Tuesday, 5 April 2016

Results of Big-Y SNP testing

Last year we raised some money for SNP testing of two of the project members from the first group in the project, Genetic Family 1 - the Limerick Spearin's.

Previously we had undertaken sequential SNP testing, with member 200083 kindly volunteering to be the "group representative" for Genetic Family 1 (GF1). The progress of this SNP testing has been covered in previous project updates. He tested positive for SNPs Z78, Z185, L1198, and Z166 and negative for Z190, Z79, F3195, and PF5268. This testing helped us move down the human evolutionary tree, placing us on sub-branches that were more and more further downstream. So that by last year, we were placed on the Z166 sub-branch of the human evolutionary tree.

The "SNP Progression" looked like this:
I- ... M438 > L460 > P214 > M223 > CTS10057 > Z161 > C6433 > Z78 > L1198 > Z166

This progression is represented diagrammatically below and shows the particular sub-branch of the evolutionary tree whereon Genetic Family 1 sits. Or at least, where it sat in February 2015. Since then, things have changed. (Note that our terminal SNP Z166 was not included in this diagram from 2013).

To move us even further down the human evolutionary tree (also known as the Haplotree), we decided to undertake Big Y testing. This test investigates up to 50,000 SNP markers on the Y-chromosome. The SNP markers are different DNA markers to the STR markers that we see on the Results pages of the project and you can read a blog post about the differences between SNP and STR markers here.

The two volunteers for Big Y testing (H1223 & 164729) were chosen on the basis that they appeared to be the most genetically different members of Genetic Family 1, based on their STR marker differences. The Genetic Distance between the two members was 5/67 (i.e. there was a 5-step difference between them on their 67 marker test results). Also, one had origins in Limerick whereas the other had been in and around Georgia since the early part of the 1800's.

The Big Y tests were conducted after our Spearin Reunion during the summer of 2015 and the first results became available in late 2015. Thereafter, they were analysed and attempts were made to place the newly discovered SNP markers on the human evolutionary tree. This can take some time to interpret because the number of tests available for comparison are limited. Since then there has been ongoing communication with the I-M223 Project Administrators trying to interpret what the results mean and what they tell us.

Firstly, we have a new terminal SNP marker for Genetic Family 1. It is Y18109. This has moved us at least two branches further down the human evolutionary tree. Our new SNP Progression looks like this:
I- ... M438 > L460 > P214 > M223 > CTS10057 > Z161 > C6433 > Z78 > CTS8584 > Z185 > Z180 > L1198 = Z166 > Y17535 > Y18109
And here is a diagram (from SNP Z78 downwards) of the new SNPs (green above) where this places us on the Haplotree (taken from FTDNA's version of the Haplotree which can be found on your own Results pages). Note that some additional SNPs (brown) have been included since the 2013 version and this is typical - more SNPs will be discovered and added as the science evolves.

The new terminal SNP for GF1 on the FTDNA Haplotree
(green = tested positive; red = tested negative)

So, this new data raises several questions: when in time did these new SNP markers emerge? How far down the human evolutionary tree are we now? And who are our neighbours on this new sub-branch? Can we learn anything from them? Does this new information tell us anything about the origins of the Spearin surname?

In order to date these new SNPs, we turn to YFULL. Their experimental Haplotree has time estimates for the emergence of these SNPs, as illustrated below.

click to enlarge

From this we see that our new terminal SNP (Y18109) is estimated to have come into existence about 2200 years ago (with a 95% Confidence Interval of 3100 to 1500 years ago). The SNP above it (Y17535) is about 2800 years old, and so came into existence about 600 years before Y18109. And the ones above that (the equivalent SNPs L1198 and Z166) are about 3000 years old. So this takes Genetic Family 1 further downstream and places us roughly at about 200 BC. But it could be anywhere from 1100BC to 500 AD. So we are still fairly far back in time, and certainly not at the point where surnames came into common usage (about 800-1000 years ago). 

To learn more about our neighbours we turn to the I-M223 project. Previously GF1 had been placed in Cont1 Group2 and we had quite a few neighbours here (see the previous post for details). But now we sit in a new group, Cont1h1, and we have lost all of our nearest neighbours. They have been split off into different adjacent sub-branches. 

GF1 now sits on its own branch - it's lonely being unique!

Our current nearest neighbour is a chap called Braz whose MDKA (Most Distant Known Ancestor) came from Portugal (green boxes in the diagram below). Neighbours on more upstream branches have ancestry from a fairly diverse number of places, but all in Western Europe, including Denmark, Finland, Netherlands, Germany, England & Scotland. So although recent SNP testing is helping to split this larger group out into smaller sub-branches, we have a long way to go as yet to narrow down the Spearin origins to a particular country or location.

Nearest neighbours (& their origins) to GF1 with dates for the various sub-branches

So what does the future hold? Well, we will continue to accrue benefits from this Big Y testing over time, so all we have to do now is wait, and keep an eye on it. As more people test, we will get more information for Genetic Family 1 in terms of both the timeline (when did our Spearin-specific branch come into existence?) and ancestral locations (where did it emerge? where did it move to?). 

In subsequent blog posts we will take a closer look at the actual SNP markers discovered for our two volunteers and what this tells us about how closely they are related. We will also explore what this means for Genetic Family 1 and generate a Mutation History Tree for this genetic family.

Maurice Gleeson
April 2016


  1. I waited months for that information. Brilliantly done, Maurice. We may have to wait to see where we end up but at least the major testing work is over! Thank yous to all participants and donors.

    1. Yes, a big thank you to our wonderful volunteers. And to everyone who donated money to the General Fund to help the project. We are certainly paving the way for other people in the I-M223 Haplogroup Project and I'm hoping that we will continue to make progress over time as more people do SNP testing..