WDYTYA – How DNA Might Have Been Used – Cynthia Nixon

I do love these Who Do You Think Your Are (WDYTYA) and similar shows, because like most everyone, I love a good mystery, especially a true story – and a good genealogy mystery tops them all.

And, of course, you never know what tidbit might be lurking for your own situation.

We had a hiatus of several months since last season, so I remembered what I liked and forgot what I didn’t.  As a long-time genealogist, I find myself talking to the TV – saying things like, “You can’t assume that,” and other similar comments to rather gargantuan leaps of faith.

I have to remind myself that it IS, after all, a TV show, and a lot of research (I hope and pray) is done behind the scenes but not shown to the audience.  After all, Ancestry.com, marketing king of easy-peasy “just enter your ancestor’s name” and it will all just be here waiting for you is sponsoring this series….so it has to look quite simple and doable for the viewing audience.  I mean, who wants to know that there could be two people in the census with the same name, in the same county….yes…really.

But my real frustration last season came with the knowledge that in many cases, DNA could have been reasonably and successfully used, and wasn’t.  So, this season, I’d like to talk about how DNA might have been used.

Ancestry provides a recap of the Cynthia Nixon episode as does TLC, and it really was a good one with lots of cliffhangers, of course.  For future episodes, GeneaBloggers published a WDYTYA bingo card.  What fun!

This episode begins as a professional genealogist puts together Cynthia’s first several generations via the census and presents her with a scroll of that information.  If you’re playing WDYTYA Bingo, I think you get two points for this.  The rest of the show focuses on Cynthia’s 3X great grandmother, Martha Curnutt.

Marriage records on Ancestry.com show a Martha Curnutt marrying Noah Casto on 15 August 1839 in Missouri. But no Martha and Noah Casto appear in the 1850 census. There’s only Martha, Mary (10), Noah (7), and Sarah (6)—all under the name Curnutt. A quick count shows Noah could have served in the Civil War. And a search of military records yields pay dirt: Noah’s mother Martha applied for a pension in 1881.

That pension record shows that Noah, the father, died in 1842, and further research shows that in 1843, Martha was indicted for murder and then found guilty of manslaughter for killing her husband, Noah Casto, with an ax “between the eyes” while he slept, after he threatened her life.  If you’d like to read a discussion about murder vs. manslaughter, Judy Russell, The Legal Genealogist, who watched the show with a group of genealogists, wrote a wonderful article about manslaughter and murder and this case.  Be sure to read the comments too.

Cynthia discovered that Martha had apparently been severely abused, based on a newspaper article.  At that time, there was no protection nor recourse for abused women.

More awful still is an unnamed informant’s account that the victim “had been in the habit of treating his wife in a manner too brutal and shocking to think of.” Cynthia is devastated to learn her 3x great-grandmother endured such horrible treatment.

But Martha fared little better in prison. Convicted of manslaughter, she was the only female inmate, was abused by people she was hired out to work for, was subjected to inhumane conditions, and in the fall of 1844 gave birth to a daughter (Sarah) fathered by someone associated with the prison. It was most likely the scandal that would accompany the story of her treatment in a state facility that led to her pardon in 1845.

An article written by a former inmate details Martha’s treatment, including the fact that she was originally allowed to work for the warden at his home, but his wife, Mrs. Brown, abused her so terribly that she ran away, was returned to prison and kept in her cell being given nothing for days, which I presume means no food or water.  That was followed by the fact that “in the fall” she delivered a child.  Knowing the dates of the trial in 1843 and that the child was born in the fall of 1844, it became evident that the child was not her deceased husband’s child, and was conceived in prison.

When Martha was in labor, Mrs. Brown would not help her, nor allow anyone else to do so.  Finally, one (male) inmate was allowed to “attend her,” but nothing, not even clothing or heat in her cell was provided for the baby.  Obviously, the warden’s wife was hoping the child would die, but Sarah didn’t, nor did Martha.  The next month, Martha was pardoned by the governor over the signatures of a long list of politicians and very influential men.  Obviously, since the mother and child didn’t die, there was a scandal brewing.

So, the question is, and certainly the scandal revolves around the identity of the Sarah’s father, the child born in prison in the fall of 1844.

We know Sarah lived at least until the 1850 census, and assuming she lived to marry and have children of her own, let’s talk about DNA options.

If Sarah were a male and had male descendants to the current generation, this would be a relatively easy case to solve….but she is a female and carries no Y chromosome, which would have been passed from the father to a male child, so we can’t test that.

Therefore, our other testing alternative would be to test the autosomal DNA of a descendant of Sarah and see if any portion of the her autosomal DNA matches with descendants of the warden’s family.  This assumes, of course, that Martha was not otherwise related to Warden Brown.

If in fact, Sarah’s descendants do match the DNA of the warden’s descendants, that would be highly suggestive that Warden Brown was Sarah’s father, especially if the amount of shared DNA would be the right percentage to be about 4 generations removed, or roughly third cousins who could be expected to share about 1% of the DNA of their common ancestor.

Not all third cousins will share DNA, or not in large enough segments to be above the matching threshold of the DNA testing companies, but many will, and all we would need would be enough and proof that the DNA in question is indeed descended from the same Brown family.

Here’s my own third cousin match at Ancestry.  He and I tested intentionally, knowing we are cousins, to map our DNA to specific ancestors (at Family Tree DNA) and to see if we match other cousins (at Ancestry.)

ancestry third cousins

Of course, Sarah is not Cynthia’s direct ancestor, the older daughter, Mary is – so finding out who Sarah’s father was does not further Cynthia’s own genealogy.  Plus, testing Cynthia’s DNA would not have been beneficial other than to have a basis for comparison on Martha’s side.  But testing a descendant of Sarah would certainly have answered a burning question about Martha’s time spent in prison – and might very likely have answered the question about why Mrs. Brown obviously hated Martha enough to try to kill her in various inhumane ways; by withholding assistance while Martha was in childbirth, not to mention essentials like food and heat.

Had Sarah’s descendants taken the Ancestry.com DNA test, especially if they had entered the warden’s name as a potential ancestor in their tree, they might well have discovered that they had “shakey leaf” hints that connected them with other people who descend from Warden Brown’s family.  If they were lucky, an actual descendant of Warden Brown himself would have tested and they would match.  In fact, maybe the producers could have found a direct descendant of Warden Brown who was interested in revealing the truth, whatever it was.

However, without a chromosome browser or any other type of comparison tools, they would be unable to prove that the match to that individual was indeed Brown family DNA – and they would have simply have to infer, allow you to believe, that the genetic match was the same as the shakey leaf match.  You can see, above, that Ancestry skates on this issue by saying “it looks like you have a shared ancestor.”  Indeed it does, but that doesn’t mean the shaky leaf ancestor is the one that you share genetically.  However, given the other leaps of faith in the series, I doubt that this “little detail” would have deterred the storyline much.  And indeed, it would have been very interesting.

In order to prove the genetic connection, one could have the people who tested, and matched on the Brown line, download their results to www.GedMatch.com and compare their actual DNA segments there.  They could also transfer their DNA to Family Tree DNA who does have comparison tools.  Of course, that opens the door to DISPROVING the shakey leaf “tree” match as well as proving it, and it’s certainly not in the same spirit or as easy as just accepting, on faith, the “shakey leaf” hint as fact.  DNA Genealogy wrote a nice summary of Ancestry.com vs GedMatch here and why those “shakey leaf” first impressions are sometimes not correct.

Am I the only one who thinks Warden Brown is the most likely candidate to be Sarah’s father?????  Whoever the father was, he was certainly important enough to warrant a pardon for Martha.  That is the one good thing in the landslide of evil that haunted Martha Curnutt.  I hope the rest of her life was much easier.

Salvaging Every Scrap of DNA Info from Ancestry

OK, it’s a given, like it or not – Ancestry.com is discontinuing their Y and mtDNA data bases on September 5th, 2014.  Let’s take every opportunity between now and then to scrape every scrap of information off of that plate before it’s so unceremoniously tossed away like so much trash.

I would suggest that you take every single family surname and enter it as a query at Ancestry.  If you already have known surname matches, then you should easily be able to eliminate those matches, by haplogroup, who assuredly aren’t yours.  For example, if there were 4 Estes males listed at Ancestry, 2 of which match my Estes line haplogroup, and 2 that do not, then the 2 that don’t I can disregard.

So let’s look at some examples.

In this demonstration case, there are no individuals who have tested by this surname at either Family Tree DNA or Sorenson, at www.smgf.org, so I’m flying blind, hoping to find anyone by that surname who has tested.

The surname is Bonnevie, an Acadian ancestor.

If you’re a registered Ancestry member, go to your DNA page and select Y.  If you’re not an Ancestry member, click on this link and it should take you there. http://ldna.ancestry.com/groups.aspx

At the top of the page, under Ancestry logo on the right, click on Groups.  You’ll see two choices – Search for Groups – which is not what you want to do since groups are no longer functional.  Enter the surname into the “Search for Individual” field.

salvage 1

In this case, Bonnevie returned no results.  Be sure to try variants.

salvage 2

I’m going on to my next surname, Vannoy.

salvage 3

Vannoy in fact returned one result.  In this case, this individual entered their results manually from another lab, which is likely, but not necessarily, Family Tree DNA.  You can tell by the “*” beside the “64 markers” under the Test category.  Because they did not test at Ancestry, there is no need to send them a message asking them if they would be interested in transferring their DNA.  If you aren’t familiar with this person through other testing or research, you might well want to contact them.  To initiate contact, click on the envelop on the far left hand side of the entry.

salvage 4

Complete this form and keep your fingers crossed.  I haven’t had a lot of luck with replies from people at Ancestry who have DNA tested, but you should at least try. Nothing ventured, nothing gained.

Crumley is another one of my surnames. In this entry, I can tell, based on the haplogroup, that they are probably a member of my Crumley line.  They tested at Ancestry (no “*”).  I can click on “View profile” to see if they have appended a tree.  They have not, so I can’t see their Crumley ancestors.

salvage 5

I can, however, contact them and see if they will enter a discussion about genealogy, if they will transfer their results to Family Tree DNA, or retest, or minimally, if they will enter their results in YSearch.  Here’s the verbiage I’ve been sending.

Hi Val,

Ancestry is planning to discontinue the Y DNA data base on September 5th.  We have a Crumley surname project at Family Tree DNA with several members.  We’d love to invite you to join us.  You can transfer your DNA results or retest.  Please contact me and I’ll be glad to explain your options.  From your haplogroup, it looks like you descend from the James Crumley/Catherine Gilkey line out of England and Virginia.  I’d love to exchange genealogy info with you as well.  Please e-mail me at robertajestes@att.net

Roberta Estes

Another approach I can take IF I have the DNA markers of the surname line is to go in and modify my own results, if they were manually entered, to reflect that surname profile.  To do this, go to your DNA page and the click on “View Results” for the Paternal lineage.

salvage 6

You will then see this page which will allow you to edit your results.  Enter the results for the lineage you are seeking.  When finished, click on “See Matches.”

salvage 7

It sometimes takes from a few minutes to a few hours to update the data base and receive matches.  If you still don’t have matches in a day, 24 hours, then you actually don’t have any matches – but do give it 24 hours.

Then, on to your next surname.

It’s sad that Ancestry’s Y and mtDNA data base resources are being discontinued, but I hope that you’ll take the time to scavenge every scrap, while you still can.  If this is the only place where that person or family ever tested, you’ll never have another opportunity.  It will be gone, forever.

10 Things to Do With Your DNAPrint, renamed AncestrybyDNA, Test

birdcage

Please note, AncestrybyDNA is NOT the same as the AncestryDNA test sold by Ancestry.com.  Both CeCe Moore and David Dowell have written about this in their respective blogs.

Back in 2002 (no, that is not a typo,) a new product called DNAPrint was introduced by a company then called DNAPrint Genomics.  It provided you, in percentages, your percentages of 4 ethnic groups: Indo-European, East-Asian, Native American and African.  Family Tree DNA remarketed this test for just over a year but ceased when they realized there were issues.

It was the first of its kind of test ever to be offered commercially, and version 2.0 utilized a whopping 71 ancestrally informative markers, according to the user’s guide delivered with the product.  The next version of the test, 2.5, titled AncestrybyDNA included 175 markers, and a third version, which I don’t believe was ever released, was to include just over 300 markers.

In 2002, this was a baby step in a brand new world.  We, as a community, were thrilled to be able to obtain this type of information.  And of course, we believed it was accurate, or relatively so.  However, the questions and ensuing debate started almost immediately and became very heated.

The company’s representatives indicated that East-Asian and Native American could be combined for those without a “Chinese grandpa” and that would have given me a whopping 25% Native American.  Even then, before pedigree analysis, I thought this was a little high.  My East Asian was shown as 15%, Native American at 10% and Indo-European at 75%.  For reference, my real Native results are probably in the 1-3% range.  Keep in mind that we were all babes in the woods, kind of stumbling around, learning, in 2002 and 2003.

Interestingly enough, I found the answer recently, quite by accident, to one of the burning questions about Native American ancestry that was asked repeatedly of Tony Frudakis during that timeframe, then a corporate officer of DNAPrint, and left unanswered.  In Carolyn Abraham’s book, The Juggler’s Children, which is a wonderful read, on page 55, the answer to the forever-hanging question was answered:

“When I finally reached Frudakis, that’s how he explained the confusion over our Native ancestry result – semantics.  The Florida company had pegged its markers as being Native American to appeal to the American market, he told me.  But it was accurate to consider them Central Asian markers, he said, that had been carried to different regions by those who migrated from that part of the globe long ago – into the Americas, into East Asia, South Asia and even southern Europe – finding their way into today’s Greeks, Italians and Turks.  ‘We may do ourselves a favour and change the name of this ancestry [component] in the test,’ he said, since apparently I wasn’t the only one baffled by it.”

So, now we know, straight from the horses mouth, via Carolyn.

Of course, since that time, many advances have occurred in this field.  Today, Family Tree DNA, 23andMe, Ancestry.com and the Genographic Project utilize chip based technology and utilize over half a million markers to achieve ethnicity predictions.  If DNAPrint, renamed AncestybyDNA was the first baby step, today we are teenagers – trying to refine our identity.  Today’s tests, although not totally accurate, are, by far, more accurate than this first baby step.  Give us another dozen years in this industry, and they’ll be spot on!

For 2003, when I ordered mine, DNAPrint was an adventure – it was exciting – it was a first step – and we learned a lot.  Unfortunately, DNAPrint under the name AncestrybyDNA is still being sold today, currently owned by the DNA Diagnostics Center.  If you are even thinking about ordering this product, take a look first at the Yelp reviews and the Better Business Bureau complaints.

I don’t regret spending the money in 2003.  Spending money on this outdated test today would be another story entirely – a total waste.  The results are entirely irrelevant today in light of the newer and more refined technology.  Unfortunately, seldom a week goes by that I don’t receive an e-mail from someone who bought this test and are quite confused and unhappy.  The test has been marketed and remarketed by a number of companies over the years.

So, here are some suggestions about what might be appropriate to do with your DNAPrint or AncestybyDNA results if you don’t want to just throw them away:

  1. Line the bottom of the birdcage.
  2. Use to light the BBQ grill or camp fire.
  3. Use under boots in the hallway in the winter.
  4. Shred, then use as confetti.
  5. Cut into strips and use as bookmarks.
  6. Use as scratch paper.
  7. Use in the garden between rows to minimize weeds.
  8. Make into a paper airplane.
  9. Roll, along with other excess paper, into logs for the fireplace.
  10. Frame, and display along with your other antiques.

Yes, it’s really that old and outdated!

Ancestry Kit Mixup

Every genealogists worst nightmare.  A DNA kit swap.  You unknowingly receive the results from someone else, and that equally in-the-dark unknown person receives yours.  And you’ll never know unless you recognize the signs and take action to see if it’s your bad luck or overactive imagination, or the answer really is a kit swap or lab error of some sort.

I’ve just spent three months unraveling this exact situation that occurred at Ancestry.com.  The person to whom this happened would like to share her story with you.  We are hoping that if something similar ever happens to you, that you’ll be able to recognize the signs and know what steps to take to figure out if this indeed has occurred.

Let me also say that a kit swap or similar lab error is really quite rare, and in most other instances when people believe their kits have been swapped, they haven’t been, although this certainly is not the first time this has happened.  CeCe Moore reported on another Ancestry.com case in 2012.

We’ll call the lady Jane. Jane’s father agreed to have his Y DNA tested some years ago at Ancestry.com.  Jane submitted his DNA for him and noticed that he had no matches to his rather common surname.  She didn’t really think anything of it at the time, other than being disappointed.  His haplogroup was estimated by Ancestry to be R1b.

As time went on, she ordered Ancestry.com’s autosomal test too for her father.  Ancestry sent another sampling kit, and her father is receiving matches to people who, at least according to their trees, share common ancestors with her father.

Last year, Jane decided to transfer her father’s Y DNA to Family Tree DNA. The markers from Ancestry.com were transferred, and Jane still didn’t have any surname matches at Family Tree DNA.

Jane then ordered the Geno2.0 test for her father.  The results were returned with haplogroup I, terminal SNP I-L22, which were at odds with Ancestry’s haplogroup R1b estimate.

About the same time, Jane upgraded her father’s STR markers as well, and the haplogroup project administrator noticed that while Jane’s father’s lower panels, meaning the ones tested at Ancestry matched haplogroup R1b, his upper panels didn’t match R1b subgroups at all.

Obviously something was wrong, very wrong, someplace.  But what, and where?  Jane contacted me and asked if I would help unravel this puzzle.

I checked Jane’s father’s page at Family Tree DNA, and when she transferred his Geno 2.0 results to his FTDNA page, apparently the transfer confused the software at FTDNA because his results reported both I-L22 and R-M269 as positive, which is impossible since I-L22 is in haplogroup I, only, and R-M269 is only found in haplogroup R.

ancestry kit swap ftdna snps

Unfortunately, this only added to the confusion.

At this point, I downloaded the raw data file from the Geno 2.0 test and verified that indeed, M269 was absent and L22 was present.

ancestry kit swap raw data

Family Tree DNA, thankfully, stepped up to the plate and ran a SNP test on Jane’s father’s second vial.  That SNP test also came back as positive for haplogroup I, matching the Geno 2.0 results.

Just to be absolutely positive, Family Tree DNA sent Jane’s father a third vial and tested the same markers that Jane had transferred from Ancestry.  You can see for yourself – the results are very different.  The results are unquestionable.  Either there was a kit swap or a lab error of some sort at Ancestry where the wrong markers were posted for Jane’s father’s results.  He has been tested three times, from separate vials, at Family Tree DNA with all of the results providing evidence that the Ancestry results were in error.

Marker Ancestry FTDNA
DYS438 12 10
DYS391 10 11
DYS392 13 11
DYS426 12 11
DYS439 13 11
DYS445 12 11
GGAAT1B07 10 11
DYS444 11 12
DYS446 13 13
DYS462 11 13
Y-GATA-A10 13 13
DYS437 15 16
DYS441 14 16
DYS458 17 16
DYS463 24 21
DYS635 23 21
DYS452 30 31

In an overabundance of caution, Family Tree DNA is going to rerun the entire test, all markers and the backbone SNP, from yet another (fourth) new vial being sent to Jane’s father.  Thank heavens Jane’s father is still available for testing and not entirely discouraged.

Jane is ecstatic, because now, she is actually receiving surname matches and in her father’s words, “we just wanted to know who we are.”  And just in time for Father’s Day!

Signs and Signals

How might you know if a kit swap has happened to you?  As we know, Ancestry has discontinued their Y and mitochondrial DNA testing and will be destroying the data base, so this won’t be an issue at Ancestry with new Y DNA kits, but it could be an issue for results already delivered, like Jane’s, and for autosomal tests.  This is one reason why retesting might not be a bad idea, even though the $19 or $58 Y DNA Ancestry to FTDNA transfer price is quite attractive.  Here are some of the signs that might tip you that there is a problem:

  1. If Y DNA, you don’t receive any surname matches, even to those you believe that you are in related to. This is one of those sticky-wickets, because if you don’t match your first cousin, for example, the most likely situation is that you have an undocumented adoption in one of the lines. My suggestion in this situation is to submit an entirely new test under a new kit number. If your first and second kits match each other, then the answer is the undocumented adoption.
  2. If autosomal DNA, and you have no matches to anyone you believe you should match, especially close relatives, submit your DNA to one of the other three testing companies – Family Tree DNA, 23andMe or Ancestry.com. The approach gives you the benefit of fishing in multiple ponds along with verifying that your results match each other. When you receive the results from both companies, download the raw data files from both to www.gedmatch.com and then match them to each other. They should match almost exactly, although there will be some small differences in terms of areas tested and possibly no-calls – but they should match very closely.

Let’s hope this never happens to anyone else.  The sad thing is that whoever, at Ancestry, received Jane’s father’s Y DNA results likely has no idea they are incorrect.

Thank you Family Tree DNA for going above and beyond to resolve this very distressing situation for Jane and her father.

Transfer DNA Results or Retest at Family Tree DNA?

confusionThe recent announcement by Ancestry.com that they are discontinuing their Y and mtDNA products and associated data bases, combined with the opportunity to transfer your Y and autosomal Y DNA results to Family Tree DNA has raised the question of whether it’s best to transfer or retest.  Let’s look at the various options, pluses and minuses, for each product involved.  As it turns out, one size does not fit all.  In other words, it depends…

Autosomal

The cost of an autosomal test transfer to Family Tree DNA is $69 and you can transfer either Ancestry.com’s autosomal test results or 23andMe’s v3 results to Family Tree DNA for that price.

However, the cost of retesting at Family Tree DNA, utilizing the Father’s Day sale, and yes, it’s valid for females too, not just men, is just $79.

So, should you transfer existing results or retest?

  1. If you retest at Family Tree DNA, you’ll have the added benefit of having your DNA archived there, available to you for other tests in the future. Archiving is free and is part of the service.
  2. If you retest at Family Tree DNA, you don’t have to deal with downloading files from Ancestry or 23andMe and then uploading them to Family Tree DNA. If you’re not a techie, this is a benefit.
  3. Ancestry has never been known for quality, so in terms of Ancestry, for a $10 difference, I would certainly retest.
  4. At 23andMe, if you tested either early (the v2 chip) or since November/December of 2013 (the v4 chip) you have no choice but to retest, because the results aren’t compatible.

In a nutshell, for a $10 difference, my vote would be to retest, unless, of course, the person isn’t available to retest then by all means, transfer the results.

If you’re going to retest, do it now while the price is still $79.  The sale ends on 6-17-2014.

Don’t forget, the Big Y, which is a nearly full sequence of the Y chromosome, is also on sale for Father’s Day for only $595.  The newly announced SNP matching in addition to the regular marker matching promises to add a second tool to those who are trying to determine family lineages.  I suggest that someone from each of your primary family surname lines take this test.  Mutations are being found every 90-150 years so this test holds great promised in combination with regular STR (37, 67 and 111 marker) testing.

Y DNA

You can transfer your Ancestry Y DNA results to Family Tree DNA for $19, and then upgrade to the Family Tree DNA standard marker test for another $39, for a total of $58.

If you transfer Ancestry’s 33 marker results, the $58 upgrade price buys you an upgrade to the 25 marker test.  If you transfer Ancestry’s 46 marker test, the upgrade buys you a standard 37 marker test.  Both of these upgrades include DNA matching to other participants.  The $19 transfer alone, does not, just the ability to join projects.

The standard 37 marker test at Family Tree DNA today costs $169 without the transfer, so transferring is definitely the way to go on Y DNA.  You save $111.  Plus, with the upgrade, you will have the added benefit of having your DNA archived at Family Tree DNA.

For Y DNA, a transfer with the upgrade is definitely your best value.  Don’t forget to do this before Sept. 5th because the Ancestry data base disappears that day.  In fact, the sooner, the better, because some of Ancestry’s DNA data base features have already been discontinued.

Mitochondrial DNA

Ancestry’s mtDNA test results weren’t compatible with Family Tree DNA’s, so you don’t have a transfer option.  The mtDNA plus at Family Tree DNA which provides you with your haplogroup and matches in the HVR1+HVR2 regions is $59, but the full sequence mitochondrial DNA test is only $199.  The full sequence test provides you with fully sequenced mitochondrial DNA results, about 10 times more locations than the HVR1+HVR2 regions, a full haplogroup designation and matching at the highest level.  It’s definitely the best value and then you’re done with mtDNA because there are no upgrades beyond the full sequence.

My recommendation would be to purchase the Full Sequence test for $199 as the best value.

The Net-Net

In short, here’s what we have:

  • Autosomal – you can retest at Family Tree DNA for $79, $10 more than the $69 transfer price, which has several benefits.
  • Y DNA – the transfer plus upgrade for $58 is your best value, saving you over $100.
  • Mitochondrial DNA – there is no transfer option, so retesting is necessary.

Click here to order.

Ancestry.com Discontinues Y and mtDNA Tests and Closes Data Base

ancestry to ftdna

Ancestry.com has not been actively selling Y and mtDNA tests for some time now.  However, today Ancestry announced the official discontinuance of those tests and that as of September 5th, their Y and mtDNA data bases will also be shuttered – meaning that the results will no longer be accessible for those who tested or for anyone wanting to do a comparison.

This is very sad news indeed for the genetic genealogy community, especially given that Ancestry has in the past purchased other vendors such as Relative Genetics and incorporated their results into their data base.

For anyone who tested their Y DNA with Ancestry, now is the time to transfer those result to the Family Tree DNA data base, now the last vendor left standing who provides those tests along with a comparison data base.  This is easy to do and you can be a part of the Family Tree DNA community, availing yourself of their surname projects for only $19.

If you want to see your matches, you can upgrade your kit from Ancestry’s 33 or 46 markers to Family Tree DNA’s standard markers for another $39 at the same time you transfer your Ancestry results.  This also has the added benefit of having your actual DNA in the lab at Family Tree DNA where it will be archived for 25 years.  I’m already hearing moans from people whose family DNA is only at Ancestry, and the original tester has passed away.

In fact, if you don’t transfer your results from Ancestry now, or before September 5th, you will lose your opportunity as your Y and mtDNA results will no longer be available at Ancestry in any format, according to their FAQ.

Ancestry states that this change does not affect their autosomal DNA testing, and in fact, that’s where they want to focus, at least for now.  Unfortunately, the shuttering of their Y and mtDNA data bases calls into question their commitment to the genetics aspect of the genealogy industry.  Autosomal DNA testing will be a priority as long as it’s profitable, just like Y and mtDNA has turned out to be.

I would suggest while you are transferring, you might also want to take advantage of this opportunity to also transfer your Ancestry autosomal results to Family Tree DNA for $69.  You can fish in a second match pool and Family Tree DNA offers many tools to participants that Ancestry does not offer.

If you’re not inclined to transfer your results to Family Tree DNA, at least avail yourself of the two free data bases, www.ysearch.org for Y results and www.mitosearch.org for mtDNA.  At least your results won’t be entirely lost forever.

I understand that Ancestry doesn’t want to sell the Y and mtDNA products any longer, but I would think that maintaining the current Y and mtDNA data bases in a static state for the tens of thousands of people who have spent a nontrivial amount of money DNA testing, and allowing comparisons, would be well worthwhile in terms of customer loyalty if nothing else.  Customers are viewing this move as abandonment and a betrayal of their trust, and it begs the question of what will eventually happen to autosomal results and matches at Ancestry.  If you’re going to test at Ancestry, make sure you also test at Family Tree DNA so your actual DNA is available there as well.

Ethnicity Percentages – Second Generation Report Card

Recently, Family Tree DNA introduced their new ethnicity tool, myOrigins as part of their autosomal Family Finder product.  This means that all of the major players in this arena using chip based technology (except for the Genographic project) have now updated their tools.  Both 23andMe and Ancestry introduced updated versions of their tools in the fall of 2013.  In essence, this is the second generation of these biogeographical or ethnicity products.  So lets take a look and see how the vendors are doing.

In a recent article, I discussed the process for determining ethnicity percentages using biogeographical ancestry, or BGA, tools.  The process is pretty much the same, regardless of which vendor’s results you are looking at.  The variant is, of course, the underlying population data base, it’s quality and quantity, and the way the vendors choose to construct and name their regions.

I’ve been comparing my own known and proven genealogy pedigree breakdown to the vendors results for some time now.  Let’s see how the new versions stack up to a known pedigree.

The paper, “Revealing American Indian and Minority Heritage using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis” was published in the Fall 2010 issue of JoGG, Vol. 6 issue 1.

The pedigree analysis portion of this document begins about page 8.  My ancestral breakdown is as follows:

Geography Pedigree Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland 0.7813
Native American 0.2933
Turkish 0.0031

This leaves about 25% unknown.

Let’s look at each vendor’s results one by one.

23andMe

23andme v2

My results using the speculative comparison mode at 23andMe are shown in a chart, below.

23andMe Category 23andMe Percentage
British and Irish 39.2
French/German 15.6
Scandinavian 7.9
Nonspecific North European 27.9
Italian 0.5
Nonspecific South European 1.6
Eastern European 1.8
Nonspecific European 4.9
Native American 0.3
Nonspecific East Asian/Native American 0.1
Middle East/North Africa 0.1

At 23andMe, if you have questions about what exact population makes up each category, just click on the arrow beside the category when you hover over it.

For example, I wasn’t sure exactly what comprises Eastern European, so I clicked.

23andme eastern europe

The first thing I see is sample size and where the samples come from, public data bases or the 23andMe data base.  Their samples, across all categories, are most prevalently from their own data base.  A rough add shows about 14,000 samples in total.

Clicking on “show details” provides me with the following information about the specific locations of included populations.

23andme pop

Using this information, and reorganizing my results a bit, the chart below shows the comparison between my pedigree chart and the 23andMe results.  In cases where the vendor’s categories spanned several of mine, I have added mine together to match the vendor category.  A perfect example is shown in row 1, below, where I added France, Holland, Germany and Switzerland together to equal the 23andMe French and German category.  Checking their reference populations shows that all 4 of these countries are included in their French and German group.

Geography Pedigree Percent 23andMe %
Germany, Holland, Switzerland & France 45.7451 15.6
France 6.6113 (above) Combined
Germany 23.8014 (above) Combined
Holland 14.5511 (above) Combined
Switzerland 0.7813 (above) Combined
British Isles 22.6104 39.2
Native American 0.2933 0.4 (Native/East Asian)
Turkish 0.0031 0.1 (Middle East/North Africa)
Scandinavian 7.9
Italian 0.5
South European 1.6
East European 1.8
European by DNA 6.8362 4.9 (nonspecific European)
Unknown 25 27.9 (North European)

I can also change to the Chromosome view to see the results mapped onto my chromosomes.

23andme chromosome view

The 23andMe Reference Population

According to the 23andMe customer care pages, “Ancestry Composition uses 31 reference populations, based on public reference datasets as well as a significant number of 23andMe members with known ancestry. The public reference datasets we’ve drawn from include the Human Genome Diversity ProjectHapMap, and the 1000 Genomes project. For these datasets as well as the data from 23andMe, we perform filtering to ensure accuracy.

Populations are selected for Ancestry Composition by studying the cluster plots of the reference individuals, choosing candidate populations that appear to cluster together, and then evaluating whether we can distinguish the groups in practice. The population labels refer to genetically similar groups, rather than nationalities.”

Additional detailed information about Ancestry Composition is available here.

Ancestry.com

ancestry v2

Ancestry is a bit more difficult to categorize, because their map regions are vastly overlapping.  For example, the west Europe category is shown above, and the Scandinavian is shown below.

ancestry scandinavia

Both categories cover the Netherlands, Germany and part of the UK.

My Ancestry percentages are:

Ancestry Category Ancestry Percentage
North Africa 1
America <1
East Asia <1
West Europe 79
Scandinavia 10
Great Britain 4
Ireland 2
Italy/Greece 2

Below, my pedigree percentages as compared to Ancestry’s categories, with category adjustments.

Geography Pedigree Percent Ancestry %
West European 52.584 (combined from below) 79
Germany 23.8041 Combined
Holland 14.5511 Combined
European by DNA 6.8362 Combined
France 6.6113 Combined
Switzerland 0.7813 Combined
British Isles 22.6104 6
Native American 0.2933 ~1 incl East Asian
Turkish 0.0031 1 (North Africa)
Unknown 25
Italy/Greece 2
Scandinavian 10

Ancestry’s European populations and regions are so broadly overlapping that almost any interpretation is possible.  For example, the Netherlands could be included in several categories – and based up on the history of the country, that’s probably legitimate.

At Ancestry, clicking on a region, then scrolling down will provide additional information about that region of the world, both their population and history.

The Ancestry Reference Population

Just below your ethnicity map is a section titled “Get the Most Out of Your Ethnicity Estimate.”  It’s worth clicking, reading and watching the video.  Ancestry states that they utilized about 3000 reference samples, pared from 4245 samples taken from people whose ethnicity seems to be entirely from that specific location in the world.

ancestry populations

You can read more in their white paper about ethnicity prediction.

Family Tree DNA’s myOrigins

I wrote about the release of my Origins recently, so I won’t repeat the information about reference populations and such found in that article.

myorigins v2

Family Tree DNA shows matches by region.  Clicking on the major regions, European and Middle Eastern, shown above, display the clusters within regions.  In addition, your Family Finder matches that match your ethnicity are shown in highest match order in the bottom left corner of your match page.

Clicking on a particular cluster, such as Trans-Ural Peneplain, highlights that cluster on the map and then shows a description in the lower left hand corner of the page.

myorigins trans-ural

Family Tree DNA shows my ethnicity results as follows.

Family Tree DNA Category Family Tree DNA Percentage
European Coastal Plain 68
European Northlands 12
Trans-Ural Peneplain 11
European Coastal Islands 7
Anatolia and Caucus 3

Below, my pedigree results reorganized a bit and compared to Family Tree DNA’s categories.

Geography Pedigree Percent Family Tree DNA %
European Coastal Plain 45.7478 68
Germany 23.8041 Combined above
Holland 14.5511 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
British Isles 22.6104 7 (Coastal Islands)
Turkish 0.0031 3 (Anatolia and Caucus)
European by DNA 6.8362
Native American 0.2933
Unknown 25
Trans-Ural Peneplain 11
European Northlands 12

Third Party Admixture Tools

www.GedMatch.com is kind enough to include 4 different admixture utilities, contributed by different developers, in their toolbox.  Remember, GedMatch is a free, meaning a contribution site – so if you utilize and enjoy their tools – please contribute.

On their main page, after signing in and transferring your raw data files from either 23andMe, Family Tree DNA or Ancestry, you will see your list of options.  Among them is “admixture.”  Click there.

gedmatch admixture

Of the 4 tools shown, MDLP is not recommended for populations outside of Europe, such as Asian, African or Native American, so I’ve skipped that one entirely.

gedmatch admix utilities

I selected Admixture Proportions for the part of this exercise that includes the pie chart.

The next option is Eurogenes K13 Admixture Proportions.  My results are shown below.

Eurogenes K13

Eurogenes K13

Of course, there is no guide in terms of label definition, so we’re guessing a bit.

Geography Pedigree Percent Eurogenes K13%
North Atlantic 75.19 44.16
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.74 combined East Asian, Siberian, Amerindian and South Asian
Turkish 0.0031 1.78 Red Sea
Unknown 25
Baltic 24.36
West Med 14.78
West Asian 6.85
Oceanian 0.86

Dodecad K12b

Next is Dodecad K12b

According to John at GedMatch, there is a more current version of Dodecad, but the developer has opted not to contribute the current or future versions.

Dodecad K12b

By the way, in case you’re wondering, Gedrosia is an area along the Indian Ocean – I had to look it up!

Geography Pedigree Percent Dodecad K12b
North European 75.19 43.50
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 3.02 Siberian, South Asia, SW Asia, East Asia
Turkish 0.0031 10.93 Caucus
Gedrosia 7.75
Northwest African 1.22
Atlantic Med 33.56
Unknown 25

Third is Harappaworld.

Harappaworld

harappaworld

Baloch is an area in the Iranian plateau.

Geography Pedigree Percent Harappaworld %
Northeast Euro 75.19 46.58
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.81 SE Asia, Siberia, NE Asian, American, Beringian
Turkish 0.0031 10.27
Unknown 25
S Indian 0.21
Baloch 9.05
Papuan 0.38
Mediterranean 28.71

The wide variety found in these results makes me curious about how my European results would be categorized using the MDLP tool, understanding that it will not pick up Native, Asian or African.

MDLP K12

mdlp k12

The Celto-Germanic category is very close to my mainland European total – but of course, many Germanic people settled in the British Isles.

Second Generation Report Card

Many of these tools picked up my Native American heritage, along with the African.  Yes, these are very small amounts, but I do have several proven lines.  By proven, I mean both by paper trail (Acadian church and other records) and genetics, meaning Yline and mtDNA.  There is no arguing with that combination.  I also have other Native lines that are less well proven.  So I’m very glad to see the improvements in that area.

Recent developments in historical research and my mitochondrial DNA matches show that my most distant maternal ancestral line in Germany have some type of a Scandinavian connection.  How did this happen, and when?  I just don’t know yet – but looking at the map below, which are my mtDNA full sequence matches, the pattern is clear.

mitomatches

Could the gene flow have potentially gone the other direction – from Germany to Scandinavia?  Yes, it’s possible.  But my relatively consistent Scandinavian ethnicity at around 10% seems unlikely if that were the case.

Actually, there is a second possibility for additional Scandinavian heritage and that’s my heavy Frisian heritage.  In fact, most of my Dutch ancestors in Frisia were either on or very near the coast on the northernmost part of Holland and many were merchants.

I also have additional autosomal matches with people from Scandinavia – not huge matches – but matches just the same – all unexplained.  The most notable of which, and the first I might add, is with my friend, Marja.

It’s extremely difficult to determine how distant the ancestry is that these tests are picking up.  It could be anyplace from a generation ago to hundreds of generations ago.  It all depends on how the DNA was passed, how isolated the population was, who tested today and which data bases are being utilized for comparison purposes along with their size and accuracy.  In most cases, even though the vendors are being quite transparent, we still don’t know exactly who the population is that we match, or how representative it is of the entire population of that region.  In some cases, when contributed data is being used, like testers at 23andMe, we don’t know if they understood or answered the questions about their ancestry correctly – and 23andMe is basing ethnicity results on their cumulative answers.  In other words, we can’t see beneath the blanket – and even if we could – I don’t know that we’d understand how to interpret the components.

So Where Am I With This?

I knew already, through confirmed paper sources that most of my ancestry is in the European heartland – Germany, Holland, France as well as in the British Isles.  Most of the companies and tools confirm this one way or another.  That’s not a surprise.  My 35 years of genealogical research has given me an extremely strong pedigree baseline that is invaluable for comparing vendor ethnicity results.

The Scandinavian results were somewhat of a surprise – especially at the level in which they are found.  If this is accurate, and I tend to believe it is present at some level, then it must be a combined effect of many ancestors, because I have no missing or unknown ancestors in the first 5 generations and only 11 of 64 missing or without a surname in generation 6.  Those missing ancestors in generation 6 only contribute about 1.5% of my DNA each, assuming they contribute an average of 50% of their DNA to offspring in each subsequent generation.

Clearly, to reach 10%, nearly all of my missing ancestors, in the US and Germany, England and the Netherlands would have to be 100% Scandinavian – or, alternately, I have quite a bit scattered around in many ancestors, which is a more likely scenario.  Still, I’m having a difficult time with that 10% number in any scenario, but I will accept that there is some Scandinavian heritage one way or another.  Finding it, however, genealogically is quite another matter.

However, I’m at a total loss as to the genesis of the South European and Mediterranean.  This must be quite ancient.  There are only two known possible ancestors from these regions and they are many generations back in time – and both are only inferred with clearly enough room to be disproven.  One is a possible Jewish family who went to France from Spain in 1492 and the other is possibly a Roman soldier whose descendants are found within a few miles of a Roman fort site today in Lancashire.  Neither of these ancestors could have contributed enough DNA to influence the outcome to the levels shown, so the South European/Mediterranean is either incorrect, or very deep ancestry.

The Eastern European makes more sense, given my amount of German heritage.  The Germans are well known to be admixed with the Magyars and Huns, so while I can’t track it or prove it, it also doesn’t surprise me one bit given the history of the people and regions where my ancestors are found.

What’s the Net-Net of This?

This is interesting, very interesting.  There are tips and clues buried here, especially when all of the various tools, including autosomal matching, Y and mtDNA, are utilized together for a larger picture.  Alone, none of these tools are as powerful as they are combined.

I look forward to the day when the reference populations are in the tens of thousands, not hundreds.  All of the tools will be far more accurate as the data base is built, refined and utilized.

Until then, I’ll continue to follow each release and watch for more tips and clues – and will compare the various tools.  For example, I’m very pleased to see Family Tree DNA’s new ethnicity matching tool incorporated into myOrigins.

I’ve taken the basic approach that my proven pedigree chart is the most accurate, by far, followed by the general consensus of the combined results of all of the vendors.  It’s particularly relevant when vendors who don’t use the same reference populations arrive at the same or similar results.  For example, 23andMe uses primarily their own clients and Nat Geo of course, although I did not include them above because they haven’t released a new tool recently, uses their own population sample results.

National Geographic’s Geno2

Nat Geo took a bit of a different approach and it’s more difficult to compare to the others.  They showed my ethnicity as 43% North European, 36% Mediterranean and 18% Southwest Asian.

nat geo results

While this initially looks very skewed, they then compared me to my two closest populations, genetically, which were the British and the Germans, which is absolutely correct, according to my pedigree chart.  Both of these populations are within a few percent of my exact same ethnicity profile, shown below.

Nat geo british 2

The description makes a lot of sense too.  “The dominant 49% European component likely reflects the earliest settlers in Europe, hunter-gatherers who arrived there more than 35,000 years ago.  The 44% Mediterranean and the 17% Southwest Asian percentages arrived later, with the spread of agriculture from the Fertile Crescent in the middle East, over the past 10,000 years.  As these early farmers moved into Europe, they spread their genetic patterns as well.”

nat geo german

So while individually, and compared to my pedigree chart, these results appear questionable, especially the Mediterranean and Southwest Asian portions, in the context of the populations I know I descend from and most resemble, the results make perfect sense when compared to my closest matching populations.  Those populations themselves include a significant amount of both Mediterranean and Southwest Asian.  Looking at this, I feel a lot better about the accuracy of my results.  Sometimes, perspective makes a world of difference.

It’s A Wrap

Just because we can’t exactly map the ethnicity results to our pedigree charts today doesn’t mean the results are entirely incorrect.  It doesn’t mean they are entirely correct, either.  The results may, in some cases, be showing where population groups descend from, not where our specific ancestors are found more recently.  The more ancestors we have from a particular region, the more that region’s profile will show up in our own personal results.  This explains why Mediterranean shows up, for example, from long ago but our one Native ancestor from 7 or 8 generations ago doesn’t.  In my case, it would be because I have many British/German/Dutch lines that combine to show the ancient Mediterranean ancestry of these groups – where I have many fewer Native ancestors.

Vendors may be picking up deep ancestry that we can’t possible know about today – population migration.  It’s not like our ancestors left a guidebook of their travels for us – at least – not outside of our DNA – and we, as a community, are still learning exactly how to read that!  We are, after all, participants on the pioneering, leading edge of science.

Having said that, I’ll personally feel a lot better about these kinds of results when the underlying technology, data bases and different vendors’ tools mature to the point where there the differences between their results are minor.

For today, these are extremely interesting tools, just don’t try to overanalyze the results, especially if you’re looking for minority admixture.  And if you don’t like your results, try a different vendor or tool, you’ll get an entirely new set to ponder!