and prolific the common ancestor, the more similar and numerous the haplotypes are in today's population. Those who closely match the key off-modal 'Rox2' (the early nickname for the cluster) 'signature' markers over 111 markers and take SNP tests consistently find they are also positive for FGC11397, FGC11369 or any other equivalent Rox2 defining SNPs when they test for them. The subclade formed centuries before the fixing of surnames, so there are many different surnames represented in the subclade today.
STR results extant between 2005 and 2012 indicated Rox2 was monophyletic clade but the deep R1b-P312 subclade it descended from (DF27) was unknown at that time. Scot, Angus Horatio Stewart, kit 142928, was the first STR cluster match to test positive (derived) for DF27 when that SNP was identified and became available to test in May 2012. From 2012 until March 2014 'Rox2' remained a R1b-DF27** yDNA subclade, ie. negative for all then known SNPs below DF27. Chip-based testing from FTDNA's Geno 2.0 and BritainsDNA's Chromo2 identified no relevant SNPs below DF27. A very large section of DF27>ZZ12, not just Rox2, remained unidentified after taking those chip-based tests. Geno 2.0 does not read P312 or DF27. Individual NGS (Next Generation Sequencing) testing by Rox2 kits N3036 and 134765 in April 2014 finally revealed the SNP trail back to DF27>ZZ12, confirming what STR testing had long suggested.
DF27 is one of the largest and most widespread R1b-P312 subclades but is one of the most difficult to identify, partly due to where DF27 is located on the Y chromosome. The technology used in chip-based SNP tests can't identify it. However, NGS testing does highlight the downstream SNPs. After more extensive post-2014 DF27 NGS testing and analysis done on it by Alex Williamson, it is now know there are two ancient groups just below DF27, ZZ12 and a subclade that has been known for several years, Z195. Rox2 is DF27>ZZ12+. Its ancestral branch below ZZ12 is ZZ19/ZZ20. Below that is Z34609. The Big Tree shows two kits who are positive for this ancient subclade but negative for the currently known SNP below it, Z2571. Those kits are N123269 from Spain and E8202 from Czech Republic. At the FTDNA project there is also another Z34609* kit from Italy, kit 10801. These ancient 'top layer' subclades were in existence at least 4500 years ago according to YFull's age estimates. Known 'son' of Z34609, Z2571, has two further subclades downstream of it, they are Rox2/FGC11397 and CTS11567. I (kit N3461) got a FGC11397+ result from YSEQ in June 2014, as have several other STR matches who have since tested single SNPs with either YSEQ or FTDNA.
Z2571 (23076115, C>G) A deep DF27 SNP. ISOGG: R1b1a2a1a2a6.
FGC11397 (7332619, G>A) A currently phylogenetically equivalent SNP, one of a block of dozens of SNPs below Z2571 that define the subclade. (Available to test at YSEQ.net and FTDNA)
The best yDNA testing approach for a Rox2 match is a combination of 111 STRs and a NGS SNP test. The subclade's key SNPs can also be tested for one at a time or in specific DF27 SNP 'packs'. FTDNA 'backbone' R1b-M343 and R-P312 SNP packs released in 2015 do not have Rox2 SNPs. A Rox2 match will only get a DF27+ result from the R1b-M343 pack and a ZZ12+ result from the R-P312 pack. The Rox2 off-modal STR 'signature' pattern of 11 key markers is reliable for identifying a Rox2 match over 111 markers. A single FGC11397 (or equivalent) test can provide SNP confirmation of a match to Rox2 if needed.
Turner (FTDNA kit N3036, FGC kit number GYBGZ) received FGC results on 3rd April 2014 (link). Many SNPs were seen to be shared with an anonymous kit in the 1000 Genomes project, HG00107. HG00107 has Orkney ancestry and matches the Rox2 off-modal STR pattern. Dickinson (FTDNA kit 134765, FGC kit WBAFF, Cumbria) received FGC results on 12th April 2014 He and Turner share dozens of SNPs in a 'phylogenetically equivalent' block below DF27>Z2571. FTDNA's BigY appears to read under half of the 45-ish Rox2 relevant SNPs present in the two FGC tests.
The phylogenetically equivalent SNP block, shared by all subclade matches, might be imagined as a chain of descent with dozens of SNP 'links' in that chain below Z2571. However, we don't know the (chronological) order of the links. Underneath the shared block there are a smaller number of reliable SNPs for each surname leading to the present day (roughly one dozen 'definite' SNPs in BigY - ie. SNPs that are not insertions/deletions or other more complex mutations). There is wide variation in the numbers of SNPs different individual lineages accumulate during the same passage of time, SNPs are random and are not as regular as clockwork. However, the numbers average out across several kits. As a very rough guide, BigY might on average identify one definite SNP (not an insertion/deletion etc.) approximately every 100 years (3-4 generations) for a Rox2 kit.
If, for example, a subclade was descended from several sons of a recent common ancestor (say, a man born in 1750 AD), then there might be very few unique definite family SNPs in evidence in each separate line of descent from that man. Also, the genetic distance (GD) between the cluster's STR haplotypes would be very low. If, however, the common ancestor was born in 1350 AD, then around half a dozen reliable SNPs could have occurred since that man was born. The STR haplotypes would usually have a higher GD too.
Looking at the Big Tree, FGC11414 is a branch point just below Rox2's block of phylogenetically equivalent SNPs, as is 'brother' subclade, Y17487.
Three kits below 'lead' SNP Y17487 (YFull use equivalent Y17484 as lead SNP), 342681, 421619 and N18197, have the same surname variation (McAuley) and BigY results indicate they share five SNPs after the Rox2 founder's time. That shared SNP block of five SNPs indicates that the kits have common ancestry - possibly for a period of several hundred years after the Rox2 founder's time. Then, the families branch from that point.
FGC11414 appears to have three branches below, or 'downstream' of it. One branch, FGC11407 (plus equivalents 7031104 C>T and FGC11419) has the two FGC tested kits, N3036 and 134765. FGC has better coverage than BigY. A second branch below FGC11414, 28519438 C>T, contains BigY kits 223803 and 273347. The third branch, FGC11414*, has kits 92933 and 330933 (the asterisk indicates no further branching known below FGC11414).
The remaining Rox2* branch containing kits HG00107, 66501, B24208 and 271969 shows no subsequent branching yet below Rox2's main phylogenetically equivalent block of SNPs. This Rox2* group have a good chance of finding their own individual branches when more of the many existing Rox2 matches get NGS results in the future.
Based on current data, it appears Rox2 has no ancient relatives - as if it arrived 'out of the blue'. There is a singular shared block of dozens of phylogenetically equivalent SNPs below 'first layer' subclade, Z2571. The Rox2 NGS results look like the teeth of a comb hanging below that large phylogenetically equivalent block. The shared block appears to exhibit no branching in the first few thousand years of its existence - so far. Further branching might become evident with more extensive and wide-reaching testing.
(click image to enlarge)
DIFFERENT 'LEAD' SNPs & SNP NAMES = SAME THING (ROX2)
A 'lead' SNP is a SNP used at the start of the phylogenetically equivalent block to represent the subclade. It is not the first, last or 'terminal' SNP, it's just one someone chose out of the few dozen equivalents to be at the start of their list. Unfortunately many different names for the same SNPs have arisen since 2014 and different equivalent SNPs also get chosen as lead SNPs by different individuals. YFull use Y8397 (FGC name FGC11374) as Rox2's lead SNP in their tree. YFull have also given their YFS names to some of the other phylogenetically equivalent Rox2 SNPs already named by FGC, eg. FGC11395 is known as Y8842. Alex Williamson has FGC11388 (YFull's Y8837) as the lead phylogenetically equivalent SNP in his Big Tree. YSEQ lead with FGC11369 (YFull's Y8407) in their DF27 Panel test. The above SNPs are getting picked as lead SNPs from the shared SNP block below Z2571 and all are currently phylogenetically equivalent to the SNP originally chosen by members of the subclade to represent their subclade, FGC11397. FGC11397 is available to test individually at YSEQ.net.
The kits on the Big Tree and YFull's tree are those who have taken expensive NGS tests and submitted results for analysis. They represent only a very small proportion of the large number of Rox2 matches distributed across several FTDNA projects. Many more STR matches at various levels of resolution exist in the databases but they have no SNP results, NGS or otherwise. Comprehensive NGS tests, like FGC or BigY, taken in conjunction with 111 STRs, are the ultimate hi-res DNA genealogy combo at the moment. Those using this combination of tests are taken as near to their 'terminal' Rox2 SNPs as is currently possible. As more matches with NGS tests share their results and appear on the phylogenetic trees like the Big Tree, more SNP defined branching under Rox2 will be revealed.
SNP 'PACK' TESTS
Rox2 and CTS11567's 'top layer' DF27 SNPs Z34609 and Z2571 were omitted from FTDNA's P312 Pack test and the M343 'Backbone' Pack test, released towards the end of 2015. Z2571, FGC11397/FGC11369 etc. were discovered and reported here and on DNA fora/message boards in April 2014. Many of the important early ZZ12 SNPs only appear on a separate DF27 Pack. It wasn't initially even considered necessary to include DF27 itself in the M343 Backbone Pack test. Had DF27 not been included, those 'backbone' packs would now be producing uninformative P312* results for Rox2 and many other DF27>ZZ12 (Z195-) subclades. A DF27* result from the M343 backbone test (DF27+ and negative for all else on the test) or a ZZ12* result (ZZ12+ and negative for all else) from the P312 Pack requires the testee to order FTDNA's 'R1b-DF27 Top-Layer and Misc Subclades SNP Pack' test. YSEQ was the first company to release a DF27 Panel test in September 2015. That test also includes Rox2's important early SNPs.
New SNPs only make it onto SNP pack tests if they've been noticed and added. Several ZZ12 subclades weren't, or are only just being discovered more recently. There is no guarantee that one's SNPs will be on an existing pack or panel test. NGS tests, like Y Elite by FullGenomes (FGC) or FTDNA's BigY, highlight your own particular family SNPs. Some of those may or may not be currently shared by others. NGS results have an advantage over SNP pack testing in that they have the potential to eventually form new branches, or fill out existing ones, when shared on phylogenetic trees, like the Big Tree. It is their presence on these trees that might eventually lead to them being represented on future 'pack' tests.
FTDNA DF27 PROJECT & Z2571
The FTDNA R1b-DF27 and Subclades Project has two sections for Rox2 matches, F8. and Uf..
Results from the new FTDNA DF27 pack and the R1b-M343 SNP 'backbone' pack are appearing. Some SNP results might be 'in progress'.
Group F8. contains Z34609+ results. Z34609 is an ancient SNP that is immediately upstream of Z2571.
Group F8a1. contains Rox2 STR matches who have taken NGS tests or SNP tested for one of the equivalent defining SNPs, like FGC11397 or FGC11369. Group Uf. contains some of the many off-modal STR matches (inc. 5 with 111 markers) who have not taken NGS tests or FGC11397 etc. as confirmation yet. Kit 10479 recently (March 2016) received DF27 Pack results and is Z34609>Z2571* (positive for Z2571 and negative for CTS11567 and FGC11369/FGC11397 Rox2 SNPs) and has been temporarily placed in group F8a1. by the project admin. This is a very interesting result because it suggests the possible existence of a new as yet unidentified ancient 'brother' clade of Rox2 and CTS11567, or perhaps an earlier branch in Rox2's long list of phylogenetically equivalent SNPs. Further NGS testing and interpretation on a phylogenetic tree should highlight the details. Kit 10479 is not a group F8a1. Rox2 STR or SNP match and belongs in a new Z2571* category under group F8.
Do get in touch here if you are unsure whether you match the Rox2 cluster.
Group F8b. contains DF27>Z2571>CTS11567 results. CTS11567 (also known as Z2572) is an ancient parallel 'brother' subclade to Rox2, below Z2571.
Carrier 46496, France, Mugford 159450, England and Norwood 85133, England are positive for CTS11567/Z2572 but are negative for DF84. Unfortunately, the 2015 'backbone' R1b-M343 SNP pack omitted DF84 (as well as Z2571 and FGC11397 etc.). It has been found that some Z2571>CTS11567 kits are negative for DF84. Therefore DF84 is not equivalent to CTS11567 and is a subclade below, or downstream of, CTS11567 (and equivalents), contrary to what some trees suggest. Recently (Feb 2016) the addition of a new sample, ERS257013, with ancestry in the south of Sardinia, to the YFull tree helped form a new branch (Z2569, containing the two South American 1000 Genomes kits) below Z2568, under DF84. This Sardinian kit comes from the Francalacci et al 2013 study of almost 2000 men with roots in Sardinia, in the Mediterranean. It seems to indicate DF84 is a very early SNP with two branches (Z2568* and Z2569) springing from it so far.
An anonymized spreadsheet containing 2000 Chromo2 results was released by BritainsDNA in 2014. I found two kits (1525 and 1903) were CTS11567+ and DF84- but one (1525) was CTS11567+ and S25893+. Therefore, S25893 possibly indicates another subclade below CTS11567/Z2572, parallel with DF84. S25893's position is 23843638 (G>C).
Anonymous 1000 Genomes kits NA19762 (Mexico) and HG01577 (Peru), who now form the new branch, Z2569, on the YFull tree,
with likely origins in Iberia, are said to share currently phylogenetic equivalent SNPs, DF84, Z2568, Z2570, and Z2572/CTS11567.
At the FTDNA DF27 project, kit N119082, Haedo, with origins in Biscay in the north of Spain is CTS11567+ and tested DF84+ in June 2015. This is the first DF84+ result I have heard of outside the 1000 Genomes data. N128161, Gelpi, from Catalunya, Spain is CTS11567+ but does not look to have tested for DF84. Neither kit has STR results but their Geno 2.0 results are listed in the DF27 project's SNP section. DF84 is not in the Geno 2.0 test but it can be ordered separately. As mentioned, above, there are kits that are CTS11567+ and DF84-, so these two SNPs are not equivalent. More NGS coverage is needed. Future NGS testing by CTS11567+ individuals and inclusion on phylogenetic trees, like YFull and the Big Tree, should further clarify subclade branching in this area of Z2571.
I made a draft SNP tree in order to visualize Z2571 in relation to other subclades of DF27.
NGS testing is beginning to uncover many interesting new subclades below DF27 that were omitted/undetected by all previously available (pre-2016) chip-based tests, like 'backbone' packs, Geno 2.0 and Chromo2.
In order to get maximum information out of BigY or FGC tests it is important to compare with other results on phylogenetic trees, like the Big Tree. To share NGS results there is a BigY files section and a FGC files section at the DF27 Yahoo Group where, after joining, you can upload zipped raw data (the .zip file which includes both the .vcf file and the .bed file) from BigY or FGC tests. Alex Williamson maintains The Big Tree here using files that are uploaded to the DF27 Yahoo Group or are sent to him via the address on the website. YFull will analyze NGS test results for you and add them to their tree for $49. Full Genomes (FGC) will analyze BAM files for $50.
Join the FTDNA DF27 and Subclades Project. It's good for matches outside a surname project to also be able to view and compare results but default privacy settings for new FTDNA kits mean new STR results (since March 2015) are invisible unless the privacy settings are changed manually by the user. Matches within a subclade like Rox2 span a number of surname projects with origins in different countries. If you test positive for Z2571, FGC11397 etc. let one of the DF27 project admins know in order for them to move you to the correct group. Ask any questions at the Yahoo DF27 group, the FTDNA forum or the FTDNA DF27 project Activity Feed. Upload STR results to YSearch.org. Check these pages regularly, they're updated often. Further understanding/progress will be made with engagement in higher resolution STR and NGS testing by the many Rox2 matches who have only 67 STRs, or less, and no SNP tests. Results need to be compared to those of others. Future ancient yDNA studies could also provide vital clues to the subclade's origins.
20th April, 2016. After an inquiry, FTDNA have fixed issues on their haplotree with regard to Rox2's 'top layer' phylogeny below DF27.
Interestingly, in that it concerns P312 (the ancient R1b subclade Rox2 is positive for), a Bell Beaker/Corded Ware burial (I0806 from Quedlinburg, Germany) was recently found to be P312+ and dated to 2296-2206 calBCE. Unfortunately they were unable to get a read for any downstream subclades. Hopefully wider testing on his yDNA will be done. His grave contained mixed cultural features, including a Corded Ware shaft-hole axe and a perfect bell beaker. (
Going by higher resolution Rox2 STR and SNP matches the subclade has a Northern European distribution and is found in England, Scotland, Northern Ireland, the Republic of Ireland, Isle of Man, Orkney, Sweden and Northern France (Normandy). The locations of most earliest known ancestors' places of birth, when known, can be approximately split into thirds; Scotland (mainly central/south west/Borders), England (mainly north and east), and Ireland (mainly the north). Recently, more matches are turning up in Southern England and Sweden. The proportion of tests of Ireland/British Isles origin is high in public hobbyist yDNA databases and this affects attempts to accurately map a subclade's geographical frequency and distribution using those databases. The majority of present-day yDNA testers are based in America and most hobbyist DNA results are from descendants of people who emigrated from the British Isles and Ireland to North America and now live there. Similarly, South America has a high proportion of people of Iberian origin. Emigration patterns to the Americas were not the same across the whole of Europe and parts of rural eastern England, Wales and especially Continental Europe are lightly represented in the hobbyist databases in comparison with Ireland and Scotland. Only a very small number of British Isles/Ireland Rox2 matches were born there. I am English and the Sweden Rox2 cluster are Swedish nationals.
A subclade founder appears to have been active in the Early Middle Ages. Of course, the Rox2 yDNA lineage existed before then (seen in the shared block of dozens of equivalent SNPs) but the similarity of many high resolution Rox2 haplotypes and branching SNPs downstream of the shared block suggest someone in the line produced a large number of descendants at that time. Time to most recent common ancestor (TMRCA) estimates suggest the founder might have lived about 1250 years ago +/- a margin of error. See (here) for how this estimate was arrived at. Possibly due to some advantage (social selection), offspring of the Rox2 founder appear to have flourished in Early Medieval society. Rox2 looks to be an Early Medieval Period founding event by a member of a small (one man) DF27>Z2571 subclade that is relatively incongruous in the British Isles.
In 2014 results from NGS testing at last identified the previously missing/unidentified block of SNPs shared by all STR cluster matches so far. This lengthy list of shared equivalent SNPs, over three quarters of the total, possibly suggests the subclade experienced a prolonged 'genetic bottleneck'. Bottlenecks can happen with a reduction in the population and/or a long period of no growth (small family), followed by a founding event and demographic expansion after near extinction. A founder might have moved from one area to another, precipitating a founding event in the new location. It is possible that distant (ancient) subclade cousins, from a time before the more recent founder, have not been picked up yet in the mainly Western European hobbyist databases. This apparent rarity/incongruity contrasts with subclades downstream of western British Isles and Ireland-heavy L21>DF13, who do know many of their anciently related 'cousin' branches. Such L21>DF13 lineages were clearly present in Bronze Age Britain and Ireland, this being confirmed through ancient yDNA testing. This is not the case for Rox2's earliest SNPs.
There are well over one hundred different surnames at 67 STR marker resolution and above represented in the cluster. Generally surnames are thought to have only become fixed and hereditary by around the fifteenth century, long after the days of the Rox2 subclade founder, although a few surnames might be fixed earlier or later. Rox2 subclade matching families usually have a name-type that is locally familiar in the region they lived (in rural England, Ireland, Scotland, Isle of Man or Sweden). Many surnames in Northern Ireland appear to have earlier Scottish roots. Surnames are not usually a reliable way of tracing back over 1000 years but can give background to the general geographical locations and origins of earliest recorded ancestors (in parish records, mostly beginning in around the sixteenth century). The Industrial Revolution of the late eighteenth century saw populations become more mobile, resulting in movement around the British Isles. Modern hobbyist DNA databases represent where some of a subclade's descendants were in relatively recent times. Modern subclade distributions can be quite different from their earliest origin. Archaeologists are now beginning to study ancient DNA and this might lead to a better understanding of where certain subclades were thousands of years ago, although no ancient DF27 has been identified anywhere yet.
The broad distribution of different, usually locally specific surnames, and the subclade's relatively young age might suggest Rox2 expanded quickly over a wide area (a rapid demographic expansion after one or more founding events). The haplotypes of all Rox2 matches are very similar and trace back to one narrow point in time. I am from an old rural North Riding of Yorkshire family that traces back to the beginning of parish records (sixteenth century) in Danby, North Yorkshire. A variation of our surname has a presence in the same general locality in earlier records, possibly as far back as the thirteenth century. Similarly, the increasing numbers of Swedish Rox2 matches are natives of their country and some also trace back to the beginning of parish records there, in the sixteenth century, in and around Bureå, Skellefteå and Northern Sweden.
No early branches have turned up yet between ancient Z2571 and the Rox2 subclade founder. As mentioned, perhaps most of the ancient branches went extinct, or maybe they are yet to be found in a less well tested place. It is possible, with more NGS testing over the next few years, that early branches could be found. Central and Eastern Europe, Western Asia and Scandinavia are not well covered by NGS yDNA testing yet. There has been poor understanding of Z195-/Z196- (ZZ12+) subclades due to the inability of chip-based SNP testing technology used for 'top-layer' tests like FTDNA's Geno 2.0 to 'see' DF27. Z2571 and other deep DF27>ZZ12 subclades were omitted from FTDNA's latest 'catch all' R1b-M343 and P312 SNP Packs. No accurate and comprehensive Europe-wide mapping of all DF27 has been done yet and no ancient DF27 yDNA has been identified. It is vital that future ancient yDNA studies use NGS technology, otherwise much of DF27 could be missed by such studies if they only use chip-based testing.
Many more potential matches exist at 37 marker resolution but their relationship to Rox2 is impossible to confirm at such low resolution with no SNP tests.
All results used in the TMRCA estimates are a minimum resolution of 111 STR markers. A match is based on a framework of eleven important R1b-P312 off-modal markers across 111 markers and not just on low genetic distance between the haplotypes. The key off-modal pattern is crucial in the identification of a Rox2 match because matches can occasionally happen between unrelated R1b haplotypes simply through coincidence (convergence). It is not unusual for a haplotype to occasionally differ on a few of the Rox2 ancestral key off-modal signature markers.
Unrelated subclades of R1b-P312 can match STRs through pure chance at only 37 marker resolution. For example, the L21>DF13>L1335>L1065 'Scots Modal' has similar key off-modal markers. Even with 67 markers, further DF27 SNP tests and/or an upgrade to the full 111 FTDNA markers are useful to confirm a Rox2 match beyond all doubt. In fact, an upgrade from 67 to 111 markers is recommended for Rox2 matches.
The Rox2 modal/base haplotype has 6 out of 67 off-modal differences from the average for all R1b-P312. Rox2 has 16 differences over 111 markers from the R1b-P312 modal. It is a genetic distance (GD) of 9/93 from Ysearch ID: XQJ7H (R1b-P312 (S116) and all Subclades Modal).
As the bar chart here illustrates, plotting Rox2 matches' genetic distances from the modal/base haplotype produced a clear bell curve. This indicates the off-modal STR markers work well in identifying common descent from a founder, even without the SNP confirmation we have now. Rox2 was always a monophyletic clade.
The cluster was named 'Rox2' around ten years ago by Jim Turner, who created the YSearch ID: 3QNM8. I first tested in 2005. The term has stuck after early discussions. It was, and is, a useful shorthand way to describe a subclade currently known by several different equivalent lead SNPs. Some of those SNPs are now gaining multiple names. Rox2 is easier to remember.
An early key defining STR marker was found to be DYS717=20. It is included in the 111 marker upgrade. Some who matched Rox2 at 67 markers have ordered this individual marker from FTDNA under 'Advanced Orders'. DYS717 is strongly off-modal in Rox2 and is considered a stable, slow mutating marker. For reference, R1b modal is DYS717=19, L21+ 'Scots Modal' is 717=21. Results matching the above extra key markers (and the 67 marker ones) make identification of a Rox2 haplotype quite unambiguous.
Less uniform key off-modal markers in the 68-111 panels: DYS712 <=20 (21), DYS714 >=26 (25).
C. Corner. April 2016.