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. 

Once Upon A Time: A SNP Fable

This SNP fable is not literally true in all regards. It is a "fictumentary" based on what we know but liberties are taken to fill in blanks where science has yet to provide more definitive answers. I hope that each time I tell it there will be less fabrication and more scientific fact. SNP discoveries are now being made so fast that such an expectation is not impossible.

SNPs are permanent changes in one location along the genomes of our ancestor that have been passed down to us. We can trace the accumulation of these SNPs, much as we could follow the paths of our ancestors backward in time as if they had left notches in tree trunks as they made their journey through time.

This journey can be traced back thousands of generations. However, in the interest of time, I will fast forward down to the last four millennium or so. This is the story of the journey of my own paternal line as I am discovering it with my results from the BIG Y test. 

As most of you have discovered, all families who share the same surname are not recently related. In my case we discovered a decade ago in early ySTR testing that the Dowells who flourished in Southern Maryland in the late 17th century were not biologically related to those who flourished in Central Virginia in the early 18th century. The surname came into use independently in more than one location. However, these two clans who were to become Dowells had traveled down the SNP highway from the beginning of time until they separated as they approached the Atlantic coast of Europe about four thousand years ago. They were both part of the great R1b migration out of Central and West Asia sometime after the last ice age receded. 

For those of you who know a little about SNPs, both of these two groups who became Dowells belonged to R-L21 which is the most prevalent haplogroup along the western coast of Europe. The timeline is still fuzzy but a few hundred years later they were both part of the SNP DF13 that was the major branch below L21. Here they came to a parting of the ways that we are just now beginning to be able to decipher with results from tests of discovery such as BIG Y, Chromo2, Full Genomes, etc. These tests are still not for the casual genetic genealogists or the timid of wallet, but they are where the fast and furious action is.

The trail of my own paternal line is being revealed to have branched off at SNP S1026. So far the Chromo2 project has discovered six individuals whose ancestors have passed this SNP down to them. Seven, including me, have been identified by the BIG Y test. And the number seems to grow weekly. 

 

Pruned from Alex Williamson's Big Tree of May 18, 2014

So far my tale is more fact than fiction, but buckle your seat belts. The chart above is thought to describe the genetic journey of seven of us over the last 3,500 years or so. However, we don't know yet in what sequence each of us passed through these various SNP junctions. We will learn more about that as more members of this clan have test results.


The Fable

However, as of now it appears that each of us have approximately thirty or so SNPs spread out over a little more than three thousand years. That averages out to about one SNP junction every one hundred years. It appears at the moment that ancestors of the man whose path is second from the left never left France for the Isles. They stopped just short on the Brittany coast across from Cornwall. The ancestors of the rest of us appear to have made the plunge at some point in the last three thousand years or so. The ancestors of the man on the left seem to have made it to Ireland. 

The ancestral lines of the five of us on the right seem to have stayed together for another five hundred years or so. We all share 5 SNPs not shared by the two on the left. 

Have you heard the one about the three brothers? It looks as if something like that happened almost 2,500 years ago. One headed for Scotland. Well, you
have heard that one before. 

My own ancestral line [the middle one in the chart above] and that of another fellow traveler continued together for about seventeen hundred years or so. The two of us already had STR matches but no common paper trail for the last three hundred years. According to my fable version of our common family history, our closest common male ancestor might have been as far back as eight hundred years ago. TiP at FTDNA predicts our connection is a little closer:  
  

Generations	Percentage
8	11.54%
12	60.70%
16	88.49%
20	97.48%
24	99.55%

Oh well.

I look forward to the opportunity to learn more about the journey of my own accumulation of SNPs. If you can correct what I have written or add to it, I would love to hear from you. That is how I learn.