5.  Historical note on L555 SNP and BigY Tests


1  Introduction

2  L555 and the single L555 SNP test

3  The Geno2 test

4  BigY results and analysis

5  L555 SNP Panel Test 

1. Introduction: SNP tests and haplotrees

SNPs and haplotrees have been introduced at “Interpreting yDNA test Results” section 3, and findings relevant to this Study at “Latest Results Analysis” especially section 3.1.  Recommendations taking SNP tests are given in “Choosing further tests section 3.  This page gives some additional background to this subject. 

2. L555 and the single L555 SNP test

The SNP L555 was first identified in 2011 in the WTY (Walk the Y) test by William Rector Irwin II (65048), which showed it to be one of an increasing number of "descendants" of R-L21.  Thanks to him then making a generous General Fund donation we learnt that most if not all members of our Borders branch were likely to test L555+.  At the same time an independent study by Robert Casey showed that many of the "sons" of L21 have tested L555-, confirming that L555 was probably another son of L21.  Robert suggested that we seek ISOGG qualification for L555.  For this we had to show that two criteria were met:

For details see http://www.rcasey.net/DNA/R_L21/R_L21_Private.html >Analysis > L555.  L555 is now recognised by ISOGG, FTDNA and National Genographic. 

This development brought the following benefits:

Initially no one outside our Study had tested L555+, but now six non-Irwin testers have tested L555+ but whose patrilineal ancestors seem unlikely to have ever used the Irwin surname.   Instead it now appears that a SNP within the block that includes FGC13746, a "grandson" of L555, is the  oldest SNP that is unique to the Border Irwins. 

Single L555 SNP tests provided a cheap method for testers whose STR signatures indicated Border Irwin branch ancestry to confirm this, and L555 Pack tests provided a cheaper method of placing the tester on the halpotree of mankind that BigY tests, but they did not "discover" SNPs other than the 86 included in the design of the chip.  During 2024 FTDNA discontinued offering single SNP tests and SNP Pack tests, in part because the relatively cheap and popular Family Finder tests can now predict mid-level SNPs such as L555. 

3.  The Geno2 test

The Geno1 test was launched by National Geographic in 2005.  Testees could transfer their ySTR test results to FTDNA's database, and 17 members of our Study took advantage of this facility, identifiable by test kit nos. prefixed by "N".

The Geno2 test was launched by National Geographic's Genographic Project in late 2012. It costs $199.95 (+$20 shipping for Europe). It is much more powerful than Geno1 and the former Deep Clade and WTY tests of FTDNA, all of which it superseded, but it is aimed primarily towards those interested in Deep Ancestry, and so has no ySTR data.  It tests for about 146,000 SNPs, but only (!!) about 12,000 of these are y-SNPs.  Of these 6,153 have been placed on a new phylogenetic tree but the remainder are "novel", although not necessarily "young".  Geno2 has been taken by several members of our Study, and includes L555, but it does not discover SNPs downstream of L555 and as I don’t think it represents value for money I cannot recommend it.  

4.   BigY test results and analysis 

FTDNA launched this test in September 2013.  It now costs $449, and less during sales or if the testers have already had an STR test.  In mid-2015 BigY covered 7,000 SNPs; by mid-2019 it coverered over 160,000 SNPs, including many "novel" SNPs younger than L555.  BigY had a "rocky" start, for several reasons, but has now matured into anincreasingly popular test and I can strongly reocmmend it for those members who are in our Borders branch and can afford its now much more reasonable price.

Although initially I did not recommend our members should order these tests, results relevant to our Study started to become available during 2014.  It was quickly apparent that the tools provided by FTDNA for their analysis – their haplotree, Matches, .csv files and .vcf files were of little use to the layman, and the BAM files, from which all this secondary data was derived, were very cumbersome to handle and even when opened not easy to comprehend. Nor were the analyses of BigY results by FGC and YFull for c.$50 much better, and I was not impressed by their probablistic STR data. 

Intelligible and informative analyses were available from Alex Williamson’s BigTree, albeit only for SNPs downstream of P312 (i.e. including L555), but Alex was threatening to withdraw his service.  I therefore felt I ought to try to learn how to handle BigY BAM data, and with help from Dennis Wright and support from Alex and Mike Walsh I eventually learned the procedures and by late 2014 was able to produce a haplotree containing our Study’s L555 BigY results. 

Concurrent with this learning process it became apparent that the expense of BigY tests was such that few members could afford such tests, while the cheaper bespoke Pack tests that FTDNA were planning would be of little use for our Study if we had not first identified the SNPs that characterised our Border Irwin sub-groups. So early in 2015 the main outstanding Border Irwin sub-groups were identified and a further six relevant BigY tests were funded by generous donations from other members of the Study.

With 12 L555 BigY test results available by mid-2015 several features were becoming clear:

- the age of the Border Irwin “starburst” as c.AD1330;

- the duration of the “bottleneck” that includes L555 as 3,000 years, a remarkably long time;

- the age of L21 as 4050bp (before present).

5.  The L555 SNP Pack (or Panel) test

FTDNA launched their SNP Pack tests in 2015.  They combine about 100 SNPs that have been identified as being relevant to a selected part of the halpotree on the basis of BigY findings.  Each SNP included is given a simple binary, i.e. yes/no test. 

The L555 Pack was designed from the findings of 12 L555 BigY tests.  It includes 86 SNPs that have been identified as being contemporary with or downstream of L555.  At $119 this works out at about $1.40 per SNP.  The Pack test is thus much cheaper than a BigY test and, per SNP, also much cheaper than a single SNP test.  And although Pack tests cannot identify “new” SNPs, an unexpected bonus is that they can, from negative results, detect the presence of hitherto unknown SNPs and show eon the haplotree that these unknown SNPs occur. However it does not discover new SNPs, or identify private SNPs unique to each tester.  W have also now learnt that the 86 SNPs it tests for donot prevode a comprehensive ppiture of the L555 haplotree.  For this reason I now recommend the BigY700 test for those who can afford its price. 

I issued analyses of our L555 Pack test results in May and September 2016 for our BigY and L555 Pack testees, but apart from demonstrating how the SNPs within the Pack were selected and how the test results make up the L555 haplotree, but the improved FTDNA haplotree made these analyses redundant.  

During 2024 FTDNA discontinued offering single SNP and SNP Pack tests.  However YSeq continue to offer similar products. 

The following websites give additional background information: