Wednesday, April 16, 2014

Power in Projects


I finally got my own BIG Y test results back Monday night. Of the kits I personally am monitoring, 2 kits remain unreported. Those were contributed by my late father-in-law and my distant cousin George. Both of their results pages still project that their results will be available by March 28th. Cousin George has been asked to provide an additional backup sample "just in case" it is needed. I haven't heard anything about my father-in-law's test. That's a little nerve wracking since he is no longer available to provide another sample.

Trying to find meaning in BIG Y results can be overwhelming -- at least at first. I am fortunate enough to belong to a haplogroup R-L21 that has a very active project that is led by some extremely talented leaders who are incredibly generous in sharing their time and expertise. 

I downloaded my raw data Tuesday without a hitch but was a little unsure about the protocol for uploading it to my haplogroup project. BIG Y results are a lot like other genetic genealogy reports. Individual reports by themselves are essentially meaningless. However, they can take on powerful meaning when they are compared with the results of others.

After some investigation I discovered the appropriate way to upload my results to my project. For our R-L21 project which contains several hundred members, the process has been automated by talented volunteer members. This morning, within a couple of hours of uploading the zip file of my raw data, I got an email from James Kane, one of the volunteers:


Hi Dave,

It looks like you are in the S1026 group in case you hadn't already known. You will be in the Big Y Matrix later this morning.

James
James was true to his word. Later this morning I started showing up in various project reports along side six other men who share this SNP. This group will grow as more test takers report their results.

S1026 is one of the new SNPs reported in the last few months by James Wilson of ScotlandsDNA. Context in genetic genealogy is everything. Where is SNP S1026 located? So far I know that it is downstream, more recent, from SNP DF13 which was the most recent SNP for my parental line than I knew about yesterday. All of you reading this, except for 1 or 2, are scratching your heads and wondering what I'm talking about. How about a picture? Thanks to the tireless work of volunteer Mike Warren I can show you one:


That is S1026 in the small red box at the bottom of the chart. Some of you may remember that a few days ago I discussed the movement of the Virginia Dowells down the SNP trail in the red box on the right side of this chart. On the vertical blue line that appears to bisect this chart, the Virginia Dowells branched off to the right and the Maryland Dowells continued to the bottom of the chart. So far we have been able to track my Maryland ancestors a step closer to the present to SNP S1026. 

Without the dedicated work and amazing expertise of those who lead our projects we would not be able to unravel the messages of our DNA. The haplogroup projects are a very powerful force in helping us learn. 

Friday, April 11, 2014

BIG Y Results Revisited


As I still await my own BIG Y results I continue to explore the results of others to familiarize myself with the test reports. In this post I am examining the report of a man with whom I have long had close STRs matches. His surname is different than mine but the STRs results suggest we share a common direct paternal ancestor in genealogical time.

In earlier testing over the years we had experienced 35/37 matches and 64/67 matches. By 111 STR markers we have 9 mismatches our unadjusted probabilities of sharing a common match according to FTDNA's TiP:


"In comparing Y-DNA 111 marker results, the probability that he and David Ray Dowell shared a common ancestor within the last..."

COMPARISON CHART
GenerationsPercentage
41.74%
827.31%
1267.71%
1690.54%
2097.93%
2499.63%
Since both of us have pretty good paper trails that seem to rule out a common male ancestor within the last 8 generations, we can refine this to run the probabilities again taking this into account:


COMPARISON CHART
GenerationsPercentage
811.54%
1260.70%
1688.49%
2097.48%
2499.55%

We have long ago reconciled ourselves to accept that we do not have a common ancestor on this side of the Atlantic although both of us have deep colonial roots. On the other hand it appears likely that we do share a common paternal ancestor within several generations before our separate departures to the colonies.


As I reported in my first attempt to find genealogical relevance in BIG Y results, I had previously done a single SNP test for DF13 but had not been able to find any more recent SNPs. My STR match had not confirmed that his DNA had progressed down the trail from L21 to DF13. We both strongly suspected that it had but it would be nice to verify this.

Verifying that he was also DF13 turned out to be a little more difficult than I thought. The indexes to BIG Y results did not include DF13 although that SNP has long been in use for the major subdivision of the large R-L21 project and FTDNA has long (at least in genetic genealogy terms) offered a single SNP test for it.

So I turned to a list on Facebook and posted a query asking if there was another name for DF13. Bob Dorr quickly came to my assistance by reposting:
"If you have tested with FTDNA as DF13+, and you search your FTDNA Big YI report for “Known SNPs” for DF13, you will not find it. You have to search for its CTS synonym CTS241 which you will find." from https://groups.yahoo.com/.../conversations/topics/20249  
It then occurred to me that I could have found this information in the ISOGG YSNP TreeCTS241/DF13/S521 are all listed as synonymous there. So many new SNPs have been loaded recently that you may have to give the page a moment to fully load. Then you can use the "Find" feature of your browser to search for a particular SNP.

Mike Wadna soon chimed in on Facebook with this piece of intelligence:
In some cases, the test read quality was low, so it will be marked as REJECTED even though it is derived/positive. The only way I know to check that is look in your raw results. DF13/CTS241's position # is 2836431 and this is the allele change, A to C.
   
So with this information in hand I was able to decoded my match's BIG Y results and determine that he too was positive for DF13/CTS241/S521. I emailed him and said, "So far that was a very expensive individual SNP test you took. ;-)" $495 for BIG Y is considerably more than an individual SNP test for $39.  However, the fun of decoding was only beginning. 

I have subsequently been able to locate BIG Y results for 12 SNPs that have been placed just below DF13 by the R L21 project team. They were all negative for my match who is serving as my temporary surogate. I'm still investigating 2 that had "?" calls and a few more that I have yet to locate in BIG Y. At this point BIG Y is becoming cost effective. Thirteen SNPs tested at $39 each would run $507. Every thing else is gravy. The fun of analyzing BIG Y results is just beginning.  

Even one more step from DF13 downstream to be closer to the present would be very exciting – at least for a couple of hours. Then we would start clamoring for more downstream SNPS!

Hope the thousands of you who ordered BIG Y are enjoying your results.

Wednesday, April 9, 2014

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.

Tuesday, April 8, 2014

Bennett Greenspan is a Pioneer


We now have new evidence that Bennett Greenspan is a pioneer and I unwittingly contributed to it. My blog post yesterday, BIG Y: Open Letter to Bennett Greenspan, was intended to be a tongue-in-cheek piece of humor. Some of my readers took it that way and some of you did not. Could I have written it more skillfully to make my intent clearer? Probably. Am I sorry I wrote it? Not really. Am I sorry it was misinterpreted? Of course. 

Based on reader comments some of you took it for the "Ha-ha!" it was intended to be. Jim Barrett accurately paraphrased my message in three short sentences: 
"I've had recent delays in my life and you've had delays in my results.  I'm about to get mine wrapped up.  I hope you are too!"
Others took it as a criticism of the BIG Y testing program or thought that I was trying somehow to get my results moved up the queue. Nothing could be further from my intent or expectations. If either of these had been my purpose, the reader who commented that I should have kept my comments between myself and Bennett would have been correct. 

It also was not my intent to become a lightning rod for criticism of FTDNA as was the case on one list. There is a proper time and manner for criticism well as there is for praise. We appear to be closing in on one of the latter.

Three pieces of intelligence did come to the fore as a result of my post. I learned that:

  • Considerably more of us jumped at the chance to be part of the BIG Y than had been expected.
  • FTDNA has gone to extraordinary lengths to manage a MAJOR groundbreaking project in an area where few guideposts and benchmarks existed. These have included borrowing an additional sequencer from Illumina.
  • Most of the remaining non-problematic test results may be expected back by next week.

I imperfectly recall a number of sayings I first heard in some version in the middle of the last century that seem to apply to the BIG Y project:

  • The only ones who don't make mistakes are those who don't try anything challenging.
  • Success is biting off more than you can chew and then chewing it.
  • You can always tell the pioneers by the arrows in their back [because they are out in front of the rest of us].

Bennett, yet again, you have given us evidence that you are a true pioneer. The test data from BIG Y reports will give us something to chew on for years. I don't know of anyone else in the world who could have pulled this off for genetic genealogy. I apologize for inadvertently adding to your stress level. It may almost be time to break out the bubbly.


Sunday, April 6, 2014

BIG Y: Open letter to Bennett Greenspan



OK Bennett, you can release my BIG Y results now. When I saw my original release date of December 31, 2013, I was thrilled to know I would have something exciting to do on New Years Eve. After all I would have just finished the manuscript for NextGen Genealogy: The DNA Connection (see other post today) and I would be needing something to do.

Well, it turns out that you knew better than I did about what was best for me. You didn't want me to be conflicted between working on my book manuscript and interpreting my BIG Y results. That was thoughtful of you. The amended February 28th release date should have given me time to get the manuscript finished but it didn't. Well at least you released a 100 or so results then. Those guys must have been all caught up on their chores. But somehow you knew that NextGen Genealogy: The DNA Connection still needed my attention. Scary. 

Then the due date got moved to March 28th. Surely I would be ready now. You released the results for a non-biologically related Dowell in our project but again none for me, for my late father-in-law or for my 6th cousin George. How did you know it wasn't time to release mine?

Last week you released Herb McDaniel's results. Herb is an STR match for me up to and including 111 markers. We are getting closer or are we? 

Bennett I really need you to keep paying attention. You do remember don't you that I ordered this test on November 11, 2013 -- the first day you were taking orders and my current expected date is the 28th of last month.

The manuscript is almost finished and out the door. Tomorrow or Tuesday at the latest. Thank you for trying to simplify my life and genetic genealogy priorities but I think I can take it from here. 

Please Bennett, free my SNPs. I want my BIG Y results and I want them NOW! I'm really not throwing a temper tantrum -- at least not yet.
  

NextGen Genealogy: The DNA Connection


Some of you may have noticed that I haven't been blogging much in the last several months. But now, finally, the manuscript is almost ready to go out the door and into the publishing process. The writing process was not at all what I had envisioned even a few months ago.

Amid the euphoria that engulfed me at the publication of my last book in June 2011, I announced on this blog that CeCe Moore and I "were talking about collaborating on a book. If all goes well you should see it in 2013." 

Then life intervened for both CeCe and me. As with most segments of life this one contained both good and not so good. My father-in-law died at age 93 and my wife Denise and I decided to sell our ocean view in Morro Bay and move to Nashville to be over 2,000 miles closer to each of our four kids and now soon to be eight grandsons. It has turned out to be a great decision for both of us but the relocation put some other parts of our lives on hold for a while. Finally last year CeCe and I signed a contract to deliver a manuscript to our publisher by December 31, 2013. The publisher came up with a cover. It is a cover you won't see later -- at least in this form:

 The title page you won't see later.


Then life intervened for CeCe in a way that was good for her professional career as a genetic genealogist but not so good for our book project. In October, 2013 CeCe became involved in solving a two decade old genetic mystery about a substituted sperm sample during an in vitro fertilization. This case reached the national media spotlight in January. By then she was immersed in work to keep up with the production schedule for "Finding Your Roots with Henry Lewis Gates, Jr." scheduled to air on public television on Tuesdays starting in September. In February CeCe withdrew from our book project.

I decided to write the autosomal part which would have been CeCe's major contribution. Angie Bush was enlisted to critique what I wrote and of other parts of book as well. Angie was a great help because she is a molecular geneticist with a background in genetics as well as genealogy. So the writing part is now a day or two from being ready to transition into the publisher's production process. The book should be out this fall.

Now I can feel free to act more like I'm really retired. I can blog, teach and research my own genealogy! :-)

Sunday, February 16, 2014

Dr D's 15 Minutes of Fame


Dr D got his 15 minutes of fame yesterday. Let me share it with you as I prepare to get back to the real world.

Dr D talks about adding DNA testing to genealogical tool kits at the
Middle Tennessee Genealogical Society in January, 2014. 
(photo courtesy of the Tennessean.)

Four weeks ago, Tony Gonzalez, a reporter for the Tennessean contacted me a couple of days before I was to present to the Middle Tennessee Genealogical Society a program on DNA as a new 21st century addition to a genealogist's toolkit. He asked for permission to bring along a photographer (see above). 

Ten days later Tony interviewed me for two and a half hours and brought along a second photographer. By then I knew that there would probably be a story published. But I had no idea what the focus would be, when it might run or what the placement in the paper would be.

A few days ago Tony told me that the article would run on Saturday unless there was breaking news that postponed it. Yesterday morning I logged in to the online version of the Tennessean before the paper version was delivered to our door. I was blown away by what I saw:



There dominating the front page of section one was Tony's story! It was continued on an inside page where the above picture was included. Click on this link to read the full story

By being considered to be "Science and Research" genealogy had moved from the hobby section of the family section to page 1, above the fold and on the left side of the page! WOW!

Now I need to come down to earth, do my laundry and get back to doing genealogy.

Saturday, February 1, 2014

X Factor: Another Adams Cousin, part 2


Four simple rules of X-chromosome DNA inheritance:
  1. 1.      Girls inherit it from their mothers.
  2. 2.      Girls inherit it from their fathers.
  3. 3.      Boys inherit it from their mothers.
  4. 4.      Boys DO NOT inherit it from their fathers.
Of these four rules the last is the most important. Anywhere on your pedigree chart where there is a father to son relationship, NO X-DNA flows. Y-DNA flows instead. As frustrating as this last rule can be sometimes, it can also be part of the solutions for some of our genealogical mysteries. But like most clues, they only help us when we are paying attention.

In December I blogged about a newly discovered 39th Adams first cousin. At the time I was operating with blinders on. Those blinders were a couple of vague recollections some of the local old timers had that an Adams boy may have had an illegitimate child that could have been my new cousin Jim. In my earlier post I had called him Joe to maintain some semblance of privacy. However, now with his blessing, I am "blowing his cover."

In my book, Crash Course in Genealogy, Rule #4 for genealogists is "Believe everything and believe nothing you hear or see in print." In my first efforts to unravel the mystery of Jim's birth, I was following the "believe everything" part of this rule but ignoring the "believe nothing" part. DNA does not lie. However, sometimes our ability to read the information it contains is considerably less than 20/20. As a result I started down a wrong path of investigating my four Adams uncles as the candidates to have been Jim's father. This effort now is revealed to have been a waste of time, money and other resources.

This week I decided to mount a second investigation. Now that I assumed that we had the investigation of his father under control and that a couple more autosomal DNA tests of strategically chosen cousins would reveal his biological father, I would start to stir the pot about his biological mother. Boy did I have that one backward.

I went to GEDMatch.com where both Jim's results from Ancestry.com and mine from various sources were parked for analysis. I decided to search Jim's X-DNA against the database to see if he matched anyone who might be related to his biological mother. Of course I came up because we were 1st cousins. So I concentrated on the others who matched Jim. Only later did I realize that I was ignoring the most important of Jim's matches. His match with me. In the chart below, the blue portions of the bar graph represent the areas where we had matching segments greater than 3 cMs long:



If Jim and I share these kind of matches on our X chromosomes our mothers were closely related. Jim's mother must be a sister of my mom. That realization turned our investigation around 180 degrees. Instead of investigating my four uncles to determine which was Jim's father, we needed to investigate my nine aunts to determine which was his mother. What a paradigm shift!

With that realization, another bit of recently acquired information took on new meaning. Jim has recently initiated an effort to find out what information court records may contain. He writes: 
The circuit court clerk was surprised that I was tagged with the family name of the father rather than the mother.  Apparently it was more common around here at that time for an unwed mother to pass her family name, not the father's, on to the child.
 When I was three years old, in the circuit court I was adopted by Morgan and Florence Jones and my name changed from James Edward Adams to James Edward Jones. The circuit court clerk will be looking at that adoption record and the birth certificate if available. It feels unlikely that there was any earlier name change.

Now based on our X-DNA we know why the file was tagged the way it was in circuit court. His mother was an Adams. So now we have a different task. Jim's mother could not be my mother. We share enough DNA to be 1st cousins. We would need to share about twice as much to be half-siblings. One of my aunts can be eliminated because she gave birth to a daughter the month before Jim was born. Another is highly unlikely because she gave birth the month Jim was conceived. Of the remaining seven, four were still living at home during the 1930 census which was recorded about a year and a half before he was conceived. These four may get our first attention. BUT if we have learned anything, it is not to overlook any possibility until it has been completely eliminated.
  

Sunday, January 26, 2014

Ethical Quagmire of DNA Testing


In an editorial entitled “DNA Standards” in the December 2013 issue of the National Genealogical Society Quarterly Melinde Lutz Byrne and Thomas W. Jones lament:
When genealogists began to apply DNA test results to family history, they had the opportunity and responsibility to set standards—not for laboratory procedures, but for acceptable linkages to individual documentation, ethics, and interpretations. It was an opportunity missed. Had they been established, such standards would have set boundaries to embrace the power of genetic testing and, the same time, to avoid abuse. As difficult as it is to cite, describe, explain, or utilize this rapidly evolving tool, the real DNA-test quagmire is ethical.

Byrne and Jones raise important questions: 
With no established standards, editors face a conundrum when considering articles from DNA-test participants. Do they publish results that might affect relatives who have not released rights? When a DNA profile becomes as easily recognizable as a cursive signature, who has what rights?

However their implication that genealogists, by being more proactive, could have influenced the practice of DNA identification in the criminal justice system seems far fetched. 


The editors acknowledge that "widespread understanding of the capabilities and limitations of DNA testing lags behind technological advances." This pattern has been repeated over and over again with all technologies probably going back to the appropriate use of clubs in the age of the cave clans. Was it OK to use it on game? Was it OK to use it for self defense? To control others?

In more recent times the Internet developed far faster than our abilities to anticipate and understand how it should be used. In the last quarter century, no areas of science and technology have expanded faster than the Internet with the possible exceptions of astronomy and genetics. It is not in our ability or interest to try to stop these developments while we figure it all out. None of us have the ability to anticipate all the possible implications of developments in these fields. If we were that clairvoyant, we would be frozen into inaction by all the possibilities. But I suppose that inaction has occurred anyway.

Ethical behavior in the application of genetics to family history research and to health related endeavors is no simple undertaking. It involves balancing the:
  1. right to know;
  2. right to privacy;
  3. right to own and benefit from intellectual property; and
  4. right to protect our communities.

Should NGS have a role is discussing and providing guidance in appropriate practice? Should ISOGG? You bet!

Friday, January 17, 2014

"Ancestry by DNA" Offers New Tests --- But What Good Are They?


Updated from the post earlier today:

Ancestry by DNA is NOT Ancestry.com although this branding is sometimes confused because the more established Ancestry.com sometimes calls itself DNAAncestry. Ancestry by DNA has announced new testing options in an offering to subscribers of Find My Past




The website makes it appear there are three product lines and of course there are: 


DNA Origins
Ancestral Ethnicity


DNA WorldView 
Compare Your Past vs. Present

Lineage Testing 
Ancestral Migration Routes


One seems to be intended to look similar to the autosomal test Ancestry.com has been offering since 2012. It is not by accident that this offering looks like Ancestry.com. Brand confusion seems to be by intent. The 15 customer reviews on Yelp gave Ancestry by DNA a generous 1.5 stars out of 5. 

One wonders why FindMyPast partnered in this deal. Perhaps it is because some kind of mt-DNA and Y-DNA tests would seem to be offered abroad:

Get 50% off a DNA kit today

Lineage testing can determine your Haplogroup which can show you how your ancient ancestors migrated out of Africa and what route they took on their journey to where you call home. Halpogroups are determined by analysing the DNA that is passed down from either your paternal or maternal side and can be traced back over 100,000 years. Your results will provide you with your Haplogroup, map, and guidebook for beginning your journey of self-discovery through DNA.


It is hard to see what the bargain is even at 50% off. Some STRs values are to be provided to males who test; but it is unclear how many. There seem to be two or possibly 3 levels of mtDNA results offered. What one gets at what price is also left open to guess. It is clear that the price for a full mtDNA test may be $199 (US) but does the 50% off apply to this? 

One more shot over our bow is the warning that:
Your certificate is accompanied by a manual, which discusses the interpretation of test results in greater detail. You will also receive a page with an in depth description of your haplogoup. All three are available for download in PDF format. Please note that results will only be available through our website for 1 year.
 
So if you take this test, be sure to download them promptly.

This is a flashy website; but what are we being offered? Check it out and give me your take. What are we being offered and at what price?

Dr D can think of no reason why persons serious about their family history would be benefited by any of these tests. Ancestry.com, FTDNA and 23andMe all offer far more useful information at comparable prices.