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. 

NextGen Sequencing and yDNA: Part 2

This post is a continuation of my post two days ago.

Within the last week several events have occurred to flesh out our small project. This is exciting but it also will take a while to absorb this influx of new data and make sense out of it all. However, relationships are emerging among project members -- some of whom had previously appeared to be living alone on almost deserted ySNP islands.

The results of an additional BIG Y kit has come back. This connected two men with at least several recent generations of documented French descent. Although they still may not have a common ancestor in genealogical times, their match appears to be within the last millennium. For one of these men whose father was adopted, this is encouragement that he is on the right track in pursuing some ySTR matches who are also of French ancestry.

One member has received Sanger confirmation through ySeq that his S1026 result from NextGen sequencing was correct. Although this analogy is very crude, NextGen sequencing is the equivalent to taking images from a space satellite. On the other hand, Sanger technology would be like driving to a specific location on earth and recording an image. 

NextGen sequencing is much faster for scanning large areas particularly those which may be almost inaccessible or those which have coordinates which were previously inexact or even unknown. It is great for discovery. 

On the other hand Sanger technology can be targeted precisely to one specific location (SNP or STR) and is considered to be much more reliable. The down side it is much more expensive drive around on the surface of our genomes and record a series of images that could be stitched together to form a coherent map. It is much faster and cost effective to start with satellite images. 

Two men who previously had close ySTR matches with others who had previous BIG Y results have tested a single downstream SNP through Sanger technology through FTDNA and confirmed they belong in this project. These men were able to target a specific SNP that had been identified by the BIG Y results of someone with whom STR results had previously suggested a distant relationship did exist. Thus at the cost of a single SNP test, these two men were able to confirm that their SNP trail takes time down into historical times and perhaps to the beginning of the genealogical era. 

One project member got this week, after a wait of three and a half months, his Chromo2 results from ScotlandsDNA. The early examination of the results confirmed that he did belong to R1b-S1026. It was in fact this test that identified and named a SNP at location 19201991 as being S1026. That is where the "S" came from in the naming protocol.

All of these results coming back within the same week has energized our tiny project which now only has a baker's dozen of confirmed members. However, it will take us a while to puzzle over what it all means and what our next steps should be to continue to trace our diverging trails down into genealogical time and hopefully connect with the documented genealogies of specific families.  

But now I must tear myself away from all this and fly to Houston today for Family Tree DNA's 10th Annual Conference on Genetic Genealogy. Don't you just hate it when your opportunities to learn more about genetic genealogy compete for your time to actually do genetic genealogy? I know, I know. I should just be grateful for my opportunities. And I am. 

NextGen Sequencing and yDNA

Genetic genealogy got its start in 2000 and yDNA dominated the first decade. mtDNA entered the scene late in that decade but has two difficulties to overcome. The first is that it is a fairly blunt instrument with only 16,569 locations to differentiate among all of us. It is good for deep ancestry but has yet to demonstrate it has potential to differentiate among related individuals. Second, to date there there have not been hundreds of thousands test their complete mitochondria -- the only level at which mtDNA seems to have much genealogical value.

By 2010 23andMe and FTDNA led the way into exploring the largest areas of our DNA -- the autosomes. These two pioneers were joined in this marketplace in 2012 by AncestryDNA. Now more than a million atDNA test kits have been sold by these three companies and the pace is accelerating. 

Autosomal DNA is great for defining close relationships -- at least when those relationships have existed within the last several few generations. Therefore it can be very useful to genealogists. However, since it is recombined in each intergenerational transfer, it soon loses its power of discernment as we investigate backward in time. This is the hottest growth area in DNA testing for genealogy and likely will continue to be so for some time. Women are on equal footing when it comes to testing autosomes.

In 2014 yDNA is making a comeback. It offers by far the longest segments of unrecombined DNA in our genomes. Therefore, it offers the best tool for looking into our deep ancestry. Although it may seem politically incorrect to say so, the less than seventeen thousand locations on our mtDNA cannot begin to be as informative as the more that fifty million locations on our yDNA. Unfortunately only men can be tested. NextGen sequencing technology is now making it possible to read SNPs at several million locations on our yDNA. This far exceeds the hundred or so ySTRs that were being sequenced by earlier technology just a couple of years ago. 

As a result of NextGen technology, tests like BIG Y, Full Y and Chromo2 have burst onto the scene. Although the prices of such tests are already coming down somewhat, they are still pricey compared to atDNA tests. However, the amount of data that they discover will take us a while to fully organize and analyze. 

Traditional genealogy emphasized starting with the present and building carefully and methodically back into the past inhabited by our ancestors. These new tests have allowed us to reverse our focus and work from prehistory down toward genealogical times. In a few cases they have already allowed us to intersect with our traditional documentary research. This trend will greatly accelerate as we get more skillful at interpreting the information written in our yDNA.

Even in earlier and simpler times we could begin to sketch the flow of our ySNPs from yADAM down toward the present. Five years ago I was offered an overview of how my SNPs and thus my paternal ancestors had migrated down to the last several thousand years. Below is how deCODEme illustrated my paternal descent down to haplogroup R1b -- the largest in Europe:

[Click on the chart to expand.]

The SNP tsunami that flows from these powerful new tests is allowing us to fill in gaps in charts like the one above. More importantly they are allowing us to build down toward the present. I will extend this SNP flow down to the last millennium in my next post.