SNP Tsunami Continues Into Third Year

Many of us spend a great deal of time, energy and money attempting to document that a particular ancestor of ours belonged to a particular tribe or ethnic group. We all get very excited when we find a family Bible or a diary of an ancestor that dates back two or three hundred years.

Don’t you wish your ancestors had carried a passport which got stamped at every branching point of their intercontinental migration route as they trudged through prehistory? Actually they did. In some cases our genomes have recorded more than a hundred thousand years of travel.

This travel is documented in the mitochondrial DNA of all of us. A separate and more detailed path is documented in the yDNA of men. Many call this anthropology. In Chapter 6 of my most recent book, NextGen Genealogy: The DNA Connection, I call this extreme genealogy. In either case it is the study of haplogroups – or the ancient clans to which our ancestors belonged.

Women ancestors were somewhat limited in what they could communicate to distant descendants because our mitochondrial DNA (mtDNA) contains only 16,569 locations in which they can record the presence of one of the four chemical bases that make up our DNA. Their paths through prehistory can be traced for our female lines using mtDNA test results. mtDNA was the basis for Bryan Sykes’ pioneering Seven Daughters of Eve.

Our men ancestors had tens of millions of additional locations where such information could be logged. What we look for today is where on our genomes these ySNPs occurred in this transcribed travel record. Once such a permanent change has occurred, it is passed down to all male descendants.

What are ySNPs and how do they differ from the ySTRs we have been testing since 2000?

Short Tandem Repeat (STR)

Pronounced "stir." This is a repeating pattern of genetic code letters at a location on the genome. The value is the number of times that pattern is repeated at that location.

Single Nucleotide Polymorphism (SNP)

Pronounced "snip." A single and permanent change in the DNA bases at a given location.

Consumer DNA testing to discover family history information began in 2000 with the focus on the Y chromosome (yDNA) which only males possess. Mitochondrial DNA testing for both genders soon followed but is somewhat limited because it has ONLY 16,569 locations to store a single bit of information. By 2010 autosomal DNA testing burst on to the scene and has become the most popular test.

By 2013 a new testing cycle for yDNA became available to genealogists. While the previous cycle had focused on testing ySTRs, the new wave examines ySNPs.

However, yDNA can record 3,500 times the data that mtDNA can. Therefore, it has the power to record a much more detailed migratory history.

Most of yDNA testing to date has been conducted on Short Tandem Repeats (ySTRs). When we talk about 12, 25, 37, 67 and 111 marker tests, we are referring to how many ySTRs were tested. STR testing is analogous to dispatching a census taker to a village which is known to have 12, 25… residences. In our scenario the locations of these residences have been defined by geneticists as being accessible and having a rate of mutation that is somewhat predictable. At each location our census taker records how many STRs are currently in residence.

In NextGen testing the focus shifts to Single Nucleotide Polymorphisms (SNPs). Instead of dispatching probes to specific, predefined locations, NextGen ySNP testing is more analogous to take satellite images along the entire Y-chromosome. Although the chromosome contains almost sixty million identifiable locations, current technology allows us to get reliable data from only about a fourth of those locations. Still this is an overwhelming amount of data. The computing power to analyze it has only recently become available.

At present ySNP chasing is only in its infancy. A vast majority of the SNPs we know today have been discovered in the last two years. The statistics in the chart below represent the number that had been placed on the International Society of Genetic Genealogists (ISOGG) yTree committee chaired by Alice Fairhurst:

Cumulative SNPs placed on the ISOGG yTree

Another way to look at this SNP tsunami is to view the new SNPs identified in a two year period (2013-2015) for R1b-L21, the most common male haplogroup in Western Europe today:

Known SNPs in R-L21 haplogroup in mid-2013 (Mike Walsh)

Known SNPs in R-L21 haplogroup in mid-2015 (Mike Walsh)

We are still working to find the exact location and sequence for many of them. In some ways our knowledge today would be like getting a SNP passport with several dozen “check point” stamps on it but in random order. We know that our genomes passed through all those points but are still trying to decipher in what sequence that journey occurred. The charts above for R1b-L21 represent ySNPs that we have been able to arrange in evolutional order. As more men are tested and we can document where they exited the main SNP trail, we can refine our chronology for all of us.

The chart below for sub-clade R-1026 is an expansion of the seven pale pink SNPs clustered at the bottom of the chart above. This subclade was unknown when the previous chart was drawn in 2013.

Courtesy of Alex Williamson -- www.ytree.net 

Even with this deluge there are many more thousands of SNPs to come. The NextGen curve is where the ySTR was in 2003 when 10,000 tests had been sold by FTDNA. Ironically, that is the number of BIG Y tests Bennett Greenspan reports FTDNA has sold to date. Full Genomes report their company has sold 1,500 NextGen tests. 

Most of the ySNPs that have been discovered have yet to be specifically placed and more will be discovered as testing numbers increase. The entire recently discovered R-S1026 haplogroup above is not yet integrated into the ISOGG ytree. It is only partially integrated into the FTDNA ytree. The R-S1026 chart contains many blocks or boxes that group newly discovered SNPs. At this point we believe we have the blocks in the correct chronological order of their appearance. However, we have yet to sort the SNPs within boxes into their correct order of appearance. And more remain to be discovered. Other haplogroups are in a similar state of discovery and growth. The SNP tsunami shows no sign of receding anytime soon. 

What's Your ySNP Testing Strategy?

In my last post Tested 67 ySTR Markers? Now What?, I discussed how you could get some idea of what your more recent ySNPs might be than the ones estimated by FTDNA. This knowledge can be useful whether or not you want to pursue further SNP chasing aggressively or not.

To build on the example in that last post, it looks like most if not all of those who had ySTR matches in that group actually belong to the R-S1026 haplogroup. This is a small clan that is now thought to have split from DF13 about 3,500 years ago. S1026 was just added to the FTDNA SNP Tree about a month ago. It still has not been added to the ISOGG yTree although the L21-DF13-S1026: R-S1026 and Subclades Project is linked from there. Our mechanisms for organizing new findings have been overwhelmed by the SNP tsunami of the last two years. 

If you have gone through the process of finding the project for your matches who have done extensive SNP chasing, you can get a general idea of where your personal ySNP trail was located. For example, in the example I have been following, S1026 is the pale pink group of boxes in the bottom right-center of the following diagram created by volunteer super SNP chaser Mike Walsh:

Only a small fraction of these SNPs were known two years ago. We are still in the early days of understanding SNPs. We are about where we were about 10 years ago in our understanding of STRs. 

Even more specific information can be found by following the SNP trails of our STR matches. The group of pink boxes associated with S1026 above have been expanded by another volunteer super SNP chaser Alex Williamson:

Now I must introduce the concept of a block of SNPs. In Alex's chart above most of the SNPs between S1026 at the top and the individuals tested at the bottom are located in blocks (or boxes). These blocks may contain only a couple of SNPs or as many as 30. We know that these SNPs in a given box are located contiguously but we are still working to determine their exact sequence chronologically. In addition it is thought that these SNP mutations occur at random but about once ever 150 years. That number will be refined as more individuals are tested and our knowledge base grows.

In the chart above some of the men listed at the bottom would be the ones that are likely to have been your 67 marker STR matches in my previous post. In this case they are the ones under the large fat SNP block in the center of the chart. Your results will differ. This example is a little skewed because several of us encouraged our closest ySTR matches to take the BIG Y test -- a strategy you may wish to employ if you do decide to take the BIG Y test.

If you are fortunate enough to be chasing a SNP that is below R-L21, you will be able to use the tools created by Mike and Alex to learn more about your own SNP path. If you are a member of a different haplogroup, hopefully there will be an experienced SNP chaser in your group who can guide your search. These volunteers are absolutely the most knowledgeable individuals about your haplogroup. 

ySNP TESTING STRATEGIES
I am going to continue to use my own haplogroup for illustration purposes. Of course your situation will differ. 

Within our haplogroup project we have proved that those with close ySTR matches also appear to have relatively close (pun intended) ySNP paths of descent down through the eons.
The three strategies from which you can choose going forward depend on your genealogical goals and the amount of disposable cash you can use to feed this addiction. This is clearly not the case where one strategy is the best fit for all.

Those three strategies are: 

1. to test one SNP at a time and hope, by lucky guess or the process of elimination, to document one's actual SNP trail;
2. to take one of the NextGen comprehensive ySNP tests such as FTDNA's BIG Y or Full Genomes Y Elite 2.0; or
3. to test with one of the bundled panels that are being assembled by various labs.

Of course you can choose a 4th option -- none of the below. That would be to travel through ySNP-land vicariously as we have been doing in this post and the post that preceded it. However, if you wish to further explore your own situation, I would encourage you to chose ONE of the strategies below and not to flip-flop back and forth between them.


Testing individual SNPs

1. The strategy that appears to be the least expensive at the beginning can become the most expensive over the long term. Both FTDNA and YSEQ offer single SNP tests for thousands of SNPs. To employ this strategy you choose a SNP to be tested from a catalog list of those offered. If you choose wisely, you may be able to advance your search for a modest cost. However, if you are ordering single SNP tests at random you can easily spend more, over time, than you would by starting with a more comprehensive test in the beginning. Ordering single tests in sequence is also time consuming because you really should order one at at time, wait weeks for the results and then decide whether another single SNP test would be useful. Single tests are currently $39 at FTDNA and about half that at YSEQ. Both are legitimate labs. FTDNA is in Houston, TX, and YSEQ is in Berlin, Germany. YSEQ is a nimble two person operation that specializes in yDNA. FTDNA offers more comprehensive DNA testing products and services including easy integration into thousands of volunteer led projects.                                                                            
2. Your needs may better by hanging on to the money you have available now and waiting until you can afford a more comprehensive test. While the single SNP testing above is somewhat like dispatching a census taker to a specific location to see in a given SNP is negative or positive, the more comprehensive testing is more similar to taking satellite photographs of the 58 million or so SNPs along your Y chromosome. Many passes are made and stitched together by a computer algorithm. While it may not be as exact in every case as the individually targeted SNP testing (Sanger), it is certainly more cost effective and gives results for locations which at present have no single SNP test yet available. At this writing the listed price for BIG Y is $575 and Y Elite 2.0 is $775. The latter is more comprehensive although both will give most genetic genealogists more data than they can process. FTDNA will not sell such advanced tests to anyone who does not yet have STR test results or Geno 2.0 results. Full Genomes has no such entry requirement. These comprehensive tests have the added advantage of yielding not only a haplogroup designation but providing a list of unique SNPs that may be approaching offering a terminal SNP that could serve the same family identifying function that did the coats of arms of old.                                                                                         
3. The newest commercial offerings to ySNP chasers are a wide variety of "panels". These are bundles that offer many tests of individual SNPs in one or two steps to narrow in on a specific haplogroup. These are offered by both YSEQ and FTDNA and generally are priced about $88 to $120. While these can screen many SNPs at one time, they generally only identify only one or two SNPs along your migratory path. Buyers should beware that such offerings actually have potential benefit for them.  

In the last analysis the advice posted in the FTDNA learning center:

Please order SNPs with the help of an expert, if you aren’t sure which SNP(s) will benefit your research.

Before ordering, you should ask the advice of an expert on your haplogroup and subclade. We recommend joining an appropiate [sic.] Y-DNA Haplogroup group project. You may then consult the administrators. 

Happy SNPing, but let the buyer beware!

Unraveling BIG Y Test Results: R-DF97

Yesterday I wrote about a BIG Y discovery that got my Maryland Dowells past SNPs R-L21 and R-DF13. The Virginia Group 1 Dowells in our surname project had long been known to have come forward in time from those two SNPs and were known to have reached R-M222. Thanks to the informative charts that citizen scientist Mike Walsh tirelessly updates at the site of the R L21 and Subclades Project, we have the opportunity to almost keep up with the current SNP tsunami:

The chart above is offered only to give overall perspective. The new subclade R-S1026 discussed in yesterday's post is represented by the four boxes colored pale pink in the middle of the chart. The more robust subclade R-DF49, which includes SNP M222, is the blue/aqua on the extreme lower left corner of the chart. Our Maryland Dowells and the Virginia Dowells have not shared a common male ancestor in about 3,500 years even though both followed the same SNP trail down from yDNA Adam to SNP DF13. You will need to visit the linked project website to be able to read the details of this chart. 

The DF49 corner of the chart is blown up below:

I request the reader's indulgence to ignore the gold and yellow boxes in the upper right corner of this part of the chart. The Virginia Group 1 Dowell who took the BIG Y test, was able to trace his SNP migration pattern several hundred years and eight SNPs closer to the present. He now is confirmed to be DF97 and beyond. DF97 is at the bottom of the third column from the left in the above chart.

Although this Dowell has been able to discover the trail of his ySNPs through a significant part of the last few millennia, he still has discoveries to make to connect his paper trail to his SNP trail. As was the case with my Maryland Dowells, The Big Tree of Alex Williamson gives many more recent SNPs to try to arrange in the proper chronological sequence. It is necessary to visit the original website to get a clear view of the SNPs that the yDNA of this Virginia Dowell has accumulated as his paternal clan moved toward the Atlantic coast of Europe. 

The Virginia Group 1 Dowell is the third column from the left in the above chart. SNP DF85 is in top row and DF97 is in row three. There are still many SNPs to arrange in the proper sequence in recent centuries as attempts are made to tie the SNP path into the documented path and to identify his nearest relatives.

Unraveling BIG Y Test Results: R-S1026

For a long time I have been stymied in my efforts to trace my SNP trail through the most recent three or four millennia down to genealogical time. Now we are beginning to make some headway due largely to the herculean efforts of the citizen scientists of the R-L21 and subclades project. The BIG Y, Full Y, Chromo2 and other discovery tests are providing multiples of the numbers of SNPs that had been identified prior to the beginning of 2014. 

R-L21 is the most prevalent male haplogroup along the western coast of Europe. In some areas it approaches 80% of the male population. Therefore, knowing that one is part of this mega clan is interesting but not very useful genealogically speaking. I had tested positive for DF13 which is a SNP just below L21. This still is not that useful as the vast majority of R-L21 men also belong to this subdivision. A dozen subclans of DF13 have been discovered in recent years but one by one I had tested negative for all of them prior to getting my BIG Y results. Now I know that I belong to the newly identified S1026 subclan. Below are the results of nine of us who have BIG Y results: 

This chart lists the SNPs for each of us that have been discovered downstream (toward the present) from S1026. At least six men have been identified by the Chromo2 project at ScotlandsDNA. 

My results are those in the middle column above. The man whose results are my closest match in the SNP chart above (just to the right of mine) is a sixth cousin-once removed. He and I share 105 of the 111 short tandem repeats (STRs) over which we previously had been tested. We appear to share five SNPs that so far separate our migration trail from that of any of the other members of this emerging group. He and I share a common ancestor who died in Southern Maryland in 1733. Even more recently I have four additional SNPs and he has seven.

The McDaniel man represented by the SNP trail in the column to my left above is my next nearest relative in this grouping. He and I previously had discovered we shared 35 of 37, 64 of 67 and 102 of 111 STR markers. He has seven identified SNP mutations since his ancestral DNA trail separated from mine and that of my Dowell cousin. The three of us share nineteen additional so far identified SNPs in common before our common trail merges with that of the three men in the columns to our right. Then the six of us share five earlier SNPs before we converge with others with whom we share SNP R-S1026.

It is going to take test results from additional men to sort out the exact sequence in which all these SNPs should be arranged chronologically. For example, we know that the five SNPs recently named (see chart above):

Z16886 Z16887 Z16888 Z16889 Z16890

are grouped together but we don't know in what chronological sequence they occurred. Only as more are tested and some are positive and others are negative will this more precise arrangement be possible. This sorting of other SNPs which are lumped together above will follow a similar process. As a result the SNPs will appear to be out of sequence as their correct ages and thus their actual locations along the migration path of our paternal DNA begin to appear. This will result in the nice orderly naming progressions to be scrambled.

Isn't genetic genealogy fun? The more we discover the more we have yet to learn. 

BIG Y: My First Genealogically Relevant Find.

The first thing I learned from the BIG Y test is that the Virginia Group 1 Dowells in our surname DNA project can finally be moved out of the logjam at SNP M222. What? You didn't know that they were jammed up there? Read on.

One of the first things we learned in 2004 in our surname project was that my Maryland Dowells were not recently related to the Virginia Group 1 Dowells. Previously we had assumed that we were closely related. We had our own variation of the multiple brothers myth. I'm sure you have heard a similar tale about one or more of the lines you have researched. 

It goes something like this. Two (or four) brothers came across the Atlantic. When they disembarked one went north and one went west. Which ever branch you descend from never heard from the other branch again. Of course there is enough truth in some such stories that they need to be investigated. However, most of them have remained impossible to verify. One of the Dowell versions I heard decades ago was that four brothers came over from Wales. I still don't know exactly where my Dowells came from before they revealed themselves in Maryland.

Prior to 2004 the working hypothesis among Dowell surname researchers was a variation of the migration myth that claimed upon arrival in Hampton Roads one Dowell turned right and sailed up the Chesapeake Bay and the other continued up the James River. Waterways were the interstate highways of the time so this story had a ring of truth. Based on this story many of us assumed that if either group would be able to extend its paper trail just one or two generations further back, we would find our common male Dowell ancestor.

Then came yDNA testing. It soon became apparent that the two groups of Dowells shared the surname only by historical coincidence. Biologically, we were no more related that we would be if we each had different surnames. Our closest shared male ancestor lived at least three thousand years ago -- long before surnames were adopted. These two groups remain the two biggest clusters in our project. 

SNPs (pronounced "snips") are permanent changes in a person's DNA that are passed down to all descendants. yDNA SNPs are permanent changes that are passed down by fathers to all their sons. As we have learned more about yDNA SNPs, we been able to sketch in more and more of our ancient ancestral lines. The BIG Y test has offered many of us an unprecedented chance to explore our SNP history in much more detail than had previously been available. This is not a test for novices. Even most of us who have considerable experience with genetic genealogy are overwhelmed by the results that are coming back.

Both groups of Dowells descend from a large haplogroup (ancient clan). Membership in this clan is distinguished by a mutation located at position called R-L21. The heat map below is from my results from the Geno 2.0 test at National Geographic which focuses on deep ancestry. The more intense the yellow and finally the red become, the larger percentage of the population carry this SNP. You will note that men who carry it are very prevalent along the Atlantic Coast of Europe and have particularly heavy concentrations in the British Isles.

The chart below shows what we thought we knew about where the two groups of Dowells had traveled down the SNP highway of history before BIG Y. The top of the chart has been truncated for simplicity. It begins as our ancestors migrated out of Central and Western Asia. You will note that L21 is represented by a green box in the upper middle of the chart below. We are very fortunate that a group of dedicated and knowledgeable citizen scientists also belong to the group and have done an immense amount of work to sort all this out. You may click on the chart to open a larger version in your browser. 
   

Before BIG Y we knew that the SNP flow of the Maryland Dowells had continued down to DF13 -- the green box just below L21 above. Then we could find no more recent SNPs. On the other hand the Virginia Group 1 Dowells could be traced through more recent SNP mutations down the left side of the chart to SNP M222. 

This chart was recently expanded to better represent newly discovered SNPs but still does not incorporate the bounty of BIG Y. Note that M222 is now shown among the blue boxes in the center right of the chart below:

The lower right part of this chart (area enclosed by the red rectangle) is blown up below for easier viewing:

Can you trace the path of SNPs from M222 in the fifth row of the family tree down to DF97 in the lower right corner of this last chart? It is sort of a connect-the-dots exercise for genetic genealogists. The Virginia Group 1 Dowells followed that genetic trail. That is what I have learned so far from BIG Y. 

How do I know that? The one Virginia Dowell who participated in BIG Y tested positive for SNPs DF85 and DF97. That means he also would be positive for the intervening SNPs along the connecting line from M222 down to DF97.

I hope we will be able to learn more from the massive amount of raw data that came back from this one test, but this is quite an advancement of our knowledge of the migration of the paternal ancestors of the Virginia Group 1 Dowells. Now we have to put it all into historical context -- a daunting task.