R1b-CTS4466 Plus- Background

Administrators

Background

CTS4466 is the SNP that defines the Irish Type II subclade, which was identified by the respected physicist and nonpareil citizen scientist Dr. Ken Nordtvedt in 2006.  It was recognized by its distinctive haplotype prior to the discovery of any SNPs associated with it. In 2011, multiple attempts to find a defining SNP through the Walk Through The Y test offered by Family Tree failed, but at the end of 2012, the more comprehensive Geno 2.0 test through National Geographic finally gave us success with two SNPs – CTS4466 and CTS5714.  Then the 1000 Genome project added two more – CTS3974 and CTS8358. Since then, an increasing number of other SNPs have been discovered through the other extensive SNP tests mentioned at the bottom of the page, particularly the BIG Y test.

 

Objectives
 
The R1b-CTS4466 Plus project will research the parameters of this major subclade which features strongly in the south of Ireland, but it is found as well in other areas of the Isles, including some in the west of Ireland, Wales, western England, an apparent branch in Northern Ireland and Scotland and a few continentals.  We hope to discover the ancient history of this subclade - where it may have originated, how old it might be, which groups within it share more recent ancestry and how different branches may have developed and migrated from the time of the common ancestor.


 
Membership Criteria

To meet the objectives of the project, we seek to limit membership to those who have tested positive for at least one of the SNPs defining Irish Type II or have a haplotype consistent with that identified through research in the Family Tree DNA database.
 
Interested parties are invited to join, even if not SNP tested, with the understanding that the Project Administrators will review the participant’s haplotype and, at their discretion, determine if there is a likelihood of it proving positive for the defining SNPs. If accepted, we expect that the participants will be willing to test for further SNPs as suggested, based on the discoveries as we progress.

Those who are deemed not to meet these criteria will be asked to leave the project or accept that the Project Administrators will remove them from it.



The Irish Type II Modal

A modal is merely a compilation of the most common values of a particular haplotype. It would be a misnomer to describe it as the ancestral modal, since we do not and cannot know what the actual haplotype was of the first man to carry the distinguishing SNP/s that define the Irish Type II haplotype, or any other subclade for that matter.
 
The modal for the SNP L21 super subclade is the base used to arrive at the Irish Type II modal. There are fourteen markers where the value for the Irish Type II differs from the L21 modal. Seven are one step up from the L21 and seven are one step down. The following chart indicates what those values are.  There is a tendency for those values to sometimes be a further step up or down,which is then no longer the actual modal, though that shift is usually consistent with the haplotype being a valid Irish Type II.
 
A few markers tend to mutate more frequently than others. For example, it is not unusual to see a 16 at DYS385b in numerous surname projects where the Irish Type II is common. This is obviously a parallel mutation, occurring with some regularity, and not indicative of any particular group.  DYS442, while modal at 13, is also seen often enough throughout the surname projects with a value of 12, the L21 modal. While some surnames may have more 13s or more 12s, again, this type of mutation or lack of one is seen with some frequency.

The defining modal of the subclade is: (Apologies, but the Family Tree system is not recognizing the chart and won't display it at the moment.  You can see it on the Munster Irish website at https://www.familytreedna.com/public/MunsterIrish/.)


The SNPs associated with Irish Type II
(Last update 30 April 2017)

Our analysis of the various extensive SNP tests has enabled us to develop a working hierarchy of the haplotree for the Irish Type II haplotype.  The following table provides a simple version of this tree.  Some of the SNPs are known by more than one designation, and we've included the alternatives in such instances.  Some SNPs have not been 'named' yet, and those are listed by their numerical position on the Y chromosome.  Some SNPs are at this time considered phylogenetically equivalent and they are noted in italics.  The indentations indicate which SNPs are downstream in the hierarchy.  Those listed in bold red font are available at Family Tree for individual testing.  We hope to see more available and will note as such as they are added.  We can sometimes get a bit behind in updating the tree here with newly identified branches, but the Results spreadsheet is always accurate.  If you see any errors or omissions, please bring them to our attention.
 

CTS4466/S1136 & equivalents CTS11267/S7938, CTS3974/S7936, CTS5714/S1137,CTS8358/Z3022
                Z16247/FGC11133,S1113, S1120, S1122, S1128, 
S7364, Z16248, Z3025/A81, Z3028A114,
                A149/FGC11137

------A7751

------------FGC43844

------S1115

------------A12402

------------A541

------------------S1121

------------------------L270.2 & equivalents M4291Z16518, Z16519,Z16520, Z16521,Z16522, Z20762

------------------------------A1133

------------------------------BY3683

------------------------------------Y29013

------------------------------BY16025 & equivalents BY16026, BY16027, PR2745

-------------------------------FGC42469

------------------------Z16252 & equivalent Z16251
------------------------------
Z18170

------------------------------------FGC29280 

--------------------------------------------S1126

------------------------------------------------A542 & equivalentsA543, S1129,A1137, A1138

--------------------------------------------------A726

------------------------------------------FGC29286 &equivalents FGC29289, FGC29290,FGC239291

------------------------------------------BY3536 & equivalents BY3518BY3519,BY3520, BY3521, BY3522, BY3523, BY3524

------------------------------------A150

------------------------------------------BY2877

------------------------------------------------FGC11145 & equivalents FGC11150,FGC11152, FGC11159,Z20764

------------------------------------------------BY2879

------------------------------------------------------A745 & equivalents A746, A747, A748, Z20763

------------------------------A159

------------------------------------BY2881

------------------------------------------BY149/Z17981

----------------------------  --------------------Z17982 & equivalent Z17983

------------------------------------------------------A664 & equivalents BY3525BY3526

------------------------------------------------------------A1511 & equivalent A1512

------------------------------------------------------------A7752 & equivalents BY3527BY3528 

------------------------------------------------------------A12015

------------------------------------------------------------BY15517

------------------------------------------------A923

------------------------------------------------------22107059

------------------------------------------------------23745816

------------------------------------------------A6507

------------------------------------------------------A6508 & equivalent A6509

------------------------------------------A9185

------------------------------A1134 &equivalent A9005

------------------------------------BY2880

------------------------------------------A804

------------------------------------------------A802 & equivalents A803, A805

------------------------------------------------------A914

------------------------------------------------FGC29067 & equivalents FGC29073,FGC29074, FGC29075

------------------------------------------------------FGC29071

------------------------------------------A2221 &equivalents A2222, A2223, A2224, A2225, A2226

------------------------------------------------A6464

------------------------------------A809 & equivalents A807. Z20766, A13625

------------------------------------------A806 &equivalents A808, A810, 13834289..303, 16840403

------------------------------------------------A2331 & equivalents A2331-A1337, 2348..., 2108..., 1914...

------------------------------------------15846113 & equivalents 18417925, 8751078, 15472749..50, 21508467..74

------------------------------------A6511 & equivalents A6512, A6513, A6514, A6515, A6516, A6517, BY4059, A6305, A6388

------------------A1135 & equivalents A1136, Z21065

------------------------A195

------------------------------A761

------------------------------------A88

------------------------------------------Z16259 equivalents Z16258, Z17985

------------------------------------------------BY2876

------------------------------------------------------ZS4590 &equivalents ZS4589, ZS4591, ZS4592, ZS4593, ZS4594

------------------------------------------------------A1333 & equivalents A1334, A1335

------------------------------------------------A2220

------------------------------------------------------A2219

------------------------------------------------------------A2295 &equivalent A2294

------------------------------------------------------A7755

-----------------------------------------BY2878

------------------------------------------------A89 & equivanentsA90, Z16256

------------------------------------------------------A155

------------------------------------------------------------A156 & equivalents A157,A158, Z16257/A159

------------------------------------------------------BY15518

-----------------------------------------A7660

------------------------------------Z16254

------------------------------------------A154 & equivalentsZ16255, Z17554

------------------------------------------------A153

------------------------------------------------------A474

------------------------------------------------------BY11841

------------------------------------------A1338

------------------------------------------------A1336 & equivalents A1337, A1339, A1340, A1341,A1342, FGC11858

------------------------------A12590

------------------------------------A12589

------------------------------A10641

------------------------A956

------------------------------A2288

------------------------------------A5312 & equivalents A5313, BY3532

------------------------------------------A8748

------------------------------------------------A7753 & equivalent A2429

------------------------------A7754

-------------------------A2427 & equivalents A2428, A2429, A2430, A2431, A2432

-------------------------------22222459

-------------------------A9426

-------------------------A11844

-------------------------------A122525

------------------A151 & equivalent A152

------------------------FGC29768

------------------------------BY139/Z17986& equivalent A1139

------------------------------------BY141/A661

------------------------------------------BY140/Z17987 & equivalents BY142/A662, Z17988

------------------------------------A9865

------------------------------------------A12087

------------------------------------------------A12149

------------------------------A743

------------------------------------FGC29773

-----------------------------------------BY15520

-----------------------------------------F3189 & equivalents BY15519, BY15520

------------------A714 & equivalents A715, A716, A717

------------------------FGC23796 & equivalents FGC23797, FGC23800, FGC23801, FGC23803,FGC23804

------------------B42

------------------------A7659

------------------------------A7654, & equivalents A7655, A7656, A7657

------------A212 & equivalent A218

------------------A206 & equivalents A210,A214, A216, A217, A292, A349, A351

------------------------A208

------------------A6518

------------------A7699

------------------------A6525

------------------------------A7756 & equivalents BY3533, BY3534, A9512

-----------------------------------A9513

------------------------A6526 & equivalents A6527,A6528, A6529, A6531, A6532, A6533

------------------------BY3535

------------------------------BY3862

------------------------A7648

------------A663 & equivalents Z17989,Z17990

------------------A2289 & equivalents A2290, A2291, A2292

------------------A5598 &equivalents A5595, A5596, A5597, A5598


There is a more detailed chart that can be seen in the Files section of our Forum (see below), where it can be downloaded at https://groups.yahoo.com/neo/groups/R1b-CTS4466-Plus/files.  James Kane's Experimental Tree is available at http://www.it2kane.org/matrix/R-FGC11134.html.  It includes the kit number and surnames of those who have tested the BIG Y and given him permission to include them in the chart.  It may not be exactly the same as the tree shown above.  More SNPs are found with each BIG Y and FG test, expanding the tree regularly.  If you see any discrepancies, please let us know and help keep the tree current.

We are making progress in our understanding of the basic hierarchy of all these SNPs, but as we receive more BIG Y and FG results, we continue to identify more. There are a number of currently equivalent to CTS4466. While CTS4466 is being used as the 'flagship' SNP, since it was identified first, any one of them may be the first or last of this series of SNPs occurring perhaps during the Bronze Age and likely into the Iron Age, defining the Irish Type II subclade before branches which have survived to this day began to appear.

SNP Testing Options

FTDNA offers individual tests for a number of those SNPs noted in the above chart in red.  The price per SNP is $39.  FTDNA continues to add the newly identified SNPs as the BIG Y tests increase the number we discover. 

FTDNA has a CTS4466 SNP Pack that includes SNPs representing most currently known subclades downstream of CTS4466.   As more branches are discovered through BIG Y tests, they will be added to the Pack.  Some equivalents are being added, in the event a tester may split that branch further, being positive for some but not all equivalents. (We have identified a new branch through this process.)  The price is $119.  Potential users should note that this Pack is unreliable in reporting certain areas of our tree, most notably that in the sequence A1135 -> A195 ->A761 and (under S1121) at BY149 (aka Z17981).  If you are predicted to fall within that branching area (your record in the spreadsheet would be included in one of the '?' categories A2. to A2a1.) you might check with one of our administrators to determine the best choice of test.

Another testing company, YSEQ - http://shop.yseq.net/ will test any SNP which can be Sanger Sequence (i.e individually) tested for the price of $17.50.  If an SNP is not listed in its price list, it may be "wished" for $1; this will also determine whether it is viable for such testing. As this is an independent company, a fresh kit will need to be ordered ($5 P&P) and its results will not display on your Family Tree pages.

YSeq offers an equivalent to the FTDNA R1b-CTS4466 Pack in its FGC11134 Panel (which includes CTS4466 and all its subclades). The price is $88 (plus the $5 for a kit if a new customer). It has one representative SNP for each known CTS4466 subclade (as longer as Sanger Sequence testable) and is kept fairly well up to date. The tree and SNPs included are listed at https://www.yseq.net/product_info.php?products_id=6309&osCsid=2d495b4f368ed77d4aacf6a81495d9b0By virtue of the method of selection of SNPs for inclusion, there are no known problems with this panel.


In addition, there are a number of more extensive DNA tests available now, through Family Tree and other companies. 

The chart at ISOGG (International Society of Genetic Genealogy) compares the various options available for extensive Y-DNA SNP testing: http://www.isogg.org/wiki/Y-DNA_SNP_testing_chart.

National Geographic offers the Geno 2.0 test for $199.95.  It tests about 150,000 already known SNPs:  http://shop.nationalgeographic.com/ngs/browse/productDetail.jsp?productId=2001246&gsk&code=MR20936At this point, it is unlikely to reveal any further SNPs than those we have already found.  It has been superseded by Geno 2.0 Next Generation, for which the current price is $179.95.  It purports to test nearly 750,000 SNPs, but we don't know how many are on the Y chromosome.

The BIG Y from FTDNA costs $575.  It covers about 65% of the Y chromosome.  There is a prominent icon for it on your homepage at Family Tree.  They have more details about the test at their link:
https://www.familytreedna.com/learn/y-dna-testing/big-y/.  

The Full Genomes Corporation offers several levels of extensive testing.  The Y Elite 2.1 is priced at $795 at the moment; and there are several levels of a Whole Genome, the most comprehensive, Whole Genome Sequencing 30x, at $1,450.  These can be seen at https://www.fullgenomes.com/ We recommend you consult with us if you are considering them.  They do cover a greater area and include SNPs not found in the BIG Y.  They also offer an Interpretation of BAM files for $40, which are the raw data files made available by Family Tree from the BIG Y tests.

YFull offers a Next Gen Sequence Interpretation of BAM files for $49.

Some participants order tests for one or more of these options. As the results become available, we provide instructions on how to share the data with the project and receive an interpretation of those results from our own analysts.

The BIG Y test at Family Tree provides a dedicated Big Y Results page with details of some of the results, both 'Known SNPs' and ''Novel Variants'.  It has a link to a .cvs file that can be downloaded that contains all that data displayed.  In addition, the participants can download a folder with a 'regions.bed' and a 'variants.vcf' file that has more information, and they can request a '.bam' file which has all the raw data by completing the contact form available on a link provided.  Due to the file size of the BAM, Family Tree will post another link on the Results page to 'Share' the link with us. Unless the participant is comfortable with handling large files (it's huge -usually about 1 gigabyte) we don't recommend they try to analyze it themselves.  We ask that all BIG Y testers send us the folder with the BED and VCF files as well as the link to the BAM file when they receive it from Family Tree (it could take a few weeks to receive).

While we analyze the data made available to us and have several spreadsheets that chart the results, there are several companies that offer an analysis of the BIG Y and FG results, such as Full Genomes sand YFull mentioned above.  If anyone is interested, please inquire for more details.



R1b-CTS4466 Plus Haplogroup Forum

We have established a Yahoo Forum for the project - http://groups.yahoo.com/neo/groups/R1b-CTS4466-Plus/infoThis is a forum for those whose paternal ancestry places them in the CTS4466/Irish Type II haplogroup/subclade. There we can network with one another, pool our efforts, discuss research and share results. Members of the project are not required to join, but you are encouraged to participate if this sparks your interest.  Likewise, you need not be in the project to join the forum.  Note that joining the Yahoo group requires you to create a Yahoo account if you don't already have one.  If you are confused by any of the science, terminology, FTDNA's website, or anything else relating to the project or genetic genealogy in general, please feel free to post your comments, questions, and concerns in the Yahoo group.


R1b-CTS4466 Plus FAQs

We've prepared a brief document with some of the questions we receive from participants.  It is available in the files section of the Forum.


Last updated 26th April 2017


General Fund

Current balance: $862.35

Type Amount Date Donor Note KitNum Donation Type
Debit $119.00 5/2/2017     124024 Unknown
Credit $30.00 4/30/2017       Individual
Credit $89.00 4/27/2017   CTS4466 SNP Pack for 124024   Individual
Debit $89.00 4/26/2017     594257 Unknown
Credit $89.00 4/26/2017   Johnny Jones SNP pack   Individual
Credit $40.00 4/25/2017 Angelia Roberson Family BigY (combine with Katie Duke's donation)   Individual
Credit $40.00 3/2/2017 Katie Duke     Individual
Debit $400.00 12/30/2016     263719 Unknown
Debit $210.00 12/30/2016     263719 Unknown
Credit $510.00 12/30/2016   mccormick/   Individual
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