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.

BIG Y: Open letter to Bennett Greenspan

Awaiting Results

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:

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! :-)

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.

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.

  

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!

"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. Buy your kit

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.  

DAR Partners with FTDNA to Offer Discounted 37 Marker Y-chromosome Tests

Wow! 2014 has already been a great year for genetic genealogists. First FTDNA introduced new X-chromosome analysis tools. This has already been blogged adequately by Roberta Estes and CeCe Moore so I will not attempt to duplicate their good work here.

Now the DAR is getting into DNA in a big way and is announcing a partnership with FTDNA for reduced prices on 37 marker Y-DNA tests:

You may click on the image above to see the details for this offer on the FTDNA site. Many more details were also released from the DAR site. The DAR is even sponsoring a new online course about using DNA evidence in support of DAR applications. Hallelujah! 

I have long been a critic of the DAR for not accepting DNA evidence to DISPROVE long accepted lines when that evidence establishes the members could not have been related to the Revolutionary patriot within genealogical time. Now I may have to initiate a new conversation with their staff.

Another Adams Cousin

I have never had a shortage of cousins – particularly on my maternal side of the family. My mother was one of 14 Adams siblings who survived infancy. These included 10 girls and 4 boys. A 5^th boy died within a few days of birth. My mom was the last surviving sibling when she died in 1998. It was interesting that of the 39 offspring these 14 produced, 18 of them were from the two oldest children. I think the timing of the Great Depression may have had as much to do with this difference in productivity as birth order but that is just speculation on my part.  

When I logged in to AncestryDNA last month, I was surprised to find the following result on my DNA page:

1st Cousin         Possible range: 1st - 2nd cousins    Confidence: 99%

The pedigree chart posted by this individual did not help me place this cousin among the twenty-five thousand or so individuals I currently have in my family tree database. The DNA information did not tell me whether this match was on my maternal or paternal side. However, the geographic locations in the pedigree chart of the “new” cousin strongly suggested this match was on my mom’s side. 

I sent an inquiry through the Ancestry message system and got this response from a person I will call Joe:

I believe ancestry.com is correct, but the exact connection may be difficult to pin down.  I was born 27 September, 1932, and adopted at birth by the parents in my ancestry.com family tree.  The doctor who delivered me was Dr. G. W. Carpenter, who I believe had an office in Utica, MO, at the time. Most of the people who had first-hand knowledge of my birth are now gone. I was reluctant to make inquiries that might embarrass anyone. A neighbor who grew up near Breckenridge vaguely recalled that my father was an Adams employed in a grocery store in Breckenridge, and my birth mother was a young employee.  As time permits, I'll try to find out more.

Only one other family member has been tested to my knowledge. That is a first cousin -- once removed who agreed to be tested so that I could establish the paternal haplogroup of my maternal (Adams) grandfather. My DNA sample establishes my paternal (Dowell) grandfather's Y-chromosome. Merrill's DNA had also been processed through the FTDNA Family Finder test.

It occurred to me that my new cousin "Joe" would be Merrill's uncle if Merrill's grandfather, my Uncle Frank, was also Joe's father. If instead Joe's father was one of the other Adams brothers, Merrill would be Joe's first cousin -- once removed. That is the same relationship I have with Merrill.
  

Since Joe had tested at Ancestry and Merrill at FTDNA, they had to be placed in the same database in order to analyze the nature of their relationship. Therefore, Joe downloaded the raw data from his test at Ancestry and uploaded it to GedMatch.com a free site that among other features allows autosomal results from a variety of labs to be compared with each other. I downloaded Merrill's raw data from FTDNA and uploaded them to GedMatch.

When Joe's results were compared with Merrill's, they shared about the same amount of DNA as I shared with Merrill as a 1st cousin -- once removed. An uncle would have shared much more with a nephew. Therefore, my Uncle Frank is also Joe's Uncle Frank and is eliminated as a candidate to be Joe's father. 

I talked to a first cousin who would have been six when Joe was born. She said she "had a feeling" that she had heard Uncle Bud might have had a child with a woman other than his wife. Even if he did this does not prove the child was Joe. Actually, we need to remember that the DNA results viewed to date do not eliminate the possibility that it was Joe's mother (not his father) who was his Adams connection. However, circumstantial evidence suggests that we are looking for an Adams father.

Our search is now focused on the three Adams brothers other than Frank. A child of one of the three (who is also one of my previously known Adams 1st cousins) has agreed to test. We should know that result sometime in February.  

Of the remaining two possible fathers, one never married and has no known descendants. We will be tracing the descendants of the other to see if we can find one willing to test.

Stay tuned for future developments.

When will you see BIG Y results?

When will we see the beginning of the SNP Tsunami from the large number of BIG Y tests many of you have ordered? 

Got a calendar on the wall for the first quarter of 2014? Got a dart? ;-)

I'm in batch 542 (see blog earlier post) which was originally predicted to be returned 12/31/2013. What great fun it would have been to decode Y-SNPs on New Years Eve!  This predicted date on my FTDNA page -- as many of you probably know -- has now eroded to 2/28/2014. The FAQ on FTDNA’s site has always said a less specific February, 2014.

On December 6^th Janine Cloud, Customer Service Manager @ FTDNA wrote:

FYI: When a kit is batched it automatically gets an expected results date. Unfortunately, it is batch-specific, not test specific. There's not currently a mechanism to set that message by test type until AFTER it's been batched.

 For example, everyone knows that a Y-12 will get results faster than a Y-111, yet both get the same expected results date if they're batched at the same time.

 Since everyone who ordered Big Y already had testing done with us, the orders batched each Wednesday as usual, even though the test has not begun running yet. Consequently, those Big Y tests got the same expected results date as all the other tests in the batch. With regular tests, we don't know that the whole group of tests will not be ready at the end of that expected results dates, but with the Big Y we did, so rather than wait until the end of the block of time, we arranged for those dates to be changed up front to help mitigate some of the potential for frustration over the test not being completed by that initial date.

 Normally those dates are updated the day after the expected date, but in this case there was reason to wait until Jan 1st, etc. to make the change. 

Then a few days later from Thomas Krahn who used to manage the SNP testing in the FTDNA lab but now runs his own company:

Good news for Big Y! I was at FTDNA yesterday and Max has told me that they have the first successful runs in house completed. He didn't say on which machine they were running (MiSeq or HiSeq) and he didn't comment on possible barcoding problems, but this gives us hope that some customers may not need to wait until next year to see their results.

We have also discussed the transfer of customer samples. It is important that those who want their samples transferred need to contact Max directly (max@genebygene.com) because apparently a commitment from the FTDNA customer support is not sufficient. However if Max approves them himself, then there doesn't seem to be a problem that samples can get transferred. Usually 50ul are sufficient. However if there is a way to get a new sample, then both companies would prefer that method instead of a sample transfer. Only samples that cannot be re-done or where laws prohibit taking a new sample should consider the transfer.

Also good news for FGC customers: YSEQ has returned the first results to our customers today. Most of the FGC markers could be confirmed right away with Sanger sequencing. It seems that Greg has done a very good job with analyzing the data. In addition to that we have kicked out a bunch of SNP candidates on repetitive and X homologue sequences during the primer design phase, so that the remaining FGC markers were almost all a hit on the first try. Especially I'd like to point out the FGC5496 marker for R1b-DF13 researchers because it has also been confirmed in another sample of the 1000 genomes project. This marker is available at http://shop.yseq.net/ already.

If you aren't confused yet, you haven’t been paying attention! Let me know when you get your results.

Happy Holidays!!