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.









   

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. 

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.