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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 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 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 - they show up as a STR cluster. Those who closely match the key off-modal 'Rox2' (the early nickname for the cluster) STR markers (listed below) and take SNP tests consistently find they are also positive for this subclade's SNPs.

Existing STR results indicated Rox2 was monophyletic clade but until 2014 (before NGS, or Next Generation Sequencing testing) 'Rox2' remained a R1b-
DF27**
 yDNA subclade, ie. negative for all then known SNPs below DF27. Those negative (ancestral) SNPs included Z196 (BritainsDNA's S355), Z195, Z215 (S357), Z225 (S225), Z229 (S359), L1245 (S1264), L1246 (S1285), (S400), L617, L194, L1231, DF79, DF81, DF83, DF84, L221, L86, L881. Scot, Angus Horatio Stewart, kit 142928, was the first match to test positive (derived) for DF27 back in May 2012Chip-based testing from FTDNA's Geno 2.0 and BritainsDNA's Chromo2 identify no relevant SNPs below DF27. Geno 2.0 does not even read P312 or DF27 itself. After more advanced NGS testing in 2014, we know there are two ancient branches just below DF27, Z195/Z196 and ZZ12. Rox2 belongs to the early DF27>ZZ12 branching subclade, ZZ19/ZZ20. Below that is Z34609 and then Z2571.

ROX2 SNPS

Extensive NGS testing is available from Full Genomes Corporation (FGC)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, where they can be read and compared in that test. 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 Big Y appears to read under half of the 45-ish Rox2 relevant SNPs present in the two FGC tests. Since 2014 there have been several Rox2 BigY tests. Depth of coverage and SNP reliability can vary from one company's test to another.

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 yet. Outside the shared block there are a smaller number of reliable SNPs for each surname leading to the present day (roughly one dozen in BigY). These 'family' SNPs are unique to each respective lineage that has taken a NGS test so far. As a very rough guide, BigY might on average identify one SNP every 70-170 years. SNPs are random and are not as regular as clockwork.

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 few, if any, unique family SNPs in evidence in each separate line of descent from that man in BigY. 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 (ones that are readable by BigY) could have occurred since that man was born. The STR haplotypes would have a higher GD too. SNPs are mutations that occasionally and randomly happen when the yDNA is replicated and a new generation is born. The less time between a common ancestor and the living descendants, the fewer family mutations/SNPs one would expect to see.

Recently (June 2015), according to Alex Williamson's Big Tree, the SNP FGC11414 is shown as a branch point just below Rox2's phylogenetically equivalent block. FGC11414 was not present in the BigY variant (.vcf) file of kit 342681 McCauley but analysis of the BAM file, confirmed by Stephen Parrish (link), indicates 342681 is negative for FGC11414. Kits N3036, 134765, 92933 and 330933 are shown downstream of FGC11414. 1000 Genomes kit HG00107 is said to be negative for FGC11414, like 342681 and 66501. Contrastingly, the YFull analysis of the Rox2 matches on their tree shows BigY kit 330933 (YF02413 SWE [SE-AC] ), 1000 Genomes kit HG00107 and BigY kit 342681 (YF03569) to be at the same level at the moment with no separate branch for 330933/YF02413, Sweden, who is FGC11414+.

In 2014, through analysis of FGC and BigY tests, Jim identified single 'one off' SNP tests to help confirm a match. These SNPs are offered for testing at Thomas and Astrid Krahn's company, YSEQ. The SNPs Z2571 and FGC11397 are also available for testing at FTDNA under 'Advanced Tests' (click 'Upgrade' then 'Advanced Tests' then choose 'SNP' and type the name in the 'Marker' box).


I (Corner, kit N3461, North Yorkshire) got a FGC11397+ result, it being one of the phylogenetically equivalent SNPs below Z2571 not read by BigY, from YSEQ in June 2014, as have several other STR matches who have since tested single SNPs with either YSEQ or FTDNA. Northern Swedish BigY and 111 STR Rox2 match, Persson FTDNA kit 330933/YFull ID 

YF02413

 was added to the YFull tree - to join HG00107 from Orkney under Z2571 - in December 2014. McCauley (BigY, 111 STRs), FTDNA kit 342681/YFull ID YF03569, Northern Ireland, was added in May 2015.


Z2571 (23076115, C>G) A deep DF27 SNP. (Available to order at YSEQ.net and FTDNA).  ISOGG: R1b1a2a1a2a6.


FGC11397 (7332619, G>A) A currently phylogenetically equivalent SNP, one of dozens below Z2571 that define the subclade. It is not read by the BigY test but is seen to be positive when tested separately by a BigY tester and those ordering individual SNP tests. (Available to test at YSEQ.net and FTDNA)

FGC11395 (14861066,  C>A) Another of the many equivalents that currently define the cluster. FGC11395 is also covered by FTDNA's BigY test. (Available to test at YSEQ.net). YFull name: Y8842.



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. YFull use Y8397 (FGC name FGC11374) as Rox2's lead SNP in their treeYFull 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 phylogenetically equivalent to the SNP originally chosen to represent the subclade, FGC11397, at the moment. It is available to test at FTDNA under 'Advanced Orders', or at YSEQ.


FTDNA DF27 PROJECT & Z2571

The FTDNA R1b-DF27 and Subclades Project has sections for Rox2 matches (on page 2 of results). Join that project if you are a Rox2 match. 

Group F8a1. contains Rox2 STR matches who have SNP tested for one of the equivalent defining SNPs. Five Rox2 STR matches are in group Uf. They are kits  241356, 122148, 115452, 202611 and 300626. Yet more Rox2 STR matches (including 328073, 228365 (DF27+), 187534 (DF27+), U2408 (DF27+), 244412, 440, 367358 (DF27+), 279300, N3285 and 382774) are distributed around the DF27 Project under four different group sections. These clear high-resolution off-modal STR pattern matches are likely to be Z2571>FGC11397 etc. and could be grouped together too.

Do get in touch here if you are unsure whether you match the Rox2 cluster. 

Group F8a. has a Z2571 result, Mugford, kit 159450, England. He is DF84-. Kit 159450, does not look to have tested for CTS11567/Z2572 yet. This SNP might be worth investigating for kit 159450 because it has been found that some Z2571>CTS11567 kits are negative for DF84. Therefore DF84 is not equivalent to CTS11567DF84 is a subclade below, or downstream of, CTS11567, contrary to what some trees currently suggest. CTS11567 

can be ordered as a single SNP at FTDNA.


Group F8b. contains Z2571>CTS11567* results. CTS11567 (also known as Z2572) is an ancient parallel 'brother' subclade to Rox2, below Z2571. Carrier, kit 46496, France, and Norwood, kit 85133, England are positive for CTS11567/Z2572. Both are negative for DF84.

An anonymized spreadsheet containing 2000 Chromo2 results was released by BritainsDNA in 2014. 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), under Z2568 on the YFull tree

could have origins in Spain and 

are said to share DF84, Z2568, Z2569, Z2570, and Z2572/CTS11567.

 At the FTDNA DF27 project, kit N119082, Haedo, with origins in Biscay in the north of Spain is CTS11567+ and has recently (June 2015) tested DF84+. 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. Future NGS testing by CTS11567+ individuals 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 missed by all previously available chip-based tests.


RESEARCH

Z2571 and FGC11397 are available for testing at FTDNA and YSEQ.net. To further research and understanding there are certain things one can do. 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. Communicate with matches and share information. Upload STR results to YSearch.org. Make sure you join your FTDNA surname project and the DF27 and Subclades Project. It's important for matches outside a surname project to also be able to view and compare results but default privacy settings for new FTDNA kits mean STR results are invisible to others. Matches within a subclade like Rox2 span a number of surname projects with origins in different countries and those relations will not find you. 'Privacy Settings' can be changed from the FTDNA dashboard by clicking your name at the top right. Next to 'My DNA Results' and 'Who can view my DNA results in group projects?' click  'Anyone'. Not much can be learned by viewing one's own results in isolation, they need to be compared. Likewise, in order to get the maximum information out of BigY or FGC tests it is necessary to compare with other results on phylogenetic trees, like YFull's or the Big Tree (mentioned above). To share 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 a 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.

LATEST NEWS

FTDNA launched a 'backbone' test, the 'R1b-M343 SNP Pack' in late July 2015. It is a $99 test aimed at identifying 'top layer' SNPs for R1b people who have not taken a SNP test yet. Anyone who matches Rox2 or knows they are DF27+ should not order this test. The initial M343 test release (SNP list) does not include DF27, or many of the other DF27>ZZ12 subclades, including Z2571. In comparison with the other subclades, the coverage for DF27>ZZ12 is patchy. Many DF27>ZZ12 will only get a P312* result because DF27 itself was not included. Only four deep ZZ12 SNPs and six downstream ones are in the test. However, if you match the Rox2 off-modal key STR markers over 67 or 111 markers (see below), there is a very good chance you will be FGC11397+ and will only need to order that less expensive test to confirm a match.

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. (

link) (link2)


DISTRIBUTION

Going by high 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 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 many Rox2 matches are descendants of people who emigrated from the British Isles and Ireland to North America and now live there. Emigration patterns were not the same across the whole of Europe and parts of rural eastern England, Wales and especially Continental Europe are less well represented.


FOUNDER


A subclade founder seems to have been active towards the end of the Early Middle Ages. Of course, the Rox2 yDNA lineage existed before then but the similarity of many high resolution modern-day Rox2 haplotypes suggests someone in the line produced a large number of descendants at that time. Time to most recent common ancestor (TMRCA) estimates agree that founder might have lived about 1250 years ago +/- a margin of error. See (here) for how this estimate was arrived at. Possibly due to social selection, several sons of the Rox2 founder appear to have survived into adulthood in early medieval society. Some of those sons may have been 'chips of the old block' and likewise distributed their ancestral yDNA widely by having several sons themselves.


Results from NGS testing at last identified the previously 'missing' SNP block of SNPs shared by all STR cluster matches so far. This lengthy list of shared equivalent SNPs, over three quarters of the total, 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. A founder might have moved from one area to another followed by a founding event in the new location. 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 origins in the distant past. 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.


The broad distribution of different locally specific surnames and the subclade's relatively young age might suggest Rox2 expanded quickly over a wide area
(a rapid demographic expansion after a 'founder effect'). The haplotypes are all similar and trace back to one 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 number of Swedish Rox2 matches are natives of their country and also trace back to the beginning of parish records there, in the sixteenth century in and around Bureå, Skellefteå and Northern Sweden.

No early branching subclades have turned up yet between ancient Z2571 and the Rox2 subclade founder. Maybe most of the ancient branches have since died out, or maybe they are yet to be found in a less well tested place. Central and Eastern Europe, Western Asia and Scandinavia are not well covered by NGS yDNA testing. Such NGS testing is the only sure means of accurately identifying DF27>ZZ12 subclades and increased use of NGS tests in places Americans (north and south) didn't emigrate from might reveal earlier relations in the future. 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 over the last few years. DF27 and Z2571 were also omitted from their latest R1b-M343 SNP Pack.


STR IDENTIFICATION


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). There are unrelated matches at 37 markers or less, SNP tests are needed at such low-resolution. High resolution Rox2 off-modal STR matches have been consistently receiving the same SNP results as each other. It is not unusual for someone to differ on one of the five Rox2 ancestral 'signature' alleles in the 67 marker resolution test.


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.


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.



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 easy to remember.

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).



KEY ROX2 OFF-MODAL MARKERS OVER 67 MARKERS:    DYS391=10 (P312 modal=11)    DYS389ii=30 (29)    DYS449=30 (29)    DYS607=14 (15)    DYS534=14 (15). The 68-111 marker section in the FTDNA test holds important key off-modal STRs for Rox2, including: 540=13 (12), 717=20 (19), 589=11 (12), 636=11 (12), 532=14 (13), 504=16 (17).

An early key defining STR marker was found to be DYS717=20It 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. August 2015.