Friday, October 10, 2014

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. 

Wednesday, October 8, 2014

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.









   



Saturday, September 27, 2014

What's Next for Dr. D?


Back in June on the eve of Genealogy Jamboree in Burbank, I had dinner with my acquisitions editor at the publisher who has published all my books to date. She had just read and forwarded to the production editor the manuscript for NextGen Genealogy: The DNA Connection. As we parted that evening she asked, "What are your going to write next?"

At the time I was not ready to answer that question. My commitment involvement to complete NextGen had not yet run its course. Now that is changing. You can now see the Table of Contents:

On Thursday I  posted on Facebook
Just sent corrected page proofs & index to publisher for NextGen Genealogy: The DNA Connection. Postpartum setting in. November publication.
I'm moving past the brief depression that comes with the realization that my ability to shape the final product has passed. For better or worse it is in the final stages of production. 

The book itself is just one of the aspects about which I now seem to be powerless. Even though Amazon has taken CeCe Moore's name off the cover, the site continues to list her as a co-author. See my earlier post about how this came to be. Once something gets into a database it seems to take a life of its own and it is next to impossible to remove/correct all locations where it resides.

Now I'm still not sure what I want to do next. I'm also not sure what the appropriate venue for that effort might be. My current publisher, Libraries Unlimited, has been a very comfortable fit up until now. As long as I was writing about library topics for library workers, this was the right market niche. With Crash Course in Genealogy it was easy to maintain this tie by slanting it toward helping library workers assist family history researchers. With NextGen Genealogy that connection became more tenuous. The title was almost shifted to Praeger -- an imprint also owned by the parent company ABC-Clio. In the end this book stayed with Libraries Unlimited. If I do undertake another book, should it be with Libraries Unlimited, Praeger, some other publisher or should it be self published?

The nature of the content may guide that choice. I have long had in the back of my mind that I might want to top off my trilogy with a book on the ethical issues surrounding DNA testing. This would go beyond testing for family history applications and wander into the even more emotionally charged area of testing for medical conditions. 

Ethics is not a new area of concern for me. In the 1970s I served on the Committee for Professional Ethics of the American Library Association. I even chaired the committee for a year. More recently, for more than a decade, I taught a short course for library workers and web designers entitled Ethics in the Information Age. However, it was only in the last three years that I came to realize that there was a significant overlap between my earlier forays into the field of professional ethics and my newer found interest in DNA testing. Chapter 7 in NextGen Genealogy is my first attempt to write about the overlap of these two fields of interest.

Now that NextGen Genealogy is about to be launched, it is becoming obvious how much has changed in the last 6 months since I turned the first draft of the manuscript over to my acquisitions editor. Print publication is such a slow process in the age of instant gratification. In addition, in NextGen Genealogy, I deliberately tried to not intimidate newcomers to genetic genealogy. Is it time to start working on NextGen Genealogy 2.0: Digging Deeper Into DNA?

Before making a final decision, I'll probably do what I have often done in the past. Do a little writing. Do a little teaching/lecturing. Get a feel for what works with people with whom I'm interacting. In the spring I may be teaching another class through the Osher Lifelong Learning Institute at Vanderbilt University. It wouldn't be appropriate for that audience to dive deeply into either of these topics but it may give me a chance to try some of the content.

Dr. D is having a hard time trying to decide what to do when he grows up or even if he wants to grow up!


Thursday, August 28, 2014

FTDNA End of Summer Sale



I'm happy to pass along this notice which just appeared in my email box because we all benefit when more people are tested and the databases of potential matches grow bigger:



Dear Beloved Bloggers,

We hope you've had a great summer!  As the season draws to a close, join us for one last celebration with our End of Summer Y-DNA Sale!  Customers can order a Y-DNA test and join the world's largest Y-DNA database today.  All Y-DNA tests and upgrades have been marked down for significant savings!

Time is limited.  The sale ends 9/3/2014.

As an added bonus, Big Y is also on sale for just
$495.  Big Y coupons acquired during the Father's Day Sale can be used on Big Y orders placed during the End of Summer Sale.  With Big Y, 340,000 years of Y-DNA ancestry is just a test away!

Standard Tests
Regular Price
Sale Price
Y-37
$169
$129
Y-67
$268
$199
Y-111
$367
$279
Big Y
$595
$495

 
Upgrades
Regular Price
Sale Price
Y-12 -> Y-37
$99
$70
Y-12 -> Y-67
$189
$148
Y-12 -> Y-111
$339
$239
Y-25 -> Y-37
$49
$35
Y-25 -> Y-67
$148
$114
Y-25 -> Y-111
$249
$209
Y-37 -> Y-67
$99
$79
Y-37 -> Y-111
$220
$179
Y-67 -> Y-111
$129
$109
 


Sunday, August 10, 2014

Unraveling BIG Y Test Results: R-DF97


Yesterday I wrote about a BIG Y discovery that got my Maryland Dowells past SNPs R-L21 and R-DF13. The Virginia Group 1 Dowells in our surname project had long been known to have come forward in time from those two SNPs and were known to have reached R-M222. Thanks to the informative charts that citizen scientist Mike Walsh tirelessly updates at the site of the R L21 and Subclades Project, we have the opportunity to almost keep up with the current SNP tsunami:


The chart above is offered only to give overall perspective. The new subclade R-S1026 discussed in yesterday's post is represented by the four boxes colored pale pink in the middle of the chart. The more robust subclade R-DF49, which includes SNP M222, is the blue/aqua on the extreme lower left corner of the chart. Our Maryland Dowells and the Virginia Dowells have not shared a common male ancestor in about 3,500 years even though both followed the same SNP trail down from yDNA Adam to SNP DF13. You will need to visit the linked project website to be able to read the details of this chart. 

The DF49 corner of the chart is blown up below:



I request the reader's indulgence to ignore the gold and yellow boxes in the upper right corner of this part of the chart. The Virginia Group 1 Dowell who took the BIG Y test, was able to trace his SNP migration pattern several hundred years and eight SNPs closer to the present. He now is confirmed to be DF97 and beyond. DF97 is at the bottom of the third column from the left in the above chart.

Although this Dowell has been able to discover the trail of his ySNPs through a significant part of the last few millennia, he still has discoveries to make to connect his paper trail to his SNP trail. As was the case with my Maryland Dowells, The Big Tree of Alex Williamson gives many more recent SNPs to try to arrange in the proper chronological sequence. It is necessary to visit the original website to get a clear view of the SNPs that the yDNA of this Virginia Dowell has accumulated as his paternal clan moved toward the Atlantic coast of Europe. 


The Virginia Group 1 Dowell is the third column from the left in the above chart. SNP DF85 is in top row and DF97 is in row three. There are still many SNPs to arrange in the proper sequence in recent centuries as attempts are made to tie the SNP path into the documented path and to identify his nearest relatives.


Saturday, August 9, 2014

NextGen Genealogy: The DNA Connection is moving toward publication


With great haste we make slow progress. I just returned the copy edits for my new book to the editor. Another step closer to the publication date but still a few steps to go. 

https://www.blogger.com/blogger.g?blogID=5415306683169000572#editor/target=post;postID=568404745683052894

For those of you who have not experienced the process, I'll review it for you. I signed the contract last September. The manuscript was due at the publisher at the end of December. That deadline was missed and my co-author had to withdraw because of success in other areas of her life as a genetic genealogist. It was April before I finished the part she was to have written. 

First the acquisition editor read the manuscript and approved it to go into production. Then it was reviewed for plagiarism, copyright and legal permissions from those whose material was being included. Here the progress seemed to bog down. I'm not sure whether this was due to an illness of the production editor or because of the cycle adopted by my publisher. The cover was developed as soon as the manuscript went into production. Authors, at least with this publisher, have no say about the cover. We can negotiate almost any other aspect but not the cover.

Manuscripts for other books I have done with this publisher were due at the end of December. This allowed the books to be available for showing to thousands of librarians who attend the American Library Association Conference typically held at the end of June. Since the current title missed that cycle, it seemed to fall into the next cycle. That cycle is to get it out in November so that it could be available for Christmas.

The production editor assigns the manuscript to a copy editor who reads it for grammar, footnote format, etc. The manuscript is returned to the author for concurrence with any changes and to answer any questions from the copy editor. This is the last point at which the author can make any changes or add new material. 

The manuscript is returned to the copy editor for final formatting. It is then converted into page proofs. These are returned to the author for one last review. At this stage only the most minute changes can be made so that the pagination will not be disrupted. The index is created at this point. I prefer to do my own indexing. Our work schedule calls for me to be indexing in mid-September. The page proofs and index are returned to the copy editor who places every thing in final form and forwards it to the publisher for printing and distribution.

If you should order this book from the publisher, be advised that the electronic format offered was designed primarily for library servers and may not be what you have come to expect from Kindle. The book also can be preordered from Amazon but the discount code shown above will not be honored there. 

Makes one want to investigate self publishing. 

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. 

Saturday, July 26, 2014

WDYTYA? Followup


If you are interested in more information on the story of Cynthia Nixon which aired on this season's first episode of the US version of Who Do You Think You Are? on TLC on Wednesday evening, I have a couple of suggestions for going deeper. If you missed the show when it was first aired, you can watch a recap online at the TLC site. Two respected bloggers offer you a chance to explore the most explosive event in Cynthia's family history in more detail. 

Judy Russell, The Legal Genealogist, covered legal aspects of the case and turns it into a legal thriller where you get to come up with your own verdict.


Roberta Estes, DNAeXplained – Genetic Genealogy discussed missed opportunities for researching deeper -- particularly with DNA.

Dr. D has long wondered why Ancestry continues to miss opportunities to market its DNA testing product. The company offers one of the three most used DNA testing programs in the US. However, no DNA test reports made it into any of the episodes of the program last season -- a trend that has continued through episode 1 this season. We are only offered about 42 minutes of content in each episode. A little of that is used to remind us what happened before commercial breaks in case our short term memory is a little challenged. 

One of the biggest challenges of the show is to film around the availability of the guest celebrities. Since it takes several weeks to get DNA tests back from the lab and to identify other potential relatives whose DNA reports might match, it is challenging from a time perspective to include such testing. Still, since Ancestry.com is the lead corporate sponsor, one would think DNA testing could be fitted in somewhere -- at least in some episodes. Is it possible that the DNA testing package being offered by Ancestry is not as conducive to genetic analysis as the tools offered by some of its competitors?

Thursday, July 24, 2014

Tennessee Ancestry Library Event (TALE)


Reserve your spot now for the Tennessee Ancestry Library Event (TALE) on Saturday, September 20th.





"Discover and celebrate your family history! This full day of genealogy classes, sponsored by Ancestry.com and the Tennessee State Library & Archives, will be held at the Sheraton Nashville Downtown Hotel (623 Union Street, Nashville, TN 37219) on Saturday, September 20. Registration for the all-day event is only $30.00. Space is limited, register today! 

Speakers will include Chuck Sherrill, J. Mark Lowe and Ancestry’s own Anne Gillespie Mitchell, Kim Harrison, Juliana Szucs Smith, Loretto (“Lou”) Szucs, and Anna Swayne. Topics include: How to Search Successfully to Tell Your Story on Ancestry.com; AncestryDNA: Another View into Your Family Story; Your Ancestor’s Lawsuit: Finding and Using Tennessee’s Supreme Court Case File; Jumpstart Your Research; and a Live Q&A Panel." 


Wednesday, July 23, 2014

Facebook account Clone


Early yesterday evening I began to receive notices from family and friends that something was amiss with my Facebook (FB) account. It seemed I had a new account which had about a half dozen pictures from my original account -- including my profile picture. Many if not all of my existing Facebook friends had been invited to accept "friend" requests to the new fake site. I had even been given a sex change. 

With some tips from savvy friends -- especially Drew Smith -- I quickly, began to understand what had happened. If I did a FB search for my name, I only got into my own original site. However, if my wife did the same search, she got 2 hits. One listed me as her husband and the other listed me as a female. My conclusion, possibly correct, was that whoever created the site was sophisticated enough to block me from findind the new site by searching from my original site. When I tried to follow a link sent me by a friend, I got this message: 

Sorry, this page isn't available

The link you followed may be broken, or the page may have been removed.

This prevented me from logging into the new site and requesting FB to take the pretender down. But my wife and others could still find the second site. 

This must have happened many times before. As I worked my way through the many FB help pages, I was first directed to log into the offending site and then contact FB. That was not possible in my case because I could not find the site from my legitimate account. 

With a little more digging, I found an option to have a friend to request that the rogue site be removed. My wife did so. I was then contacted by FB to verify that I wanted the second site removed. They took it down within minutes. 

If you ever get a friend request from an existing friend, be a real friend and notify the person immediately of this anomaly. Apparently 40 of my friends accepted the fake friend requests. If this happens to you, contact FB immediately.

I have no idea who did this or why. Be vigilant.